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How to publish your research

A step-by-step guide to getting published.

Publishing your research is an important step in your academic career. While there isn’t a one-size-fits-all approach, this guide is designed to take you through the typical steps in publishing a research paper.

Discover how to get your paper published, from choosing the right journal and understanding what a peer reviewed article is, to responding to reviewers and navigating the production process.

Jump to section

Step 1: choosing a journal.

Choosing which journal to publish your research paper in is one of the most significant decisions you have to make as a researcher. Where you decide to submit your work can make a big difference to the reach and impact your research has.

It’s important to take your time to consider your options carefully and analyze each aspect of journal submission – from shortlisting titles to your preferred method of publication, for example open access .

Don’t forget to think about publishing options beyond the traditional journals format – for example, open research platform F1000Research , which offers rapid, open publication for a wide range of outputs.

Why choose your target journal before you start writing?

The first step in publishing a research paper should always be selecting the journal you want to publish in. Choosing your target journal before you start writing means you can tailor your work to build on research that’s already been published in that journal. This can help editors to see how a paper adds to the ‘conversation’ in their journal.

In addition, many journals only accept specific manuscript formats of article. So, by choosing a journal before you start, you can write your article to their specifications and audience, and ultimately improve your chances of acceptance.

To save time and for peace of mind, you can consider using manuscript formatting experts while you focus on your research.

How to select the journal to publish your research in

Choosing which journal to publish your research in can seem like an overwhelming task. So, for all the details of how to navigate this important step in publishing your research paper, take a look at our choosing a journal guide . This will take you through the selection process, from understanding the aims and scope of the journals you’re interested in to making sure you choose a trustworthy journal.

Don’t forget to explore our Journal Suggester to see which Taylor & Francis journals could be right for your research.

Go to guidance on choosing a journal

Step 2: Writing your paper

Writing an effective, compelling research paper  is vital to getting your research published. But if you’re new to putting together academic papers, it can feel daunting to start from scratch.

The good news is that if you’ve chosen the journal you want to publish in, you’ll have lots of examples already published in that journal to base your own paper on. We’ve gathered advice on every aspect of writing your paper, to make sure you get off to a great start.

How to write your paper

How you write your paper will depend on your chosen journal, your subject area, and the type of paper you’re writing. Everything from the style and structure you choose to the audience you should have in mind while writing will differ, so it’s important to think about these things before you get stuck in.

Our  writing your paper guidance  will take you through everything you need to know to put together your research article and prepare it for submission. This includes getting to know your target journal, understanding your audiences, and how to choose appropriate keywords.

You can also use this guide to take you through your research publication journey .

You should also make sure you’re aware of all the Editorial Policies  for the journal you plan to submit to. Don’t forget that you can contact our  editing services  to help you refine your manuscript.

Discover advice and guidance for writing your paper

Step 3: Making your submission

Once you’ve chosen the right journal and written your manuscript, the next step in publishing your research paper is  to make your submission .

Each journal will have specific submission requirements, so make sure you visit  Taylor & Francis Online  and carefully check through the  instructions for authors  for your chosen journal.

How to submit your manuscript

To submit your manuscript you’ll need to ensure that you’ve gone through all the steps in our  making your submission  guide. This includes thoroughly understanding your chosen journal’s instructions for authors, writing an effective cover letter, navigating the journal’s submission system, and making sure your research data is prepared as required.

You can also  improve your submission experience  with our guide to avoid obstacles and complete a seamless submission.

To make sure you’ve covered everything before you hit ‘submit’ you can also take a look at our  ‘ready to submit’ checklist  (don’t forget, you should only submit to one journal at a time).

Understand the process of making your submission

Step 4: Navigating the peer review process

Now you’ve submitted your manuscript, you need to get to grips with one of the most important parts of publishing your research paper –  the peer review process .

What is peer review?

Peer review is the independent assessment of your research article by independent experts in your field. Reviewers, also sometimes called ‘referees’, are asked to judge the validity, significance, and originality of your work.

This process ensures that a peer-reviewed article has been through a rigorous process to make sure the methodology is sound, the work can be replicated, and it fits with the aims and scope of the journal that is considering it for publication. It acts as an important form of quality control for research papers.

Peer review is also a very useful source of feedback, helping you to improve your paper before it’s published. It is intended to be a collaborative process, where authors engage in a dialogue with their peers and receive constructive feedback and support to advance their work.

Almost all research articles go through peer review, although in some cases the journal may operate post-publication peer review, which means that reviews and reader comments are invited after the paper is published.

If you’ll like to feel more confident before getting your work peer reviewed by the journal, you may want to consider using an  in-depth technical review service from experts.

Understanding peer review

Peer review can be a complex process to get your head around. That’s why we’ve put together a  comprehensive guide to understanding peer review . This explains everything from the many different types of peer review to the step-by-step peer review process and how to revise your manuscript. It also has helpful advice on what to do if your manuscript is rejected.

Visit our peer review guide for authors

Step 5: The production process

If your paper is accepted for publication, it will then head into  production . At this stage of the process, the paper will be prepared for publishing in your chosen journal.

A lot of the work to produce the final version of your paper will be done by the journal production team, but your input will be required at various stages of the process.

What do you need to do during production?

During production, you’ll have a variety of tasks to complete and decisions to make. For example, you’ll need to check and correct proofs of your article and consider whether or not you want to  produce a video abstract  to accompany it.

Take a look at  our guide to the production process  to find out what you’ll need to do in this final step to getting your research published.

Your research is published – now what?

You’ve successfully navigated publishing a research paper – congratulations! But the process doesn’t stop there. Now your research is published in a journal for the world to see, you’ll need to know  how to access your article  and  make sure it has an impact .

Here’s a  quick tip on how to boost your research impact  by investing in making your accomplishments stand out.

Below you’ll find helpful tips and post-publication support. From how to communicate about your research to how to request corrections or translations.

How to access your published article

When you publish with Taylor & Francis, you’ll have access to a new section on Taylor & Francis Online called  Authored Works . This will give you and all other named authors perpetual access to your article, regardless of whether or not you have a subscription to the journal you have published in.

You can also  order print copies of your article .

How to make sure your research has an impact

Taking the time to make sure your research has an impact can help drive your career progression, build your networks, and secure funding for new research. So, it’s worth investing in.

Creating a real impact with your work can be a challenging and time-consuming task, which can feel difficult to fit into an already demanding academic career.

To help you understand what impact means for you and your work, take a look at  our guide to research impact . It covers why impact is important, the different types of impact you can have, how to achieve impact – including tips on communicating with a variety of audiences – and how to measure your success.

Keeping track of your article’s progress

Through your  Authored Works access , you’ll be able to get real-time insights about your article, such as views, downloads and citation numbers.

In addition, when you publish an article with us, you’ll be offered the option to sign up for email updates. These emails will be sent to you three, six and twelve months after your article is published to let you know how many views and citations the article has had.

Corrections and translations of published articles

Sometimes after an article has been published it may be necessary to make a change to the  Version of Record . Take a look at our dedicated  guide to corrections, expressions of concern, retractions and removals  to find out more.

You may also be interested in translating your article into another language. If that’s the case, take a look at our  information on article translations .

Go to your guide on moving through production

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How to Publish a Research Paper

Last Updated: August 17, 2023 References Approved

This article was co-authored by Matthew Snipp, PhD and by wikiHow staff writer, Christopher M. Osborne, PhD . C. Matthew Snipp is the Burnet C. and Mildred Finley Wohlford Professor of Humanities and Sciences in the Department of Sociology at Stanford University. He is also the Director for the Institute for Research in the Social Science’s Secure Data Center. He has been a Research Fellow at the U.S. Bureau of the Census and a Fellow at the Center for Advanced Study in the Behavioral Sciences. He has published 3 books and over 70 articles and book chapters on demography, economic development, poverty and unemployment. He is also currently serving on the National Institute of Child Health and Development’s Population Science Subcommittee. He holds a Ph.D. in Sociology from the University of Wisconsin—Madison. There are 7 references cited in this article, which can be found at the bottom of the page. wikiHow marks an article as reader-approved once it receives enough positive feedback. This article received 30 testimonials and 93% of readers who voted found it helpful, earning it our reader-approved status. This article has been viewed 678,820 times.

Publishing a research paper in a peer-reviewed journal is an important activity within the academic community. It allows you to network with other scholars, get your name and work into circulation, and further refine your ideas and research. Getting published isn’t easy, but you can improve your odds by submitting a technically sound and creative yet straightforward piece of research. It’s also vital to find a suitable academic journal for your topic and writing style, so you can tailor your research paper to it and increase your chances of publication and wider recognition.

Submitting (and Resubmitting) Your Paper

• Have two or three people review your paper. At least one should be a non-expert in the major topic — their “outsider’s perspective” can be particularly valuable, as not all reviewers will be experts on your specific topic.

• Journal articles in the sciences often follow a specific organizational format, such as: Abstract; Introduction; Methods; Results; Discussion; Conclusion; Acknowledgements/References. Those in the arts and humanities are usually less regimented.

• Submit your article to only one journal at a time. Work your way down your list, one at a time, as needed.
• When submitting online, use your university email account. This connects you with a scholarly institution, which adds credibility to your work.

• Accept with Revision — only minor adjustments are needed, based on the provided feedback by the reviewers.
• Revise and Resubmit — more substantial changes (as described) are needed before publication can be considered, but the journal is still very interested in your work.
• Reject and Resubmit — the article is not currently viable for consideration, but substantial alterations and refocusing may be able to change this outcome.
• Reject — the paper isn’t and won’t be suitable for this publication, but that doesn’t mean it might not work for another journal.

• Do not get over-attached to your original submission. Instead, remain flexible and rework the paper in light of the feedback you receive. Use your skills as a researcher and a writer to create a superior paper.
• However, you don’t have to “roll over” and meekly follow reviewer comments that you feel are off the mark. Open a dialogue with the editor and explain your position, respectfully but confidently. Remember, you’re an expert on this specific topic! [6] X Research source

• Remember, a rejected paper doesn’t necessarily equal a bad paper. Numerous factors, many of them completely out of your control, go into determining which articles are accepted.
• Move on to your second-choice journal for submission. You might even ask for guidance on finding a better fit from the editor of the first journal.

Choosing the Right Journal for Submission

• Read academic journals related to your field of study.
• Search online for published research papers, conference papers, and journal articles.
• Ask a colleague or professor for a suggested reading list.

• “Fit” is critical here — the most renowned journal in your field might not be the one best suited to your specific work. At the same time, though, don’t sell yourself short by assuming your paper could never be good enough for that top-shelf publication.

• However, always prioritize peer-reviewed journals — in which field scholars anonymously review submitted works. This is the basic standard for scholarly publishing.
• You can increase your readership dramatically by publishing in an open access journal. As such, it will be freely available as part of an online repository of peer-reviewed scholarly papers. [11] X Research source

Strengthening Your Submission

• “This paper explores how George Washington’s experiences as a young officer may have shaped his views during difficult circumstances as a commanding officer.”
• “This paper contends that George Washington’s experiences as a young officer on the 1750s Pennsylvania frontier directly impacted his relationship with his Continental Army troops during the harsh winter at Valley Forge.”

• This is especially true for younger scholars who are breaking into the field. Leave the grand (yet still only 20-30 page) explorations to more established scholars.

• Your abstract should make people eager to start reading the article, but never disappointed when they finish the article.
• Get as many people as you can to read over your abstract and provide feedback before you submit your paper to a journal.

Research Paper Help

Expert Q&A

• Do not immediately revise your paper if you are upset or frustrated with the journal's requests for change. Set your paper aside for several days, then come back to it with "fresh eyes." The feedback you received will have percolated and settled, and will now find a comfortable place within your article. Remember this is a big project and final refinements will take time. Thanks Helpful 1 Not Helpful 0

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• ↑ https://owl.excelsior.edu/research/revising-and-editing-a-research-paper/
• ↑ http://www.canberra.edu.au/library/start-your-research/research_help/publishing-research
• ↑ http://www.apa.org/monitor/sep02/publish.aspx
• ↑ Matthew Snipp, PhD. Research Fellow, U.S. Bureau of the Census. Expert Interview. 26 March 2020.
• ↑ https://www.timeshighereducation.com/news/how-to-get-your-first-research-paper-published/2015485.article#survey-answer
• ↑ https://www.webarchive.org.uk/wayback/archive/20140615095526/http://www.jisc.ac.uk/media/documents/publications/briefingpaper/2010/bppublishingresearchpapersv1final.pdf
• ↑ https://libguides.usc.edu/writingguide/abstract

About This Article

To publish a research paper, ask a colleague or professor to review your paper and give you feedback. Once you've revised your work, familiarize yourself with different academic journals so that you can choose the publication that best suits your paper. Make sure to look at the "Author's Guide" so you can format your paper according to the guidelines for that publication. Then, submit your paper and don't get discouraged if it is not accepted right away. You may need to revise your paper and try again. To learn about the different responses you might get from journals, see our reviewer's explanation below. Did this summary help you? Yes No

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How to Write and Publish a Research Paper in 7 Steps

What comes next after you're done with your research? Publishing the results in a journal of course! We tell you how to present your work in the best way possible.

This post is part of a series, which serves to provide hands-on information and resources for authors and editors.

Things have gotten busy in scholarly publishing: These days, a new article gets published in the 50,000 most important peer-reviewed journals every few seconds, while each one takes on average 40 minutes to read. Hundreds of thousands of papers reach the desks of editors and reviewers worldwide each year and 50% of all submissions end up rejected at some stage.

In a nutshell: there is a lot of competition, and the people who decide upon the fate of your manuscript are short on time and overworked. But there are ways to make their lives a little easier and improve your own chances of getting your work published!

Well, it may seem obvious, but before submitting an academic paper, always make sure that it is an excellent reflection of the research you have done and that you present it in the most professional way possible. Incomplete or poorly presented manuscripts can create a great deal of frustration and annoyance for editors who probably won’t even bother wasting the time of the reviewers!

This post will discuss 7 steps to the successful publication of your research paper:

• Check whether your research is publication-ready
• Choose an article type
• Choose a journal
• Construct your paper
• Decide the order of authors
• Check and double-check
• Submit your paper

1. Check Whether Your Research Is Publication-Ready

Should you publish your research at all?

If your work holds academic value – of course – a well-written scholarly article could open doors to your research community. However, if you are not yet sure, whether your research is ready for publication, here are some key questions to ask yourself depending on your field of expertise:

• Have you done or found something new and interesting? Something unique?
• Is the work directly related to a current hot topic?
• Have you checked the latest results or research in the field?
• Have you provided solutions to any difficult problems?
• Have the findings been verified?
• Have the appropriate controls been performed if required?
• Are your findings comprehensive?

If the answers to all relevant questions are “yes”, you need to prepare a good, strong manuscript. Remember, a research paper is only useful if it is clearly understood, reproducible and if it is read and used .

2. Choose An Article Type

The first step is to determine which type of paper is most appropriate for your work and what you want to achieve. The following list contains the most important, usually peer-reviewed article types in the natural sciences:

Full original research papers disseminate completed research findings. On average this type of paper is 8-10 pages long, contains five figures, and 25-30 references. Full original research papers are an important part of the process when developing your career.

Review papers present a critical synthesis of a specific research topic. These papers are usually much longer than original papers and will contain numerous references. More often than not, they will be commissioned by journal editors. Reviews present an excellent way to solidify your research career.

Letters, Rapid or Short Communications are often published for the quick and early communication of significant and original advances. They are much shorter than full articles and usually limited in length by the journal. Journals specifically dedicated to short communications or letters are also published in some fields. In these the authors can present short preliminary findings before developing a full-length paper.

3. Choose a Journal

Are you looking for the right place to publish your paper? Find out here whether a De Gruyter journal might be the right fit.

Submit to journals that you already read, that you have a good feel for. If you do so, you will have a better appreciation of both its culture and the requirements of the editors and reviewers.

Other factors to consider are:

• The specific subject area
• The aims and scope of the journal
• The type of manuscript you have written
• The significance of your work
• The reputation of the journal
• The reputation of the editors within the community
• The editorial/review and production speeds of the journal
• The community served by the journal
• The coverage and distribution
• The accessibility ( open access vs. closed access)

4. Construct Your Paper

Each element of a paper has its purpose, so you should make these sections easy to index and search.

Don’t forget that requirements can differ highly per publication, so always make sure to apply a journal’s specific instructions – or guide – for authors to your manuscript, even to the first draft (text layout, paper citation, nomenclature, figures and table, etc.) It will save you time, and the editor’s.

Also, even in these days of Internet-based publishing, space is still at a premium, so be as concise as possible. As a good journalist would say: “Never use three words when one will do!”

Let’s look at the typical structure of a full research paper, but bear in mind certain subject disciplines may have their own specific requirements so check the instructions for authors on the journal’s home page.

4.1 The Title

It’s important to use the title to tell the reader what your paper is all about! You want to attract their attention, a bit like a newspaper headline does. Be specific and to the point. Keep it informative and concise, and avoid jargon and abbreviations (unless they are universally recognized like DNA, for example).

4.2 The Abstract

This could be termed as the “advertisement” for your article. Make it interesting and easily understood without the reader having to read the whole article. Be accurate and specific, and keep it as brief and concise as possible. Some journals (particularly in the medical fields) will ask you to structure the abstract in distinct, labeled sections, which makes it even more accessible.

A clear abstract will influence whether or not your work is considered and whether an editor should invest more time on it or send it for review.

4.3 Keywords

Keywords are used by abstracting and indexing services, such as PubMed and Web of Science. They are the labels of your manuscript, which make it “searchable” online by other researchers.

Include words or phrases (usually 4-8) that are closely related to your topic but not “too niche” for anyone to find them. Make sure to only use established abbreviations. Think about what scientific terms and its variations your potential readers are likely to use and search for. You can also do a test run of your selected keywords in one of the common academic search engines. Do similar articles to your own appear? Yes? Then that’s a good sign.

