Biology Department

Bioinformatics seminar @ Boston College

Chuang lab

Clote lab

Marth lab


The seminar is a joint initiative of three of the bioinformatics labs (Chuang, Clote and Marth) of the Biology Department at Boston College. It primarily aims at strengthening ties and facilitating exchanges between these three groups, without precluding any external attendance.

Time and location

Time: The seminar will take place on Fridays at 2pm, starting from January 2008.
Location: Boston College [directions], Biology department, Higgins building [map].
Room to be announced.
Location and schedules subject to changes, please check out this page regularly or leave us your email if you wish to be kept updated.


  Date Speaker Title Abstract
[+] 2008-01-25 Claire Herrbach
LRI/IGM, Orsay (France)
Pairwise RNA secondary structures alignment PDF
[+] 2008-02-08 Ivan Dotu
Brown University
Towards Hybrid Methods for Solving Hard Combinatorial Optimization Problems PDF
[+] 2008-02-29 William Andrew Lorenz
Boston College
A Self-Adaptive Random Walk Algorithm to Identify Genetic Epistatic Effects
[+] 2008-03-07 Jerome Waldispuhl
Modeling ensembles of transmembrane beta-barrel proteins PDF
Transmembrane beta-barrel (TMB) proteins are embedded in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Despite their importance, very few nonhomologous TMB structures have been determined by X-ray diffraction because of the experimental difficulty encountered in crystallizing transmembrane proteins. We introduce the program partiFold to investigate the folding landscape of TMBs. By computing the Boltzmann partition function, partiFold estimates inter--strand residue interaction probabilities, predicts contacts and per-residue X-ray crystal structure B-values, and samples conformations from the Boltzmann low energy ensemble. This broad range of predictive capabilities is achieved using a single, parameterizable grammatical model to describe potential beta-barrel supersecondary structures, combined with a novel energy function of stacked amino acid pair statistical potentials. PartiFold outperforms existing programs for inter--strand residue contact prediction on TMB proteins, offering both higher average predictive accuracy as well as more consistent results. Moreover, the integration of these contact probabilities inside a stochastic contact map can be used to infer a more meaningful picture of the TMB folding landscape, which cannot be achieved with other methods. Partifold's predictions of B-values are competitive with recent methods specifically designed for this problem. Finally, we show that sampling TMBs from the Boltzmann ensemble matches the X-ray crystal structure better than single structure prediction methods. A webserver running partiFold is available at


Organizer: Yann Ponty