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Author Guidelines

Revisions to these Guidelines

 

PLEASE NOTE THAT MOLECULAR SYSTEMS BIOLOGY NOW REQUIRES A COMPLETE AUTHOR CHECKLIST (RIGHT CLICK AND 'SAVE AS') TO BE SUBMITTED WITH ALL REVISED MANUSCRIPTS.

 

About the journal

Editorial Policies

Editorial Process

Manuscript Preparation

Submission

For Acceptance and Publication

Help and Contact

 

About the Journal

Aims and Scope

Systems biology is an integrative discipline that seeks to explain the properties and behaviour of complex biological systems in terms of their components and their interactions.

Molecular Systems Biology is a peer-reviewed author-pays online journal that publishes high-quality research in the fields of systems biology, synthetic biology and systems medicine. The Editors select manuscripts based on their novelty and wide biological significance. Although the primary emphasis of the journal is on molecular components and their interactions, systems studies at the organ level may also be considered. Works describing large-scale datasets will be judged, in part, by the extent to which these datasets are integrated both with each other and with computational models, with the ultimate aim to better understand the dynamic and complex nature of living systems. Reports of new experimental methods will also be considered in the context of this policy.

Topics falling within the scope of the journal include, but are not limited to: integrative genome-scale biology, quantitative biology, computational biology, metabolic and regulatory networks, evolution of genomes and biological networks, clinical and translational systems biology, synthetic biology and genome-scale biological engineering.

Molecular Systems Biology publishes research articles as full-length Articles or short Reports. The journal publishes also Reviews, Perspectives, News & Views, Correspondences and Editorials.

Bibliometrics

Impact Factor (2013): 14.1 (Thomson Reuters)

5-year Impact Factor (2013): 12.3 (Thomson Reuters

Immediacy Index (2013): 2.4 (Thomson Reuters)

SJR (2013): 9.8 (JournalM3trics)

SNIP (2013): 2.9 (JournalM3trics)

h4 (2009-2013): 71 (Google Scholar)

 

Subject Categories

Subject Categories are used to structure the current and archived online content of Molecular Systems Biology, and to help readers interested in particular areas of molecular biology find relevant information more easily. Authors should suggest appropriate Subject Categories for the submitted manuscript. One or two categories may be selected from the following list:

 

Systems & Synthetic Biology categories
Quantitative Biology & Dynamical Systems Genome-Scale & Integrative Biology
Network Biology Synthetic Biology & Biotechnology
Systems Medicine Computational Biology
Methods & Resources  

 

Molecular & Cell Biology categories
Ageing Metabolism
Cancer
Microbiology, Virology & Host Pathogen Interaction
Cell Adhesion, Polarity & Cytoskeleton Molecular Biology of Disease
Cell Cycle Neuroscience
Cell Death & Autophagy Pharmacology & Drug Discovery
Chemical Biology Plant Biology
Chromatin, Epigenetics, Genomics & Functional Genomics Post-translational Modifications, Proteolysis & Proteomics
Development & Differentiation Protein Biosynthesis & Quality Control
DNA Replication, Repair & Recombination RNA Biology
Evolution Signal Transduction
Genetics, Gene Therapy & Genetic Disease Stem Cells
Immunology Structural Biology
Membrane & Intracellular Transport Transcription

 

Editorial Policies

Submission of a manuscript implies that it reports unpublished work and that neither itself, nor parts of it, have been published or are under consideration for publication elsewhere. By submitting a manuscript, the authors guarantee that they have the appropriate authority from their employers and/or funding agencies to publish the work. Any related work under consideration, review, revision or accepted for publication elsewhere must accompany the submission if they are relevant to its scientific assessment.

The journal reserves the right not to publish material that has already been formally published, completely or substantially, including in established digital media such as blogs. All EMBO Press journals encourage prior publication on recognized non-peer-reviewed, community preprint servers such as arXiv and bioRxiv for commenting by other scientists before formal submission to the journal. The details of the preprint server concerned and any accession numbers or DOIs must be included in the cover letter accompanying submission of the manuscript.

Transparent Process

All EMBO Press journals have made the editorial process transparent for all accepted manuscripts by publishing as an online supplementary document all correspondence between authors and the editorial office relevant to the decision process. This will by default include all referee comments directed to the authors, as well as the authors' point-by-point responses. Internal communications and informal consultations between editors and editorial advisors will remain excluded from these policies. Likewise, referee anonymity will be strictly maintained, unless a referee chooses to sign his or her report. Authors who are, for specific reasons or as a matter of principle, not comfortable with these disclosures will have the possibility to opt out of the transparent process at any stage prior to publication. More information about the EMBO Press Transparent Process can be found below and on the EMBO Press website.

Authorship Guidelines

Submission of a manuscript requires that all authors have seen and approved the manuscript and its contents, and that they are aware of the responsibilities connected to authorship. Each of the listed authors has to concur with the text of the submitted manuscript, confirm the integrity of the data and its presentation, and agree with its interpretation as discussed in the manuscript. Signatures from all the authors are not required; it is the corresponding author’s responsibility to obtain agreement from all authors supporting the submission. All authors will be notified upon peer-review of a new manuscript and upon acceptance of a manuscript, but the editorial office generally corresponds only with the Corresponding Author, whose responsibility it is to communicate information sent from the editorial office with all other authors. Editors may send information such as referee reports to all the authors where they consider this to be essential

Submission of a manuscript requires that all authors agree to the authorship as listed in the manuscript. The nature of every author’s contribution must be specified both in the manuscript submission system and in the manuscript under the heading “Author Contributions”.

Our authorship policies conform to international standards (see, for example, ICMJE authorship guidelines).

The journal encourages the submission of a completed author checklist (right click to download) at submission (which covers animal welfare, human subjects, data deposition and ethics), and will require it to be filled and returned to the editorial office at revision, either via the online submission system (upload as a supplementary file) or by email to the editorial office. All information covered in the checklist should be included in the manuscript.

Use of living organisms

For Research Articles submitted to EMBO Press journals reporting experiments on live vertebrates and/or higher invertebrates, the corresponding author must confirm that all experiments were performed in accordance with relevant guidelines and regulations. The manuscript must include a statement in the Materials and Methods identifying the institutional and/or licensing committee approving the experiments, including any relevant details. For experiments involving human subjects, authors must identify the committee approving the experiments, and include with their submission a statement confirming that informed consent was obtained from all subjects.

Right click to download and complete the author checklist here.

Animal welfare

For studies reporting experiments on live vertebrates and/or higher invertebrates, the corresponding author must confirm that all experiments were performed in accordance with relevant guidelines and regulations. The manuscript must include a statement in the Materials and Methods identifying the institutional and/or licensing committee approving the experiments. The editors reserve the right to consult with board members or external experts and reject manuscripts that contain animal experiments that do not conform to NIH or MRC guidelines for animal welfare. For further information see: Office of Laboratory Animal Welfare; The journal encourages authors to follow the ARRIVE guidelines (PLoS Biol. 8(6), e1000412, 2010) for reporting studies involving animals. Please see the following website for details: http://www.equator-network.org/reporting-guidelines/improving-bioscience-research-reporting-the-arrive-guidelines-for-reporting-animal-research/

Right click to download and complete the author checklist here.

Human Subjects

For experiments involving human subjects the corresponding author must identify the committee approving the experiments and include a statement that informed consent was obtained from all subjects and that the experiments conformed to the principles set out in the WMA Declaration of Helsinki and the Department of Health and Human Services Belmont Report. Editors or referees may request further documentation confirming that this is the case. 

Any restrictions on the availability or on the use of human data or samples should be clearly specified in the manuscript. Any restrictions that may detract from the overall impact of a study or undermine its reproducibility will be taken into account in the editorial decision. 

