LaTeX Style and BiBTeX Bibliography Formats for Biologists:
TeX and LaTeX Resources

by Tom Schneider

Can your word processor do these?

     
Examples from The TeX showcase

LaTeX is a typesetting language that runs circles around standard word processing programs because ... it is a true language. This means you can define new commands and do rather complex things. It is not really any harder to use than standard word processing programs such as wordY or wordIMperfect but it beats them hands down.

Because it is a vastly superior, permanent document preparation method, I write all my scientific papers, in LaTeX and then convert them automatically to html with latex2html, and to postscript and (more recently) to pdf with ghostscript. An example is the Information Theory Primer.

BiBTeX is a program associated with LaTeX that creates bibliographies. The format of the bibliographies is defined by a "bst" file, which is a programming language. The nice thing about BiBTeX is that you simply insert things like \cite{Shannon1948} into your text and the programs take over from there, automatically formatting and sorting the references.

Why Use Latex?

When used in conjunction with the atchange program, LaTeX and BiBTeX become automated and act like a WYSIWYG-AIWYW (What You See Is What You Get - And It's What You Wanted). The program medlinebib will convert from Medline bibliography format to BiBTeX. Atchange can be used to automate the process. (New as of 1999 September 9)

This page has three major parts:

BiBTeX Bibliography and LaTeX Style Formats for Biologists

I cannot guarantee that these formats are exactly the same as the journal formats, in part because the journals change them and in part because the journals sometimes use rather complex rules. They are pretty good and we have published all of our papers using them (since 1987). Generally a journal will modify a format at typesetting stage.

LaTeX2e for class and package writers

To use:
  • Store the file. There are two methods:
      If you are the systems administrator: The program texhash will register any thing beyond the main (texmf) directory. The man page for texhash has more information.
    • Put the style in the texmf directory
    • Run texhash
      If you are not the systems administrator (or can't get them to do it):
    • put the whatever.sty and whatever.bst file in your archive directory.
    • Make a link to the archive copy (eg, use lk)
  • mention the whatever.sty file like this: \usepackage{whatever} before your \begin{document}.
  • mention the whatever.bst file like this: \bibliographystyle{whatever} after the \begin{document}.
  • How to control capitalization. Normally BiBTex calls a routine to decapitalize everything except the first character of the title. However, BiBTex in general will leave the capitalization alone when you surround the text with braces like this: "{CAPITALS left alone}". If you have looked at atchange and the medlinebib programs, you will see that they take the pubmed formats and put {} around all of the text to preserve it. This probably will solve your problem for specific cases where you want capitals, without you having to change any code.

BiBTeX Style
A yellow box indicates that the journal accepts LaTeX. 		LaTeX Style other files and comments
  Acta Biotheoretica (Springer)
amnat.bst, amnat.dbj   The American Naturalist.
According to their instructions they prefer the AASTeX format but according to Dr. Kopp, they will accept LaTeX. The dbj was used to produce the bst. Thanks to Dr. Michael Kopp for this bst. as of 2007 Dec 23
animcog.bst   Animal Cognition (Springer)
Thanks to Joanna J. Bryson (Artificial models of natural Intelligence - AMONI) for this bst.
ajhg.bst
Use it in conjunction with the nature.sty style file (for unbracketed references), the citesupernumber.sty file (for superscript citation numbers) and the citecollapse.sty file (for concise citation numbers as 1-4 instead of 1,2,3,4). American Journal of Human Genetics
The first version was: ajhg1.01.bst by Stefan Böhringer . The University of Chicago Press, which publishes AJHG says: "Special Instructions for Mathematical and Other Non-ASCII Symbols. Authors of math-intensive articles are strongly urged to format their articles in LaTeX. This is particularly important if the articles contain numerous or complex equations." BRAVO!!
The second version, by Amy L. Williams was based on the more recent AJHG_Information_for_Authors.pdf.
biochemistry.bst the sty file is not available yet Biochemistry Thanks to Sonja M. Schwarzl, sonja.schwarzl@iwr.uni-heidelberg.de, for this. She notes: 
One has to add
  \usepackage[round, comma, sort&compress]{natbib}
into the preamble and
  \makeatletter
  \renewcommand\@biblabel[1]{#1.}
  \makeatother
right after the \begin{document}.
The only thing that is missing is that the
numbers should be italics rather than normal text
when citing something. I did not manage to change
this. however, I hope that this is a minor detail
and the journal editors can change it
themselves.
Theoretically these things could/should be done in a sty file ...
BiochemJ2008.bst a sty file is not available yet Biochemical Journal Thanks to Karl Blum RdSnp4@gmx.net for this. (new as of 2008 May 19):
Use the files from the journal! (Our old file: bioinformatics.bst) Use the files from the journal! (Our old file: bioinformatics.sty) Bioinformatics (formerly CABIOS). Thanks to Bruce Shapiro for the initial files. At PREPARING YOUR MANUSCRIPT Bioinformatics now provides LaTeX templates, but they are not compulsory!

