Tracing the Early Cell Divisions of Mouse Embryos by Single Cell RNA-Seq (Invited Keynote Talk) Catalin Barbacioru 1
Successes and Failures of Elegant Algorithms in Computational Biology (Invited Keynote Talk) Piotr Berman 2
Modeling without Borders: Creating and Annotating VCell Models 3
Using the Web Michael L. Blinov Oliver Ruebenacker James C. Schaff Ion I. Moraru 18
Touring Protein Space with Matt Noah Daniels Anoop Kumar Lenore Cowen Matt Menke 29
Fixed-Parameter Algorithm for General Pedigrees with a Single Pair of Sites Duong D. Doan Patricia A. Evans 29
Analysis of Temporal-spatial Co-variation within Gene Expression Microarray Data in an Organogenesis Model Martin Ehler Vinodh Rajapakse Barry Zeeberg Brian Brooks Jacob Brown Wojciech Czatja Robert F. Bonner 38
Human Genome Annotation (Invited Keynote Talk) Mark Gerstein 50
Extensions and Improvements to the Chordal Graph Approach to the Multi-state Perfect Phylogeny Problem Rob Gysel Dan Gusfield 52
Analysis of Gene Interactions Using Restricted Boolean Networks and Time-Series Data Carlos H.A. Higa Vitor H.P. Louzada Ronaldo F. Hashimoto 61
Residue Contexts: Non-sequential Protein Structure Alignment Using Structural and Biochemical Features Jay W. Kim Rahul Singh|77
Essential Proteins Discovery from Weighted Protein Interaction Networks Min Li Jianxin Wang Huan Wang Yi Pan 89
Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets Bo Liu Mihai Pop 101
A Novel Approach for Compressing Phylogenetic Trees Suzanne J. Matthews Seung-Jin Sul Tiffani L. Williams 113
Structure of Proximal and Distant Regulatory Elements in the Human Genome (Invited Keynote Talk) Ivan Ovcharenko 125
Combinatorics in Recombinational Population Genomics (Invited Keynote Talk) Laxmi Parida 126
Uncovering Hidden Phylogenetic Consensus Nicholas D. Pattengale Krister M. Swenson Bernard M.E. Moret 128
An Agglomerate Algorithm for Mining Overlapping and Hierarchical Functional Modules in Protein Interaction Networks Jun Ren Jianxin Wang Jianâer Chen Min Li Gang Chen 140
Fast Protein Structure Alignment Yosi Shibberu Allen Holder Kyla Lutz 152
Predicting and Analyzing Cellular Networks (Invited Keynote Talk) Mona Singh 166
A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure Ming-Chi Tsai Guy Blelloch R. Ravi Russell Schwartz 167
Inferring Evolutionary Scenarios for Protein Domain Compositions John Wiedenhoeft Roland Krause Oliver Eulenstein 179
Local Structural Alignment of RNA with Affine Gap Model Thomas K.F. Wong Brenda W.Y. Cheung T.W. Lam S.M. Yiu 191
Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees Yufeng Wu Jiayin Wang 203
"Master-Slave" Biological Network Alignment Nicola Ferraro Luigi Palopoli Simona Panni Simona B. Rombo 215
Deciphering Transcription Factor Binding Patterns from Genome-Wide High Density ChIP-chip Tiling Array Data Juntao Li Lei Zhu Majid Eshaghi Jianhua Liu Radha Krishna Murthy Karuturi 230
The Expected Fitness Cost of a Mutation Fixation under the One-Dimensional Fisher Model Liqing Zhang Layne T. Watson 241
Author Index 253
Overview
The 20 revised full papers and 6 invited talks presented were carefully reviewed and selected out of 57 submissions. Topics presented span all areas of bioinformatics and computational biology, including the development of experimental or commercial systems.