ISMB 2010 Conference Proceedings are now available on-line
here
Proceedings Track: PT01
Low-homology protein threading
Date: Sunday, July 11 - 10:45 a.m. - 11:10 a.m.
Room: 302
Presenting Author: Jian Peng, Toyota Technological Institute of Chicago, Chicago, IL
TOPProceedings Track: PT02
TEAM: Efficient Two-Locus Epistasis Tests in Human Genome-Wide Association Study
Date: Sunday, July 11 - 10:45 a.m. - 11:10 a.m.
Room: 304
Presenting Author: Xiang Zhang, Univ of NC, Chapel Hill, NC
ISMB2010 BlogPT02: Xiang Zhang - TEAM: Efficient Two-Locus Epistasis Tests in Human Genome-Wide Association Study Proceedings Track: PT03
Fragment-free Approach to Protein Folding Using Conditional Neural Fields
Date: Sunday, July 11 - 11:15 a.m. - 11:40 a.m.
Room: 302
Presenting Author: Feng Zhao, Toyota Technological Institute of Chicago, Chicago, IL
ISMB2010 BlogPT03: Feng Zhao - Fragment-free Approach to Protein Folding Using Conditional Neural Fields Proceedings Track: PT04
Robust Unmixing of Tumor States in Array Comparative Genomic Hybridization Data
Date: Sunday, July 11 - 11:15 a.m. - 11:40 a.m.
Room: 304
Presenting Author: David Allan Tolliver, Carnegie Mellon Univ, Pittsburgh, PA
ISMB2010 BlogPT04: David Tolliver - Robust Unmixing of Tumor States in Array Comparative Genomic Hybridization Data Proceedings Track: PT05
MOTIF-EM: an Automated Computational Tool for Identifying Conserved Regions in CryoEM Structures
Date: Sunday, July 11 - 11:45 a.m. - 12:10 p.m.
Room: 302
Presenting Author: Mitul Saha, Univ of TX, Galveston, TX
ISMB2010 BlogPT05: Mitul Saha - MOTIF-EM: an Automated Computational Tool for Identifying Conserved Regions in CryoEM Structures Proceedings Track: PT06
Sparse Multitask Regression for Identifying Common Mechanism of Response to Therapeutic Targets
Date: Sunday, July 11 - 11:45 a.m. - 12:10 p.m.
Room: 304
Presenting Author: Kai Zhang, Lawrence Berkeley National Laboratory, Berkeley, CA
ISMB2010 BlogPT06: Kai Zhang - Sparse Multitask Regression for Identifying Common Mechanism of Response to Therapeutic Targets Proceedings Track: PT07
Thermodynamics of RNA structures by Wang-Landau sampling
Date: Sunday, July 11 - 12:15 p.m. - 12:40 p.m.
Room: 302
Presenting Author: Peter G Clote, Boston College, Chestnut Hill, MA
ISMB2010 BlogPT07: Peter Clote - Thermodynamics of RNA structures by Wang-Landau sampling Proceedings Track: PT08
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
Date: Sunday, July 11 - 12:15 p.m. - 12:40 p.m.
Room: 304
Presenting Author: Charles J. Vaske, Princeton Univ, Princeton, NJ
ISMB2010 BlogPT08: Charles Vaske - Inference of patient-speci?c pathway activities from multi-dimensional cancer genomics data using PARADIGM Proceedings Track: PT09
Recognition of Beta-Structural Motifs Using Hidden Markov Models Trained with Simulated Evolution
Date: Sunday, July 11 - 2:30 p.m. - 2:55 p.m.
Room: 302
Presenting Author: Anoop Kumar, Tufts Univ, Medford, MA
ISMB2010 BlogPT09: Anoop Kumar - Recognition of Beta-Structural Motifs Using Hidden Markov Models Trained with Simulated Evolution Proceedings Track: PT10
Efficient identification of identical-by-descent status in pedigrees with many untyped individuals
Date: Sunday, July 11 - 2:30 p.m. - 2:55 p.m.
