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General Author Guidelines

Before reading these guidelines, please read the information about Manuscripts Types.

All manuscripts should be written using American English spelling and grammar and be concise. Use at least 1.5 spaces between lines, and 1 inch (25 mm) page margins. They should conform to the guidelines in the Council of Science Editors Style Manual (7th ed., 2006) and to the style conventions described here. You should use correct diacritics for non-English words. Use standard fonts, e.g., Symbol, Times/Times New Roman, Helvetica/Arial, Courier/Courier new, Computer Modern, and mathematical or symbol fonts. It is better to avoid hyphenation, justification, linked and embedded objects and images, and other advanced word processing features. Be consistent in representing symbols and distinguish clearly between similar-looking symbols, e.g., letter x, multiplication sign, and Greek chi; minus sign, hyphen, and dash. Do not approximate characters by creating your own symbols (e.g., superscript o for degree symbol) and approximate formatting, e.g., linebreak + tab for hanging indent. It is not advisable to use underlining to indicate italics or in plus-minus signs. Organize the manuscript in the order below. Please note that upon initial submission a complete (text, figure legends, tables, and figures) PDF document only is required. For revised manuscripts, you will receive instructions at an appropriate time.

Cover Page
Text
Acknowledgements and funding information
Tables
Figure Legends
arXiv
References
Figures
Terminology and Style Conventions
LaTeX Submissions
Getting help

Cover Page

On the top right corner of the first page, clearly indicate if the submission is intended as an Article, Letter, Brief Communication, Perspective, Protocol, or Review. For Articles and Letters, clearly indicate whether the work best fits in the Discoveries, Methods, or Resources section of MBE. The cover page should contain a brief and informative Title that should be accessible to general readers of MBE. Below the title, list all author names and their current affiliations, including institution(s) at which research was done. Then, list the name and e-mail address of the corresponding author.

Text

For all manuscripts, the text begins with an abstract, which should follow the word limits indicated in the Manuscript Types and Formats section for different types of contributions. The rest of the main text should be organized exactly as described for Articles, Letters, Brief Communications, Protocols, Perspectives, and Reviews in the Manuscript Types page.

Acknowledgments and funding information

All manuscript types may have an Acknowledgment section to thank individuals and to provide information on funding. Include accession numbers for GenBank and other public databases for all newly-reported sequences and structural coordinates. Details of all funding sources for the work in question should be included in the Acknowledgments section. A full list of RIN-approved UK funding agencies may be found here. Please apply the following rules:

  • The sentence should begin: "This work was supported by …” The full official funding agency name should be given, i.e. "the National Cancer Institute at the National Institutes of Health” or simply "National Institutes of Health” not "NCI” (one of the sub-institutions) or "NCI at NIH” (click here for the full RIN-approved list of UK funding agencies).
  • Grant numbers should be complete and accurate and provided in parentheses as follows: (grant number ABX CDXXXXXX). Multiple grant numbers should be separated by a comma as follows: (grant numbers ABX CDXXXXXX, EFX GHXXXXXX). Agencies should be separated by a semi-colon (plus "and” before the last funding agency).
  • Where individuals need to be specified for certain sources of funding the following text should be added after the relevant agency or grant number: to [author initials]. An example is given here: This work was supported by the National Institutes of Health (P50 CA098252 and CA118790 to R.B.S.R.) and the Alcohol & Education Research Council (HFY GR667789).

Oxford Journals will deposit all NIH-funded articles in PubMed Central. See http://www.oxfordjournals.org/for_authors/repositories.html for details. Authors must ensure that manuscripts are clearly indicated as NIH-funded using the guidelines above.

Tables

When preparing tables, the following guidelines should be considered. All tables should be included after the figure legends.

  • Number them consecutively following the sequence in which they are mentioned in the text.

  • Each table should have a short title that describes content (no legends, no vertical lines).

  • Tables are numbered with Arabic numerals.

  • Arrange data so that columns of like material read down, not across.

  • Include sufficient information that the meaning of the data is clear without reference to the text.

  • Use abbreviations to conserve space.

  • Include explanatory material as footnotes immediately below the table.

  • Reference explanatory footnotes by superscripted lower case letters except for significance levels, for which asterisks are used.

  • Do not include detailed descriptions of experiments in explanatory footnotes.

  • Use only when six or more individual data are presented.

