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PLoS Genetics Guidelines for Authors

Contents:

  1. About PLoS Genetics
  2. Open Access
  3. Publication Charges
  4. Criteria for Publication
  5. Overview of the Editorial Process
  6. Presubmission Inquiries
  7. Preparation of Research Articles
    1. Organization of the Manuscript
    2. Nomenclature
    3. Accession Numbers
    4. Abbreviations
  8. Materials Required for Manuscript Submission
    1. Cover Letter
    2. Author Status
    3. Financial Disclosure
    4. Competing Interests
    5. Electronic Formats
      1. Manuscript and Tables File
      2. Figure Files
      3. Multimedia Files and Supporting Information
    6. Ready to Submit Your Manuscript?
  9. Interviews, Reviews, and Special Reports
  10. Overview of the Production Process
  11. Blogs, Wikis, Embargoes, and the Media

1. About PLoS Genetics

The techniques of genetics and genomics are being applied to a wealth of biological questions and experimental systems. PLoS Genetics reflects the full breadth and interdisciplinary nature of this research by publishing outstanding original contributions in all areas of biology. With immediate free access to all content, PLoS Genetics provides a unique venue for publishing genetics and genomics research, ensuring that authors reach the widest possible audience.

PLoS Genetics publishes human studies as well as research on model organisms—from mice and flies, to plants and bacteria. Our emphasis is on studies of broad interest that provide significant mechanistic insight into a biological process or processes. Topics include (but are not limited to) gene discovery and function, population genetics, genome projects, comparative and functional genomics, medical genetics, disease biology, evolution, gene expression, complex traits, chromosome biology, and epigenetics.

2. Open Access

The Public Library of Science (PLoS) applies the Creative Commons Attribution License (CCAL) to all works we publish. Under the CCAL, authors retain ownership of the copyright for their article, but authors allow anyone to download, reuse, reprint, modify, distribute, and/or copy articles in PLoS journals, so long as the original authors and source are cited. No permission is required from the authors or the publishers.

3. Publication Charges

To provide open access, PLoS journals use a business model in which our expenses—including those of peer review, journal production, and online hosting and archiving—are recovered in part by charging a publication fee to the authors or research sponsors for each article they publish. For PLoS Genetics the publication fee is US$2200. Authors who are affiliated with one of our Institutional Members are eligible for a discount on this fee.

We offer a complete or partial fee waiver for authors who do not have funds to cover publication fees. Editors and reviewers have no access to payment information, and hence inability to pay will not influence the decision to publish a paper.

For further information, see our Publication Fee FAQ.

4. Criteria for Publication

To be considered for publication in PLoS Genetics, any given manuscript must satisfy the following criteria:

5. Overview of Editorial Process

Our aim is to provide all authors with an efficient, courteous, and constructive editorial process. To achieve its required level of quality, PLoS Genetics is highly selective in the manuscripts that it publishes; rejection rates are high. To ensure the fairest and most objective decision-making, the editorial process is run as a partnership between the PLoS Genetics Editor-in-Chief, a Deputy Editor, a team of Section Editors (SEs), and a group of academic experts who act as Associate Editors (AEs). These individuals are leaders in their fields and represent the full breadth of genetics and genomics.

Submitted manuscripts are first reviewed by the EIC, Deputy Editor, or one of the SEs, who may decide to reject the paper or send it on to an AE for further review. The AE is most often a member of the PLoS Genetics Editorial Board, but occasionally a guest of the Board is invited to serve in this capacity. The AE evaluates the paper and decides whether it describes a sufficient body of work to support a major advance in a particular field. If so, the paper is sent out for external peer review, at which stage the technical and scientific merits of the work are carefully considered. Once the reviews have been received and considered by the editors, a decision letter to the corresponding author is drafted and sent.

The decision will be within one of the following categories:

6. Presubmission Inquiries

When authors are unsure whether their work satisfies the basic requirements for publication in PLoS Genetics, we are happy to consider presubmission inquiries. If you would like to submit an informal presubmission inquiry to see if a manuscript is appropriate in principle, please login or register for a new account within our online submission system, choosing 'Submit Presubmission Inquiry' from the list of Author Tasks. Required for all Presubmission Inquiries are contact information, a cover letter, and an abstract.

Responses to these inquiries are normally provided within a few working days. Responses may take longer if consultation between members of the editorial board is required. If you are invited to submit your manuscript, we will do our best to provide an expeditious initial assessment of the complete manuscript for suitability and then, if warranted, external peer review.

