Problems and Perspectives in Computational Molecular
Biology
Cornell University
Spring 2002
The next presentation
Wednesday May 1
Edward Choi (Electrical Engineering)
(1) Correlated mutations contain information about protein-protein interaction.
abstract, paper
(2) Coevolving Protein Residues: Maximum Likelihood Identification
and Relationship to Structure.
abstract, paper
(3) Co-evolution of Proteins with their Interaction Partners.
abstract, paper
Future presentations (schedule your presentation)
Previous presentations and presentation files
(Fall 2001)
Time and Place
Wednesdays 1:25 pm to 2:40 pm
Upson Hall 205
1 credit, S/U only.
Prerequisites:� Permission of instructor.
The seminar is required from students of the Computational Molecular
Biology Program.
Instructors
Golan Yona (CS),
Marty Wells (BSCB),
Doug Knipple
(Entomology)
This course is cross-listed as CS 726 (Computer Science),
PB 726 (Plant Breeding) and BSCB 726 (Biometrics)
Links
Introduction
This is a weekly seminar series discussing timely topics in
computational molecular biology. The course addresses methodological
approaches to sequence and structure analysis, function prediction,
study of evolutionary relationships, and analysis of large biological
system. Statistical and deterministic computational approaches will
be covered and specific and detailed biological examples will be
discussed.
After a successful fall semester, we decided to continue in a similar
format. In each topic we will select one or two representative papers
that made significant advances in this field. The lectures will be
given by faculty and students. The seminar is open to all from the
life sciences, computational sciences, and the physical sciences. We
will try to bridge these disciplines by pairing students/faculty from
complementary backgrounds.
The topics that will be covered in the spring 2002 semester:
- Protein structure analysis
- Protein-protein interactions
- Co-evolution
- Gene networks
- Whole-cell simulations
Suggested Papers
Structure analysis
Fold recognition, Threading, Structure prediction
session 1
Prof. Ron Elber
session 2 (two papers out of five)
- Rost, B., Schneider, R. & Sander, C. (1997). Protein fold
recognition by prediction-based threading. J. Mol. Biol.
270, 471-480. abstract
- Jaroszewski, L., Rychlewski, L., Zhang, B. & Godzik,
A. (1998). Fold prediction by a hierarchy of sequence,
threading, and modeling methods. (1998). Protein Sci 7,
1431-1440. abstract
- Olmea, O., Rost, B. & Valencia, A. (1999). Effective use of
sequence correlation and conservation in fold recognition. J
Mol Biol. 293, 1221-1239. abstract
- Karplus, K., Barrett, C., Cline, M., Diekhans, M., Grate, L.
& Hughey, R. (1999). Predicting protein structure using only
sequence information. Proteins 37, 121-125. abstract
- Jones, D. T. (1999). GenTHREADER: an efficient and reliable
protein fold recognition method for genomic sequences.
J. Mol. Biol. 287, 797-815. abstract
session 3 (two papers out of four)
- Lemer, C. M., Rooman, M. J. & Wodak, S. J. (1995). Protein
structure prediction by threading methods: evaluation of current
techniques. Proteins 23, 337-355. abstract
- Bryant, S. H. (1996). Evaluation of threading specificity
and accuracy. Proteins 26, 172-185. abstract
-
Mirny, L. A. & Shakhnovich, E. I. (1998). Protein structure
prediction by threading. Why it works and why it does not.
J. Mol. Biol. 283, 507-526. abstract
- Bienkowska JR, Yu L, Zarakhovich S, Rogers RG Jr, Smith TF. (2000).
Protein fold recognition by total alignment probability.
Proteins 40, 451-62. abstract
Structure comparison (Dali, CE, Structal, Geometric hashing)
session 4 (two papers our of three)
- Nussinov R, Wolfson HJ. (1991). Efficient detection of
three-dimensional structural motifs in biological
macromolecules by computer vision techniques.
