Bioinformatics Reading Group, Fall 2007

CSE department, UConn


Model-based inference of haplotype block variation, G Greenspan and D Geiger, RECOMB 2003 (Link).
Ion Mandoiu
RNA Folding Including Pseudoknots: A New Parameterized Algorithm and Improved Upper Bound (PDF), WABI 2007 by C. Liu, et al.
Yoo-Ah Kim
Exact inference algorithms: sum-product and junction tree algorithms.
Yufeng Wu
Incremental Paradigm of Motif Discovery (PDF) by Alberto Apostolico, Laxmi Parida,  Journal of Computational Biology, 2004.
Sanguthevar Rajasekaran
Exact inference algorithm: elimination and sum-product algorithms. See the following two articles by M. Jordan for reference: [Link] and [Link].
Ion Mandoiu
Introduction to graphical models. In particular, what the graph tell us and how the graph is associated with a family of probablistic distributions?
Yufeng Wu

Suggested Paper Lists

Graphical models and their applications to bioinformatics

1. On more advanced topics on graphical model:

An Introduction to Variational Methods for Graphical Models
MI Jordan, Z Ghahramani, TS Jaakkola, LK Saul - Machine Learning, 1999 - Springer

Variational methods for the Dirichlet process (2004), Link
David M. Blei, Michael I. Jordan.

Learning Module Networks, Eran Segal, et al., Journal of Machine Learning Research, 2005.

2. On sequences, binding sites, motif, and gene regulation

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data,
Eran Segal, et al., Nature Genetics, 2003.

Modeling dependencies in protein-DNA binding sites
Y Barash, G Elidan, N Friedman, T Kaplan, RECOMB 2003.

A discriminative model for identifying spatial cis-regulatory modules
E Segal, R Sharan, RECOMB 2004.

3. On haplotypes

Model-based inference of haplotype block variation -
G Greenspan, D Geiger, RECOMB 2003.
High density linkage disequilibrium mapping using models of haplotype block variation -
G Greenspan, D Geiger, ISMB 2004.

4. On genetic linkage analysis:

Exact genetic linkage computations for general pedigrees, M Fishelson, D Geiger - Bioinformatics, 2002.  Link

Optimizing exact genetic linkage computations
M Fishelson, D Geiger - Proceedings of the seventh annual international conference. Link

5. Phylognenetics

Combining phylogenetic and hidden Markov models in biosequence analysis, Siepel and Haussler, RECOMB 2003. Link

Vladimir Jojic, Nebojsa Jojic, Christopher Meek, Dan Geiger, Adam C. Siepel, David Haussler, David Heckerman: Efficient approximations for learning phylogenetic HMM models from data. ISMB/ECCB (Supplement of Bioinformatics) 2004: 161-168

Ydo Wexler, Dan Geiger: Variational Upper Bounds for Probabilistic Phylogenetic Models. 226-237, RECOMB 2007.

Motif and structural prediction

Incremental Discovery of the Irredundant Motif Bases for all Suffixes of a String
in $O(|\Sigma|n^2 \log n)$ Time.
Alberto Apostolico (Univ of Padova and Georgia Tech, Italy)
Claudia Tagliacollo (Univ of Padova & Georgia Tech, Italy)

A Graph Clustering Approach to Weak Motif Recognition.
Christina Boucher (Univ of Waterloo, Canada)
Daniel Brown (Cheriton School of Comp Sci, Univ of Waterloo, Canada)
Paul Church (Univ of Waterloo, Canada)

Informative Motifs in Protein Family Alignments.
Hatice Gulcin Ozer (Ohio State Univ, USA)
William C Ray (The Ohio State Univ, USA)

Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for
Protein Structure Prediction.
Vincenzo Cutello (Dept of Mathematics and Comp Sci, Univ of Catania, Italy)
Giuseppe Nicosia (Univ of Catania, Italy)
Giovanni Stracquadanio (Univ of Catania, Italy)

When Less is More: Improving Classification of Protein Families with a Minimal
Set of Global Features.
Roy Varshavsky (Hebew Univ, Jerusalem, Israel)
Menachem Fromer (Hebew Univ, Jerusalem, Israel)
Amit Man (Hebew Univ, Jerusalem, Israel)
Michal Linial (The Hebrew Univ of Jerusalem, Israel)

RNA Folding Including Pseudoknots: A New Parameterized Algorithm and
Improved Upper Bound.
Chunmei Liu (Howard Univ, USA)
Yinglei Song (Univ of Maryland, Eastern Shore, USA)
Louis Shapiro (Dept of Math, Howard Univ, USA)

HFold: RNA Pseudoknotted Secondary Structure Prediction Using
Hierarchical Folding.
Hosna Jabbari (Univ of British Columbia, Canada)
Anne Condon (Univ of British Columbia, Canada)
Ana Pop (Univ of British Columbia, Canada)
Cristina Pop (Univ of British Columbia, Canada)
Yinglei Zhao (Univ of British Columbia, Canada)