For clinical trials reporting, the authors should fill out a CONSORT flow diagram and submit it as supplementary information. The journal also encourages authors to follow the CONSORT reporting guidelines http://www.consort-statement.org. Please see the EQUATOR website for details. Clinical trials should also be registered as recommended by the International Committee of Medical Journal Editors, and the trial registration number should be provided.

Right click to download and complete the author checklist here.

Reporting Guidelines

Authors are encouraged to follow the EQUATOR Network reporting guidelines for the following:

Type of Study Guidelines
Animal research ARRIVE
Parallel group randomized trials CONSORT
Conensus-based Clinical Case Reporting CARE
Prognostic marker studies REMARK
Diagnostic Accuracy STARD
Meta-analysis of observational studies MOOSE
Systematic reviews and meta-analysis PRISMA
Observational studies STROBE
Genetic association studies STREGA
Statistical analyses and methods STAMPL
Microarray/deep sequencing studies MIAME
Studies using biospecimens BRISQ

Biosecurity

Planned research and results from experiments should be evaluated at an early stage for possible dual use concerns. In such cases, authors should first consult with an appropriate local body concerning the implications for biosecurity and public health. For further information see the U.S. National Science Advisory Board for Biosecurity's recommendations and the US National Select Agent Registry.

Authors should explicitly describe any potential biosecurity implications and the local body's assessment in their cover letter at submission and in the author checklist. The threat posed by the potential abuse of certain experimental data or material for bioweapons, terrorist or other criminal activities may require that editors balance the risks and benefits of publication. The ultimate decision whether to publish the paper as submitted or with suggested changes is the prerogative of the editors after consultation with board members or external experts in biosafety, biosecurity, or public and environmental health.

Right click to download and complete the author checklist here.

Availability of published material, data and software

It is understood that by publishing a paper in this journal, the authors agree to make available to colleagues in academic research all new reagents, including organisms (or means to produce them), viruses, cells, nucleic acids and antibodies, that were used in the research reported and that are not available from public repositories or commercial suppliers. Human patient samples and data should be made available in accordance with the relevant ethical standards. Materials must be made available at a reasonable cost that reflects production and distribution. The distribution of published materials does not automatically confer a right of co-authorship. The guidelines below were inspired, in part, by the recommendations formulated by the Board on Life Sciences from the National Academies Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences (National Academies Press, 2003). Right click to download and complete the author checklist here.

  • Organisms, viruses, cells, nucleic acids, antibodies, and other reagents that were used in the research reported and that are not available from commercial suppliers should be freely available to colleagues in academic research. Human patient samples and data should be made available in accordance with the relevant ethical standards.
  • Datasets obtained by experimentation, computation or data mining, should be made freely available, without restriction. This holds without exception to data that are central and integral to the findings reported in the paper and it is strongly recommended for any remaining associated data.
  • Software should be described in sufficient detail to allow reproduction of the underlying algorithms by others. This may be achieved by providing the appropriate narrative or mathematical description, pseudocode and, possibly but not obligatorily, the source code. If a specific implementation is the focus of the study, it is strongly recommended that non-commercial users are granted free access to this implementation.
  • If a piece of software is central to the study, it is strongly recommended that it provides appropriate mechanisms (eg data import and export functionalities) for a reasonable integration in other workflows.
  • Any restrictions on the availability or on the use of included data, software and databases should be clearly specified in the paper. These restrictions may detract from the overall impact of a study, in particular when datasets, software or databases are central to the findings reported, and, therefore, will be taken into account in the final editorial decision.

The journal will only review and publish manuscripts if the authors agree to make all data that cannot be published in the journal itself (e.g. novel nucleotide sequences, structural data, or data from large-scale gene expression experiments) freely available, where possible in an appropriate public database (detailed guidelines can be found below).

Right click to download and complete the author checklist here.

Conflicts of interest

In the interests of transparency and to help editors and reviewers assess any potential bias, the journal requires authors of original research papers to declare any competing commercial interests in relation to the submitted work. It is difficult to specify a threshold at which a financial interest becomes significant, but as a practical guideline, we would suggest this to be any undeclared interest that could embarrass you were it to become publicly known. Referees and editors are also subject to Conflict of Interest regulations.

Scientific Integrity

The editorial staff are committed to maintaining high standards of integrity of the published scientific record. Journal staff undertake routine image analysis of data in manuscripts submitted for publication and will request source data and an author response to image aberrations.

The journal requests that authors take note of and adhere to national standards, as well as guidelines established by the U.S. Department of Health and Human Services Office of Research Integrity (http://ori.dhhs.gov). The journal will investigate suspected instances of scientific fraud, inappropriate image manipulation or processing, plagiarism, misrepresentation, duplicate publication and other cases that violate research ethics in submitted manuscripts or published papers. Depending on the outcome of these investigations, the journal may opt to publish errata or corrigenda (see below), or, in cases of serious scientific misconduct, either to ask authors to retract their paper, or to impose retraction on them. In such cases, the authors’ current employers and the research institution of the corresponding author at the time of publication of the paper will also be informed. The journal may also issue an editorial note attached to the paper to alert readers to an ongoing investigation. As a matter of policy, the journal will collaborate with independent institutional investigations into misconduct and, where appropriate, will accept the outcome of such investigations.

All EMBO Press journals are members of the Committee on Publication Ethics (COPE).

Corrigenda, errata, addenda and refutations

Correction and additions to a paper are published at the sole discretion of the editors.

An erratum is notification of a significant error made by the journal that would mislead the readership if left uncorrected.

A corrigendum is notification of a significant error made by the author(s). A corrigendum may include a communication by the authors and/or an editorial statement.

An editorial note may be used to alert readers to a specific issue related to a paper.

An addendum may be published in rare cases where additional data directly relevant to central aspects of a paper emerge and it is apparent that publication would strengthen the paper in question fundamentally. All additional data is subject to peer review.

Refutations of articles published in the journal can be considered for the Correspondence section of the journal. Such correspondence will almost always include data to support the arguments of the correspondent and will have to concern central aspects of a paper. The original authors of the article will be offered the opportunity to respond side-by-side with the correspondence. Both the refutation and the response will be peer reviewed at the discretion of the editor and acceptance depends on the strength of the arguments raised as well as the importance of the matter to a general readership. Publication of the correspondence does not automatically entail publication of a response of the authors of the challenged research paper. After one round of correspondence, the journal will consider the matter closed and will not publish further exchanges.

Data collection and presentation

Presented data must represent the findings in an unbiased, accurate and transparent manner. This includes appropriate statistical analysis and image processing. For further details, please refer to these guidelines.

The Editors reserve the right to request minimally processed versions of figures and the source data that were used to assemble the figure from the authors of a paper under consideration, or of a paper already published in the journal.

Originality and Plagiarism

The editors require that any information published in the journal represents a substantially novel contribution to the scientific record. Any manuscript submitted to the journal should therefore not contain content that has been formally published in a peer reviewed journal or another formally citable manner, whether in print or electronic. This includes websites, blogs and the news media. Recognized, non-peer-reviewed pre-print servers and conference presentations (including summaries) are not considered prior publication (see below).

Subject to licensing restrictions, the journal will consider manuscripts based on information that has been previously discussed by the authors at scientific conferences in the form of posters, talks, abstract books, meeting reports or webcasts. Manuscripts may be posted prior to or at the time of submission on recognised non-peer reviewed pre-publication platforms dedicated to discussion among peers, including the preprint servers bioRXiv, arXiv, PeerJ Preprint and Faculty1000 posters. The details of the preprint server concerned and any accession numbers must be included in the cover letter accompanying submission of the manuscript. The journal will also consider manuscripts based on unpublished academic theses released in accordance with institutional rules. If your institution requires formal publication of your thesis, please contact the editorial office.
 