Room: 304
Presenting Author: Xin Li, CaseWestern Reserve Univ, Cleveland, OH
ISMB2010 BlogPT10: Xin Li - Efficient identification of identical-by-descent status in pedigrees with many untyped individuals Proceedings Track: PT11
Markov Dynamic Models for Long-Timescale Protein Motion
Date: Sunday, July 11 - 3:00 p.m. - 3:25 p.m.
Room: 302
Presenting Author: Tsung-Han Chiang, National University of Singapore, Singapore
ISMB2010 BlogPT11: Tsung-Han Chiang - Markov Dynamic Models for Long-Timescale Protein Motion Proceedings Track: PT12
Efficient Genome Ancestry Inference in Complex Pedigrees with Inbreeding
Date: Sunday, July 11 - 3:00 p.m. - 3:25 p.m.
Room: 304
Presenting Author: Eric Yi Liu, Univ of NC, Chapel Hill, NC
ISMB2010 BlogPT12: Eric Liu - Efficient Genome Ancestry Inference in Complex Pedigrees with Inbreeding Proceedings Track: PT13
A fast mathematical programming procedure for simultaneous fitting of assembly components into cryo-EM density maps
Date: Sunday, July 11 - 3:30 p.m. - 3:55 p.m.
Room: 302
Presenting Author: Shihua Zhang, USC, Los Angeles, CA
ISMB2010 BlogPT13: Shihua Zhang - A fast mathematical programming procedure for simultaneous fitting of assembly components into cryo-EM density maps Proceedings Track: PT14
Multi-Population GWA Mapping via Multi-Task Regularized Regression
Date: Sunday, July 11 - 3:30 p.m. - 3:55 p.m.
Room: 304
Presenting Author: Kriti Puniyani, Carnegie Mellon Univ, Pittsburgh, PA
ISMB2010 BlogPT14: Kriti Puniyani - Multi-Population GWA Mapping via Multi-Task Regularized Regression Proceedings Track: PT15
Open MS/MS Spectral Library Search to Identify Unanticipated Post-Translational Modifications and Increase Spectral Identification Rate
Date: Sunday, July 11 - 4:00 p.m. - 4:25 p.m.
Room: 302
Presenting Author: Ding Ye, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
ISMB2010 BlogPT15: Ding Ye - Open MS/MS Spectral Library Search to Identify Unanticipated Post-Translational Modifications and Increase Spectral Identification Rate Proceedings Track: PT16
Estimating genomewide IBD-sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping
Date: Sunday, July 11 - 4:00 p.m. - 4:25 p.m.
Room: 304
Presenting Author: Sivan Bercovici, Technion, Haifa, Israel
ISMB2010 BlogPT16: Sivan Bercovici - Estimating genomewide IBD-sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping Proceedings Track: PT17
TRStalker: an Efficient Heuristic for Finding Fuzzy Tandem Repeats
Date: Monday, July 12 - 10:45 a.m. - 11:10 a.m.
Room: 302
Presenting Author: Marco Pellegrini, Institute for Informatics and Telematics of C.N.R., Pisa, Italy
ISMB2010 BlogPT17: Marco Pellegrini - TRStalker: an Efficient Heuristic for Finding Fuzzy Tandem Repeats Proceedings Track: PT18
Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation
Date: Monday, July 12 - 10:45 a.m. - 11:10 a.m.
Room: 304
Presenting Author: Rendong Yang, China Agricultural Univ, Beijing, China
ISMB2010 BlogPT18: Rendong Yang - Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation Proceedings Track: PT19
Model-Based Detection of Alternative Splicing Signals
Date: Monday, July 12 - 11:15 a.m. - 11:40 a.m.
Room: 302
Presenting Author: Yoseph Barash, Univ of Toronto, Toronto, Canada
ISMB2010 BlogPT19: Yoseph Barash - Model-Based Detection of Alternative Splicing Signals Proceedings Track: PT20
Multivariate multi-way analysis of multi-source data
Date: Monday, July 12 - 11:15 a.m. - 11:40 a.m.
