CS 726: Problems and perspective in computational molecular biology

Spring 2005 Faculty: Uri Keich

Fridays 2-3 at 484 Rhodes Hall

Choose your paper(s) from the list of abstracts.

Announcements:

4/29/05 -

Shafquat Rahman will present:

Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods - Ohlson T, Wallner B, Elofsson A.

Proteins. 2004 Oct 1;57(1):188-97.

A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues - Capriotti E, Fariselli P, Rossi I, Casadio R.

Proteins. 2004 Feb 1;54(2):351-60.

4/22/05 -

Niranjan Nagarajan will present:

COMPASS: A Tool for Comparison of Multiple Protein Alignments with Assessment of Statistical Significance - Ruslan Sadreyev and Nick Grishin

J. Mol. Biol. (2003) 326:317-336

4/8/05 -

Qin Hu will present:

Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments - Chang, M.S.S. and Benner, S.A.

J. Mol. Biol. (2004) 341:617-631

4/1/05 -

Ori Weitz will present:

A Method for Simultaneous Alignment of Multiple Protein Structures - Shatsky M, Nussinov R, Wolfson HJ.

Proteins. 2004 Jul 1;56(1):143-56

3/18/05 -

Qin Hu will present:

Local homology recognition and distance measures in linear time using compressed amino acid alphabets – Edgar RC

Alignment-free sequence comparison-a review - Vinga S, Almeida J

3/11/05 -

Helgi Ingolfsson will present:

Combining phylogenetic and hidden Markov models in biosequence analysis - Siepel A, Haussler D.

follow this link to download from JCB 2004;11(2-3):413-28

3/4/05 -

Huhn-Kie Lee will present:

Genome sequence of the Brown Norway rat yields insights into mammalian evolution – Gibbs et al.

2/25/05 -

Ori Weitz will present:

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution – Hillier et al.

2/18/05 -

Yonatan Ben-Simhon will present:

Comparative recombination rates in the rat, mouse, and human genomes - Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ.

2/16/05 -

Cameron Wellock will present today at 2:30 (RH484):

Ultraconserved elements in the human genome - Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D.

Into the heart of darkness: large-scale clustering of human non-coding DNA - Bejerano G, Haussler D, Blanchette M.

2/4/05 -

Liviu Popescu will present the following papers:

Predicting protein complex membership using probabilistic network reliability - Asthana S, King OD, Gibbons FD, Roth FP.

Filling gaps in a metabolic network using expression information - Kharchenko P, Vitkup D, Church GM.