Any text, data, material, images, ideas or quotes should be attributed to the original source, even if it is by the same authors. If necessary, authors should seek permission to use the material from the copyright holder in accordance to licensing stipulations. The journal's policies on attribution follow the standards set by the Associated Press. It is at the discretion of the editors whether prior publication of such related material prevents subsequent publication in the journal.
 
Plagiarism is the misappropriation of intellectual property and the substantial unattributed textual copying of another's work. The journal uses CrossCheck, a multi-publisher initiative to screen submitted content for plagiarism, to detect overlapping and similar text (including self-plagiarism) prior to publication. To find out more about CrossCheck visit http://www.crossref.org/crosscheck/index.html. If you do reproduce text from other publications, it should be obvious that the text is a quotation and you must cite the source (the journal has no limit on references).

Embargo Policy

The content of papers and any associated press releases is strictly embargoed until the official date of publication of a manuscript. Accepted contributions can be discussed with the media from one week before the publication date provided the journalist respects the embargo date. We will press release selected papers with summaries. Authors may arrange their own publicity, but must adhere to the embargo conditions. Further details can be provided by the editorial office.

Citation

Comprehensive and accurate citation of the relevant literature is essential. We require citation of the primary literature wherever appropriate. There are no limits on the total number of references in the bibliography, and the reference list is not subject to manuscript length format requirements (for details, see below). Similarly, page charges will apply only to the body of a published article, not to the reference list.

Editorial Process

All submissions are initially assessed by a dedicated scientific editor specialised in the scientific topics covered in the manuscript, and may also be evaluated by an appropriate Editorial Advisory Board member, Senior Editor, or another external expert advisor. All research manuscripts and reviews published in the journal are subject to peer-review. Non-research articles, editorial material and commentaries are usually not reviewed, although editors may elect to undertake review in the interest of authoritative and balanced reporting.

Double blind review: As a default, the referees are aware of the identities of the authors and referee names are withheld from authors (single-blind review). We will withhold author names from referees on request by the authors. The authors may chose this option during the submission process, but it is the authors’ responsibility to anonymize their manuscript. The editorial offices will not edit the manuscript files submitted for anonymity and will not alert authors who have chosen the anonymization option, but who have not anonymized the manuscript files. The journal may consult with the referees after conditional acceptance of a manuscript on a de-anonymized manuscript to assess the changes applied in revision.

Research manuscripts judged by the editors to be potentially suitable for publication in the journal with realistic experimental revision are sent out for formal peer review, so that manuscripts with a low probability of success can be returned to the authors without delay. Manuscripts are typically reviewed by three appropriate independent experts selected by the editors. Authors may exclude a small number of experts if they are concerned of a conflict of interest or bias.

Referee Cross-commenting: Referees are routinely invited to comment on each other’s reports and may discuss issues under moderation of the editors. Referees are not informed of each other’s identities.

Based on the arguments and recommendations of the referees, the editors decide whether to offer publication or revision, or whether to reject the manuscript. This decision might involve further consultation with the referees, the Editorial Advisory Board and/or the authors. Revisions are invited only for manuscripts that have a high probability of acceptance after one major round of experimental revision.

‘Scooping’: During the editorial and peer review process and the agreed author revision period, other studies that may appear in the literature are not taken into account in assessing the conceptual advance of a study. Please inform editors once you become aware of other studies directly relevant to your study.

Authors may appeal decisions if there is concrete evidence for a misunderstanding or mistake at the editorial or referee level. Appeals are evaluated in depth and without prejudice.

Transparent Process: The journal makes the editorial process transparent for all accepted manuscripts, by publishing as an online supplementary document (the Review Process File, RPF) all correspondence between authors and the editorial office relevant to the decision process. This will include all referee comments directed to the authors, as well as the authors’ point-by-point responses. Internal communications and informal consultations between editors, editorial advisors or referees will remain excluded from these documents. Importantly, referee anonymity will be strictly maintained. Authors have the possibility to opt out of the transparent process at any stage prior to publication.

To further facilitate transparency, the journal has removed the “Confidential Comments” field from our referee reporting forms. This is to ensure that the authors receive all information pertinent to the decision made on a manuscript. Referees should be aware that all comments will be transmitted to the authors and the other referees. Should there be any issues with the manuscript, in particular concerns about ethical standards, data integrity, biosecurity, or conflicts of an academic or commercial nature that need to be communicated directly and confidentially to the editor, this can be done by email.

Please see the EMBO Press website for more information on these policies.

Transfer policies

The EMBO Press journals are editorially independent from their publishers, one another and EMBO.

Authors can choose to transfer manuscripts rejected from any one of the EMBO Press journals to any other of the EMBO Press journals by following the instructions appended to the editorial decision letter. Manuscripts transferred post-review will automatically include the referees’ reports and identities, and authors are invited to include a point-by-point rebuttal and a revised manuscript as part of the transfer. The editors will aim to use the transferred referee reports in arriving at a rapid decision – they may involve an arbitrating expert, who is asked to adjudicate based on the information provided by the authors and referees. Editors may choose to seek additional advice from referees or editorial advisory board members in cases where this would enhance informed decision-making.

Transfers of manuscripts with referee reports from Journals unrelated to EMBO Press are also possible at the editor’s discretion. If anonymous, authenticated referee reports are available, the editors will aim to work with this information to arrive at a timely decision without entering a de novo review process. This may involve expert advice in an adjudicating function. Please contact the editors to discuss options. EMBO Press is committed to a rapid, efficient and fair editorial process.

 

Manuscript Preparation

Molecular Systems Biology publishes the following article types:

Research Article Submission

YOU DO NOT NEED TO REFORMAT YOUR MANUSCRIPT FOR A FIRST SUBMISSION

The following guidelines refer to Research Articles. While published manuscripts are expected to conform tightly to the following guidelines, this is not a requirement at first submission.

Manuscripts must be written in clear and concise English and be intelligible to a broad readership. Prior to submission, authors may benefit from having their manuscript reviewed for clarity by colleagues and/or by using one of the many English language-editing services that are available.

Text Format

The Editorial Office will only accept text files in RTF or MS Word format. The final character count must be clearly indicated on the title page of the manuscript. Revised manuscripts that do not comply with the formatting guidelines, or exceed the length restrictions, may be returned to the authors for amendment.

Please submit the full text (including figure legends, expanded view figure legends, tables, and references) as a single MS Word or RTF file.

Submitted manuscripts should be divided into the following sections:

  • Title page
  • Abstract
  • Introduction
  • Results
  • Discussion
  • Materials and Methods
  • Acknowledgements
  • Author Contributions
  • Conflict of Interest
  • References
  • Figure Legends
  • Table Legends
  • Expanded View Figure Legends

Title Page

The title should be short and informative, and should not contain any abbreviations (for example, Epithelial-Mesenchymal Transition should not be abbreviated to EMT). However, commonly used gene or protein acronyms are acceptable. The total length of the title should not exceed 100 characters (including spaces). Serial titles are not accepted.

The full name of each author should be given. Multiple first-authorships are acceptable and should be indicated. Numbers in superscript should be used to indicate the department, institution, city with postal code and country, for each author. Any changes of address may also be given in numbered footnotes. It is possible to name more than one author as the correspondent of a published article, although we will by default address all correspondence to the single author listed as Corresponding Author upon submission.

Please provide a running title of no more than 50 characters including spaces.

Up to five keywords, which may or may not appear in the title, should be given in alphabetical order, below the abstract, each separated by a slash (/).

Abstract

This should be a single paragraph not exceeding 175 words. The Abstract should be comprehensible to readers before they have read the paper, and abbreviations should be avoided where possible (as for the title). Reference citations within the abstract are not permitted. The abstract should describe all key novel findings of the study.

