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Bioinformatics Journal Latex Template Assignment

Instructions to Authors

Please note that the journal now encourages authors to complete their copyright licence to publish form online. Upon receipt of accepted manuscripts at Oxford Journals authors will be invited to complete an online copyright licence to publish form.

Please note that by submitting an this article for publication you confirm that you are the corresponding/submitting author and that Oxford University Press ("OUP") may retain your email address for the purpose of communicating with you about the article. You agree to notify OUP immediately if your details change. If your article is accepted for publication OUP will contact you using the email address you have used in the registration process.

ALL ARTICLES MUST BE SUBMITTED ONLINE. Once you have prepared your manuscript according to the Instructions below please visit the online submission website.

Instructions on submitting your manuscript online, along with the compulsory Word and LaTex* templates, are available. [*If you use bibtex, please use the bibliography style named natbib.bst]. Help with inserting figures into the templates may be found here.

Please read these instructions carefully and follow them strictly so that the publication process is efficient and as rapid as possible. The Editors and the Editorial Office reserve the right to return submissions that are not prepared in accordance with the following instructions.

SCOPE

Bioinformatics provides a forum for the exchange of information in the fields of computational molecular biology and post-genome bioinformatics, with emphasis on the documentation of new algorithms and databases that allows the progress of bioinformatics and biomedical research in a significant manner.

Upon submission you will be asked to provisionally select one of the following categories for your manuscript:

  • Genome analysis
  • Sequence analysis
  • Phylogenetics
  • Structural bioinformatics
  • Gene expression
  • Genetic and population analysis
  • Systems biology
  • Data and text mining
  • Databases and ontologies
  • Bioimage informatics

Detailed Scope Guidelines are also available for the above categories.

FORMAT-FREE SUBMISSION

Bioinformatics manuscripts can now be submitted without being formatted into journal style. Manuscripts will need to be formatted for revision, after acceptance. Follow the below guide to ensure your submission will be within page limits.

Original papers: approximately 5,000 words or approximately 25-30 format-free pages

Discovery notes: approximately 3,000 words or approximately 18-20 format free pages

Application notes: approximately 1,300 words or 1,000 words plus one figure, or 16-18 format-free pages

Note that the page count approximation above is based on a) a paper without illustrations (figure/table) b) formatted in Times New Roman font, double-spaced in 12 font size c) single column format.

TYPES OF MANUSCRIPT

The following types of paper may be submitted for publication. Please note the page limits for each type of paper formatted in the journal template, as well as the word and figure limitations for papers submitted Format-Free.

Original Papers (up to 7 pages; this is approx. 5,000 words): Original papers that describe new research developments in computational molecular biology, for example: models, algorithms, software involving new methods, biological databases and network information services, and their impact on molecular biology or computer science. Actual biological data, as opposed to purely simulated data, must be used.

Discovery Notes (up to 4 pages, this is approx. 3,000 words): Discovery notes report biologically interesting discoveries using computational techniques. Topics may include sequence motif detection, definition of new domains, structural similarities, gene structure prediction, comparative genomics, biomolecular networks and other aspects of computational molecular biology.

The results presented should present new discoveries, bringing insight to a relevant biological problem, and not be the simple extension of current knowledge. The results are expected to proceed from the specialized use of tools, methods, and databases. The inclusion of experimental results is considered very positively.

Application Notes (up to 2 pages; this is approx. 1,300 words or 1,000 words plus one figure): Applications Notes are short descriptions of novel software or new algorithm implementations, databases and network services (web servers, and interfaces). Software or data must be freely available to non-commercial users. Availability and Implementation must be clearly stated in the article. Authors must also ensure that the software is available for a full TWO YEARS following publication. Web services must not require mandatory registration by the user. Additional Supplementary data can be published online-only by the journal. This supplementary material should be referred to in the abstract of the Application Note. If describing software, the software should run under nearly all conditions on a wide range of machines. Web servers should not be browser specific. Application Notes must not describe trivial utilities, nor involve significant investment of time for the user to install. The name of the application should be included in the title.

Reviews (3-8 pages): Most review papers are commissioned, although the editors welcome suggestions from prospective authors who should in the first instance submit a draft or abstract/summary no longer than a page.

Letters to the Editor: Bioinformatics publishes "letters to the editors" on the broad range of topics covered by the journal, including political, technical and scientific analyses of issues related to bioinformatics and computational biology. The letters can also include the discussion of papers published by the journal.

Conference Papers: Bioinformatics considers proposals for publishing conference proceeding papers, as supplementary issues or as special sections of the journal. Please be sure to include the following information in your proposal:

  • What is the theme of the conference and submitted papers?
  • What numbers of papers are expected to be submitted and published?
  • What peer review process will be put in place by the conference organisers to recommend papers for publication in the journal?
  • How many delegates are expected to attend the conference?
  • Assurance that the papers proposed for publication have not and will not be published elsewhere prior to publication in Bioinformatics, or afterwards without the permission of the journal’s publisher.

PAGE CHARGES

The journal strongly discourages authors from exceeding the page limits. Manuscripts exceeding the recommended limits may be rejected without review - for example manuscripts that exceed the limit by 20% or more are usually returned by the Editorial Office immediately. In the event that a manuscript does exceed the page limits we make the following charges:

  • Original papers: £100/$190 per excess page (over 7 published pages*)
  • Discovery notes: £100/$190 per excess page (over 4 published pages*)
  • Application notes: £100/$190 per excess page (over 2 published pages*)

Orders from the UK will be subject to the current UK VAT charge. For orders from elsewhere in the EU you or your institution should account for VAT by way of a reverse charge. Please provide us with your or your institution’s VAT number.

