19th Annual International Conference on
Intelligent Systems for Molecular Biology and
10th European Conference on Computational Biology


Proceedings Track Presentation Schedule
As of March 29, 2011 (schedule subject to change)

Proceedings Track: PT01
Sorting the nuclear proteome
Date: Sunday, July 17 - 10:45 a.m. - 11:10 a.m.
Room: Hall L/M
Presenting Author: Mikael Boden, The University of Queensland, Australia
Session Chair: Anna Tramontano

ISMB/ECCB 2011 Blog
PT01: Mikael Boden - Sorting the nuclear proteome
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Proceedings Track: PT02
vipR: Variant identification in pooled DNA using R
Date: Sunday, July 17 - 10:45 a.m. - 11:10 a.m.
Room: A353
Presenting Author: Andre Altmann, Max Planck Institute of Psychiatry, Germany
Session Chair: John Kececioglu

ISMB/ECCB 2011 Blog
PT02: Andre Altmann - vipR: Variant identification in pooled DNA using R
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Proceedings Track: PT03
Environment specific substitution tables improve membrane protein alignment
Date: Sunday, July 17 - 11:15 a.m. - 11:40 a.m.
Room: Hall L/M
Presenting Author: Jamie R. Hill, University of Oxford, United Kingdom
Session Chair: Anna Tramontano

ISMB/ECCB 2011 Blog
PT03: Jamie R. Hill - Environment specific substitution tables improve membrane protein alignment
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Proceedings Track: PT04
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
Date: Sunday, July 17 - 11:15 a.m. - 11:40 a.m.
Room: A353
Presenting Author: Kengo Sato, University of Tokyo, Japan
Session Chair: John Kececioglu

ISMB/ECCB 2011 Blog
PT04: Kengo Sato - IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
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Proceedings Track: PT05
Sequence-based prediction of protein crystallization, purification, and production propensity
Date: Sunday, July 17 - 11:45 a.m. - 12:10 p.m.
Room: Hall L/M
Presenting Author: Marcin J. Mizianty, University of Alberta, Canada
Session Chair: Anna Tramontano

ISMB/ECCB 2011 Blog
PT05: Marcin J. Mizianty - Sequence-based prediction of protein crystallization, purification, and production propensity
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Proceedings Track: PT06
Meta-IDBA: De Novo Assembler for Mixed Species in Metagenomic Data
Date: Sunday, July 17 - 11:45 a.m. - 12:10 p.m.
Room: A353
Presenting Author: Yu Peng, The University of Hong Kong, Hong Kong
Session Chair: John Kececioglu

ISMB/ECCB 2011 Blog
PT06: Yu Peng - Meta-IDBA: De Novo Assembler for Mixed Species in Metagenomic Data
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Proceedings Track: PT07
A method for probing the mutational landscape of amyloid structure
Date: Sunday, July 17 - 12:15 p.m. - 12:40 p.m.
Room: Hall L/M
Presenting Author: Charles W. O'Donnell, Massachusetts Institute of Technology, United States
Session Chair: Anna Tramontano

ISMB/ECCB 2011 Blog
PT07: Charles W. O'Donnell - A method for probing the mutational landscape of amyloid structure
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Proceedings Track: PT08
A Conditional Random Fields Method for RNA Sequence-Structure Relationship Modeling and Conformation Sampling
Date: Sunday, July 17 - 12:15 p.m. - 12:40 p.m.
Room: A353
Presenting Author: Zhiyong Wang, Toyota Technological Institute at Chicago, United States
Session Chair: John Kececioglu

ISMB/ECCB 2011 Blog
PT08: Zhiyong Wang - A Conditional Random Fields Method for RNA Sequence-Structure Relationship Modeling and Conformation Sampling
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Proceedings Track: PT09
Piecewise Linear Approximation of Protein Structures using the Principle of Minimum Message Length
Date: Sunday, July 17 - 2:30 p.m. - 2:55 p.m.
Room: Hall L/M
Presenting Author: Arun Konagurthu, Monash University, Australia
Session Chair: Yves Moreau

ISMB/ECCB 2011 Blog
PT09: Arun Konagurthu - Piecewise Linear Approximation of Protein Structures using the Principle of Minimum Message Length
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Proceedings Track: PT10
Discovering and visualising indirect associations between biomedical concepts
Date: Sunday, July 17 - 2:30 p.m. - 2:55 p.m.
Room: A353
Presenting Author: Sophia Ananiadou, The University of Manchester, United Kingdom
Session Chair: Eric Xing