7. Preparation of Research Manuscripts

PLoS Genetics publishes original research that clearly demonstrates novelty, importance to a particular field, biological significance, and conclusions that are justified by the study.

Our aim is to make the editorial process rigorous and consistent, and to offer the best possible support to our authors throughout this process. Authors are encouraged to decide how best to present their ideas, results, and conclusions. The writing style should be concise and accessible. Editors may make suggestions for how to achieve this, as well as suggestions for cuts or additions that could be made to the article to strengthen the argument.

Although we encourage submissions from around the globe, we require that manuscripts be submitted in English. As a step towards overcoming language barriers, we encourage authors fluent in other languages to provide copies of their full articles or abstracts in other languages. Translations should be submitted as supporting information and listed, together with other supporting information files, at the end of the article text.

Organization of the Manuscript

Most articles published in PLoS Genetics are organized into the following sections: Title, Authors, Affiliations, Abstract, Author Summary, Introduction, Results, Discussion, Materials and Methods, Acknowledgments, References, Figure Legends, and Tables. Uniformity in format facilitates the experience of readers and users of the journal. To provide flexibility, however, authors are also able to include the Materials and Methods section before the Results section or before the Discussion section. Please also note that the Results and Discussion can be combined into one Results/Discussion section. Although we have no firm length restrictions for the entire manuscript, we urge authors to present and discuss their findings concisely.

Title (150 characters or less)

The title should be specific to the project, yet concise. It should be comprehensible to readers outside your field. Avoid specialist abbreviations, if possible. Titles should be presented in title case, meaning that all words except for prepositions, articles, and conjunctions should be capitalized. Please also provide a brief "running head" of no more than 30 characters.

Example:
Detection of Specific Sequences among DNA Fragments Separated by Gel Electrophoresis.

Authors and Affiliations

Provide the first names or initials (if used), middle names or initials (if used), surnames, and affiliations—department, university or organization, city, state/province (if applicable), and country—for all authors. One of the authors should be designated as the corresponding author. It is the corresponding author's responsibility to ensure that the author list, and the summary of the author contributions to the study, is accurate and complete. If the article has been submitted on behalf of a consortium, all consortium members and affiliations should be listed after the Acknowledgments.

Abstract

The abstract of the paper should be succinct; it should not exceed 250-300 words. Authors should mention the techniques used without going into methodological detail and should summarize the most important results. The abstract is conceptually divided into the following three sections for the purpose of submission and review: Background, Methodology/Principal Findings, and Conclusions/Significance. While the text of the abstract in the submission form and article file should be exactly the same, please do not apply these distinct headings to the abstract within the article file. Please do not include any citations and avoid specialist abbreviations.

Author Summary

We ask that all authors of research articles include a 150-200 word non-technical summary of the work as part of the manuscript to immediately follow the abstract. This text is subject to editorial change, should be written in the first-person voice, and should be distinct from the scientific abstract. Aim to highlight where your work fits within a broader context; present the significance or possible implications of your work simply and objectively; and avoid the use of acronyms and complex terminology wherever possible. The goal is to make your findings accessible to a wide audience that includes both scientists and non-scientists. Authors may benefit from consulting with a science writer or press officer to ensure they effectively communicate their findings to a general audience. Examples are available at:

Complex Seizure Disorder Caused by Brunol4 Deficiency in Mice

Genome-Wide Association Scan Shows Genetic Variants in the FTO Gene Are Associated with Obesity-Related Traits

A Mutation in the Myostatin Gene Increases Muscle Mass and Enhances Racing Performance in Heterozygote Dogs

Introduction

The introduction should put the focus of the manuscript into a broader context. As you compose the introduction, think of readers who are not experts in this field. Include a brief review of the key literature. If there are relevant controversies or disagreements in the field, they should be mentioned so that a non-expert reader can delve into these issues further. The introduction should conclude with a brief statement of the overall aim of the experiments and a comment about whether that aim was achieved.

Results

The results section should provide details of all of the experiments that are required to support the conclusions of the paper. There is no specific word limit for this section, but details of experiments that are peripheral to the main thrust of the article and that detract from the focus of the article should not be included. The section may be divided into subsections, each with a concise subheading. Large datasets, including raw data, should be submitted as supporting files; these are published online alongside the accepted article. The results section should be written in the past tense.

Discussion

The discussion should spell out the major conclusions of the work along with some explanation or speculation on the significance of these conclusions. How do the conclusions affect the existing assumptions and models in the field? How can future research build on these observations? What are the key experiments that must be done? The discussion should be concise and tightly argued. The results and discussion may be combined into one section, if desired.