Room: 304
Presenting Author: Ilkka Huopaniemi, Aalto Univ, Aalto, Finland
ISMB2010 BlogPT20: Ilkka Huopaniemi - Multivariate multi-way analysis of multi-source data Proceedings Track: PT21
A dynamic Bayesian network for identifying protein binding footprints from single molecule based sequencing data
Date: Monday, July 12 - 11:45 a.m. - 12:10 p.m.
Room: 302
Presenting Author: Xiaoyu Chen, Univ of WA, Seattle, WA
ISMB2010 BlogPT21: Xiaoyu Chen - A dynamic Bayesian network for identifying protein binding footprints from single molecule based sequencing data Proceedings Track: PT22
Discovering Transcriptional Modules by Bayesian Data Integration
Date: Monday, July 12 - 11:45 a.m. - 12:10 p.m.
Room: 304
Presenting Author: Richard Savage, Univ of Warwick, Coventry, UK
ISMB2010 BlogPT22: Richard Savage - Discovering Transcriptional Modules by Bayesian Data Integration Proceedings Track: PT23
A statistical method for the detection of variants from next-generation resequencing of DNA pools
Date: Monday, July 12 - 12:15 p.m. - 12:40 p.m.
Room: 302
Presenting Author: Vikas Bansal, Scripps Translational Science Institute, La Jolla, CA
ISMB2010 BlogPT23: Vikas Bansal - A statistical method for the detection of variants from next-generation resequencing of DNA pools Proceedings Track: PT24
Inferring Combinatorial Association Logic Networks in Multimodal Genome-Wide Screens
Date: Monday, July 12 - 12:15 p.m. - 12:40 p.m.
Room: 304
Presenting Author: Jeroen de Ridder, Delft Univ of Tech/ Delft, The Netherlands
ISMB2010 BlogPT24: Jeroen de Ridder - Inferring Combinatorial Association Logic Networks in Multimodal Genome-Wide Screens Proceedings Track: PT25
Optimal Algorithms for Haplotype Assembly From Whole-Genome Sequence Data
Date: Monday, July 12 - 2:30 p.m. - 2:55 p.m.
Room: 302
Presenting Author: Dan He, UCLA, Los Angeles, CA
ISMB2010 BlogPT25: Dan He - Optimal Algorithms for Haplotype Assembly From Whole-Genome Sequence Data Proceedings Track: PT26
Modularity and Directionality in Genetic Interaction Maps
Date: Monday, July 12 - 2:30 p.m. - 2:55 p.m.
Room: 304
Presenting Author: Ruty Rinott, The Hebrew University of Jerusalem
ISMB2010 BlogPT26: Ruty Rinott - Modularity and Directionality in Genetic Interaction Maps Proceedings Track: PT27
Next Generation VariationHunter : Combinatorial Algorithms for Transposon Insertion Discovery
Date: Monday, July 12 - 3:00 p.m. - 3:25 p.m.
Room: 302
Presenting Author: Fereydoun Hormozdiari, Simon Fraser Univ, Burnaby, Canada
ISMB2010 BlogPT27: Fereydoun Hormozdiari - Next Generation VariationHunter : Combinatorial Algorithms for Transposon Insertion Discovery Proceedings Track: PT28
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework
Date: Monday, July 12 - 3:00 p.m. - 3:25 p.m.
Room: 304
Presenting Author: Yoshihiro Yamanishi, Mines Paris Tech, Fontainebleau Cedex, France
ISMB2010 BlogPT28: Yoshihiro Yamanishi - Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework Proceedings Track: PT29
Efficient construction of an assembly string graph using the FM-index
Date: Monday, July 12 - 3:30 p.m. - 3:55 p.m.