ISMB/ECCB 2011 Blog
PT10: Sophia Ananiadou - Discovering and visualising indirect associations between biomedical concepts
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Proceedings Track: PT11
QAARM: Quasi-anharmonic auto-regressive model reveals molecular recognition pathways in ubiquitin
Date: Sunday, July 17 - 3:00 p.m. - 3:25 p.m.
Room: Hall L/M
Presenting Author: Andrej Savol, University of Pittsburgh, United States
Session Chair: Yves Moreau

ISMB/ECCB 2011 Blog
PT11: Andrej Savol - QAARM: Quasi-anharmonic auto-regressive model reveals molecular recognition pathways in ubiquitin
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Proceedings Track: PT12
MeSH: A Window into Full-Text for Document Summarization
Date: Sunday, July 17 - 3:00 p.m. - 3:25 p.m.
Room: A353
Presenting Author: Sanmitra Bhattacharya, The University of Iowa, United States
Session Chair: Eric Xing

ISMB/ECCB 2011 Blog
PT12: Sanmitra Bhattacharya - MeSH: A Window into Full-Text for Document Summarization
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Proceedings Track: PT13
Multi-view Methods for Protein Structure Comparison using Latent Dirichlet Allocation
Date: Sunday, July 17 - 3:30 p.m. - 3:55 p.m.
Room: Hall L/M
Presenting Author: Ashish Tendulkar, IT Madras, India
Session Chair: Yves Moreau

ISMB/ECCB 2011 Blog
PT13: Ashish Tendulkar - Multi-view Methods for Protein Structure Comparison using Latent Dirichlet Allocation
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Proceedings Track: PT14
A Folding Algorithm for Extended RNA Secondary Structures
Date: Sunday, July 17 - 3:30 p.m. - 3:55 p.m.
Room: A353
Presenting Author: Christian Hoener Zu Siederdissen, University of Vienna, Austria
Session Chair: Eric Xing

ISMB/ECCB 2011 Blog
PT14: Christian Hoener Zu Siederdissen - A Folding Algorithm for Extended RNA Secondary Structures
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Proceedings Track: PT15
Template-free detection of macromolecular complexes in cryo electron tomograms
Date: Sunday, July 17 - 4:00 p.m. - 4:25 p.m.
Room: Hall L/M
Presenting Author: Min Xu, University of Southern California, United States
Session Chair: Yves Moreau

ISMB/ECCB 2011 Blog
PT15: Min Xu - Template-free detection of macromolecular complexes in cryo electron tomograms
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Proceedings Track: PT16
Error correction of high-throughput sequencing datasets with non-uniform coverage
Date: Sunday, July 17 - 4:00 p.m. - 4:25 p.m.
Room: A353
Presenting Author: Paul Medvedev, University of California, San Diego, United States
Session Chair: Eric Xing

ISMB/ECCB 2011 Blog
PT16: Paul Medvedev - Error correction of high-throughput sequencing datasets with non-uniform coverage
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Proceedings Track: PT17
Generative Probabilistic Models for Protein-Protein Interaction Networks – The Biclique Perspective
Date: Monday, July 18 - 10:45 a.m. - 11:10 a.m.
Room: Hall L/M
Presenting Author: Regev Schweiger, The Hebrew University of Jerusalem, Israel
Session Chair: Robert Russell

ISMB/ECCB 2011 Blog
PT17: Regev Schweiger - Generative Probabilistic Models for Protein-Protein Interaction Networks – The Biclique Perspective Show Comments
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Proceedings Track: PT18
Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs
Date: Monday, July 18 - 10:45 a.m. - 11:10 a.m.
Room: A353
Presenting Author: Tony Kam-Thong, Max Planck Institute of Psychiatry, Germany
Session Chair: Niko Beerenwinkel

ISMB/ECCB 2011 Blog
PT18: Tony Kam-Thong - Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs
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Proceedings Track: PT19
RINQ: Reference-based Indexing for Network Queries
Date: Monday, July 18 - 11:15 a.m. - 11:40 a.m.
Room: Hall L/M
Presenting Author: Gunhan Gulsoy, University of Florida, United States
Session Chair: Robert Russell

ISMB/ECCB 2011 Blog
PT19: Gunhan Gulsoy - RINQ: Reference-based Indexing for Network Queries Show Comments
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Proceedings Track: PT20
Detecting epistatic effect in association studies at a genomic level based on an ensemble approach
Date: Monday, July 18 - 11:15 a.m. - 11:40 a.m.
Room: A353
Presenting Author: Jing Li, Case Western Reserve University, United States
Session Chair: Niko Beerenwinkel