* Please note that the Word and LaTex author templates used for submission to Manuscript Central (ScholarOne) are not an exact reflection of the final typeset article, and therefore cannot be used to estimate exactly how many published pages your final typeset article will be. Please use the following word count guidelines for a more accurate indication:

Original papers: up to 7 pages, this is approx. 5000 words, Discovery notes: up to 4 pages, this is approx. 3000 words, Application notes: up to 2 pages; this is approx. 1300 words or 1000 words plus one figure.

GENERAL POLICIES

Previous publication

Submission of a manuscript implies that it reports unpublished work, that it is not under consideration for publication elsewhere and that, if accepted, it will not be published elsewhere in the same form, either in English or in any other language, without the consent of the publisher. Authors should provide the references of similar work that they have already published, or which is currently under consideration by another journal. If the work has previously been presented at a conference, authors should provide details in the covering letter. The journal will consider publication of work that has previously been presented as either a short abstract or poster at a conference, but not as a full paper. If previously published tables, illustrations or more than 200 words of text are to be included, then the copyright holder's written permission must be obtained. Include copies of any such permission letters with your paper. Please note that if considered appropriate, plagiarism checking software may be applied to your manuscript during the editorial review process.

Authors retain the right to make a preprint version of the article available on their own personal website and/or that of their employer and/or in free public servers of preprints and/or articles in their subject area.
Authors making their manuscripts available in this way must clearly note this in their submission.
Once the manuscript has been accepted the authors must acknowledge that the article has been accepted for publication as follows:
"This article has been accepted for publication in [Journal Title] ©: [year] [owner as specified on the article]Published by Oxford University Press [on behalf of xxxxxx]. All rights reserved."
Please read the full policy on self-archiving here.

Authorship

All persons designated as authors should qualify for authorship. Each author should have participated sufficiently in the work to take public responsibility for the content. Authorship credit should be based on substantial contribution to conception and design, execution, or analysis and interpretation of data. All authors should be involved in drafting the article or revising it critically for important intellectual content, and must have read and approved the final version of the manuscript.

Other than in exceptional circumstances the Journal does not allow addition or removal of author names after submission. A satisfactory explanation for any proposed changes in authorship will be required. We will also require a letter of consent from any person whose name has been removed indicating that they agree to the removal of their name from the author list. Owing to the complexity of these rules we strongly advise authors to fix the author list before submission and not to attempt to make changes later.

Conflicts of Interest

At the point of submission, Bioinformatics policy requires that each author reveal any financial interests or connections, direct or indirect, or other situations that might raise the question of bias in the work reported or the conclusions, implications, or opinions stated - including pertinent commercial or other sources of funding for the individual author(s) or for the associated department(s) or organization(s), personal relationships, or direct academic competition. When considering whether you should declare a conflicting interest or connection please consider the conflict of interest test: Is there any arrangement that would embarrass you or any of your co-authors if it was to emerge after publication and you had not declared it?

As an integral part of the online submission process, Corresponding authors are required to confirm whether they or their co-authors have any conflicts of interest to declare, and to provide details of these. If the Corresponding author is unable to confirm this information on behalf of all co-authors, the authors in question will then be required to submit a completed Conflict of Interest form to the Editorial Office. It is the Corresponding author’s responsibility to ensure that all authors adhere to this policy.

If the manuscript is published, Conflict of Interest information will be communicated in a statement in the published paper.

Software

If the manuscript describes new software tools or the implementation of novel algorithms the software must be freely available to non-commercial users at the time of submission, and appropriate test data should be made available. Availability must be clearly stated in the article. Authors must also ensure that the software and test data is available for a full TWO YEARS following publication. The editors of Bioinformatics encourage authors to make their source code available and, if possible, to provide access through an open source license (see www.opensource.org for examples). Authors should make every effort to use URLs that will remain stable. At the minimum, authors must provide one of: webserver, source code or binary. The name of the software should be included in the title of the paper wherever possible.

Supporting Data

All data on which the conclusions given in the publication are based must be publicly available. Bioinformatics fully supports the recommendations of the National Academies regarding data sharing (see Board on Life Sciences, Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences. Available at www.nap.edu/books/0309088593/html). If the analysis is based on new datasets, authors are encouraged to submit these to appropriate public repositories. In particular, microarray data should be submitted to one of the recognized public repositories in a MIAME compliant way (see C. A. Ball et al., Submission of Microarray Data to Public Repositories. PLoS Biology, 2, e317). In any event, all data should be made available to the journal for the purpose of peer review. If your manuscript describes a three-dimensional model of a protein that has been manually built, you should deposit it in the PMDB database (https://bioinformatics.cineca.it/PMDB/, see also NAR 34, 306-309). The database will return a unique identifier which you can include in your manuscript, thereby allowing readers to have access to your model.

Supplementary Data

Only directly relevant material should be included in the full text of manuscripts. Supporting materials and Appendices which are not essential for inclusion in the full text, but would nevertheless benefit the reader, can be published as online-only Supplementary Data. Supplementary Data should be submitted for review, in a separate file or files from the manuscript. Authors should make sure that all additional text, figures and tables are presented in a single file to minimise the number of files. Authors should ensure that the Supplementary Data is referred to in the main manuscript at an appropriate point in the text. It cannot be altered or replaced after the paper has been accepted for publication. For the purpose of long-term preservation of this information, we require supplementary material to be published and stored on our website. It is acceptable for authors to post supplementary material on their own website in addition to this, but not in place of this.

Pre-screening

At present the journal accepts 30% of manuscripts that are submitted. Therefore, to increase the efficiency of the publication process, manuscripts received in the Bioinformatics office undergo a pre-screening process. Papers that are considered to be of low significance to the readership of the journal are returned without review.

The review process

At least four recommended reviewers must be provided by the author at the submission stage. A manuscript will not be assigned to an Associate Editor until this information has been provided. Manuscripts that pass the pre-screening phase but have not yet been formatted in journal style will then be returned to the author for formatting. Following this, the manuscript will be sent to two or more referees, who agree to undertake the refereeing within a short period. Authors should normally carry out any revision within four weeks including formatting the manuscript into journal style. Revisions that are not received within 90 days will be treated as new submissions.

