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

2. 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

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

4. 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

5. 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

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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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)

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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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)

20. 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

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

22. Proteomics, RNA Structure
Geometric Algorithms for the Analysis of 2D-Electrophoresis Gels
Separation technique for proteins : picking robot, mass spectrometry
CAROL : .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