ISMB/ECCB 2011 Blog
PT20: Jing Li - Detecting epistatic effect in association studies at a genomic level based on an ensemble approach
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Proceedings Track: PT21
Construction of Co-complex Score Matrix for Protein Complex Prediction from AP-MS Data
Date: Monday, July 18 - 11:45 a.m. - 12:10 p.m.
Room: Hall L/M
Presenting Author: Xiaoli Li, Nanyang Technological University, Singapore
Session Chair: Robert Russell

ISMB/ECCB 2011 Blog
PT21: Xiaoli Li - Construction of Co-complex Score Matrix for Protein Complex Prediction from AP-MS Data Show Comments
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Proceedings Track: PT22
Efficient spatial segmentation of large imaging mass spectrometry data sets with spatially-aware clustering
Date: Monday, July 18 - 11:45 a.m. - 12:10 p.m.
Room: A353
Presenting Author: Theodore Alexandrov, University of Bremen, Germany
Session Chair: Niko Beerenwinkel

ISMB/ECCB 2011 Blog
PT22: Theodore Alexandrov - Efficient spatial segmentation of large imaging mass spectrometry data sets with spatially-aware clustering
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Proceedings Track: PT23
Uncover disease genes by maximizing information flow in the phenome-interactome network
Date: Monday, July 18 - 12:15 p.m. - 12:40 p.m.
Room: Hall L/M
Presenting Author: Rui Jiang, Tsinghua University, China
Session Chair: Robert Russell

ISMB/ECCB 2011 Blog
PT23: Rui Jiang - Uncover disease genes by maximizing information flow in the phenome-interactome network
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Proceedings Track: PT24
Automatic Tracing of 3D Neuron Structures Using All-Path Pruning
Date: Monday, July 18 - 12:15 p.m. - 12:40 p.m.
Room: A353
Presenting Author: Hanchuan Peng, Howard Hughes Medical Institute, United States
Session Chair: Niko Beerenwinkel

ISMB/ECCB 2011 Blog
PT24: Hanchuan Peng - Automatic Tracing of 3D Neuron Structures Using All-Path Pruning
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Proceedings Track: PT25
Physical Module Networks: an Integrative Approach for Reconstructing Transcription Regulation
Date: Monday, July 18 - 2:30 p.m. - 2:55 p.m.
Room: Hall L/M
Presenting Author: Noa Novershtern, The Hebrew University of Jerusalem, Israel
Session Chair: Trey Ideker

ISMB/ECCB 2011 Blog
PT25: Noa Novershtern - Physical Module Networks: an Integrative Approach for Reconstructing Transcription Regulation
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Proceedings Track: PT26
Tanglegrams for Rooted Phylogenetic Trees and Networks
Date: Monday, July 18 - 2:30 p.m. - 2:55 p.m.
Room: A353
Presenting Author: Celine Scornavacca, ZBIT, University of Tuebingen, Germany
Session Chair: Teresa Przytycka

ISMB/ECCB 2011 Blog
PT26: Celine Scornavacca - Tanglegrams for Rooted Phylogenetic Trees and Networks
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Proceedings Track: PT27
Identification of metabolic network models from incomplete high-throughput datasets
Date: Monday, July 18 - 3:00 p.m. - 3:25 p.m.
Room: Hall L/M
Presenting Author: Sara Berthoumieux, INRIA, France
Session Chair: Trey Ideker

ISMB/ECCB 2011 Blog
PT27: Sara Berthoumieux - Identification of metabolic network models from incomplete high-throughput datasets
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Proceedings Track: PT28
Mapping ancestral genomes with massive gene loss: a matrix sandwich problem
Date: Monday, July 18 - 3:00 p.m. - 3:25 p.m.
Room: A353
Presenting Author: Eric Tannier, INRIA, France
Session Chair: Teresa Przytycka

ISMB/ECCB 2011 Blog
PT28: Eric Tannier - Mapping ancestral genomes with massive gene loss: a matrix sandwich problem
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Proceedings Track: PT29
TREEGL: Reverse Engineering Tree-Evolving Gene Networks Underlying Developing Biological Lineages
Date: Monday, July 18 - 3:30 p.m. - 3:55 p.m.
Room: Hall L/M
Presenting Author: Ankur Parikh, Carnegie Mellon University, United States
Session Chair: Trey Ideker

