CONTENTS

• Biomolecular Networks: From Analysis to Synthesis
• Computational Challenges in Comparative Genomics: Gene Family Evolution, Ancestral Genome Reconstruction, and Applications to Human Genetics
• Dynamics of Biological Networks
• Emerging Challenges in Multi-Scale Modeling in Biology
• Knowledge-Driven Analysis and Data Integration for High-Throughput Biological Data
• Molecular Bioinformatics for Diseases
• Workshops

Biomolecular Networks: From Analysis to Synthesis

Session Introduction

Gil Alterovitz, Judith A. Blake, Jonathan M. Dreyfuss, Drew Endy, and Marco F. Ramoni; Pacific Symposium on Biocomputing 14:1-3(2009)

Stochastic Transient Analysis of Biochemical Systems and Its Application to the Design of Biochemical Logic Gates

Bin Cheng and Marc Riedel; Pacific Symposium on Biocomputing 14:4-14(2009)

Data-Driven Ontologies

James C. Costello, Dan Schrider, Jeff Gehlhausen, Mehmet Dalkilic; Pacific Symposium on Biocomputing 14:15-26(2009)

Identification of Discriminating Biomarkers for Human Disease Using Integrative Network Biology

Joel T. Dudley and Atul J. Butte; Pacific Symposium on Biocomputing 14:27-38(2009)

Learning the Structure of Protein-Protein Interaction Networks

Oleksii Kuchaiev and Natasa Przulj; Pacific Symposium on Biocomputing 14:39-50(2009)

Inference of Functional Networks of Condition-Specific Response--A Case Study Of Quiescence In Yeast

Sushmita Roy, Terran Lane, Margaret Werner-Washburne, and Diego Martinez; Pacific Symposium on Biocomputing 14:51-62(2009)

Learning Cyclic Signaling Pathway Structures While Minimizing Data Requirements

K. Sachs, S. Itani, J. Fitzgerald, L. Wille, B. Schoeberl, M.A. Dahleh, and G.P. Nolan; Pacific Symposium on Biocomputing 14:63-74(2009)

Context-Specific Gene Regulations in Cancer Gene Expression Data

Ina Sen, Michael P. Verdicchio, Sungwon Jung, Robert Trevino, Michael Bittner, and Seungchan Kim; Pacific Symposium on Biocomputing 14:75-86(2009)

Querying Parse Tree Database of Medline Text to Synthesize User-Specific Biomolecular Networks

Luis Tari, Jorg Hakenberg, Graciela Gonzalez, Chitta Baral; Pacific Symposium on Biocomputing 14:87-98(2009)

Pairwise Alignment of Interaction Networks by Fast Identification of Maximal Conserved Patterns

Wenhong Tian and Nagiza F. Samatova; Pacific Symposium on Biocomputing 14:99-110(2009)

Computational Challenges in Comparative Genomics: Gene Family Evolution, Ancestral Genome Reconstruction, and Applications to Human Genetics

Session Introduction

Bernard Moret, Webb Miller, Pavel Pevzner, and David Sankoff; Pacific Symposium on Biocomputing 14:111-113(2009)

Identifying Parent-Daughter Relationships Among Duplicated Genes

Mira V. Han And Matthew W. Hahn; Pacific Symposium on Biocomputing 14:114-125(2009)

A Parsimony Approach to Analysis of Human Segmental Duplications

Crystal L. Kahn and Benjamin J. Raphael; Pacific Symposium on Biocomputing 14:126-137(2009)

An Exact Solver for the DCJ Median Problem

Meng Zhang, William Arndt, and Jijun Tang; Pacific Symposium on Biocomputing 14:138-149(2009)

Inferring Genome-Wide Mosaic Structure

Qi Zhang, Wei Wang, Leonard Mcmillan, Fernando Pardo-Manuel De Villena, and David Threadgill; Pacific Symposium on Biocomputing 14:150-161(2009)

Simultaneous History Reconstruction for Complex Gene Clusters in Multiple Species

Yu Zhang, Giltae Song, Chih-Hao Hsu, and Webb Miller; Pacific Symposium on Biocomputing 14:162-173(2009)

Dynamics of Biological Networks

Session Introduction

Tanya Berger-Wolf, Teresa Przytycka, and Mona Singh; Pacific Symposium on Biocomputing 14:174-177(2009)