4.4 Introduction

This first part of the main text should introduce the problem, as well as any existing solutions you are aware of and the main limitations. Also, state what you hope to achieve with your research.

Do not confuse the introduction with the results, discussion or conclusion.

4.5 Methods

Every research article should include a detailed Methods section (also referred to as “Materials and Methods”) to provide the reader with enough information to be able to judge whether the study is valid and reproducible.

Include detailed information so that a knowledgeable reader can reproduce the experiment. However, use references and supplementary materials to indicate previously published procedures.

4.6 Results

In this section, you will present the essential or primary results of your study. To display them in a comprehensible way, you should use subheadings as well as illustrations such as figures, graphs, tables and photos, as appropriate.

4.7 Discussion

Here you should tell your readers what the results mean .

Do state how the results relate to the study’s aims and hypotheses and how the findings relate to those of other studies. Explain all possible interpretations of your findings and the study’s limitations.

Do not make “grand statements” that are not supported by the data. Also, do not introduce any new results or terms. Moreover, do not ignore work that conflicts or disagrees with your findings. Instead …

Be brave! Address conflicting study results and convince the reader you are the one who is correct.

4.8 Conclusion

Your conclusion isn’t just a summary of what you’ve already written. It should take your paper one step further and answer any unresolved questions.

Sum up what you have shown in your study and indicate possible applications and extensions. The main question your conclusion should answer is: What do my results mean for the research field and my community?

4.9 Acknowledgments and Ethical Statements

It is extremely important to acknowledge anyone who has helped you with your paper, including researchers who supplied materials or reagents (e.g. vectors or antibodies); and anyone who helped with the writing or English, or offered critical comments about the content.

Learn more about academic integrity in our blog post “Scholarly Publication Ethics: 4 Common Mistakes You Want To Avoid” .

Remember to state why people have been acknowledged and ask their permission . Ensure that you acknowledge sources of funding, including any grant or reference numbers.

Furthermore, if you have worked with animals or humans, you need to include information about the ethical approval of your study and, if applicable, whether informed consent was given. Also, state whether you have any competing interests regarding the study (e.g. because of financial or personal relationships.)

4.10 References

The end is in sight, but don’t relax just yet!

De facto, there are often more mistakes in the references than in any other part of the manuscript. It is also one of the most annoying and time-consuming problems for editors.

Remember to cite the main scientific publications on which your work is based. But do not inflate the manuscript with too many references. Avoid excessive – and especially unnecessary – self-citations. Also, avoid excessive citations of publications from the same institute or region.

5. Decide the Order of Authors

In the sciences, the most common way to order the names of the authors is by relative contribution.

Generally, the first author conducts and/or supervises the data analysis and the proper presentation and interpretation of the results. They put the paper together and usually submit the paper to the journal.

Co-authors make intellectual contributions to the data analysis and contribute to data interpretation. They review each paper draft. All of them must be able to present the paper and its results, as well as to defend the implications and discuss study limitations.

Do not leave out authors who should be included or add “gift authors”, i.e. authors who did not contribute significantly.

6. Check and Double-Check

As a final step before submission, ask colleagues to read your work and be constructively critical .

Make sure that the paper is appropriate for the journal – take a last look at their aims and scope. Check if all of the requirements in the instructions for authors are met.

Ensure that the cited literature is balanced. Are the aims, purpose and significance of the results clear?

Conduct a final check for language, either by a native English speaker or an editing service.

7. Submit Your Paper

When you and your co-authors have double-, triple-, quadruple-checked the manuscript: submit it via e-mail or online submission system. Along with your manuscript, submit a cover letter, which highlights the reasons why your paper would appeal to the journal and which ensures that you have received approval of all authors for submission.

It is up to the editors and the peer-reviewers now to provide you with their (ideally constructive and helpful) comments and feedback. Time to take a breather!

If the paper gets rejected, do not despair – it happens to literally everybody. If the journal suggests major or minor revisions, take the chance to provide a thorough response and make improvements as you see fit. If the paper gets accepted, congrats!

It’s now time to get writing and share your hard work – good luck!

If you are interested, check out this related blog post

[Title Image by Nick Morrison via Unsplash]

David Sleeman

David Sleeman worked as Senior Journals Manager in the field of Physical Sciences at De Gruyter.

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The 5 Best Platforms to Publish Your Academic Research

Academic research is a central component of scientific advancements and breakthrough innovations. However, your research journey is complex and ever-changing. You must take into consideration funding options, how to securely store your information, choosing where to publish your research, finding manuscript peer reviewers, and many more.

To keep up with the change, you and other researchers require modern, easy-to-navigate research platforms to help you uncover, store, verify, compile, and share content, data, and important insights to continue to carry out breakthrough research.

This article explains how to identify the best platforms for publishing your research and gives you a list of five platforms to help you publish. Towards the end, you’ll also see a mention of how Orvium can further assist you with publishing.

How to Identify the Best Platforms for Publishing

When trying to identify the best platforms for publishing your research, you have to consider several factors, including:

• Does the platform support your research journey ? Can you collaborate with other authors and researchers, discover public groups and research papers and manuscripts (including Open Access work), view interactive graphs, images, tables, etc., track citations, and build a professional research profile?
• Is the platform easy to use ? Does it offer rich functionalities that are easy to understand, and if so, which ones?
• Does it use artificial intelligence and machine learning ? Automated actions (email alerts, etc.) can help you unlock breakthroughs faster and deliver deeper insights.
• What security and governance does it have ? Platforms must be secure and compliant according to local regulations since researchers often deal with sensitive data.

The 5 Best Platforms to Publish Academic Research

Researchgate.

ResearchGate is a platform hosting over 135 million publication pages with a community of 20 million scientists. The platform allows you to show off your work, access papers and advice from other researchers, make contacts and even find jobs. Some of its more prominent features include:

• Dedicated Q&A section with searchable keywords to target experts in your particular field or area of study
• Ability to create a personal profile page where you can display all research-specific details about yourself, including up to five pieces of work (including datasets and conference papers)
• In-depth stats on who reads your work and the ability to track your citations
• A private messaging service that allows you to send messages to other researchers
• A comments section to provide feedback when viewing a paper
• A “projects” section to tell others about your upcoming work.

In addition, it's completely free to use!

Academia is a research-sharing platform with over 178 million users, 29 million papers uploaded, and 87 million visitors per month. Their goal is to accelerate research in all fields, ensure that all research is available for free and that the sharing of knowledge is available in multiple formats (videos, datasets, code, short-form content, etc.). Some of their more prominent features include:

• Mentions and search alerts that notify you when another researcher cites, thanks, or acknowledges your work, and automatic reports of search queries
• Ability to create a personal profile page
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• A “grants” feature to allow you to find new grants and fellowships in your field
• Advanced research discovery tools allow you to see full texts and citations of millions of papers.

The platform is based on a “freemium” business model, which provides free access to research for everyone, and paid capabilities to subscribers.

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ScienceOpen is a discovery platform that empowers researchers to make an impact in their communities. The platform is committed to Open Science, combining decades of experience in traditional publishing, computing, and academic research to provide free access to knowledge to drive creativity, innovation, and development. Some of their more prominent features include:

• You can publish your most recent paper as a preprint that’s citable and includes a DOI to share with peers immediately and enhance visibility
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The platform is free to use, although some features (like publishing your preprint) may cost money.

IOPscience is a platform that embraces innovative technologies to make it easier for researchers to discover and access technical, scientific, and medical content while managing their own research content. They participate in several programs that offer researchers in developing countries several ways to gain access to journals at little or no cost. Some of their other features include:

• An enhanced search filtering feature allows you to find relevant research faster
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• Ability to create a personal profile, customize your alerts, view recently published articles within your field or area of interest, and save relevant papers or articles
• Ability to receive email alerts and RSS feeds once new content is published.

IOPscience is free to use and functions on an Open Access policy, which you can check here .

Orvium is an open, community-based research platform that allows researchers, reviewers, and publishers to share, publish, review, and manage their research. Orvium protects your work with built-in blockchain integration to ensure that you maintain the copyright of your work and not only. Some of our more notable features include:

• Access to a modern web platform with Google indexing, notifications, and mobile-ready features
• Ability to manage your entire publication process, with control over when you submit, receive peer reviews, and publish your paper
• “Collaboration” and “full traceability” features allow you to track your profile impact, get in touch with other researchers, and have ownership over your work
• Recognition badges or economic rewards are given when you peer-review.

Orvium is completely free to use.

Orvium Makes Choosing a Platform Easy

No matter what platform or community you choose to be a part of, you now know what you need to look for when choosing one. You also learned about five excellent platforms where you can publish your academic research. Orvium will remain your one-stop-shop platform for all your research needs. Do you want to know how Orvium and our communities work? Check out our platform or contact us with any questions you may have.

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• Publication Recognition

How to Submit a Paper for Publication in a Journal

• 4 minute read
• 49.7K views

Table of Contents

Whether you’ve done it before, or not, submitting a paper for publication in a journal is, to say the least, a process that brings great anxiety and stress. After all your hard work for many months, or even years, recognition is finally at your grasp. That is why there no room for mistakes.

What to Expect of the Scientific Publishing Process

If you are a beginner, you might be struggling to know exactly what to do. After all, it is a step-by-step process, sometimes with a lot of players and paperwork involved; it’s not always evident what to do next. An excellent, high-quality manuscript is the best way to give a good impression from the beginning, putting your paper on the right track for a successful submission. At Elsevier, with our Language Editing services , we not only revise your manuscript, but guarantee there are no text errors.

If, on the other hand, you have already published articles, you might have enough experience to know that each paper submission in a journal is different. Either the journal is different, or the context has changed, or the peers are new. You never know what can go right or wrong, other than the variable that lies under your control – that the manuscript is error-free and spot-on for successful acceptance. In this case, you might consider Elsevier’s professional Language Editing services to amend your text to the target journal’s requirements, helping you focus on other projects.

Scientific Paper Submission. Are you ready? Let’s go!

For many researchers, putting their paper through the professional journal submission process is stressful. Here is a simple to-do list which might help you go through all of it with some peace of mind:

• Use an external editing service, such as Elsevier’s Author Services if you need assistance with language.
• Free e-learning modules on preparing your manuscript can be found on Researcher Academy.
• Mendeley makes your life easier by helping you organize your papers, citations and references, accessing them in the cloud on any device, wherever you are.
• Do not rush submitting your article for publication Carefully re-read and revise your manuscript. Re-reading is essential in the research field and helps identify the most common problems and shortcomings in the manuscript, which might otherwise be overlooked. Often, reading your text out loud will uncover more errors than reading silently to yourself. If you are doubtful about the quality of your text, consider Elsevier’s Professional Language Editing services . Our professional team is trained to provide you with an optimal text for successful submission.
• Read the journal’s aims and scope to make sure they match your paper.
• Check whether you can submit – some journals are invitation only.
• Use the journal’s metrics to measure its impact. In fact, you can also check other additional info – like speed and reach to understand if it’s the right one for you.
• If you’re a post doc, check out our free access program.
• Read the aims and scope and author guidelines of your target journal carefully Once you think your manuscript is ready for submission, the next important step is to read the aims and scope of the journals in your target research area. Doing so will improve the chances of having your manuscript accepted for publishing.
• Submit a cover letter with the manuscript Never underestimate the importance of a cover letter addressed to the editor or editor-in-chief of the target journal. A good cover letter should underline 3 main aspects: the main theme of the paper, its originality/novelty and the relevance of the manuscript to the target journal.
• Make a good first impression with your title and abstract The title and abstract are incredibly important components of a manuscript as they are the first elements a journal editor sees. They create interest and curiosity about the whole work.

Now, what happens if your paper gets rejected by the journal ? It is, by no means, the end of the world. There are very real steps you can take to ultimately get published in a reputable journal.

The Science of Article Publishing

Article publishing is every researcher’s aim. It brings visibility and recognition, essential factors for those who intend to build a full career in research. However, most scientists feel handicapped or lost when it comes to conveying their findings or ideas to others. For many, it can be difficult to re-format a certain type of text to another, be aware of formatting requirements and translate their work into visually appealing outcomes. Additionally, keeping track of all the steps needed to submit an article for publication can be overwhelming and take too much time that could be spent doing new research.

At Elsevier, we believe everyone should be doing what they do best: in this case, leave research for scientists and leave the science of turning the best ideas into excellent quality text to our professionals.

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How to Write and Publish a Research Paper for a Peer-Reviewed Journal

• Open Access
• Published: 30 April 2020
• volume  36 ,  pages 909–913 ( 2021 )

You have full access to this open access article

• Clara Busse   ORCID: orcid.org/0000-0002-0178-1000 1 &
• Ella August   ORCID: orcid.org/0000-0001-5151-1036 1 , 2  

188k Accesses

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Cite this article

Communicating research findings is an essential step in the research process. Often, peer-reviewed journals are the forum for such communication, yet many researchers are never taught how to write a publishable scientific paper. In this article, we explain the basic structure of a scientific paper and describe the information that should be included in each section. We also identify common pitfalls for each section and recommend strategies to avoid them. Further, we give advice about target journal selection and authorship. In the online resource 1 , we provide an example of a high-quality scientific paper, with annotations identifying the elements we describe in this article.

Working on a manuscript?

Introduction.

Writing a scientific paper is an important component of the research process, yet researchers often receive little formal training in scientific writing. This is especially true in low-resource settings. In this article, we explain why choosing a target journal is important, give advice about authorship, provide a basic structure for writing each section of a scientific paper, and describe common pitfalls and recommendations for each section. In the online resource 1 , we also include an annotated journal article that identifies the key elements and writing approaches that we detail here. Before you begin your research, make sure you have ethical clearance from all relevant ethical review boards.

Select a Target Journal Early in the Writing Process

We recommend that you select a “target journal” early in the writing process; a “target journal” is the journal to which you plan to submit your paper. Each journal has a set of core readers and you should tailor your writing to this readership. For example, if you plan to submit a manuscript about vaping during pregnancy to a pregnancy-focused journal, you will need to explain what vaping is because readers of this journal may not have a background in this topic. However, if you were to submit that same article to a tobacco journal, you would not need to provide as much background information about vaping.

Information about a journal’s core readership can be found on its website, usually in a section called “About this journal” or something similar. For example, the Journal of Cancer Education presents such information on the “Aims and Scope” page of its website, which can be found here: https://www.springer.com/journal/13187/aims-and-scope .

Peer reviewer guidelines from your target journal are an additional resource that can help you tailor your writing to the journal and provide additional advice about crafting an effective article [ 1 ]. These are not always available, but it is worth a quick web search to find out.

Identify Author Roles Early in the Process

Early in the writing process, identify authors, determine the order of authors, and discuss the responsibilities of each author. Standard author responsibilities have been identified by The International Committee of Medical Journal Editors (ICMJE) [ 2 ]. To set clear expectations about each team member’s responsibilities and prevent errors in communication, we also suggest outlining more detailed roles, such as who will draft each section of the manuscript, write the abstract, submit the paper electronically, serve as corresponding author, and write the cover letter. It is best to formalize this agreement in writing after discussing it, circulating the document to the author team for approval. We suggest creating a title page on which all authors are listed in the agreed-upon order. It may be necessary to adjust authorship roles and order during the development of the paper. If a new author order is agreed upon, be sure to update the title page in the manuscript draft.

In the case where multiple papers will result from a single study, authors should discuss who will author each paper. Additionally, authors should agree on a deadline for each paper and the lead author should take responsibility for producing an initial draft by this deadline.

Structure of the Introduction Section

The introduction section should be approximately three to five paragraphs in length. Look at examples from your target journal to decide the appropriate length. This section should include the elements shown in Fig.  1 . Begin with a general context, narrowing to the specific focus of the paper. Include five main elements: why your research is important, what is already known about the topic, the “gap” or what is not yet known about the topic, why it is important to learn the new information that your research adds, and the specific research aim(s) that your paper addresses. Your research aim should address the gap you identified. Be sure to add enough background information to enable readers to understand your study. Table 1 provides common introduction section pitfalls and recommendations for addressing them.

The main elements of the introduction section of an original research article. Often, the elements overlap

Methods Section

The purpose of the methods section is twofold: to explain how the study was done in enough detail to enable its replication and to provide enough contextual detail to enable readers to understand and interpret the results. In general, the essential elements of a methods section are the following: a description of the setting and participants, the study design and timing, the recruitment and sampling, the data collection process, the dataset, the dependent and independent variables, the covariates, the analytic approach for each research objective, and the ethical approval. The hallmark of an exemplary methods section is the justification of why each method was used. Table 2 provides common methods section pitfalls and recommendations for addressing them.

Results Section

The focus of the results section should be associations, or lack thereof, rather than statistical tests. Two considerations should guide your writing here. First, the results should present answers to each part of the research aim. Second, return to the methods section to ensure that the analysis and variables for each result have been explained.

Begin the results section by describing the number of participants in the final sample and details such as the number who were approached to participate, the proportion who were eligible and who enrolled, and the number of participants who dropped out. The next part of the results should describe the participant characteristics. After that, you may organize your results by the aim or by putting the most exciting results first. Do not forget to report your non-significant associations. These are still findings.

Tables and figures capture the reader’s attention and efficiently communicate your main findings [ 3 ]. Each table and figure should have a clear message and should complement, rather than repeat, the text. Tables and figures should communicate all salient details necessary for a reader to understand the findings without consulting the text. Include information on comparisons and tests, as well as information about the sample and timing of the study in the title, legend, or in a footnote. Note that figures are often more visually interesting than tables, so if it is feasible to make a figure, make a figure. To avoid confusing the reader, either avoid abbreviations in tables and figures, or define them in a footnote. Note that there should not be citations in the results section and you should not interpret results here. Table 3 provides common results section pitfalls and recommendations for addressing them.