Proc Natl Acad Sci USA. 88, 10495-10499. abstract
- Holm, L. & Sander, C. (1997). Dali/FSSP classification
of three-dimensional protein folds. Nucl. Acids Res. 25, 231-234.
abstract
- Shindyalov, I. N. \& Bourne, P. E. (1998). Protein structure
alignment by incremental combinatorial extension (CE) of the
optimal path. Protein Eng. 11, 739-747. abstract
session 5 (two papers out of three)
- Levitt, M & Gerstein, M. (1998). A Unified Statistical Framework
for Sequence Comparison and Structure Comparison.
Proc. Natl. Acad. Sci. USA 95, 5913-5920. abstract
- Jongsun Jung and Byungkook Lee. (2000). Protein structure
alignment using environmental profiles. Protein Eng. 13,
535-543. abstract
- Hadley, C. & Jones, D. T. (1999). A systematic comparison of
protein structure classifications: SCOP, CATH and FSSP.
Structure Fold Des. 7, 1099-1112. abstract
Automatic detection of domains
session 6 (two papers out of three)
- Holm, L. & Sander, C. (1994). Parser for protein folding units.
Proteins 19, 256-268. abstract
- Sowdhamini R, Blundell TL. (1995). An automatic method involving
cluster analysis of secondary structures for the identification of
domains in proteins. Protein Sci 4, 506-520. abstract
-
Jones, S., Stewart, M., Michie, A., Swindells, M. B., Orengo, C.
& Thornton, J. M. (1998). Domain assignment for protein structures
using a consensus approach: characterization and analysis.
Protein Sci. 7, 233-242. abstract
session 7 (two papers out of three)
- Taylor, W. R. (1999). Protein structural domain identification.
Protein Eng. 12, 203-216. abstract
- Xu, Y., Xu, D. & Gabow, H. N. (2000). Protein domain decomposition
using a graph-theoretic approach. Bioinformatics 16, 1091-1104.
abstract
- Kael F. Fischer, Susan Marqusee. (2000). A Rapid Test for
Identification of Autonomous Folding Units in Proteins. J Mol
Biol. 302, 701-12. abstract
Structural/evolutionary profiles
session 8 (two papers out of four)
- Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D,
Yeates TO. (1999). Assigning protein functions by comparative
genome analysis: protein phylogenetic profiles. Proc Natl
Acad Sci USA. 96, 4285-8. abstract
- Marcotte EM, Xenarios I, van Der Bliek AM, Eisenberg D. (2000).
Localizing proteins in the cell from their phylogenetic profiles.
Proc Natl Acad Sci USA 97, 12115-20. abstract
- Kelley, L. A., MacCallum, R. M. & Sternberg, M. J. (2000).
Enhanced genome annotation using structural profiles in the
program 3D-PSSM. J. Mol. Biol. 299, 499-520. abstract
- Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D.
(1999).A combined algorithm for genome-wide prediction of protein
function. Nature 402, 83-6. abstract
Co-evolution, Protein-protein interaction
session 9
- Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D.
(1999). Detecting protein function and protein-protein
interactions from genome sequences. Science 285, 751-3.
abstract
- Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. (1999).
Protein interaction maps for complete genomes based on gene fusion
events. Nature 402, 86-90. abstract
session 10 (two papers out of three)
- Schwikowski B, Uetz P, Fields S. (2000). A network of protein-protein interactions
in yeast. Nat Biotechnol. 18, 1257-61. abstract
- Gallet X, Charloteaux B, Thomas A, Brasseur R. (2000).
A fast method to predict protein interaction sites from sequences.
J Mol Biol. 302, 917-26. abstract
- Park J, Lappe M, Teichmann SA. (2001). Mapping protein family
interactions: intramolecular and intermolecular protein family
interaction repertoires in the PDB and yeast. J Mol Biol.