Biomed Central
As of 2002 April 8, Biomed Central accepts DVI files for paper submissions.
biophysj.bst bj_latex_template.tex
bj_bibtex_template.bib
template pdf 		Biophysical Journal. These links are mentioned in the Instructions for Authors. Thanks to Nuno Loureiro Ferreira nunolf@ci.uc.pt for this. (new as of 2007 Mar 27):
cell.bst cell.sty

cite.sty the most modern control of citations within text

citecollapse.sty

citeparens.sty

citesupernumber.sty makes citations be superscript
control.bst control.sty Basic format for building bst files.
cv.bst cv.sty

doublespace.sty
ecology.bst natbib.sty (part of LaTeX) Ecology (journal published by the Ecological Society of America) Thanks to Henrique Miguel Pereira, PhD, http://www.stanford.edu/~hpereira, hpereira@stanford.edu, who provided it.
ecol_let.bst
Ecology Letters, thanks to Dr. Michael Kopp. The ecol_let_raw.dbj file is also available for regenerating the bst file.

emboj.sty
evolution.bst
Evolution (volume index) now accepts LaTeX files. The evolution.dbj file is also available for regenerating the bst file. Thanks to Dr. Michael Kopp for pointing this out.

floatfig.sty


Elsevier Journals: Gene Preparing Documents with LaTeX.
2008 Jul 30: See Elsevier publisher information.
genetics.bst Genetics accepts LaTeX! Thanks to Stuart Macgregor who published a paper (Genetics, 171:1365-1376, 2005) there using LaTeX. He made the bst using makebst. Stuart has also kindly supplied two small template files that people can use for Genetics, genetics.tex and genetics.bib. There is no sty file.
Dr. Michael Kopp modified the bst slightly to add a comma before the 'and' in the author list. Looking at the example above one can see that their rules are rather whacky: add a comma only if there are two authors! The other whacky rule of Genetics is that the first author is listed in the form "LAST, INITIALS" but all later authors are of the form "INITIALS LAST".
2008 May 12. Rutger Hermsen notes:
1. Jarle Tufto has a simple style file for Genetics to correct the appearance of the headers: http://www.math.ntnu.no/~jarlet/latex/
2. The bibliography style "genetics.bst" correctly formats the bibliography for Genetics, but the citations in the text are not entirely correct. In the Genetics style, there is no interpunction between the author and the year, while by default natbib.sty inserts a comma. This can easily be fixed by putting the following line in the preamble of the article (after loading natbib):
\bibpunct{(}{)}{;}{author-year}{}{,}
3. The name of the References Section is "Literature Cited" in Genetics; before the \bibliography statement one should therefore add the following line:
\renewcommand\refname{Literature Cited}