Discussion Section

Opposite the introduction section, the discussion should take the form of a right-side-up triangle beginning with interpretation of your results and moving to general implications (Fig.  2 ). This section typically begins with a restatement of the main findings, which can usually be accomplished with a few carefully-crafted sentences.

Major elements of the discussion section of an original research article. Often, the elements overlap

Next, interpret the meaning or explain the significance of your results, lifting the reader’s gaze from the study’s specific findings to more general applications. Then, compare these study findings with other research. Are these findings in agreement or disagreement with those from other studies? Does this study impart additional nuance to well-accepted theories? Situate your findings within the broader context of scientific literature, then explain the pathways or mechanisms that might give rise to, or explain, the results.

Journals vary in their approach to strengths and limitations sections: some are embedded paragraphs within the discussion section, while some mandate separate section headings. Keep in mind that every study has strengths and limitations. Candidly reporting yours helps readers to correctly interpret your research findings.

The next element of the discussion is a summary of the potential impacts and applications of the research. Should these results be used to optimally design an intervention? Does the work have implications for clinical protocols or public policy? These considerations will help the reader to further grasp the possible impacts of the presented work.

Finally, the discussion should conclude with specific suggestions for future work. Here, you have an opportunity to illuminate specific gaps in the literature that compel further study. Avoid the phrase “future research is necessary” because the recommendation is too general to be helpful to readers. Instead, provide substantive and specific recommendations for future studies. Table 4 provides common discussion section pitfalls and recommendations for addressing them.

Follow the Journal’s Author Guidelines

After you select a target journal, identify the journal’s author guidelines to guide the formatting of your manuscript and references. Author guidelines will often (but not always) include instructions for titles, cover letters, and other components of a manuscript submission. Read the guidelines carefully. If you do not follow the guidelines, your article will be sent back to you.

Finally, do not submit your paper to more than one journal at a time. Even if this is not explicitly stated in the author guidelines of your target journal, it is considered inappropriate and unprofessional.

Your title should invite readers to continue reading beyond the first page [ 4 , 5 ]. It should be informative and interesting. Consider describing the independent and dependent variables, the population and setting, the study design, the timing, and even the main result in your title. Because the focus of the paper can change as you write and revise, we recommend you wait until you have finished writing your paper before composing the title.

Be sure that the title is useful for potential readers searching for your topic. The keywords you select should complement those in your title to maximize the likelihood that a researcher will find your paper through a database search. Avoid using abbreviations in your title unless they are very well known, such as SNP, because it is more likely that someone will use a complete word rather than an abbreviation as a search term to help readers find your paper.

After you have written a complete draft, use the checklist (Fig. 3 ) below to guide your revisions and editing. Additional resources are available on writing the abstract and citing references [ 5 ]. When you feel that your work is ready, ask a trusted colleague or two to read the work and provide informal feedback. The box below provides a checklist that summarizes the key points offered in this article.

Checklist for manuscript quality

Data Availability

Michalek AM (2014) Down the rabbit hole…advice to reviewers. J Cancer Educ 29:4–5

Article   Google Scholar  

International Committee of Medical Journal Editors. Defining the role of authors and contributors: who is an author? http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authosrs-and-contributors.html . Accessed 15 January, 2020

Vetto JT (2014) Short and sweet: a short course on concise medical writing. J Cancer Educ 29(1):194–195

Brett M, Kording K (2017) Ten simple rules for structuring papers. PLoS ComputBiol. https://doi.org/10.1371/journal.pcbi.1005619

Lang TA (2017) Writing a better research article. J Public Health Emerg. https://doi.org/10.21037/jphe.2017.11.06

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Acknowledgments

Ella August is grateful to the Sustainable Sciences Institute for mentoring her in training researchers on writing and publishing their research.

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Clara Busse & Ella August

Department of Epidemiology, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA

Ella August

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Busse, C., August, E. How to Write and Publish a Research Paper for a Peer-Reviewed Journal. J Canc Educ 36 , 909–913 (2021). https://doi.org/10.1007/s13187-020-01751-z

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How to Write and Publish a Research Paper for a Peer-Reviewed Journal

Clara busse.

1 Department of Maternal and Child Health, University of North Carolina Gillings School of Global Public Health, 135 Dauer Dr, 27599 Chapel Hill, NC USA

Ella August

2 Department of Epidemiology, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109-2029 USA

Associated Data

Communicating research findings is an essential step in the research process. Often, peer-reviewed journals are the forum for such communication, yet many researchers are never taught how to write a publishable scientific paper. In this article, we explain the basic structure of a scientific paper and describe the information that should be included in each section. We also identify common pitfalls for each section and recommend strategies to avoid them. Further, we give advice about target journal selection and authorship. In the online resource 1 , we provide an example of a high-quality scientific paper, with annotations identifying the elements we describe in this article.

Electronic supplementary material

The online version of this article (10.1007/s13187-020-01751-z) contains supplementary material, which is available to authorized users.

Introduction

Writing a scientific paper is an important component of the research process, yet researchers often receive little formal training in scientific writing. This is especially true in low-resource settings. In this article, we explain why choosing a target journal is important, give advice about authorship, provide a basic structure for writing each section of a scientific paper, and describe common pitfalls and recommendations for each section. In the online resource 1 , we also include an annotated journal article that identifies the key elements and writing approaches that we detail here. Before you begin your research, make sure you have ethical clearance from all relevant ethical review boards.

Select a Target Journal Early in the Writing Process

We recommend that you select a “target journal” early in the writing process; a “target journal” is the journal to which you plan to submit your paper. Each journal has a set of core readers and you should tailor your writing to this readership. For example, if you plan to submit a manuscript about vaping during pregnancy to a pregnancy-focused journal, you will need to explain what vaping is because readers of this journal may not have a background in this topic. However, if you were to submit that same article to a tobacco journal, you would not need to provide as much background information about vaping.

Information about a journal’s core readership can be found on its website, usually in a section called “About this journal” or something similar. For example, the Journal of Cancer Education presents such information on the “Aims and Scope” page of its website, which can be found here: https://www.springer.com/journal/13187/aims-and-scope .

Peer reviewer guidelines from your target journal are an additional resource that can help you tailor your writing to the journal and provide additional advice about crafting an effective article [ 1 ]. These are not always available, but it is worth a quick web search to find out.

Identify Author Roles Early in the Process

Early in the writing process, identify authors, determine the order of authors, and discuss the responsibilities of each author. Standard author responsibilities have been identified by The International Committee of Medical Journal Editors (ICMJE) [ 2 ]. To set clear expectations about each team member’s responsibilities and prevent errors in communication, we also suggest outlining more detailed roles, such as who will draft each section of the manuscript, write the abstract, submit the paper electronically, serve as corresponding author, and write the cover letter. It is best to formalize this agreement in writing after discussing it, circulating the document to the author team for approval. We suggest creating a title page on which all authors are listed in the agreed-upon order. It may be necessary to adjust authorship roles and order during the development of the paper. If a new author order is agreed upon, be sure to update the title page in the manuscript draft.

In the case where multiple papers will result from a single study, authors should discuss who will author each paper. Additionally, authors should agree on a deadline for each paper and the lead author should take responsibility for producing an initial draft by this deadline.

Structure of the Introduction Section

The introduction section should be approximately three to five paragraphs in length. Look at examples from your target journal to decide the appropriate length. This section should include the elements shown in Fig.  1 . Begin with a general context, narrowing to the specific focus of the paper. Include five main elements: why your research is important, what is already known about the topic, the “gap” or what is not yet known about the topic, why it is important to learn the new information that your research adds, and the specific research aim(s) that your paper addresses. Your research aim should address the gap you identified. Be sure to add enough background information to enable readers to understand your study. Table ​ Table1 1 provides common introduction section pitfalls and recommendations for addressing them.

The main elements of the introduction section of an original research article. Often, the elements overlap

Common introduction section pitfalls and recommendations

Methods Section

The purpose of the methods section is twofold: to explain how the study was done in enough detail to enable its replication and to provide enough contextual detail to enable readers to understand and interpret the results. In general, the essential elements of a methods section are the following: a description of the setting and participants, the study design and timing, the recruitment and sampling, the data collection process, the dataset, the dependent and independent variables, the covariates, the analytic approach for each research objective, and the ethical approval. The hallmark of an exemplary methods section is the justification of why each method was used. Table ​ Table2 2 provides common methods section pitfalls and recommendations for addressing them.

Common methods section pitfalls and recommendations

Results Section

The focus of the results section should be associations, or lack thereof, rather than statistical tests. Two considerations should guide your writing here. First, the results should present answers to each part of the research aim. Second, return to the methods section to ensure that the analysis and variables for each result have been explained.

Begin the results section by describing the number of participants in the final sample and details such as the number who were approached to participate, the proportion who were eligible and who enrolled, and the number of participants who dropped out. The next part of the results should describe the participant characteristics. After that, you may organize your results by the aim or by putting the most exciting results first. Do not forget to report your non-significant associations. These are still findings.

Tables and figures capture the reader’s attention and efficiently communicate your main findings [ 3 ]. Each table and figure should have a clear message and should complement, rather than repeat, the text. Tables and figures should communicate all salient details necessary for a reader to understand the findings without consulting the text. Include information on comparisons and tests, as well as information about the sample and timing of the study in the title, legend, or in a footnote. Note that figures are often more visually interesting than tables, so if it is feasible to make a figure, make a figure. To avoid confusing the reader, either avoid abbreviations in tables and figures, or define them in a footnote. Note that there should not be citations in the results section and you should not interpret results here. Table ​ Table3 3 provides common results section pitfalls and recommendations for addressing them.

Common results section pitfalls and recommendations

Discussion Section

Opposite the introduction section, the discussion should take the form of a right-side-up triangle beginning with interpretation of your results and moving to general implications (Fig.  2 ). This section typically begins with a restatement of the main findings, which can usually be accomplished with a few carefully-crafted sentences.

Major elements of the discussion section of an original research article. Often, the elements overlap

Next, interpret the meaning or explain the significance of your results, lifting the reader’s gaze from the study’s specific findings to more general applications. Then, compare these study findings with other research. Are these findings in agreement or disagreement with those from other studies? Does this study impart additional nuance to well-accepted theories? Situate your findings within the broader context of scientific literature, then explain the pathways or mechanisms that might give rise to, or explain, the results.

Journals vary in their approach to strengths and limitations sections: some are embedded paragraphs within the discussion section, while some mandate separate section headings. Keep in mind that every study has strengths and limitations. Candidly reporting yours helps readers to correctly interpret your research findings.

The next element of the discussion is a summary of the potential impacts and applications of the research. Should these results be used to optimally design an intervention? Does the work have implications for clinical protocols or public policy? These considerations will help the reader to further grasp the possible impacts of the presented work.

Finally, the discussion should conclude with specific suggestions for future work. Here, you have an opportunity to illuminate specific gaps in the literature that compel further study. Avoid the phrase “future research is necessary” because the recommendation is too general to be helpful to readers. Instead, provide substantive and specific recommendations for future studies. Table ​ Table4 4 provides common discussion section pitfalls and recommendations for addressing them.

Common discussion section pitfalls and recommendations

Follow the Journal’s Author Guidelines

After you select a target journal, identify the journal’s author guidelines to guide the formatting of your manuscript and references. Author guidelines will often (but not always) include instructions for titles, cover letters, and other components of a manuscript submission. Read the guidelines carefully. If you do not follow the guidelines, your article will be sent back to you.

Finally, do not submit your paper to more than one journal at a time. Even if this is not explicitly stated in the author guidelines of your target journal, it is considered inappropriate and unprofessional.

Your title should invite readers to continue reading beyond the first page [ 4 , 5 ]. It should be informative and interesting. Consider describing the independent and dependent variables, the population and setting, the study design, the timing, and even the main result in your title. Because the focus of the paper can change as you write and revise, we recommend you wait until you have finished writing your paper before composing the title.

Be sure that the title is useful for potential readers searching for your topic. The keywords you select should complement those in your title to maximize the likelihood that a researcher will find your paper through a database search. Avoid using abbreviations in your title unless they are very well known, such as SNP, because it is more likely that someone will use a complete word rather than an abbreviation as a search term to help readers find your paper.

After you have written a complete draft, use the checklist (Fig. ​ (Fig.3) 3 ) below to guide your revisions and editing. Additional resources are available on writing the abstract and citing references [ 5 ]. When you feel that your work is ready, ask a trusted colleague or two to read the work and provide informal feedback. The box below provides a checklist that summarizes the key points offered in this article.

Checklist for manuscript quality

(PDF 362 kb)

Acknowledgments

Ella August is grateful to the Sustainable Sciences Institute for mentoring her in training researchers on writing and publishing their research.

Code Availability

Not applicable.

Data Availability

Compliance with ethical standards.

The authors declare that they have no conflict of interest.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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7 steps to publishing in a scientific journal

Before you hit “submit,” here’s a checklist (and pitfalls to avoid)

As scholars, we strive to do high-quality research that will advance science. We come up with what we believe are unique hypotheses, base our work on robust data and use an appropriate research methodology. As we write up our findings, we aim to provide theoretical insight, and share theoretical and practical implications about our work. Then we submit our manuscript for publication in a peer-reviewed journal.

In my seven years of research and teaching, I have observed several shortcomings in the manuscript preparation and submission process that often lead to research being rejected for publication. Being aware of these shortcomings will increase your chances of having your manuscript published and also boost your research profile and career progression.

In this article, intended for doctoral students and other young scholars, I identify common pitfalls and offer helpful solutions to prepare more impactful papers. While there are several types of research articles, such as short communications, review papers and so forth, these guidelines focus on preparing a full article (including a literature review), whether based on qualitative or quantitative methodology, from the perspective of the management, education, information sciences and social sciences disciplines.

Writing for academic journals is a highly competitive activity, and it’s important to understand that there could be several reasons behind a rejection. Furthermore, the journal peer-review process is an essential element of publication because no writer could identify and address all potential issues with a manuscript.

1. Do not rush submitting your article for publication.

In my first article for Elsevier Connect – “ Five secrets to surviving (and thriving in) a PhD program ” – I emphasized that scholars should start writing during the early stages of your research or doctoral study career. This secret does not entail submitting your manuscript for publication the moment you have crafted its conclusion. Authors sometimes rely on the fact that they will always have an opportunity to address their work’s shortcomings after the feedback received from the journal editor and reviewers has identified them.

A proactive approach and attitude will reduce the chance of rejection and disappointment. In my opinion, a logical flow of activities dominates every research activity and should be followed for preparing a manuscript as well. Such activities include carefully re-reading your manuscript at different times and perhaps at different places. Re-reading is essential in the research field and helps identify the most common problems and shortcomings in the manuscript, which might otherwise be overlooked. Second, I find it very helpful to share my manuscripts with my colleagues and other researchers in my network and to request their feedback. In doing so, I highlight any sections of the manuscript that I would like reviewers to be absolutely clear on.

2. Select an appropriate publication outlet.

I also ask colleagues about the most appropriate journal to submit my manuscript to; finding the right journal for your article can dramatically improve the chances of acceptance and ensure it reaches your target audience.

Elsevier provides an innovative Journal Finder search facility on its website. Authors enter the article title, a brief abstract and the field of research to get a list of the most appropriate journals for their article. For a full discussion of how to select an appropriate journal see Knight and Steinbach (2008).

Less experienced scholars sometimes choose to submit their research work to two or more journals at the same time. Research ethics and policies of all scholarly journals suggest that authors should submit a manuscript to only one journal at a time. Doing otherwise can cause embarrassment and lead to copyright problems for the author, the university employer and the journals involved.

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3. Read the aims and scope and author guidelines of your target journal carefully.

Once you have read and re-read your manuscript carefully several times, received feedback from your colleagues, and identified a target journal, the next important step is to read the aims and scope of the journals in your target research area. Doing so will improve the chances of having your manuscript accepted for publishing. Another important step is to download and absorb the author guidelines and ensure your manuscript conforms to them. Some publishers report that one paper in five does not follow the style and format requirements of the target journal, which might specify requirements for figures, tables and references.

Rejection can come at different times and in different formats. For instance, if your research objective is not in line with the aims and scope of the target journal, or if your manuscript is not structured and formatted according to the target journal layout, or if your manuscript does not have a reasonable chance of being able to satisfy the target journal’s publishing expectations, the manuscript can receive a desk rejection from the editor without being sent out for peer review. Desk rejections can be disheartening for authors, making them feel they have wasted valuable time and might even cause them to lose enthusiasm for their research topic. Sun and Linton (2014), Hierons (2016) and Craig (2010) offer useful discussions on the subject of “desk rejections.”

4. Make a good first impression with your title and abstract.

The title and abstract are incredibly important components of a manuscript as they are the first elements a journal editor sees. I have been fortunate to receive advice from editors and reviewers on my submissions, and feedback from many colleagues at academic conferences, and this is what I’ve learned:

• The title should summarize the main theme of the article and reflect your contribution to the theory.
• The abstract should be crafted carefully and encompass the aim and scope of the study; the key problem to be addressed and theory; the method used; the data set; key findings; limitations; and implications for theory and practice.

Dr. Angel Borja goes into detail about these components in “ 11 steps to structuring a science paper editors will take seriously .”

Learn more in Elsevier's free Researcher Academy

5. Have a professional editing firm copy-edit ( not just proofread) your manuscript, including the main text, list of references, tables and figures.

The key characteristic of scientific writing is clarity. Before submitting a manuscript for publication, it is highly advisable to have a professional editing firm copy-edit your manuscript. An article submitted to a peer-reviewed journal will be scrutinized critically by the editorial board before it is selected for peer review. According to a statistic shared by Elsevier , between 30 percent and 50 percent of articles submitted to Elsevier journals are rejected before they even reach the peer-review stage, and one of the top reasons for rejection is poor language. A properly written, edited and presented text will be error free and understandable and will project a professional image that will help ensure your work is taken seriously in the world of publishing. On occasion, the major revisions conducted at the request of a reviewer will necessitate another round of editing.

