PSB 2014 Online Proceedings

PSB 2014

PSB Proceedings for All Years



Cancer Panomics: Computational Methods and Infrastructure for Integrative Analysis of Cancer High-Throughput "Omics" Data

Session Introduction
Soren Brunak, Francisco M. De La Vega, Gunnar Raetsch, Joshua M. Stuart; Pacific Symposium on Biocomputing 19:1-2(2014)
Tumor Haplotype Assembly Algorithms for Cancer Genomics
Derek Aguiar, Wendy S.W. Wong, Sorin Istrail; Pacific Symposium on Biocomputing 19:3-14(2014)
Extracting Significant Sample-Specific Cancer Mutations Using Their Protein Interactions
Liviu Badea; Pacific Symposium on Biocomputing 19:15-26(2014)
The Stream Algorithm: Computationally Efficient Ridge-Regression via Bayesian Model Averaging, and Applications to Pharmacogenomic Prediction of Cancer Cell Line Sensitivity
Elias Chaibub Neto, In Sock Jang, Stephen H. Friend, Adam A. Margolin; Pacific Symposium on Biocomputing 19:27-38(2014)
Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous Diseases
Anthony Gitter, Alfredo Braunstein, Andrea Pagnani, Carlo Baldassi, Christian Borgs, Jennifer Chayes, Riccardo Zecchina, Ernest Fraenkel; Pacific Symposium on Biocomputing 19:39-50(2014)
Detecting Statistical Interaction Between Somatic Mutational Events and Germline Variation from Next-Generation Sequence Data
Hao Hu, Chad D. Huff; Pacific Symposium on Biocomputing 19:51-62(2014)
Systematic Assessment of Analytical Methods for Drug Sensitivity Prediction from Cancer Cell Line Data
In Sock Jang, Elias Chaibub Neto, Justin Guinney, Stephen H. Friend, Adam A. Margolin; Pacific Symposium on Biocomputing 19:63-74(2014)
Integrative Analysis of Two Cell Lines Derived from a Non-Small-Lung Cancer Patient - A Panomics Approach
Oleg Mayba, Florian Gnad, Michael Peyton, Fan Zhang, Kimberly Walter, Pan Du, Melanie A. Huntley, Zhaoshi Jiang, Jinfeng Liu, Peter M. Haverty, Robert C. Gentleman, Ruiqiang Li, John D. Minna, Yingrui Li, David S. Shames, Zemin Zhang; Pacific Symposium on Biocomputing 19:75-86(2014)
An Integrated Approach To Blood-Based Cancer Diagnosis And Biomarker Discovery
Martin Renqiang Min, Salim Chowdhury, Yanjun Qi, Alex Stewart, Rachel Ostroff; Pacific Symposium on Biocomputing 19:87-98(2014)
Multiplex Meta-Analysis of Medulloblastoma Expression Studies with External Controls
Alexander A. Morgan, Matthew D. Li, Achal S. Achrol, Purvesh J. Khatri, Samuel H. Cheshier; Pacific Symposium on Biocomputing 19:99-109(2014)

Computational Approaches to Drug Repurposing and Pharmacology

Session Introduction
S. Joshua Swamidass, Zhiyong Lu, Pankaj Agarwal, Atul Butte; Pacific Symposium on Biocomputing 19:110-113(2014)
Challenges in Secondary Analysis of High Throughput Screening Data
Aurora S. Blucher, Shannon K. McWeeney; Pacific Symposium on Biocomputing 19:114-124(2014)
Drug Intervention Response Predictions with Paradigm (DIRPP) Identifies Drug Resistant Cancer Cell Lines and Pathway Mechanisms of Resistance
Douglas Brubaker, Analisa Difeo, Yanwen Chen, Taylor Pearl, Kaide Zhai, Gurkan Bebek, Mark Chance, Jill Barnholtz-Sloan; Pacific Symposium on Biocomputing 19:125-135(2014)
Anti-Infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology Approach
Clara Ng, Ruth Hauptman, Yinliang Zhang, Philip E. Bourne, Lei Xie; Pacific Symposium on Biocomputing 19:136-147(2014)
Drug-Target Interaction Prediction by Integrating Chemical, Genomic, Functional and Pharmacological Data
Fan Yang, Jinbo Xu, Jianyang Zeng; Pacific Symposium on Biocomputing 19:148-159(2014)
Prediction of Off-Target Drug Effects Through Data Fusion
Emmanuel R. Yera, Ann E. Cleves, Ajay N. Jain; Pacific Symposium on Biocomputing 19:160-171(2014)
Exploring the Pharmacogenomics Knowledge Base (PharmGKB) for Repositioning Breast Cancer Drugs by Leveraging Web Ontology Language (OWL) and Cheminformatics Approaches
Qian Zhu, Cui Tao, Feichen Shen, Christopher Chute; Pacific Symposium on Biocomputing 19:172-182(2014)

Detecting and Characterizing Pleiotropy: New Methods for Uncovering the Connection Between the Complexity of Genomic Architecture and Multiple Phenotypes

Session introduction
Anna L. Tyler, Dana C. Crawford, Sarah A. Pendergrass; Pacific Symposium on Biocomputing 19:183-187(2014)
Using the Bipartite Human Phenotype Network to Reveal Pleiotropy and Epistasis Beyond the Gene
Christian Darabos, Samantha H. Harmon, Jason H. Moore; Pacific Symposium on Biocomputing 19:188-199(2014)
Environment-Wide Association Study (EWAS) for Type 2 Diabetes in the Marshfield Personalized Medicine Research Project Biobank
Molly A. Hall, Scott M. Dudek, Robert Goodloe, Dana C. Crawford, Sarah A. Pendergrass, Peggy Peissig, Murray Brilliant, Catherine A. McCarty, Marylyn D. Ritchie ; Pacific Symposium on Biocomputing 19:200-211(2014)
Dissection of Complex Gene Expression Using the Combined Analysis of Pleiotropy and Epistasis
Vivek M. Philip, Anna L. Tyler, Gregory W. Carter; Pacific Symposium on Biocomputing 19:200-211(2014)

