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PSB 2018 proceedings are published as Open Access chapters by World Scientific Publishing Company and distributed under the terms of the Creative Commons Attribution (CC BY) 4.0 License.
PSB Proceedings for All Years
Contents
Preface
- Session Introduction
- Richard Bourgon, Frederick E. Dewey, Zhengyan Kan, Shuyu D. Li;
Pacific Symposium on Biocomputing 23:1-7(2018)
- Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology
- Xintong Chen, Sander Houten, Kimaada Allette, Robert P. Sebra, Gustavo Stolovitzky, Bojan Losic;
Pacific Symposium on Biocomputing 23:8-19(2018)
- Prediction of protein-ligand interactions from paired protein sequence motifs and ligand
substructures
- Peyton Greenside, Maureen Hillenmeyer, Anshul Kundaje;
Pacific Symposium on Biocomputing 23:20-31(2018)
- Cell-specific prediction and application of drug-induced gene expression
- Rachel Hodos, Ping Zhang, Hao-Chih Lee, Qiaonan Duan, Zichen Wang, Neil R. Clark, Avi Ma’ayan, Fei Wang, Brian Kidd, Jianying Hu, David Sontag, Joel Dudley ;
Pacific Symposium on Biocomputing 23:32-43(2018)
- Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action
- Yunan Luo, Sheng Wang, Jinfeng Xiao, Jian Peng;
Pacific Symposium on Biocomputing 23:44-55(2018)
- Chemical reaction vector embeddings: towards predicting drug metabolism in the human gut microbiome
- Emily K. Mallory, Ambika Acharya, Stefano E. Rensi, Peter J Turnbaugh, Roselie A. Bright, Russ B. Altman;
Pacific Symposium on Biocomputing 23:56-67(2018)
- Loss-of-function of neuroplasticity-related genes confers risk for human neurodevelopmental disorders
- Milo R. Smith, Benjamin S. Glicksberg, Li Li, Rong Chen, Hirofumi Morishita, Joel T. Dudley;
Pacific Symposium on Biocomputing 23:68-79(2018)
- Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders
- Gregory P. Way, Casey S. Greene;
Pacific Symposium on Biocomputing 23:80-91(2018)
- Diffusion mapping of drug targets on disease signaling network elements reveals drug combination strategies
- Jielin Xu, Kelly Regan-Fendt, Siyuan Deng, William E. Carson III, Philip R.O. Payne, Fuhai Li;
Pacific Symposium on Biocomputing 23:92-103(2018)
- Session Introduction
- Shefali Setia Verma, Anurag Verma, Anna Okula Basile, Marta-Byrska Bishop, Christian Darabos;
Pacific Symposium on Biocomputing 23:104-110(2018)
- Large-scale analysis of disease pathways in the human interactome
- Monica Agrawal, Marinka Zitnik, Jure Leskovec;
Pacific Symposium on Biocomputing 23:111-122(2018)
- Mapping patient trajectories using longitudinal extraction and deep learning in the MIMIC-III Critical Care Database
- Brett K. Beaulieu-Jones, Patryk Orzechowski, Jason H. Moore;
Pacific Symposium on Biocomputing 23:123-132(2018)
- OWL-NETS: Transforming OWL representations for improved network inference
- Tiffany J. Callahan, William A. Baumgartner Jr., Michael Bada, Adrianne L. Stefanski, Ignacio Tripodi, Elizabeth K. White, Lawrence E. Hunter;
Pacific Symposium on Biocomputing 23:133-144(2018)
- Automated disease cohort selection using word embeddings from Electronic Health Records
- Benjamin S. Glicksberg, Riccardo Miotto, Kipp W. Johnson, Khader Shameer, Li Li, Rong Chen, Joel T. Dudley;
Pacific Symposium on Biocomputing 23:145-156(2018)
- Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses
- Lia X. Harrington, Gregory P. Way, Jennifer A. Doherty, Casey S. Greene;