Materials and Methods (also called Methods or Models)

This section should provide enough detail for reproduction of the findings. Protocols for new methods should be included, but well-established protocols may simply be referenced. While we do encourage authors to submit all appendices, detailed protocols, or details of the algorithms for newer or less well-established methods, please do so as Supporting Information files. These are not included in the typeset manuscript, but are downloadable and fully searchable from the HTML version of the article.

Acknowledgments

People who contributed to the work but do not fit the criteria for authors should be listed in the Acknowledgments, along with their contributions. You must also ensure that anyone named in the Acknowledgments agrees to being so named.

Details of the funding sources that have supported the work should be confined to the funding statement provided in the online submission system. Do not include them in the Acknowledgments.

References

Only published or accepted manuscripts should be included in the reference list. Meetings abstracts, conference talks, or papers that have been submitted but not yet accepted should not be cited. Limited citation of unpublished work should be included in the body of the text only. All personal communications should be supported by a letter from the relevant authors.

PLoS uses the numbered citation (citation-sequence) method. References are listed and numbered in the order that they appear in the text. In the text, citations should be indicated by the reference number in brackets. Multiple citations within a single set of brackets should be separated by commas. Where there are three or more sequential citations, they should be given as a range. Example: "...has been shown previously [1,4–6,22]." Make sure the parts of the manuscript are in the correct order for the relevant journal before ordering the citations. Figure captions and tables should be at the end of the manuscript.

Because all references will be linked electronically as much as possible to the papers they cite, proper formatting of the references is crucial. Please use the following style for the reference list:

Published Papers
1. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74: 5463–5467.

Please list the first five authors and then add "et al." if there are additional authors. Use of a DOI number to the full-text article is acceptable as an alternative to or in addition to traditional volume and page numbers.

Accepted Papers
Same as above, but "In press" appears instead of the page numbers. Example: Adv Clin Path. In press.

Electronic Journal Articles
1. Loker WM (1996) "Campesinos" and the crisis of modernization in Latin America. Jour Pol Ecol 3. Available: http://www.library.arizona.edu/ej/jpe/volume_3/ascii-lokeriso.txt. Accessed 11 August 2006.

Books
1. Bates B (1992) Bargaining for life: A social history of tuberculosis. Philadelphia: University of Pennsylvania Press. 435 p.

Book Chapters
1. Hansen B (1991) New York City epidemics and history for the public. In: Harden VA, Risse GB, editors. AIDS and the historian. Bethesda: National Institutes of Health. pp. 21–28.

Figure Legends

The aim of the figure legend should be to describe the key messages of the figure, but the figure should also be discussed in the text. An enlarged version of the figure and its full legend will often be viewed in a separate window online, and it should be possible for a reader to understand the figure without switching back and forth between this window and the relevant parts of the text. Each legend should have a concise title of no more than 15 words. The legend itself should be succinct, while still explaining all symbols and abbreviations. Avoid lengthy descriptions of methods.

Tables

Tables should be included at the end of the manuscript file and cited sequentially in the text. All tables should have a concise title. Footnotes can be used to explain abbreviations. Citations should be indicated using the same style as outlined above. Tables occupying more than one printed page should be avoided, if possible. Larger tables can be published as online supporting information. Tables must be cell-based; do not use picture elements, text boxes, tabs, or returns in tables. Please ensure that all tables conform to our Guidelines for Figure and Table Preparation when preparing them.

Nomenclature

The use of standardized nomenclature in all fields of science and medicine is an essential step toward the integration and linking of scientific information reported in published literature. We will enforce the use of correct and established nomenclature wherever possible:

Accession Numbers

All appropriate datasets, images, and information should be deposited in public resources. Please provide the relevant accession numbers (and version numbers, if appropriate). Accession numbers should be provided in parentheses after the entity on first use. Suggested databases include, but are not limited to:

In addition, as much as possible, please provide accession numbers or identifiers for all entities such as genes, proteins, mutants, diseases, etc., for which there is an entry in a public database, for example:

Providing accession numbers allows linking to and from established databases and integrates your article with a broader collection of scientific information.

Abbreviations

Please keep abbreviations to a minimum and define them upon first use in the text. Non-standard abbreviations should not be used unless they appear at least three times in the text.

8. Materials Required for Manuscript Submission

Cover Letter

It is important that you include a cover letter with your manuscript. Please explain why this manuscript is suitable for publication in PLoS Genetics; why will your paper inspire the other members of your field, and how will it drive research forward? You are free to recommend a suitable Associate Editor to handle your submission; however, the editors reserve the right to contact an alternative—either from the board or a guest editor—if it is considered more appropriate. Please note that the cover letter will be available to the editors and to external peer reviewers as necessary, so be careful not to reveal anything of a confidential nature.