Introduction

The Introduction should be succinct and without subheadings. It should provide only the necessary background information, rather than comprise a comprehensive review of the field. Citation of the primary literature is required where appropriate (see section on Citation Policy).

Results

The Results section, and associated figures, tables and Expanded View information, must accurately describe the findings of the study. Figure order should follow the text. Detailed methodological descriptions should be restricted to the Materials and Methods section. ‘Data not shown’ is not permitted (see below): all significant data should be displayed in the main figures or Expanded View information.

Discussion

The Discussion should accurately interpret the results, but not be repetitive with the Results section. Authors are encouraged to discuss their work in the broader context. Related published data must be appropriately discussed and cited. Speculation is allowed but should be clearly labelled as such. For shorter articles, the Results and Discussion sections can be combined.

Materials and methods

This section should contain sufficient detail so that all experimental procedures can be repeated by others, in conjunction with cited references. Reagents must be described in such a way as to allow readers to identify them unequivocally and/or reproduce them. For example, antibodies epitopes should be described and siRNA and other probe sequences must be provided. In cases where detailed methods cannot be described within the length limits of the article, additional Materials and Methods can be included as part of the Expanded View Appendix. This additional information should, however, not be of immediate importance for the understanding of the manuscript, and it is not permissible to move the entire “Materials and methods” section into the Appendix.

Acknowledgements

These should be placed at the end of the text and not in footnotes. Personal acknowledgements should precede those of institutions or agencies. Grant numbers are permissible. Dedications are discouraged.

Author Contribution

The journal requires a statement specifying the contributions of every author. Further details on authorship can be found here.

Conflict of Interest

The journal requires a statement specifying whether or not the authors have a Conflict of Interest (see above for details). In the case of a Conflict of Interest, this must be specified.

References

As a matter of policy, the journal requires the citation of primary literature (over review articles) wherever appropriate. Authors are responsible for the accuracy of the references. Authors are responsible for ensuring that the related literature is accurately and comprehensively discussed and cited. Review articles should only be cited for general background information, the proposal of certain concepts or similar purposes, whereas primary research articles should preferentially be referenced to introduce the question being addressed or to support the conclusions and interpretations of the results. Articles in press can be cited with the explicit permission corresponding author of the study; the journal name has to be included and, where available, the Digital Object Identifier.

Only articles that have been published or that are accepted for publication at a named publication should be cited in the reference list. In the text of the manuscript, a reference should be cited by author and year of publication; no more than two authors may be cited per reference; ‘et al’ should be used if there are more than two authors (i.e. Smith & Jones, 2003; Smith et al, 2000). Papers accepted for publication must be cited with the corresponding author’s permission and should include title and all author names (or initials if any of the authors are co-authors of the present contribution), as well as either the DOI, if available, or the term ‘in press’. In the reference list, citations should be listed in alphabetical order and then chronologically, with the authors’ surnames and initials inverted; where there are more than 20 authors on a paper, the first 20 will be listed, followed by ‘et al.’. Publications by the same author(s) in the same year should be identified with a, b, c after the year of publication. The name of each journal should be abbreviated according to Index Medicus and italicized. References should therefore be listed (and will subsequently appear in print) as follows:

    Akhmedkhanov A, Toniolo P, Zeleniuch-Jacquotte A, Koenig KL, Shore RE (2002) Aspirin and lung cancer in women. Br J Cancer 87: 49-53

Book chapters and books can be cited in the following way:

    Price SR, Oubridge C, Varani G, Nagai K (1998) Preparation of RNA-protein complexes for X-ray crystallography and NMR. In RNA-Protein Interaction: Practical Approach, Smith C (ed) pp 37-74. Oxford: Oxford University Press

    Sambrook J, Fritsch E & Maniatis T (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbour Press, Cold Spring Harbour, New York, USA

Links to online resources and websites should be cited in the text only, and should be available long-term (e.g. permalinks or DOI wherever possible). URLs should not appear in the reference list.

Tables

Tables should be typed on separate sheets and numbered consecutively with Roman numerals (I, II, III, IV,). Tables should be self-explanatory and include a brief descriptive title. Footnotes to tables indicated by lower-case superscript letters are acceptable, but they should not include extensive experimental detail.

Conventions and Abbreviations

In general, the journal follows conventions given in Scientific Style and Format: The CBE Manual for Authors, Editors and Publishers (1994) Cambridge University Press, Cambridge, UK, 6th edn. Please follow Chemical Abstracts and its indexes for chemical names. For guidance in the use of biochemical terminology follow the recommendations issued by the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature. In general, genes and genotypes should be indicated in italics; proteins and phenotypes should not be italicized.

Authors should use approved gene and gene product nomenclature and apply the italicization and capitalization formatting as appropriate for each organism’s standard nomenclature. Please consult the appropriate nomenclature databases for correct gene names and symbols. Some useful general resources are: Entrez Gene (http://www.ncbi.nlm.nih.gov/gene); UniProt (http://www.uniprot.org/).

Try to restrict the use of abbreviations to SI symbols (standard units of measurements) and those recommended by the International Union of Pure and Applied Chemistry (IUPAC). Abbreviations should be defined in brackets after their first mention in the text, not in a list of abbreviations. SI symbols and symbols of chemical elements may be used without definition in the body of the paper. Abbreviations of standard biochemical compounds, e.g. ATP, DNA, nucleotides in nucleic acids, and amino acids in proteins, need not be defined. Common language abbreviations, such as e.g. or i.e., should not be used.

Figures

Figure Legends

Figure legends should contain sufficient information to allow the reader to follow the data presented without referring back to the text, but should not be redundant with the Results section. Each figure must contain a heading, and each panel a subheading. All symbols and abbreviations used in the figure must be defined, unless they are common abbreviations or have already been defined in the text. Experimental details should, where possible, be given in the Materials and Methods section, and not repeated in the figure legends. Figure legends should be formatted such that each panel, or group of panels, has its own entry with the panel letter (or range) on the left and the description on the right. The description of specific panels can be preceded or followed by free text describing features, statistics or values pertinent to all panels.

 

Figure 1 - Generation of hiPSCs from a patient with type-2 long-QT syndrome.

    A  Genetic screening in the patient revealed the heterozygous single-nucleotide mutation Aright arrowT in exon 13 of the KCNH2 gene, in position 2987 of the coding sequence (CDS) (c.A2987T, NM_000238.3), resulting in the substitution of an asparagine with an isoleucine at position 996 of the protein (N996I, NP_000229.1).
    B  The N996I mutation (red dot) is located in the C-terminal of the HERG protein, which is made of six trans-membrane domains (S1-S6), an amino (NH2) domain, a carboxyl (COOH) domain, and a pore (P) region.
    C  Example of a hiPSC colony harbouring the c.A2987T (N996I) KCNH2 mutation (LQT2-hiPSCsN996I). Scale bar: 400 mu;m.
    D  Immunofluorescence analysis of pluripotency markers SSEA4 (green) and NANOG (red) in a representative LQT2-hiPSCN996I clone, with nuclear staining (DNA, blue). The image on the right is a magnification of the area framed in the left image. Scale bars: 100 mu;m (left image); 50 mu;m (right image).

 

Figure Formatting

Figures and Expanded View figures should be presented in the order they are mentioned in the text. Figures use the numbering system Fig 1, while Expanded View figures use the system Fig EV1. The figure count in each is separate, such that there will be both a Fig 1 and a Fig EV1 (and so on) in a manuscript.

The final size of figures will be between 82 mm and 172 mm wide on the printed page. Please bear this in mind when submitting your manuscript for review and allow for sufficient resolution at a suitable size.

