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Author Guidelines

About The EMBO Journal

Editorial Policies

Manuscript Preparation

General Formatting Guidelines

Submission

For Acceptance and Publication

Help and Contact

 

About the Journal

Aims and Scope

Launched in 1982, The EMBO Journal is an international print and online publication dedicated to rapid publication of research papers in all areas of molecular biology. The Journal is one of four journals owned and run by the European Molecular Biology Organization (EMBO) and published through EMBO Press with support from Wiley and HighWire Press.

The EMBO Journal publishes full-length papers describing original research in all areas of molecular biology, with an emphasis on mechanistic insight and physiological significance. Manuscripts will be selected on the basis of conceptual advance, general interest and technical quality.

As a guide, the journal welcomes submission of articles on the following biological processes, investigated at any level of organization (from the structural and molecular through to the organismal) and in any model system (including plants and micro-organisms):

  • Ageing
  • Autophagy
  • Cancer
  • Cell Adhesion, Polarity & Cytoskeleton
  • Cell Cycle
  • Cell Death
  • Developmental Biology
  • DNA Replication, Repair & Recombination
  • Chromatin, Epigenetics & Genomics
  • Immunology
  • Membrane & Intracellular Transport
  • Metabolism
  • Microbiology, Virology & Host Pathogen Interaction
  • Molecular Biology of Disease
  • Neuroscience
  • Plant Biology
  • Post-translational Modifications, Proteolysis & Proteomics
  • RNA Biology
  • Signal Transduction
  • Stem Cells
  • Structural Biology
  • Systems, Chemical & Computational Biology
  • Transcription
  • Protein Biosynthesis & Quality Control
  • Vascular Biology

For papers submitted from January 2009 onwards, The EMBO Journal will make the editorial process transparent for all accepted manuscripts by publishing as an online supplementary document containing 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. 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.

Authors of accepted peer-reviewed original articles may choose to pay a fee in order for their published article to be made freely accessible to all immediately upon publication. Please visit the section on Charges below.

Article Types

The EMBO Journal publishes the following article types:

Research Articles

Full-length original research papers, reporting novel findings in all molecular biology-related fields. Papers are assessed with regard to mechanistic insight, physiological relevance, and the level of conceptual advance.

Reviews

Focus Issue Reviews - Series of commissioned reviews highlighting diverse aspects of a topical biological theme.

EMBO Member Reviews - Reviews contributed by newly elected EMBO Members, providing an overview of the current state and future directions of the Member’s field.

Have You Seen?

Commissioned short commentaries on specific articles, discussing the advance and the broader implications of the respective study.

Editorials

Policies, news and comment.

Correspondence

Correspondence concerning the validity of data or its interpretation in articles published in The EMBO Journal (see below for further information).
 

 

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 to The EMBO Journal, 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 EMBO Journal reserves the right not to publish material that has already been pre-published (either in electronic or other media). The EMBO Journal does allow prior publication on recognized community preprint servers (e.g. arXiv or Nature Precedings) for review by other scientists in the field before formal submission to the journal. The details of the preprint server concerned and any accession numbers must be included in the cover letter accompanying submission of the manuscript.

Authorship Guidelines

Submission of a paper implies that all authors have seen and approved the manuscript and its contents, and that they are aware of the responsibilities connected to authorship. 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 receipt of a new manuscript and upon acceptance of a manuscript, but the editorial office corresponds only with the Corresponding Author, whose responsibility it is to communicate with all other authors.

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, http://www.icmje.org/ethical_1author.html).

Use of living organisms

For Research Articles submitted to The EMBO Journal 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.

Animal welfare

For experiments involving animals, authors must include with their submission a statement that the experiments have been approved by the appropriate review board and conform to local laws and regulations. The editors reserve the right to consult with board members or external experts and to reject manuscripts that contain experiments with animals which do not adhere to internationally accepted standards for animal welfare. For further information see the International Guiding Principles for Biomedical Research Involving Animals (1985) from CIOMS and the European Commission's legislation and guidance on laboratory animals.

Human Subjects

For experiments involving human subjects, authors must include with their submission 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 NIH Belmont report. Editors or referees may request further documentation confirming that this is the case. Additionally, authors must identify the institutional committee that approved the experiments. The editors reserve the right to consult appropriate board members or external experts.

Any restrictions on the availability or use of human data or samples should be clearly specified in the manuscript. Such restrictions may undermine reproducibility and violate the journal's materials & data sharing guidelines. Any restrictions that might detract from the overall impact of a study and that are central to the findings reported will be taken into account in the editorial decision. 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.

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. 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.