Pacific Symposium on Biocomputing 23:157-167(2018)
- An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data
- Hyun-Hwan Jeong, Hari Krishna Yalamanchili, Caiwei Guo, Joshua M. Shulman, Zhandong Liu;
Pacific Symposium on Biocomputing 23:168-179(2018)
- Causal inference on electronic health records to assess blood pressure treatment targets: An application of the parametric g formula
- Kipp W. Johnson, Benjamin S. Glicksberg, Rachel Hodos, Khader Shameer, Joel T. Dudley;
Pacific Symposium on Biocomputing 23:180-191(2018)
- Data-driven advice for applying machine learning to bioinformatics problems
- Randal S. Olson, William La Cava, Zairah Mustahsan, Akshay Varik, Jason H. Moore;
Pacific Symposium on Biocomputing 23:192-203(2018)
- Improving the explainability of Random Forest classifier – user centered approach
- Dragutin Petkovic, Russ B. Altman, Mike Wong, Arthur Vigil;
Pacific Symposium on Biocomputing 23:204-215(2018)
- Tree-based methods for characterizing tumor density heterogeneity
- Katherine Shoemaker, Brian P. Hobbs, Karthik Bharath, Chaan S. Ng, Veerabhadran Baladandayuthapani;
Pacific Symposium on Biocomputing 23:216-227(2018)
- How powerful are summary-based methods for identifying expression-trait associations under different genetic architectures?
- Yogasudha Veturi, Marylyn D. Ritchie;
Pacific Symposium on Biocomputing 23:228-239(2018)
- Session introduction
- Philip R.O Payne, Nigam H. Shah, Jessica D. Tenenbaum, Lara Mangravite;
Pacific Symposium on Biocomputing 23:240-246(2018)
- ClinGen Cancer Somatic Working Group – Standardizing and democratizing access to cancer molecular diagnostic data to drive translational research
- Subha Madhavan, Deborah Ritter, Christine Micheel, Shruti Rao, Angshumoy Roy, Dmitriy Sonkin, Matthew McCoy, Malachi Griffith, Obi L Griffith, Peter Mcgarvey,
Shashikant Kulkarni on Behalf of the ClinGen Somatic Working Group;
Pacific Symposium on Biocomputing 23:247-258(2018)
- A heuristic method for simulating open-data of arbitrary complexity that can be used to compare and evaluate machine learning methods
- Jason H. Moore, Maksim Shestov, Peter Schmitt, Randal S. Olson;
Pacific Symposium on Biocomputing 23:259-267(2018)
- Identifying natural health product and dietary supplement information within adverse event reporting systems
- Vivekanand Sharma, Indra Neil Sarkar;
Pacific Symposium on Biocomputing 23:268-279(2018)
- Best practices and lessons learned from reuse of 4 patient-derived metabolomics datasets in Alzheimer’s disease
- Jessica D. Tenenbaum, Colette Blach;
Pacific Symposium on Biocomputing 23:280-291(2018)
- Democratizing data science through data science training
- John Darrell Van Horn, Lily Fierro, Jeana Kamdar, Jonathan Gordon, Crystal Stewart, Avnish Bhattrai,
Sumiko Abe, Xiaoxiao Lei, Caroline O’Driscoll, Aakanchha Sinha, Priyambada Jain, Gully Burns, Kristina Lerman,
José Luis Ambite;
Pacific Symposium on Biocomputing 23:292-303(2018)
- Session introduction
- Heng Huang, Li Shen, Paul M. Thompson, Kun Huang, Junzhou Huang, Lin Yang
Pacific Symposium on Biocomputing 23:304-306(2018)
- Heritability estimates on resting state fMRI data using the ENIGMA analysis
pipeline
- Bhim M. Adhikari, Neda Jahanshad, Dinesh Shukla, David C. Glahn, John Blangero,
Richard C. Reynolds, Robert W. Cox, Els Fieremans, Jelle Veraart, Dmitry S. Novikov,
Thomas E. Nichols, L. Elliot Hong, Paul M. Thompson, Peter Kochunov;
