Guide for Authors

An International Journal of Functional and Evolutionary Genomics


!!! Important information for NIH authors !!!


Sponsored Articles
Gene offers authors the option to sponsor non-subscriber access to their articles on Elsevier's electronic publishing platforms. For more information please view our Sponsored Articles page.




INTRODUCTION
Speed of Peer Review - Types of paper - Contact details for submission
BEFORE YOU BEGIN
Ethics in Publishing - Conflict of interest - Submission declaration - Copyright - Retained author rights - Role of the funding source - Funding body agreements and policies - Language and language services - Submission - Referees
PREPARATION
Use of wordprocessing software - Article structure - Subdivision - numbered sections - Introduction - Material and methods - - Results - Discussion - - Conclusions - Appendices - Essential title page information - Abstract - Keywords - - Abbreviations - Acknowledgements - Accession numbers - Math formulae - Footnotes - Electronic artwork - Non-electronic artwork - - - Color artwork - Figure captions - Tables - References - Citation in text - Web references - References in a special issue - Reference style - Journal Abbreviations Source - Supplementary material - Submission checklist
AFTER ACCEPTANCE
Use of the Digital Object Identifier - Proofs - Offprints
AUTHOR INQUIRIES


INTRODUCTION

Before preparing a paper for submission to Gene, the author(s) should carefully read these instructions, and Gene's List of Abbreviations, thus avoiding needless delays during the editorial process. Papers should be carefully prepared in Gene's style. When a paper is submitted to Gene, the corresponding author is responsible for all authors having seen and approved the original paper and, eventually, the proofs.

The paper should be accompanied by a letter of transmittal, in which the authors are invited to suggest the names of two editorial board members who could handle the manuscript as Handling Editors, and to specify the names of five or more potential referees (including complete addresses, phone and fax numbers, e-mail addresses and areas of expertise). In order to ensure a maximum of objectivity, the names of scientists the authors do not wish to be consulted in the reviewing process can also be provided, as well as any other special requests.

Gene requires all new nucleotide and amino acid sequences to be deposited. Obtain and include an accession number with all sequences. The most convenient method for submitting sequence data is by World Wide Web:

EMBL
GenBank
DDBJ

Alternatively, the stand-alone submission tool "Sequin" is available from NCBI.

If requested the database will withhold release of data until publication.

If references are quoted as 'In press', the relevant manuscript(s) should also be attached. Should authors be requested by the Editor to modify the text prior to publication, the revised version should be submitted within 2 months. After this period, the manuscript will be dealt with as a new one.

Speed of Peer Review

All possible effort will be made by the Editors in order to obtain referees' comments rapidly. In principle, the authors will be informed of a decision within 6 weeks.

Types of paper

Regular research papers, method papers, reviews, letters to the editor. All reports should explicitly state the biological relevance of the function that is the subject of the paper.

Methods papers will be considered only if they are of general importance with considerable original and useful information. Minor improvements to existing methods are not acceptable.

Letters to the Editor are selected for publication that are pertinent to material published in GENE or that discuss problems of general interest. The author of a paper in question is usually given an opportunity to reply.

Reviews or Mini-reviews will be generally solicited by the Editors of the journal. However, prospective authors interested in contributing such a paper are invited to contact the Editor-in-Chief.

Contact details for submission

Papers should be submitted to Gene's online submission system, http://ees.elsevier.com/gene/. For questions on the submission and reviewing process, please contact the Editorial Office at gene@elsevier.com.

BEFORE YOU BEGIN

Ethics in Publishing

For information on Ethics in Publishing and Ethical guidelines for journal publication see http://www.elsevier.com/publishingethics and http://www.elsevier.com/ethicalguidelines.

Conflict of interest

All authors are requested to disclose any actual or potential conflict of interest including any financial, personal or other relationships with other people or organizations within three years of beginning the submitted work that could inappropriately influence, or be perceived to influence, their work. See also http://www.elsevier.com/conflictsofinterest.

