Submitting your work to the JCI

The Journal of Clinical Investigation (JCI) is a general-interest biomedical journal with a broad readership. Among top-tier research journals, the JCI is alone in providing barrier-free online access to its research articles, and it has done so since 1996. The JCI is the publication of the American Society for Clinical Investigation (ASCI) and has been published continuously since 1924.

Revised December 3, 2012 | Revision history

Scope of publication

The JCI publishes original articles of the highest quality pertaining to the genetic, molecular, cellular, or physiological basis of human biology and disease (see categories of submission). Single, complete papers are preferred to a series of interdependent ones.

Manuscript submission

The JCI requires that manuscripts be submitted online. An account is required to proceed with submission; authors can register for accounts or access their existing accounts by following the instructions at https://www.the-jci.org. Briefly, a submission must be prepared as described below in Manuscript preparation and format, with particular attention paid to the submitted PDF:

  • The manuscript must be supplied in a single PDF and must include all information related to the submission: the complete manuscript text, all figures, and all tables. (Supplemental data, information for reviewers, and PDFs of manuscripts in press must be uploaded separately.)
  • Each figure (including all parts, if applicable) with its corresponding legend must be presented together on its own page within the manuscript PDF.
  • Each table must be presented complete on its own page within the manuscript PDF.

Other information about the submission — for example, title, author list, and abstract — will need to be supplied as required during the submission process. Once all required information has been provided, submitters of original and de novo submissions will be asked to pay a submission fee.

Submission fee. A nonrefundable fee of US$75 is required for original and de novo submissions in Regular, Brief Report, and Technical Advance categories. (Beginning January 1, 2014, this fee also applies to Clinical Medicine submissions.) The fee is not required for revised submissions. Payment by credit card (Visa/MasterCard/American Express only) is strongly encouraged; checks drawn in US dollars are acceptable (a US$25 fee is assessed for returned checks). The JCI does not accept purchase orders or bankwire transfers. Manuscripts will not be considered until payment is received. Please note that the submission fee is charged regardless of whether the manuscript is sent for external review.

Policies

The corresponding author must verify that the manuscript, including related data, figures, and tables, has not been previously reported or published; that the manuscript is not under consideration elsewhere; and that it will not be submitted elsewhere while under review by the JCI. If any related preliminary report (for example, in symposia, proceedings, transactions, books, invited articles, etc.) other than an abstract of 400 words or fewer has been published or submitted, a copy must accompany the submission. Related unpublished articles by any of the authors must also be submitted online for editors and reviewers.

All clinical investigation must have been conducted according to Declaration of Helsinki principles. All human and animal studies must have been approved by the appropriate institutional review board(s). A specific declaration of such approval must be made in a stand-alone paragraph at the end of the Methods section; in the case of human studies, this includes a statement indicating that written informed consent was received from participants prior to inclusion in the study. Participants should be identified by number, not by name. Manuscripts without declaration of ethical approval for experiments will not be reviewed.

All authors must disclose any commercial affiliations as well as consultancies, stock or equity interests, and patent-licensing arrangements that could be considered a conflict of interest. A detailed conflict of interest policy is available on the JCI website. Specifics of such disclosures will remain confidential until publication, when an appropriate statement regarding any conflicts will be noted in the manuscript. Please note your conflict of interest statement on the title page.

As of the date of publication, authors will be required to make materials and methods used available to academic researchers for their own use. No exceptions will be made to this policy. This requirement includes antibodies, cell lines, and any newly created mutant animals. Animals can be made available through the authors' institution or, via a publicly available repository. Other reagents, methods, etc. must be made available to the academic community. A pictorial representation of the structure of any new drug described in the manuscript must be provided. Failure to adhere to these guidelines will be considered a violation of the authorship agreement and could result in retraction of the published article.

Authors must submit original nucleotide or amino acid sequence data to GenBank, European Molecular Biology Laboratory (EMBL), DNA Databank of Japan (DDBJ), or another appropriate publicly available database in general use in the field that gives free access to researchers from the date of publication. Microarray data must be deposited in a MIAME-compliant public database. High-throughput sequencing data for RNA (RNA-Seq) and chromatin immunoprecipitation (ChIP-Seq) must be deposited in a MINSEQE-compliant public database. Accession numbers must be provided in the submitted manuscript. Other supporting datasets must be made available to any interested reader on the publication date from the authors directly. Researchers who encounter a persistent refusal by an author of a paper to comply with these guidelines should contact the Editor's office by e-mail at editors@the-jci.org.

