SCOPE
JOURNAL OF COMPUTATIONAL BIOLOGY provides a forum for communication of scientific and technical issues associated with the analysis and management of biological information at the molecular level. It will accept papers on the computational, mathematical, and statistical aspects of molecular biology. This includes sequence comparison; sequence analysis and searching; DNA and protein sequence determination; DNA topological structure; protein structure; RNA secondary and tertiary structure; genetic mapping; physical mapping; molecular evolution, including phylogenetic reconstructions; parallel methods of computation; design and implementation of biological data- bases; biological expert system design and use; and application of artificial intelligence methods to biological systems.
Manuscripts must be submitted online using the following URL:
http://mc.manuscriptcentral.com/jcb
Please read ALL instructions to authors before submitting.
EDITORIAL OFFICE
The editorial process is handled by the Coeditors-in-Chief and the Editorial Board, plus peer reviewers. Press releases, conference announcements, workshops, and the like, should be submitted to the following e-mail address: jcb@cs.brown.edu. Address questions about manuscript status and editorial management to
Erin Klopfenstein, Editorial Assistant:ehk@cs.brown.edu
SUBMISSION REQUIREMENTS
Please follow the Instructions for Authors carefully to help ensure that the review and publication of your paper is as rapid as possible. The Editors reserve the right to return manuscripts that are not prepared in accordance with these instructions. If there is
a question about the suitability of a manuscript, please contact a member of the Executive Editorial Board.
Submitted manuscripts must be previously unpublished and not submitted for publication elsewhere. If published in JOURNAL OF COMPUTATIONAL BIOLOGY, the paper cannot be published anywhere else in the same form, regardless of language, without the consent of the Publisher. Either American or British English
is acceptable, but be consistent. Text must be informative without being terse or wordy. Manuscripts will not be extensively copy- edited and it is expected that proofs will require only typographical corrections. There may be an extra charge for extensive changes made in proof.
MANUSCRIPT SUBMISSION AND COPYRIGHT AGREEMENT FORM
The Copyright Agreement form (available from web site at transfer_of_copyright.pdf) should be submitted once your paper has been accepted for publication. Manuscripts cannot be published without this form. The corresponding author is responsible for obtaining signatures of coauthors. Authors not permitted to release copyright must still return the form signed under the statement of the reason for not releasing the copyright. Upon acceptance of your paper, please fax the Copyright Agreement form to 914-740-2108.
MANUSCRIPT PREPARATION
Manuscripts must be prepared in either LaTex format or Microsoft Word.
Please submit individual files for text (with embedded *.bbl file when applicable), figures, and tables; do NOT submit a single PDF file containing these elements. Manuscript Central creates a PDF proof when all files are uploaded.
The entire manuscript must be double spaced, including references and tables. Font sizes must be no smaller than 12 points (proportional or fixed width). Clearly identify unusual or Greek letters. The position of each table and figure must be marked in the margin at the location it should appear.
FORMATS
Mini-Review/News/Perspectives: These papers should typically be 2–4 pages long. Contacting one of the senior editors before beginning such a paper is suggested. The purpose of the mini- review is to provide a forum for the informal exchange of theories and experimental approaches.
Reviews: Brief outlines from prospective contributors are welcome, and these will also be solicited on specific subjects. Papers: Standard journal papers should report unique findings not previously published.
Communications: These papers should typically be 2 pages long; this section is for communications too brief for a full paper. Software, Hardware, and Book Reviews: These reviews will usually be commissioned by the Editor-in-Chief or the Editorial Board, but a short (1–2 page) outline can be sent to the Editor-in-Chief unsolicited. Typical reviews will be one or two typeset pages, with a maximum of three figures.
TABLES
Each table should be on a separate page following the references. Tables should be numbered with Arabic numerals and given a short, descriptive title. Indicate footnotes by superscript lower case letters rather than numbers. Cite all tables in the text where they should appear. Information in the general text should not be repeated, nor should abbreviations used in the text be spelled out. Tables should be understandable to readers without having to refer to the text.
FIGURES
Each figure should be in separate files. Figures should be numbered consecutively in Arabic numerals and given a short, descriptive title. Cite all figures in the text where they should appear. The legends should define all symbols and new abbreviations not used in the text.
Photographs or screen dumps should be presented in final-sized form. Reproduction of color art will be made at the expense of the author. The charge will be $1,200 for each page that includes color art, plus $275 per piece of color art printed.
Provide clear, sharp line art that is suitable for reproduction. No additional relettering, redrawing, or typesetting will be done; therefore, all labeling should preferably be made with lettering set. The final size of lettering in line art should be no less than 2 mm high. The size of the lettering should be in proportion to the overall dimension of the drawing. Ideally, line drawings should be submitted in the desired final size to avoid reduction.
MANUSCRIPT ELEMENTS
Papers should have a title page, abstract, introduction, paper body (including such sections as methods, algorithms, findings, proofs, and discussion), acknowledgments, and references. Begin each section on a separate page.
Title Page: The title should be short, specific, and avoid jargon. The name of each author should be followed by her or his department, institution, city, with zip (postal) code, and country. We require the full mailing address and contact information (telephone, fax, and e-mail address) for EACH author listed on your paper. Please include the address(es) either on the title page or on a separate sheet. Please also indicate the corresponding author with an asterisk. Any changes of address may be added to the footnotes. Running heads should be 50 characters or less. Up to five key words or key phrases should be supplied to assist indexing services.
