General information

Submission process

Manuscripts must be submitted by one of the authors of the manuscript, and should not be submitted by anyone on their behalf. The submitting author takes responsibility for the article during submission and peer review.

To facilitate rapid publication and to minimize administrative costs, Immunome Research accepts only online submission.

Files can be submitted as a batch, or one by one. The submission process can be interrupted at any time - when users return to the site, they can carry on where they left off.

See below for examples of acceptable word processor and graphics file formats. Additional files of any type, such as movies, animations, or original data files, can also be submitted as part of the publication.

During submission you will be asked to provide a cover letter. Please use this to explain why your manuscript should be published in the journal and to elaborate on any issues relating to our editorial policies detailed in the instructions for authors.

Assistance with the process of manuscript preparation and submission is available from the customer support team ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ).

We also provide a collection of links to useful tools and resources for scientific authors, on our Tools for Authors page.

Publication and peer review processes

Immunome Research uses online peer review to speed up the publication process. The time taken to reach a final decision depends on whether reviewers request revisions, and how quickly authors are able to respond.

Once an article is accepted, it is published in Immunome Research immediately as a provisional PDF file. The paper will subsequently be published in both fully browseable web form, and as a formatted PDF. The article will then be available through Immunome Research, BioMed Central and PubMed Central, and will also be included in PubMed.

The ultimate responsibility for any decision lies with the Editor-in-Chief, to whom any appeals against rejection should be addressed.

Article-processing charges

Immunome Research levies an article-processing charge for every accepted article, to cover the costs incurred by open access publication. In 2011 the article-processing charge is US$1000.  Waivers may be granted, particularly for authors from developing countries.

Editorial policies

Any manuscripts, or substantial parts of it, submitted to the journal must not be under consideration by any other journal. In general, the manuscript should not have already been published in any journal or other citable form, although it may have been deposited on a preprint server. The journal is willing to consider peer-reviewing manuscripts that are translations of articles originally published in another language. In this case, the consent of the journal in which the article was originally published must be obtained and the fact that the article has already been published must be made clear on submission and stated in the abstract.  Authors are required to ensure that no material submitted as part of a manuscript infringes existing copyrights, or the rights of a third party. Authors who publish in Immunome Research retain copyright to their work (more information). Correspondence concerning articles published in Immunome Research is encouraged.

Submission of a manuscript to Immunome Research implies that all authors have read and agreed to its content, and that any experimental research that is reported in the manuscript has been performed with the approval of an appropriate ethics committee. Research carried out on humans must be in compliance with the Helsinki Declaration, and any experimental research on animals must follow internationally recognized guidelines. A statement to this effect must appear in the Methods section of the manuscript, including the name of the body which gave approval, with a reference number where appropriate. Informed consent must also be documented. Manuscripts may be rejected if the editorial office considers that the research has not been carried out within an ethical framework, e.g. if the severity of the experimental procedure is not justified by the value of the knowledge gained.

Immunome Research's publisher, Nikolai Petrovsky Publishing, has a legal responsibility to ensure that its journals do not publish material that infringes copyright, or that includes libellous or defamatory content. If, on review, your manuscript is perceived to contain potentially libellous content the journal Editors, with assistance from the publisher if required, will work with authors to ensure an appropriate outcome is reached.

Generic drug names should generally be used. When proprietary brands are used in research, include the brand names in parentheses in the Methods section.

We ask authors of Immunome Research papers to complete a declaration of competing interests, which should be provided as a separate section of the manuscript, to follow the Acknowledgements. Where an author gives no competing interests, the listing will read 'The author(s) declare that they have no competing interests'. Much has been written about competing interests (or conflict of interest, as other journals call it) within scientific research, but the following articles provide some background:

R Smith: Beyond conflict of interest. BMJ 1998, 317 :291-292

R Smith: Making progress with competing interests. BMJ 2002, 325 :1375-1376

CD DeAngelis, PB Fontanarosa, A Flanagin: Reporting financial conflicts of interest and relationships between investigators and research sponsors. JAMA 2001, 286 :89-9

K Morin, H Rakatansky, FA Riddick Jr, LJ Morse, JM O'Bannon 3rd, MS Goldrich, P Ray, M Weiss, RM Sade, MA Spillman: Managing conflicts of interest in the conduct of clinical trials. JAMA 2002, 287 :78-84

For all articles that include information or clinical photographs relating to individual patients, written and signed consent from each patient to publish must also be mailed or faxed to the editorial staff. The manuscript should also include a statement to this effect in the Acknowledgements section, as follows: "Written consent for publication was obtained from the patient or their relative."