Availability of published material and data

It is understood that by publishing a paper in The EMBO 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 EMBO 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).

Conflicts of interest

In the interests of transparency and to help editors and reviewers assess any potential bias, The EMBO 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 of The EMBO Journal is strongly committed to maintaining high standards of integrity of the published scientific record. The journal requests that authors take note of and adhere to 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, plagiarism, duplicate publication and other cases that violate research ethics. Depending on the outcome of these investigations, the journal may opt to publish errata or corrigenda, 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’ employers may also be contacted. As a matter of policy, the journal will collaborate with independent institutional investigations into misconduct and usually accept the outcome of such investigations.

An erratum is notification of an important error made by the journal, whereas a corrigendum is notification of an important error made by the author(s).

Refutations of articles published in The EMBO 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. The original authors of that article will be offered the opportunity to respond side-by-side with the correspondence. Both pieces 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 EMBO Journal will consider the matter closed and will not publish further exchanges.

The EMBO Journal is a member of the Committee on Publication Ethics (COPE).

Data collection and presentation

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

The Editors reserve the right to request original 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 EMBO 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 EMBO 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.

Subject to licensing restrictions, The EMBO Journal will consider for publication 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 submission on recognised non-peer reviewed pre-publication platforms dedicated to discussion among peers, including the preprint servers bioRXiv and arXiv, 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 EMBO Journal will also consider manuscripts based on unpublished academic theses released in accordance with institutional rules.
 
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 EMBO 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 includes both the theft or misappropriation of intellectual property and the substantial unattributed textual copying of another's work. The EMBO 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.html.

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 (contact@embojournal.org).

Citation

Comprehensive and accurate citation of the relevant literature is essential. We require citation of the primary literature wherever appropriate. To enable this, we have removed any limits on the total number of references in the bibliography, and the reference list is no longer 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 in-house editor specialised in the scientific topics covered in the manuscript, and may also be evaluated by an appropriate Editorial Advisory Board member, or other external expert advisor. Only manuscripts judged by the editors to be potentially suitable for publication in The EMBO Journal 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 generally reviewed by three appropriate experts selected by the editors. Based on their arguments and recommendations, the decision concerning publication, revision or rejection is taken, sometimes after further consultation with the referees, the editorial advisory board or indeed the authors. Revisions are invited only for manuscripts that have a high probability of acceptance after one major round of revision. 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.

The EMBO Journal makes the editorial process transparent for all accepted manuscripts, by publishing as an online supplementary document (the Peer Review Process File, PRPF) 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 EMBO 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 (contact@embojournal.org).

Please see the following editorials for more information on these policies.
The EMBO Journal 2009: New Initiatives
A Transparent Black Box

Transfer policies

The EMBO Journal is editorially independent of its publishers and of the other EMBO Scientific Publications.
Authors can choose to transfer manuscripts rejected from The EMBO Journal to any of the other three EMBO Publications (EMBO reports, Molecular Systems Biology, EMBO Molecular Medicine) by following the instructions appended to the editorial decision letter. Manuscripts transferred post-review will automatically include the referees’ reports and identities, and the editors will aim to use these reports in arriving at a rapid decision. Editors may choose to seek additional advice from referees or editorial advisory board members in cases where this would enhance informed decision-making.

 

Manuscript Preparation

General Guidelines for Submission

The following guidelines refer to Research Articles, although many also apply to other, commissioned, article types. The Editors reserve the right to return manuscripts that are not in accordance with the following instructions. However, manuscript will not be rejected out of hand for format reasons: 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.

Manuscripts for primary research articles can be up to approximately 55,000 characters (including spaces) in length. This includes title page, abstract and figure legends, but excludes references, tables and Expanded View material. Articles can include up to 9 figures.

Manuscript Format

Text

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
  • Figures
  • Tables
  • Expanded View (replaces Supplementary Information)

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 Citations).

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.

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. 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 online supplement.

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

Conflict of Interest

The EMBO 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 EMBO 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. Reference formatting information can be found here.

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. For example:

 

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).

Expanded View (replacing Supplementary Information)

[Note: authors do NOT need to reformat their manuscript at first submission. The guidelines below are to be followed when submitting a revision.]

All data and information that are essential to support the scientific arguments made in the paper should be presented in figures that will be included in the main paper. Figures, tables or text sections that are not required by the general reader to understand the principle findings of the paper and that would disrupt the flow of paper should be submitted as 'Expanded View', which will be displayed in collapsible form and will replace Supplementary Information.

The printed article must be complete and self-explanatory without the Expanded View content. Please refer to each Expanded View item in the body of the text or the figure legends. You should also include the text “Expanded View information is available at The EMBO Journal Online’ at the end of the article and before the references.