Room: 302
Presenting Author: Jared Simpson, Wellcome Trust Sanger Institute, Hinxton, UK
ISMB2010 BlogPT29: Jared Simpson - Efficient construction of an assembly string graph using the FM-index Proceedings Track: PT30
Integrating Quantitative Proteomics and Metabolomics with a Genome-scale Metabolic Network Model
Date: Monday, July 12 - 3:30 p.m. - 3:55 p.m.
Room: 304
Presenting Author: Keren Yizhak, Tel Aviv Univ, TelAviv, Israel
ISMB2010 BlogPT30: Keren Yizhak - Integrating Quantitative Proteomics and Metabolomics with a Genome-scale Metabolic Network Model Proceedings Track: PT31
VARiD: A Variation Detection Framework for Colorspace and Letterspace platforms
Date: Monday, July 12 - 4:00 p.m. - 4:25 p.m.
Room: 302
Presenting Author: Adrian V. Dalca, MIT, Cambridge, MA
ISMB2010 BlogPT31: Adrian Dalca - VARiD: A Variation Detection Framework for Colorspace and Letterspace platforms Proceedings Track: PT32
PathText: A Text Mining Integrator for Biological Pathway Visualizations
Date: Monday, July 12 - 4:00 p.m. - 4:25 p.m.
Room: 304
Presenting Author: Sophia Ananiadou, National Centre for Text Mining, Manchester, UK
ISMB2010 BlogPT32: Sophia Ananiadou - PathText: A Text Mining Integrator for Biological Pathway Visualizations Proceedings Track: PT33
Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph
Date: Tuesday, July 13 - 10:45 a.m. - 11:10 a.m.
Room: 302
Presenting Author: Adam Richards, Medical University of South Carolina, Charleston, SC
ISMB2010 BlogPT33: Adam Richards - Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph Proceedings Track: PT34
A Spectral Graph Theoretic Approach to Quantification and Calibration of Collective Morphological Differences in Cell Images
Date: Tuesday, July 13 - 10:45 a.m. - 11:10 a.m.
Room: 304
Presenting Author: Chun-Nan Hsu, USC, Los Angeles, CA
ISMB2010 BlogPT34: Chun-Nan Hsu - A Spectral Graph Theoretic Approach to Quantification and Calibration of Collective Morphological Differences in Cell Images Proceedings Track: PT35
Semi-automated ontology generation within OBO-Edit
Date: Tuesday, July 13 - 11:15 a.m. - 11:40 a.m.
Room: 302
Presenting Author: Thomas Wächter, University of Technology, Dresden, Germany
ISMB2010 BlogPT35: Thomas Wächter - Semi-automated ontology generation within OBO-Edit Proceedings Track: PT36
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets
Date: Tuesday, July 13 - 11:15 a.m. - 11:40 a.m.
Room: 304
Presenting Author: Stephan Saalfeld, Max Planck Institute of Molecular Cell Bio & Genetics, Dresden, Germany
ISMB2010 BlogPT36: Stephan Saalfeld - As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets Proceedings Track: PT37
Using Semantic Web Rules To Reason On An Ontology Of Pseudogenes
Date: Tuesday, July 13 - 11:45 a.m. - 12:10 p.m.
Room: 302
Presenting Author: Matt Holford, Yale University, New Haven, CT
ISMB2010 BlogPT37: Matt Holford - Using Semantic Web Rules To Reason On An Ontology Of Pseudogenes Proceedings Track: PT38
A Soft Kinetic Data Structure for Lesion Border Detection
Date: Tuesday, July 13 - 11:45 a.m. - 12:10 p.m.
Room: 304
Presenting Author: Sinan Kochara, Univ of Central AR, Conway, AR
ISMB2010 BlogPT38: Sinan Kochara - A Soft Kinetic Data Structure for Lesion Border Detection Proceedings Track: PT39
Complex Event Extraction at PubMed Scale
Date: Tuesday, July 13 - 12:15 p.m. - 12:40 p.m.