Ideally, the template by Stuart Macgregor could be adjusted to include these points. This amounts to replacing the line
\usepackage[authoryear]{natbib}
in that file by:
\usepackage{natbib} \bibpunct{(}{)}{;}{author-year}{}{,} \usepackage{genetics}
and inserting
\renewcommand\refname{Literature Cited}
directly after
\bibliographystyle{genetics}

html.sty This style file allows LaTeX to be converted to html by latex2html. You can find these files at CTAN, search for 'latex2html'.
latex2html at CTAN
gastroent.bst gastroent.sty Gastroenterology Requires natbib.sty in the document. Written by Herbert Plass, herbert.plass@meduniwien.ac.at, Vienna, Austria.
Genome Biology: Use BioMed Central's TeX template to prepare your manuscript for submission Use BioMed Central's TeX template to prepare your manuscript for submission Genome Biology accepts TeX and LaTeX! Instructions for Authors say: Use BioMed Central's TeX template to prepare your manuscript for submission
Thanks to Ramón Díaz-Uriarte for his version, GenomeBiology.bst (This is a link to Ramón Díaz-Uriarte's file.) (new as of 2005 Sep 5):
genres.bst genres.sty Genome Research. The style uses package natbib to allow control over references. TO DO CITATIONS:
\citep*{Petitjean.Olivier2007,Soussi2000,Soussi.Ishioka2005}.
gives (Petitjean, 2007; ...);
\citet{el-Deiry.Vogelstein1992}
gives
el-Deiry (1992).
For additional example documentation, see the Reference sheet for natbib usage.
gcb.bst natbib.sty   Global Change Biology as of 2008 Dec 18. Thanks to Marissa Baskett who notes: "to be used with natbib.sty".
heredity.bst   Heredity as of 2008 Jul 22. Thanks to Thibaut Jombart (or this page) who notes: "It requires the natbib package. ... To comply with the requirement of the journal, one should also use abbreviations for journal titles, but I do not think this is up to the bibtex style (I did it using jabref)."
humanmutation.bst humanmutation.sty Human Mutation