Acceptance

When accepted by the editors, authors may be asked to send the files of the final manuscript to the editorial office. These files are used for typesetting and should be either Word or LaTex files.

Because accepted manuscripts are published online following acceptance, it is important that the final version of the manuscript supplied by the author contains no information regarding the citation information (volume, issue, year) or a copyright line as this will mislead readers.

Licence to Publish

It is a condition of publication in Bioinformatics that authors grant an exclusive licence to Oxford University Press. This ensures that requests from third parties to reproduce articles are handled efficiently and consistently and will also allow the article to be as widely disseminated as possible. As part of the licence agreement, Authors may use their own material in other publications provided that Bioinformatics is acknowledged as the original place of publication and Oxford University Press as the Publisher. Information about the New Creative Commons licence can be found here.

Scientific Misconduct

When dealing with potential cases of misconduct the journal follows the guidelines provided by the Committee on Publication Ethics (COPE).

Bioinformatics Advance Access

Bioinformatics Advanced Access articles are initially published in their 'Accepted Manuscript' form as soon as possible post acceptance. Subsequently, a copyedited, typeset, corrected version of the 'Corrected Proof' is also published on the Advanced Access page. More information, including how to cite Advance Access papers, can be found on the Advance Access Page.

Complimentary ISCB memberships for authors

Bioinformatics is an official journal of the ISCB and as part of our partnership with the Society we have 200 complimentary ISCB memberships to offer our authors each year. If you are the corresponding author of a Bioinformatics paper then the ISCB will be in touch after your article has been published.

OPEN ACCESS OPTION FOR AUTHORS

Bioinformatics authors have the option, at an additional charge, to make their paper freely available online immediately upon publication, under the Oxford Open initiative. After your manuscript is accepted, as part of the mandatory licence form required of all corresponding authors, you will be asked to indicate whether or not you wish to pay to have your paper made freely available immediately. If you do not select the Open Access option, your paper will be published with standard subscription-based access and you will not be charged.

Oxford Open articles are published under Creative Commons licences. Authors publishing in Bioinformatics can use the following Creative Commons licences for their articles:

  • Creative Commons Attribution licence (CC BY)
  • Creative Commons Non-Commercial licence (CC BY-NC)

Please click here for more information about the Creative Commons licences.

Charges also vary depending on the manuscript category. Please see below for details:

Original Paper/Review/Special issue article - optional Oxford Open charges:
Regular charge - £1850/ $3000 / €2450
Reduced Rate Developing country charge* - £925 / $1500 / €1225
Free Developing country charge * - £0 /$0 / €0

Application Note/Letter to the Editor/Message from ISCB/Discovery Note
– optional Oxford Open charges:
Regular charge - £900 / $1600 / €1350
Reduced Rate Developing country charge* - £450 / $800 / €675
Free Developing country charge* - £0 / $0 / €0

* Visit our Developing Countries page for a list of qualifying countries.

ISCB members are entitled to a 15% discount on the open access fee to publish in Bioinformatics. In order to receive this discount, ISCB members must claim this discount prior to signing a license to publish. Please do so by contacting the production editor (bioinformatics@oup.com) and informing them that you are an ISCB member.

The above Open Access charges are in addition to any page charges and colour charges that might apply.

Orders from the UK will be subject to the current UK VAT charge. For orders from the rest of the EU, we will assume that the service is provided for business purposes, please provide a VAT number for yourself or your institution and ensure you account for your own local VAT correctly.

You can pay Open Access charges using our Author Services site. This will enable you to pay online with a credit/debit card, or request an invoice by email or post.

Third-Party Content in Open Access papers

If you will be publishing your paper under an Open Access licence but it contains material for which you do not have Open Access re-use permissions, please state this clearly by supplying the following credit line alongside the material:

Title of content
Author, Original publication, year of original publication, by permission of [rights holder]
This image/content is not covered by the terms of the Creative Commons licence of this publication. For permission to reuse, please contact the rights holder.

MANUSCRIPT PREPARATION

Papers must be clearly and concisely written in English and within the recommended length. In the interests of speed, manuscripts are not extensively copyedited and authors are requested to check their texts carefully before submitting them so that proofs will require only correction of typographical errors.

How to prepare text and figures

For guidelines on the types of documents that can be uploaded to the online submission system, please click here.

Prepare your figures at publication quality resolution, using applications capable of generating high-resolution .tif files (1200 d.p.i. for line drawings and 350 d.p.i. for colour and half-tone artwork). The printing process requires your figures to be in this format if your paper is accepted and printed. For useful information on preparing your figures for publication, please click here. For online submission, please also prepare a second version of your figures at low-resolution for use in the review process; these versions of the figures can be saved in .jpg, .gif, .tif or .eps format. For INITIAL submission, it is preferable that you insert the low-resolution versions of the figures and tables into the word processing but you can also upload these versions as separate files.

Sections of the manuscript

Please subdivide manuscripts into the following sequence of sections, according to the type of paper:

  • Original papers: Title page, Structured Abstract, Introduction, System and methods, Algorithm, Implementation, Discussion, References.
  • Reviews: May be in a format best suited to subject matter, but should include Title page, Structured Abstract, Text, References. For clarity the main body of text should be sub-divided into sections.
  • Applications notes: Title page, Short Structured Abstract, Text.
  • Discovery notes: The description of the analysis can be up to four pages long including one or two figures. Please include an abstract. Sequences must be freely available in the database and the results of the analyses should not have been published elsewhere.

