Manuscript Preparation

A cover letter MUST include:
(1) name, address, telephone number, FAX number, and e-mail address of author responsible for correspondence regarding the manuscript
(2) paragraph highlighting the main points of the work
(3) statement that the manuscript has been seen and approved by all listed authors
(4) a list of potential referees (referees' names, institution, and e-mail), and, if desired, a reasonable list of individuals with potential conflict, as we work very hard to avoid sending manuscripts to competitors
(5) status of any statements of personal communication or other permissions needed (any data presented as unpublished results from individuals other than the authors require permission for use)
(6) statement regarding databank submission of data and
(7) a list of all gene/protein names and symbols used in the paper - these must all 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 can be uploaded as supplementary information online or mailed to the office.

The title page should include: the title, all authors' names and institutions, the corresponding author's complete contact information, a running title (50 characters or less, including spaces), and at least two keywords.

Manuscript Type: The general format for all manuscript types (Article, Letter, Methods, Resource) is identical (as described below). The selection of type is based on the content of the manuscript, and will ultimately be decided by the Editor. Research: ARTICLES generally contain extensive conceptual advances as well as extensive analyses with wide appeal for a variety of readers. LETTERS are the most common manuscript published in Genome Research and contain a solid advance of general interest to readers, but are likely of greatest interest to specific fields. Methods and Resources: METHODS are manuscripts where the primary focus is on a novel methodology; these manuscripts often contain extensive 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: We prefer the manuscript be written in active rather than passive voice. Manuscript sections should be presented in the following order: TITLE PAGE, ABSTRACT (the abstract cannot exceed 250 words. There should be a second paragraph [not counted in the 250 words] that indicates if there are going to be accession numbers [for all data types] and/or supplementary material, followed by INTRODUCTION, RESULTS, DISCUSSION, METHODS, ACKNOWLEDGMENTS, FIGURE LEGENDS, FIGURES, TABLES, and REFERENCES. Tables providing information (such as primers and sequences) that are essential for reproducing the work but not essential for understanding the content of the paper should be included only as supplementary data. In addition, extremely lengthy tables are best presented in complete form as online supplementary material. We recommend that authors with long 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 an online supplement. Some consideration for altered layout format (e.g., inclusion of extra-long tables, or METHODS preceding RESULTS) for manuscripts will be taken into account for reports where an altered format aids in subject comprehension; altering the format MUST be discussed with the Editor. The methods should be detailed enough to allow any qualified researcher to duplicate the results. Additional material for reviewers can be included and marked as such (especially appreciated, when possible, are disks containing material from Web sites that need to be examined by referees as Web sites with passwords may compromise referee anonymity).

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 Web site, or in the absence of such a Web site on the Genome Research Web site. There are NO exceptions.

You MUST use approved nomenclature for gene and protein names and symbols (including appropriate use of italics [using italics is a standard for genes, so put 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. Proteins should appear in Roman 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 Web site links for data submission, or for nomenclature rules or for submission of gene or protein names, see [Web Site Links for Data Submission and Appropriate Nomenclature]

Article and book references Cite as (name date) in text, not by number. 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 10 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: Last name, first initial, for up to 10 authors. Year. Article title. Journal title, abbrev. Volume: Complete article page range.

e.g., Saiki, R.K., Scharf, S., Faloona, F., Mullis, K.B., Horn, G.T., Erlich, H.A., and 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: Last name, first initial of up to 10 authors. The year. Chapter title, if used. Book title. (editors, if included) Chapter page range. Publisher, city, state.

e.g., Sambrook, J., Fritsch, E.F., and Maniatis, T. 1989. Molecular cloning: A laboratory manual, 2nd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Miller, J.H. 1972. Generalized transduction; use of P1 in strain construction. In Experiments in molecular genetics (ed. J.H. Miller), pp. 201-205. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

If the paper includes Web site URLs as references to places where material was obtained for doing the work, the URL should be included next to that information in the text.

Figures 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 caps. In general, it is best to avoid heavy letters, which often close up when reduced. Likewise, colors of similar shades should be avoided because, depending on final art sizing to conform to journal style, similar shades may become difficult to differentiate. Also, avoid using very light colors, since these typically do not reproduce well. NOTE ALSO: For publication purposes, file type and format are very stringent and ONLY .tif and .eps electronic art formats can be used by the printer. For details on figure format for accepted manuscripts see Submission of Electronic Figures for Accepted Manuscripts: Detailed Instructions. Authors wishing to publish color art must pay the associated publication costs; price estimates will be provided on acceptance of the paper. In cases where the authors cannot cover color art fees, but it is clear the figure must be presented in color, such fees may be waived at the discretion of the Editor. A letter explaining the circumstances should be sent to the hsussman{at}cshl.edu.

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.

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