Dense Graphlet Statistics of Protein Interaction and Random Networks

R. Colak, F. Hormozdiari, F. Moser, A. Schonhuth, J. Holman, M. Ester and S.C. Sahinalp; Pacific Symposium on Biocomputing 14:178-189(2009)

Reverse Engineering the Evolution of Protein Interaction Networks

Todd A. Gibson and Debra S. Goldberg; Pacific Symposium on Biocomputing 14:190-202(2009)

Identifying Dynamic Network Modules with Temporal and Spatial Constraints

Ruoming Jin, Scott Mccallen, Chun-Chi Liu, Yang Xiang, Eivind Almaas, and Xianghong Jasmine Zhou; Pacific Symposium on Biocomputing 14:203-214(2009)

Efficient and Robust Prediction Algorithms for Protein Complexes Using Gomory-Hu Trees

A. Mitrofanova, M. Farach-Colton, and B. Mishra; Pacific Symposium on Biocomputing 14:215-226(2009)

Parameter Estimation of In Silico Biological Pathways with Particle Filtering Towards a Petascale Computing

Kazuyuki Nakamura, Ryo Yoshida, Masao Nagasaki, Satoru Miyano, and Tomoyuki Higuchi; Pacific Symposium on Biocomputing 14:227-238(2009)

From ODES to Language-Based, Executable Models of Biological Systems

A. Palmisano, I. Mura, and C. Priami; Pacific Symposium on Biocomputing 14:239-250(2009)

Unraveling Dynamic Activities of Autocrine Pathways that Control Drug-Response Transcriptome Networks

Yoshinori Tamada, Hiromitsu Araki, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Yukiko Nakanishi, Yuki Tomiyasu, Kaori Yasuda, Ben Dunmore, Deborah Sanders, Sally Humphreys, Cristin Print, D. Stephen Charnock-Jones, Kousuke Tashiro, Satoru Kuhara, and Satoru Miyano; Pacific Symposium on Biocomputing 14:251-263(2009)

Dissecting the Interface Between Signaling and Transcriptional Regulation in Human B Cells

Kai Wang, Mariano J. Alvarez, Brygida C. Bisikirska, Rune Linding, Katia Basso, Riccardo Dalla Favera, and Andrea Califano; Pacific Symposium on Biocomputing 14:264-275(2009)

Emerging Challenges in Multi-Scale Modeling in Biology

Session Introduction

Roy Kerckhoffs, James Bassingthwaighte, Jeff Reinbolt, and Peter Arzberger; Pacific Symposium on Biocomputing 14:276-280(2009)

Finite Element Analysis of Drug Electrostatic Diffusion: Inhibition Rate Studies in N1 Neuraminidase

Yuhui Cheng, Michael J. Holst And J. A. Mccammon; Pacific Symposium on Biocomputing 14:281-292(2009)

Multi-Scale Modeling of the Human Vertebral Body: Comparison of Micro-CT Based High-Resolution and Continuum-Level Models

Senthil K. Eswaran, Aaron J. Fields, Prem Nagarathnam, and Tony M. Keaveny; Pacific Symposium on Biocomputing 14:293-303(2009)

Advances in Semantic Representation for Multiscale Biosimulation: A Case Study in Merging Models

Maxwell Lewis Neal, John H. Gennari, Theo Arts, and Daniel L. Cook; Pacific Symposium on Biocomputing 14:304-315(2009)

Integration of Angiogenesis Modules at Multiple Scales: From Molecular to Tissue

Amina A. Qutub, Gang Liu, Prakash Vempati, and Aleksander S. Popel; Pacific Symposium on Biocomputing 14:316-327(2009)

Towards Computational Modeling of Excitation-Contraction Coupling in Cardiac Myocytes: Reconstruction of Structures and Proteins from Confocal Imaging

Frank B. Sachse, Eleonora Savio-Galimberti, Joshua I. Goldhaber, and John H. B. Bridge; Pacific Symposium on Biocomputing 14:328-339(2009)

A Multiscale Approach to Sampling Nascent Peptide Chains in the Ribosomal Exit Tunnel

V. A. Voelz, P. Petrone, and V. S. Pande; Pacific Symposium on Biocomputing 14:340-352(2009)

Knowledge-Driven Analysis and Data Integration for High-Throughput Biological Data

Session Introduction

Michael Ochs, John Quackenbush, Ramana Davuluri, and Habtom Ressom; Pacific Symposium on Biocomputing 14:353-355(2009)

