ISMB 2010 TALKS

The full listing of talks can be found below.

**Not all presenters provided permission to make talks available.

Type Title Presenter Keywords
HL01 Genomic privacy and limits of individual detection in a pool Sriram Sankararaman ,
HL02 Species Tree Inference by Minimizing Deep Coalescences Luay Nakhleh ,
HL03 Can literature analysis identify innovation drivers in drug discovery? Pankaj Agarwal ,
HL04 DNA Sudoku Yaniv Erlich ,
HL05 Finding co-occurrence of copy number changes in tumors. Christiaan Klijn ,
HL06 Genome-wide Identification of Human RNA Editing Sites by Massively Parallel DNA Capturing and Sequencing Erez Levanon ,
HL07 Novel statistics reveal cancer universal miRNA activity Roy Navon ,
HL08 The effect of histone sequence preferences on nucleosome organization and gene regulation Noam Kaplan ,
HL09 High-throughput analysis of miRNAs regulating the Estrogen Receptor Pekka Kohonen ,
HL10 Cracking the genetic code of heart regulatory elements Ivan Ovcharenko ,
HL11 The robustness of disease signatures across tissues and experiments Joel Dudley ,
HL12 Interrogating high-level DNA structure from ChIA-PET Data Han Xu ,
HL13 Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning Richard Lathrop ,
HL14 Systems-level dynamic analyses of fate change in murine embryonic stem cells Florian Markowetz ,
HL15 Comparative Network Analysis of Complex Diseases Rune Linding ,
HL16 A systems approach shows competition and saturation drives microRNA and siRNA target gene regulation - its more than target site efficacy Debora Marks ,
HL17 Systematic prediction of human membrane receptor interactions Yanjun Qi ,
HL18 Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns Robert Murphy ,
HL19 Automating Biology Using Robot Scientists Ross King ,
HL20 Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling Smita Agrawal ,
HL21 FragBag: representing protein structures as 'bags-of-fragments' allows efficient exploration of protein structure space. Rachel Kolodny ,
HL22 The Genetic Landscape of a Cell Anastasia Baryshnikova ,
HL23 A probabilistic approach to the design of interfaces in proteins with multiple partners: Tradeoff between stability and promiscuity Menachem Fromer ,
HL24 A 3D Digtial Atlas of C. elegans and Its Application to Single-Cell Gene Expression and Cell Fate Analyses Fuhui Long ,
HL25 Protein Folding Requires Crowd Control in a Simulated Cell Benjamin Jefferys ,
HL26 Protein interactions and ligand binding: from protein subfamilies to functional specificity Antonio Rausell ,
HL27 Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima Ying Zhang ,
HL28 An Integrative Proteomics Approach to Identify Functional Sub-networks In Cancer Rod Nibbe ,
HL29 Fast and accurate large-scale co-estimation of alignments and trees Tandy Warnow ,
HL30 Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes Rohith Srivas ,
HL31 Selection for hotspot mutations in core genes of Escherichia coli Sujay Chattopadhyay ,
HL32 Network models for understanding what 'omic data really mean. Ernest Fraenkel ,
HL33 Neofunctionalization in interaction network evolution Todd Gibson ,
HL34 Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Claus Jørgensen ,
HL35 A universal relationship between gene compactness and expression level in multicellular eukaryotes Liran Carmel ,
HL36 Pathway and network based approaches to prioritize reliable hits from high throughput RNAi screening experiments Zhidong Tu ,
HL37 Scaling to PubMedCentral: Bringing Ontology-based Biomedical Language Processing into the Full Text Era Lawrence Hunter ,
HL38 Applying histone modification information to genome-wide prediction of transcription factor binding sites Kyoungjae Won ,
HL39 Modeling the temporal interplay of molecular signalling and gene expression by using dynamic nested effects models Benedict Anchang ,
HL40 Histone modification levels are predictive for gene expression Martin Vingron ,
HL41 Illuminating Complete Functional Networks: Automation, Computation and the Single Cell Michael Fero ,
HL42 Modeling information flow from metabolomics to transcriptomics Xinghua Lu ,
Keynote Ultraconserved nonsense: gene regulation by splicing & RNA surveillance Steven Brenner ,
Keynote Protein Folding and Environmental Stress REDRAW the Relationship between Genotype and Phenotype Susan Lindquist ,
Keynote Analyses of Pleistocene Genomes Svante Pääbo ,
Keynote Systems Biology of Cancer Cells Chris Sander ,
Keynote Genomic Variation and the Inherited Basis of Common Disease David Altshuler ,
Keynote BI/O: Reading and Writing Genomes George Church ,
PT01 Low-homology protein threading Jian Peng Protein Stucture and Function,
PT02 TEAM: Efficient Two-Locus Epistasis Tests in Human Genome-Wide Association Study Xiang Zhang Population Genomics,
PT03 Fragment-free Approach to Protein Folding Using Conditional Neural Fields Feng Zhao Protein Stucture and Function,
PT04 Robust Unmixing of Tumor States in Array Comparative Genomic Hybridization Data David Tolliver Disease Models and Epidemiology,
PT05 MOTIF-EM: an Automated Computational Tool for Identifying Conserved Regions in CryoEM Structures Mitul Saha Protein Stucture and Function,
PT06 Sparse Multitask Regression for Identifying Common Mechanism of Response to Therapeutic Targets Kai Zhang Disease Models and Epidemiology,
PT07 Thermodynamics of RNA structures by Wang-Landau sampling Peter Clote Protein Stucture and Function,
