You can check out the pictorial history of Wheaton's Genomics Group.

It is time of exciting science. The extreme complexity and enormous length of DNA molecules have made their study a daunting task, far more than any scientist could tackle alone. However, aided by cleverly designed computer programs as tools, it is possible to study, search, and analyze entire DNA strands in seconds.

Our research continues to pour over into our teaching. Our work in the lab has influenced the undergraduate curricula in biology and computer science (see Educational Materials). This in turn contributes to a pipeline of students who work with us on our research; for example, applying authorship attribution techniques in search of genomic signatures and the construction of a Motif Lexicon or DNA Dictionary. In addition, LeBlanc and Dyer have team-taught three iterations of a course called "DNA" where non-majors creatively use regular expressions and Perl to explore DNA sequences. They have written a book to help novice programmers learn to write programs for sequence analyses Perl for Exploring DNA (Oxford University Press, 2007).

Dr. Betsey Dexter Dyer a Professor of Biology at Wheaton College, is most responsible for keeping the software-types busy. She is interested in the grammar and syntax of gene regulation.

Dr. Mark D. LeBlanc is Professor of Computer Science at Wheaton College. Mark tries to manage the software-types. He is interested in pattern matching and computational sylistics.

Dr. Michael J. Kahn is Professor of Mathematics and Statistics at Wheaton College. Mike recently introduced the group to the programming language "R" and serves as the group's current lead on statistical analysis. He also makes strong coffee which is working out quite well.

Neil Kathok '10 wrote Perl scripts to test all the examples in our new book and ported each example to the book's companion website. Neil is currently building a new database of microbial genomes and associated suite of scripts to automatically seed the database when new microbial genomes become available at NCBI. Neil currently serves as our student project leader.

Amos Jones '11 joins the group this summer 2008. When he isn't found playing GTA4, you can find him cutting code in the lab.

Christina Nelson '11 joins the group this summer 2008. When she's not running long distances, she is applying her new skills in C++ and Perl.

Past Performances

Evan Ferri '08 , a biology major, was quickly recruited to join our group after finishing our Perl DNA course. Evan kept the software types honest as we searched for genomic signatures between plasmids and their hosts durring 2007 and early 2008. Evan plans to go on to medical school.

Matt Brown '10 joined our weekly journal clubs in 2007 and 2008. He led SQL tutorials for the group as we began a new database design.

Greg Williams '02 was a former computer science major and a current computer science Ph.D. student at RPI. Greg continues to sport wild hair and served as our hacker supreme for years. He reviewed our entire manuscript of our Perl book (Oxford, 2007), serving as our in-house Perl expert. He also helped finish off a database of microbial genomes.

Robbie Grossman '07 was a computer science major who lent considerable expertise in database design and Perl scripts to automatically seed our a database of microbial genomes.

Nguni Phakela '06, was Wheaton's first double major in computer science and biochemistry. Nguni prototyped some of first experimental software in phylogenetics under the guidance of Biology Professor Shawn McCafferty.

Sarah Milewski '07 was a computer science major. Sarah implemented routines to seed our new microbial database.

Stephen Benz '05 was a computer science major and biochemistry minor and is now a Ph.D. student in Bioinformatics (starting in Fall 2007). Steve was our lead programmer for two years in 2004 and 2005. Steve worked from the west coast during the summer of 2002 completing the redesign of our GUI for the Motif Lexicon v2.0. Steve was funded for the 2002-2003 academic year and worked on the design and implementation of regular expressions and software to search for putative zinc-finger binding sites. 

Patrick Sagui '04 computer science major. Patrick is a jack-of-all-boxes. Pat ported our Perl and C++ CGIs to a new Linux box over the summer of 2002 and helped with the upgrade of the Motif Lexicon to v2.0.

Pete Cahalan '04 Pete scripted in C++ and Perl during the summer of 2003 as the Motif Lexicon moved to v3.0. Pete and Brian left scripts and directions for handling new organisms that are added to the Motif Lexicon.

Brian Donorfio '04 Brian moved the Motif Lexicon to v3.0 during the summer of 2003; v3.0 handles multiple organisms.

Pete and Brian worked during the summer of 2003 on the Motif Lexicon. They shipped v3.0 of the lexicon so that it includes the functionality of handling multiple organisms.

Austin Jordan '03 computer science major. Austin worked as a consultant during the summer of 2003 on a redesign of the Genomics Research Group web site.

Adam Villa '03, computer science major, honors thesis student, and French minor. Adam started with the group in January 2001. He first helped prototype an HTML-wrapper for the software framework for our Motif Lexicon. Adam completed an honors thesis in genomics subtitled "Giving DNA a Trie" where he implemented the "Neighborhood" CGI in the Motif Lexicon. Adam is a PhD student in computer science at UNH.

Jonah Cool '04 Jonah worked with Steve Benz on the favGene application. Jonah researched the literature for Zinc Finger transcription factors and their associated DNA binding sites. Jonah is working on his Ph.D. in Biology.

Martin Baron '03 double major: computer science and mathematics. Martin put the finishing touches on the statistical module in the summer of 2002 and prototyped a "relateds" module as we shipped version 2.0 of the Motif Lexicon.

Missy Kimball '02 dual mathematics and computer science major. A jack of all trades, you could usually find her proving abstract theorems, working on programs in C, or belting out tunes with the Whims, the acappella group. Missy prototyped the initial motif lexicon in Perl and C and added a new statistical module in January 2002. Missy is a graduate student at UNH.

Nick Doolittle '03 computer science major who was a lead on the implementation of a C++ class for handling the caching of results for the Motif Lexicon in January 2001. He started a new module to find all repeats of various configurations with loops of any length in January 2002.

Jon Lister '03 dual math/computer science major. Jon created a database of biology and computer science programs in the northeast in support of our NSF workshops on incorporating genomics into the undergraduate curriculum.

Trevor Agnitti '02 dual computer science and physics major. In addition to his contributions in the genomics group, he was known for his hallway scootering and a wide selection of really spiffy shirts.

Chris Wilbur '05 biology major. Chris put together a DNA helix model, a beautiful addition to our lab.

Glen Aspeslagh '00 computer science major. When he wasn't working on some C++ dynamic programming or Perl data viewers, he could be found programming his Palm Pilot. Glen implemented the first browser tool on our site and started the "Favorite Gene Project" with his thesis work on repeats in the Krebs cycle.

Nathan Buggia '01 computer science major. When he wasn't found clutching a copy of von Heijne's Sequence Analysis in Molecular Biology, he was probably cranking out some C++ or Perl as he served coffee at the Lyon's Den. Nathan left the group a software framework for the motif lexicon to facilitate continued student development on the project.

Andrea Christoforou '01 , double-major in Mathematics and Chemistry and a Fulbright Scholar studying bioinformatics in England. Andrea worked on closed form equations to compute the liklihood of finding all possible repeats.

Jen Tobin '01 , Biochemistry major. Jenn searched MedLine for all possible current functions for intergenic motifs of length L=4bp.

You can check out the history of the Wheaton College Genomics Group.