Artificial Intelligence and Heuristic
Methods for Bioinformatics

A NATO Advanced Studies Institute

San Miniato, Italy October 1-11, 2001

Co-directors: Paolo Frasconi (University of Florence) Ron Shamir (Tel Aviv University)

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Schedule and program of lectures (updated)

Online lecture notes and links (new)

Submitted papers (new)

Organizing Committee and Lecturers

Participation and Application form

Location, traveling, accommodation

Lecture notes and weblinks

This is a partial set of slides used during the Institute. They are generously provided by some of the lecturers/speakers and hosted in this server as a means to disseminate the contents of the Institute.

Slides

ASI Lectures
P. Frasconi	Introduction to neural networks and machine learning
P. Frasconi	Connectionist models for learning in sequential and structured domains
D. Geiger	Inference in Bayesian networks
D. Geiger	Learning Bayesian networks with applications to bioinformatics
M. Gelfand	Recognition of Regulatory Signals
N. Kolchanov	Activity: computer system for prediction of functional sites activity on the basis of their nucleotide sequences
N. Kolchanov	B-DNA unit of the genenetworks computer system: conformational and physico-chemical properties of functional sites
N. Kolchanov	Nucleosome formation sites: coding, organization and function
N. Kolchanov	CRASP: software package for analysis of physicochemical parameters of aligned sequences of protein families
N. Kolchanov	Genenetworks system: computational approaches to RNA structure and function analysis
N. Kolchanov	Transcription factor binding sites recognition by consensus and weight matrix
N. Kolchanov	GeneNetWorks: integrated system on gene expression regulation
H. Mueller	Statistically robust E2F induced gene expression patterns in functional gene expression data mining
S. Muggleton	Knowledge-mining in biological and chemical domains
R. Serra	Introduction to Genetic Network Models
R. Serra	Tumors as Complex Systems
B. Shoelkopf	SVMs and Kernel Methods for High-Dimensional Data
Other presentations

D. Gilbert	Techniques for pattern matching, pattern discovery and structure comparison From sequences to protein structure
H. Kestler	Cluster analysis of comparative genomic hybridization data

Links

This is a collection of links to webpages directly related to material or services presented in the lectures and talks. Suggestions for additions/updates are welcome (click here)

Algorithms for Molecular Biology: Course Archive.
(by R. Shamir)
CBS prediction servers: including DictyOGlyc (O-(alpha)-GlcNAc glycosylation sites), NetPhos (Serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins) and many others
(S. Brunak's group)
EVA: Real time analysis of protein structure prediction servers
(B. Rost's group)
Human Genome Working Draft at UCSC
(D. Haussler's group)
Initial Sequencing and Analysis of the Human Genome (Nature 409, 860 - 921, Feb. 2001), paper by the International Human Genome Sequencing Consortium.
(partially covers the lectures by D. Haussler)
PDG software and web services: PDGcon (residue contacts), Threadlize (threading visualization), Plotcorr (residue contacts from correlated mutations), GeneQuiz (Sequence analysis), EUCLID (protein functional classification), abXtract (mining protein function from scientific abstracts)
(A. Valencia's group)
PredictProtein (secondary structure prediction).
(B. Rost's group)
Prion freely available predictors: CORNET (residue contacts), CYSPRED (bonding state of proteins), RCDPRED (residue coordination number), SECPRED (secondary structure)
(R. Casadio's group)
Promoter predictors: SSPro (secondary structure), CONpro (number of residue contacts), ACCpro (residue solvent accessibility)
(P. Baldi's group)
TOPS (Protein topology)
(D. Gilbert's group)
Verbunculus (detecting under- and over-represented words in sequences)
(A. Apostolico's group)

Artificial Intelligence and Heuristic Methods for Bioinformatics