Figures divided into parts should be labelled with an upper-case, bold letter (Helvetica Font). Figures with several parts should also be in proportion, with consistently sized lettering so that the whole figure can be reduced by the same amount to the smallest size at which the essential details are visible. Use Courier font for sequence data and Symbol font for any symbols.

All lettering should be done using standard fonts (Helvetica, Times, Symbol, Courier) and retained in a separate layer (if possible) so that the production team can adapt any labels to the journal’s style if necessary. All fonts used for labelling the figures should also be embedded in the final files if the software package offers this option.

Scale bars, rather than magnification factors, should be used, with the length of the bar defined in the legend rather than on the bar itself. In general, visual cues on the figure itself are preferred rather than verbal explanations (for example, ‘broken line’ or ‘filled black triangles’) in the legend.

When preparing figures of microscopy images, please note that we strongly encourage the use of colours that are suitable for colour-blind readers: for example, the use of magenta/green is preferred over red/green for 2-channel images.

For publication, we require PowerPoint, TIFF or EPS files in PC or Macintosh format, preferably from PhotoShop or Illustrator software. We cannot accept Freehand, Canvas, CorelDRAW or MacDrawPro files. These files must be converted to postscript (eps) format. For any figures submitted in photoshop or tiff format we require layered files to be sent whereby all text, arrows or additional attributes are placed on individual layers within the file. For line art/charts/graphs we prefer to work with Adobe Illustrator AI or EPS files. We can also accept high-resolution PDF files.

All colour artwork must be submitted in CMYK colour mode. When converting files from RGB, please consider that the final figures will be printed on coated paper, using Euroscale process inks. If you are not familiar with these specifications, or are not sure how to apply them within your software package, please consult a local graphics expert. Ultimately, it is important that all colours look satisfactory after conversion to CMYK, both on screen and when printed on different printers.

Non-vector graphics should be preserved at high resolution: 300 dpi minimum at final size for greyscale or colour halftone images, and 600 dpi minimum for bitmap (b/w) artwork. Combinations of monochrome and greyscale/photographs should be at 600 dpi.

Further detailed guidelines regarding the preparation of artwork is available to download in this document [pdf].

The journal does not have colour charges for figures, and the authors are therefore welcome to submit full colour figures.

Figure/Data Presentation

Figures must accurately reflect the results of the experiments. Appropriate controls, markers and scale bars should be included in all panels. Statistical tests must be clearly defined and appropriate to the data.

Image Processing
Images submitted with a manuscript for review should be minimally processed (for instance, to add arrows to a micrograph). Authors should retain their unprocessed data and metadata files, as editors may request them to aid in manuscript evaluation. If unprocessed data are unavailable, manuscript evaluation may be stalled until the issue is resolved.

A certain degree of image processing is acceptable for publication (and for some experiments, fields and techniques is unavoidable), but the final image must correctly represent the original data and conform to community standards. The guidelines below will aid in accurate data presentation at the image processing level; authors must also take care to exercise prudence during data acquisition, where misrepresentation must equally be avoided. Where appropriate, manuscripts should include further Methods as part of the Expanded View that describe for each figure the pertinent instrument settings, acquisition conditions and processing changes.

Authors should list all image acquisition tools and image processing software packages used. Authors should document key image-gathering settings and processing manipulations in the Methods.

Images gathered at different times or from different locations should not be combined into a single image, unless it is stated that the resultant image is a product of time-averaged data or a time-lapse sequence. If juxtaposing images is essential, the borders should be clearly demarcated in the figure and described in the legend.

The use of touch-up tools, such as cloning and healing tools in Photoshop, or any feature that deliberately obscures manipulations, is to be avoided.

Processing (such as changing brightness and contrast) is appropriate only when it is applied equally across the entire image and is applied equally to controls. Contrast should not be adjusted so that data disappear. Excessive manipulations, such as processing to emphasize one region in the image at the expense of others (for example, through the use of a biased choice of threshold settings), is inappropriate, as is emphasizing experimental data relative to the control.

When submitting revised final figures upon conditional acceptance, authors may be asked to submit original, minimally processed images.

Electrophoretic gels and blots
Positive and negative controls, as well as molecular size markers, should be included on each gel and blot. For previously characterized antibodies, a citation must be provided. For antibodies less well characterized in the system under study, a detailed characterization that demonstrates not only the specificity of the antibody, but also the range of reactivity of the reagent in the assay, should be published as part of the Expanded View. The display of cropped gels and blots in the main paper is permitted if it improves the clarity and conciseness of the presentation. Cropped gels in the paper must retain all important bands, and space (several band-widths) should be retained above and below the relevant band(s). Vertically sliced images that juxtapose lanes that were non-adjacent in the gel must have a clear separation or a black line delineating the boundary between the gels. Quantitative comparisons between samples on different gels/blots are discouraged; if this is unavoidable, the figure legend must state that the samples derive from the same experiment and that gels/blots were processed in parallel. Loading controls must be run on the same blot. High-contrast gels and blots are discouraged, as overexposure may mask additional bands. Authors should strive for exposures with gray backgrounds. Multiple exposures should be presented in the Expanded View information if high contrast is unavoidable. Immunoblots should be surrounded by a black line to indicate the borders of the blot, if the background is faint. For quantitative comparisons, appropriate reagents, controls and imaging methods with linear signal ranges should be used.

Microscopy
Authors should be prepared to supply the editors with original data on request, at the resolution collected, from which their images were generated. Cells from multiple fields should not be juxtaposed in a single field; instead multiple supporting fields of cells should be shown as part of the Expanded View. Specific guidelines: Adjustments should be applied to the entire image. Threshold manipulation, expansion or contraction of signal ranges and the altering of high signals should be avoided. If ‘Pseudo-colouring’ and nonlinear adjustment (for example ‘gamma changes’) are used, this must be disclosed. Adjustments of individual colour channels are sometimes necessary on ‘merged’ images, but this should be noted in the figure legend. We encourage inclusion of the following with the final revised version of the manuscript for publication: In the Methods, specify the type of equipment (microscopes/objective lenses, cameras, detectors, filter model and batch number) and acquisition software used. Although we appreciate that there is some variation between instruments, equipment settings for critical measurements should also be listed. A further Methods section as part of the Expanded View (or part of a larger Methods section) titled ‘equipment and settings’ should list for each image: acquisition information, including time and space resolution data (xyzt and pixel dimensions); image bit depth; experimental conditions such as temperature and imaging medium; and fluorochromes (excitation and emission wavelengths or ranges, filters, dichroic beamsplitters, if any). The display lookup table (LUT) and the quantitative map between the LUT and the bitmap should be provided, especially when rainbow pseudocolor is used. If the LUT is linear and covers the full range of the data, that should be stated. Processing software should be named and manipulations indicated (such as type of deconvolution, three-dimensional reconstructions, surface and volume rendering, ‘gamma changes’, filtering, thresholding and projection). Authors should state the measured resolution at which an image was acquired and any downstream processing or averaging that enhances the resolution of the image.

Statistical analysis
All statistical analyses performed in the work must be clearly described, including the name of the test performed and the number (n) of independent experiments underlying each analysis. Authors must justify the use of a particular test and explain whether their data conform to the assumptions of the tests. In particular:

  • When using statistical methods based on the normal distribution authors should explain how they tested their data for normality. If the data do not meet the assumptions of the test, then a non-parametric alternative should be used.
  • When making multiple statistical comparisons on a single data set, authors should explain how they adjusted the alpha level to avoid an inflated Type I error rate, or they should select statistical tests appropriate for multiple groups.
  • For each experiment, the number of both technical and biological replicates should be clearly stated. Biological replicates are derived from independent experiments using separately obtained biological samples, while technical replicates are created by repeated measurements on the same biological sample. In general, technical replicates should be averaged before any statistical inference tests are performed.
  • In cases where n is small, appropriate statistical tests should be employed and justified in the text.