Abstract: Abstracts should have a maximum of 250 words and be understandable to readers who have not yet read the paper. They should state the aims, results, and conclusions drawn from the study. Reference citations are not permitted in an abstract. When genetic sequences are analyzed, the inclusion of appropriate accession numbers is recommended to aid cross referencing in Medline.
Text Elements: The introduction should briefly outline the paper’s field, review previous relevant work, and establish the background for the work being reported.
The body of the paper should include the well described and documented findings of the work as well as the information necessary for the reader to independently verify the findings. Authors should comment on the availability of reported programs from their own work and commercially, including availability by anonymous FTP, state from which media, and also provide program costs. Software submission to one of the public molecular biology or biology archive sites may be required, if appropriate. The discussion section should describe the applicability of the technique and other uses for which the technique can be employed. Authors are encouraged to discuss important feature constraints that they perceive in their system software.
Chemical Formulae and Mathematical Equations: Wherever possible, write mathematical equations and chemical formulae on a single line. Please submit complex chemical structures as figures. Number equations sequentially in Arabic numerals at the right margin.
Disclosure Statement
Immediately following the Acknowledgments section, include a section entitled “Author Disclosure Statement.” In this portion of the paper, authors must disclose any commercial associations that might create a conflict of interest in connection with submitted manuscripts. This statement should include appropriate information for EACH author, thereby representing that competing financial interests of all authors have been appropriately disclosed according to the policy of the Journal. It is important that all conflicts of interest, whether they are actual or potential, be disclosed. This information will remain confidential while the paper is being reviewed and will not influence the editorial decision. Please see the Uniform Requirements for Manuscripts Submitted to Biomedical Journals at http://www.icmje.org/index.htlm#conflicts for further guidance. If no conflicts exist, the authors must state “No competing financial interests exist."
If no conflicts exist, the authors must state “No competing financial interests exist."
References: Authors are responsible for the accuracy of the references. Published papers and those in press (state the journal that has accepted them) may be included. Text references should be cited by author and date (Smith 1976), not numbered. If more than two authors have written the paper, use the first author, then et al. References should be typed in alphabetical order and follow the acknowledgments. Journal names should be abbreviated according to the World List of Scientific Periodicals. References should be presented in the following style:
Journal Paper: Fujar, B.R., and Smith, R.N. 1996. Navigating gopherspace with neural implants. J. Neurol Impl. 10, 275–280.
Book: Hillis, D.M., and Moritz, C. 1991. Molecular Systematics. Sinaur Associates, Sunderland, MA.
Chapter within edited book: Knight, J.R., and Myers, E.W.
1992. Approximate regular expression pattern matching with concave gap penalties, 66–76. In Chrochemore, M., and Galil, Z., eds., Combinational Pattern Matching. Lecture Notes in Computer Science, Springer-Verlag, New York.
Acknowledgments: List collaborations, sources of research funds, and other acknowledgments in a separate section at the end of the text.
ABBREVIATIONS
Try to restrict the use of abbreviations to SI symbols and those recommended by the IUPAC. Abbreviations should be given in parentheses after their first mention in the text if the term is used more than once. Standard units of measurement and chemical symbols of elements may be used without definition in the body of the paper.
PERMISSIONS
Use of copyrighted material requires the copyright holder’s written permission, which must accompany the manuscript. Failure to do so will considerably delay the processing of your manuscript.
PERSONAL COMMUNICATIONS
Personal communication references can be used only when permission has been obtained in writing, and such permission must be provided to the editor before the manuscript can proceed to publication.
CONVENTIONS
In general, JOURNAL OF COMPUTATIONAL BIOLOGY follows the conventions of the CBE Style Manual (Council of Biology Editors, Bethesda, MD, 1983, 5th ed.).
Follow Chemical Abstracts and its indices for chemical names. For guidance in the use of biochemical terminology, follow the recommendation issued by the IUPAC-IUB Commission on Biochemical Nomenclature, as given in Biochemical Nomenclature and Related Documents, published by the Biochemical Society, UK. For enzymes, use the recommended name assigned by the IUPAC-IUB Committee on Biochemical Nomenclature, 1978, as given in Enzyme Nomenclature, published by Academic Press, New York, 1980. Where possible, use the recommended SI (Système Internationale) units.
Genotypes should be italicized (underline in typed copy); phenotypes should not be italicized. For bacterial genetics nomenclature, follow Demerec et al. (1977), Genetics, 54, 61–761.
SUBMISSION TO DATA BANKS
All sequences, clones, etc. that are reported must be deposited with the appropriate archive (GenBank, GDB, ATCC, etc.). Papers reporting sequences must have an accession number before submission.
PAGE PROOFS
All authors will receive a link to page proofs of their papers via email. To avoid delay, proofs should be checked immediately for typographical errors and returned within 48 hours to the Publisher’s production editor by express mail or fax according to the directions in the letter accompanying proofs.
REPRINTS
Reprints may be ordered by using the special reprint forms that will accompany the page proofs. These forms should be returned with the proofs. Reprints ordered after the issue is printed will be charged at a significantly higher rate.
PUBLISHER
The Journal is published by Mary Ann Liebert, Inc., 140 Huguenot Street, 3rd Floor, New Rochelle, NY 10801-5215. Telephone: (914) 740-2100; fax: (914) 740-2102; e-mail: info@ liebertpub.com; Web: www.liebertpub.com