Immunome Research supports initiatives to improve the performance and reporting of clinical trials, part of which includes prospective registering and numbering of trials. The International Committee of Medical Journal Editors (ICMJE) defines a clinical trial as any research study that prospectively assigns human subjects to one or more health related interventions to evaluate the effects on health outcomes. Authors of protocols or reports of such clinical trials, where the primary purpose of the research is to understand the causes, development and effects of disease, or to improve preventative, diagnostic or therapeutic interventions, must register their trial prior to submission in a suitable publicly accessible registry. Registries which meet the requirements of the ICMJE include WHO Primary Registries. The trial registration number should be included as the last line of the abstract of the manuscript.

Immunome Research also supports initiatives aimed at improving the reporting of biomedical research. Checklists have been developed for a number of study designs, including randomized controlled trials (CONSORT), systematic reviews (PRISMA), meta-analyses of observational studies (MOOSE), diagnostic accuracy studies (STARD) and qualitative studies (RATS). We recommend authors refer to the EQUATOR network website for further information on the available reporting guidelines for health research, and the MIBBI Portal for prescriptive checklists for reporting biological and biomedical research where applicable. Authors are requested to make use of these when drafting their manuscript and peer reviewers will also be asked to refer to these checklists when evaluating these studies. For authors of systematic reviews, a supplementary file, linked from the Methods section, should reproduce all details concerning the search strategy. For an example of how a search strategy should be presented, see the Cochrane Reviewers' Handbook.

Authors from pharmaceutical companies, or other commercial organizations that sponsor clinical trials, should adhere to the Good Publication Practice guidelines for pharmaceutical companies, which are designed to ensure that publications are produced in a responsible and ethical manner. The guidelines also apply to any companies or individuals that work on industry-sponsored publications, such as freelance writers, contract research organizations and communications companies.

The involvement of medical writers or anyone else who assisted with the preparation of the manuscript content should be acknowledged, along with their source of funding, as described in the European Medical Writers Association (EMWA) guidelines on the role of medical writers in developing peer-reviewed publications. If medical writers are not listed among the authors, it is important that their role be acknowledged explicitly. We suggest wording such as 'We thank Jane Doe who provided medical writing services on behalf of XYZ Pharmaceuticals Ltd.'.

Any 'in press' articles cited within the references and necessary for the reviewers' assessment of the manuscript should be made available if requested by the editorial office.

Submission of a manuscript to Immunome Research implies that readily reproducible materials described in the manuscript, including all relevant raw data, will be freely available to any scientist wishing to use them for non-commercial purposes. Nucleic acid sequences, protein sequences, and atomic coordinates should be deposited in an appropriate database in time for the accession number to be included in the published article. In computational studies where the sequence information is unacceptable for inclusion in databases because of lack of experimental validation, the sequences must be published as an additional file with the article.

Nucleotide sequences

Nucleotide sequences can be deposited with the DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory (EMBL/EBI) Nucleotide Sequence Database, or GenBank (National Center for Biotechnology Information).

Protein sequences

Protein sequences can be deposited with SwissProt or the Protein Information Resource (PIR).

Structures

Protein structures can be deposited with one of the members of the Worldwide Protein Data Bank. Nucleic Acids structures can be deposited with the Nucleic Acid Database at Rutgers. Crystal structures of organic compounds can be deposited with the Cambridge Crystallographic Data Centre.

Chemical structures and assays

Structures of chemical substances can be deposited with PubChem Substance. Bioactivity screens of chemical substances can be deposited with PubChem BioAssay.