Expanded View Figures, tables or text represent an integral part of the published paper and benefit from the same peer-review and editorial production process as the other sections of the paper. Please note the Expanded View items are restricted to information essential to support the scientific arguments made in the paper. Peripheral, tangential or further reaching data and information should not be presented. Reference to 'data not shown' is discouraged'.

Expanded View items (Figures, Tables, Text) are displayed inline in the HTML version of the paper and are individually expandable/collapsible [note: currently files are linked to for download but full HTML rendering will come in the near future].

The article should be self-explanatory without the Expanded View sections. The scope of Expanded View sections should therefore be limited to the following categories:

  • controls and results from technical optimization experiments
  • replication or confirmation of previous results
  • negative results
  • extended methods and detailed protocols
  • mathematical demonstrations, algorithms, computer code and models
  • datasets

Note that controls and replicates to directly support the data presented in a figure should be supplied as 'Source Data' file linked to the relevant figure.

All Expanded View items should be cited in the text as "Figure E1", "Figure E2", Table E1", "Table E2", etc..., throughout the text.

Every Expanded View item should be accompanied by a legend that explains the content of the item. Expanded View legends should simply be included in the main manuscript file after the legends to the Figures and use the conventional format:

  • "Figure E1. Title of the item. Explanatory legend."

Each Expanded View item should in principle be supplied as an individual file. If this is not possible due to the nature of the information provided in Expanded View and the way it needs to be presented, a single PDF file (including a Table of Contents) can also be provided in exceptional cases and in agreement with the editors.

The following formats are accepted:

  • Expanded View Figure: jpg, gif, tiff, eps, pdf
  • Expanded View Tables (less than 50 rows): Word, Excel
  • Expanded View Text: Word, LaTeX
  • Expanded View Datasets and large tables (more than 50 rows): Excel, tab-delimited text, comma-separated values (csv), XML
  • Expanded View Code and Models: plain text, XML, ZIP compressed archives (including a README text file at the top level to detail the content and nature of each file included in the archive)
  • Expanded View Movie: mpeg, mov, avi

For the PDF version of the article, all displayable Expanded View items (Figures, Text and small tables) are automatically converted into PDF format and appended to the end of the article as part of a single downloadable 'PDF+' file. Files marked 'PDF' display the paper without Expandable View Items.

Unpublished Data

The EMBO 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 below)

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.

General Formatting Guidelines

Text

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. 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, tables, and references) as a single MS Word or RTF file.

Figures

Figures and Expanded View figures should be presented in the order they are mentioned in the text.

Figures should be labelled in consecutive Arabic numerals. 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 use TIFF and 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 1,000 dpi minimum for bitmap (b/w) artwork.

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

The EMBO Journal does not have colour charges for figures, and the authors are therefore welcome to submit full colour figures. Details on page charges can be found in the Charges section below.

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. All digitized images submitted with the final revision of the manuscript must be of high quality and have resolutions of at least 300 d.p.i. for colour, 600 d.p.i. for greyscale and 1,200 d.p.i. for line art.

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, as described in this guide.

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, unprocessed 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
The description of all reported data that includes statistical testing must state the name of the statistical test used to generate error bars and P values, the number (n) of independent experiments underlying each data point (not replicate measures of one sample), and the actual P value for each test (not merely ‘significant’ or ‘P < 0.05’). Descriptive statistics should include a clearly labelled measure of centre (such as the mean or the median), and a clearly labelled measure of variability (such as standard deviation or range). Ranges are more appropriate than standard deviations or standard errors for small data sets. Standard error or confidence interval is appropriate to compare data to a control. Graphs must include clearly labelled error bars for cases where more than two independent experiments have been performed (error bars for replicate samples are less useful). Authors must state whether a number that follows the ± sign is a standard error (s.e.m.) or a standard deviation (s.d.) Figure legends should contain a basic description of n, P and the test applied, and the Methods should contain further discussion of statistical methodology. 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.

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

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.

References

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.

 

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 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).

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 EMBO 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.

 

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://emboj.msubmit.net) or by e-mail (contact@embojournal.org) and should minimally include a list of all authors, a cover letter and an abstract.

If you have already prepared a manuscript, please 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 at The EMBO Journal is usually rapid, with an average decision time of four days (details of our handling statistics can be found here).

How to Submit

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

In order to submit, you must have registered for an account. 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. 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 [contact@embojournal.org] 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. Please remember that your manuscript will not be submitted until you have approved the converted 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 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 [contact@embojournal.org] 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 as well as the editorial decision letter, in PDF or Word format. To facilitate the re-evaluation, we encourage authors to intercalate their response with the referee comments.