Since for complex biological experiments the number of independent repeats of a measurement often has to be limited for practical reasons, statistical measures with a very small n are commonplace. However, statistical measures applied to too small a sample size are not significant and they can suggest a false level of significance. We recommend that the actual individual data from each experiment should be plotted if n < 5, alongside an error bar. In cases where n is small, a justification for the use of the statistical test employed has to be provided. Presenting a single ‘typical result’ of n experiments is sometimes unavoidable, but should be accompanied by an indication of the variability of data between independent experiments. If n is not based on independent experiments (that is, n merely represents replicates of a measurement), statistics may still be useful, but a detailed description of the repeated measurement is required. Figure legends should contain a basic description of n, P, and any relevant statistical tests or error bars.

For more information on the appropriate use of standard deviation, standard error, and confidence intervals please refer to Cumming et al (2007).

Graphs must include clearly labelled error bars for cases where more than two independent experiments have been performed (error bars should not be shown for technical replicates).

Authors must justify the use of a particular test and explain whether their data conform to the assumptions of the tests.

Expanded View (replacing Supplementary Information)

YOU DO NOT NEED TO REFORMAT YOUR MANUSCRIPT FOR A FIRST SUBMISSION.

Please follow the guidelines below when submitting a revision.

EMBO Press journals encourage the inclusion of extra figures in the HTML version of the main manuscript. These figures are presented in an expandable format inline in the main text so that readers who are interested can access them directly as they read in the context of the article. They are also provided for download in a separate PDF to accompany the Article PDF.

Figures appropriate for the Expanded View format are those of particular value to specialist readers, but which are not essential to follow the main thread of the paper for the general reader. Previously, important data would have been difficult to find and access as Supplementary Information. EMBO Press strongly encourages authors to select a limited number (typically 5) of supplementary figures for inclusion in the article proper as Expanded View figures in order to improve their accessibility, visibility and utility. Any extra figures that are not promoted to the Expanded View should be included in a 'traditional' supplementary PDF (along with supplementary text and tables) now called the Appendix.

We intend that by promoting only the essential elements of the supplementary information to be fully integrated in the main manuscript, authors and journals can reduce the often excessive amounts of information that is largely hidden in supplementary information sections. Note that it is explicit policy at all four EMBO Press journals to only include data directly relevant to the scientific claims of the paper.

Our editors will be happy to help you to decide which figures to promote to the Expanded View, or to explain about the Expanded View in more detail. There is no extra typesetting cost for figures that you choose promote in this way. However, please keep in mind the limit of 5 extra figures, unless agreed otherwise with the editor.

Your paper will now include 4 levels of information designed to add more structure and more flexibility to read or browse:

LEVEL 1 (Main manuscript and figures)

Main manuscript text, main figures and simple tables (Figures nomenclature: Figure 1, Table 1 etc.)
UPLOAD using file types: Manuscript File (including main text and tables), Figure File (as separate image files).

LEVEL 2 (Expanded View)

Expanded View figures (Expanded View figure nomenclature: Figure EV1)
[These figures will be displayed in the main HTML of the paper in a collapsible format. They will also be collected by the publisher into a single PDF and made available for download]
UPLOAD as separate image files using the file type Figure File (as for Main Figures, but note the different nomenclature when naming your Expanded View figures in the system).

Expanded View large tables and files (nomenclature: Table EV1, Dataset EV1 etc.)
[These extra files will be collected at the end of the manuscript in the Expanded View section]
UPLOAD as separate files (.txt, .xls., .ZIP etc.) using the file type Expanded View File.

LEVEL 3 (Appendix PDF)

Appendix PDF: Extra figures not promoted to the Expanded View, simple Tables not provided as separate Excel files and extra text (e.g. extra methods) provided in a single PDF (nomenclature to name and refer to Appendix items in the main text: Appendix Figure S1, Appendix Table S1, Appendix Supplementary Methods)
Please use this format for figures/tables/text beyond the limitations set of the main manuscript (level 1) and Expanded View (level 2). The Appendix should begin with a short table of contents.
[The Appendix will be provided at the end of the manuscript at as PDF]
UPLOAD as a single PDF using the file type Expanded View File

LEVEL 4 (Source Data)

Source Data for main figures: Source Data should be uploaded using the Source Data file type to link source data underlying regular figures (level 1) or Expanded View figures (level 2) to the relevant figures. Source Data can include minimally processed version of data presented in figures, numerical data underlying plots or charts, as well as replicates.
UPLOAD as single files using the file type Source Data

Source Data for Expanded View and Appendix figures: We cannot currently link Source Data to Expanded View Figures (level 2) and Appendix files (level 3) for technical reasons. It should therefore be uploaded using the Expanded View File filetype in a single ZIP file containing all the Source Data for Expanded View and Appendix content.
UPLOAD as a single ZIP file containing multiple folders/files relating to individual Expanded View items using the file type Expanded View File

 

To take advantage of the Expanded View

Authors will need to:

1. Select from their current Supplementary Information up to 5 figures for inclusion in the Expanded View.
2. Provide these figures as separate figure files (as for main figures in EPS, TIFF, PPT format etc.) using the file type Figure File in our manuscript submission system.
3. Include the legends for these figures in the main manuscript document file in a section called Expanded View Figure Legends after the main Figure Legends section.
4. Use the nomenclature Figure EV1 (and so on) for the figure legends and making reference to the figures in the text. The figures should be included in numerical sequential order (note that the EV sequence is separate from the sequence for regular figures).

For the figures that are not promoted to Expanded View format, and for supplementary text and tables, we ask authors to provide a single PDF file titled Appendix, containing:

1. A table of contents on the first page
2. Supplementary figures, text and simple tables and their legends (i.e. traditional Supplementary Information)
3. Use the nomenclature Appendix Figure S1, Appendix Table S1, Appendix Supplementary Methods etc. to ensure readers are not confused between Appendix figures and Expanded View figures
4. Reference these items in the manuscript text as: Appendix Figure S1, Appendix Table S1, Appendix Supplementary Methods
5. The Appendix PDF should be uploaded using the file type Expanded View File in our manuscript submission system.

For complex tables (more than 5 columns or 20 rows), datasets, computer code and so on, authors are asked to supply individual ZIP files using the nomenclature: Dataset EV1, Table EV1 and so on. Each ZIP file should contain the data file (movie, excel file, computer code) AND a separate plain text README file with item title and description. Submit these using the file type Expanded View File in our manuscript submission system.

Source data for Expanded View figures, Appendix content and individual files should be provided in a single ZIP file called Source Data for Expanded View and Appendix. Within the ZIP file, the Source Data should be included in individual folders pertaining to the figure/table that the Source Data is for. Submit this using the file type Expanded View File in our manuscript submission system.

