Journal of Computational Biology

Manuscript Submission

SCOPE

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: akm@cs.brown.edu.  Address questions about manuscript status and editorial management to Angel Murakami, Editorial Assistant: akm@cs.brown.edu

MANUSCRIPT SUBSMISSION FEE

Effective August 12, 2013, JOURNAL OF COMPUTATIONAL BIOLOGY instituted a non-refundable manuscript submission fee of $75.00 USD per submitted paper. This fee is charged regardless of the outcome of editorial decision of acceptance or rejection. In addition to the benefits of publishing your work in JOURNAL OF COMPUTATIONAL BIOLOGY, your submission provides unique opportunities to increase the visibility of your work through the robust AuthorCite™ services platform, including a link to freely share your article for 30 days.  SUBMIT YOUR MANUSCRIPT

Submission fees/codes are NOT required for revisions to papers submitted prior to August 12, 2013. To upload a revision of a paper, the submitting author must log in to their Author Center and click on the “Revised Manuscripts in Draft” link. The paper will appear there, and the submitting author will be able to proceed without paying a submission fee or entering a submission code.

SUBMITTING MANUSCRIPTS

Please be sure to follow the Instructions for Authors below on Manuscript Preparation. Authors whose submissions that do not comply with these Instructions will have their papers returned to them without peer review, and the submission fee will not be refunded. In this circumstance, if you wish to resubmit a returned paper, the standard submission fee of $75.00 USD will be charged again. (This does NOT refer to revisions of peer-reviewed papers.) CLICK HERE TO SUBMIT YOUR MANUSCRIPT

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 copyedited and it is expected that proofs will require only typographical corrections. There may be an extra charge for extensive changes made in proof.

 
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. 

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.

Additional Notes:

• 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.

FORMATS

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.

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   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

MANUSCRIPT  ELEMENTS

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.

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.
 

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." 

Acknowledgments: List collaborations, sources of research funds, and  other  acknowledgments in a separate  section  at  the  end  of the text.

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.

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.

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.  Include appropriate credit line.
 

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;  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, email, or fax according to the directions in the letter accompanying proofs.
 

REPRINTS

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.

PUBLISHER

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