ISMB/ECCB 2011 Blog
PT29: Ankur Parikh - TREEGL: Reverse Engineering Tree-Evolving Gene Networks Underlying Developing Biological Lineages Show Comments
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Proceedings Track: PT30
Predicting site-specific human selective pressure using evolutionary signatures
Date: Monday, July 18 - 3:30 p.m. - 3:55 p.m.
Room: A353
Presenting Author: Javad Sadri, McGill University, Canada
Session Chair: Teresa Przytycka

ISMB/ECCB 2011 Blog
PT30: Javad Sadri - Predicting site-specific human selective pressure using evolutionary signatures
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Proceedings Track: PT31
Optimal Discriminating Subnetwork Markers Predict Responses To Cancer Treatments
Date: Monday, July 18 - 4:00 p.m. - 4:25 p.m.
Room: Hall L/M
Presenting Author: Phuong Dao, Simon Fraser University, Canada
Session Chair: Trey Ideker

ISMB/ECCB 2011 Blog
PT31: Phuong Dao - Optimal Discriminating Subnetwork Markers Predict Responses To Cancer Treatments
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Proceedings Track: PT32
PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions
Date: Monday, July 18 - 4:00 p.m. - 4:25 p.m.
Room: A353
Presenting Author: Michael Lin, Massachusetts Institute of Technology, United States
Session Chair: Teresa Przytycka

ISMB/ECCB 2011 Blog
PT32: Michael Lin - PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions
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Proceedings Track: PT33
The role of proteosome-mediated proteolysis in modulating the activity of potentially harmful transcription factor activity in Saccharomyces cerevisiae
Date: Tuesday, July 19 - 10:45 a.m. - 11:10 a.m.
Room: Hall L/M
Presenting Author: Jasmin Fisher, Microsoft Research Cambridge, United Kingdom
Session Chair: Phil Bourne

ISMB/ECCB 2011 Blog
PT33: Jasmin Fisher - The role of proteosome-mediated proteolysis in modulating the activity of potentially harmful transcription factor activity in Saccharomyces cerevisiae
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Proceedings Track: PT34
ccSVM: Correcting Support Vector Machines for confounding factors in biological data classification
Date: Tuesday, July 19 - 10:45 a.m. - 11:10 a.m.
Room: A353
Presenting Author: Limin Li, MPIs Tübingen, Germany
Session Chair: Hagit Shatkay

ISMB/ECCB 2011 Blog
PT34: Limin Li - ccSVM: Correcting Support Vector Machines for confounding factors in biological data classification
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Proceedings Track: PT35
Mixed Model Coexpression (MMC): calculating gene coexpression while accounting for expression heterogeneity
Date: Tuesday, July 19 - 11:15 a.m. - 11:40 a.m.
Room: Hall L/M
Presenting Author: Nicholas Furlotte, University of California Los Angeles, United States
Session Chair: Phil Bourne

ISMB/ECCB 2011 Blog
PT35: Nicholas Furlotte - Mixed Model Coexpression (MMC): calculating gene coexpression while accounting for expression heterogeneity
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Proceedings Track: PT36
Ontology Patterns for Tabular Representations of Knowledge on Neglected Tropical Diseases
Date: Tuesday, July 19 - 11:15 a.m. - 11:40 a.m.
Room: A353
Presenting Author: Filipe Santana da Silva, Universidade Federal de Pernambuco, Brazil
Session Chair: Hagit Shatkay

ISMB/ECCB 2011 Blog
PT36: Filipe Santana da Silva - Ontology Patterns for Tabular Representations of Knowledge on Neglected Tropical Diseases
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Proceedings Track: PT37
A generalized model for multi-marker analysis of cell-cycle progression in synchrony experiments
Date: Tuesday, July 19 - 11:45 a.m. - 12:10 p.m.
Room: Hall L/M
Presenting Author: Michael B. Mayhew, Duke University, United States
Session Chair: Phil Bourne

ISMB/ECCB 2011 Blog
PT37: Michael B. Mayhew - A generalized model for multi-marker analysis of cell-cycle progression in synchrony experiments Show Comments
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Proceedings Track: PT38
Detection and interpretation of metabolite-transcript co-responses using combined profiling data
Date: Tuesday, July 19 - 11:45 a.m. - 12:10 p.m.
Room: A353
Presenting Author: Henning Redestig, RIKEN Plant Science Center, Japan
Session Chair: Hagit Shatkay