 

File naming conventions

Files should be named based on manuscript number, file type and sequence position as in the following examples. Your Manuscript ID can be seen at the top of the page when you begin submission.

manuscriptID_Fig1.tiff
manuscriptID_SourceDataForFigure1A-F.PDF
manuscriptID_SourceDataForFigure2E.xls
manuscriptID_FigEV1.tiff
manuscriptID_MovieEV1.zip
manuscriptID_DatasetEV1.zip
manuscriptID_ComputerCodeEV1.zip
manuscriptID_Appendix.PDF
manuscriptID_SourceDataForExpandedView.zip

Unpublished Data

The journal does not permit citation of “Data not shown”. All data referred to in the paper should be displayed in the main or Expanded View figures. “Unpublished observations” may be referred to in exceptional cases, where these are data peripheral to the major message of the paper and are intended to form part of a future or separate study. Personal communications (Author name(s), personal communications) must be authorised in writing by those involved, and the authorisation sent to the editorial office at time of submission. Care should be taken that embargo policies are not contravened. References to manuscripts in preparation or submitted, but not yet accepted, should be cited in the text as (Author names(s), in preparation), and should not be included in the list of references. Copies of such manuscripts should be enclosed at submission for reviewing purposes where relevant, as should manuscripts in press, which should be cited in the reference list (see above)

Data deposition

Large-scale datasets, sequences, atomic coordinates and computational models should be deposited in one of the relevant public databases prior to submission (provided private access is available at the database) and authors should include accession codes in the Materials & Methods section. The suggested wording for referring to accession identifiers in a manuscript is the following: “The [protein interaction | microarray | mass spectrometry ] data from this publication have been submitted to the [name of the database] database [URL] and assigned the identifier [accession | permalink | hashtag ].” If necessary, please include in the manuscript the relevant information (username and password) for confidential access by peer-reviewers.

Data for which no suitable public database exists should be included, if possible, as dataset files in the Expanded View. In cases where data can not be confidentially deposited in a public database, and is too large to be included in the Expanded View, please contact the editorial office for advice on how to make these data available for refereeing purposes.

Functional genomics data

Microarray and sequencing-based functional genomics data should be deposited in the ArrayExpress (http://www.ebi.ac.uk/arrayexpress/), GEO (http://www.ncbi.nlm.nih.gov/geo/) or CIBEX (http://cibex.nig.ac.jp/index.jsp) databases in compliance to the MIAME (http://www.mged.org/Workgroups/MIAME/miame.html) standards and the MINSEQE (http://www.mged.org/minseqe/) draft proposal.

Proteomics, metabolomics and molecular interactions

Mass spectrometry datasets should be deposited in a machine-readable format (e.g. mzML if possible) in one of the major public database, for example Pride (http://www.ebi.ac.uk/pride/) or PeptideAtlas (http://www.peptideatlas.org) and authors should follow the MIAPE recommendations (http://www.psidev.info/index.php?q=node/91).

Molecular interaction data should be deposited with a member of the International Molecular Exchange Consortium (IMEx, http://www.imexconsortium.org) prior to submission of the manuscript. Authors should follow the MIMIx recommendations (http://www.psidev.info/index.php?q=node/278).

Metabolomics data should be deposited following the recommendations of the Metabolomics Standards Initiative (MSI) (http://metabolomicssociety.org/index.php/resources/metabolomics-standards) in a recognised repository such as MetaboLights (http://www.ebi.ac.uk/metabolights/).

Sequence data

Nucleotide sequence data should be submitted to an International Nucleotide Sequence Database Collaboration member: GenBank (http://www.ncbi.nlm.nih.gov/genbank/), EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) or DDBJ (http://www.ddbj.nig.ac.jp/).

Structural data

The journal accepts and follows the recommendations of the International Union of Crystallography (IUCr), with regard to the deposition and release of macromolecular structural data. These guidelines are set out in the article by the IUCr Commission on Biological Macromolecules in Acta Crystallographica (2000), D56, 2. In summary, they state that all publications must be accompanied by deposition of both the atomic coordinates and the structure-factor amplitudes in the appropriate database (PDB or NDB). In the case of low-resolution structures for which only a chain trace is reported, a set of C alpha positions and structure-factor amplitudes may be sufficient.

For NMR structures, data deposited should include resonance assignments, and all restraints used in structure determination (NOEs, spin-spin coupling constants, amide exchange rates, etc) and the derived atomic coordinates for both an individual structure and for a family of acceptable structures.

Structures of biological macromolecules solved by electron microscopy must be submitted to the EMDB database at http://emdatabank.org. For a brief description of the database, see Lawson et al. (2011) Nucleic Acids Res. 39: D456-D464.

Human clinical and genomic datasets

The journal encourages authors to provide access to genotype and clinical data with as few restrictions as possible while respecting ethical obligations to the patients and relevant medical and legal issues. If practically possible and compatible with the individual consent agreement used in the study, such data should be deposited in one of the major public access-controlled repositories such as dbGAP (http://www.ncbi.nlm.nih.gov/gap) or EGA (http://www.ebi.ac.uk/ega). Simple genetic polymorphisms should be submitted to dbSNP (http://www.ncbi.nlm.nih.gov/SNP/).

Right click to download and complete the author checklist here.

 

Other Article Types

Reports

Reports are short publications focusing on a particularly provocative and novel aspect of a study. They should have an Abstract phrased in terms that are comprehensible to readers outside the discipline. Results and Discussion sections can be combined. The remaining sections are organized as described above for Articles.

 

The total character count (including spaces) for Reports, excluding the Methods section, tables and Expanded View material, but including title page, abstract, figure legends and references should not exceed 22,000 characters (the exact character count to be stated on the title page). Reports have, in principle, a maximum of 3 Figures.

In all other regards, reports should follow the same instructions as Research Articles.

Reviews

Review articles aim to provide accessible, authoritative overviews of a field or topic. Reviews should communicate a sense of enthusiasm, weaving background information with the latest advances, and placing both of these elements in the context of the rest of the field. The readership of Molecular Systems Biology encompasses a wide range – from advanced undergraduate and graduate students to group leaders and professors. Technical terms and specialist jargon should be avoided or clearly defined.

 

Reviews are usually commissioned but can also be submitted. After submission, all articles are refereed.

The main text should be about 5,000 words. References should be limited to ~100 for a long Review concentrating on significant original research papers. Referencing guidelines are the same as for Research Articles.

Perspective

Perspective papers provide a platform to expose hypotheses and concepts that open up new avenues in Systems and Synthetic Biology. A Perspective paper has a more focused scope than a Review in the sense that it may highlight the work of a single laboratory and may present a particular viewpoint on a field.

 

This format can also accommodate proposals, in which existing knowledge is used to delineate the plan of an ambitious project that would provide decisive and novel insight in the fields of Systems and Synthetic Biology. The proposed goal has to be highly original and of broad interest to the community. A proposal should detail the various aspects of the project such as its objectives, main concrete steps and milestones, utility and implications while in development and after completion.

Perspectives are usually commissioned but can also be submitted. After submission, all articles are refereed.

The main text should be about 5,000 words. References should be limited to ~100. Referencing guidelines are the same as for research articles.

News & Views

Molecular Systems Biology’s News & Views section provides a forum in which scientific news can be communicated to a wide audience spanning the varied disciplines covered in systems biology. News & Views articles are short (usually 800-900 words), and have as much in common with journalistic news reports as the formal scientific literature. They should therefore make clear the news and opinions being discussed, and communicate a sense of excitement, yet provide a critical evaluation of the research or approach concerned. Referencing guidelines are the same as for research articles.

 

Correspondence

A Correspondence is a flexible format that may include anything of interest to the journal’s readers, from policy debates to announcements to ‘matters arising’ from research papers. A Correspondence may describe primary research data, but only one Figure and one Table are allowed. A Correspondence has no abstract and should be limited to 1000 words in principle. The number of references should not exceed 10 for either the Correspondence or its Reply. Expanded View information can in principle only be in the form of structured data or dataset files.

 

Authors must submit a competing financial interests statement, which is printed only if they declare that they have competing interests. In cases where a Correspondence is critical of a previous research paper, the authors are normally given the option of publishing a brief reply. Criticism of opinions or other secondary matter does not involve an automatic right of reply.

Refutations and commentaries on previously published articles are always peer reviewed. Other types of Correspondence may be peer reviewed at the editors' discretion. Referencing guidelines are the same as for research articles.