Authors can facilitate the editing of their manuscripts by taking precautions at their end. These include proofreading their own manuscript for accuracy and wordiness (avoid unnecessary or normative descriptions like “it should be noted here” and “the authors believe) and sending it for editing only when it is complete in all respects and ready for publishing. Professional editing companies charge hefty fees, and it is simply not financially viable to have them conduct multiple rounds of editing on your article. Applications like the spelling and grammar checker in Microsoft Word or Grammarly are certainly worth applying to your article, but the benefits of proper editing are undeniable. For more on the difference between proofreading and editing, see the description in Elsevier’s WebShop.

6. Submit a cover letter with the manuscript.

Never underestimate the importance of a cover letter addressed to the editor or editor-in-chief of the target journal. Last year, I attended a conference in Boston. A “meet the editors” session revealed that many submissions do not include a covering letter, but the editors-in-chief present, who represented renewed and ISI-indexed Elsevier journals, argued that the cover letter gives authors an important opportunity to convince them that their research work is worth reviewing.

Accordingly, the content of the cover letter is also worth spending time on. Some inexperienced scholars paste the article’s abstract into their letter thinking it will be sufficient to make the case for publication; it is a practice best avoided. A good cover letter first outlines the main theme of the paper; second, argues the novelty of the paper; and third, justifies the relevance of the manuscript to the target journal. I would suggest limiting the cover letter to half a page. More importantly, peers and colleagues who read the article and provided feedback before the manuscript’s submission should be acknowledged in the cover letter.

7. Address reviewer comments very carefully.

Editors and editors-in-chief usually couch the acceptance of a manuscript as subject to a “revise and resubmit” based on the recommendations provided by the reviewer or reviewers. These revisions may necessitate either major or minor changes in the manuscript. Inexperienced scholars should understand a few key aspects of the revision process. First, it important to address the revisions diligently; second, is imperative to address all the comments received from the reviewers and avoid oversights; third, the resubmission of the revised manuscript must happen by the deadline provided by the journal; fourth, the revision process might comprise multiple rounds.

The revision process requires two major documents. The first is the revised manuscript highlighting all the modifications made following the recommendations received from the reviewers. The second is a letter listing the authors’ responses illustrating they have addressed all the concerns of the reviewers and editors. These two documents should be drafted carefully. The authors of the manuscript can agree or disagree with the comments of the reviewers (typically agreement is encouraged) and are not always obliged to implement their recommendations, but they should in all cases provide a well-argued justification for their course of action.

Given the ever increasing number of manuscripts submitted for publication, the process of preparing a manuscript well enough to have it accepted by a journal can be daunting. High-impact journals accept less than 10 percent of the articles submitted to them, although the acceptance ratio for special issues or special topics sections is normally over 40 percent. Scholars might have to resign themselves to having their articles rejected and then reworking them to submit them to a different journal before the manuscript is accepted.

The advice offered here is not exhaustive but it’s also not difficult to implement. These recommendations require proper attention, planning and careful implementation; however, following this advice could help doctoral students and other scholars improve the likelihood of getting their work published, and that is key to having a productive, exciting and rewarding academic career.

Acknowledgements

I would like to thank Professor Heikki Karjaluoto, Jyväskylä University School of Business and Economics for providing valuable feedback on this article.

• Sun, H., & Linton, J. D. (2014). Structuring papers for success: Making your paper more like a high impact publication than a desk reject , Technovation.
• Craig, J. B. (2010). Desk rejection: How to avoid being hit by a returning boomerang , Family Business Review .
• Hierons, R. M. (2016). The dreaded desk reject , Software Testing, Verification and Reliability .
• Borja, A (2014): 11 steps to structuring a science paper editors will take seriously , Elsevier Connect
• Knight, L. V., & Steinbach, T. A. (2008). Selecting an appropriate publication outlet: a comprehensive model of journal selection criteria for researchers in a broad range of academic disciplines , International Journal of Doctoral Studies .
• Tewin, K. (2015). How to Better Proofread An Article in 6 Simple Steps ,
• Day, R, & Gastel, B: How to write and publish a scientific paper. Cambridge University Press (2012)

Contributors

Aijaz Shaikh, PhD

Aijaz Shaikh has a PhD in Marketing from the Jyväskylä University School of Business & Economics (AMBA accredited), Finland, an MSc from Hanken School of Economics (AACSB / EQUIS/AMBA accredited), Finland. He is Member-Editorial Review Board of the  International Journal of E-Business Research and  special issue Guest Editor of the International Journal of E-Business Research. His academic specialty is in Marketing (consumer behaviour), Information Technology Adoption, and Mobile Financial Services.

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• Research paper

How to Write a Research Paper | A Beginner's Guide

A research paper is a piece of academic writing that provides analysis, interpretation, and argument based on in-depth independent research.

Research papers are similar to academic essays , but they are usually longer and more detailed assignments, designed to assess not only your writing skills but also your skills in scholarly research. Writing a research paper requires you to demonstrate a strong knowledge of your topic, engage with a variety of sources, and make an original contribution to the debate.

This step-by-step guide takes you through the entire writing process, from understanding your assignment to proofreading your final draft.

Table of contents

Understand the assignment, choose a research paper topic, conduct preliminary research, develop a thesis statement, create a research paper outline, write a first draft of the research paper, write the introduction, write a compelling body of text, write the conclusion, the second draft, the revision process, research paper checklist, free lecture slides.

Completing a research paper successfully means accomplishing the specific tasks set out for you. Before you start, make sure you thoroughly understanding the assignment task sheet:

• Read it carefully, looking for anything confusing you might need to clarify with your professor.
• Identify the assignment goal, deadline, length specifications, formatting, and submission method.
• Make a bulleted list of the key points, then go back and cross completed items off as you’re writing.

Carefully consider your timeframe and word limit: be realistic, and plan enough time to research, write, and edit.

Prevent plagiarism. Run a free check.

There are many ways to generate an idea for a research paper, from brainstorming with pen and paper to talking it through with a fellow student or professor.

You can try free writing, which involves taking a broad topic and writing continuously for two or three minutes to identify absolutely anything relevant that could be interesting.

You can also gain inspiration from other research. The discussion or recommendations sections of research papers often include ideas for other specific topics that require further examination.

Once you have a broad subject area, narrow it down to choose a topic that interests you, m eets the criteria of your assignment, and i s possible to research. Aim for ideas that are both original and specific:

• A paper following the chronology of World War II would not be original or specific enough.
• A paper on the experience of Danish citizens living close to the German border during World War II would be specific and could be original enough.

Note any discussions that seem important to the topic, and try to find an issue that you can focus your paper around. Use a variety of sources , including journals, books, and reliable websites, to ensure you do not miss anything glaring.

Do not only verify the ideas you have in mind, but look for sources that contradict your point of view.

• Is there anything people seem to overlook in the sources you research?
• Are there any heated debates you can address?
• Do you have a unique take on your topic?
• Have there been some recent developments that build on the extant research?

In this stage, you might find it helpful to formulate some research questions to help guide you. To write research questions, try to finish the following sentence: “I want to know how/what/why…”

A thesis statement is a statement of your central argument — it establishes the purpose and position of your paper. If you started with a research question, the thesis statement should answer it. It should also show what evidence and reasoning you’ll use to support that answer.

The thesis statement should be concise, contentious, and coherent. That means it should briefly summarize your argument in a sentence or two, make a claim that requires further evidence or analysis, and make a coherent point that relates to every part of the paper.

You will probably revise and refine the thesis statement as you do more research, but it can serve as a guide throughout the writing process. Every paragraph should aim to support and develop this central claim.

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A research paper outline is essentially a list of the key topics, arguments, and evidence you want to include, divided into sections with headings so that you know roughly what the paper will look like before you start writing.

A structure outline can help make the writing process much more efficient, so it’s worth dedicating some time to create one.

Your first draft won’t be perfect — you can polish later on. Your priorities at this stage are as follows:

• Maintaining forward momentum — write now, perfect later.
• Paying attention to clear organization and logical ordering of paragraphs and sentences, which will help when you come to the second draft.
• Expressing your ideas as clearly as possible, so you know what you were trying to say when you come back to the text.

You do not need to start by writing the introduction. Begin where it feels most natural for you — some prefer to finish the most difficult sections first, while others choose to start with the easiest part. If you created an outline, use it as a map while you work.

Do not delete large sections of text. If you begin to dislike something you have written or find it doesn’t quite fit, move it to a different document, but don’t lose it completely — you never know if it might come in useful later.

Paragraph structure

Paragraphs are the basic building blocks of research papers. Each one should focus on a single claim or idea that helps to establish the overall argument or purpose of the paper.

Example paragraph

George Orwell’s 1946 essay “Politics and the English Language” has had an enduring impact on thought about the relationship between politics and language. This impact is particularly obvious in light of the various critical review articles that have recently referenced the essay. For example, consider Mark Falcoff’s 2009 article in The National Review Online, “The Perversion of Language; or, Orwell Revisited,” in which he analyzes several common words (“activist,” “civil-rights leader,” “diversity,” and more). Falcoff’s close analysis of the ambiguity built into political language intentionally mirrors Orwell’s own point-by-point analysis of the political language of his day. Even 63 years after its publication, Orwell’s essay is emulated by contemporary thinkers.

Citing sources

It’s also important to keep track of citations at this stage to avoid accidental plagiarism . Each time you use a source, make sure to take note of where the information came from.

You can use our free citation generators to automatically create citations and save your reference list as you go.

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The research paper introduction should address three questions: What, why, and how? After finishing the introduction, the reader should know what the paper is about, why it is worth reading, and how you’ll build your arguments.

What? Be specific about the topic of the paper, introduce the background, and define key terms or concepts.

Why? This is the most important, but also the most difficult, part of the introduction. Try to provide brief answers to the following questions: What new material or insight are you offering? What important issues does your essay help define or answer?

How? To let the reader know what to expect from the rest of the paper, the introduction should include a “map” of what will be discussed, briefly presenting the key elements of the paper in chronological order.

The major struggle faced by most writers is how to organize the information presented in the paper, which is one reason an outline is so useful. However, remember that the outline is only a guide and, when writing, you can be flexible with the order in which the information and arguments are presented.

One way to stay on track is to use your thesis statement and topic sentences . Check:

• topic sentences against the thesis statement;
• topic sentences against each other, for similarities and logical ordering;
• and each sentence against the topic sentence of that paragraph.

Be aware of paragraphs that seem to cover the same things. If two paragraphs discuss something similar, they must approach that topic in different ways. Aim to create smooth transitions between sentences, paragraphs, and sections.

The research paper conclusion is designed to help your reader out of the paper’s argument, giving them a sense of finality.

Trace the course of the paper, emphasizing how it all comes together to prove your thesis statement. Give the paper a sense of finality by making sure the reader understands how you’ve settled the issues raised in the introduction.

You might also discuss the more general consequences of the argument, outline what the paper offers to future students of the topic, and suggest any questions the paper’s argument raises but cannot or does not try to answer.

You should not :

• Offer new arguments or essential information
• Take up any more space than necessary
• Begin with stock phrases that signal you are ending the paper (e.g. “In conclusion”)

There are four main considerations when it comes to the second draft.

• Check how your vision of the paper lines up with the first draft and, more importantly, that your paper still answers the assignment.
• Identify any assumptions that might require (more substantial) justification, keeping your reader’s perspective foremost in mind. Remove these points if you cannot substantiate them further.
• Be open to rearranging your ideas. Check whether any sections feel out of place and whether your ideas could be better organized.
• If you find that old ideas do not fit as well as you anticipated, you should cut them out or condense them. You might also find that new and well-suited ideas occurred to you during the writing of the first draft — now is the time to make them part of the paper.

The goal during the revision and proofreading process is to ensure you have completed all the necessary tasks and that the paper is as well-articulated as possible.

Global concerns

• Confirm that your paper completes every task specified in your assignment sheet.
• Check for logical organization and flow of paragraphs.
• Check paragraphs against the introduction and thesis statement.

Fine-grained details

Check the content of each paragraph, making sure that:

• each sentence helps support the topic sentence.
• no unnecessary or irrelevant information is present.
• all technical terms your audience might not know are identified.

Next, think about sentence structure , grammatical errors, and formatting . Check that you have correctly used transition words and phrases to show the connections between your ideas. Look for typos, cut unnecessary words, and check for consistency in aspects such as heading formatting and spellings .

Finally, you need to make sure your paper is correctly formatted according to the rules of the citation style you are using. For example, you might need to include an MLA heading  or create an APA title page .

Scribbr’s professional editors can help with the revision process with our award-winning proofreading services.

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Checklist: Research paper

I have followed all instructions in the assignment sheet.

My introduction presents my topic in an engaging way and provides necessary background information.

My introduction presents a clear, focused research problem and/or thesis statement .

My paper is logically organized using paragraphs and (if relevant) section headings .

Each paragraph is clearly focused on one central idea, expressed in a clear topic sentence .

Each paragraph is relevant to my research problem or thesis statement.

I have used appropriate transitions  to clarify the connections between sections, paragraphs, and sentences.

My conclusion provides a concise answer to the research question or emphasizes how the thesis has been supported.

My conclusion shows how my research has contributed to knowledge or understanding of my topic.

My conclusion does not present any new points or information essential to my argument.

I have provided an in-text citation every time I refer to ideas or information from a source.

I have included a reference list at the end of my paper, consistently formatted according to a specific citation style .

I have thoroughly revised my paper and addressed any feedback from my professor or supervisor.

I have followed all formatting guidelines (page numbers, headers, spacing, etc.).

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How to publish a scientific paper: writing the paper.

• Writing the paper
• Submitting the manuscript
• Editorial process
• Maximizing impact

Image (detail): Subhashish Panigrahi, Wikimedia Commons , CC-BY-SA 4.0

Writing a scientific paper

Before you begin.

• Review the literature: Ensure that the research question has not been investigated before and that the experimental methods are appropriate. Librarians can help!
• Research data management (UC Berkeley): Ensure that your data meet disciplinary guidelines, and that you will be able to comply with funder and journal policies for data deposit and sharing.

Quick writing guides

• 11 steps to structuring a science paper editors will take seriously (Borja 2014, updated 2021)
• The Science of Science Writing (Gopen and Swan 1990)
• Short Guide to Scientific Writing (Sawyer n.d.)
• Ten simple principles for structuring papers (Mensh and Kording 2017)
• Writing workshop program PLOS Neglected Tropical Diseases, 2015; includes general as well as journal-specific guidelines. General guidelines begin at slide 13.

Image (detail): istock/Thomas Shanahan ( Elsevier Connect )

In-depth writing guides and resources

• Nature Masterclass on Scientific Writing and Publishing Requires creating free Nature account, accessing from Berkeley IP address or using the Berkeley VPN with Library Access - Full Tunnel gateway, and enabling popups.
• How to Write a Good Scientific Paper (Mack 2018)
• Writing science: how to write papers that get cited and proposals that get funded (Schimel 2012)
• Graduate Writing Center (UC Berkeley)

Image (detail): Nature Masterclasses

Reporting guidelines

• Digital Curation Centre (DCC): https://www.dcc.ac.uk/guidance/standards/metadata
• Enhancing the QUAlity and Transparency Of health Research (EQUATOR): https://www.equator-network.org/reporting-guidelines/ for human- and animal-subjects research
• FAIRsharing: https://fairsharing.org/standards/

Writing tools

• Manage your citations : Citation managers EndNote, Mendeley, RefWorks, and Zotero (UC Berkeley Library guide)

• Writing + Citing in the Sciences : LaTeX editor Overleaf and citation managers (UC Berkeley Library guide)

• LaTeX in Engineering & Physical Sciences : The document formatting markup language LaTeX, which is especially useful for rendering mathematical and chemical symbols and equations (UC Berkeley Library guide)
• Virtual Online Library Tutorials (VOLT): LaTeX : Self-paced exercises for learning LaTeX

For more help

Writing tips & tools

Writing tips.

Avoid fragmentation (breaking a single study into multiple short papers) and redundant publication (submitting multiple papers that are very similar).

When writing a scientific paper, think about the structure familiar to you from reading scientific papers. A common structure for scientific research articles is termed IMRAD: Introduction, Methods, Results, And Discussion. A fuller outline is provided below:

• Title: most important element; include standard, searchable terms (keywords) to call attention to your work. Articles with short titles describing the results are cited more often (Paiva et al. 2012); cited 200 times (Google Scholar)  
•  What is the problem domain (system under investigation)?
•  What is the specific research question ? 
•  What were the methods and results ? 
•  What are the conclusions ?
• Introduction: describes the general problem domain (system under investigation) and then focuses on the specific research question addressed and/or the hypothesis tested by this paper.  
• Methods and materials: provides enough detail to enable experiment to be reproduced by another researcher in your field. Standard experimental methods can be indicated by a reference to a published protocol. Some journals have adopted STAR Methods (Structured, Transparent, Accessible Reporting), which includes a Key Resources Table listing all reagents, antibodies, cell lines, software, or other resources required for the experiment. Use of identifiers such as Research Resource Identifiers (RRIDs) is strongly encouraged. Protocols can be shared publicly or privately on protocols.io . If they are original they can be published in a protocol journal such as bio-protocol , STAR protocols , or JoVE .  
• Figures: clear and compelling; each figure should tell a single story: Data Visualization Guide (UC Berkeley Library)  
• Discussion: explains meaning and significance of results (how do they advance the field?) and how they relate to the research question; describes limitations and further work suggested by study.  
• Data availability statement: Some publishers require a statement describing how the data can be accessed and reused, or the data protection concerns (such as privacy or commercial sensitivity) that prevent sharing.  
• Acknowledgements: Unless there are separate sections for this information, name funding sources , declare any potential competing interests , and thank contributors who are not co-authors. For human- and animal-subject research, an ethics statement may be required identifying the review committee that approved the study and the relevant guidelines and regulations that governed the research.  
• References : A list of sources cited in your paper. Citations (both in-text and in the reference list) must be accurate and formatted in the journal's required style. Use a citation manager .  
• Supplementary information : supporting technical information (figures, protocols, methods, tables, additional data) too long or detailed to fit into the body of the paper.