Figure Legends

All submissions with figures must have legends that define abbreviations and contain enough information so the figure can be understood independently of the text. Legends should be listed one after the other as part of the text document.

arXiv

All manuscripts published in arXiv are considered unpublished works. Manuscripts that appear on arXiv may be submitted to MBE for consideration for publication. Manuscripts that contain text citations to papers published on arXiv must format such citations as unpublished data (see References section below), listing all authors and including the URL. For example: Blumenstiel JP, Chen X, He M, Bergman CM, unpublished data, http://arxiv.org/abs/1209.3456, last accessed June 26, 2013.

References

Please note that the journal style now conforms to The Council of Science Editors Style Manual (7th ed., 2006), with one exception: the use of "et al." will be retained in text citations and within the reference section.

All submissions will have references and must follow the format listed below. References within the text must:

  • be cited by author and year,

  • include relevant pages for direct quotations,

  • be in chronological order when grouped (alphabetical order if published in the same year),

  • follow CSE citation style (e.g., Thomas and Wilson 1991; Okimoto et al. 1992; Powers ST and Powers JD 1993a, 1993b),

  • include the name of the first author and "et al." when there are three or more authors,

  • refer to unpublished work of authors as "name AB, unpublished data", and

  • refer to unpublished work of others as "name AB, name CD, personal communication" (authors are responsible for securing permissions to cite).

Reference section must:

  • be arranged alphabetically by name of author(s) and then chronologically for references with identical authors,
  • contain only works cited in the text; works cited in Supplementary files only should NOT be included in this list,
  • refer to manuscripts accepted for publication but which have not yet been published as "forthcoming",
  • not include manuscripts that have not been formally accepted for publication,
  • follow the guidelines for abbreviations of periodicals given in The Council of Science Editors Style Manual (7th ed., 2006), and
  • formatted as in recent issues of the journal and as follows:
    • Journal articles: Pensole G, Gissi C, Lanave C, Saccone C. 1995. Glutamine synthetase gene evolution in bacteria. Mol Biol Evol. 12:189-197.
    • (>10 co-authors): Wilson R, Ainscough R, Anderson K, Baynes C, Berks M, Bonfield J, Burton J, Connell M, Copsey T, Cooper J, et al. 1994. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature 368:32-38.
    • Books: Ingram VM. 1963. The hemoglobins in genetics and evolution. New York: Columbia University Press.
    • Book chapters: Hall BG. 1983. Evolution of new metabolic functions in laboratory organisms. In: Nei M, Koehn RK, editors. Evolution of genes and proteins. Sunderland (MA): Sinauer Associates. p. 234-257.

Figures

For initial submissions, include all figures in the main text in the single PDF file containing the manuscript. At the time of manuscript revision, we will request high quality figures in separate files (high-resolution .tif files: 1200 dots per inch for line drawings and 300 dots per inch for color and half-tone artwork). For additional useful information on preparing your figures for publication, click here. Follow these rules for figures:

  • Number them consecutively following the sequence in which they are mentioned in the text.
  • Include scale bars where appropriate. These should not be placed in the legend.
  • Size figures for the publication: maximum single column width = 8.2 cm/3.25 inches; 2 columns = 16.9 cm/6.75 inches; depth = 24 cm/9.25 inches.
  • Must have uniform lettering style.
  • Figures should not include sequences and alignments that exceed one journal page. Larger alignments must be submitted as Supplementary Material and their availability indicated in print in the Supplementary Materials section.
  • Legends must define abbreviations and contains enough information so the figure can be understood independently of the text.

Figures must:

  • Be in Adobe postscript fonts.
  • Be converted to grayscale or bitmap mode if originally in color but to be printed in black and white.
  • Have any unnecessary white space cropped from around the outside of the image if the file is a TIFF file. Be careful not to crop any of the intended image.
  • Each be saved in a separate file. If a figure has multiple parts (e.g., Fig. 1A, Fig. 1B) all parts should be saved into one file.
  • Be submitted for publication at resolutions of 1200 dots per inch for line figures and 300 dots per inch for half tones.
  • Always use the latest version of the software program available. Files from older versions often lose integrity when opened in newer versions.
  • Figures must be submitted as .tif, .eps, .ppt, .xls, .doc, .pdf, .gif, or .jpg files.

Color figures must be:

  • In CMYK mode, not RGB.
  • Saved at resolution of 300 dpi.
  • Paid for (see charges) except in the case of Open Access articles.
  • Given names that include both the manuscript handling number and the corresponding author’s name.

