Manuscript Preparation
A cover letter MUST include:
(1) a paragraph highlighting the main points of the work and its suitability for Genome Research;
(2) status of any statements of personal communication or other permissions needed (any data presented as unpublished results
from individuals other than the authors require permission for use);
(3) statement regarding databank submission of data; and
(4) assurance that all gene/protein names and symbols used in the paper adhere to approved nomenclature guidelines for specific
species.
All related manuscripts in press, submitted, or in preparation MUST be disclosed. Additional supplemental files are encouraged as necessary for a thorough review process. These should be uploaded as Supplemental Material online.
Paper length in the journal is between two and 12 journal pages. A manuscript of 28-32 typed, DOUBLE-SPACED pages with 27 lines of 11-point text per page (a manuscript of 50,000 characters) with four to six figures and one or two tables will translate to 12 printed pages in the journal.
The title page should include: the title, all authors' names and institutions, the corresponding author's complete contact information, and a running title (50 characters or less, including spaces). The title should reflect the most novel advance and/or insights offered by the work. Please note that we prefer a title that does not include any punctuation (e.g., a colon).
Manuscript Type: The general format for all manuscript types (Research, Methods, Resource) is identical (as described below). However, RESOURCE articles are expected to be much more succinct. The selection of type is based on the content of the manuscript, and will ultimately be decided by the Editor. RESEARCH articles generally contain significant conceptual advances and novel genomic insights as well as extensive analyses with wide appeal for a variety of readers. METHODS are manuscripts where the primary focus is on a novel methodology; these manuscripts include appropriate comparisons to other approaches in the field and supportive biological data. RESOURCE reports present information on useful tools, databases, or large-scale informational resources, such as detailed maps or data sources, that hold broad appeal for the community at large and include novel biological information or technology.
General manuscript format: Please number all pages for review purposes and ensure in-text references are set in journal format (see below). We prefer the manuscript be written in active rather than passive voice. In the Abstract, past research relevant to the current study should be written in the present perfect tense, whereas findings from the current study should be written in the present tense.
Manuscript sections should be presented in the following order: TITLE PAGE, ABSTRACT (the abstract cannot exceed 250 words), INTRODUCTION, RESULTS, DISCUSSION, METHODS (including a Software availability section at the end, as appropriate), DATA ACCESS (including public database accession numbers for all newly generated data and/or reviewer links to deposited data when accessions are not yet public. Previously published accessions should be included in the Methods section where appropriate), COMPETING INTEREST STATEMENT, ACKNOWLEDGMENTS, and REFERENCES. Author Contributions should appear at the end of ACKNOWLEDGMENTS. First version submissions are required to include all FIGURES and TABLES embedded near the place of first citation within the text of the main document file (.pdf). Figure legends should appear adjacent to the relevant figure. Figures must be of sufficient quality for review. Tables providing information (such as primer sequences) that are essential for reproducing the work but not essential for understanding the content of the paper should be included as Supplemental Material. In addition, lengthy tables are best presented in complete form as online Supplemental Material. We recommend that authors with lengthy tables,--e.g., more than one page at 6.5" X 9" with no smaller than 8 pt. type--create a sample single page table for inclusion in print (it should include anything discussed in the text) and include a copy (electronic) of the complete table for display as Supplemental Material. Some consideration for altered section order (e.g., METHODS preceding RESULTS) will be considered for reports where an altered format aids in subject comprehension; altering the format MUST be discussed with the Editor in advance. RESULTS and DISCUSSION may not be combined. METHODS should be detailed enough to allow any qualified researcher to reproduce the results. Additional material for reviewers should be included as Supplemental Material and marked as such (related manuscripts submitted elsewhere, source code for software, etc.).
All sequence data, SNP data, array data, molecular interaction data, and any other data where there is a publicly held database MUST be submitted to these databases. Genome Research will NOT consider manuscripts where data used in the paper is not freely available on either a publicly held website, or in the absence of such a website on the Genome Research website. There are NO exceptions.
Please use the following examples of our boilerplate language to be used in the Data access section, located after Methods and before Acknowledgments:
All raw and processed sequencing data generated in this study have been submitted to the NCBI Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE123456.
The [specify data types] data generated in this study have been submitted to the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) under accession number PRJNA123456.
Authors must ensure that all relevant previously published work is properly acknowledged and cited at the appropriate point in the main text, with the correct bibliographic information given in the Reference list. Quotation marks (" "), with the appropriate citation and Reference, should be used where statements made in a previously published work are reproduced verbatim. The journal reserves the right to employ automated tools to identify any instances of plagiarism and to withdraw the article if detected.
Authors are also responsible for obtaining permission from the rights holder to adapt or reproduce material previously published elsewhere (typically, this will be the publisher) and for including any required permission statement alongside the citation.