General tips:

• first focus on the results (including figures and tables ), discussion and methods (communicating the experimental outcomes, significance and procedures)
• then work on the introduction , abstract and title (increasingly concise summaries of the work).
• Use simple, concrete, active language ("We determined..." not "It was determined that...")
• Start paragraphs with a topic sentence
• Consider your audience: narrowly specialized or interdisciplinary ?
• Be as clear and concise as possible
• Next: Submitting the manuscript >>
• Last Updated: Jul 7, 2023 8:30 AM
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Where is the best place to publish my research?

Identifying the best place to publish research involves consideration of many factors, including:

• Journal aim and scope
• Publication of similar work
• Journal rankings and measures of journal impact
• Demonstration of good publishing practices

Welch compiled the information below to help guide a researcher through the decision-making process.

 Think. Check. Submit.

“Think. Check. Submit. is a campaign to help researchers identify trusted journals for their research.  It is a simple checklist researchers can use to assess the credentials of a journal or publisher.”

 Retrieved from  http://thinkchecksubmit.org/about/

 Locating Journals

• Welch Medical Library Journals by Subject Select the subject to view available journals by subject. Journals are sorted according to the following journal rankings: Journal Impact Factor, Citescore, Scimago Journal & Country Rank, and Source Normalized Impact per Paper (SNIP).
• Elsevier Journal Finder Enter the unpublished article’s title and abstract info into this tool to determine possible sites for publication. Note: Covers only journals published by Elsevier.
• Journal/Author Name Estimator Enter the unpublished article’s title and/or abstract to determine possible sites for publication. It only covers journals in MEDLINE, regardless of publisher.
• Springer Journal Suggester Enter the unpublished article’s title and abstract into this tool to determine possible sites for publication. Note: Covers only journals published by Springer.
• HelioBlast A search tool that allows you to paste in text and identify similar text in MEDLINE. Note: Only covers journals in MEDLINE.
• Directory of Open Access Journals (DOAJ) Use the Browse Subjects feature, and select Journals to find quality Open Access Journals. Note: Covers only Open Access Journals.
• JANE Relies on data in PubMed to help you determine where to publish your research. Note: JANE tags journals indexed and found in MEDLINE and DOAJ.
• Edanz Journal Selector Allows you to search by keyword, journal name, abstract and more. Pulls results from publicly available data sources like Thomson Reuters’ annual Journal Citation Reports®.

Journal Metrics

• InCites™ Journal Citation Reports® Find a variety of metrics for journal quality, including impact factor, immediacy index, Eigenfactor score, and article influence score. Searchable by journal name and browsable by research category.
• SCImago Journal & Country Rank Access journal rankings based on citation data from the Scopus database. Journals can be grouped by major thematic areas and specific subject categories.
• Scopus In search results, click on the journal title to view journal metrics. Scopus will give you SJR (SCImago Journal Rank), IPP (Impact per Publication), and SNIP (Source Normalized Impact per Paper) measurements.
• Web of Science In search results, click on the journal title to view journal metrics. In Web of Science, view its IF (Impact Factor) and JCR (Journal Citation Reports) rankings.
• Eigenfactor Find an article’s Eigenfactor ®  and  Article Influence Score ®  to evaluate the influence of a journal.

General Information About Journals

• JHU Catalog (Catalyst) : Use the “Journal title” search in the catalog to determine if the JHU Libraries subscribe to a particular journal.
• Journals in PubMed and Other NCBI Databases : Search the catalog of the National Library of Medicine (NLM) for journals referenced by NCBI databases, including PubMed.  Each catalog record indicates key journal details, including ISSN, abbreviations, and whether its articles are currently indexed for MEDLINE.
• Ulrich's Periodical Directory : Search this comprehensive database of serial publications for key details about journals, including previous titles, publishers, ISSNs, URLs, indexing, and English versions of foreign titles.

  Search for Open Access Journals

• Enago Open Access Journal Finder : Paste in content from your publication to access a shortlist of quality Open Access Journals that are relevant to you. This tool searches against DOAJ’s list of journals.

Publishing in an Open Access Journal allows you to share your work widely and bypass permission and paywall barriers so the public has greater access to your work. However, predatory publishers, many disguised as Open Access Journals, may solicit you for your research. If you encounter a potential predatory publisher, take the time to analyze the journal or publisher before submitting work to make sure they are not a predatory journal or publisher. Use the Think.Check.Submit method to assess a potential journal.

You can also take the following steps:

• Search DOAJ and MEDLINE to see if the journal is listed
• Search Google for the journal/publisher
• Look up the location of the publisher to see what appears on a map
• Look for spelling errors on the publisher's website and in the solicitation email message
• Check the editorial board for names you may recognize
• Ask your Welch informationist

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• Research & Preparation

Which journal should I publish in?

To decide which journal you can submit your manuscript to, you can use JournalFinder.

Follow these steps to find out which journal matches with your manuscript:

• Enter your paper title in the 'Paper title' field.
• Enter your paper abstract in the 'Paper abstract' field.
• Click 'Find journal' .
• What can I do if I'm using JournalFinder and cannot see the journals displayed on the screen
• Read the aims and scope in the expanded state of a journal on the search results list or on the journal homepage to make sure the journal is a match.
• Check whether you can submit your manuscript yourself. If online submission is available for your chosen journal, this is stated in the expanded state of a journal on the search results list or on the journal homepage along with a link to the relevant online submission site.
• Read the journal's Guide for Author to ensure that your paper adheres to the rules and guidelines for submission to the journal.
• Check the  open access options on the journal homepage, if you want to publish open access.

Find out more about JournalFinder with these FAQs .

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For further assistance:

How to Write and Publish a Research Paper for a Peer-Reviewed Journal

Affiliations.

• 1 Department of Maternal and Child Health, University of North Carolina Gillings School of Global Public Health, 135 Dauer Dr, 27599, Chapel Hill, NC, USA.
• 2 Department of Maternal and Child Health, University of North Carolina Gillings School of Global Public Health, 135 Dauer Dr, 27599, Chapel Hill, NC, USA. [email protected].
• 3 Department of Epidemiology, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA. [email protected].
• PMID: 32356250
• PMCID: PMC8520870
• DOI: 10.1007/s13187-020-01751-z

Communicating research findings is an essential step in the research process. Often, peer-reviewed journals are the forum for such communication, yet many researchers are never taught how to write a publishable scientific paper. In this article, we explain the basic structure of a scientific paper and describe the information that should be included in each section. We also identify common pitfalls for each section and recommend strategies to avoid them. Further, we give advice about target journal selection and authorship. In the online resource 1, we provide an example of a high-quality scientific paper, with annotations identifying the elements we describe in this article.

Keywords: Manuscripts; Publishing; Scientific writing.

© 2020. The Author(s).

• Communication
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• Journal Selection Tips

Q: How should I choose the best platform to publish my research paper?

I want to know the steps and factors that I have to keep in mind for choosing the best platform to publish my research article.

Asked on 11 Feb, 2021

Firstly, by ‘platform,’ we understand you mean a journal or even a publisher.

Coming to your query, there are actually quite a few points to keep in mind, such as the scope and focus of the journal (whether the topic of your paper is aligned with the topics published by the journal), the frequency of its publication, and its quality/stature, to name a few. One thing you need to be watchful of though is the presence of predatory/bogus journals that look to dupe unwary researchers. Finally, to improve your chances of acceptance, once you have shortlisted a few journals, you may send them presubmission inquiries in order to gauge their interest in considering and possibly publishing your paper. For the points discussed above, we have provided a few links for you to get started.

• Journal selection guide: Questions you should ask to make the right choice
• Can I write to the editor to inquire if my article's topic matches the journal's scope?
• How to write a presubmission inquiry: Dos and don'ts
• 10 Point checklist to identify predatory publishers

Apart from the above, you may do your own search (looking up relevant databases) or even use a journal selection service (such as ours ).

Hope that helps. In fact, identifying the right target journal can be a sort of research too. :) So, happy re/searching!

Answered by Editage Insights on 16 Feb, 2021

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Search Help

Get the most out of Google Scholar with some helpful tips on searches, email alerts, citation export, and more.

Finding recent papers

Your search results are normally sorted by relevance, not by date. To find newer articles, try the following options in the left sidebar:

• click "Since Year" to show only recently published papers, sorted by relevance;
• click "Sort by date" to show just the new additions, sorted by date;
• click the envelope icon to have new results periodically delivered by email.

Locating the full text of an article

Abstracts are freely available for most of the articles. Alas, reading the entire article may require a subscription. Here're a few things to try:

• click a library link, e.g., "FindIt@Harvard", to the right of the search result;
• click a link labeled [PDF] to the right of the search result;
• click "All versions" under the search result and check out the alternative sources;
• click "Related articles" or "Cited by" under the search result to explore similar articles.

If you're affiliated with a university, but don't see links such as "FindIt@Harvard", please check with your local library about the best way to access their online subscriptions. You may need to do search from a computer on campus, or to configure your browser to use a library proxy.

Getting better answers

If you're new to the subject, it may be helpful to pick up the terminology from secondary sources. E.g., a Wikipedia article for "overweight" might suggest a Scholar search for "pediatric hyperalimentation".

If the search results are too specific for your needs, check out what they're citing in their "References" sections. Referenced works are often more general in nature.

Similarly, if the search results are too basic for you, click "Cited by" to see newer papers that referenced them. These newer papers will often be more specific.

Explore! There's rarely a single answer to a research question. Click "Related articles" or "Cited by" to see closely related work, or search for author's name and see what else they have written.

Searching Google Scholar

Use the "author:" operator, e.g., author:"d knuth" or author:"donald e knuth".

Put the paper's title in quotations: "A History of the China Sea".

You'll often get better results if you search only recent articles, but still sort them by relevance, not by date. E.g., click "Since 2018" in the left sidebar of the search results page.

To see the absolutely newest articles first, click "Sort by date" in the sidebar. If you use this feature a lot, you may also find it useful to setup email alerts to have new results automatically sent to you.

Note: On smaller screens that don't show the sidebar, these options are available in the dropdown menu labelled "Year" right below the search button.

Select the "Case law" option on the homepage or in the side drawer on the search results page.

It finds documents similar to the given search result.

It's in the side drawer. The advanced search window lets you search in the author, title, and publication fields, as well as limit your search results by date.

Select the "Case law" option and do a keyword search over all jurisdictions. Then, click the "Select courts" link in the left sidebar on the search results page.

Tip: To quickly search a frequently used selection of courts, bookmark a search results page with the desired selection.

Access to articles

For each Scholar search result, we try to find a version of the article that you can read. These access links are labelled [PDF] or [HTML] and appear to the right of the search result. For example:

A paper that you need to read

Access links cover a wide variety of ways in which articles may be available to you - articles that your library subscribes to, open access articles, free-to-read articles from publishers, preprints, articles in repositories, etc.

When you are on a campus network, access links automatically include your library subscriptions and direct you to subscribed versions of articles. On-campus access links cover subscriptions from primary publishers as well as aggregators.

Off-campus access

Off-campus access links let you take your library subscriptions with you when you are at home or traveling. You can read subscribed articles when you are off-campus just as easily as when you are on-campus. Off-campus access links work by recording your subscriptions when you visit Scholar while on-campus, and looking up the recorded subscriptions later when you are off-campus.

We use the recorded subscriptions to provide you with the same subscribed access links as you see on campus. We also indicate your subscription access to participating publishers so that they can allow you to read the full-text of these articles without logging in or using a proxy. The recorded subscription information expires after 30 days and is automatically deleted.

In addition to Google Scholar search results, off-campus access links can also appear on articles from publishers participating in the off-campus subscription access program. Look for links labeled [PDF] or [HTML] on the right hand side of article pages.

Anne Author , John Doe , Jane Smith , Someone Else

In this fascinating paper, we investigate various topics that would be of interest to you. We also describe new methods relevant to your project, and attempt to address several questions which you would also like to know the answer to. Lastly, we analyze …

You can disable off-campus access links on the Scholar settings page . Disabling off-campus access links will turn off recording of your library subscriptions. It will also turn off indicating subscription access to participating publishers. Once off-campus access links are disabled, you may need to identify and configure an alternate mechanism (e.g., an institutional proxy or VPN) to access your library subscriptions while off-campus.

Email Alerts

Do a search for the topic of interest, e.g., "M Theory"; click the envelope icon in the sidebar of the search results page; enter your email address, and click "Create alert". We'll then periodically email you newly published papers that match your search criteria.

No, you can enter any email address of your choice. If the email address isn't a Google account or doesn't match your Google account, then we'll email you a verification link, which you'll need to click to start receiving alerts.

This works best if you create a public profile , which is free and quick to do. Once you get to the homepage with your photo, click "Follow" next to your name, select "New citations to my articles", and click "Done". We will then email you when we find new articles that cite yours.

Search for the title of your paper, e.g., "Anti de Sitter space and holography"; click on the "Cited by" link at the bottom of the search result; and then click on the envelope icon in the left sidebar of the search results page.

First, do a search for your colleague's name, and see if they have a Scholar profile. If they do, click on it, click the "Follow" button next to their name, select "New articles by this author", and click "Done".

If they don't have a profile, do a search by author, e.g., [author:s-hawking], and click on the mighty envelope in the left sidebar of the search results page. If you find that several different people share the same name, you may need to add co-author names or topical keywords to limit results to the author you wish to follow.

We send the alerts right after we add new papers to Google Scholar. This usually happens several times a week, except that our search robots meticulously observe holidays.

There's a link to cancel the alert at the bottom of every notification email.

If you created alerts using a Google account, you can manage them all here . If you're not using a Google account, you'll need to unsubscribe from the individual alerts and subscribe to the new ones.

Google Scholar library

Google Scholar library is your personal collection of articles. You can save articles right off the search page, organize them by adding labels, and use the power of Scholar search to quickly find just the one you want - at any time and from anywhere. You decide what goes into your library, and we’ll keep the links up to date.

You get all the goodies that come with Scholar search results - links to PDF and to your university's subscriptions, formatted citations, citing articles, and more!

Library help

Find the article you want to add in Google Scholar and click the “Save” button under the search result.

Click “My library” at the top of the page or in the side drawer to view all articles in your library. To search the full text of these articles, enter your query as usual in the search box.

Find the article you want to remove, and then click the “Delete” button under it.

• To add a label to an article, find the article in your library, click the “Label” button under it, select the label you want to apply, and click “Done”.
• To view all the articles with a specific label, click the label name in the left sidebar of your library page.
• To remove a label from an article, click the “Label” button under it, deselect the label you want to remove, and click “Done”.
• To add, edit, or delete labels, click “Manage labels” in the left column of your library page.

Only you can see the articles in your library. If you create a Scholar profile and make it public, then the articles in your public profile (and only those articles) will be visible to everyone.

Your profile contains all the articles you have written yourself. It’s a way to present your work to others, as well as to keep track of citations to it. Your library is a way to organize the articles that you’d like to read or cite, not necessarily the ones you’ve written.

Citation Export

Click the "Cite" button under the search result and then select your bibliography manager at the bottom of the popup. We currently support BibTeX, EndNote, RefMan, and RefWorks.

Err, no, please respect our robots.txt when you access Google Scholar using automated software. As the wearers of crawler's shoes and webmaster's hat, we cannot recommend adherence to web standards highly enough.

Sorry, we're unable to provide bulk access. You'll need to make an arrangement directly with the source of the data you're interested in. Keep in mind that a lot of the records in Google Scholar come from commercial subscription services.

Sorry, we can only show up to 1,000 results for any particular search query. Try a different query to get more results.

Content Coverage

Google Scholar includes journal and conference papers, theses and dissertations, academic books, pre-prints, abstracts, technical reports and other scholarly literature from all broad areas of research. You'll find works from a wide variety of academic publishers, professional societies and university repositories, as well as scholarly articles available anywhere across the web. Google Scholar also includes court opinions and patents.

We index research articles and abstracts from most major academic publishers and repositories worldwide, including both free and subscription sources. To check current coverage of a specific source in Google Scholar, search for a sample of their article titles in quotes.

While we try to be comprehensive, it isn't possible to guarantee uninterrupted coverage of any particular source. We index articles from sources all over the web and link to these websites in our search results. If one of these websites becomes unavailable to our search robots or to a large number of web users, we have to remove it from Google Scholar until it becomes available again.

Our meticulous search robots generally try to index every paper from every website they visit, including most major sources and also many lesser known ones.

That said, Google Scholar is primarily a search of academic papers. Shorter articles, such as book reviews, news sections, editorials, announcements and letters, may or may not be included. Untitled documents and documents without authors are usually not included. Website URLs that aren't available to our search robots or to the majority of web users are, obviously, not included either. Nor do we include websites that require you to sign up for an account, install a browser plugin, watch four colorful ads, and turn around three times and say coo-coo before you can read the listing of titles scanned at 10 DPI... You get the idea, we cover academic papers from sensible websites.

That's usually because we index many of these papers from other websites, such as the websites of their primary publishers. The "site:" operator currently only searches the primary version of each paper.

It could also be that the papers are located on examplejournals.gov, not on example.gov. Please make sure you're searching for the "right" website.

That said, the best way to check coverage of a specific source is to search for a sample of their papers using the title of the paper.

Ahem, we index papers, not journals. You should also ask about our coverage of universities, research groups, proteins, seminal breakthroughs, and other dimensions that are of interest to users. All such questions are best answered by searching for a statistical sample of papers that has the property of interest - journal, author, protein, etc. Many coverage comparisons are available if you search for [allintitle:"google scholar"], but some of them are more statistically valid than others.