Submission declaration

Submission of an article implies that the work described has not been published previously (except in the form of an abstract or as part of a published lecture or academic thesis), that it is not under consideration for publication elsewhere, that its publication is approved by all authors and tacitly or explicitly by the responsible authorities where the work was carried out, and that, if accepted, it will not be published elsewhere in the same form, in English or in any other language, without the written consent of the copyright-holder.

Copyright

Upon acceptance of an article, authors will be asked to complete a 'Journal Publishing Agreement' (for more information on this and copyright see http://www.elsevier.com/copyright). Acceptance of the agreement will ensure the widest possible dissemination of information. An e-mail will be sent to the corresponding author confirming receipt of the manuscript together with a 'Journal Publishing Agreement' form or a link to the online version of this agreement.
Subscribers may reproduce tables of contents or prepare lists of articles including abstracts for internal circulation within their institutions. Permission of the Publisher is required for resale or distribution outside the institution and for all other derivative works, including compilations and translations (please consult http://www.elsevier.com/permissions). If excerpts from other copyrighted works are included, the author(s) must obtain written permission from the copyright owners and credit the source(s) in the article. Elsevier has preprinted forms for use by authors in these cases: please consult http://www.elsevier.com/permissions.

Retained author rights

As an author you (or your employer or institution) retain certain rights; for details you are referred to: http://www.elsevier.com/authorsrights.

Role of the funding source

You are requested to identify who provided financial support for the conduct of the research and/or preparation of the article and to briefly describe the role of the sponsor(s), if any, in study design; in the collection, analysis and interpretation of data; in the writing of the report; and in the decision to submit the paper for publication. If the funding source(s) had no such involvement then this should be stated. Please see http://www.elsevier.com/funding.

Funding body agreements and policies

Elsevier has established agreements and developed policies to allow authors whose articles appear in journals published by Elsevier, to comply with potential manuscript archiving requirements as specified as conditions of their grant awards. To learn more about existing agreements and policies please visit http://www.elsevier.com/fundingbodies.

Language and language services

Please write your text in good English (American or British usage is accepted, but not a mixture of these). Authors who require information about language editing and copyediting services pre- and post-submission please visit http://www.elsevier.com/languagepolishing or our customer support site at http://epsupport.elsevier.com for more information. Please note Elsevier neither endorses nor takes responsibility for any products, goods or services offered by outside vendors through our services or in any advertising. For more information please refer to our Terms & Conditions: http://www.elsevier.com/termsandconditions.

Submission

Submission to this journal proceeds totally online and you will be guided stepwise through the creation and uploading of your files. The system automatically converts source files to a single PDF file of the article, which is used in the peer-review process. Please note that even though manuscript source files are converted to PDF files at submission for the review process, these source files are needed for further processing after acceptance. All correspondence, including notification of the Editor's decision and requests for revision, takes place by e-mail removing the need for a paper trail.

Referees

Please submit, with the manuscript, the names, addresses and e-mail addresses of 3 potential referees. Note that the editor retains the sole right to decide whether or not the suggested reviewers are used.

PREPARATION

Use of wordprocessing software

It is important that the file be saved in the native format of the wordprocessor used. The text should be in single-column format. Keep the layout of the text as simple as possible. Most formatting codes will be removed and replaced on processing the article. In particular, do not use the wordprocessor's options to justify text or to hyphenate words. However, do use bold face, italics, subscripts, superscripts etc. Do not embed "graphically designed" equations or tables, but prepare these using the wordprocessor's facility. When preparing tables, if you are using a table grid, use only one grid for each individual table and not a grid for each row. If no grid is used, use tabs, not spaces, to align columns. The electronic text should be prepared in a way very similar to that of conventional manuscripts (see also the Guide to Publishing with Elsevier: http://www.elsevier.com/guidepublication). Do not import the figures into the text file but, instead, indicate their approximate locations directly in the electronic text and on the manuscript. See also the section on Electronic illustrations.
To avoid unnecessary errors you are strongly advised to use the "spell-check" and "grammar-check" functions of your wordprocessor.