 

Submission

Presubmission Enquiries

Presubmission enquires allow authors to receive rapid feedback on whether a manuscript in preparation is likely to be of interest to the journal. Presubmission enquiries should be submitted via our online submission system (http://msb.msubmit.net) or by e-mail and should minimally include a list of all authors, a cover letter and an abstract.

If you have already prepared a manuscript, you should submit this via our online system as an article, rather than sending a presubmission enquiry. This allows the editors to make a more informed decision as to whether or not the manuscript is potentially appropriate for the journal. Initial editorial assessment of full submissions is usually rapid, with an average decision time of four days. Full manuscripts should not have been submitted elsewhere, even if they are sent as a presubmission enquiry.

How to Submit

YOU DO NOT NEED TO REFORMAT YOUR MANUSCRIPT AT FIRST SUBMISSION

We use an online manuscript submission and tracking system: http://msb.msubmit.net

In order to submit, you must have registered for an account (on any of the four EMBO Press journals). After this, please consult the following instrutions for submission via our secure server. Please be sure that your browser is set to accept cookies. Our tracking system requires cookies for proper operation.

Please refrain from submitting your manuscript by e-mail attachment.

For original submissions, you will need to upload a cover letter, a Word file of the text of the manuscript (including figure legends), and a PDF file containing all the figures. Alternatively, individual figure files can be uploaded separately, but please note that this can be more time-consuming than a PDF submission. You can also submit all of these files within a single ZIP file. The system will expand it for you. Additional Expanded View files can also be uploaded when applicable (please refer to the section ‘Expanded View’ above).

Once you have submitted your files and the conversion is in progress, it can take up to 30 minutes before the PDF, created in the conversion process, is ready for approval. Please contact the editorial office if the conversion engine takes longer than this. It is important to check the quality of the figures in the converted PDF before approving the submission. You can also upload your own PDF for each file if this is faster and/or provides the quality you require. Please remember that your manuscript will not be submitted until you have approved the converted or uploaded PDF files.

To avoid any unnecessary delays, please refer to the most current electronic formatting guidelines when preparing your manuscript for submission. Authors using computer systems with non-Western type encoding are strongly encouraged to eliminate all occurrences of non-standard fonts in both the manuscript and the figures. We suggest using only the fonts Times, Symbol, Courier and Helvetica.

We will acknowledge receipt of a submitted manuscript by e-mail to the Corresponding author as soon as the quality check (appropriate manuscript format and image quality) has been completed. All further correspondence will also be by e-mail. Please ensure that your servers are set up to allow e-mails from the journal, and contact us if you do not receive an acknowledgement e-mail within a few days of submission.

Manuscript Status

You can check the status of your manuscript at any time in the review process by:

  1. Accessing the system with your password or link sent to you in the acknowledgement e-mail.
  2. Clicking on the link represented by your manuscript tracking number and abbreviated title.
  3. Clicking on the “Check Status” link at the bottom of the displayed page.

This procedure will display tracking information about where your manuscript is in the submission/peer review process.

Please feel free to contact the editorial office with status queries.

Submission of Revisions

When a manuscript is returned to authors for revision, the revised version should be submitted within three months of the authors’ receipt of the referee reports, unless another date is specified in the decision letter. Please contact the editor by the deadline in cases where extra time is required for revision. Additional time may be granted upon request at the Editors’ discretion, assuming the conceptual advance of the study stands (with regard to the current literature). As a matter of policy, we do not consider any competing manuscripts published during the specified revision period as negatively impacting on the conceptual advance presented by your study. However, we request that you contact the editor as soon as possible upon publication of any related work, to discuss how to proceed. Only a single round of revision is generally permitted. The initial decision letter on the original version of the manuscript provides a URL that should be used for submission of revised manuscripts. Please do not upload revisions as new submissions.

Revisions should be accompanied by a point-by-point response to the referees’ comments and editorial decision letter, in PDF or Word format. To facilitate the re-evaluation, we encourage authors to intercalate their response with the referee comments.

Revisions must also be accompanied by a completed author checklist. Right click to download and complete the author checklist here.

At this stage, you must also conform for our formatting guidelines.

 

For Acceptance and Publication

Before acceptance and transfer to our publishers, manuscripts will be checked for appropriate formatting and image processing, and for plagiarism. We cannot proceed to acceptance until data are available in public databases when required; see above for details.

Speed of publication

The journal aims for rapid publication of papers, usually within 15 to 20 working days. Please help the Editors and publisher avoid delays by providing current e-mail address(es), telephone and fax numbers at which author(s) can be contacted.

The journal offers a fast-track (10 working day) publication route for manuscripts under competition. Please notify the editor as soon as possible in such circumstances.

Proofs

Authors will be sent an e-mail with a link to access and annotate their proof. It is the authors’ responsibility to check that the final proof is accurate. In the interests of speed, corrections should be submitted within 24 hours. If you have any trouble submitting corrections through the system, please contact the production office immediately. Essential changes of an extensive nature may be made only by insertion of a ‘Note added in proof’, and only with the approval of the Editors. A charge will be made to authors who insist on extensive amendment within the text at the page proof stage. Excessive alterations may delay publication of the article.

Press Embargo

When discussing unpublished data (including data in accepted papers not yet published) with the press, authors should take care not to break the journal embargo policy (see above for details)

Open Access and Charges

The journal levies an Article Processing Charge (APC) of 2,950 EUROS (3,900 USD/GBP 2,500) for Research Articles or Reports accepted for publication. There are no additional costs (such as page charges or submission charges).

No charges apply for Reviews, News & Views, Perspectives or Correspondence.

At revision stage, authors are prompted by the system to fill in their funding and payment details.

We will automatically waive or discount charges for corresponding authors working in countries covered by the Research4Life Initiative (see the Wiley Open Access Waiver Country List). In exceptional circumstances charges may be reduced for authors who can provide evidence that they are unable to pay the fees.

Upon acceptance, the corresponding author will receive instructions by email for completing the relevant license forms.

Processing of an accepted manuscript for publication can only proceed once the funding and payment details have been provided via the system and the licence to publish has been returned.

Authors who receive funding from an agency or institution with a Wiley Open Access Account do not pay directly - the charge is paid by the institution or funder. Authors whose institutions have paid the Wiley Open Access partner fee are eligible for a discount on the publication charge - on acceptance a discounted fee is payable by the author. Please see additional details on the online payment page when you submit your revised manuscript.

The journal's articles are freely accessible to all via the Internet and are also deposited immediately upon publication, without embargo, to the Open Access repository PubMed Central.

Copyright on any article published by the journal is retained by the author(s).

The journal publishes articles under the Creative Commons Attribution CC BY 4.0 License. This license permits users to access, download, copy, display and redistribute the journal's articles, as well as adapt, translate, text- and data-mine the content subject to the following conditions:

  • The authors' moral rights are not compromised. These rights include the right of "paternity" (also known as "attribution" - the right for the author to be identified as such) and "integrity" (the right for the author not to have the work altered in such a way that the author's reputation or integrity may be impugned).
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Please note that any file labeled “Source Data”, “Dataset” or “Resource” is released under a Creative Commons CC0 1.0 Universal Licence. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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EMBO Press and its publishers assign a unique digital object identifier (DOI) to every article it publishes. The DOI initiative is an international effort for electronic content identification and is guided by the International DOI Foundation, composed primarily of academic publishers and societies. The DOI appears on the title page of the article. It is assigned after the article has been accepted for publication and persists throughout the lifetime of the article. It is important to include the article’s DOI in the reference, as volume and page information is not always available for articles published online.

 

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If you need additional help, you can click on the help signs (icon) spread throughout the system. A help dialogue will pop up with context sensitive help. For questions regarding our policies and guidelines, please contact Molecular Systems Biology editorial office (msb@embo.org).