Microarray data

Where appropriate, authors should adhere to the standards proposed by the Microarray Gene Expression Data Society and must deposit microarray data in one of the public repositories, such as ArrayExpress, Gene Expression Omnibus (GEO) or the Center for Information Biology Gene Expression Database (CIBEX).

Computional modeling

We encourage authors to prepare models of biochemical reaction networks using the Systems Biology Markup Language and to deposit the model with the BioModels database, as well as submitting it as an additional file with the manuscript.

Plasmids

We encourage authors to deposit copies of their plasmids as DNA or bacterial stocks with Addgene, a non-profit repository, or PlasmID, the Plasmid Information Database at Harvard.

Preparing main manuscript text

File formats

The following word processor file formats are acceptable for the main manuscript document:

• Microsoft Word (version 2 and above)
• Rich text format (RTF)
• Portable document format (PDF)

Users of other word processing packages should save or convert their files to RTF before uploading. Many free tools are available which ease this process.

Note that figures must be submitted as separate image files, not as part of the submitted DOC/ PDF file.

Article types

When submitting your manuscript, you will be asked to assign one of the following types to your article

• Research
• Commentary
• Database
• Hypothesis
• Meeting report
• Methodology
• Review
• Short Report
• Software

Please read the descriptions of each of the article types, choose which is appropriate for your article and structure it accordingly. If in doubt, your manuscript should be classified as Research, the structure for which is described below.

Manuscript sections for Research articles

Manuscripts for Research articles submitted to Immunome Research should be divided into the following sections:

• Title page
• Abstract
• Background
• Results
• Discussion
• Conclusions
• Methods
• List of abbreviations used(if any)
• Competing interests
• Authors' contributions
• Authors' information (if any)
• Acknowledgements and Funding
• References
• Figure legends (if any)
• Tables and captions (if any)
• Description of additional data files (if any)

You can download a template (Mac and Windows compatible; Microsoft Word 98/2000) for your article. For instructions on use, see below.

The Accession Numbers of any nucleic acid sequences, protein sequences or atomic coordinates cited in the manuscript should be provided, in square brackets and include the corresponding database name; for example, [EMBL:AB026295, EMBL:AC137000, DDBJ:AE000812, GenBank:U49845, PDB:1BFM, Swiss-Prot:Q96KQ7, PIR:S66116].

The databases for which we can provide direct links are: EMBL Nucleotide Sequence Database (EMBL), DNA Data Bank of Japan (DDBJ ), GenBank at the NCBI (GenBank), Protein Data Bank (PDB), Protein Information Resource (PIR) and the Swiss-Prot Protein Database (Swiss-Prot).

Title page

This should list the title of the article. The title should include the study design, for example:

A versus B in the treatment of C: a randomized controlled trial

X is a risk factor for Y: a case control study

The full names, institutional addresses, and e-mail addresses for all authors must be included on the title page. The corresponding author should also be indicated.

Abstract

The abstract of the manuscript should not exceed 350 words and must be structured into separate sections: Background, the context and purpose of the study; Results, the main findings; Conclusions, brief summary and potential implications. Please minimize the use of abbreviations and do not cite references in the abstract. Trial Registration, if your research article reports the results of a controlled health care intervention, please list your trial registry, along with the unique identifying number, e.g. Trial registration: Current Controlled Trials ISRCTN73824458. Please note that there should be no space between the letters and numbers of your trial registration number.

Background

The background section should be written from the standpoint of researchers without specialist knowledge in that area and must clearly state - and, if helpful, illustrate - the background to the research and its aims. Reports of clinical research should, where appropriate, include a summary of a search of the literature to indicate why this study was necessary and what it aimed to contribute to the field. The section should end with a very brief statement of what is being reported in the article.

Results and Discussion

The Results and Discussion may be combined into a single section or presented separately. Results of statistical analysis should include, where appropriate, relative and absolute risks or risk reductions, and confidence intervals. The results and discussion sections may also be broken into subsections with short, informative headings.

Conclusions

This should state clearly the main conclusions of the research and give a clear explanation of their importance and relevance. Summary illustrations may be included.

Methods (can also be placed after Background)

This should include the design of the study, the setting, the type of participants or materials involved, a clear description of all interventions and comparisons, and the type of analysis used, including a power calculation if appropriate.