You MUST use approved nomenclature for gene and protein names and symbols, including appropriate use of italics (format ALL gene symbols and loci in italics) and capitalization as it applies for each organism's standard nomenclature format, in text, tables, and figures. Full gene names are generally not in italics and Greek symbols are NEVER used in gene names or symbols. Protein symbols should appear in Roman (non-italic) type. To help you in doing this, you will find links below to nomenclature sites for a variety of organisms. You MUST submit novel genes and proteins to the appropriate databases prior to submission. Novel gene and protein names must be approved prior to publication. For website links for data submission, or for nomenclature rules or for submission of gene or protein names, see [Website Links for Data Submission and Appropriate Nomenclature]
Article and book references Cite as (name date) in text, not by number. Do NOT include a comma between surname and first initials or periods in initials. Journal abbreviations also should not include punctuation.
For citations with two authors, cite as (surname and surname date). For citations with more than two authors, do not list all authors. Cite as (first author last name et al. date) in text. Undated citations (unpublished, in preparation, personal communication) should include first initials and last names of all authors up to three before et al.--e.g., (F Smith, pers. comm.)--and do not appear in the reference list.
The reference list should be presented in alphabetical order. Note ALL authors' names should be included when there are 10 or fewer names. If more than 10 names, the reference should include the first 10 names, followed by et al. Bibliographic information should be supplied in the following order.
For journal articles: Surname First Initials (NOTE: up to 10 authors before et al.). Year. Article title. Abbrev journal title Volume: Complete article page range. (If no page range but an epub article number, please also include DOI.)
e.g., Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N. 1985. Enzymatic amplification of X-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230: 1350-1354.
For books: Surname First Initials (NOTE: up to 10 authors before et al.). Year. Chapter title, if used. In Book title (Editors, if included), Chapter page range (if chapter is cited). Publisher, city, state.
e.g., Fischmann DA, Vaugh K, Weber F, Einheber S. 1991. Myosin binding proteins: intracellular members of the immunoglobulin super family. In Frontiers of muscle research: muscle contraction and muscle dystrophy, 2nd ed. (ed. Ozawa E, et al.), pp. 211–222. Elsevier, Amsterdam.
Miller JH. 1972. Generalized transduction; use of P1 in strain construction. In Experiments in molecular genetics (ed. JH Miller), pp. 201-205. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
For preprint servers: Preprints deposited in bioRxiv, for example, should be cited using their digital object identifier (doi).
e.g., Author AN, Author BT. 2013. My article title. bioRxiv doi: 10.1101/123456.
If the paper includes website URLs as references to places where material was obtained for doing the work (with the exception of preprint servers, such as bioRxiv.org, whose papers are fully citable—see details above), the URL should be included next to that information in the text.
Figures The journal will not accept artwork that is manipulated to hide, add, remove, merge, or otherwise change any of the original data. Adjustments to the brightness or contrast of artwork are acceptable, providing they are applied to the entire image and do not obscure any feature of the original. Tools that detect the manipulation of data may be utilized by the journal to ensure that original data have been preserved in the final image.
Acceptable Image and Table file formats for reviewing purposes are GIF, TIFF, EPS, PDF, and JPEG. Electronic files for figures should be named with the first author's name and the figure number; for example, Smith_Fig1. Also be sure to include the figure number on the figure in the file. If the manuscript is accepted for publication, the size of the figures will be adjusted to fit the journal format; therefore, please try to keep labels, symbols, and other call-out devices in proportion to the figure size and detail (use Helvetica or a similar typeface in point sizes no smaller than 8 pt and no larger than 10 pt. Main callouts [e.g., A, B, C, etc.] should be 10 pt. bold capital letters. In general, it is best to avoid heavy letters, which often close up when reduced. Very light colors or colors of similar shades should be avoided. Please also ensure that figures are accessible to readers with color vision deficiency. NOTE ALSO: For publication purposes, file type and format must conform to our printer's parameters for TIFF, EPS, PDF, JPEG, or AI. For details on figure format and specifications for manuscripts that are accepted, see Digital Art Guidelines.
Permissions It is the author's responsibility to obtain permission from the publisher to reproduce/modify/adapt any previously published figure or table for use both in print and online in Genome Research. Authors must include the permissions letter at the time of manuscript submission. The figure or table legend should contain the following information: (Reprinted [or Modified or Adapted] from author year [regular Reference citation] with permission from publisher year, URL [include URL if publisher requires it, as stated in permissions letter]). In addition, the complete reference must be included in the Reference list.
Supplemental Material Supplemental Material is peer-reviewed and must be directly relevant to the conclusions offered in the main text but non-essential for reader understanding. We strongly recommend it be succinct (preferably presented in a single PDF file with a Table of Contents), organized carefully, and labeled appropriately. File sizes should be as small as possible. Each supplemental figure, table, movie, or data file must be cited in the main text; citations and supplemental files themselves must be named as follows, with underscores connecting all segments in each filename and with the file-type extension in view: Supplemental_Fig_S1.pdf, Supplemental_Fig_S2.eps, Supplemental_Table_S1.xls, Supplemental_Table_S2.pdf, Supplemental_Movie_S1.mov, Supplemental_Methods.pdf, etc. Authors submitting papers that describe or present a new computer program or algorithm or papers where in-house software is uniquely necessary to reproduce the work should be prepared to make that software freely available for academic and nonprofit use. We encourage authors to also make the source code available as Supplemental Material, for posterity. When submitting a manuscript initially, supplemental files should also include related papers in press or under consideration and permission letters.
[Back to Instructions to Authors]