Title page

The title should be short, specific and informative, avoiding if possible version number and the words: tool, package, application, software (and similar). If novel software is being described, the name of the software should be included in the title. The surname and initials of each author should be followed by his/her department, Institution, city with postal code and country. Any changes of address may be added to the footnotes. The author to whom offprint requests are to be sent should be indicated by an asterisk and the footnote 'To whom correspondence should be addressed'. Please provide a running head of not more than 50 characters.

Structured Abstract (see recent issues of journal for examples)

Original papers

Abstracts are structured with a standard layout such that the text is divided into sub-sections under the following five headings: Motivation, Results, Availability and Implementation, Contact and Supplementary Information. In cases where authors feel the headings inappropriate, some flexibility is allowed. The abstracts should be succinct and contain only material relevant to the headings. A maximum of 150 words is recommended. If internet hyperlinks are available for any part of the abstract, then this should be given in the form of 'clickable text', i.e.{{http://www...}}.

  • Motivation: This section should specifically state the scientific question within the context of the field of study.
  • Results: This section should summarize the scientific advance or novel results of the study, and its impact on computational biology.
  • Availability and Implementation: This section should state software availability if the paper focuses mainly on software development or on the implementation of an algorithm. Examples are: 'Freely available on the web at http://www.example_url.org.' Website implemented in Perl, MySQL and Apache, with all major browsers supported'; or 'Source code and binaries freely available for download at URL, implemented in C++ and supported on linux and MS Windows'. The complete address (URL) should be given. If the manuscript describes new software tools or the implementation of novel algorithms the software must be freely available to non-commercial users. Authors must also ensure that the software is available for a full TWO YEARS following publication. The editors of Bioinformatics encourage authors to make their source code available and, if possible, to provide access through an open source license (see www.opensource.org for examples).
  • Contact: Full email address to be given, preferably an institution email address.
  • Supplementary information: Links to additional figures/data available on a web site, pr reference to online-only supplementary data available at the journal's web site.

Applications Notes

Abstracts for Applications Notes are much shorter than those for an Original Paper. They are structured with four headings: Summary, Availability and Implementation, Contact and Supplementary Information.

  • Summary: This section should summarize the purpose/novel features of the program in one or two sentences.
  • Availability and Implementation: See above for advice and examples for this section.
  • Contact: Full E-mail address to be supplied, preferably an institution address.
  • Supplementary information: Links to additional figures/data available on a web site, or reference to online-only Supplementary data available at the journal's web site.

Acknowledgements

These should be included at the end of the text and not in footnotes. Please ensure you acknowledge all sources of funding, see funding section below.

Details of all funding sources for the work in question should be given in a separate section entitled 'Funding'. This should appear before the 'Acknowledgements' section.

Funding information

The following rules should be followed:

• The sentence should begin: ‘This work was supported by …’ • The full official funding agency name should be given, i.e. ‘National Institutes of Health’, not ‘NIH’ (full RIN-approved list of UK funding agencies) Grant numbers should be given in brackets as follows: ‘[grant number xxxx]’ • Multiple grant numbers should be separated by a comma as follows: ‘[grant numbers xxxx, yyyy]’ • Agencies should be separated by a semi-colon (plus ‘and’ before the last funding agency) • Where individuals need to be specified for certain sources of funding the following text should be added after the relevant agency or grant number 'to [author initials]'.

An example is given here: ‘This work was supported by the National Institutes of Health [AA123456 to C.S., BB765432 to M.H.]; and the Alcohol & Education Research Council [hfygr667789].’

Oxford Journals will deposit all NIH-funded articles in PubMed Central. See Depositing articles in repositories – information for authors for details. Authors must ensure that manuscripts are clearly indicated as NIH-funded using the guidelines above.

Crossref Funding Data Registry

In order to meet your funding requirements authors are required to name their funding sources, or state if there are none, during the submission process. For further information on this process or to find out more about the CHORUS initiative please click here.

References

These should conform to standard scientific reporting style. Previous work in the field should be mentioned. Sufficient information should be given so that an application can be re-implemented. A test data set and results must be provided (where appropriate).

Authors are responsible for the accuracy of the References. Published articles and those in press (state the journal which has accepted them) may be included. In the text, a reference should be cited by author and date and enclosed by round brackets; not more than two authors may be cited per reference; if there are more than two authors use et al. References must NOT be numbered. At the end of the manuscript, the citations should be given in alphabetical order, with the author's surname followed by the initial. References should include in the following order: author, year, paper title, journal title, volume number, inclusive page numbers. The name of the journal should be abbreviated according to the World List of Scientific Periodicals. Book references should also include the editors and the name and address of the publisher. References should therefore be listed as follows:

Personal communications (J.Smith, personal communication) should be authorized by those involved in writing, and unpublished data should be cited as (unpublished data). Both should be used as sparingly as possible and only when the unpublished data referred to is peripheral rather than central to the discussion. Personal communications, unpublished results, manuscripts submitted or in preparation, statistical packages, computer programs and web sites should be cited in the text only, NOT included in the References section. References to manuscripts accepted for publication but not yet published should be included in the reference list as 'in press'.

Examples are given here:

  • Myasnikova,E. et al. (2000) Registration of the expression patterns of Drosophila segmentation genes by two independent methods. Bioinformatics, 17, 3-12.
  • Schäfer,J. and Strimmer,K. (2005) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics, 21, 754-764.

Tables

Tables should be embedded within the main document file and be numbered consecutively. Tables should be self-explanatory and include a brief descriptive title. Footnotes to tables should be indicated by lower case letters but should not include extensive experimental detail.

Figures

All figures should be embedded within the text inside the main document file and referred to in the text as Figure 1 etc. All figures should be formatted to fit into, or be reduced to, a single (86 mm) or double (178 mm) column width. Figure legends should appear adjacent to the relevant figure.

