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Program MLCB 2007

Program of the MLCB workshop on December 7 & 8, 2007.

The abstracts are available here.

Friday December 7

Morning session – Interactions and function prediction: 7:30am–10:30am

7:45am Gene Function Prediction from Multiple Data Sources Using GO Priors, Sara Mostafavi, Debajyoti Ray, David Warde-Farley, Chris Grouios and Quaid Morris

8:10am Kernel methods for in silico chemogenomics, Laurent Jacob and Jean-Phlippe Vert.

8:35am Searching for functional gene modules with interaction component models, Juuso Parkkinen and Samuel Kaski

9:00am coffee break

9:15am Reaction graph kernels for discovering missing enzymes in the plant secondary metabolism, Hiroto Saigo, Masahiro Hattori and Koji Tsuda

9:40am An Automated Combination of Kernels for Predicting Protein Subcellular Localization, Alexander Zien and Cheng Soon Ong

10:05am Discussion

Afternoon session – Gene expression and regulation: 3:30pm–6:30pm

3:30pm Growth-specific programs of gene expression, Edo Airoldi, , Curtis Huttenhower, David Gresham, David Botstein and Olga Troyanskaya.

3:55pm Stochastic Multiscale Modeling Methods for Stem Cell Niches, Guy Yosiphon, Kimberly Gokoffski, Anne Calof, Arthur Lander and Eric Mjolsness

4:20pm coffee break

4:35pm Invited talk:

Comparative genomics in flies and mammals: signal discovery, regulatory networks, and evolutionary dynamics, Manolis Kellis

5:20pm Nucleosome Positioning from Tiling Microarray Data, Moran Yassour, Tommy Kaplan, Ariel Jaimovich and Nir Friedman

5:45pm Deconvolution yields a high-resolution view of global gene expression during the cell cycle, Allister Bernard, David Orlando, Charles Lin, Edwin Iversen, Steven Haase and Alexander Hartemink

6:10pm Discussion: Future plans for the Computational Biology workshop, The organizers

Saturday, December 8

Morning session – Proteomics and Imaging: 7:30am–10:30am

7:45am Markov Random Field Based Automatic Image Alignment for Electron Tomography, Farshid Moussavi, Fernando Amat, Mark Horowitz, Gal Elidan, Luis Comolli and Kenneth Downing

8:10am Spatial Querying of Imaging Mass Spectrometry Data: A Nonnegative Least Squares Approach, Raf Van de Plas, Kristiaan Pelckmans, Bart De Moor and Etienne Waelkens

8:35am Automatic mining of whole cell tomograms for cancer detection, Rajesh Narasimha, Hua Ouyang, Alexander Gray, Steven W. McLaughlin and Sriram Subramaniam

9:00am coffee break

9:15am A Generalized Framework for Protein Sequence Annotation, Huzefa Rangwala, Chris Kauffman and George Karypis

9:40am Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics, Nico Pfeifer, Andreas Leinenbach, Christian Huber and Oliver Kohlbacher

10:05am Discussion

Afternoon session – Genetic variation and evolution: 3:30pm–6:30pm

3:30pm A phylogenetically-corrected dependency network for HIV immune-adaptation, Jonathan Carlson, C. Kadie, Z. Brumme, C. Brumme, P. R. Harrigan and D. Heckerman

3:55pm Machine Learning Algorithms for Polymorphism Detection, George Zeller, G. Schweikert, R. Clark, S. Ossowski, P. Shin, … , B. Schölkopf and G. Rätsch

4:20pm coffee break

4:35pm Invited talk:

Informative positional priors for DNA motif discovery: nucleosome positioning, sequence conservation, DNA stability, Alex Hartemink (tentative)

5:20pm A finite state transducer approach to haplotype phasing, Sean O’Rourke and Eleazar Eskin

5:45pm Positional Oligomer Importance Matrices, Soeren Sonnenburg, Alexander Zien, Petra Philips and Gunnar Rätsch

6:10pm Closing remarks, The organizers

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