 

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, using Advance Online Publication of every paper to expedite the process. 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.

Proofs

Authors will be sent an e-mail with a link to download their proof. It is the authors’ responsibility to check that the final proof is accurate. In the interests of speed, corrections should be returned within 24 hours. 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)

Charges

The pricing structure for The EMBO Journal for page and colour charges has been consolidated into a single processing fee called Page Charge, applicable for all articles submitted on or after 1st March 2011. This covers some of the costs of processing and producing the article for online and print publication. After final layout for publication, each page of an article will occur a fixed charge of 185 EUROS (other currencies are accepted). There are no additional charges for colour, and - in line with our citation policies - we will not charge for reference only pages.

It should be noted that the new page charges generate a similar income to the previous charges (page and colour printing) combined, and that these charges had not changed for five years.

20% VAT will be added to the total page charge amount upon invoicing. This also applies to all EU authors who do not provide a valid VAT number upon returning this form.

Please note that if EMBO OPEN is chosen, in addition to the page charges an Article Processing Charge of $3,900 will apply.

Open Access & Self Archiving

Authors of original research articles are encouraged to submit the author’s version of the accepted paper (the unedited manuscript) to their funding body’s archive, for public release six months after publication. In addition, authors are encouraged to archive this version of the manuscript in their institution’s repositories and on their personal websites, also six months after the original publication. This is in line with EMBO Press’ self-archiving policy.

Authors of research articles can also opt to pay an article processing charge of $3,900 (+VAT where applicable) for their accepted articles to be open access online immediately upon publication. By paying this charge authors are also permitted to post the final, published PDF of their article on a website, institutional repository or other free public server, immediately on publication.

Please note that EMBO OPEN charges will have to be levied in addition to the page charges, in order to cover some of the costs associated with the production process for a paper.

EMBO Press’ publishing policies ensure that authors can fully comply with the public access requirements of the major funding bodies worldwide - please see www.sherpa.ac.uk for more information. However, it is the author’s responsibility to take the necessary actions to achieve compliance. These may include self archiving, opting into EMBO Press' manuscript deposition service and / or choosing open access publication.

Author licence agreement

The corresponding author must complete and sign the Licence to Publish form upon acceptance of the manuscript. Failure to do so will result in delays to the publication of your paper. The corresponding author will receive instructions in the decision letter sent from the journal. Signing the license will involve following a link to the Wiley Online Author Serivces system.

EMBO Press does not require authors of original research papers to assign release copyright of their published contributions. Authors grant EMBO Press and its publishers an exclusive licence to publish, in return for which they can re-use their papers in their future printed work. Authors are encouraged to submit their version of the accepted, peer-reviewed manuscript to their funding body’s archive, for public release six months after publication. In addition, authors are encouraged to archive their version of the manuscript in their institution’s repositories (as well as on their personal websites), also six months after the original publication. Authors should cite the publication reference and DOI number on any deposited version, and provide a link from it to the published article. This policy is consistent with the policies of the US National Institutes of Health, the Wellcome Trust and other research funding bodies around the world. EMBO Press and its publishers recognise the efforts of funding bodies to increase access of the research they fund, and strongly encourage authors to participate in such efforts. Upon submission, authors of original research articles can opt for EMBO Press and its publishers to deposit their author accepted paper on PMC and UKPMC via the manuscript deposition service automatically after six months.

After 12 months all articles in The EMBO Journal will be converted to open access on PubMedCentral in their final published form.

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Under the Creative Commons Attribution 3.0 Unported Licence (CC BY), users are free to share (copy, distribute and transmit) and to adapt (edit, rewrite or remix) the contribution including for commercial purposes, but with formal attribution. Users must attribute the contribution in the manner specified by the author or licensor (but not in any way that suggests that they or their use of the contribution is endorsed by the author or licensor). (see full legal code at http://creativecommons.org/licenses/by/3.0/)

The use of the CC-BY licence is mandatory for open access publication by recipients of funding from Research Councils UK (RCUK) and the Wellcome Trust after April 2013.

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None of these Creative Commons Licence impairs or restricts the author’s moral rights. Additionally, the following terms hold:

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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 (legal code at http://creativecommons.org/publicdomain/zero/1.0). This allows unrestricted re-use without the explicit requirement of attribution. We encourage attribution where this is warranted by good scholarly practice.

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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.

 

Help and Contact

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. Should further assistance be required, then please contact MTS help. For questions regarding our policies and guidelines, please contact The EMBO Journal editorial office (contact@embojournal.org).