List of abbreviations

If abbreviations are used in the text, either they should be defined in the text where first used, or a list of abbreviations can be provided, which should precede the competing interests and authors' contributions.

Competing interests

A competing interest exists when your interpretation of data or presentation of information may be influenced by your personal or financial relationship with other people or organizations. Authors should disclose any financial competing interests but also any non-financial competing interests that may cause them embarrassment were they to become public after the publication of the manuscript.

Authors are required to complete a declaration of competing interests. All competing interests that are declared will be listed at the end of published articles. Where an author gives no competing interests, the listing will read 'The author(s) declare that they have no competing interests'.

When completing your declaration, please consider the following questions:

Financial competing interests

• In the past five years have you received reimbursements, fees, funding, or salary from an organization that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Is such an organization financing this manuscript (including the article-processing charge)? If so, please specify.
• Do you hold any stocks or shares in an organization that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? If so, please specify.
• Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? If so, please specify.
• Do you have any other financial competing interests? If so, please specify.

Non-financial competing interests

Are there any non-financial competing interests (political, personal, religious, ideological, academic, intellectual, commercial or any other) to declare in relation to this manuscript? If so, please specify.

If you are unsure as to whether you or one of your co-authors has a competing interest, please discuss it with the editorial office.

Authors' contributions

In order to give appropriate credit to each author of a paper, the individual contributions of authors to the manuscript should be specified in this section.

An "author" is generally considered to be someone who has made substantive intellectual contributions to a published study. To qualify as an author one should 1) have made substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; 2) have been involved in drafting the manuscript or revising it critically for important intellectual content; and 3) have given final approval of the version to be published. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content. Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship.

We suggest the following kind of format (please use initials to refer to each author's contribution): AB carried out the molecular genetic studies, participated in the sequence alignment and drafted the manuscript. JY carried out the immunoassays. MT participated in the sequence alignment. ES participated in the design of the study and performed the statistical analysis. FG conceived of the study, and participated in its design and coordination and helped to draft the manuscript. All authors read and approved the final manuscript.

All contributors who do not meet the criteria for authorship should be listed in an acknowledgements section. Examples of those who might be acknowledged include a person who provided purely technical help, writing assistance, or a department chair who provided only general support.

Authors' information

You may choose to use this section to include any relevant information about the author(s) that may aid the reader’s interpretation of the article, and understand the standpoint of the author(s). This may include details about the authors' qualifications, current positions they hold at institutions or societies, or any other relevant background information. Please refer to authors using their initials. Note this section should not be used to describe any competing interests.

Acknowledgements and Funding

Please acknowledge anyone who contributed towards the study by making substantial contributions to conception, design, acquisition of data, or analysis and interpretation of data, or who was involved in drafting the manuscript or revising it critically for important intellectual content, but who does not meet the criteria for authorship. Please also include their source(s) of funding. Please also acknowledge anyone who contributed materials essential for the study.

The role of a medical writer must be included in the acknowledgements section, including their source(s) of funding.

Authors should obtain permission to acknowledge from all those mentioned in the Acknowledgements.

Please list the source(s) of funding for the study, for each author, and for the manuscript preparation in the acknowledgements section. Authors must describe the role of the funding body, if any, in study design; in the collection, analysis, and interpretation of data; in the writing of the manuscript; and in the decision to submit the manuscript for publication.

References

All references must be numbered consecutively, in square brackets, in the order in which they are cited in the text, followed by any in tables or legends. Reference citations should not appear in titles or headings. Each reference must have an individual reference number. Please avoid excessive referencing. If automatic numbering systems are used, the reference numbers must be finalized and the bibliography must be fully formatted before submission.

Only articles and abstracts that have been published or are in press, or are available through public e-print/preprint servers, may be cited; unpublished abstracts, unpublished data and personal communications should not be included in the reference list, but may be included in the text and referred to as "unpublished data", "unpublished observations", or "personal communications" giving the names of the involved researchers. Notes/footnotes are not allowed. Obtaining permission to quote personal communications and unpublished data from the cited author(s) is the responsibility of the author. Journal abbreviations follow Index Medicus/MEDLINE. Citations in the reference list should contain all named authors, regardless of how many there are.