Currently, Google Scholar allows you to search and read published opinions of US state appellate and supreme court cases since 1950, US federal district, appellate, tax and bankruptcy courts since 1923 and US Supreme Court cases since 1791. In addition, it includes citations for cases cited by indexed opinions or journal articles which allows you to find influential cases (usually older or international) which are not yet online or publicly available.

Legal opinions in Google Scholar are provided for informational purposes only and should not be relied on as a substitute for legal advice from a licensed lawyer. Google does not warrant that the information is complete or accurate.

We normally add new papers several times a week. However, updates to existing records take 6-9 months to a year or longer, because in order to update our records, we need to first recrawl them from the source website. For many larger websites, the speed at which we can update their records is limited by the crawl rate that they allow.

Inclusion and Corrections

We apologize, and we assure you the error was unintentional. Automated extraction of information from articles in diverse fields can be tricky, so an error sometimes sneaks through.

Please write to the owner of the website where the erroneous search result is coming from, and encourage them to provide correct bibliographic data to us, as described in the technical guidelines . Once the data is corrected on their website, it usually takes 6-9 months to a year or longer for it to be updated in Google Scholar. We appreciate your help and your patience.

If you can't find your papers when you search for them by title and by author, please refer your publisher to our technical guidelines .

You can also deposit your papers into your institutional repository or put their PDF versions on your personal website, but please follow your publisher's requirements when you do so. See our technical guidelines for more details on the inclusion process.

We normally add new papers several times a week; however, it might take us some time to crawl larger websites, and corrections to already included papers can take 6-9 months to a year or longer.

Google Scholar generally reflects the state of the web as it is currently visible to our search robots and to the majority of users. When you're searching for relevant papers to read, you wouldn't want it any other way!

If your citation counts have gone down, chances are that either your paper or papers that cite it have either disappeared from the web entirely, or have become unavailable to our search robots, or, perhaps, have been reformatted in a way that made it difficult for our automated software to identify their bibliographic data and references. If you wish to correct this, you'll need to identify the specific documents with indexing problems and ask your publisher to fix them. Please refer to the technical guidelines .

Please do let us know . Please include the URL for the opinion, the corrected information and a source where we can verify the correction.

We're only able to make corrections to court opinions that are hosted on our own website. For corrections to academic papers, books, dissertations and other third-party material, click on the search result in question and contact the owner of the website where the document came from. For corrections to books from Google Book Search, click on the book's title and locate the link to provide feedback at the bottom of the book's page.

General Questions

These are articles which other scholarly articles have referred to, but which we haven't found online. To exclude them from your search results, uncheck the "include citations" box on the left sidebar.

First, click on links labeled [PDF] or [HTML] to the right of the search result's title. Also, check out the "All versions" link at the bottom of the search result.

Second, if you're affiliated with a university, using a computer on campus will often let you access your library's online subscriptions. Look for links labeled with your library's name to the right of the search result's title. Also, see if there's a link to the full text on the publisher's page with the abstract.

Keep in mind that final published versions are often only available to subscribers, and that some articles are not available online at all. Good luck!

Technically, your web browser remembers your settings in a "cookie" on your computer's disk, and sends this cookie to our website along with every search. Check that your browser isn't configured to discard our cookies. Also, check if disabling various proxies or overly helpful privacy settings does the trick. Either way, your settings are stored on your computer, not on our servers, so a long hard look at your browser's preferences or internet options should help cure the machine's forgetfulness.

Not even close. That phrase is our acknowledgement that much of scholarly research involves building on what others have already discovered. It's taken from Sir Isaac Newton's famous quote, "If I have seen further, it is by standing on the shoulders of giants."

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How to Publish a research paper

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• Published: 23 August 2023

The complete sequence of a human Y chromosome

• Arang Rhie   ORCID: orcid.org/0000-0002-9809-8127 1   na1 ,
• Sergey Nurk 1   na1   nAff51 ,
• Monika Cechova 2 , 3   na1 ,
• Savannah J. Hoyt   ORCID: orcid.org/0000-0001-7804-3236 4   na1 ,
• Dylan J. Taylor   ORCID: orcid.org/0000-0001-5806-4494 5   na1 ,
• Nicolas Altemose   ORCID: orcid.org/0000-0002-7231-6026 6 ,
• Paul W. Hook   ORCID: orcid.org/0000-0002-3912-1999 7 ,
• Sergey Koren   ORCID: orcid.org/0000-0002-1472-8962 1 ,
• Mikko Rautiainen 1 ,
• Ivan A. Alexandrov 8 , 9   nAff52 ,
• Jamie Allen   ORCID: orcid.org/0000-0002-8677-2225 10 ,
• Mobin Asri 11 ,
• Andrey V. Bzikadze   ORCID: orcid.org/0000-0002-7928-7950 12 ,
• Nae-Chyun Chen 13 ,
• Chen-Shan Chin   ORCID: orcid.org/0000-0003-4394-2455 14 , 15 ,
• Mark Diekhans   ORCID: orcid.org/0000-0002-0430-0989 11 ,
• Paul Flicek 10 , 16 ,
• Giulio Formenti 17 ,
• Arkarachai Fungtammasan   ORCID: orcid.org/0000-0003-2398-0358 18 ,
• Carlos Garcia Giron 10 ,
• Erik Garrison   ORCID: orcid.org/0000-0003-3821-631X 19 ,
• Ariel Gershman 7 ,
• Jennifer L. Gerton   ORCID: orcid.org/0000-0003-0743-3637 20 , 21 ,
• Patrick G. S. Grady 4 ,
• Andrea Guarracino   ORCID: orcid.org/0000-0001-9744-131X 19 , 22 ,
• Leanne Haggerty 10 ,
• Reza Halabian 23 ,
• Nancy F. Hansen   ORCID: orcid.org/0000-0002-0950-0699 1 , 24 ,
• Robert Harris 25 ,
• Gabrielle A. Hartley 4 ,
• William T. Harvey 26 ,
• Marina Haukness   ORCID: orcid.org/0000-0001-9991-8089 11 ,
• Jakob Heinz 7 ,
• Thibaut Hourlier   ORCID: orcid.org/0000-0003-4894-7773 10 ,
• Robert M. Hubley 27 ,
• Sarah E. Hunt   ORCID: orcid.org/0000-0002-8350-1235 10 ,
• Stephen Hwang 28 ,
• Miten Jain   ORCID: orcid.org/0000-0002-4571-3982 29 ,
• Rupesh K. Kesharwani 30 ,
• Alexandra P. Lewis 26 ,
• Heng Li 31 , 32 ,
• Glennis A. Logsdon   ORCID: orcid.org/0000-0003-2396-0656 26 ,
• Julian K. Lucas 3 , 11 ,
• Wojciech Makalowski   ORCID: orcid.org/0000-0003-2303-9541 23 ,
• Christopher Markovic 33 ,
• Fergal J. Martin   ORCID: orcid.org/0000-0002-1672-050X 10 ,
• Ann M. Mc Cartney 1 ,
• Rajiv C. McCoy   ORCID: orcid.org/0000-0003-0615-146X 5 ,
• Jennifer McDaniel 34 ,
• Brandy M. McNulty 3 , 11 ,
• Paul Medvedev 35 , 36 , 37 ,
• Alla Mikheenko 9 , 38 ,
• Katherine M. Munson   ORCID: orcid.org/0000-0001-8413-6498 26 ,
• Terence D. Murphy   ORCID: orcid.org/0000-0001-9311-9745 39 ,
• Hugh E. Olsen 3 , 11 ,
• Nathan D. Olson 34 ,
• Luis F. Paulin   ORCID: orcid.org/0000-0003-2567-3773 30 ,
• David Porubsky   ORCID: orcid.org/0000-0001-8414-8966 26 ,
• Tamara Potapova   ORCID: orcid.org/0000-0003-2761-1795 20 ,
• Fedor Ryabov   ORCID: orcid.org/0000-0001-8728-9465 40 ,
• Steven L. Salzberg   ORCID: orcid.org/0000-0002-8859-7432 41 ,
• Michael E. G. Sauria 5 ,
• Fritz J. Sedlazeck   ORCID: orcid.org/0000-0001-6040-2691 30 , 42 ,
• Kishwar Shafin   ORCID: orcid.org/0000-0001-5252-3434 43 ,
• Valery A. Shepelev 44 ,
• Alaina Shumate 7 ,
• Jessica M. Storer 27 ,
• Likhitha Surapaneni 10 ,
• Angela M. Taravella Oill 45 ,
• Françoise Thibaud-Nissen   ORCID: orcid.org/0000-0003-4957-7807 39 ,
• Winston Timp   ORCID: orcid.org/0000-0003-2083-6027 7 ,
• Marta Tomaszkiewicz   ORCID: orcid.org/0000-0003-1523-200X 25 , 46 ,
• Mitchell R. Vollger   ORCID: orcid.org/0000-0002-8651-1615 26 ,
• Brian P. Walenz   ORCID: orcid.org/0000-0001-8431-1428 1 ,
• Allison C. Watwood 25 ,
• Matthias H. Weissensteiner 25 ,
• Aaron M. Wenger 47 ,
• Melissa A. Wilson 45 ,
• Samantha Zarate   ORCID: orcid.org/0000-0001-5570-2059 13 ,
• Yiming Zhu 30 ,
• Justin M. Zook   ORCID: orcid.org/0000-0003-2309-8402 34 ,
• Evan E. Eichler   ORCID: orcid.org/0000-0002-8246-4014 26 , 48 ,
• Rachel J. O’Neill   ORCID: orcid.org/0000-0002-1525-6821 4 , 49 , 50 ,
• Michael C. Schatz   ORCID: orcid.org/0000-0002-4118-4446 5 , 13 ,
• Karen H. Miga   ORCID: orcid.org/0000-0002-3670-4507 3 , 11 ,
• Kateryna D. Makova 25 &
• Adam M. Phillippy   ORCID: orcid.org/0000-0003-2983-8934 1  

Nature ( 2023 ) Cite this article

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• Chromosomes
• Genetic variation
• Genome informatics

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications 1 , 2 , 3 . As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished 4 , 5 . Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY , DAZ and RBMY ; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome 4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

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Data availability

The T2T-CHM13v2.0 (T2T-CHM13+Y) assembly, reference analysis set, complete list of resources—including gene annotation, repeat annotation, epigenetic profiles, variant-calling results from 1KGP and SGDP, gnomAD, ClinVar, GWAS and dbSNP datasets—are available for download at https://github.com/marbl/CHM13 . The assembly is also available from NCBI and EBI with GenBank accession GCA_009914755.4 . Annotation and associated resources are also browsable as ‘hs1’ from the UCSC Genome Browser ( http://genome.ucsc.edu/cgi-bin/hgTracks?db=hub_3671779_hs1 ), the Ensembl Genome Browser ( https://projects.ensembl.org/hprc/ ) (assembly name T2T-CHM13v2.0) and NCBI data-hub ( https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_009914755.1/ ). Potential assembly issues are listed and can be tracked at https://github.com/marbl/CHM13-issues . 1KGP and SGDP short-read alignments and variant calls are available within AnVIL at https://anvil.terra.bio/#workspaces/anvil-datastorage/AnVIL_T2T_CHRY . Original data from the Gerton lab underlying this manuscript can be accessed from the Stowers Original Data Repository at http://www.stowers.org/research/publications/libpb-2358 . Sequencing data used in this study are listed in Supplementary Table 1 .

Code availability

Custom codes developed for data analysis and visualization are available at https://github.com/arangrhie/T2T-HG002Y , https://github.com/snurk/sg_sandbox and https://github.com/schatzlab/t2t-chm13-chry and are deposited with Zenodo 159 . Software and parameters used are stated in the  Supplementary Methods with further details.

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Acknowledgements

We thank P. Hallast, M. C. Loftus, M. K. Konkel, P. Ebert, T. Marschall and C. Lee for coordination and discussions, J.C.-I. Lee for sharing the GRCh38-Y coordinates used in Y-Finder and members of the Telomere-to-Telomere consortium and HPRC for constructive feedback. This work utilized the computational resources of the National Institutes of Health (NIH) HPC Biowulf cluster ( https://hpc.nih.gov ). Computational resources were partially provided by the e-INFRA CZ project (no. 90140), supported by the Ministry of Education, Youth and Sports of the Czech Republic and Computational Biology Core, Institute for Systems Genomics, University of Connecticut. Certain commercial equipment, instruments and materials are identified to specify adequately experimental conditions or reported results. Such identification does not imply recommendation or endorsement by the NIST, nor does it imply that the equipment, instruments or materials identified are necessarily the best available for the purpose. We thank the Intramural Research Program of NHGRI, NIH no. HG200398 (A.R., S.N., S.K., M.R., A.M.M., B.P.W. and A.M.P.); NIH no. GM123312 (S.J.H., P.G.S.G., G.A.H. and R.J.O.); NIH no. GM130691 (P.M., M.H.W. and K.D.M.); HHMI Hanna Gray Fellowship (N.A.); NIH no. CA266339 (J.G. and T.P.); NIH no. GM147352 (G.A.L.); NIH nos. HG002939 and HG010136 (R.M.H. and J.M.S.); NIH no. HG009190 (P.W.H., A. Gershman and W.T.); NIH nos. HG010263, HG006620 and CA253481 and NSF no. DBI-1627442 (M.C.S.); NIH no. GM136684 (K.D.M.); NIH nos. HG011274 and HG010548 (K.H.M.); NIH nos. HG010961 and HG010040 (H.L.); NIH no. HG007234 (M.D.); NIH no. HG011758 (F.J.S.); NIH no. DA047638 (E.G.); NIH no. GM124827 (M.A.W.); NIH no. GM133747 (R.C.M.); NIH no. CA240199 (R.J.O.); NIH nos. HG002385, HG010169 and HG010971 (E.E.E.); Stowers Institute for Medical Research (J.L.G. and T.P.); National Center for Biotechnology Information of the National Library of Medicine, NIH (F.T.-N. and T.D.M.); intramural funding at NIST (J.M.Z.); NIST no. 70NANB20H206 (M.J.); and NIH nos. HG010972 and WT222155/Z/20/Z and the European Molecular Biology Laboratory (J.A., P.F., C.G.G., L.H., T.H., S.E.H., F.J.M. and L.S.). RNA generation was supported by NIST no. 70NANB21H101 and NIH no. 1S10OD028587; the Ministry of Science and Higher Education of the Russian Federation, St. Petersburg State University, no. PURE 73023672 (I.A.A.); the Computation, Bioinformatics, and Statistics Predoctoral Training Program awarded to Penn State by the NIH (A.C.W.); and Achievement Rewards for College Scientists Foundation, The Graduate College at Arizona State University (A.M.T.O.). E.E.E. is an investigator for HHMI.

Author information

Sergey Nurk

Present address: Oxford Nanopore Technologies Inc., Oxford, UK

Ivan A. Alexandrov

Present address: Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel

These authors contributed equally: Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, Dylan J. Taylor

Authors and Affiliations

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA

Arang Rhie, Sergey Nurk, Sergey Koren, Mikko Rautiainen, Nancy F. Hansen, Ann M. Mc Cartney, Brian P. Walenz & Adam M. Phillippy

Faculty of Informatics, Masaryk University, Brno, Czech Republic

Monika Cechova

Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA

Monika Cechova, Julian K. Lucas, Brandy M. McNulty, Hugh E. Olsen & Karen H. Miga

Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA

Savannah J. Hoyt, Patrick G. S. Grady, Gabrielle A. Hartley & Rachel J. O’Neill

Department of Biology, Johns Hopkins University, Baltimore, MD, USA

Dylan J. Taylor, Rajiv C. McCoy, Michael E. G. Sauria & Michael C. Schatz

Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA

Nicolas Altemose

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA

Paul W. Hook, Ariel Gershman, Jakob Heinz, Alaina Shumate & Winston Timp

Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia

Center for Algorithmic Biotechnology, Saint Petersburg State University, St Petersburg, Russia

Ivan A. Alexandrov & Alla Mikheenko

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK

Jamie Allen, Paul Flicek, Carlos Garcia Giron, Leanne Haggerty, Thibaut Hourlier, Sarah E. Hunt, Fergal J. Martin & Likhitha Surapaneni

UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA

Mobin Asri, Mark Diekhans, Marina Haukness, Julian K. Lucas, Brandy M. McNulty, Hugh E. Olsen & Karen H. Miga

Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, CA, USA

Andrey V. Bzikadze

Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA

Nae-Chyun Chen, Samantha Zarate & Michael C. Schatz

GeneDX Holdings Corp, Stamford, CT, USA

Chen-Shan Chin

Foundation of Biological Data Science, Belmont, CA, USA

Department of Genetics, University of Cambridge, Cambridge, UK

Paul Flicek

The Rockefeller University, New York, NY, USA

Giulio Formenti

DNAnexus, Inc., Mountain View, CA, USA

Arkarachai Fungtammasan

Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA

Erik Garrison & Andrea Guarracino

Stowers Institute for Medical Research, Kansas City, MO, USA

Jennifer L. Gerton & Tamara Potapova

University of Kansas Medical Center, Kansas City, MO, USA

Jennifer L. Gerton

Genomics Research Centre, Human Technopole, Milan, Italy

Andrea Guarracino

Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany

Reza Halabian & Wojciech Makalowski

Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA

Nancy F. Hansen

Department of Biology, Pennsylvania State University, University Park, PA, USA

Robert Harris, Marta Tomaszkiewicz, Allison C. Watwood, Matthias H. Weissensteiner & Kateryna D. Makova

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA

William T. Harvey, Alexandra P. Lewis, Glennis A. Logsdon, Katherine M. Munson, David Porubsky, Mitchell R. Vollger & Evan E. Eichler

