Statistical Applications in Genetics and Molecular Biology seeks to publish significant research on the application of statistical ideas to problems arising from computational biology. The focus of the papers should be on the relevant statistical issues but should contain a succinct description of the relevant biological problem being considered. The range of topics is wide and will include topics such as linkage mapping, association studies, gene finding and sequence alignment, protein structure prediction, design and analysis of microarray data, molecular evolution and phylogenetic trees, DNA topology, and data base search strategies. Both original research and review articles will be warmly received.
As one of the bepress family of journals, we are also dedicated to changes in the academic publishing process. In particular:
This document provides details on copyediting, typesetting, and layout requirements and recommendations pertaining to final manuscript submission to a bepress journal. Authors interested in the technical details of producing quality electronic documents in Adobe's Portable Document Format (PDF) should consult the manual:
A Guide to PDF for Scholars Using the bepress System1
Copyediting
The bepress system has been designed to improve the scholarly publication process for authors. Among the many improvements we offer over traditional journals, the most significant is that we have dramatically shortened the period between initial submission and the final publication of a peer-reviewed article. Much of this time savings is due to innovative use of electronic publication. These innovations, however, require subtle, but important changes in the way authors need to prepare accepted manuscripts for electronic publication.
bepress does not copyedit the manuscripts, and with the exception of adding the title page, pagination, and headers/footers, bepress does not make any formatting changes to the submissions. Therefore, authors are their own copyeditors and typesetters. This means that authors need to pay greater attention to the editing and look of their manuscripts than is typically required by print journals, which may do copyediting and typesetting—but not, however, without headaches such as the introduction of errors and the need for authors to do careful reviews of page proofs.
If you have reasons to doubt your proficiency with respect to spelling, grammar, etc. (e.g., because English is not your native language), then you may also wish to employ—at your expense—the services of a professional copyeditor.
Formatting Requirements
- Do not include a title page or abstract. (Begin the document with the introduction; a title page, including the abstract, will be added to your paper by the bepress system.)
- Do not include page numbers, headers, or footers. (The bepress system will add the appropriate header with page numbers).
- Write your article in English (unless the journal expressly permits non-English submissions).
- Submit your manuscript, including tables, figures, appendices, etc., as a single file (Word, WordPerfect, RTF, or PDF files are accepted).
- Page size should be 8.5 x 11-inches.
- All margins (left, right, top and bottom) should be 1.5 inches (3.8 cm), including your tables and figures.
- Single space your text.
- Use a single column layout with both left and right margins justified.
- Font:
- Main Body—12 pt. Times or the closest comparable font available
- Footnotes—10 pt. Times or the closest comparable font available
- Include a proper bibliography following the bepress guidelines2.
- If figures are included, use high-resolution figures, preferably encoded as encapsulated PostScript (eps).
- Copyedit your manuscript.
- When possible, there should be no pages where more than a quarter of the page is empty space.
- Use the following document structure (remember there is no title page):
- Introduction (titling this section is optional)
- Subsequent sections including all tables, figures, and footnotes referenced in the text.
- Appendices (if any)
- References
Please note that acknowledgments should be entered in the submission form so that they may be incorporated into the title page produced for publication.
Additional Recommendations
Indenting, Line Spacing, and Justification
Indent all paragraphs except those following a section heading. An indent should be at least 2 em-spaces.
Do not insert extra space between paragraphs of text with the exception of long quotations, theorems, propositions, special remarks, etc. These should be set off from the surrounding text by additional space above and below.
Don't "widow" or "orphan" text (i.e., ending a page with the first line of a paragraph or beginning a page with the last line of a paragraph).
All text should be left-justified (i.e., flush with the left margin—except where indented). Where possible, it should also be right-justified (i.e., flush with the right margin). "Where possible" refers to the quality of the justification. For example, LaTeX3 and TeX4 do an excellent job of justifying text. Word does a reasonable job. But some word processors do a lousy job (e.g., they achieve right justification by inserting too much white space within and between words). We prefer flush right margins. However, it is better to have jagged right margins than to have flush right margins with awkward intra- and inter-word spacing. Make your decision on whichever looks best.
