RECOMB 2001 The Fifth Annual International Conference On Computational Molecular Biology Montreal, Canada

The Trip Seoul -> Tokyo -> Chicago -> Montreal (about 22 hours) Montreal Royal mountain About 5 hours from New York by car (in my thought) Skyscrapers and the old European French and English Good water and beer

The Conference About 650 participants from biology, biocheimistry, biophysics, drug company and computer science Oral presentations: 35 Poster: 130 Several keynotes Software demonstration

Keynotes 4.22 4.23 4.24 4.25 Sequencing is unfinished yet. RNA interference experiments (biochemistry) Drug design 4.23 Chemical knockout >> Temporal knockout (technologies?) Information processing by cells (bioinformatics) 4.24 Collaboration 4.25 Shotgun method Gene annotation

Statistics Protein Structure: 5 Molecular Interactions: 2 Protein folding process and protein structures Molecular Interactions: 2 Protein interaction and protein docking (divide and conquer) Expression Patterns: 5 Gene clustering, regulatory genes and the combination of heterogeneous data Yeast cell-cycle regulation is the major (4 papers out of 5) Sequencing By Hybridization: 2 Computational theory (emerging?) Sequence Analysis I: 5 Sleepy and HMM

Statistics Phylogeny and Gene Duplications: 5 Sequence Analysis II: 3 Sequencing: 5 Proteomics, RNA Structure: 3

Protein Structure Using Motion Planning to Study Protein Folding Pathways Method: Probabilistic Roadmap Issue: Folding process Studied data: IMB Jena Image Library of Biological Macromolecules Experimental data: Protein Data Bank 101 Optimal PDB Structure Alignments: a Branch-and-Cut Algorithm for the Maximum Contact Map Overlap Problem Algorithmic approach to the protein structure comparison Integer programming formulation for protein structure contact map overlapping Minimum independent set problem Data: Protein Data Bank

Protein Structure Algorithms for Identifying Protein Cross-links Via Tandem Mass Spectrometry (MS-MS): protein-protein interaction and protein structures Detecting cross-linked peptides and amino-acids from (MS-MS) Data: Cross-linked Hemoglobin protein Predicting The Beta-Helix Fold From Protein Sequence Data Predict Beta-helix super-secondary structural motif using Beta-strand interactions Data: Protein Data Bank

Protein Structure Extracting Structural Information Using Time-Frequency Analysis of Protein NMR Data Nuclear magnetic resonance (NMR) structural biology based on time-frequency analysis of chemical shift dynamics

Molecular Interactions Toward Predicting Coiled-Coil Protein Interactions Using both genomic sequence data and experimental data A NMR-spectra-based Scoring Function for Protein Docking Protein docking problem Scoring function for the protein structure

Expression Patterns Class Discovery in Gene Expression Data Amir Ben-Dor et al Tissues clustering with subset of genes from microarray data New class discovery via some statistical scores 3 Datasets Regulatory Element Detection Using Correlation with Expression Also accepted in Nature Genetics S. cerevisiae data

Expression Patterns Gene Function Classification From Heterogeneous Data Microarray and while genome sequence data Yeast data and its phylogenetic profiles Support vector machines Context-Specific Bayesian Clustering for Gene Expression Data Learning a combined probability model of binding sites and expression patterns Extended naïve Bayesian clustering 2 yeast data (from Spellman and Gacsh)

Expression Patterns Analysis Techniques for Microarray Time-Series Data Hamming distance and correlation coefficient of sequences Yeast data Putative genetic network

Sequencing By Hybridization Large Scale Sequencing By Hybridization The probability of (un)ambiguous reconstruction Optimal Sequencing by Hybridization in Rounds Use a series of small SBH chips to sequence long strings

Sequence Analysis I Fast and Simple Character Classes and Bounded Gaps Pattern Matching, With Application to Protein Searching CBG matching and regular expression matching Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems Cross-species gene finding DNA-cDNA and DNA-protein alignment A Gibbs Sampling Method to Detect Over-represented Motifs in the Upstream Regions of Co-expressed Genes A probability distribution to estimate the number of copies of the motif in a sequence G-box motif

Sequence Analysis I On the Predictive Power of Sequence Similarity in Yeast 6280 yeast ORFs DNA Segmentation as A Model Selection Process Bayesian Information Criterion

Phylogeny and Gene Duplications A Structural EM Algorithm for Phylogenetic Inference reconstruction of a phylogenetic tree from sequences good quality, and fast compared with MOLPHY Algorithms for Phylogenetic Footprinting identifying regulatory elements by finding conserved regions in non-coding DNA sequences from multiple species Fast Recovery of Evolutionary Trees With Thousands of Nodes distance based algorithm, just simulation Efficient Algorithms for Lateral Gene Transfer Problems between gene trees and species tree partial order of evolution implied by S

Phylogeny and Gene Duplications Zinc Finger Gene Clusters and Tandem Gene Duplication cluster appearing in a tandem array on chromosome inferring the series of gene duplication events

Sequence Analysis II A New Approach to Sequence Comparison: Normalized Sequence Alignment maximal degree of similarity than maximal score fractional programming, slower thant S-W algorithm Rapid Significance Estimation in Local Sequence Alignment With Gaps Assessing the significance of sequence alignments, Gumbel distribution, importance sampling Finding Motifs Using Random Projections (15, 4) : difficult problem (14, 4), (16, 5) (18, 6)

Sequencing A New Approach to Fragment Assembly in DNA Sequencing Problem of resolving repeats in “shotgun methods” Variation of Eulerian Superpath approach Separating Repeats in DNA Sequence Assembly Repeat separation problem K-median problem, integer programming Comparing Sequence Scaffolds The Greedy Path-Merging Algorithm for Sequence Assembly Clone-by-clone, whole genome shotgun Hierachical assembly, Bactig Ordering Problem

Sequencing An Optimal Procedure for Gap Closing in Whole Genome Shotgun Sequencing Use a multiplex PCR strategy, pairing primers

Proteomics, RNA Structure Geometric Algorithms for the Analysis of 2D-Electrophoresis Gels Separation technique for proteins : picking robot, mass spectrometry CAROL : http://gelmatching .inf.fu-berlin.de Gene-Finding via Tandem Mass Spectrometry HPLC (high performance liquid chromatography) tandem mass spectrometry Edit Distance Between Two RNA Structures Arc-annotated sequence for structural information of RNA sequences