  • Web screen dumps: The editors prefer tables or figures instead of web screen dumps. All figures should have a white background to increase the contrast between the illustration and the background, so that the figure is easy to read.
  • Line illustrations: These must be of sufficient quality for publication as submitted, i.e. clear, sharp, clean and of even density. Figures will NOT be redrawn or relabelled. Any lettering or text should be in proportion with the rest of the figure.
  • Photographs: These must be of sufficient quality with respect to detail, contrast, and fineness of grain to withstand the unavoidable loss of contrast inherent in the printing process.
  • Colour figures: Inclusion of colour figures is subject to a special charge (£350/US$600/€525 to print a figure in colour). Online colour figures are free of charge. Orders from the UK will be subject to the current UK VAT charge. For orders from elsewhere in the EU you or your institution should account for VAT by way of a reverse charge. Please provide us with your or your institution’s VAT number.

Conventions

In general, the journal follows the conventions of the CBE Style Manual (Council of Biology Editors, Bethesda, MD, 1983, 5th edition). Follow Chemical Abstracts and its indices for chemical names. For guidance in the use of biochemical terminology follow the recommendations issued by the IUPAC-IUB Commission on Biochemical Nomenclature, as given in Biochemical Nomenclature and Related Documents, published by the Biochemical Society, UK. For enzymes, use the recommended name assigned by the IUPAC-IUB Committee on Biochemical Nomenclature, 1978, as given in Enzyme Nomenclature, published by Academic Press, New York, 1980. Where possible, use the recommended SI units. Genotypes should be italicized. Phenotypes should not be italicized. For bacterial agents nomenclature follow Demarc et al. (1966) Genetics, 54, 61-76.

LATEX

TEX-based manuscripts should be produced using the LATEX article style format only. The document style options used must indicate two-column text with 86 mm column widths.

English Language Editing

Language editing, if your first language is not English, to ensure that the academic content of your paper is fully understood by journal editors and reviewers is optional. Language editing does not guarantee that your manuscript will be accepted for publication. For further information on this service, please click here. Several specialist language editing companies offer similar services and you can also use any of these. Authors are liable for all costs associated with such services.

Proofs

Authors are sent page proofs by email. These should be checked immediately and returned to the publishers by email or fax (further details are supplied with the proof). A charge may be made to authors who insist on amendment within the text at the page proof stage.

Offprints

A URL providing free access to the online version of the article will be e-mailed to the corresponding author. This link may then be distributed to interested parties. Paper offprints may be ordered during production of your paper using the Author Services site. Orders from the UK will be subject to the current UK VAT charge. For orders from elsewhere in the EU you or your institution should account for VAT by way of a reverse charge. Please provide us with your or your institution’s VAT number.

Author information pack



Genomics, Proteomics & Bioinformatics publishes papers from all over the world in the fields of genomics, proteomics and bioinformatics. The Journal aims to achieve fast science broadcasting by publishing efficiently. For manuscripts submitted to GPB, direct rejection, direct acceptance or further review will be decided within 5 days. Besides, GPB offers Article-in-Press, by which all the accepted manuscripts can be freely accessible online ahead of its printed issue print for fast dissemination. Featured areas and particular interests of GPB include but are not limited to:

•Genomics: functional genomics, evolutionary genomics, comparative genomics, epigenetics, transcriptomics

•Proteomics: protein expression profiling, protein complexes in terms of structure, function, properties and interactions, metabolomics

•Bioinformatics: genome analysis, sequence analysis, genetic and population analysis, phylogenetics, gene expression, database, web server, algorithm, tools and software, with emphasis on large-scale data analysis based on high-throughput sequencing technologies

GPB welcomes submissions from all over the world in the following types:

•High-quality research papers presenting novel data and ideas •Papers describing innovative methods, tools and techniques as well as resources providing primary scientific information to a broad readership •Comprehensive reviews either as full articles or mini-reviews related with author's own research •Commentaries and opinions about new discoveries, scientific policies, and research proposals

Sections:

•Editorials •Essays •Commentaries •Reviews •Research Articles •Letters •Methods •Application Notes •Research Resources

Page Charges

Genomics, Proteomics & Bioinformatics is an open access journal: all articles will be immediately and permanently free for everyone to read and download. Beijing Institute of Genomics, the Chinese Academy of Sciences and the Genetics Society of China charges a publication fee of USD 50 per published page, color print will be charged extra USD 100 per page for international submissions while Yen 200 per print page and extra Yen 800 per color print page will be charged for submissions from China excluding taxes (also known as an article publishing charge APC) which needs to be paid by the authors or on their behalf e.g. by their research funder or institution. If accepted for publication in the journal following peer-review, authors will be notified of this decision and requested to pay the article processing charge in due time when proofreading is requested after the accepted manuscripts are typeset by Elsevier. Following payment of this charge, the article will be published by Beijing Institute of Genomics, the Chinese Academy of Sciences and the Genetics Society of China in Genomics, Proteomics & Bioinformatics which is made freely available at no further charge through ScienceDirect (Open Access). No article will be published until page fees are paid in full and proof of payment has been received by the Editorial Office. The page charges may be waived under some circumstances, subjected to the editorial justification case by case. The completed form is required for further processing.

Genomics Proteomics and Bioinformatics is under the CC BY license, however if necessary, the authors have a choice of CC BY-NC-ND for their article. The licenses give users the following rights:

Creative Commons Attribution (CC BY): lets others distribute and copy the article, to create extracts, abstracts, and other revised versions, adaptations or derivative works of or from an article (such as a translation), to include in a collective work (such as an anthology), to text or data mine the article, even for commercial purposes, as long as they credit the author(s), do not represent the author as endorsing their adaptation of the article, and do not modify the article in such a way as to damage the author's honor or reputation.

Creative Commons Attribution-NonCommercial-NoDerivs (CC BY-NC-ND): for non-commercial purposes, lets others distribute and copy the article, and to include in a collective work (such as an anthology), as long as they credit the author(s) and provided they do not alter or modify the article.

