BIOE598 Spring 2007: Current Topics in Bioinformatics

Papers for discussion

Cis-regulation:

Regulatory motif finding by logic regression

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/16/2799

Chieh-Chun Chen, Jan 17

Coupling Hidden Markov Models for the Discovery of Cis-Regulatory Modules in Multiple Species

Zhou Q, Wong W (In press), Annals of Applied Statistics

Dan Xie, Feb 28

Physical Constraints and Functional Characteristics of Transcription Factor-DNA Interaction

U. Gerland, J.D. Moroz and T. Hwa. PNAS 99: 12015-12020 (2002).

http://matisse.ucsd.edu/~hwa/pub/TF-DNA.pdf

On schemes of combinatorial transcription logic

Nicolas E. Buchler, Ulrich Gerland, and Terence Hwa (2003)

http://matisse.ucsd.edu/%7Ehwa/pub/logic.pdf

Feng Hong, Jan 31

Large-scale turnover of functional transcription factor binding sites in Drosophila

Alan M. Moses, …, Michael Eisen (2006).

Chieh-Chun Chen, Feb 7

arrayCGH and tiling array:

Hidden Markov models approach to the analysis of array CGH data

http://portal.acm.org/citation.cfm?id=1016469.1016476

Yanen Li, Jan 24

MAT: Model-based Analysis of Tiling-arrays for ChIP-chip.

Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS (2006).Proc Natl Acad Sci U S A. 103: 12457-12462

Tze-Howe Charn, Feb 14

Clustering:

Hierarchical Beta Processes and the Indian Buffet Process

R. Thibaux, and M. I. Jordan, Technical Report 719, Department of Statistics, University of California, Berkeley, 2006

http://www.stat.berkeley.edu/tech-reports/719.pdf

David Unger, Feb 21

Branching process:

An Application of a General Branching Process in the Study of the Genetics of Aging. Journal of Computational Biology, 2001

http://www.math.tulane.edu/~polofsson/aging.pdf

Supplementary reading:

1. Fengzhu Sun. The polymerase chain reaction and branching process. Journal of Computational Biology, 2(1):63--86, 1995

2. http://www.stat.berkeley.edu/users/terry/Classes/s260.1998/Week9b/week9b/node4.html

Papers for the second semester:

Evolution of Gene Expression:

The following paper will be presented by Dan Xie on April 18.

Evolution of primate gene expression

Philipp Khaitovich, Wolfgang Enard, Michael Lachmann and Svante Pääbo

Nature Reviews Genetics 7, 693-702 (September 2006) | doi:10.1038/nrg1940

http://www.nature.com/nrg/journal/v7/n9/abs/nrg1940.html

Toward a neutral evolutionary model of gene expression

Khaitovich, P. , Paabo, S. & Weiss, G. Genetics 170, 929–939 (2005)

http://www.genetics.org/cgi/content/abstract/170/2/929

Dirichlet Process:

The following paper will be presented by David Unger on April 4.

A Split-Merge Markov Chain Sampling Algorithm For Bayesian Mixture Models
Sonia Jain and Radford Neal. Technical Report No. 2003, Dept. of Statistics, University of Toronto
http://www.cs.toronto.edu/~radford/papers-online.html
http://www.cs.toronto.edu/~radford/ftp/mixsplit.pdf

arrayCGH:

The following two papers will be presented by Yanen Li on April 11.

COMPARATIVE GENOMIC HYBRIDIZATION

Daniel Pinkel and Donna G. Albertson. Annu. Rev. Genomics Hum. Genet. 2005. 6:331–54

http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genom.6.080604.162140?cookieSet=1

Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data

Weil R. Lai, Mark D. Johnson, Raju Kucherlapati and Peter J. Park.

Bioinformatics Volume 21, Number 19 Pp. 3763-3770

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/19/3763

Transcription:

The following paper will be presented by Feng Hong on April 25.

Interacting models of cooperative gene regulation. PNAS 2004

http://www.pnas.org/cgi/content/full/101/46/16234