IUCR (International Union of Crystallography) journals such as Acta Crystallographica Section D: Biological Crystallography
download from IEEE download from IEEE IEEE ( Institute of Electrical and Electronics Engineers).
IEEEtran.cls is the official IEEE LaTeX class for authors of the Institute of Electrical and Electronics Engineers (IEEE) Transactions journals and conferences. Support sites: http://www.michaelshell.org/tex/ieeetran/ http://www.ctan.org/tex-archive/macros/latex/contrib/IEEEtran/ and http://www.ieee.org/.
jbact.bst jbact.sty
jeb.bst, jeb.dbj   Journal of Evolutionary Biology.
They accept LaTeX. The dbj was used to produce the bst. Thanks to Dr. Michael Kopp for this bst. as of 2007 Dec 23
Journal of Mathematical Biology "Springer Verlag has developed TeX and LaTeX macro packages for different journals." Apparently the above contains outdated files, but more recent ones can be found at their ftp site (Thanks to Michel Durinx for pointing this out!)
HOWEVER those are (still) dated 2004. In 2007 Ted Pavlic wrote to me "I've been trying to fix and modernize some of the Springer LaTeX support files for the Journal of Mathematical Biology (JMB). I've come up with these..." Preamble for Journal of Mathematical Biology and LaTeX Support :: Fixes and Suggestions for Springer's Journal of Mathematical Biology"
JMB: elsart-num.bst or elsart-harv.bst elsart.cls (standard file), elsartUSA.cls (my modification for USA) Journal of Molecular Biology NEW FORMAT CHANGE!! (as of 2003 Feb 14) JMB is now under Elsevier, and they accept LaTeX! Elsevier LaTeX file guidelines and Preparing Articles with LaTeX. The links given are for LaTeX 2e (upgrade if you still have 2.09!). Preparing Documents with LaTeX
As of 2004 April 26, all submissions are online: Online submission and editorial system for the Journal of Molecular Biology
2008 Jul 30: See Elsevier publisher information.
jss.bst. See notes jss.sty. See notes Journal of Statistical Software provide their own LaTeX Style Files! Please obtain the files from them so you get the latest version.
jsupercomp.bst jsupercomp.sty
jtb.bst jtb.sty Journal of Theoretical Biology Note: JMB changed their reference format so JTB is now completely separated.
As part of Elsevier, Journal of Theoretical Biology now accepts LaTeX! Elsevier LaTeX file guidelines
2008 Jul 30: See Elsevier publisher information.
methenz.bst
Methods in Enzymology
molcellbiol.bst molcellbiol.sty
nci.bst nci.sty and ulem.doc (part of LaTeX2e, call in preamble as \usepackage[normalem]{ulem}) National Cancer Institute bibliography format as defined for application forms in the NCI RedBook. There are two test files, nci.bib, which is a BiBTex bibliography, and nci.tex, which is a LaTeX file to test the bibliography. New as of 2000 Nov 28
nih nih.sty (link to another web site) Using LaTeX for NIH Grant Applications by Bruce Donald. New as of 2004 March 15, corrected 2008 Nov 15.
nar.bst The new style file is: narfront.cls (the old one is nar.sty) Nucleic Acids Research instructions to authors
  • 2000 Sep 13: nar.bst includes titles as specified by NAR.
  • 2001 Jun 15: now periods after titles!!
  • 2003 May 28: front mechanism for authors using narfront.cls!
  • 2004 June 7: LaTeX is an accepted format!
  • 2004 Dec 13: revision to nar.sty to make nicer sections/subsections.
  • 2005 Feb 5: narfront.cls is functional. A complete working example is narsample.tar.Z. Note: the files narfront.cls and nar.sty have not been fully merged.
  • 2008 Jan 7: Manuscript central now takes zip files. This means one can download the LaTeX files together.
  • 2008 May 22: For fonts we recently used:
    \usepackage{pslatex} % Times New Roman Font
namedplus.bst namedplus.sty Journal of Neuroscience and other similar (apalike, but different) styles. They use parens around citations and allow four types of citation macros: \cite, \citeauthor, \citeyear, \citenoparens, and \citetext \citenoparens gives you the standard Darwin, 1873 with no parentheses so you can do stuff like (see \citenoparens{darwin1873}). \citetext gives you Darwin (1873). The output comes out as a full list of authors (year) and then the standard rest of the stuff. I've used it for Journal of Neuroscience, Hippocampus, and other similar journals. (new as of 2000 April 12).
nature.bst nature.sty
citesupernumber.sty
naturefem.sty 		Nature. use in conjunction with citesupernumber.sty. Nature Guide To Authors says: " We cannot accept TeX and LaTeX: if no other format is possible, please ask the manuscript editor's advice. " Of course this is a terrible policy!! Their "natural" rival, Science is doing much better (see below). (new as of 2000 Dec 12): naturefem.sty provides a function that converts from LaTeX footnote numbers to the ones demanded by Nature.
2004 April 5: Please see the UPDATED VERSIONS AT CTAN. I have not had a chance to inspect these but they are probably more advanced than the ones on this web site.

Nature Nanotechnology, How to submit "Authors submitting LaTeX files may use any of the standard class files such as article.cls, revtex.cls or amsart.cls."

noReferences.sty remove the word "References" from your bibliography.

nihgrant.sty see also: nih.template.txt . (If that has gone away , you can use my mirror.)