Article structure

Subdivision - numbered sections

Divide your article into clearly defined and numbered sections. Subsections should be numbered 1.1 (then 1.1.1, 1.1.2, ...), 1.2, etc. (the abstract is not included in section numbering). Use this numbering also for internal cross-referencing: do not just refer to "the text". Any subsection may be given a brief heading. Each heading should appear on its own separate line.

Introduction

State the objectives of the work and provide an adequate background, avoiding a detailed literature survey or a summary of the results.

Material and methods

Provide sufficient detail to allow the work to be reproduced. Methods already published should be indicated by a reference: only relevant modifications should be described.
Please add to legends (for figures) or footnotes (for tables) details such as [temp.,time(s), voltage, concentrations, type and % of gel, markers,sizes (bp,kb,kDa), etc.], but outline methods themselves in the main text.

Results

Results should be clear and concise.

Discussion

This should explore the significance of the results of the work, not repeat them. A combined Results and Discussion section is often appropriate. Avoid extensive citations and discussion of published literature.
The Results and Discussion sections should refer to the data shown in the figures and tables, and briefly discuss their significance. Divide these sections into numbered subsections with short subtitles (lower-case, Roman, not underlined). Where the Results section is combined with the Discussion section, the last subsection, subtitled Conclusions, should be short and be divided into points.

Conclusions

The main conclusions of the study may be presented in a short Conclusions section, which may stand alone or form a subsection of a Discussion or Results and Discussion section.

Appendices

If there is more than one appendix, they should be identified as A, B, etc. Formulae and equations in appendices should be given separate numbering: Eq. (A.1), Eq. (A.2), etc.; in a subsequent appendix, Eq. (B.1) and so on.

Essential title page information

• Title. Concise and informative. Titles are often used in information-retrieval systems. Avoid abbreviations and formulae where possible.
• Author names and affiliations. Where the family name may be ambiguous (e.g., a double name), please indicate this clearly. Present the authors' affiliation addresses (where the actual work was done) below the names. Indicate all affiliations with a lower-case superscript letter immediately after the author's name and in front of the appropriate address. Provide the full postal address of each affiliation, including the country name, and, if available, the e-mail address of each author.
• Corresponding author. Clearly indicate who will handle correspondence at all stages of refereeing and publication, also post-publication. Ensure that telephone and fax numbers (with country and area code) are provided in addition to the e-mail address and the complete postal address.
• Present/permanent address. If an author has moved since the work described in the article was done, or was visiting at the time, a "Present address" (or "Permanent address") may be indicated as a footnote to that author's name. The address at which the author actually did the work must be retained as the main, affiliation address. Superscript Arabic numerals are used for such footnotes.

Abstract

A concise and factual abstract is required. The abstract should state briefly the purpose of the research, the principal results and major conclusions. An abstract is often presented separately from the article, so it must be able to stand alone. For this reason, References should be avoided, but if essential, then cite the author(s) and year(s). Also, non-standard or uncommon abbreviations should be avoided, but if essential they must be defined at their first mention in the abstract itself.

Keywords

Immediately after the abstract, provide a maximum of 6 keywords, using American spelling and avoiding general and plural terms and multiple concepts (avoid, for example, "and", "of"). Be sparing with abbreviations: only abbreviations firmly established in the field may be eligible. These keywords will be used for indexing purposes.
Use only words not already present in the title.

Abbreviations

Consult Gene's List of Abbreviations and the pertinent literature for accepted abbreviations, especially for genes and proteins; list all those used, even if already in Gene's list (create new abbreviations if necessary). Be meticulous with symbols. For proteins, use Roman letters with at least the first letter capitalized (e.g., Hprt, HPRT or βGal; for genes (or DNA) use italicized letters (e.g., lacZ, hprt, HPRT or cat gene, not HPRTor CAT gene). Consult the nomenclature (or usage) for the particular organism concerned to use (or create) proper gene/protein abbreviations.

Acknowledgements

Collate acknowledgements in a separate section at the end of the article before the references and do not, therefore, include them on the title page, as a footnote to the title or otherwise. List here those individuals who provided help during the research (e.g., providing language help, writing assistance or proof reading the article, etc.).