Institute for Systems Biology, Seattle, WA, USA

Robert M. Hubley & Jessica M. Storer

XDBio Program, Johns Hopkins University, Baltimore, MD, USA

Stephen Hwang

Department of Bioengineering, Department of Physics, Northeastern University, Boston, MA, USA

Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA

Rupesh K. Kesharwani, Luis F. Paulin, Fritz J. Sedlazeck & Yiming Zhu

Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA

Genome Technology Access Center at the McDonnell Genome Institute, Washington University, St. Louis, MO, USA

Christopher Markovic

Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA

Jennifer McDaniel, Nathan D. Olson & Justin M. Zook

Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA

Paul Medvedev

Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA

Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA

UCL Queen Square Institute of Neurology, UCL, London, UK

Alla Mikheenko

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

Terence D. Murphy & Françoise Thibaud-Nissen

Masters Program in National Research University Higher School of Economics, Moscow, Russia

Fedor Ryabov

Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, USA

Steven L. Salzberg

Department of Computer Science, Rice University, Houston, TX, USA

Fritz J. Sedlazeck

Google Inc., Mountain View, CA, USA

Kishwar Shafin

Institute of Molecular Genetics, Moscow, Russia

Valery A. Shepelev

Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA

Angela M. Taravella Oill & Melissa A. Wilson

Department of Biomedical Engineering, Pennsylvania State University, State College, PA, USA

Marta Tomaszkiewicz

Pacific Biosciences, Menlo Park, CA, USA

Aaron M. Wenger

Investigator, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA

Evan E. Eichler

Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA

Rachel J. O’Neill

Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA

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Contributions

V.A.S. is retired from the Institute of Molecular Genetics. Assembly was carried out by S.N., S.K. and M.R. Validation was performed by A.R., S.K., M.A., A.V.B., G.F., A.F., A.M.M., J.M., A.M., L.F.P., D.P., F.J.S., K.S., P.M., J.M.Z. and K.D.M. ChrY haplogroups were determined by A.R. and A.C.W. Alignment was done by C.-S.C., M.D., R. Harris, M.R.V. and K.D.M. Satellite annotation was performed by N.A., I.A.A., G.A.L., F.R., V.A.S. and K.H.M. N.A., J.G. and T.P. carried out FISH. Repeat annotation was done by S.J.H., P.G.S.G., G.A.H., R.M.H., J.M.S. and R.J.O. Retro-elements were dealt with by R. Halabian and W.M. Non-B DNA was dealt with by M.H.W. and K.D.M. Gene annotation was undertaken by A.R., M.D., P.F., C.G.G., L.H., M.H., J.H., T.H., F.J.M., T.D.M., S.L.S., A.S. and F.T.-N. A.R., R. Harris, W.T.H., P.M., M.T. and K.D.M. dealt with ampliconic genes. Structural annotation was performed by A.R., M.C., H.L., P.M. and K.D.M. Epigenetic analysis was performed by A.R., P.W.H., A. Gershman, W.T. and A.M.W. Mappability was performed by A.M.T.O., M.A.W. and J.M.Z. Non-B DNA was dealt with by M.H.W. and K.D.M. Variants and liftover were carried out by A.R., D.J.T., S.K., J.A., N.-C.C., M.D., E.G., A. Guarracino, N.F.H., W.T.H., S.E.H., S.H., R.C.M., N.D.O., M.E.G.S., L.S., M.R.V., S.Z., J.M.Z., E.E.E. and A.M.P. A.R., S.L.S., B.P.W. and A.M.P. dealt with contamination. Data generation was carried out by M.J., R.K.K., A.P.L., J.K.L., C.M., B.M.M., K.M.M., H.E.O., F.J.S. and Y.Z. Data management was undertaken by A.R., M.D., M.J. and J.K.L. Computational resources were sourced by R.J.O., M.C.S. and A.M.P. A.R., S.N., M.C., S.J.H., D.J.T., N.A., I.A.A., N.-C.C., E.G., J.G., P.G.S.G., A. Guarracino, R. Halabian, W.M., J.M., T.P., F.R., S.L.S., J.M.S., A.M.T.O., A.C.W., M.A.W., S.Z., J.M.Z., E.E.E., R.J.O., M.C.S., K.H.M., K.D.M. and A.M.P. wrote the manuscript draft. A.R. and A.M.P. edited the manuscript, with the assistance of all authors. J.M.Z., E.E.E., R.J.O., M.C.S., K.H.M., K.D.M. and A.M.P. supervised the research. Conceptualization was the responsibility of A.R., S.N., M.C., E.E.E., K.H.M., K.D.M. and A.M.P.

Corresponding author

Correspondence to Adam M. Phillippy .

Ethics declarations

Competing interests.

S.N. is now an employee of ONT. S.K. has received travel funding for speaking at events hosted by ONT. A.F. is an employee of DNAnexus. C.-S.C. is an employee of GeneDX Holdings Corp. N.-C.C. is an employee of Exai Bio. L.F.P. receives research support from Genetech. F.J.S. receives research support from Pacific Biosciences, ONT, Illumina and Genetech. K.S. is an employee of Google LLC and owns Alphabet stock as part of the standard compensation package. W.T. has two patents (nos. 8,748,091 and 8,394,584) licensed to ONT. E.E.E. is a scientific advisory board member of Variant Bio, Inc. The remaining authors declare no competing interests.

Peer review

Peer review information.

Nature thanks John Lovell, Mikkel Heide Schierup and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data figures and tables

Extended data fig. 1 assembling the x and y chromosomes of hg002..

a . Chromosome X and Y components of the assembly string graph built from HiFi reads, detected based on node sequence alignments to T2T-CHM13 and GRCh38 references. Each node is colored according to the excess of paternal-specific (blue) and maternal-specific (red) k-mers, obtained from parental Illumina reads, indicating if they exclusively belong to chromosome Y or X, respectively. Most complicated tangles are localized within the heterochromatic satellite region on the Y q-arm. The X and Y subgraphs are connected in PAR1 and PAR2. Graph discontinuities are due to a lack of HiFi sequence coverage in these regions caused by contextual sequencing bias, with 9 out of 11 observed breaks falling within PAR1 on either chromosome (5 out of 5 for chromosome Y). Note that for visualization purposes the length of shorter nodes is artificially increased making the extent of the tangles appear larger than reality. b . The effects of manual pruning and semi-automated ONT read integration is illustrated from top to bottom. Top, zoomed in view of a tangle encoding the P1–P3 palindromic region in Y (approx. 22.86–27.08 Mb, see Fig. 4 ). Middle, corresponding subgraph following the manual pruning and recompaction. Nodes excluded from the curated “single-copy” list for automated ONT-based repeat resolution are shown in yellow. Three hairpin structures are highlighted, which form almost-perfect inverted tandem repeats encompassing the entire P3 and two P2 (red) palindromes. Node outlines in the palindromes are colored according to the palindromic arms as in Fig. 4 . Bottom, corresponding subgraph following the repeat resolution using ONT read-to-graph alignments. Remaining ambiguities were resolved by evaluating ONT read alignments to all candidate reconstructions of the corresponding sub-regions. c . PAR1 subgraph labeled with HiFi read coverage on each node. Gaps (green edges) and uneven node coverage estimates indicate biases in HiFi sequencing across the region. Figure 1 shows an enrichment of SINE repeats and non-B DNA motifs in PAR1 that may underlie the sequencing gaps in this region.

Extended Data Fig. 2 Validation and polishing of the T2T-Y.

a . Evaluation and polishing workflow performed on T2T-CHM13v1.1 autosomes + HG002 XY assemblies. b . Venn diagram of the k-mers from the parents and child. On the left, hap-mers 18 represent haplotype specific k-mers inherited by the child. The darker outlined circle inside the child k-mers represent single-copy k-mers (k-mers occurring once in the assembly and single-copy in the child’s genome). Right figure shows an example of the paternal specific, “single-copy” and “marker” k-mers. The marker set includes both multi-copy and single-copy k-mers specific to the paternal haplotype that were inherited by the child. Unlike polishing the nearly haploid CHM13 assembly 17 , both single-copy k-mers and marker k-mers were used for the marker-assisted alignments to HG002 XY. This helped align more reads within repetitive regions to the correct chromosome for evaluation during polishing. Right panel shows counts of the k-mers and coverage of HiFi and ONT reads using the marker-assisted Winnowmap2 alignment, in addition to alignments from VerityMap, which uses locally unique k-mers for anchoring the reads. c . Aggregated Strand-seq coverage profile across all 65 libraries on GRCh38-Y (top) and T2T-Y (bottom). Each bar represents read counts in every 20 kb bin supporting the reference in forward direction (light green) or reverse direction (dark green). Multiple spikes in reverse direction (black asterisks) in GRCh38-Y indicate inversion polymorphisms relative to HG002, likely due to differences between the haplogroups. Such spikes in coverage are not observed on T2T-X and T2T-Y, which confirm the structural and directional accuracy of the HG002 assemblies. A 3 kb inversion of the unique sequence between the P5 palindromic arms was identified as erroneous in T2T-Y (red asterisk), but was confirmed to be polymorphic in the population and left uncorrected in this version of the assembly.

Extended Data Fig. 3 Large structural differences between T2T-Y and previous GRCh Y assemblies.

a - b . Ampliconic genes and X-degenerate sequences revealed from alignments between GRCh38-Y (Y-axis) and T2T-Y (X-axis). a . Dotplot generated using LastZ 93 after softmasking with WindowMasker 94 . b . Identity was computed from matches and mismatches over positions with alignments, excluding gaps. c . Structural differences revealed using PRG-TK 95 against GRCh38-Y and GRCh37-Y in the euchromatic region of the Y chromosome.

Extended Data Fig. 4 Repeat discovery and annotation of T2T-Y.

a . Assembly completion allowed for a full assessment of repeats and resulted in the identification of previously unknown satellite arrays (predominantly in the PAR1) and subunit repeats that fall within one of three composite repeat units ( TSPY , RBMY , DAZ ). b . Ideogram of TE density (per 100 kb bin). This is an extension of Fig. 1 with non-SINEs expanded into separate TE classes (SVA, LTR, LINE, DNA/RC). Density scale ranges from low (white, zero) to high (black, relative to total density) and sequence classes are denoted by color. c . Summary (in terms of base coverage per region) across all five TE classes and two specific families: Alu /SINE and L1/LINE. The satellites in ( b ) were kept separate as two categories; Cen/Sat as the left satellite block including alpha satellites and DYZ19, while all other categories were combined per sequence classes.

Extended Data Fig. 5 Non-B DNA motifs along the T2T-Y.

HSat3 on the Yq and satellite sequences around the centromere are more enriched with A-phased repeats, direct repeats and STRs, while HSat1B is more enriched with inverted repeats and mirror repeats. Enrichment of non-B DNA sequences were also observed in the PAR region. Notably, the TSPY gene array is enriched for G4 and Z-DNA motifs, as shown in Extended Data Fig. 6b .

Extended Data Fig. 6 Phylogenetic tree analysis of the ampliconic TSPY gene family and pattern of non-B DNA structure.

a . Phylogenetic tree analysis using protein-coding TSPY s from a Sumatran Orangutan ( Pongo abelii ) and a Silvery gibbon ( Hylobates moloch ) as outgroups confirmed TSPY2 (distal to the array) and TSPY copies within the array originated from the same branch, distinguished from the rest of the TSPY pseudogenes. Rectangular inset shows a cartoon representation of the simplified tree. Numbers next to the triangles indicate the number of TSPY genes in the same branch. b . G4 and Z-DNA structures predicted for a typical TSPY copy inside the TSPY array. All TSPY copies in the array have the same signature, with one G4 peak present ~500 bases upstream of the TSPY (arrow). Higher Quadron score 122 (Q-score) indicates a more stable G4 structure, with scores over 19 considered stable (dotted line).

Extended Data Fig. 7 Recurrent inversions identified with Strand-seq.

a . Five out of 15 individuals have the inverted variant as present in HG002 at the P3 palindrome (white arrow). Although inversions across P1–P2 (yellow and red arrows) are difficult to confirm with Strand-seq because of the high sequence similarity between the palindromic arms, different orientations are observable in these samples. b . Strand states for 65 Strand-seq libraries of HG002. Depending on the mappings of directional Strand-seq reads (+ reads: ‘Crick’, C, – reads: ‘Watson’, W), reference sequence was assigned in three states: WC, WW, and CC. WC, roughly equal mixture of plus and minus reads; WW, all reads mapped in minus orientation; CC, all reads mapped in plus orientation. Changes in strand state along a single chromosome are normally caused by a double-strand-break (DSBs) that occurred during DNA replication 160 in a random fashion and we refer to them as sister-chromatid-exchanges (SCEs, yellow thunderbolts). Recurrent change in strand state over the same region in multiple Strand-seq cells indicates misassembly. Similarly, collapsed or incomplete assembly of a certain genomic region will result in a recurrent strand state change as observed for GRCh38-Y (black arrowheads). In contrast, T2T-Y shows strand state changes randomly distributed along each Strand-seq library with no evidence of misassembly or collapse. c . Strand-seq profile of selected libraries over T2T-Y summarized in bins (bin size: 500 kb, step size: 50 kb). Teal, Crick read counts; orange, Watson read counts. As ChrY is haploid, reads are expected to map only in Watson or Crick orientation. Light gray rectangles highlight regions where SCEs were detected in the heterochromatic Yq12 despite a lower coverage of Strand-seq reads. A modified breakpointR parameter was used (windowsize = 500000 minReads = 20) in order to refine detected SCEs presented in panel b and c .

Extended Data Fig. 8 Satellite annotation and recent expansion events in the Yq heterochromatin.

a . A plot showing the top repeat periodicities detected by NTRprism 44 in 50 kb blocks tiled across T2T-Y, with centromeric satellite annotations overlaid on the X axis. Large arrays are labeled with their historic nomenclature 1 , HSat subfamilies 61 , and predominant repeat periodicities. b . An exact 2000-mer match dotplot of the Yq region (a dot is plotted when an identical 2000 base sequence is found at positions X and Y). The lower triangle has DYZ1/DYZ2 annotations overlaid as yellow and blue bars, respectively. Circled patterns in the upper triangle correspond to recent iterative duplication events, which are illustrated below the X axis. c . A reconstruction of a possible sequence of recent iterative duplications that could explain the observed dotplot patterns. d . A 2000-mer dotplot comparison of two ~800 kb HSat1B sub-arrays that were part of a recent large duplication event, along with self-self comparisons of the same arrays, revealing sites of more recent and smaller-scale deletions and expansions (annotated in yellow and red, with a possible sequence of events illustrated by the schematic on the right).

Extended Data Fig. 9 Genomic similarity in PARs and XTR and improved MAPQ of the PARs through informed sex chromosome complement reference.

a . Dotplots from LASTZ alignments of the CHM13-X, HG002-X, and HG002-Y (T2T-Y) over 96% sequence identity. Dashed gray lines represent the start and end of the approximate PARs or XTR boundaries. Disconnected diagonal lines indicate the presence of genomic diversity between each paired region. More genomic differences are observed in the PAR1 between the HG002-Y and CHM13-X. b - c . Average mapping quality (MAPQ) across GRCh38-X from simulated reads of an XX ( b ) and XY ( c ) sample. Top, a default version of GRCh38 (with two copies of identical PARs on XY). Middle, a version of GRCh38 informed on the sex chromosome complement (SCC) of the sample (entire Y hard-masked for the XX sample vs. only PARs on the Y hard-masked for the XY sample). Bottom, the difference in average MAPQ between the SCC and default approaches. MAPQ was averaged in 50 kb windows, sliding 10 kb across the chromosome. A positive value means MAPQ score is higher with SCC reference alignment compared to default alignment.

Extended Data Fig. 10 Number of variants called from 1KGP and SGDP individuals.

a . More variants are called on the X-PARs when using the sex chromosome complement reference approach (calling variants in diploid mode on PARs) than the non-masked approach (calling variants in haploid mode on PARs). The 1KGP results for GRCh38-Y are from Aganezov et al. 66 , which was performed on CHM13v1.0+GRCh38-Y. b . Num. of variants called from each 1KGP XY sample on chromosome GRCh38-Y and T2T-Y c . Num. of variants called in the syntenic region between the two Ys. A large num. of additional variants are called on each sample attributed to the newly added, non-syntenic sequences on T2T-Y. Within the syntenic regions, a reduction in the number of variants is observed for each population except for samples from R1 haplogroups as shown in Fig. 6c . d . Aggregated total number of variants for the 279 SGDP samples per chromosome. e . SGDP genome-wide counts of variants per-sample (n = 279) demonstrate increased variation in African samples regardless of reference. Each bar in the box plot represents the 1st, 2nd (median), and 3rd quartile of the number of variants in each population. Whiskers are bound to the 1.5 × interquartile range. Data outside of the whisker ranges are shown as dots. For the SGDP samples, variants were called using T2T-CHM13+Y or GRCh38 as the reference. All variants shown in this figure were filtered for “high quality (PASS)”.

Extended Data Fig. 11 Human contaminants in bacterial reference genomes.

a . Number of distinct RefSeq accessions in every 10 kb window containing 64-mers of GRCh38-Y (top), T2T-Y (middle), and in T2T-Y only (bottom). Here, RefSeq sequences with more than 20 64-mers or matching over 10% of the Y chromosome are included. b . Length distribution of the sequences from ( a ) in log scale. Majority of the shorter (<1 kb) sequences contain 64-mers found in HSat1B or HSat3. c . Number of bacterial RefSeq entries by strain identified to contain sequences of T2T-Y and not GRCh38-Y, visualized with Krona 158 .

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Rhie, A., Nurk, S., Cechova, M. et al. The complete sequence of a human Y chromosome. Nature (2023). https://doi.org/10.1038/s41586-023-06457-y

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DOI : https://doi.org/10.1038/s41586-023-06457-y

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Error bars represent 95% CIs. GAS indicates gender-affirming surgery.