nrotate.sty
openmind.bst openmind.sty files for Open Mind Journals. instructions for authors
Philosophical Transactions series A.
bst not available 		rspublic.cls (not required) The Philosophical Transactions series A of the Royal Society (Phil. Trans. A) Instructions to Authors says "The Society encourages authors to use LaTeX for the preparation of all papers submitted for publication, especially those with a large amount of mathematics."
PLoS-Biology.bst
(PLoS-Biology.bst is a link to Ramón Díaz-Uriarte's original file.) 		use with the natbib package, with \usepackage[authoryear, round, sort]{natbib} in the preamble. PLoS: Public Library of Science accepts TeX and LaTeX! See also PLoS Biology Guidelines for Authors.
Thanks to Ramón Díaz-Uriarte for this one! (new as of 2005 Sep 5)
2005 Oct 20: Thomas Grotkjaer writes: "Unfortunately PLoS has recently changed the citation style and now they are using a sort of Nature style with numbering. However, the actual reference list has not changed, i.e. authors, journal names are written in the same way."
2007 Jul 30: apparently they changed their policy.
Text files can be submitted for review in the following formats: DOC, RTF or PDF. Any articles that have been prepared in LaTeX will be accepted for review, but only in PDF format. After acceptance, only text files (RTF or DOC) of the revised manuscript and tables can be accepted for use in the pre-production and copyediting processes."
They let you give them a PDF generated by LaTeX for review, but only accept stupid formats later. The solution is to give them an ugly RTF using latex2rtf (see below).
proteins.bst proteins.sty also uses citesupernumber.sty
pnas.bst from CTAN.
If that is not available or slow you can get my copy of pnas.bst.
You can also try pnas-bolker.bst from Ben Bolker (2008 Jan 30) which I have not tested. pnas-bolker.zip is a complete zipped directory for testing the bst file. 		Use article.sty for LaTeX 2.09 and article.cls for LaTeX2e. To set the proper dashes in references and format of numbering in the bibliography you can use pnas.sty Proceedings of the National Academy of Science now accepts TeX and LaTeX (new as of 1999 October 8). PDF describing PNAS Style for TeX and LaTeX. Instructions for Authors. Note: PNAS will not accept the raw reference database; the paper.bbl might be acceptable. See the discussion on improving the pnas.bst. Also, pnas.sty uses natbib.sty.
psfg.bst
(New as of 2002 September 1)
(The old 1999 version, probably no longer useful, is still available as protsci.bst) 		protsci.sty (the same as jmb.sty for now) Protein Science instructions. I have put their journal example into a tiny bibliography, protsci.bib
Science.bst (Science.bst is my copy; use only if the Science link is down) scicite.sty (scicite.sty is my copy; use only if the Science link is down) Instructions at Science: Preparing Your Text and Tables -- Using LaTeX WOW!! 2002 May 6: Thanks to Edoardo ''Dado'' Marcora",Edoardo.Marcora@colorado.edu, for pointing out that Science now supports LaTeX!

section.sty
spec.bst spec.sty


Wiley LaTeX styles! NOTE that the pdf instructions given are older than the one in the tar file.

How to upload files (reminder to Tom): ftp://tug.ctan.org/pub/tex-archive/README.uploads

Publishers who use TeX/LaTeX

House Confirmed:
has author instructions
or other pages that
mention TeX/LaTeX		 Source
aaai www.aaai.org author instructions #11
AAAS/science www.sciencemag.org author instructions #11
Addison-Wesley
They published LaTeX: A Document Preparation System, 2/E
by Leslie Lamport, but I can't locate LaTeX in their instructions! 		must exist
but cannot locate! 		#1
American Institute of Physics www.aip.org author instructions #3, #11
American Mathematical Society author instructions #3,#6
American Meteorological Society www.ametsoc.org author instructions #11
American Physical Society authors.aps.org author instructions #3,#11
ATLIS Customize the CIA World Factbook from ATLIS
TeX Sample Pages from ATLIS 		#12
Beech Stave Press in preparation #10
Birkhäuser FAQs #2
Cambridge University Press author instructions #2,#3
Cambridge University Press authornet.cambridge.org author instructions #11
CRC author instructions
page 4 		#9
Documenta Mathematica www.math.uiuc.edu author instructions #11
 