307, 929-38. abstract
session 11 (two papers out of three)
- Pazos, F., Helmer-Citterich, M., Ausiello, G. \& Valencia,
A. (1997). Correlated mutations contain information about
protein-protein interaction. J. Mol. Biol. 271, 511-523.
abstract
- David D. Pollock, William R. Taylor, Nick Goldman. (1999).
Coevolving Protein Residues: Maximum Likelihood Identification
and Relationship to Structure. Journal of Molecular Biology
287, 187-198. abstract
- Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE. (2000).
Co-evolution of Proteins with their Interaction Partners.
J Mol Biol. 299, 283-93. abstract
Gene networks, Whole-cell simulations
session 12
- Wessels LF, van Someren EP, Reinders MJ. (2001).
A comparison of genetic network models. Pac Symp Biocomput. 508-19.
abstract
- Maki Y, Tominaga D, Okamoto M, Watanabe S, Eguchi Y. (2001).
Development of a system for the inference of large scale genetic networks. Pac Symp Biocomput. 446-58.
abstract
- Saqi MA, Sternberg MJ. (2001).
A structural census of metabolic networks for E. coli.
J Mol Biol. 313, 1195-206.
abstract
session 13
- Friedman N, Linial M, Nachman I, Pe'er D. (2000).
Using Bayesian networks to analyze expression data.
J Comput Biol. 7, 601-20. abstract
- Pe'er D, Regev A, Elidan G, Friedman N. (2001).
Inferring subnetworks from perturbed expression profiles.
Bioinformatics 17
abstract
session 14
- Karp PD. (2001).
Pathway databases: a case study in computational symbolic theories.
Science. 293, 2040-4.
abstract
- Ideker T, Galitski T, Hood L. (2001).
A new approach to decoding life: systems biology.
Annu Rev Genomics Hum Genet. 2, 343-72.
abstract
Books
- Waterman, M. S. (1995). Introduction to computational biology.
Chapman & Hall, London.
- Setubal, J. C. & Meidanis, J. (1996).
Introduction to computational molecular biology.
PWS Publishing Co., Boston.
- Methods in Enzymology, vol 266 (1996). Edited by R. F. Doolittle.
- Durbin, Eddy, Krogh, Mitchison (1998). Biological sequence analysis.
- Baldi, P. & Brunak, S. (1998). Bioinformatics: the machine
learning approach.
- Bioinformatics: Sequence, structure, and databanks.
Edited by D. Higgins and W. Taylor. Oxford University Press.
Journals
Science
Nature
Nature Structural Biology
Cell
Proceedings of the National Academy of Sciences
JMB
Protein Science
Proteins: Structure, Function, and Genetics
Protein Engineering
Nucleic Acids Research
Bioinformatics
Journal of Computational Biology
Trends in Biochemical Sciences
Molecular Microbiology
Web journals
Science's Next Wave
BioMedNet 'webzine'
GenomeBiology
Paper Search and Misc.
Biochemistry and Molecular Biology Journals
IDEAL homepage
PubMed (Medline)
NEC archive
e-Print archive
citation reports (impact factor of scientific journals)
Background reading
For a survey of the classic algorithms for sequence comparison
and the statistics of sequence alignment (topics covered
in the fall semester 2001) you can download one
of the following documents
Recommended books and book chapters on
- Sequence alignment.
Books: Waterman (1995), Setubal & Meidanis (1996),
Durbin, Eddy, Krogh, Mitchison (1998).
Book chapters: Pearson (Methods Enzymol 1996),
Yona & Brenner (Bioinformatics 2000).
- multiple sequence alignment and profiles
Books: Waterman (1995), Setubal & Meidanis (1996),
Durbin, Eddy, Krogh, Mitchison (1998).
Book chapters: Gribskov (Methods Enzymol 1996),
Taylor (Methods Enzymol 1996), Duret & Abdeddaim (Bioinformatics 2000).
- Hidden Markov Models
Books: Durbin, Eddy, Krogh, Mitchison (1998), Baldi & Brunak (1998).
Book chapters: Birney (Bioinformatics 2000)