For all experiments involving genetically engineered mice, inbred strain background effects have become an important concern. The Editorial Board generally prefers littermate controls, but will evaluate the controls used on a case by case basis (authors must fully describe the source of animals and number of backcrosses). If an alternative control was used, an explanation must be included in the cover letter to the Editor and within the manuscript.

Authors may suggest a member of the Editorial Board with appropriate expertise to handle their submission. In addition, authors may note up to 2 reviewers they wish to exclude and reason(s) for exclusion.

Manuscript preparation and format

Authors are encouraged to provide a concise summary (1-2 paragraphs) of the key findings in the submission cover letter. 

Refer to categories of submission for a quick overview of require manuscript elements. Note that Clinical Medicine submissions have additional guidelines beyond those described here.

Start each section on a new page using the guidelines that follow. Manuscripts should be double spaced (including references and tables); however, figure legends may be single spaced if necessary to keep a figure and its corresponding legend on the same page. Number all pages. Ensure that gene and protein names and symbols conform to official Entrez Gene nomenclature and are presented according to JCI style: see Gene Nomenclature and Style. Nonstandard abbreviations must be spelled out at first mention, with the abbreviated form appearing in parentheses. Thereafter, they should be used without definition. Standard JCI abbreviations do not need to be defined.

List the manuscript title, first and last names of all authors, as well as their affiliations (departments, institutions, and locations) during the period when the work was performed. Assign affiliation footnotes consecutively using superscript numbers (1, 2, 3, etc.). If any author's affiliation has changed since completion of the work, specify the present affiliation and location. The complete name, address, telephone and fax numbers (including country code, where applicable), and e-mail address of the corresponding author must be provided. Also include a conflict of interest statement on the title page.

The manuscript title should be clear, concise, descriptive and limited to 10 words including conjunctions. Subtitles, colons, and nonstandard abbreviations are unacceptable. For publication, titles may be revised by the JCI to ensure clarity and accessibility to our wide readership, with the final approval of the authors.

Examples

  • Iron metabolism regulates graft immune tolerance in human liver transplantation
  • Effect of H56 vaccine in active and latent tuberculosis
  • NF-κB and Notch signaling pathways in pancreatic cancer progression

The abstract may not exceed 200 words and should state the rationale, objectives, findings, and conclusions of the manuscript. References and primary data should not be presented in abstracts, and nonstandard abbreviations must be defined. For publication, abstracts may be revised by the JCI to ensure clarity and accessibility to our wide readership, with the final approval of the authors.

In Acknowledgments, state sources of support in the form of grants, equipment, or drugs. Authors may include other appropriate acknowledgments (for example, to other scientists for their help or advice).

Indicate references in the text by sequential numbers in parentheses (do not use superscript). In the Reference section, list references numbered in the order in which they appear in the text. Follow AMA style (AMA Manual of Style, 10th edition, pages 39-79), and abbreviate names of journals according to the PubMed Journals list. Reference styling examples are provided here.

Upload all related unpublished manuscripts cited. Submitted manuscripts, manuscripts in preparation, unpublished observations, personal communications, and preliminary report citations must appear parenthetically in the text and not in the References section. Obtain and submit written permission (an e-mail is sufficient) when citing a personal communication or unpublished observation.

Figures and tables

Data integrity: It is strongly encouraged that data are displayed in their raw form and not in a way that conceals their distribution. We recommend that individual data be presented as dot plots next to the average for the group with appropriate error bars. Presenting data as columns with error bars (dynamite plunger plots) conceals data. For animal experiments, small sample sizes of less than 5 animals per group are discouraged.

Authors of new submissions that contain cropped gels/blots are encouraged, but not required, to submit a file that contains the entire unedited gel for all representative cropped gels in the submission. Each gel should be annotated as "Full unedited gel for Figure X," and the authors should highlight which lanes of the unedited gel correspond to those shown in the cropped images within the manuscript. This file should be separate from the primary submission PDF and distinct from any other supplementary data provided. For authors of revised submissions, this file is required. Authors may choose whether to publish full uncut blot data if their submission is ultimately accepted.