Room: 302
Presenting Author: Jari Bjorne, Univ of Turku, Turku, Finland
ISMB2010 BlogPT39: Jari Bjorne - Complex Event Extraction at PubMed Scale Proceedings Track: PT40
Reconstruction of the Neuromuscular Junction Connectome
Date: Tuesday, July 13 - 12:15 p.m. - 12:40 p.m.
Room: 304
Presenting Author: Ranga Srinivasan, The Methodist Hospital Research Institute, Houston, TX
ISMB2010 BlogPT40: Ranga Srinivasan - Reconstruction of the Neuromuscular Junction Connectome Proceedings Track: PT41
Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters
Date: Tuesday, July 13 - 2:15 p.m. - 2:40 p.m.
Room: 302
Presenting Author: Steven Kelk, Centrum voor Wiskunde en Informatica (CWI), Amsterdam, The Netherlands
ISMB2010 BlogPT41: Steven Kelk - Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters Proceedings Track: PT42
Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos
Date: Tuesday, July 13 - 2:15 p.m. - 2:40 p.m.
Room: 304
Presenting Author: Steffen Jaensch, Max Planck Institute of Molecular Cell Bio & Genetics, Dresden, Germany
ISMB2010 BlogPT42: Steffen Jaensch - Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos Proceedings Track: PT43
SUPERTRIPLETS: A triplet-based supertree approach to phylogenomics
Date: Tuesday, July 13 - 2:45 p.m. - 3:10 p.m.
Room: 302
Presenting Author: Emmanuel Douzery, Institut des Sciences de l'Evolution de Montpellier, Montpellier Cedex, France
ISMB2010 BlogPT43: Emmanuel Douzery - SUPERTRIPLETS: A triplet-based supertree approach to phylogenomics Proceedings Track: PT44
SPEX^2 : Automated Concise Extraction of Spatial Gene Expression Patterns from Fly Embryo ISH Images
Date: Tuesday, July 13 - 2:45 p.m. - 3:10 p.m.
Room: 304
Presenting Author: Kriti Puniyani, Carnegie Mellon Univ, Pittsburgh, PA
ISMB2010 BlogPT44: Kriti Puniyani - SPEX^2 : Automated Concise Extraction of Spatial Gene Expression Patterns from Fly Embryo ISH Images Proceedings Track: PT45
Time and memory efficient likelihood-based tree searches on gappy phylogenomic alignments
Date: Tuesday, July 13 - 3:15 p.m. - 3:40 p.m.
Room: 302
Presenting Author: Nikolaos Alachiotis, Technical Univ of Munich, Munich, Germany
ISMB2010 BlogPT45: Nikolaos Alachiotis - Time and memory efficient likelihood-based tree searches on gappy phylogenomic alignments Proceedings Track: PT46
Automatic Reconstruction of 3D Neuron Structures Using a Graph-Augmented Deformable Model
Date: Tuesday, July 13 - 3:15 p.m. - 3:40 p.m.
Room: 304
Presenting Author: Hanchuan Peng, Howard Hughes Medical Institute, Ashburn, VA
ISMB2010 BlogPT46: Hanchuan Peng - Automatic Reconstruction of 3D Neuron Structures Using a Graph-Augmented Deformable Model Proceedings Track: PT47
Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees
Date: Tuesday, July 13 - 3:45 p.m. - 4:10 p.m.
Room: 302
Presenting Author: Yufeng Wu, Univ of CT, Storrs, CT
ISMB2010 BlogPT47: Yufeng Wu - Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees Proceedings Track: PT48
Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing
Date: Tuesday, July 13 - 3:45 p.m. - 4:10 p.m.
Room: 304
Presenting Author: Tao Peng, Carnegie Mellon Univ, Pittsburgh, PA
ISMB2010 BlogPT48: Tao Peng - Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing 
Show Comments
arne: "Not sure I really got the idea, but the results looked quite good."
arne: "Seems Like Raptor-X is doing OK (but not better than HHPRED) http://www.pdc.kth.se/~bjornw/CASP9/"