Author Status

It is the responsibility of the corresponding author to ensure that all authors are aware of and approve the submission of the manuscript, its content, authorship, and order of authorship. Confirmation of this action is required at submission of all manuscripts.

The involvement of any professional medical writer in publication must be declared. We encourage authors to consult the European Medical Writers' Association Guidelines on the role of medical writers.

PLoS Genetics bases its criteria for authorship on those outlined in the Uniform Requirements for Manuscripts Submitted to Biomedical Journals, which are summarized below. However, if you believe that a particular individual should be an author, you may include them, provided they are able to take responsibility for a given part of the study. The contributions of all authors must be described. Contributions that fall short of authorship should be mentioned in the acknowledgments.

"Authorship credit should be based on

  1. substantial contribution to conception and design, or acquisition of data, or analysis and interpretation of data;
  2. drafting the article or revising it critically for important intellectual content; and
  3. final approval of the version to be published
Authors should meet conditions 1, 2, and 3.

When a large, multi-center group has conducted the work, the group should identify the individuals who accept direct responsibility for the manuscript (3). These individuals should fully meet the criteria for authorship defined above and editors will ask these individuals to complete journal-specific author and competing interests disclosure forms. When submitting a group author manuscript, the corresponding author should clearly indicate the preferred citation and should clearly identify all individual authors as well as the group name.

Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship. All persons designated as authors should qualify for authorship, and all those who qualify should be listed. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content."

Financial Disclosure

Before submitting your manuscript, please collect information on the sources of funding that have supported the work. When you submit your manuscript, you will be required to provide a statement in the online submission system declaring the funding sources, and also stating the role of the study sponsor(s), if any, in study design; collection, analysis, and interpretation of data; writing of the paper; and decision to submit it for publication.

Competing Interests

The submitting author is asked at submission to declare, on behalf of all authors, whether there are any financial, personal, or professional interests that could be construed to have influenced the paper. Reviewers are also asked to declare any interests that might interfere with their objective assessment of a manuscript. Any relevant competing interests of authors must be available to editors and reviewers during the review process and will be stated in published articles. Read more about the policy of PLoS regarding competing interests.

Electronic Formats

Our submission system supports a limited range of formats for text and graphics. The following file formats/types and manuscript information are required before submission. If you are concerned about the suitability of your files, please contact us at plosgenetics [at] plos.org.

Manuscript and Tables File

Text files should be submitted in DOC or RTF format. Tables should be placed at the end of the manuscript file.

Manuscripts prepared in LaTeX may be submitted in PDF format for use during the review process. Post acceptance, however, these authors will be asked to submit their .tex files and formatting information as a zipped file. Please consult our LaTeX Guidelines for a list of what will be required.

Please note: At this time we cannot accept for review or revision any documents created in Microsoft Office 2007, even if "saved down" to the 2003 version. Major changes made in Word 2007, relative to earlier versions of Word, are incompatible with the established workflow processes of many publishers (e.g. the handling of mathematical equations). PLoS is actively seeking solutions to this problem.

Figure Files

For the article to be accepted for publication, the author will need to supply high-resolution versions of the figures in TIF or EPS format only. When preparing your figures, please ensure that the files conform to our Guidelines for Figure and Table Preparation. Please do not upload panels for a single figure separately (for example, Figure 1A, Figure 1B-1D, Figure 1E); each figure file should be a single montage of all panels. Queries can be sent to figures [at] plos.org.

If you are uploading your files in EPS format, please use the "create outlines" option under the type menu in Illustrator so that all text and fonts appear as intended in print. If you need additional help with figure preparation, please contact figures [at] plos.org.

All figures will be published under a Creative Commons Attribution License, which allows them to be freely used, distributed, and built upon as long as proper attribution is given. Please do not submit any figures that have been previously copyrighted unless you have express written permission from the copyright holder to publish under the CCAL license.

Multimedia Files and Supporting Information

We encourage authors to submit essential supporting files and multimedia files along with their manuscripts. All supporting material will be subject to peer review, and should be smaller than 10 MB in size because of the difficulties that some users will experience in loading or downloading files of a greater size.

Supporting files should fall into one of the following categories: Dataset, Figure, Table, Text, Protocol, Audio, or Video. All supporting information should be referred to in the manuscript with a leading capital S (e.g., Figure S4 for the fourth supporting information figure). The numbered title and caption for each supporting information file should be entered into the appropriate fields in the online submission system. The information entered here will appear in the published version, so no supporting information titles or captions should be listed in the manuscript file.

