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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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