Accession numbers

Accession numbers are unique identifiers in bioinformatics allocated to nucleotide and protein sequences to allow tracking of different versions of that sequence record and the associated sequence in a data repository [e.g., databases at the National Center for Biotechnical Information (NCBI) at the National Library of Medicine ('GenBank') and the Worldwide Protein Data Bank]. There are different types of accession numbers in use based on the type of sequence cited, each of which uses a different coding. Authors should explicitly mention the type of accession number together with the actual number, bearing in mind that an error in a letter or number can result in a dead link in the online version of the article. Please use the following format: accession number type ID: xxxx (e.g., MMDB ID: 12345; PDB ID: 1TUP). Note that in the final version of the electronic copy, accession numbers will be linked to the appropriate database, enabling readers to go directly to that source from the article.

Math formulae

Present simple formulae in the line of normal text where possible and use the solidus (/) instead of a horizontal line for small fractional terms, e.g., X/Y. In principle, variables are to be presented in italics. Powers of e are often more conveniently denoted by exp. Number consecutively any equations that have to be displayed separately from the text (if referred to explicitly in the text).

Footnotes

Footnotes should be used sparingly. Number them consecutively throughout the article, using superscript Arabic numbers. Many wordprocessors build footnotes into the text, and this feature may be used. Should this not be the case, indicate the position of footnotes in the text and present the footnotes themselves separately at the end of the article. Do not include footnotes in the Reference list.
Table footnotes
Indicate each footnote in a table with a superscript lowercase letter.

Electronic artwork

General points
• Make sure you use uniform lettering and sizing of your original artwork.
• Save text in illustrations as "graphics" or enclose the font.
• Only use the following fonts in your illustrations: Arial, Courier, Times, Symbol.
• Number the illustrations according to their sequence in the text.
• Use a logical naming convention for your artwork files.
• Provide captions to illustrations separately.
• Produce images near to the desired size of the printed version.
• Submit each figure as a separate file.

A detailed guide on electronic artwork is available on our website:
http://www.elsevier.com/artworkinstructions
You are urged to visit this site; some excerpts from the detailed information are given here.
Formats
Regardless of the application used, when your electronic artwork is finalised, please "save as" or convert the images to one of the following formats (note the resolution requirements for line drawings, halftones, and line/halftone combinations given below):
EPS: Vector drawings. Embed the font or save the text as "graphics".
TIFF: color or grayscale photographs (halftones): always use a minimum of 300 dpi.
TIFF: Bitmapped line drawings: use a minimum of 1000 dpi.
TIFF: Combinations bitmapped line/half-tone (color or grayscale): a minimum of 500 dpi is required.
DOC, XLS or PPT: If your electronic artwork is created in any of these Microsoft Office applications please supply "as is".
Please do not:
• Supply embedded graphics in your wordprocessor (spreadsheet, presentation) document;
• Supply files that are optimised for screen use (like GIF, BMP, PICT, WPG); the resolution is too low;
• Supply files that are too low in resolution;
• Submit graphics that are disproportionately large for the content.

Non-electronic artwork

Provide all illustrations as high-quality printouts, suitable for reproduction (which may include reduction) without retouching. Number illustrations consecutively in the order in which they are referred to in the text. They should accompany the manuscript, but should not be included within the text. Clearly mark all illustrations on the back (or - in case of line drawings - on the lower front side) with the figure number and the author's name and, in cases of ambiguity, the correct orientation.
Mark the appropriate position of a figure in the article
Only if a laser-quality printer is not available (dot matrix printers are unsatisfactory) should you present professionally drawn figures in black ink on white paper. Always use large and bold lettering and heavy smoothlines to permit photographic reduction. Ensure that all symbols in the figure are large and match the explanations in the legend. Sequence figures should be either 60 nucleotides (or amino acids) in width (to fit into a single printed column), or 120-150 nt. As a rule no more than a single page is allowed for sequence figures. Add bp, nt, kb or kDa symbols above the numerals in marker lanes. Legends should be typed/printed double-spaced, on pages separate from the figures themselves. The maximum size of figures is A4: present larger figures on two or more sheets.
In review articles, colour illustrations will be reproduced free of charge if essential for the presentation of results. This will be at the discretion of the Editor-in-Chief.

