Funding : We thank the generous support and funding that we have received from the National Science Foundation, Mars Fellowships, Davis Educational Grants, The Filene Center for Work and Learning, Wheaton Research Partners, Wheaton Foundation Grants, and Wheaton's Provost Office.

1998

In the beginning... Mark and Betsey experiment with their first "linking" of a computer science course and a biology course.

1999

Our initial search and browse tools went online in the fall of 1999.

2000

In the spring of 2000, Glen Aspeslagh finished the "Favorite Gene Project" with his thesis work entitled: Software for Locating Potential Regulatory Motifs in the Promotors of the Kreb's Cycle Genes of Caenorhabditis elegans.

Results from initial experimental runs by Nathan Buggia '01 and Glen Aspeslagh '00 were published:
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.

In the fall semester, Nathan Buggia enrolled in an independent research course entitled: "System design engineering for data storage and analysis in genomics research." Nate's work set the foundation for the Jan. 2001 system redesign.

2001

During January break, the group implented a Motif Lexicon for C.elegans (Nathan Buggia '01 Computer Science, Melissa Kimball '02 Mathematics & Computer Science, Nick Doolittle '03 Computer Science, Adam Villa '03 Computer Science).

During the spring semester, Andrea Christoforou '01, a double major in Chemistry and Mathematics worked on counting problems in genomics under Professor of Mathematics Shelly Leibowitz and Professor of Biology Betsey Dyer.

Andrea Christoforou '01, a double major in Chemistry and Mathematics and Melissa Kimball '01, a double major in Computer Science and Mathematics presented their research projects in genomics at the annual conference of Computer Science in Colleges at Middlebury College, VT, April 2001.

Professors Dyer and LeBlanc were awarded a grant from the National Science Foundation (NSF DUE 0126643) to encourage other faculty in biology and computer science to work together and encorporate genomics into their curriculums.

Spring 2001 Images

June 2001 Images

During the fall semester Greg Williams '03 searched for the top-10 motifs of any lengths from local neighborhoods as well as genome wide in C.elegans . Adam Villa '03 included a new module into the motif lexicon for searching "neighborhoods".

Some of the meetings of the Genomics Group happen at the Lyon's Den.

2002

During January break Nick Doolittle '03 started a new module to find all repeats of any length with unlimited loop size. Missy Kimball '02 integrated a new module to give the statistical liklihood of a requested motif. This module was the result of earlier work by Andrea Chritoforou '01. Greg Williams '02 wrote a very cool "Etymology" module which searches PubMed for all published abstracts for one's requested motif.

In the spring Greg Williams '02 enrolled in COMP 499 - Genomics Research - and implemented a suite of filters for motifs in the regulatory regions of some of the genes involved in making the flagella in bacteria. His version of the "favorite gene project" is due in the Fall of 2002.

Martin Baron '03 and Patrick Sagui '04 (above) were Mars Fellows for the summer . Martin and Pat moved the motif lexicon to version 2.0, implementing a number of enhancements to the GUI and statistics module. Martin added a new "relateds" module for the lexicon while Pat ported our CGIs to a new Linux box.

In the August 19 , 2002, v17 issue of The Scientist, Dyer, B. and LeBlanc, M. published Free user-friendly genomics software.

Fall 2002 Images

At the 14th International Genome Sequencing and Analysis Conference, on October 4th in Boston, MA, Professors Mark LeBlanc and Betsy Dyer along with students Baron, M. '03, Christoforou, A. '01, Doolittle, N. '03, Kimball, M. '02, Villa, A. '03, Williams, G. '02 presented The DNA Motif Lexicon -- cataloguing and annotating genomes.

Glen returns for a party and checks out our latest software.

In the Winter 2002 issue of Cell Biology Education (101-104), Betsy Dyer and Mark LeBlanc published a workshop report - Incorporating Genomics Research into Undergraduate Curricula.

On December 14th , Professors Mark LeBlanc and Betsy Dyer presented Collaborations in Genomics - Connecting Courses in Genetics and Computer Science at the workshop New Paradigms in Teaching Introductory and Cell Biology at the Annual Meeting of the American Society for Cell Biology in San Francisco, CA.

Two days later on December 16th, Professors LeBlanc and Dyer along with Steve Benz, '05 and Jonah Cool, '04 attended The 42nd Annual Meeting of the American Society for Cell Biology to present Towards a DNA Dictionary.

2003

By January of 2003, Greg Williams '02 had set up a MySQL database (with worm, yeast, and Ecoli genomes) and written Perl utilities that search and/or create files of DNA sequence of the upstream, downstream, and genic regions of a family of genes (favGene v1.0).

At Dickison College in Carlisle, PA on March 21st and 22nd , Dyer, B. and LeBlanc, M. presented Genomics in the Undergraduate Curriculum.

The following month, April , professors LeBlanc and Dyer presented Teaching together: A three-year case study in genomics at the Northeastern Conference on Computing in Small Colleges and published in The Journal of Computing Sciences.

The abstract of Adam Villa's ('03) Searching DNA Neighborhoods was published in The Journal of Computing Sciences in Colleges, April 2003 , p245.

Also published that April was Mark LeBlanc and Betsy Dyer's Teaching together: A three-year case study in genomics in The Journal of Computing Sciences in Colleges, v18(5), April 2003, p85-95.

