Date

Topic and readings

Discussion Leader

Keywords (goals, ML techniques used)

1

3/29

Introduction & overview of topics

Su-In Lee

2

3/31

Introduction & overview of topics

Su-In Lee

Lecture note 2 [ppt]

3

4/5

A feature-based approach to modeling protein-DNA interactions, Sharon E, Lubliner S, Segal E. PLoS Comput Biol. 2008.

(shorter version: Sharon E, Segal E, RECOMB 2007)

Optional readings:

Efficient structure learning of Markov networks using L1-regularization, Lee SI, Ganapathi V, Koller D. NIPS 2007.

4

Module networks: identifying regulatory modules and their conditional specific regulators from gene expression data, Segal E, Shapira M, Regev A, Pe’er D, Botstein D, Koller D, Friedman N. Nat Genet. 2003.

Optional readings:

Learning module networks, Segal E, Pe’er D, Regev A, Koller D, Friendman N. J Machine Learning Research (JMLR) 2005.

Inferring transcriptional regulatory networks; structure/parameter learning of Bayesian network

5

4/12

Probabilistic discovery of overlapping cellular processes and their regulation, Battle A, Segal E, Koller D. J Comput Biol. 2005.

(shorter version: Battle A, Segal E, Koller D. RECOMB 2004)

Clustering genes based on expression data; probabilistic relational models

6

Learning a Prior on Regulatory Potential from eQTL Data, Lee SI, Dudley AM, Drubin D, Silver PA, Krogan N, Koller D. PLoS Genet. 2009.

Optional readings:

Learning a meta-level prior for feature relevance from multiple related tasks, Lee SI, Chatalbashev V, Vickrey D, Koller D. ICML 2007.

Inferring the effect of sequence variation on regulatory networks; Bayesian network, LASSO

7

An integrative genomics approach to infer causal associations between gene expression and disease, Schadt EE et al. Nat Gen. 2005.

Inferring transcriptional regulatory networks, Bayesian network

8

Characterizing dynamic changes in the human blood transcriptional network, Zhu J, Chen Y, Leonardson AS, Wang K, Lamb JR, Emilsson V, Schadt EE. PLoS Comp Biol. 2010.

Inferring temporal changes of regulatory networks, Dynamic Bayesian network

9

Statistical estimation of correlated genome associations to a quantitative trait network, Kim SY, Xing E, PLoS Genet. 2010.

(shorter version: Kim SY, Xing E. ISMB 2009)

Identifying genetic factors for human diseases, LASSO

10

Population structure and eigenanalysis, Patterson N, Price AL, Reich D. PLoS Genet 2006.

Principal components analysis corrects for stratification in genome-wide association studies, Price AL, Patternson N, Plenge RM, Weinblatt M, Shadick NA, Reich D. Nat Gen. 2006.

Population stratification, PCA

11

SNP imputation in association studies, Halperin E, Stephan DA. Nat Biotechnology. 2009.

One of the methods listed in Table 1 or

Bayesian multi-population haplotype inference via a hierarchical Dirichlet process mixture, Xing E, Sohn KA, Jordan MI, The YW. ICML 2006.

Haplotype reconstruction & imputation, HMM or Dirichlet process

12

Reconstructing genetic ancestry blocks in admixed individuals, Tang H, Coram M, Wang P, Zhu X, Risch N. American Journal of Human Genetics (AJHG) 2006.

Inferring the local ancestry of DNA segments, Markov HMM

13

Tag SNP selection in genotype data for maximizing SNP prediction accuracy. Halperin E, Kimmel G, Shamir R. Bioinformatics 2005.

BNTagger: improved tagging SNP selection using Bayesian networks. Lee PH, Shatkay H. Bioinformatics 2006.

Tag SNP selection, Bayesian network, information theory

14

Kristi Tsukida

Inferring signaling network, Bayesian network

15

CONTRAfold: RNA secondary structure prediction without physics-based models, Do CB, Woods DA, Batzoglou S. Bioinformatics 2006.

A max-margin model for efficient simultaneous alignment and folding of RNA sequences, Do CB, Foo CS, Batzoglou S. Bioinformatics 2008.

RNA secondary structure prediction

16

Automatic parameter learning for multiple network alignment, Flannick J, Novak A, Do CB, Srinizasan, Batzoglou S. J Comput Biol. 2009.

Optional readings:

Modeling cellular machinery through biological network comparison, Sharan R, Ideker T, Nat Biotech. 2006.

Comparison of biological networks

17

Cancer classification based on genotype (TBD)

18

Evolution of regulatory networks (TBD)

19

Something on Tandem Mass Spec (TBD)