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.

Fall 2007

Date Speaker Title Abstract
Jan 11 Prof. Dr. Rolf Backofen (Lehrstuhl für Bioinformatik Institut für Informatik) Motif Detection under RNA Structural Constraints PDF
Jan 23 Claire Herrbach Pairwise RNA secondary structures alignment PDF
Feb 6 Bonnie Berger (MIT) Comparative Genomics: Sequence, Structure and Networks
Feb 13 Peter Clote (BC) Riboswitches, RNA conformational switches and prokaryotic gene regulation PDF
Feb 20 Jinbo Xu (TTI-C) Protein conformation sampling using conditional random fields PDF
Feb 27 Liise Holm (Univ of Helsinki/Radcliffe) Sequence space graph and some applications PDF
Mar 5 Arjun Bhutkar (BU, Harvard) Comparative Genomics: Synteny and genome rearrangements PDF
Mar 12 Jerome Waldispuhl Algorithms for exploring the mutation landscape of RNA molecules PDF
Mar 19 Dr. Shobha Polturi (Pfizer) Predictive Models for Toxicity using rat in-vivo Gene Expression Data (ToxExpress) PDF
Apr 2 Yann Ponty (BC) Statistical sampling of RNA structures: Analysis and algorithmic improvements PDF
Apr 9 Eric Xing (CMU) Nonparametric Bayesian Methods for Genetic Inference PDF
Apr 16 Jadwiga Bienskowska (Biogen/CSAIL) Convergent Random Forest Predictor: A new method for designing predictors of drug response. Predicting response to anti-TNFs in Rheumatoid Arthritis using whole blood gene expression. PDF
Apr 23 Leonid Mirney (Harvard, MIT) How gene order is influenced by the biophysics of transcription regulation PDF
Apr 30 Joseph Lehar (CombinatoRx) Systems Biomedicine and the Multi-Node Drug Target PDF
May 7 Yoel Shkolnisky (Yale) Reference Free Cryo-EM Structure Determination through Eigenvectors of Sparse Matrices PDF
May 14 Lenore Cowen (Tufts) Comparative Modeling for Protein Structure Prediction 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.