JOURNAL OF COMPUTATIONAL BIOLOGY provides a forum for communicating 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 databases biological expert system design and use application of artificial intelligence methods to biological systems.
Manuscripts must be submitted online using the following URL: http://mc.manuscriptcentral.com/jcb
To help defray the cost of processing, the publisher requests that page charges of $80 per typeset page be paid by all authors who have funds available from research grants or from their institutions. It should be noted that ability to pay page charges is not a prerequisite for publication in the Journal.
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: email@example.com. Address questions about manuscript status and editorial management to Angel Murakami, Editorial Assistant: firstname.lastname@example.org
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Submitted manuscripts must be previously unpublished and not submitted for publication elsewhere.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 copyedited and it is expected that proofs will require only typographical corrections. There may be an extra charge for extensive changes made in proof.
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.
Basic Guidelines for Uploading a LaTeX Formatted Manuscript:
- Always upload the main LaTeX file first, selecting the file designation of Main Document.
- Then, upload each file that is related to the main .TEX file as is needed for processing, selecting the file designation of TeX/LaTeX Suppl File.
- Be sure to upload all style sheets, and reference and bibliography files that are a part of the document.
- All image files must be saved and uploaded in .EPS format in order for the file to properly format and convert.
- If changes are made to the main LaTeX document after all of the related files have been uploaded, all supplementary LaTeX files will have to be removed and re-uploaded.
Research Articles: Manuscripts should be limited to 3,000 words, excluding tables, figures, legends, abstract, disclosure or references.
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.
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.
Each figure should be in a separate file. 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 shots should be presented in final-sized form.
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 12 points. 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.
Art should be provided in the following formats:
- Line illustrations should be submitted at 900 DPI.
- Halftones and color photos should be submitted at a minimum of 300 DPI.
- Save art in either TIFF or EPS formats. Do not submit JPEG files. (JPEG files are for screen representation-quality only and will print very poorly during the printing process.)
- Color art should be saved in CYMK format. (If RGB files are submitted, the files will be converted to CYMK and some color variation will occur.)
- Label figures inside the files in addition to naming the file with the figure number (i.e., when figures files are opened, the figure number should appear inside the file.)
- When naming your figure files, please label them with your last name, followed by a period (.), and then list the figure number, for example, Smith.Fig_1
Papers should contain a title page, abstract, introduction, paper body (including such sections as methods, algorithms, findings, proofs, and discussion), acknowledgments, author disclosure(s), 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 be structured and 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.
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.
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.
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."
Acknowledgments: List collaborations, sources of research funds, and other acknowledgments in a separate section at the end of the text.
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.
References: Authors are responsible for the accuracy of the references.
Citation of references in the text: References in the text should be cited by author names and publication year. When a text citation includes one or two authors, list all authors and the publication year, e.g., Smith (2008) or Smith and Jones (2008), but for text citations for three or more authors, cite the first author only followed by et al. and the publication year, e.g., Smith et al. (2008).
Reference list at the end of the article: References should be typed in alphabetical order by first author, and the entire list should appear after the Acknowledgments and Disclosure Statement sections. Journal names should be abbreviated according to the Index Medicus or World List of Scientific Periodicals. In the reference list, provide up to three authors only. For references with four or more authors, use et al. after three authors (e.g., Lifshitz, J., Kelley, B.J., Povlishock, J.T., et al.). Distinguish citations with the same author-year with a letter appended to the year, e.g., Hall (1981a,b). Type reference list in double space with author names in upper and lower case followed by year. Page numbers should be inclusive.
References should be presented in the following style:
Journal Paper: Fujar, B.R., Smith, R.N., Jackson, T.R., et al. 1996. Navigating gopherspace with neural implants. J. Neurol. 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. Combinatorial Pattern Matching. Springer-Verlag, New York.
Edited Book: Branden, C., and Tooze, J., eds. 1991. Introduction to Protein Structure, 2nd ed. Garland Publishing, New York.
Abstract: Angluin, D. 1979. Fast algorithms. Comput. Biol. 18, 155-193(abst).
Conference presentation (not published): Ladd, A. 2002. Motion planning. Presented at the 5th International Workshop on Algorithms, Boston.
Technical report (not published): Haussler, D. 1999. Convolution kernels on discrete structures. Technical Report UCSCCRL-99-10. University of California at Santa Cruz.
Dissertation: Kellogg, L. 2003. Computational protein design [Ph.D. dissertation]. MIT, Cambridge, MA.
Online article: Sayle, R. 1995. Protein visualization tool. Available at: www.umass.edu. Accessed June 1, 2006.
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. Include appropriate credit line.
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; 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.
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, email, or fax according to the directions in the letter accompanying proofs.
Reprints may be ordered by following the special instructions that will accompany page proofs, and should be ordered at the time the corresponding author returns the corrected page proofs to the Publisher. Reprints ordered after an issue is printed will be charged at a substantially higher rate.
The Journal is published by Mary Ann Liebert, Inc., 140 Huguenot Street, New Rochelle, NY 10801-5215. Telephone: (914) 740-2100; fax: (914) 740-2101; e-mail: info@ liebertpub.com; Web: www.liebertpub.com
The views, opinions, findings, conclusions and recommendations set forth in any Journal article are solely those of the authors of those articles and do not necessarily reflect the views, policy or position of the Journal, its Publisher, its editorial staff or any affiliated Societies and should not be attributed to any of them.