Submission checklist

You can use this list to carry out a final check of your submission before you send it to the journal for review. Please check the relevant section in this Guide for Authors for more details.

Ensure that the following items are present:

One author has been designated as the corresponding author with contact details:
• E-mail address
• Full postal address

All necessary files have been uploaded:
Manuscript:
• Include keywords
• All figures (include relevant captions)
• All tables (including titles, description, footnotes)
• Ensure all figure and table citations in the text match the files provided
• Indicate clearly if color should be used for any figures in print
Graphical Abstracts / Highlights files (where applicable)
Supplemental files (where applicable)

Further considerations
• Manuscript has been 'spell checked' and 'grammar checked'
• 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 Internet)
• A competing interests statement is provided, even if the authors have no competing interests to declare
• Journal policies detailed in this guide have been reviewed
• Referee suggestions and contact details provided, based on journal requirements

For further information, visit our Support Center.

Ethics in publishing

Please see our information pages on Ethics in publishing and Ethical guidelines for journal publication.

CONFLICTS OF INTEREST

A declaration of Conflict of Interest section must be included in the manuscript. A conflict of interest occurs when an individual’s objectivity is potentially compromised by a desire for financial gain, prominence, professional advancement or a successful outcome. GPB Editors strive to ensure that what is published in the Journal is as balanced, objective and evidence-based as possible. Since it can be difficult to distinguish between an actual conflict of interest and a perceived conflict of interest, by declaring no conflict of interest, the Journal requires authors to disclose all and any potential conflicts of interest including:

Section I

The authors certify that they have NO affiliations with or involvement in any organization or entity with any financial interest (such as honoraria; educational grants; participation in speakers’ bureaus; membership, employment, consultancies, stock ownership, or other equity interest; and expert testimony or patent-licensing arrangements), or non-financial interest (such as personal or professional relationships, affiliations, knowledge or beliefs) in the subject matter or materials discussed in this manuscript.

Section II

The authors report the following details of affiliation or involvement in an organization or entity with a financial or non-financial interest in the subject matter or materials discussed in the manuscript. Please specify the nature of the conflict on a separate sheet of paper.

By submitting to GPB

By submitting to GPB, the corresponding author certified that all Authors have seen and approved the manuscript being submitted. Authors warrant that the article is the Authors' original work. Authors warrant that the article has not received prior publication and is not under consideration for publication elsewhere. On behalf of all Co-Authors, the corresponding Author shall bear full responsibility for the submission. Authors attest to the fact that all Authors listed on the title page have contributed significantly to the work, have read the manuscript, attest to the validity and legitimacy of the data and its interpretation, and agree to its submission to Genomics, Proteomics & Bioinformatics (GPB). All authors agree that author list is correct in its content and order and that no modification to the author list can be made without the written acceptance of all authors and the formal approval of the Editor-in-Chief. All authors accept that the Editor-in-Chief's decisions over acceptance or rejection or in the event of any breach of the Principles of Ethical Publishing in Genomics, Proteomics & Bioinformatics (GPB) being discovered, of retraction are final.

Submission declaration and verification

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 or as an electronic preprint, see 'Multiple, redundant or concurrent publication' section of our ethics policy for more information), 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, including electronically without the written consent of the copyright-holder. To verify originality, your article may be checked by the originality detection service Crossref Similarity Check.

Authorship Policy

All persons who meet authorship criteria are listed as authors, and all authors certify that they have participated sufficiently in the work to take public responsibility for the content, including participation in the concept, design, analysis, writing, or revision of the manuscript. Furthermore, each author certifies that this material or similar material has not been and will not be submitted to or published in any other publication. The manuscript must include the Author Contribution section, which includes the specific contributions made by each author (list the authors’ initials and contributions). The name of each author must appear at least once in each of the three categories below.

Category 1

Conception and design of study; acquisition of data;analysis and/or interpretation of data.

Category 2

Drafting the manuscript;revising the manuscript critically for important intellectual content.

Category 3

Approval of the version of the manuscript to be published (the names of all authors must be listed).

Changes to Authorship Policy

This policy concerns the addition, deletion, or rearrangement of author names in the authorship of all submitted manuscripts:

Before the manuscript is accepted by journal editor: Requests to add or remove an author, or to rearrange the author names, must be sent to the Journal Editor from the corresponding author of the submitted manuscript and must include: (a) the reason the name should be added or removed, or the author names rearranged and (b) written confirmation (e-mail, fax, letter) from all authors that they agree with the addition, removal or rearrangement. In the case of addition or removal of authors, this includes confirmation from the author being added or removed. Requests that are not sent by the corresponding author will be forwarded by the Journal Editor to the corresponding author, who must follow the procedure as described above. Note that: Further process of the manuscript will be halted until authorship has been agreed.

Before the accepted manuscript is published in an online issue: Requests to add or remove an author, or to rearrange the author names, must be sent to the Journal Manager from the corresponding author of the accepted manuscript and must include: (a) the reason the name should be added or removed, or the author names rearranged and (b) written confirmation (e-mail, fax, letter) from all authors that they agree with the addition, removal or rearrangement. In the case of addition or removal of authors, this includes confirmation from the author being added or removed. Please click to download and fill the Authorship Agreement (http://www.elsevier.com/__data/promis_misc/Authorship Agreement.pdf) with all necessary signatures if any changes made on authorship. Requests that are not sent by the corresponding author will be forwarded by the Journal Manager to the corresponding author, who must follow the procedure as described above. Note that: (1) Journal Managers will inform the Journal Editors of any such requests and (2) publication of the accepted manuscript in an online issue is suspended until authorship has been agreed.

After the accepted manuscript is published in an online issue: Any requests to add, delete, or rearrange author names in an article published in an online issue will follow the same policies as noted above and result in a corrigendum.

Elsevier supports responsible sharing
Find out how you can share your research published in Elsevier journals.