Color artwork

Please make sure that artwork files are in an acceptable format (TIFF, EPS or MS Office files) and with the correct resolution. If, together with your accepted article, you submit usable color figures then Elsevier will ensure, at no additional charge, that these figures will appear in color on the Web (e.g., ScienceDirect and other sites) in addition to color reproduction in print. For further information on the preparation of electronic artwork, please see http://www.elsevier.com/artworkinstructions.

Figure captions

Ensure that each illustration has a caption. Supply captions separately, not attached to the figure. A caption should comprise a brief title (not on the figure itself) and a description of the illustration. Keep text in the illustrations themselves to a minimum but explain all symbols and abbreviations used.

Tables

Number tables consecutively in accordance with their appearance in the text. Place footnotes to tables below the table body and indicate them with superscript lowercase letters. Avoid vertical rules. Be sparing in the use of tables and ensure that the data presented in tables do not duplicate results described elsewhere in the article.

References

Citation in text

Please ensure that every reference cited in the text is also present in the reference list (and vice versa). Any references cited in the abstract must be given in full. Unpublished results and personal communications are not recommended in the reference list, but may be mentioned in the text. If these references are included in the reference list they should follow the standard reference style of the journal and should include a substitution of the publication date with either "Unpublished results" or "Personal communication" Citation of a reference as "in press" implies that the item has been accepted for publication.

Web references

As a minimum, the full URL should be given. Any further information, if known (DOI, author names, dates, reference to a source publication, etc.), should also be given. Web references can be listed separately (e.g., after the reference list) under a different heading if desired, or can be included in the reference list.

References in a special issue

Please ensure that the words 'this issue' are added to any references in the list (and any citations in the text) to other articles in the same Special Issue.

Reference style

Text: All citations in the text should refer to:
1. Single author: the author's name (without initials, unless there is ambiguity) and the year of publication;
2. Two authors: both authors' names and the year of publication;
3. Three or more authors: first author's name followed by "et al." and the year of publication.
Citations may be made directly (or parenthetically). Groups of references should be listed first alphabetically, then chronologically.
Examples: "as demonstrated (Allan, 1996a, 1996b, 1999; Allan and Jones, 1995). Kramer et al. (2000) have recently shown ...."
List: References should be arranged first alphabetically and then further sorted chronologically if necessary. More than one reference from the same author(s) in the same year must be identified by the letters "a", "b", "c", etc., placed after the year of publication.
Examples:
Reference to a journal publication:
Van der Geer, J., Hanraads, J.A.J., Lupton, R.A., 2000. The art of writing a scientific article. J. Sci. Commun. 163, 51-59.
Reference to a book:
Strunk Jr., W., White, E.B., 1979. The Elements of Style, third ed. Macmillan, New York.
Reference to a chapter in an edited book:
Mettam, G.R., Adams, L.B., 1999. How to prepare an electronic version of your article, in: Jones, B.S., Smith , R.Z. (Eds.), Introduction to the Electronic Age. E-Publishing Inc., New York, pp. 281-304.

Journal Abbreviations Source

Journal titles should be abbreviated according to the 'List of Serials Indexed for Online Users' which can be found on http://www.nlm.nih.gov. For reviews with a large number of references, employ the system used in Gene 1991; 100: 13-26.

Supplementary material

Elsevier accepts electronic supplementary material to support and enhance your scientific research. Supplementary files offer the author additional possibilities to publish supporting applications, movies, animation sequences, high-resolution images, background datasets, sound clips and more. Supplementary files supplied will be published online alongside the electronic version of your article in Elsevier Web products, including ScienceDirect: http://www.sciencedirect.com. In order to ensure that your submitted material is directly usable, please ensure that data are provided in one of our recommended file formats. Authors should submit the material in electronic format together with the article and supply a concise and descriptive caption for each file. Video files: please supply 'stills' with your files: you can choose any frame from the video or make a separate image. These will be used instead of standard icons and will personalize the link to your supplementary information. For more detailed instructions please visit our artwork instruction pages at http://www.elsevier.com/artworkinstructions.