 
Elsevier
www.elsevier.com
 
 
author instructions #1
author instructions #2
2008 Jul 02: Preparing Documents with LaTeX
"New document class for typeset journal articles, elsarticle.cls, now available for user testing" August 2008 		#1, #11
Fondo de Cultura Económica   #4
Informs joc.pubs.informs.org author instructions #11
Institut Mittag-Leffler (Royal Swedish Academy of Sciences)
www.arkivformatematik.org 		author instructions #11
IOP (institute of physics) authors.iop.org author instructions #11
John Benjamins Publishing Company Guidelines for Contributors for the journal Interaction Studies #13
London Mathematical Society Journals
(see paragraph beginning "before filling in the form) www.lms.ac.uk 		author instructions #2,#11
London Mathematical Society books www.lms.ac.uk author instructions #2,#11
Louisiana State University Press see footnote #8
Mathematical Association of America www.maa.org author instructions #11
Oxford University Press author instructions #1
Oxford University Press (see last paragraph) www.oup.co.uk author instructions #11
Princeton University Press press.princeton.edu author instructions #11
Publications de l'Institut Math\'ematique (Beograd) www.emis.de author instructions #11
SIAM author instructions #7
SIAM journals www.siam.org author instructions #11
SIAM books www.siam.org author instructions #11
Springer math www.springer.com author instructions #2,#3,#11
Springer physics www.springer.com author instructions #2,#3,#11
Thomson Delmar Learning not mentioned
in author guide 		#1
Unipress (Institute of High Pressure Physics, Polish Academy of Sciences)
www.unipress.waw.pl 		author instructions #11
Wiley www.wiley.com author instructions #1,#11
William Andrew Publishing Accept LaTeX files but
author guidelines do not
mention TeX/LaTeX.
example 		#2
World Scientific author instructions #3
WordTech see footnote #8
This table comes from a discussion on the group texhax under the thread [texhax] Publishing houses using TeX or LaTeX.
"Confirmed" means that a link to author instructions which allow, encourage or demand (!) TeX/LaTeX is given.

Other Publiser Lists:
Link Notes Source
http://www.juergenfenn.de/tex/verlage/verlage.html (La)TeX-freundliche Verlage in Deutschland
"A list of German publishing houses that LaTeX authors have reported to accept either LaTeX source or a ready PDF/PS output from LaTeX source was compiled by Henrik Grotjahn a while ago. He donated it to my website when he re-organised his own." 		Juergen Fenn juergen.fenn at GMX.DE
http://www-lsi.upc.es/~valiente/journals.html Journals accepting Manuscripts written using LaTeX
Gabriel Valiente's Publisher List 		Karl Berry karl at freefriends.org
http://tug.org/interest.html#publishers Publisher information at tug.org Karl Berry karl at freefriends.org
http://www.ccrnp.ncifcrf.gov/~toms/beeton/ Barbara Beeton's List of TeX/LaTeX Publishers Barbara Beeton, personal communication
"by going to the princeton press site http://press.princeton.edu/ and searching for "instructions for authors", an amazing selection of possibilities is found." Search Princeton University Press via Google for 'instructions for authors' Barbara Beeton, personal communication

Source Notes:
  1. William Adams will.adams at frycomm.com senior graphic designer, Fry Communications, "Places I'm aware of", 2007 June 12
  2. William Adams will.adams at frycomm.com senior graphic designer, Fry Communications, "Places that I've worked with", 2007 June 12
  3. Philip G. Ratcliffe philip.ratcliffe at uninsubria.it 2007 June 13
  4. Axel E. Retif axretif at igo.com.mx 2007 June 12
  5. (now unused)
  6. Stephen Moye stephenmoye at mac.com, Publications Technical Support, American Mathematical Society 2007 June 13
  7. William Adams will.adams at frycomm.com, 2007 June 13
  8. John Burt burt at brandeis.edu, 2007 June 13. Neither LSU nor WordTech support TeX, but both published his books from using PDF made using LaTeX.
  9. Morten Høgholm "Note: Taylor and Francis has style files available for FrameMaker, InDesign, and LaTEX (version 2e). Please consult your Project Coordinator or Acquiring Editor if you are interested in obtaining these. No Microsoft products or WordPerfect versions may be used to prepare author produced books." 2007 June 14
  10. Personal communication from Steve Peter 2007 June 13
  11. Personal communication from Barbara Beeton 2007 June 14
  12. William Adams will.adams at frycomm.com, 2008 July 03
  13. Joanna Bryson, 2008 July 09

TeX and LaTeX Resources




Schneider Lab
origin:   1998 Mar 3
updated: 2008 Jul 30
counting unique visitors since 2005 Sep 5