Guide for Authors
An International Journal of Functional and Evolutionary Genomics
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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.
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.
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.
Artwork
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.
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.
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.
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