ISMB/ECCB 2011 Blog
PT38: Henning Redestig - Detection and interpretation of metabolite-transcript co-responses using combined profiling data
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Proceedings Track: PT39
Systematic exploration of error sources in pyrosequencing flowgram data
Date: Tuesday, July 19 - 12:15 p.m. - 12:40 p.m.
Room: Hall L/M
Presenting Author: Susanne Balzer, Institute of Marine Research, Norway
Session Chair: Phil Bourne

ISMB/ECCB 2011 Blog
PT39: Susanne Balzer - Systematic exploration of error sources in pyrosequencing flowgram data
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Proceedings Track: PT40
From Sets to Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems
Date: Tuesday, July 19 - 12:15 p.m. - 12:40 p.m.
Room: A353
Presenting Author: Ludwig Geistlinger, LMU München, Germany
Session Chair: Hagit Shatkay

ISMB/ECCB 2011 Blog
PT40: Ludwig Geistlinger - From Sets to Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems
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Proceedings Track: PT41
An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data
Date: Tuesday, July 19 - 2:30 p.m. - 2:55 p.m.
Room: Hall L/M
Presenting Author: Stephen Wong, The Methodist Hospital Research Institute & Cornell Weill Medical College, United States
Session Chair: Eleazer Eskin

ISMB/ECCB 2011 Blog
PT41: Stephen Wong - An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data
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Proceedings Track: PT42
Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning
Date: Tuesday, July 19 - 2:30 p.m. - 2:55 p.m.
Room: A353
Presenting Author: Katherine A. Heller, University of Cambridge, United Kingdom
Session Chair: Robert Murphy

ISMB/ECCB 2011 Blog
PT42: Katherine A. Heller - Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning
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Proceedings Track: PT43
Accurate Estimation of Heritability in Genome Wide Studies using Random Effects Models
Date: Tuesday, July 19 - 3:00 p.m. - 3:25 p.m.
Room: Hall L/M
Presenting Author: David Golan, Tel Aviv University, Israel
Session Chair: Eleazer Eskin

ISMB/ECCB 2011 Blog
PT43: David Golan - Accurate Estimation of Heritability in Genome Wide Studies using Random Effects Models
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Proceedings Track: PT44
Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling
Date: Tuesday, July 19 - 3:00 p.m. - 3:25 p.m.
Room: A353
Presenting Author: Paweł P. Łabaj, Boku University Vienna, Austria
Session Chair: Robert Murphy

ISMB/ECCB 2011 Blog
PT44: Paweł P. Łabaj - Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling Show Comments
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Proceedings Track: PT45
StructHDP: Automatic inference of number of clusters from admixed genotype data
Date: Tuesday, July 19 - 3:30 p.m. - 3:55 p.m.
Room: Hall L/M
Presenting Author: Suyash Shringarpure, Carnegie Mellon University, United States
Session Chair: Eleazer Eskin

ISMB/ECCB 2011 Blog
PT45: Suyash Shringarpure - StructHDP: Automatic inference of number of clusters from admixed genotype data
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Proceedings Track: PT46
An Integrative Clustering and Modeling Algorithm for Dynamical Gene Expression Data
Date: Tuesday, July 19 - 3:30 p.m. - 3:55 p.m.
Room: A353
Presenting Author: Julia Sivriver, Hebrew University of Jerusalem, Israel
Session Chair: Robert Murphy

ISMB/ECCB 2011 Blog
PT46: Julia Sivriver - An Integrative Clustering and Modeling Algorithm for Dynamical Gene Expression Data Show Comments
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Proceedings Track: PT47
Reconstruction of genealogical relationships with applications to Phase III of HapMap
Date: Tuesday, July 19 - 4:00 p.m. - 4:25 p.m.
Room: Hall L/M
Presenting Author: Sofia Kyriazopoulou-Panagiotopoulou, Stanford, United States
Session Chair: Eleazer Eskin

ISMB/ECCB 2011 Blog
PT47: Sofia Kyriazopoulou-Panagiotopoulou - Reconstruction of genealogical relationships with applications to Phase III of HapMap
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Proceedings Track: PT48
A novel computational framework for simultaneous integration of multiple functional genomic data to identify microRNA-gene regulatory modules
Date: Tuesday, July 19 - 4:00 p.m. - 4:25 p.m.
Room: A353
Presenting Author: Shihua Zhang, University of Southern California, United States
Session Chair: Robert Murphy

ISMB/ECCB 2011 Blog
PT48: Shihua Zhang - A novel computational framework for simultaneous integration of multiple functional genomic data to identify microRNA-gene regulatory modules
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