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  • Publications

    LeBlanc, M.D., Dyer, B.D., DeMolles, C., and Li, M. (2013). The Natural Variability of Inverted Repeats in Bacterial and Archaeal Genomes. Abstract published in proceedings and presented at BIT’s 4th World Genome Day, Nanjing, China, April 26, 2013.

    LeBlanc, M.D., Baldwin, E., Hichens, K., Bass, D., Kahn, M. and Dyer, B.D. (2012). Classifying Stages of Retention and Loss of DNA Acquired by Horizontal Transfer between Bacteria and Archaea. Abstract published in proceedings and presented at BIT’s 3rd World Genome Day, Xi’an, China, April 27, 2012.

    LeBlanc, M.D. (2008). Bio Meets Big Oh: Turning Research into Programming Assignments. SIGCSE 2008. Portland, OR. (See Infusing Genomics into a Computer Science Course on Educational Materials)

    Dyer, B.D., Kahn, M.J., and LeBlanc, M.D. (2007). Classification and Regression Tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of Archaea and Bacteria. Archaea 2:159-167.

    LeBlanc, M.D. and Dyer, B.D. (2004). Bioinformatics and Computing Curricula 2001 — Why Computer Science is well positioned in a post-genomic world. ACM SIGCSE Bulletin, v36(4), Dec. 2004.

    Dyer, B.D., LeBlanc, M.D., Benz, S., Cahalan, P., Donorfio, B., Sagui, P., Villa, A., and Williams, G. (2004). A DNA motif lexicon: cataloguing and annotating sequences. In Silico Biology, v4, 0039.

    Benz, S. ’05, Grossman, R. ’07, Dyer, B. and LeBlanc, M. (2004). Genomics Research and the Liberal Arts: Building a Database for Exploring Your Favorite Set of Genes (favGene v2.0). Transformations-Liberal Arts in the Digital Age, v2(1), May 2004.

    Benz, Steve ’05 and Grossman, Robby ’07 (2004). FavGene 2.0 — A Perl and MySQL System for Exploring a Set of Genes . Journal of Computing Sciences in Colleges. v19(5), 311-312.

    Benz, Steve and Cool, Jonah (2003). Using Regular Expressions to Locate Putative Zinc Finger Binding Sites. Abstract appears in The Journal of Computing Sciences in Colleges, v18(4).

    LeBlanc, M. and Dyer, B. (2003). Teaching Together: A three-year case study in genomics. The Journal of Computing in Colleges.v18(5), 85-95.

    Villa, Adam (2003). Giving DNA a Trie. Abstract appears in The Journal of Computing Sciences in Colleges , v18(4).

    Dyer, B. and M. LeBlanc (2002). A DNA Motif Lexicon. The Scientist. August 19, 2002.

    Dyer, B. and M. LeBlanc (2002). Meeting Report: Incorporating Genomics Research into Undergraduate Curricula. Cell Biology Education , v1(4), Winter Issue 2002, 101-104.

    Christoforou, Andrea (2001). Counting Problems in Genomics. Abstract appears in Journal of Computing in Small Colleges, v16(4):343. Andrea won a 2001 Great Britain Fulbright scholarship and has completed her M.S. in Genomics in Scotland.

    Kimball, Melissa (2001). A Motif Lexicon for the Genomic Analysis of DNA. Abstract appears in Journal of Computing in Small Colleges, v16(4):344. Melissa is in graduate school in Mathematics at UNH.

    LeBlanc, M., G. Aspeslagh, N. Buggia, B. Dyer (2000).
    An Annotated Catalog of Inverted Repeats of Caenorhabditis elegans
    Chromosomes III and X, with Observations Concerning Odd/Even Biases and Conserved Motifs
    , Genome Research, v10(9):1381-1392, Cold Spring Harbor Laboratory Press, September 2000.

  • Grants

    LeBlanc, M. and Dyer B. (May 2004 – May 2007). NSF DUE 0340761 “Teaching Genomics to Undergraduate Computer Science and Biology Majors: A model involving infusion and strategic linking.” (See Linking CS and Biology Courses on Educational Materials)

  • Undergraduate Honors Theses
    • Cluster Validation Using Non-parametric Bootstrap and Parallel Processing: Applications in Unsupervised Machine
      Learning of Shimodaira’s Method to Text Mining and Genomics. Undergraduate thesis, Spring 2012. Donald went on to graduate work at Northeastern University.
    • Supporting Analyses of Gene Regulation in DNA Neighborhoods. Undergraduate thesis, Spring 2003. Adam received his Ph.D. from UNH and is a faculty member at Providence College.
    • Aspeslagh, Glen (2000).Software for Locating Potential Regulatory Motifs in the Promotors of the Kreb’s Cycle Genes of Caenorhabditis elegans. Undergraduate thesis, Spring 2000.

Teaching with Python: A course called “DNA”. (So, no … we don’t use our own Perl book anymore. Python is just the best choice of language when sharing computational programming with novices, from play to scikit-learn machine learning modules. The spirit of our collaboration in the book lives on in our course materials and the next iteration of the course.)

Perl for Exploring DNAPerl for Exploring DNA. Marc LeBlanc and Betsey Dexter Dyer (2007).  Oxford University Press.

This was a fun take on teaching scripting to life science students (but again, see our first link (above) to our current iteration of this course that uses Python).

- A Field Guide to Bacteria. Betsey Dexter Dyer (2003). Cornell University Press.

We love microbes. The human microbiome projects have spawned a gold mine of data to explore. Did we mention that we love microbes?