Bioinformatics Seminar

The Bioinformatics Seminar is co-sponsored by the Department of Mathematics at the Massachusetts Institute of Technology and the Theory of Computation group at MIT's Computer Science and Artificial Intelligence Laboratory (CSAIL). The seminar series focuses on highlighting areas of research in the field of computational biology. This year, we are hoping to highlight three topics: (1) language models and their uses in biology and biomedicine, (2) ethical and societal issues in biomedical data (e.g. privacy, fairness), and (3) single-cell biology.

Spring 2004

Date Speaker Title Abstract
Feb. 9 John Aach
Multicellular genetic network modeling: directions and issues PDF
Feb. 16 Holiday
President's Day
Feb. 23 Guest Lecturer: Phil Bradley
In Conjunction with AMC
Folding Algorithms for Protein Structure Prediction PDF
Mar. 1 Peter Clote
Boston College
Efficiently Computing the Landscape of Locally Optimal RNA Secondary Structures
Mar. 10 Matt Menke
Berger Lab Member, MIT/CSAIL
Wrap-and-Pack: A New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils PDF
Mar. 15 No Lecture
Mar. 22 Spring Vacation
Mar. 29 Tandy Warnow
Department of Computer Sciences, University of Texas at Austin
The CIPRES Project: Inferring the Tree of Life PDF
Apr. 5 Shamil Sunyaev
Harvard Medical School and Brigham and Women's Hospital
Computational Analysis of the Genome Variation... PDF
Apr. 12 Temple Smith
Boston University
The tale of two protein domain problems... PDF
Apr. 19 Holiday
(Patriot's Day)
Apr. 26 Bonnie Berger
Mathematical Challenges in Molecular Biology PDF
May 3 Gary Benson
Searching for Inverted Repeats in Genomic Sequences PDF
May 5 Sorin Istrail
On the General and Logical Theory of Genomic Regulatory Systems PDF
May 11 Qicheng Ma
Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks PDF
Jun. 2 Paul Vitanyi
CWI and the University of Amsterdam
Clustering by Compression --- the Similarity metric PDF

Past Terms

A listing of the Bioinformatics Seminar series home pages from prior terms.

Organizers and Information

The Bioinformatics Seminar is hosted by MIT Simons Professor of Mathematics and head of the Computation and Biology group at CSAIL Bonnie Berger. Professor Berger is also Faculty of Harvard-MIT Health Sciences & Technology, Associate Member of the Broad Institute of MIT and Harvard, Faculty of MIT CSB, and Affiliated Faculty of Harvard Medical School.

The seminar is announced weekly via email to members of the seminar's mailing list and to those on CSAIL's event calendar list. It is also posted in the BioWeek calendar.

Bonnie Berger:

Shuvom Sadhuka (TA):

To be added to the seminar's email announcement list or for any questions you have about the seminar, please mail

If you plan to enroll in the associated course, 18.418/HST.504: Topics in Computational Molecular Biology, please contact Professor Berger ( and cc TA Shuvom Sadhuka ( for more information.