Language & Grammar
All submissions must be in English (unless the particular bepress journal explicitly states submissions in other languages are permitted). Except for common foreign words and phrases, the use of foreign words and phrases should be avoided.
Authors should use proper, standard English grammar. The Elements of Style by William Strunk, Jr. and E. B. White (now in its fourth edition) is the "standard" guide, but other excellent guides (e.g., The Chicago Manual of Style, University of Chicago Press) exist as well.
Article Length
Because bepress publishes electronically, page limits are not as relevant as they are in the world of print publications. We are happy, therefore, to let authors take advantage of this greater "bandwidth" to include material that they might otherwise have to cut to get into a print journal. This said, authors should exercise some discretion with respect to length.
Fonts
The following is a brief guide to fonts with respect to layout. See also the discussion in "A Guide to PDF for Scholars Using the bepress System" (http://www.bepress.com/manuals.html1) for font-related issues in the production of good PDF files. We cannot accept Type3 fonts.
Colored text
Set the font color to black for the majority of the text. bepress encourages authors to take advantage of the ability to use color in the production of figures, maps, etc., however, you need to appreciate that this will cause some of your readers problems when they print the document on a black & white printer. For this reason, you are advised to avoid the use of colors in situations where their translation to black and white would render the material illegible or incomprehensible.
Please ensure that there are no colored mark-ups or comments in the final version, unless they are meant to be part of the final text. (You may need to "accept all changes" in track changes or set your document to "normal" in final markup.)
Emphasized text
Whenever possible use italics to indicate text you wish to emphasize rather than underlining it. The use of color to emphasize text is discouraged.
Font faces
Except, possibly, where special symbols are needed, use Times or the closest comparable font available. If you desire a second font, for instance for headings, use a sans serif font (e.g., Arial or Computer Modern Sans Serif).
Font size
The main body of text should be set in 12pt. Avoid the use of fonts smaller than 6pt.
Foreign terms
Whenever possible, foreign terms should be set in italics rather than underlined.
Headings
Headings (e.g., start of sections) should be distinguished from the main body text by their fonts or by using small caps. Use the same font face for all headings and indicate the hierarchy by reducing the font size. There should be space above and below headings.
Main text
The font for the main body of text must be black and, if at all possible, in Times or closest comparable font available.
Titles
Whenever possible, titles of books, movies, etc., should be set in italics rather than underlined.
Footnotes
Footnotes should appear at the bottom of the page on which they are referenced rather than at the end of the paper. Footnotes should be in 10 pt. Times or closest comparable font available, they should be single spaced, and there should be a footnote separator rule (line). Footnote numbers or symbols in the text must follow, rather than precede, punctuation. Excessively long footnotes are probably better handled in an appendix. All footnotes should be left and right-justified (i.e., flush with the right margin), unless this creates awkward spacing.
Tables and Figures
To the extent possible, tables and figures should appear in the document near where they are referenced in the text. Large tables or figures should be put on pages by themselves. Avoid the use of overly small type in tables. In no case should tables or figures be in a separate document or file. All tables and figures must fit within 1.5" margins on all sides (top, bottom, left and right) in both portrait and landscape view.
See the appropriate discussion in A Guide to PDF for Scholars Using the bepress System1 for details on how best to prepare figures electronically.
Mathematics
Roman letters used in mathematical expressions as variables should be italicized. Roman letters used as part of multi-letter function names should not be italicized. Whenever possible, subscripts and superscripts should be a smaller font size than the main text.
Short mathematical expressions should be typed inline. Longer expressions should appear as display math. Also expressions using many different levels (e.g., such as the fractions) should be set as display math. Important definitions or concepts can also be set off as display math.
Equations should be numbered sequentially. Whether equation numbers are on the right or left is the choice of the author(s). However, you are expected to be consistent in this.
Symbols and notation in unusual fonts should be avoided. This will not only enhance the clarity of the manuscript, but it will also help insure that it displays correctly on the reader's screen and prints correctly on her printer. When proofing your document under PDF pay particular attention to the rendering of the mathematics, especially symbols and notation drawn from other than standard fonts.