Examples of the Immunome Research reference style are shown below. Please take care to follow the reference style precisely; references not in the correct style may be retyped, necessitating tedious proofreading.

[http://tumor.informatics.jax.org/mtbwi/index.do]

Immunome Research reference style

Article within a journal

1. Koonin EV, Altschul SF, Bork P: BRCA1 protein products: functional motifs. Nat Genet 1996, 13:266-267.

Article within a journal supplement

2. Orengo CA, Bray JE, Hubbard T, LoConte L, Sillitoe I: Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins 1999, 43(Suppl 3):149-170.

In press article

3. Kharitonov SA, Barnes PJ: Clinical aspects of exhaled nitric oxide. Eur Respir J, in press.

Published abstract

4. Zvaifler NJ, Burger JA, Marinova-Mutafchieva L, Taylor P, Maini RN: Mesenchymal cells, stromal derived factor-1 and rheumatoid arthritis [abstract]. Arthritis Rheum 1999, 42:s250.

Article within conference proceedings

5. Jones X: Zeolites and synthetic mechanisms. In Proceedings of the First National Conference on Porous Sieves: 27-30 June 1996; Baltimore. Edited by Smith Y. Stoneham: Butterworth-Heinemann; 1996:16-27.

Book chapter, or article within a book

6. Schnepf E: From prey via endosymbiont to plastids: comparative studies in dinoflagellates. In Origins of Plastids. Volume 2. 2nd edition. Edited by Lewin RA. New York: Chapman and Hall; 1993:53-76.

Whole issue of journal

7. Ponder B, Johnston S, Chodosh L (Eds): Innovative oncology. In Breast Cancer Res 1998, 10:1-72.

Whole conference proceedings

8. Smith Y (Ed): Proceedings of the First National Conference on Porous Sieves: 27-30 June 1996; Baltimore. Stoneham: Butterworth-Heinemann; 1996.

Complete book

9. Margulis L: Origin of Eukaryotic Cells. New Haven: Yale University Press; 1970.

Monograph or book in a series

10. Hunninghake GW, Gadek JE: The alveolar macrophage. In Cultured Human Cells and Tissues. Edited by Harris TJR. New York: Academic Press; 1995:54-56. [Stoner G (Series Editor): Methods and Perspectives in Cell Biology, vol 1.]

Book with institutional author

11. Advisory Committee on Genetic Modification: Annual Report. London; 1999.

PhD thesis

12. Kohavi R: Wrappers for performance enhancement and oblivious decision graphs. PhD thesis. Stanford University, Computer Science Department; 1995.

[http://tumor.informatics.jax.org/mtbwi/index.do]

Microsoft Word template

Although we can accept manuscripts prepared as Microsoft Word, RTF or PDF files, we have designed a Microsoft Word template that can be used to generate a standard style and format for your article. It can be used if you have not yet started to write your paper, or if it is already written and needs to be put into Immunome Research style.

Download the template (compatible with Mac and Windows Word 97/98/2000/2003/2007) from our site, and save it to your hard drive. Double click the template to open it.

How to use the Immunome Research template

The template consists of a standard set of headings that make up a Immunome Research Research manuscript, along with dummy fragments of body text. Follow these steps to create your manuscript in the standard format:

• Replace the dummy text for Title, Author details, Institutional affiliations, and the other sections of the manuscript with your own text (either by entering the text directly or by cutting and pasting from your own manuscript document).
• If there are sections which you do not need, delete them (but check the rest of the Instructions for Authors to see which sections are compulsory).
• If you need an additional copy of a heading (e.g. for additional figure legends) just copy and paste.
• For the references, you may either manually enter the references using the reference style given, or use bibliographic software to insert them automatically. We provide style files for EndNote, Reference Manager and Zotero.

For extra convenience, you can use the template as one of your standard Word templates. To do this, put a copy of the template file in Word's 'Templates' folder, normally C:\Program Files\Microsoft Office\Templates on a PC. The next time you create a new document in Word using the File menu, the template will appear as one of the available choices for a new document.