BIOL368/S20:Citation Guidelines

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

Spring 2020

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Academic Honesty Resources

Use your own words

In addition to the general guidelines set forth in “The Davidson College Department of Biology Statement on Plagiarism”, use these specific guidelines when preparing your wiki pages or other written work for this course.

  • Direct quotations are rarely, if ever, used in scientific papers. So, you should not use any in your work.
  • In a nutshell, you must synthesize the information that you have read and then write about it in your own words. You might think that there is no better way or even no different way to say it other than what your source has. This is not true. Think about what point your sentence is making, and then say it out loud as if you were explaining it to a friend. Translate the scientific jargon into regular English.
  • The only case in which it is OK to copy directly in this course is when documenting a protocol you followed as part of your electronic lab notebook. However, in this case, you must then modify the protocol as to what you actually did (using past tense) and provide appropriate attribution in your Acknowledgments and References section.

In text (in-line) citations

  • You must then cite the reference from which you obtained your information, in the body of the text, as close to where you write about it as possible.
  • A good practice is to cite once at the end of the first sentence in which you use information from that source and then again at the end of the paragraph, if the source you took the information from has not changed in the preceding sentences.
  • If you change sources, then you must cite that new source. Err on the side of too many citations. I will be looking for a minimum of two citations per expository paragraph in your written work.
  • You should only cite references that you have personally read. If you are citing information from an article that has cited another article for it, cite the one you read. You can say: (Dahlquist et al., 2002, cited in Baxevanis and Ouelette, 2005)
  • For this course, you must use the (Name, Year) format for in text citations, referring to the citation in the text at the end of the sentence. Follow the format of the following examples:
    • (Dahlquist, 2004), one author
    • (Dahlquist & Puglisi, 2000), two authors
    • (Dahlquist et al., 2002), more than two authors
  • DO NOT USE (Dahlquist, page 1000)
  • If you want to use the authors of a paper as the subject of your sentence, you can say:
    • “Dahlquist (2004) showed that…”
    • “Dahlquist and Puglisi (2000) showed that…”
    • “Dahlquist et al. (2002) showed that…”

References section

  • The references section at the end of your paper should list the full citations for each work cited in the text of the paper and no others.
  • List the citations in alphabetical order by the first author’s last name.
  • Do not change the order of the authors of a paper.
  • Each journal in the biological sciences has its own idiosyncratic formatting for the references section. For consistency of style, in this course, you will follow the APA style (see for examples).
  • The most common formats that you will use for this course are shown below.
    • A full citation for a journal article includes: author(s), year published, title, journal, volume, issue number (optional), page numbers, and DOI (if available)
      • Dahlquist, K. D., Salomonis, N., Vranizan, K., Lawlor, S. C., & Conklin, B. R. (2002). GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature genetics, 31(1), 19-20. DOI:10.1038/ng0502-19
    • A full citation for a book includes: authors(s), year published, title, publishing company, location of publisher, page numbers
      • Baxevanis, B.D. & Ouelette, B.F.F. (2005) Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins (3rd ed.), Hoboken, NJ: John Wiley and Sons, pp. 253-291.
    • A full citation for a website includes: the author of the web site, the date last updated, the name of web site, the URL listed like this, and date accessed
  • Note: The “shortcut” way to get an APA-formatted citation that you can copy and paste into your page or document is to look up the citation in Google Scholar.
    • Click on the “cite” link under the article in the search results (the icon looks like quotation marks).
    • This will open a pop-up window showing the properly formatted bibliographic citation that you can copy and paste.
    • However, this citation does not automatically provide the DOI number, so you will need to add that to your citation, if it is available.
    • The DOI number can be found on the PubMed abstract page, the publisher full text page, or on the PDF of the article iteslf.