Supporting files will not be included in the typeset PDF, but will be referenced in the text and hosted online.

Supporting files may be submitted in a variety of formats, but should be publication-ready, as these files are not copyedited. Carefully consider whether your supporting information needs to be searchable and/or editable, and choose the most suitable format accordingly.

Some preferred formats for PLoS Genetics are:

Ready to Submit Your Manuscript?

We have provided a Submission Checklist to help you prepare your materials for submission and to make the online submission process as straightforward as possible. Please take the time to look through the list before submitting your article.

Please login or register at our online submission system to begin the submission process. Files should be uploaded individually, and are automatically combined into a single PDF file, which must be approved by the author at the end of the submission process. This merged PDF is for internal and external peer review only. Original source files will be used to prepare accepted articles for publication.

9. Interviews, Reviews, and Special Reports

In addition to weekly research articles, PLoS Genetics also provides a forum for the publication of articles of broad interest to the genetics and genomics community. These articles are by invitation only; however, we encourage you to send your feedback and ideas to plosgenetics [at] plos.org.

Interviews

Jane Gitschier brings her unique conversational style to an ongoing collection of interviews of interesting people in the world of science and genetics — from Nicholas Wade to Sir John Sulston, from David Botstein to Shirley Tilghman.

Reviews

These succinct, synthetic, well-focused, and engaging mini reviews should appeal to a broad genetics readership. Aim for no more than 2,500 words, 50 references, and two or three display items. The article will include an overview of the existing literature but should focus on the future: where is the field going; what exciting developments are expected?

Because these articles are by invitation only, the topic and scope will have been agreed with an editor. It is advisable to forward on a short summary or draft in advance of the full submission. Mini reviews are peer reviewed externally; if accepted for publication, a publication charge does not apply.

Structure the mini review as follows: Title, Authors, Affiliations, Abstract, Introduction, Main Text (broken into subsections as appropriate), Conclusions, Acknowledgments, References, Figure Legends, and Tables. Please refer to the information above about the specifics of manuscript, figure, and table preparation. Email plosgenetics [at] plos.org if you are in any doubt about how our guidelines for research articles differ from those of mini reviews.

Special Reports

PLoS Genetics editors occasionally recruit a special report of a conference or meeting. This article should be concise and well written, no longer than 1,500 words, with up to 2 display items. The style should be progressive and punchy, and the author should bring his or her own perspective or a particular theme to the report, engaging readers with a range of professional scientific interests and levels of experience. It should inform and inspire novice readers and experts alike by: identifying the overall purpose of the meeting; synthesizing the focus of the scientific discussion in key presentations; and, most importantly, explaining why this conference or meeting is relevant to and generated excitement in the larger scientific community.

Because these are by invitation only, the scope of the report will have been agreed with an editor. Authors should work closely with the recruiting editor, forwarding a draft for review before the final report is submitted. The report may or may not be subject to external peer review; if accepted for publication, a publication charge does not apply.

Please refer to the information above about the specifics of manuscript, figure, and table preparation and email plosgenetics [at] plos.org if you are in any doubt about how our guidelines for research articles differ from those of special reports.

10. Overview of the Production Process

Before formal acceptance of the article for publication, the manuscript and all related files will be checked by PLoS staff to ensure that they comply with all essential formatting and manuscript preparation requirements; they are not subject to detailed copyediting. Therefore, please carefully review your manuscript paying special attention to spelling, punctuation, and grammar, as well as scientific content. Authors who believe their manuscripts would benefit from in-depth professional copyediting are encouraged to use language-editing and copyediting services, such as the ones offered below:

PLoS neither endorses nor takes responsibility for contracting with any of these individuals/companies, but we do recognize the value of the services they provide.

When an article has been accepted for publication, the manuscript files are transferred into our production system and will be published in PDF and HTML formats, with an XML download option. Articles are published online weekly and archived in PubMed Central/PubMed within 5 to 10 days of publication.

11. Blogs, Wikis, Embargoes, and the Media

Authors are of course at liberty to present their findings at medical or scientific conferences ahead of publication. We recommend, however, that authors not contact the media or respond to such contact unless an article has been accepted for publication and an embargo date has been established. Respect for press embargoes will help to ensure that your work is reported accurately in the popular media. If a journalist has covered a piece of work ahead of publication, this will not affect consideration of the work for publication. See also our embargo guidelines for journalists.

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