References
It is the author's obligation to provide complete references with the necessary information. After the last sentence of your submission, please insert a line break—not a page break—and begin your references on the same page, if possible. References should appear right after the end of the document, beginning on the last page if possible. References should have margins that are both left and right- justified. You may choose not to right-justify the margin of one or more references if the spacing looks too awkward. Each reference should give the last names of all the authors, their first names or first initials, and, optionally, their middle initials. The hierarchy for ordering the references is:
- Last name of first author
- First name of first author
- Last name of second author (if any). Co-authored work is listed after solo-authored work by the same first author (e.g., Edlin, Aaron S. would precede Edlin, Aaron S. and Stefan Reichelstein).
- First name of second author
- Publication date
- Order cited in text
The information to be given with each citation in the references is as follows:
Articles in traditional journals:
Required: Author's (authors') name(s), title of article, name of journal, year of publication (or "n.d." if no date), volume number, page numbers.
Optional (but desirable): issue number and month/season of publication. For forthcoming (in press) articles, put expected year of publication and substitute "forthcoming" for the volume and page numbers.
Article in a bepress journal:
Required: Author's (authors') name(s), title of article, name of journal, series name (if journal has different series), year of publication, volume number, issue number, article number.
Optional(but desirable): A hyperlink to the article.
Books:
Required: Author's (authors') name(s), title of book, year of publication (or "n.d." if no date), publisher, publisher's address, edition (if not first). For forthcoming (in press) books, put expected year of publication and add "forthcoming."
Chapters in collections or anthologies:
Required: Name(s) of author(s) of chapter, name(s) of editor(s) of book, title of chapter, title of book, year of publication (or "n.d." if no date), publisher, publisher's address, and edition (if not first). For forthcoming (in press) books, put expected year of publication and add "forthcoming."
Working papers:
Required: Author's (authors') name(s), title of working paper, year (or "n.d." if no date), location (e.g., "Department of Economics Working Paper, University of California, Berkeley" or "Author's web site: http://www.someurl.edu/author." If the working paper is part of series, then the series name and the number of the working paper within the series must also be given.
Other works:
Required: Author's (authors') name(s), title of work, year (or "n.d." if no date), and information about how the reader could obtain a copy.
Within the references section, the citations can be formatted as you like, provided (i) the formatting is consistent and (ii) each citation begins with the last name of the first author. That is, the following would all be acceptable:
Smith, Adam (1776) The Wealth of Nations, . . .
Smith, A., The Wealth of Nations, . . . , 1776.
Smith, Adam: The Wealth of Nations, 1776, . . .
Use hanging indents for citations (i.e., the first line of the citation should be flush with the left margin and all other lines should be indented from the left margin by a set amount). Citations should be single-spaced with extra space between citations.
When works by the same author are listed in a row, use — instead of writing the name again. Hence, one might have
Smith, Adam: The Wealth of Nations, . . .
—: The Theory of Moral Sentiments, . . .
Similarly, instead of repeating two names use
For instance,
Edlin, A. and S. Reichelstein (1995) . . .
— and — (1996) . . .
Within the text of your manuscript, use the author-date method of citation. For instance,
"As noted by Smith (1776)."
When there are two authors, use both last names. For instance,
"Edlin and Reichelstein (1996) claim . . . "
If there are three or more authors give the last name of the first author and append et al. For instance, a 1987 work by Abel, Baker, and Charley, would be cited as
If two or more cited works share the same authors and dates, use "a," "b," and so on to distinguish among them. For instance,
"Jones (1994b) provides a more general analysis of the model introduced
in Example 3 of Jones (1994a)."
After the first cite in the text using the author-date method, subsequent cites can use just the last names if that would be unambiguous. For example, Edlin and Reichelstein (1996) can be followed by just Edlin and Reichelstein provided no other Edlin & Reichelstein article is referenced; if one is, then the date must always be attached.
When citations appear within parentheses, use commas—rather than parentheses or brackets—to separate the date from the surrounding text. For instance,
" . . . (see Smith, 1776, for an early discussion of this)."
刊名字顺( Alphabetical List of Journals):
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