During the entire 2002-2003 academic year, Steve Benz '05 and Jonah Cool '04, worked jointly on designing regular expressions and Perl programs to search for putative zinc finger binding sites. Steve and Jonah presented their research at the annual conference of Computer Science in Colleges at Rhode Island College, RI, April 2003.

To be presented at the Northeastern Conference on Computing in Small Colleges (2003) by Benz, S. '05 and Cool, J. '04 is Using Regular Expressions to Locate Putative Zinc Finger Binding Sites. Also the abstract has been published in The Journal of Computing Sciences in Colleges.

Adam Villa '03 completed an honors thesis in computer science in the Spring . Adam's thesis was entitled, "Supporting Exploratory Analyses of Gene Regulation in Localized DNA Neighborhoods." Adam presented his research at the annual conference of Computer Science in Colleges at Rhode Island College, RI, April 2003 .

Also during that April , in The Journal of Computing Sciences in Colleges, Benz, S. '05 and Cool, J. '04 published Using Regular Expressions to Locate Putative Zinc Finger Binding Sites.

Spring 2003 Images

Presented at the Northeastern Conference on Computing in Small Colleges (2003) was Adam Villa's, '03, Searching DNA Neighborhoods. The abstract was also published in The Journal of Computing Sciences in Colleges.

In June , Dyer, B. and LeBlanc, M. presented  "A Second Workshop for Professors teaching Undergraduate Biology or Computer Science with an interest in incorporating "Genomics" (the analysis of DNA sequences) into their curricula." (NSF DUE #0126643).

Summer 2003 Images

During July 28th through the 30th , in Boulder, CO, at MathFest 2003, Professor LeBlanc will present a two-day short course on 'Reading the Book of Life: How Bioinformatics Makes Sense of Molecular Messages' -- Moving Research to the Classroom: Linking courses in Biology and Computer Science.

2004

In a year-long project, Steve Benz '05, Robby Grossman '07, and Nguni Phakela '06 worked on version 2.0 of the "favorite gene" project. favGene is an application that stores genomes in a MySQL database on the backend to facilitate a user (via Perl scripts on the frontend) in selecting and assembling the DNA sequences in the upstream, downstream, and/or genic regions of their "favorite" set of genes. Additional Perl scripts allow the user to either take home their sequences or search just those regions for various motifs using regular expressions.

Steve and Robby presented their work at the northeast regional conference on computer science education (CCSCNE 2004) at Union College in April 2004.
As part of a new NSF grant (NSF DUE # 0340761), Robby and Steve will work during the summer of 2004 on favGene.

Spring 2004 Images

Steve Benz '05	Robby Grossman '07	Nguni Phakela '06

CCSCNE 2004 at Union College

Steve, Brian and Robby outside of the Knatt Memorial, where they presented their posters

 

Steve and Robby in front of their poster

 

Steve explains favGene to professors from various New England colleges

2005

Steve Benz finished his senior year helping Betsey upgrade the favGene tool. Betsey presented some of her work at ASM.

Mark taught and did research at the University of Wollongong (UoW), Australia for the year. He presented the group's work on favGene at the International Conference on Bioinformatics in Auckland, New Zealand. Mark worked with Paul White (UoW) '06 on a set of routines to automate experimental runs that test authorship attribution techniques, typically used on English texts, in the context of identifying the kingdom, genus, and species of a given sequence of DNA.

2006

Mark and Betsey made inroads with reaching the national community of computer science professors as they presented workshops at CCSC-Eastern (Iona College, NY) and SIGCSE (Houston, TX). With "pre-doc" Greg Williams '02 as a consultant, Mark and Betsey shipped their manuscript for their new book, 'Perl for Exploring Biological Sequences' (Oxford University Press, due out in early 2007). The group received additional funding and a one-year extension on their NSF grant (NSF DUE # 0340761), to help finish their book.

Under the leadership of Wheaton Biology Professor Shawn McCafferty, Mark and Nguni Phakela '06 developed some software to help Shawn with his research in phylogenetic analyses. In particular, Nguni and Mark implemented routines to compute patristic distances of a variable number of organisms.

Sarah Milewski '07 and Robbie Grossman '07 designed and prototyped a database to store the entire chromosomal and plasmid DNA for over 300 prokaryotic genomes. Greg Williams '02 helped implement a final version. The database is a huge move forward for the group as it holds metadata on the each organism (e.g., salinity, mobility, temperature range, etc), thus facilitating the range of questions to pose of microbial genomes.

2007

While on year-long sabatticals, Betsey and Mark joined colleague Mike Kahn (Statistics) in a series of experiments to classify 200+ bacteria and archaea genomes by temperature regime (hyperthermophile, thermophile, or mesophile). Mike introduced the group to the statistical programming language "R" where Mark and Mike developed models using CART (Classification and Regression Trees). The work led to a publication in the journal Archaea 2:159-167, 2007.

Neil Kathok '10 joined the Genomics Group in the Spring of 2007 to help test all of the Perl routines to appear in our new book, Perl for Exploring DNA. Neil also created a website which will appear on the book's Oxford University Press companion website to allow users of the text to download all of the Perl examples.

2008

Throught the fall of 2007 and spring of 2008, the Genomics Group consisted of students Neil Kathok '10, Evan Ferri '08, and Matt Brown '10. Neil, Evan, and Matt worked with Professors Dyer, Kahn, and LeBlanc to update the group's microbial database and to design experiments that use genomic signature to investigate relationships between microbial plasmids and pathogenicity.