PT08 Inference of patient-speci?c pathway activities from multi-dimensional cancer genomics data using PARADIGM Charles Vaske Protein Interactions and Molecular Networks,
PT09 Recognition of Beta-Structural Motifs Using Hidden Markov Models Trained with Simulated Evolution Anoop Kumar Protein Stucture and Function,
PT10 Efficient identification of identical-by-descent status in pedigrees with many untyped individuals Xin Li Population Genomics,
PT11 Markov Dynamic Models for Long-Timescale Protein Motion Tsung-Han Chiang Protein Stucture and Function,
PT12 Efficient Genome Ancestry Inference in Complex Pedigrees with Inbreeding Eric Liu Population Genomics,
PT13 A fast mathematical programming procedure for simultaneous fitting of assembly components into cryo-EM density maps Shihua Zhang Protein Stucture and Function,
PT14 Multi-Population GWA Mapping via Multi-Task Regularized Regression Kriti Puniyani Population Genomics,
PT15 Open MS/MS Spectral Library Search to Identify Unanticipated Post-Translational Modifications and Increase Spectral Identification Rate Ding Ye Other,
PT16 Estimating genomewide IBD-sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping Sivan Bercovici Population Genomics,
PT17 TRStalker: an Efficient Heuristic for Finding Fuzzy Tandem Repeats Marco Pellegrini Sequence Analysis,
PT18 Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation Rendong Yang Gene Regulation and Transcriptomics,
PT19 Model-Based Detection of Alternative Splicing Signals Yoseph Barash Sequence Analysis,
PT20 Multivariate multi-way analysis of multi-source data Ilkka Huopaniemi Other,
PT21 A dynamic Bayesian network for identifying protein binding footprints from single molecule based sequencing data Xiaoyu Chen Sequence Analysis,
PT22 Discovering Transcriptional Modules by Bayesian Data Integration Richard Savage Gene Regulation and Transcriptomics,
PT23 A statistical method for the detection of variants from next-generation resequencing of DNA pools Vikas Bansal Sequence Analysis,
PT24 Inferring Combinatorial Association Logic Networks in Multimodal Genome-Wide Screens Jeroen de Ridder Gene Regulation and Transcriptomics,
PT25 Optimal Algorithms for Haplotype Assembly From Whole-Genome Sequence Data Dan He Population Genomics,
PT26 Modularity and Directionality in Genetic Interaction Maps Ruty Rinott Protein Interactions and Molecular Networks,
PT27 Next Generation VariationHunter : Combinatorial Algorithms for Transposon Insertion Discovery Fereydoun Hormozdiari Sequence Analysis,
PT28 Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework Yoshihiro Yamanishi Protein Interactions and Molecular Networks,
PT29 Efficient construction of an assembly string graph using the FM-index Jared Simpson Sequence Analysis,
PT30 Integrating Quantitative Proteomics and Metabolomics with a Genome-scale Metabolic Network Model Keren Yizhak Protein Interactions and Molecular Networks,
PT31 VARiD: A Variation Detection Framework for Colorspace and Letterspace platforms Adrian Dalca Sequence Analysis,
PT32 PathText: A Text Mining Integrator for Biological Pathway Visualizations Sophia Ananiadou Text Mining,
PT33 Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph Adam Richards Databases and Ontologies,
PT34 A Spectral Graph Theoretic Approach to Quantification and Calibration of Collective Morphological Differences in Cell Images Chun-Nan Hsu Bioimaging,
PT35 Semi-automated ontology generation within OBO-Edit Thomas Wächter Databases and Ontologies,
PT36 As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets Stephan Saalfeld Bioimaging,
PT37 Using Semantic Web Rules To Reason On An Ontology Of Pseudogenes Matt Holford Databases and Ontologies,
PT38 A Soft Kinetic Data Structure for Lesion Border Detection Sinan Kochara Bioimaging,
PT39 Complex Event Extraction at PubMed Scale Jari Bjorne Text Mining,
PT40 Reconstruction of the Neuromuscular Junction Connectome Ranga Srinivasan Bioimaging,
PT41 Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters Steven Kelk Evolution and Comparative Genomics,
PT42 Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos Steffen Jaensch Bioimaging,
PT43 SUPERTRIPLETS: A triplet-based supertree approach to phylogenomics Emmanuel Douzery Evolution and Comparative Genomics,
PT44 SPEX^2 : Automated Concise Extraction of Spatial Gene Expression Patterns from Fly Embryo ISH Images Kriti Puniyani Bioimaging,
PT45 Time and memory efficient likelihood-based tree searches on gappy phylogenomic alignments Nikolaos Alachiotis Evolution and Comparative Genomics,
PT46 Automatic Reconstruction of 3D Neuron Structures Using a Graph-Augmented Deformable Model Hanchuan Peng Bioimaging,
PT47 Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees Yufeng Wu Evolution and Comparative Genomics,
PT48 Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing Tao Peng Bioimaging,
SPL Cancer Stem Cells and the Evolution of Malignancy Dr. Robert Weinberg ,
SS03A Identification and Pharmacogenomic Characterization of Liver Membrane Transporter Enhancers Nadav Ahituv ,
SS03C Genetic factors affecting severe adverse effects for common drugs Itsik Pe'er ,
SS04 Future of Scientific Publishing Jennifer Boyd ,
SS04 Future of Scientific Publishing Theodora Bloom ,
SS05A Visualization of biological networks Igor Jurisica ,
SS05B Visualization of large networks Frank van Ham ,
SS05C Visual interpretation of biological data using networks Gary Bader ,
SS06A Development of analytic methods in genome-scale RNAi researches Xiaohua Zhang ,
SS06C Data Analysis in Genome-scale RNAi Research Xiaohua Zhang ,