Citations and References in ISB articles

Alphabetical citation system:

  1. One or two-author-papers are cited by last names and the publication year, the latter separated by a comma. Two names are connected by "and" (not: "&"). Initials are to be put ahead only is necessary to diffentiate between authors with the same last name. If the cited paper has mor than 2 authors, only the first name is given followed by "et al." (italics!).
  2. If the citation is distinct from the remainder of the sentence, i. e. is not gramatically incorporated, it is put into brackets. The content of the brackets (not the brackets themselves) are linked.
    • - The aim of these models is to predict the system dynamics [Heinrich and Schuster, 1998].
  3. If there are several reference from the same authors, only the years are given for the second and following citations, to be separated by semicolon. The first reference is linked as usual, for the following ones only the year is linked.
    • - Other contributions followed, using various types of Petri nets like stochastic nets [Goss and Peccoud, 1998; 1999]
  4. If there are several citations cumulated in this way, they are altogether put into one set of brackets, separated by semicolon. Within these brackets, they are to be ordered (1) chronologically, (2) alphabetically within one year. The individual citations within the brackets, neither the brackets nor the semicolon, are linked.
    • - The aim of these models is to predict the system dynamics" [Heinrich and Schuster, 1998; Schuster et al., 2000a].
  5. Citations syntactically incorporated in the running text are not put into brackets. The year is after the names, and both the names and the year are linked to avoid interrupting the general referencing scheme of names and years by an opening bracket or the beginning of the link. This also applies if the phrase where the reference is incoporated is put into parentheses.
    • - A thorough analysis of an extended form of this pathway was performed by Koch et al., 2000, which forms the starting point for this paper.
    • - Executable high-level net models of metabolic pathways, and their (almost automated) construction, simulation, and quantitative analysis are described in Genrich et al., 2001.
    • - ... have been developed (for a review, see Heinrich and Schuster, 1996).
  6. Deviating from the third example in 5, (a) citation(s) in parentheses may be put in brackets instead if the additional wording is minor and does not form an own phrase (see first citation in the example).
    • - This is why most tools developed for gene prediction [e. g. Borodovsky and McIninch, 1993; Frishman et al., 1998; Salzberg et al., 1998; Besemer et al., 2001; Guo et al., 2003] implement algorithms, which rely on statistical concepts (reviewed e. g. in Fickett, 1996; Burge and Karlin, 1998).
  7. If both rules 3 and 5 apply, i. e. several papers of the same author(s) are referenced in the syntactic context of a sentence, the name(s) is/are repeated in brackets with the years following as in No. 3, to avoid a sequence of years to be separated by semicolon within a sentence.
    • - The application of Petri nets to this field began in the nineties with the publications of Reddy et al. [Reddy et al., 1993; 1996].
  8. If there are several citations in one pair of brackets, they should be (1) chronologically, (2) alphabetically ordered (see example under 6).
References List:
  1. Usually, all author names are given in the Reference list. Exceptions can be made if there are more than 20 authors. In these cases, only the first author may be given, including initials, with "et al." (italics, no comma before). If the authors collective has (a ) name(s), the may be given as well separated by semicolon; no dot at the end, before the year, unless required for an abbreviation.
    • - Okazaki, Y. et al.; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team (2002). Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563-573.
  2. Spelling of authors' names should be a close to the original as possible, i. e. with accents, umlauts, all initials (not just the two given by PubMed), dashes between initials etc.
  3. The initials are only the first letter of each given name, put after the family name, separated by comma from it and by space from each other, each appreviated with a dot.
  4. The year of publication is given in parentheses, plus a letter if neccesary for distinction (see above, 4), followed by a dot after the closing parenthesis.
  5. The title is given as in the original paper, including italics and special characters (e.g., Greek letters); however, any general capitalization of first letters is omitted.
  6. NAR Database issue citations (and similar specials) have an own unambiguous page numbering system. Thus, addition of "Database issue" is not required:
    • - Pospisil, H., Herrmann, A., Bortfeldt, R. H. and Reich, J. G. (2004). EASED: Extended Alternatively Spliced EST Database. Nucleic Acids Res. 32, D70-D74.

Numerical citation system:

  1. The references in the text body are given by numbers, in square brackets, in the order of their appearance.
  2. Several references may appear in one pair of brackets, separated by commata; consecutive references may be given as range:
    • - ... the participation of hydrophobic interactions in the protein folding process is rather significant [5, 19-21].

References list:

All references are listed in the order of their citation in the text, with the corresponding number ahead; otherwise, the same rules apply as for the References list in the alphabetical citation system.