Personalized Medicine: from genotypes and molecular phenotypes towards therapy

Session introduction
Jennifer Listgarten, Oliver Stegle, Quaid Morris, Steven E. Brenner, Leopold Parts; Pacific Symposium on Biocomputing 19:247-249(2014)
PATH-SCAN: A Reporting Tool for Identifying Clinically Actionable Variants
Roxana Daneshjou, Zachary Zappala, Kim Kukurba, Sean M Boyle, Kelly E Ormond, Teri E Klein, Michael Snyder, Carlos D Bustamante, Russ B Altman, Stephen B Montgomery; Pacific Symposium on Biocomputing 19:229-240(2014)
Imputation-based Assessment of Next Generation Rare Exome Variant Arrays
Alicia R. Martin, Gerard Tse, Carlos D. Bustamante, Eimear E. Kenny; Pacific Symposium on Biocomputing 19:262-272(2014)
Utilization of an EMR-Biorepository to Identify the Genetic Predictors of Calcineurin-Inhibitor Toxicity in Heart Transplant Recipients
Matthew Oetjens, William S. Bush, Kelly A. Birdwell, Holli H. Dilks, Erica A. Bowton, Joshua C. Denny, Russell A. Wilke, Dan M. Roden, Dana C. Crawford; Pacific Symposium on Biocomputing 19:253-264(2014)
Robust Reverse Engineering of Dynamic Gene Networks Under Sample Size Heterogeneity
Ankur P. Parikh, Wei Wu, Eric P. Xing; Pacific Symposium on Biocomputing 19:265-276(2014)
Variant Priorization and Analysis Incorporating Problematic Regions of the Genome
Anil Patwardhan, Michael Clark, Alex Morgan, Stephen Chervitz, Mark Pratt, Gabor Bartha, Gemma Chandratillake, Sarah Garcia, Nan Leng, Richard Chen; Pacific Symposium on Biocomputing 19:277-287(2014)
Bags of Words Models of Epitope Sets: HIV Viral Load Regression with Counting Grids
Alessandro Perina, Pietro Lovato, Nebojsa Jojic; Pacific Symposium on Biocomputing 19:288-300(2014)
Joint Association Discovery and Diagnosis of Alzheimer's Disease by Supervised Heterogeneous Multiview Learning
Shandian Zhe, Zenglin Xu, Yuan Qi, Peng Yu; Pacific Symposium on Biocomputing 19:300-311(2014)

Text and Data Mining for Biomedical Discovery

Session introduction
Graciela H. Gonzalez, Kevin Bretonnel Cohen, Robert Leaman, Casey Greene, Nigam Shah, Maricel G. Kann, Jieping Ye; Pacific Symposium on Biocomputing 19:312-315(2014)
Vector Quantization Kernels for the Classification of Protein Sequences and Structures
Wyatt T. Clark, Predrag Radivojac; Pacific Symposium on Biocomputing 19:316-327(2014)
Combining Heterogenous Data for Prediction of Disease Related and Pharmacogenes
Christopher S. Funk, Lawrence E. Hunter, K. Bretonnel Cohen; Pacific Symposium on Biocomputing 19:328-339(2014)
A Novel Profile Biomarker Diagnosis for Mass Spectral Proteomics
Henry Han; Pacific Symposium on Biocomputing 19:340-351(2014)
Towards Pathway Curation Through Literature Mining - A Case Study Using PharmGKB
Ravikumar K.E., Kavishwar B. Wagholikar, Hongfang Liu; Pacific Symposium on Biocomputing 19:352-363(2014)
Sparse Generalized Functional Linear Model for Predicting Remission Status of Depression Patients
Yashu Liu, Zhi Nie, Jiayu Zhou, Michael Farnum, Vaibhav A Narayan, Gayle Wiittenberg, Jieping Ye; Pacific Symposium on Biocomputing 19:364-375(2014)
Development of a Data-Mining Algorithm to Identify Ages at Reproductive Milestones in Electronic Medical Records
Jennifer Malinowski, Eric Farber-Eger, Dana C. Crawford; Pacific Symposium on Biocomputing 19:376-387(2014)
An Efficient Algorithm to Integrate Network and Attribute Data for Gene Function Prediction
Shankar Vembu, Quaid Morris; Pacific Symposium on Biocomputing 19:388-399(2014)
Matrix Factorization-Based Data Fusion for Gene Function Prediction in Baker's Yeast and Slime Mold
Marinka Zitnik, Blaz Zupan; Pacific Symposium on Biocomputing 19:400-411(2014)


Applications of Bioinformatics to Non-Coding RNAs in the Era of Next-Generation Sequencing
Chao Cheng, Jason Moore, Casey Greene; Pacific Symposium on Biocomputing 19:412-416(2014)
Building the Next Generation of Quantitative Biologists
Kristine A. Pattin, Anna C. Greene, Russ B. Altman, Lawrence E. Hunter, David A. Ross, James A. Foster, Jason H. Moore; Pacific Symposium on Biocomputing 19:417-421(2014)
Uncovering the Etiology of Autism Spectrum Disorders: Genomics, Bioinformatics, Environment, Data Collection and Exploration, and Future Possibilities
Sarah A. Pendergrass, Santhosh Girirajan, Scott Selleck; Pacific Symposium on Biocomputing 19:422-426(2014)

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