Submission checklist

It is hoped that this list will be useful during the final checking of an article prior to sending it to the journal's Editor for review. Please consult this Guide for Authors for further details of any item.
Ensure that the following items are present:
One Author designated as corresponding Author:
• E-mail address
• Full postal address
• Telephone and fax numbers
All necessary files have been uploaded
• Keywords
• All figure captions
• All tables (including title, description, footnotes)
Further considerations
• Manuscript has been "spellchecked" and "grammar-checked"
• References are in the correct format for this journal
• All references mentioned in the Reference list are cited in the text, and vice versa
• Permission has been obtained for use of copyrighted material from other sources (including the Web)
• color figures are clearly marked as being intended for color reproduction on the Web (free of charge) and in print or to be reproduced in color on the Web (free of charge) and in black-and-white in print
• If only color on the Web is required, black and white versions of the figures are also supplied for printing purposes
For any further information please visit our customer support site at http://epsupport.elsevier.com.

AFTER ACCEPTANCE

Use of the Digital Object Identifier

The Digital Object Identifier (DOI) may be used to cite and link to electronic documents. The DOI consists of a unique alpha-numeric character string which is assigned to a document by the publisher upon the initial electronic publication. The assigned DOI never changes. Therefore, it is an ideal medium for citing a document, particularly 'Articles in press' because they have not yet received their full bibliographic information. The correct format for citing a DOI is shown as follows (example taken from a document in the journal Physics Letters B):
doi:10.1016/j.physletb.2003.10.071
When you use the DOI to create URL hyperlinks to documents on the web, they are guaranteed never to change.

Proofs

One set of page proofs (as PDF files) will be sent by e-mail to the corresponding author (if we do not have an e-mail address then paper proofs will be sent by post) or, a link will be provided in the e-mail so that authors can download the files themselves. Elsevier now provides authors with PDF proofs which can be annotated; for this you will need to download Adobe Reader version 7 (or higher) available free from http://www.adobe.com/products/acrobat/readstep2.html. Instructions on how to annotate PDF files will accompany the proofs (also given online). The exact system requirements are given at the Adobe site: http://www.adobe.com/products/acrobat/acrrsystemreqs.html#70win.
If you do not wish to use the PDF annotations function, you may list the corrections (including replies to the Query Form) and return them to Elsevier in an e-mail. Please list your corrections quoting line number. If, for any reason, this is not possible, then mark the corrections and any other comments (including replies to the Query Form) on a printout of your proof and return by fax, or scan the pages and e-mail, or by post. Please use this proof only for checking the typesetting, editing, completeness and correctness of the text, tables and figures. Significant changes to the article as accepted for publication will only be considered at this stage with permission from the Editor. We will do everything possible to get your article published quickly and accurately. Therefore, it is important to ensure that all of your corrections are sent back to us in one communication: please check carefully before replying, as inclusion of any subsequent corrections cannot be guaranteed. Proofreading is solely your responsibility. Note that Elsevier may proceed with the publication of your article if no response is received.

Offprints

The corresponding author, at no cost, will be provided with a PDF file of the article via e-mail. The PDF file is a watermarked version of the published article and includes a cover sheet with the journal cover image and a disclaimer outlining the terms and conditions of use. Additional paper offprints can be ordered by the authors. An order form with prices will be sent to the corresponding author.

AUTHOR INQUIRIES

For inquiries relating to the submission of articles (including electronic submission where available) please visit this journal's homepage. You can track accepted articles at http://www.elsevier.com/trackarticle and set up e-mail alerts to inform you of when an article's status has changed. Also accessible from here is information on copyright, frequently asked questions and more. Contact details for questions arising after acceptance of an article, especially those relating to proofs, will be provided by the publisher.