Characterization of Unknown Adult Stem Cell Samples by Large Scale Data Integration and Artificial Neural Networks

G. Bidaut and C.J. Stoeckert Jr.; Pacific Symposium on Biocomputing 14:356-367(2009)

Biofilter: A Knowledge-Integration System for the Multi-Locus Analysis of Genome-Wide Association Studies

William S. Bush, Scott M. Dudek, and Marylyn D. Ritchie; Pacific Symposium on Biocomputing 14:368-379(2009)

Interpreting Genetics Of Gene Expression: Integrative Architecture In Bioconductor

V. J. Carey and R. Gentleman; Pacific Symposium on Biocomputing 14:380-390(2009)

High Throughput Interaction Data Reveals Degree Conservation of Hub Proteins

A. Fox, D. Taylor, and D. K. Slonim; Pacific Symposium on Biocomputing 14:391-402(2009)

Unison: An Integrated Platform for Computational Biology Discovery

Reece K. Hart and Kiran Mukhyala; Pacific Symposium on Biocomputing 14:403-414(2009)

TreeQA: Quantitative Genome Wide Association Mapping Using Local Perfect Phylogeny Trees

Feng Pan, Leonard Mcmillan, Fernando Pardo-Manuel De Villena, David Threadgill, and Wei Wang; Pacific Symposium on Biocomputing 14:415-426(2009)

Improving the Efficiency of Biomarker Identification Using Biological Knowledge

John H. Phan, Qiqin Yin-Goen, Andrew N. Young, and May D. Wang; Pacific Symposium on Biocomputing 14:427-438(2009)

Towards a Cytokine-Cell Interaction Knowledgebase of the Adaptive Immune System

Shai S. Shen-Orr, Ofir Goldberger, Yael Garten, Yael Rosenberg-Hasson, Patricia A. Lovelace, David L. Hirschberg, Russ B. Altman, Mark M. Davis, and Atul J. Butte; Pacific Symposium on Biocomputing 14:439-450(2009)

A Bayesian Integration Model of High-Throughput Proteomics and Metabolomics Data for Improved Early Detection of Microbial Infections

Bobbie-Jo M. Webb-Robertson, Lee Ann Mccue, Nathanial Beagley, Jason E. Mcdermott, David S. Wunschel, Susan M. Varnum, Jian Zhi Hu, Nancy G. Isern, Garry W. Buchko, Kathleen Mcateer, and Joel G. Pounds; Pacific Symposium on Biocomputing 14:451-463(2009)

Molecular Bioinformatics for Disease

Session Introduction

Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Atul Butte, and Maricel Kann; Pacific Symposium on Biocomputing 14:464-466(2009)

Supervised Classification of Array CGH Data with HMM-Based Feature Selection

Anneleen Daemen, Olivier Gevaert, Karin Leunen, Eric Legius, Ignace Vergote, and Bart De Moor; Pacific Symposium on Biocomputing 14:468-479(2009)

Inferring Disease-Related Pathways Using A Probabilistic Epistasis Model

P.N. Kanabar, C.J. Vaske, C.H. Yeang, F.H. Yildiz, and J.M. Stuart; Pacific Symposium on Biocomputing 14:480-491(2009)

Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin

Peter M. Kasson and Vijay S. Pande; Pacific Symposium on Biocomputing 14:492-503(2009)

Master Regulators Used As Breast Cancer Metastasis Classifier

Wei Keat Lim, Eugenia Lyashenko, Andrea Califano; Pacific Symposium on Biocomputing 14:504-515(2009)

Prediction of Interactions Between HIV-1 and Human Proteins by Information Integration

Oznur Tastan, Yanjun Qi, Jaime G. Carbonell, and Judith Kleinseetharaman; Pacific Symposium on Biocomputing 14:516-527(2009)

FastChi: An Efficient Algorithm for Analyzing Gene-Gene Interactions

Xiang Zhang, Fei Zou, and Wei Wang; Pacific Symposium on Biocomputing 14:528-539(2009)

Workshops

Open Science: Tools, Approaches, and Implications

Cameron Neylon and Shirley Wu; Pacific Symposium on Biocomputing 14:540-544(2009)

Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization

Benjamin Blencowe, Steven Brenner, Timothy Hughes, and Quaid Morris; Pacific Symposium on Biocomputing 14:545-548(2009)

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Updated: December 29, 2008