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 article for publication. If the funding source(s) had no such involvement then this should be stated.

The open access publication fee for this journal is , excluding taxes. Learn more about Elsevier's pricing policy: http://www.elsevier.com/openaccesspricing.

Elsevier Researcher Academy
Researcher Academy is a free e-learning platform designed to support early and mid-career researchers throughout their research journey. The "Learn" environment at Researcher Academy offers several interactive modules, webinars, downloadable guides and resources to guide you through the process of writing for research and going through peer review. Feel free to use these free resources to improve your submission and navigate the publication process with ease.

Language (usage and editing services)
Please write your text in good English (American or British usage is accepted, but not a mixture of these). Authors who feel their English language manuscript may require editing to eliminate possible grammatical or spelling errors and to conform to correct scientific English may wish to use the English Language Editing service available from Elsevier's WebShop.

Submission

Our online submission system guides you stepwise through the process of entering your article details and uploading your files. The system converts your article files to a single PDF file used in the peer-review process. Editable files (e.g., Word, LaTeX) are required to typeset your article for final publication. All correspondence, including notification of the Editor's decision and requests for revision, is sent by e-mail.

Submit your article
Please submit your article via http://ees.elsevier.com/gpb/default.asp.

Peer review

This journal operates a single blind review process. All contributions will be initially assessed by the editor for suitability for the journal. Papers deemed suitable are then typically sent to a minimum of two independent expert reviewers to assess the scientific quality of the paper. The Editor is responsible for the final decision regarding acceptance or rejection of articles. The Editor's decision is final. More information on types of peer review.

Article Structure

General manuscript format: Manuscripts must be written in English. Manuscript sections should be presented in the following order: title page, Abstract (less than 200 words), Introduction, Results, Discussion, Conclusions (optional), Materials and methods, Authors' contributions, Competing interests, Acknowledgments, References, followed by Figure legends and Supplementary materials (if any). Please provide each table and figure separately. A manuscript template for research articles is available.

Original Article

Identification of A Novel SBF2 Frameshift Mutation in Charcot-Marie-Tooth Disease Type 4B2 Using Whole-exome Sequencing

Structure samples for other article types:

Life-time Achievement Review

My Journey to DNA Repair

Comprehensive Review

N6-methyl-adenosine (m6A) in RNA: An Old Modification with A Novel Epigenetic Function

Minireview

Systems Approaches to Biology and Disease Enable Translational Systems Medicine

Resource Review

Web Resources for Stem Cell Research

Letter

Complete Sequence of pABTJ2, A Plasmid from Acinetobacter baumannii MDR-TJ, Carrying Many Phage-like Elements

Method

FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein-Protein Networks

Application Note

nuMap: A Web Platform for Accurate Prediction of Nucleosome Positioning

Protocol

Systematic Characterization of Cell Cycle Phase-dependent Protein Dynamics and Pathway Activities by High-content Microscopy-assisted Cell Cycle Phenotyping

Introduction

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

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.

Conclusions

The main conclusions of the study may be presented in a short Conclusions section, which may stand a

Essential Title Page Information

A title page should include: the title, all authors' names and complete affiliations, the corresponding author's complete contact information, a running title (50 characters or less, including spaces), 2-6 key words, and sources of grants or funding supports and personal acknowledgments).

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.

Acknowledgments

All persons who have made substantial contributions to the work reported in the manuscript (e.g., technical help, writing and editing assistance, general support), but who do not meet the criteria for authorship, are named in the Acknowledgments and have given their written permission to be named. If no Acknowledgements was involved, it indicates that no substantial contributions from non-authors were received.

Formatting of funding sources
List funding sources in this standard way to facilitate compliance to funder's requirements:

Funding: This work was supported by the National Institutes of Health [grant numbers xxxx, yyyy]; the Bill & Melinda Gates Foundation, Seattle, WA [grant number zzzz]; and the United States Institutes of Peace [grant number aaaa].

It is not necessary to include detailed descriptions on the program or type of grants and awards. When funding is from a block grant or other resources available to a university, college, or other research institution, submit the name of the institute or organization that provided the funding.

If no funding has been provided for the research, please include the following sentence:

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Artwork

Electronic artwork
General points
• Make sure you use uniform lettering and sizing of your original artwork.
• Embed the used fonts if the application provides that option.
• Aim to use the following fonts in your illustrations: Arial, Courier, Times New Roman, Symbol, or use fonts that look similar.
• Number the illustrations according to their sequence in the text.
• Use a logical naming convention for your artwork files.
• Provide captions to illustrations separately.
• Size the illustrations close to the desired dimensions of the published version.
• Submit each illustration as a separate file.
A detailed guide on electronic artwork is available.
You are urged to visit this site; some excerpts from the detailed information are given here.
Formats
If your electronic artwork is created in a Microsoft Office application (Word, PowerPoint, Excel) then please supply 'as is' in the native document format.
Regardless of the application used other than Microsoft Office, when your electronic artwork is finalized, 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 (or PDF): Vector drawings, embed all used fonts.
TIFF (or JPEG): Color or grayscale photographs (halftones), keep to a minimum of 300 dpi.
TIFF (or JPEG): Bitmapped (pure black & white pixels) line drawings, keep to a minimum of 1000 dpi.
TIFF (or JPEG): Combinations bitmapped line/half-tone (color or grayscale), keep to a minimum of 500 dpi.
Please do not:
• Supply files that are optimized for screen use (e.g., GIF, BMP, PICT, WPG); these typically have a low number of pixels and limited set of colors;
• Supply files that are too low in resolution;
• Submit graphics that are disproportionately large for the content.