Terminology and Style Conventions

  • Abbreviations and symbols should follow the International System of Units (SI).
  • Nonstandard abbreviations must be defined at first occurrence, in both abstract and main text.
  • Species must be identified by italicized scientific binomens. Generic names that are also common names should not be italicized unless they form part of a binomen (thus an investigation may involve Drosophila melanogaster or D. melanogaster, but a comparison would be made between Drosophila and human genes). Binomen abbreviations of the form "Gsp" (Genus, species) as, for example, "Hsa" for Homo sapiens may be used in tables and figures.
  • Genetic loci must be italicized and must follow the established rules of genetic nomenclature that have been established for the various organisms (e.g. HUGO Nomenclature Committee, the International Immunogenetics Database, Mouse Nomenclature Guidelines, or Mendel-GFDb (plants).
  • The International Union of Pure and Applied Chemistry and the International Union of Biochemistry and Molecular Biology rules of nomenclature must be followed for amino acids, peptides, proteins, enzymes, nucleic acids, polynucleotides, carbohydrates, and lipids.
  • Mathematical equations must be presented with correct spacing between characters. Characters in equations and their counterparts in the text will be set in italics unless the author specifies otherwise the first time a character appears. Equations must be numbered sequentially, in Arabic numerals in parentheses, on the right-hand side of the page.
  • Statistical inferences, including those used for phylogenetic estimation, must be soundly based. Where appropriate, the assumptions underlying statistical inferences should be made explicit and sources of error should be clearly identified.
  • The IUBMB single-letter code for nucleotide bases including ambiguity is as follows: A = adenine; C = cytosine; G = guanine; T = thymine; U = uracil; R = A/G (purine); Y = C/T (pyrimidine); M = A/C; W = A/T; S = C/G; K = G/T; B = C/G/T (not A); D = A/G/T (not C); H = A/C/T (not G); V = A/C/G (not T); and N = X = A/C/G/T (any or unknown). For ambiguous nucleotides, T and U are equivalent.
  • Effective interdisciplinary communication requires that the precise meaning of words be understood in all disciplines. The following conventions should generally be followed:
    • When aligned sequences are compared, differences, not changes, may be observed. Changes can only be inferred, and a single difference may result from multiple changes.
    • The word "invariant" has two common but different meanings, invariable and unvaried. Either can be used, but the meaning must be clear.
    • A mutation generally occurs in a single individual and gives rise to an allele. If an allele achieves some frequency in a population it can be referred to as a polymorphism (not a "common [or rare] mutation"). If it has become fixed in a population it may be referred to as a substitution.
    • If two molecules are alike in some degree, they are similar. If it is inferred from their similarity that they have a common ancestor, then they are homologous, but if their similarity was acquired by convergence, they are analogous. When homology arises via a gene duplication (all or part), it is paralogy; when it arises via speciation, it is orthology; when it arises by horizontal gene transfer, it is xenology.
    • The phrase "insertions and/or deletions" may be reduced to "indels."
    • Gaps are introduced into sequences to increase their similarity rather than to optimize similarity, unless an algorithm is employed that guarantees an optimized result according to the way similarity is defined (e.g., as maximum matches).
    • Similarity should not be asserted to be significant unless accompanied by a probability statement and its method of determination.

LaTeX Submissions

While you should prepare your typescript text using a word-processing package (save in .doc or .rtf format), PDF files may be acceptable if you have used LaTeX to write your manuscript. Typescripts should be double-spaced. Please number each page. LaTeX: When creating the pdf file from standard word processing packages, it is important to select the option "embed all fonts" (or equivalent) to ensure that mathematical symbols appear correctly. Failure to do so may result in an unreadable submission. Instructions for generating correct PDF files can be found at https://gemini.econ.umd.edu/e-editor/pdftips.html. Manuscripts must be prepared using the TeX class file (available here as a .zip file, accompanied by notes on usage). Once a Tex file is created, it can be submitted to the editorial office. Please see our LaTeX submissions FAQ page for more detailed instructions for LaTeX submissions.

Getting help

If you experience any problems during the online submission process please consult the Author's User Guide which provides more detailed submission instructions and 'movie tutorials' explaining how to submit your paper. Alternatively, please contact the Journal's Editorial Office who will be pleased to assist you.

Updated on 15th October 2012