Percentages are based on the number of procedures divided by number of patients; thus, as some patients underwent multiple procedures the total may be greater than 100%. Error bars represent 95% CIs.

eTable.  ICD-10 and CPT Codes of Gender-Affirming Surgery

eFigure. Percentage of Patients With Codes for Gender Identity Disorder Who Underwent GAS

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Wright JD , Chen L , Suzuki Y , Matsuo K , Hershman DL. National Estimates of Gender-Affirming Surgery in the US. JAMA Netw Open. 2023;6(8):e2330348. doi:10.1001/jamanetworkopen.2023.30348

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National Estimates of Gender-Affirming Surgery in the US

• 1 Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, New York
• 2 Department of Obstetrics and Gynecology, University of Southern California, Los Angeles

Question   What are the temporal trends in gender-affirming surgery (GAS) in the US?

Findings   In this cohort study of 48 019 patients, GAS increased significantly, nearly tripling from 2016 to 2019. Breast and chest surgery was the most common class of procedures performed overall; genital reconstructive procedures were more common among older individuals.

Meaning   These findings suggest that there will be a greater need for clinicians knowledgeable in the care of transgender individuals with the requisite expertise to perform gender-affirming procedures.

Importance   While changes in federal and state laws mandating coverage of gender-affirming surgery (GAS) may have led to an increase in the number of annual cases, comprehensive data describing trends in both inpatient and outpatient procedures are limited.

Objective   To examine trends in inpatient and outpatient GAS procedures in the US and to explore the temporal trends in the types of GAS performed across age groups.

Design, Setting, and Participants   This cohort study includes data from 2016 to 2020 in the Nationwide Ambulatory Surgery Sample and the National Inpatient Sample. Patients with diagnosis codes for gender identity disorder, transsexualism, or a personal history of sex reassignment were identified, and the performance of GAS, including breast and chest procedures, genital reconstructive procedures, and other facial and cosmetic surgical procedures, were identified.

Main Outcome Measures   Weighted estimates of the annual number of inpatient and outpatient procedures performed and the distribution of each class of procedure overall and by age were analyzed.

Results   A total of 48 019 patients who underwent GAS were identified, including 25 099 (52.3%) who were aged 19 to 30 years. The most common procedures were breast and chest procedures, which occurred in 27 187 patients (56.6%), followed by genital reconstruction (16 872 [35.1%]) and other facial and cosmetic procedures (6669 [13.9%]). The absolute number of GAS procedures rose from 4552 in 2016 to a peak of 13 011 in 2019 and then declined slightly to 12 818 in 2020. Overall, 25 099 patients (52.3%) were aged 19 to 30 years, 10 476 (21.8%) were aged 31 to 40, and 3678 (7.7%) were aged12 to 18 years. When stratified by the type of procedure performed, breast and chest procedures made up a greater percentage of the surgical interventions in younger patients, while genital surgical procedures were greater in older patients.

Conclusions and Relevance   Performance of GAS has increased substantially in the US. Breast and chest surgery was the most common group of procedures performed. The number of genital surgical procedures performed increased with increasing age.

Gender dysphoria is characterized as an incongruence between an individual’s experienced or expressed gender and the gender that was assigned at birth. 1 Transgender individuals may pursue multiple treatments, including behavioral therapy, hormonal therapy, and gender-affirming surgery (GAS). 2 GAS encompasses a variety of procedures that align an individual patient’s gender identity with their physical appearance. 2 - 4

While numerous surgical interventions can be considered GAS, the procedures have been broadly classified as breast and chest surgical procedures, facial and cosmetic interventions, and genital reconstructive surgery. 2 , 4 Prior studies 2 - 7 have shown that GAS is associated with improved quality of life, high rates of satisfaction, and a reduction in gender dysphoria. Furthermore, some studies have reported that GAS is associated with decreased depression and anxiety. 8 Lastly, the procedures appear to be associated with acceptable morbidity and reasonable rates of perioperative complications. 2 , 4

Given the benefits of GAS, the performance of GAS in the US has increased over time. 9 The increase in GAS is likely due in part to federal and state laws requiring coverage of transition-related care, although actual insurance coverage of specific procedures is variable. 10 , 11 While prior work has shown that the use of inpatient GAS has increased, national estimates of inpatient and outpatient GAS are lacking. 9 This is important as many GAS procedures occur in ambulatory settings. We performed a population-based analysis to examine trends in GAS in the US and explored the temporal trends in the types of GAS performed across age groups.

To capture both inpatient and outpatient surgical procedures, we used data from the Nationwide Ambulatory Surgery Sample (NASS) and the National Inpatient Sample (NIS). NASS is an ambulatory surgery database and captures major ambulatory surgical procedures at nearly 2800 hospital-owned facilities from up to 35 states, approximating a 63% to 67% stratified sample of hospital-owned facilities. NIS comprehensively captures approximately 20% of inpatient hospital encounters from all community hospitals across 48 states participating in the Healthcare Cost and Utilization Project (HCUP), covering more than 97% of the US population. Both NIS and NASS contain weights that can be used to produce US population estimates. 12 , 13 Informed consent was waived because data sources contain deidentified data, and the study was deemed exempt by the Columbia University institutional review board. This cohort study followed the Strengthening the Reporting of Observational Studies in Epidemiology ( STROBE ) reporting guideline.

We selected patients of all ages with an International Statistical Classification of Diseases and Related Health Problems, Tenth Revision ( ICD-10 ) diagnosis codes for gender identity disorder or transsexualism ( ICD-10 F64) or a personal history of sex reassignment ( ICD-10 Z87.890) from 2016 to 2020 (eTable in Supplement 1 ). We first examined all hospital (NIS) and ambulatory surgical (NASS) encounters for patients with these codes and then analyzed encounters for GAS within this cohort. GAS was identified using ICD-10 procedure codes and Common Procedural Terminology codes and classified as breast and chest procedures, genital reconstructive procedures, and other facial and cosmetic surgical procedures. 2 , 4 Breast and chest surgical procedures encompassed breast reconstruction, mammoplasty and mastopexy, or nipple reconstruction. Genital reconstructive procedures included any surgical intervention of the male or female genital tract. Other facial and cosmetic procedures included cosmetic facial procedures and other cosmetic procedures including hair removal or transplantation, liposuction, and collagen injections (eTable in Supplement 1 ). Patients might have undergone procedures from multiple different surgical groups. We measured the total number of procedures and the distribution of procedures within each procedural group.

Within the data sets, sex was based on patient self-report. The sex of patients in NIS who underwent inpatient surgery was classified as either male, female, missing, or inconsistent. The inconsistent classification denoted patients who underwent a procedure that was not consistent with the sex recorded on their medical record. Similar to prior analyses, patients in NIS with a sex variable not compatible with the procedure performed were classified as having undergone genital reconstructive surgery (GAS not otherwise specified). 9

Clinical variables in the analysis included patient clinical and demographic factors and hospital characteristics. Demographic characteristics included age at the time of surgery (12 to 18 years, 19 to 30 years, 31 to 40 years, 41 to 50 years, 51 to 60 years, 61 to 70 years, and older than 70 years), year of the procedure (2016-2020), and primary insurance coverage (private, Medicare, Medicaid, self-pay, and other). Race and ethnicity were only reported in NIS and were classified as White, Black, Hispanic and other. Race and ethnicity were considered in this study because prior studies have shown an association between race and GAS. The income status captured national quartiles of median household income based of a patient’s zip code and was recorded as less than 25% (low), 26% to 50% (medium-low), 51% to 75% (medium-high), and 76% or more (high). The Elixhauser Comorbidity Index was estimated for each patient based on the codes for common medical comorbidities and weighted for a final score. 14 Patients were classified as 0, 1, 2, or 3 or more. We separately reported coding for HIV and AIDS; substance abuse, including alcohol and drug abuse; and recorded mental health diagnoses, including depression and psychoses. Hospital characteristics included a composite of teaching status and location (rural, urban teaching, and urban nonteaching) and hospital region (Northeast, Midwest, South, and West). Hospital bed sizes were classified as small, medium, and large. The cutoffs were less than 100 (small), 100 to 299 (medium), and 300 or more (large) short-term acute care beds of the facilities from NASS and were varied based on region, urban-rural designation, and teaching status of the hospital from NIS. 8 Patients with missing data were classified as the unknown group and were included in the analysis.

National estimates of the number of GAS procedures among all hospital encounters for patients with gender identity disorder were derived using discharge or encounter weight provided by the databases. 15 The clinical and demographic characteristics of the patients undergoing GAS were reported descriptively. The number of encounters for gender identity disorder, the percentage of GAS procedures among those encounters, and the absolute number of each procedure performed over time were estimated. The difference by age group was examined and tested using Rao-Scott χ 2 test. All hypothesis tests were 2-sided, and P  < .05 was considered statistically significant. All analyses were conducted using SAS version 9.4 (SAS Institute Inc).

A total of 48 019 patients who underwent GAS were identified ( Table 1 ). Overall, 25 099 patients (52.3%) were aged 19 to 30 years, 10 476 (21.8%) were aged 31 to 40, and 3678 (7.7%) were aged 12 to 18 years. Private insurance coverage was most common in 29 064 patients (60.5%), while 12 127 (25.3%) were Medicaid recipients. Depression was reported in 7192 patients (15.0%). Most patients (42 467 [88.4%]) were treated at urban, teaching hospitals, and there was a disproportionate number of patients in the West (22 037 [45.9%]) and Northeast (12 396 [25.8%]). Within the cohort, 31 668 patients (65.9%) underwent 1 procedure while 13 415 (27.9%) underwent 2 procedures, and the remainder underwent multiple procedures concurrently ( Table 1 ).

The overall number of health system encounters for gender identity disorder rose from 13 855 in 2016 to 38 470 in 2020. Among encounters with a billing code for gender identity disorder, there was a consistent rise in the percentage that were for GAS from 4552 (32.9%) in 2016 to 13 011 (37.1%) in 2019, followed by a decline to 12 818 (33.3%) in 2020 ( Figure 1 and eFigure in Supplement 1 ). Among patients undergoing ambulatory surgical procedures, 37 394 (80.3%) of the surgical procedures included gender-affirming surgical procedures. For those with hospital admissions with gender identity disorder, 10 625 (11.8%) of admissions were for GAS.

Breast and chest procedures were most common and were performed for 27 187 patients (56.6%). Genital reconstruction was performed for 16 872 patients (35.1%), and other facial and cosmetic procedures for 6669 patients (13.9%) ( Table 2 ). The most common individual procedure was breast reconstruction in 21 244 (44.2%), while the most common genital reconstructive procedure was hysterectomy (4489 [9.3%]), followed by orchiectomy (3425 [7.1%]), and vaginoplasty (3381 [7.0%]). Among patients who underwent other facial and cosmetic procedures, liposuction (2945 [6.1%]) was most common, followed by rhinoplasty (2446 [5.1%]) and facial feminizing surgery and chin augmentation (1874 [3.9%]).

The absolute number of GAS procedures rose from 4552 in 2016 to a peak of 13 011 in 2019 and then declined slightly to 12 818 in 2020 ( Figure 1 ). Similar trends were noted for breast and chest surgical procedures as well as genital surgery, while the rate of other facial and cosmetic procedures increased consistently from 2016 to 2020. The distribution of the individual procedures performed in each class were largely similar across the years of analysis ( Table 3 ).

When stratified by age, patients 19 to 30 years had the greatest number of procedures, 25 099 ( Figure 2 ). There were 10 476 procedures performed in those aged 31 to 40 years and 4359 in those aged 41 to 50 years. Among patients younger than 19 years, 3678 GAS procedures were performed. GAS was less common in those cohorts older than 50 years. Overall, the greatest number of breast and chest surgical procedures, genital surgical procedures, and facial and other cosmetic surgical procedures were performed in patients aged 19 to 30 years.

When stratified by the type of procedure performed, breast and chest procedures made up the greatest percentage of the surgical interventions in younger patients while genital surgical procedures were greater in older patients ( Figure 2 ). Additionally, 3215 patients (87.4%) aged 12 to 18 years underwent GAS and had breast or chest procedures. This decreased to 16 067 patients (64.0%) in those aged 19 to 30 years, 4918 (46.9%) in those aged 31 to 40 years, and 1650 (37.9%) in patients aged 41 to 50 years ( P  < .001). In contrast, 405 patients (11.0%) aged 12 to 18 years underwent genital surgery. The percentage of patients who underwent genital surgery rose sequentially to 4423 (42.2%) in those aged 31 to 40 years, 1546 (52.3%) in those aged 51 to 60 years, and 742 (58.4%) in those aged 61 to 70 years ( P  < .001). The percentage of patients who underwent facial and other cosmetic surgical procedures rose with age from 9.5% in those aged 12 to 18 years to 20.6% in those aged 51 to 60 years, then gradually declined ( P  < .001). Figure 2 displays the absolute number of procedure classes performed by year stratified by age. The greatest magnitude of the decline in 2020 was in younger patients and for breast and chest procedures.

These findings suggest that the number of GAS procedures performed in the US has increased dramatically, nearly tripling from 2016 to 2019. Breast and chest surgery is the most common class of procedure performed while patients are most likely to undergo surgery between the ages of 19 and 30 years. The number of genital surgical procedures performed increased with increasing age.

Consistent with prior studies, we identified a remarkable increase in the number of GAS procedures performed over time. 9 , 16 A prior study examining national estimates of inpatient GAS procedures noted that the absolute number of procedures performed nearly doubled between 2000 to 2005 and from 2006 to 2011. In our analysis, the number of GAS procedures nearly tripled from 2016 to 2020. 9 , 17 Not unexpectedly, a large number of the procedures we captured were performed in the ambulatory setting, highlighting the need to capture both inpatient and outpatient procedures when analyzing data on trends. Like many prior studies, we noted a decrease in the number of procedures performed in 2020, likely reflective of the COVID-19 pandemic. 18 However, the decline in the number of procedures performed between 2019 and 2020 was relatively modest, particularly as these procedures are largely elective.

Analysis of procedure-specific trends by age revealed a number of important findings. First, GAS procedures were most common in patients aged 19 to 30 years. This is in line with prior work that demonstrated that most patients first experience gender dysphoria at a young age, with approximately three-quarters of patients reporting gender dysphoria by age 7 years. These patients subsequently lived for a mean of 23 years for transgender men and 27 years for transgender women before beginning gender transition treatments. 19 Our findings were also notable that GAS procedures were relatively uncommon in patients aged 18 years or younger. In our cohort, fewer than 1200 patients in this age group underwent GAS, even in the highest volume years. GAS in adolescents has been the focus of intense debate and led to legislative initiatives to limit access to these procedures in adolescents in several states. 20 , 21

Second, there was a marked difference in the distribution of procedures in the different age groups. Breast and chest procedures were more common in younger patients, while genital surgery was more frequent in older individuals. In our cohort of individuals aged 19 to 30 years, breast and chest procedures were twice as common as genital procedures. Genital surgery gradually increased with advancing age, and these procedures became the most common in patients older than 40 years. A prior study of patients with commercial insurance who underwent GAS noted that the mean age for mastectomy was 28 years, significantly lower than for hysterectomy at age 31 years, vaginoplasty at age 40 years, and orchiectomy at age 37 years. 16 These trends likely reflect the increased complexity of genital surgery compared with breast and chest surgery as well as the definitive nature of removal of the reproductive organs.

This study has limitations. First, there may be under-capture of both transgender individuals and GAS procedures. In both data sets analyzed, gender is based on self-report. NIS specifically makes notation of procedures that are considered inconsistent with a patient’s reported gender (eg, a male patient who underwent oophorectomy). Similar to prior work, we assumed that patients with a code for gender identity disorder or transsexualism along with a surgical procedure classified as inconsistent underwent GAS. 9 Second, we captured procedures commonly reported as GAS procedures; however, it is possible that some of these procedures were performed for other underlying indications or diseases rather than solely for gender affirmation. Third, our trends showed a significant increase in procedures through 2019, with a decline in 2020. The decline in services in 2020 is likely related to COVID-19 service alterations. Additionally, while we comprehensively captured inpatient and ambulatory surgical procedures in large, nationwide data sets, undoubtedly, a small number of procedures were performed in other settings; thus, our estimates may underrepresent the actual number of procedures performed each year in the US.

These data have important implications in providing an understanding of the use of services that can help inform care for transgender populations. The rapid rise in the performance of GAS suggests that there will be a greater need for clinicians knowledgeable in the care of transgender individuals and with the requisite expertise to perform GAS procedures. However, numerous reports have described the political considerations and challenges in the delivery of transgender care. 22 Despite many medical societies recognizing the necessity of gender-affirming care, several states have enacted legislation or policies that restrict gender-affirming care and services, particularly in adolescence. 20 , 21 These regulations are barriers for patients who seek gender-affirming care and provide legal and ethical challenges for clinicians. As the use of GAS increases, delivering equitable gender-affirming care in this complex landscape will remain a public health challenge.

Accepted for Publication: July 15, 2023.

Published: August 23, 2023. doi: 10.1001/jamanetworkopen.2023.30348

Open Access: This is an open access article distributed under the terms of the CC-BY License . © 2023 Wright JD et al. JAMA Network Open .

Corresponding Author: Jason D. Wright, MD, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, 161 Fort Washington Ave, 4th Floor, New York, NY 10032 ( [email protected] ).

Author Contributions: Dr Wright had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis.

Concept and design: Wright, Chen.

Acquisition, analysis, or interpretation of data: All authors.

Drafting of the manuscript: Wright.

Critical review of the manuscript for important intellectual content: All authors.

Statistical analysis: Wright, Chen.

Administrative, technical, or material support: Wright, Suzuki.

Conflict of Interest Disclosures: Dr Wright reported receiving grants from Merck and personal fees from UpToDate outside the submitted work. No other disclosures were reported.

Data Sharing Statement: See Supplement 2 .

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