Color artwork
Please make sure that artwork files are in an acceptable format (TIFF (or JPEG), EPS (or PDF), 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 online (e.g., ScienceDirect and other sites) regardless of whether or not these illustrations are reproduced in color in the printed version. For color reproduction in print, you will receive information regarding the costs from Elsevier after receipt of your accepted article. Please indicate your preference for color: in print or online only. Further information on the preparation of electronic artwork.

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

Please submit tables as editable text and not as images. Tables can be placed either next to the relevant text in the article, or on separate page(s) at the end. Number tables consecutively in accordance with their appearance in the text and place any table notes below the table body. Be sparing in the use of tables and ensure that the data presented in them do not duplicate results described elsewhere in the article. Please avoid using vertical rules and shading in table cells.

References
The reference style for GPB is Vancouver system. In order to follow the Vancouver system for references, the typesetters requires the full author name list of references in order to implement for your article.

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.

Reference Style

Text: Indicate references by number(s) in square brackets in line with the text. The actual authors can be referred to, but the reference number(s) must always be given.

List: Number the references (numbers in square brackets) in the list in the order in which they appear in the text.

Examples:

Reference to a journal publication: [1] Van der Geer J, Hanraads JAJ, Lupton RA. The art of writing a scientific article. J Sci Commun 2010;163:51-9.

Reference to a book: [2] Strunk Jr W, White EB. The elements of style. 4th ed. New York: Longman; 2000.

Reference to a chapter in an edited book: [3] Mettam GR, Adams LB. How to prepare an electronic version of your article. In: Jones BS, Smith RZ, editors. Introduction to the electronic age, New York: E-Publishing Inc; 2009, p. 281-304.

Reference to an ebook or online pdf: [4] Smith K. A brief history of NCBI's formation and growth. In: The NCBI handbook [Internet]. Bethesda: National Center for Biotechnology Information; 2013, http://www.ncbi.nlm.nih.gov/books/NBK148949/

Please do not put webpage links into the reference section. The links can be added in a parenthesis right after the citing materials in the main text.

Note shortened form for last page number. e.g., 51-9, and that for more than 6 authors the first 6 should be listed followed by 'et al.' For further details you are referred to 'Uniform Requirements for Manuscripts submitted to Biomedical Journals' (J Am Med Assoc 1997;277:927-34) (see also http://www.nlm.nih.gov/bsd/uniform_requirements.html). A GPB reference style for Endnote is available for downloading http://www.elsevier.com/__data/promis_misc/GPB-Endnote-Template.ens.

Data policy

Data policy

Authors are encouraged to enable other scientists the use of their data that are deposited in public databases on genes, proteins, genomics, diseases, etc. To do so, authors please identify the data accession numbers, tagging identifiers, or any specific IDs generated and/or cited in their papers in parenthesis with the following format:

Database abbreviation accession No: data identifier

eg. The obtained ITS and psbA-trnH sequences were deposited in the GenBank of NCBI database (GenBank Accessions: HQ386701, HQ386689, HQ386691, HQ386695, HQ386696, HQ407399, HQ386690 and JF423303) at http://www.sciencedirect.com/science/article/pii/S1672022912000915.

Authors should check accession numbers, tagging identifiers, or any specific IDs very carefully. An error in a letter or number can result in a dead link. In the final version of the electronic copy, the text for accession number, tagging identifier or other specific ID will be linked to the appropriate source in the databases, enabling the readers to go directly to that source from the article. In the final version of the printed article, the text of accession number, tagging identifier or other specific ID will appear in the same font as regular text.

Detailed information is available regarding the types of data and the corresponding data repositories given in the listing of databases supported by Elsevier at the following link: http://www.elsevier.com/?a=57755.

Video data

Elsevier accepts video material and animation sequences to support and enhance your scientific research. Authors who have video or animation files that they wish to submit with their article are strongly encouraged to include links to these within the body of the article. This can be done in the same way as a figure or table by referring to the video or animation content and noting in the body text where it should be placed. All submitted files should be properly labeled so that they directly relate to the video file's content. In order to ensure that your video or animation material is directly usable, please provide the files in one of our recommended file formats with a preferred maximum size of 150 MB. Video and animation files supplied will be published online in the electronic version of your article in Elsevier Web products, including ScienceDirect: http://www.sciencedirect.com. Please supply 'stills' with your files: you can choose any frame from the video or animation or make a separate image. These will be used instead of standard icons and will personalize the link to your video data. For more detailed instructions please visit our video instruction pages at https://www.elsevier.com/artworkinstructions. Note: since video and animation cannot be embedded in the print version of the journal, please provide text for both the electronic and the print version for the portions of the article that refer to this content.

Supplementary material

Supplementary material such as applications, images and sound clips, can be published with your article to enhance it. Submitted supplementary items are published exactly as they are received (Excel or PowerPoint files will appear as such online). Please submit your material together with the article and supply a concise, descriptive caption for each supplementary file. If you wish to make changes to supplementary material during any stage of the process, please make sure to provide an updated file. Do not annotate any corrections on a previous version. Please switch off the 'Track Changes' option in Microsoft Office files as these will appear in the published version.

Proofs

Accepted articles will be published online on ScienceDirect as an article in press and assigned an issue at a later date. You can track the status of your accepted article throughout this process in our production tracking system (http://authors.elsevier.com/TrackPaper.html) using the reference No (e.g. GPB12) we sent to you in the acknowledgement e-mail.
As soon as your article has been typeset, a page proof in the form of a PDF file will be sent to the corresponding author(s) for checking and correction of typographical errors and should be returned before the date specified. This usually happens 4-5 weeks after we receive your completed article. Accurate proofreading and clear marking of corrections are essential for the production of a quality article. Please note that careful proofreading is solely your responsibility. We will do everything we can to have your article corrected and published as quickly and accurately as possible. Therefore, it is important to ensure that all of your corrections are sent back to us in one communication.



Visit the Elsevier Support Center to find the answers you need. Here you will find everything from Frequently Asked Questions to ways to get in touch.
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