Style: Type appearing within figures (axis labels, for example) should be in Helvetica or a similar typeface, and it must be of sufficient size and contrast to retain clarity if reduced in size. When using scale bars, define scales in figure legends, not in the figures themselves. Use standard abbreviations whenever possible. Avoid gratuitous use of color for decorative effect, boxes around graphs and figures, and small type and symbols on large graphs; avoid pairing red and green in graphs to ensure legibility for colorblind readers. Whenever possible, do not place labels over any part of a color figure. Do not include tabular material within figures. Additional figure instructions can be found on the figure instructions page.

Figures must be cited sequentially in the text using Arabic numerals (for example, Figure 7). Provide a short title (in the legend, not in the figure itself) and an explanation in brief but sufficient detail to make the figure intelligible without reference to the main text (unless a similar explanation has been given in a preceding figure). Do not exceed 250 words for each legend. Provide a key to any symbols used. Each figure (including all parts, if applicable) with corresponding legend must be presented on its own page.

All tables should be double-spaced on manuscript pages. Tables should be self-contained and self-explanatory. Provide brief titles, and assign footnotes to tables by superscript capital letters starting with A and continuing in alphabetical order. Tables with sections (for example, Table 1A, 1B, 1C) are not acceptable. Each table must be presented complete on its own page.

For graphic material, we have adopted a policy taken from the Journal of Cell Biology: No specific feature within an image may be enhanced, obscured, moved, removed, or introduced. The groupings of images from different parts of the same gel, or from different gels, fields or exposures must be made explicit by the arrangement of the figure (e.g., using dividing lines) and in the text of the figure legend. Adjustments of brightness, contrast, or color balance are acceptable if and as long as they do not obscure or eliminate any information present in the original. Nonlinear adjustments (e.g., changes to gamma settings) must be disclosed in the figure legend.

The Editors reserve the right to consult the Office of Research Integrity or the appointed official at the authors' home institution if the figures appear to have been manipulated.

Accepted manuscripts

The following items are of note to authors of accepted manuscripts, although all authors submitting their work to the JCI should be aware of the journal's policies regarding accepted manuscripts.

The JCI deposits all articles in PubMed Central immediately upon publication. Authors of articles published in the JCI do not need to submit their accepted articles separately to PubMed Central. This satisfies the NIH Public Access Policy and other similar funder requirements.

Detailed instructions for figure preparations

Authors of accepted manuscripts may provide related supplemental data to be posted online along with the published manuscript. This may include figures, tables, videos, or appendices but excludes large datasets (see Policies). All Supplemental Data information (except videos) should be combined into a single PDF file. Before submission, carefully review all files, they will not be checked by a copy editor. The JCI is not responsible for any errors contained in data supplements.

All JCI research articles are freely available online immediately upon publication (and, in most instances, prior to print publication). Charges (in US$) assessed to authors help support publication of the JCI. Authors will receive an invoice with their publication proofs. For publication of Regular articles and Technical Advances, authors will be assessed $0.26 per word, including the text of legends, tables, and references, based on the word count of the accepted manuscript. Authors will be billed $175 per figure and $75 per table. For publication of Brief Reports, the publication fee is $2,500. Authors will be charged $300 for supplemental data to appear online with accepted articles. The JCI is not responsible for assuming the cost of correcting errors in supplemental data or the cost of scanning supplemental images.

Upon acceptance of an article, all authors associated with the submission are sent an e-mail requesting assignment of copyright to the ASCI prior to publication.


Revision history

  • March 25, 2014: Added requirement to deposit ChIP-Seq and RNA-Seq data.
  • December 3, 2012: Added Clinical Medicine category.
  • August 23, 2012: Added clarification that full uncut gels/blots be highlighted to demonstrate which lanes apply to the submitted manuscript.
  • August 6, 2012: Posting of "Gene nomenclature and style" document.
  • April 8, 2012: Upload of full uncut gels/blots for first-time submissions no longer required.

 

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