Pacific Symposium on Biocomputing 23:307-318(2018)
- Discriminative bag-of-cells for imaging-genomics
- Benjamin Chidester, Minh N. Do, Jian Ma;
Pacific Symposium on Biocomputing 23:319-330(2018)
- MRI to MGMT: Predicting methylation status in glioblastoma patients using
convolutional recurrent neural networks
- Lichy Han, Maulik R. Kamdar;
Pacific Symposium on Biocomputing 23:331-342(2018)
- Deep integrative analysis for survival prediction
- Chenglong Huang, Albert Zhang, Guanghua Xiao;
Pacific Symposium on Biocomputing 23:343-352(2018)
- Genotype-Phenotype association study via new multi-task learning model
- Zhouyuan Huo, Dinggang Shen, Heng Huang;
Pacific Symposium on Biocomputing 23:353-364(2018)
- Codon bias among synonymous rare variants is associated with Alzheimer’s
disease imaging biomarker
- Jason E. Miller, Manu K. Shivakumar, Shannon L. Risacher, Andrew J. Saykin, Seunggeun Lee,
Kwangsik Nho, Dokyoon Kim, for the Alzheimer’s Disease Neuroimaging Initiative (ADNI);
Pacific Symposium on Biocomputing 23:365-376(2018)
- Building trans-omics evidence: using imaging and ‘omics’ to characterize
cancer profiles
- Arunima Srivastava, Chaitanya Kulkarni, Parag Mallick, Kun Huang, Raghu Machiraju;
Pacific Symposium on Biocomputing 23:377-388(2018)
- Session Introduction
- Dana C. Crawford, Alexander A. Morgan, Joshua C. Denny, Bruce J. Aronow, Steven E. Brenner;
Pacific Symposium on Biocomputing 23:389-399(2018)
- Single subject transcriptome analysis to identify functionally signed
gene set or pathway activity
- Joanne Berghout, Qike Li, Nima Pouladi, Jianrong Li, Yves A. Lussier;
Pacific Symposium on Biocomputing 23:400-411(2018)
- Using simulation and optimization approach to improve outcome through warfarin
precision treatment
- Chih-Lin Chi, Lu He, Kourosh Ravvaz, John Weissert, Peter J. Tonellato;
Pacific Symposium on Biocomputing 23:412-423(2018)
- Local ancestry transitions modify snp-trait associations
- Alexandra E. Fish, Dana C. Crawford, John A. Capra, William S. Bush;
Pacific Symposium on Biocomputing 23:424-435(2018)
Coalitional game theory as a promising approach to identify candidate
autism genes
- Anika Gupta, Min Woo Sun, Kelley M. Paskov, Nate T. Stockham, Jae-Yoon Jung,
Dennis P. Wall;
Pacific Symposium on Biocomputing 23:436-447(2018)
- Evaluation of PrediXcan for prioritizing GWAS associations and predicting
gene expression
- Binglan Li, Shefali S. Verma, Yogasudha C. Veturi, Anurag Verma, Yuki Bradford,
David W. Haas, Marylyn D. Ritchie;
Pacific Symposium on Biocomputing 23:448-459(2018)
- Considerations for automated machine learning in clinical metabolic
profiling: Altered homocysteine plasma concentration associated with metformin exposure
- Alena Orlenko, Jason H. Moore, Patryk Orzechowski, Randal S. Olson, Junmei Cairns,
Pedro J. Caraballo, Richard M. Weinshilboum, Liewei Wang, Matthew K. Breitenstein;
Pacific Symposium on Biocomputing 23:460-471(2018)
- Addressing vital sign alarm fatigue using personalized alarm thresholds
- Sarah Poole, Nigam Shah;
Pacific Symposium on Biocomputing 23:472-483(2018)
- Emergence of pathway-level composite biomarkers from converging gene set
signals of heterogeneous transcriptomic responses
- Samir Rachid Zaim, Qike Li, A. Grant Schissler, Yves A. Lussier;
Pacific Symposium on Biocomputing 23:484-495(2018)
- Analyzing metabolomics data for association with genotypes using
two-component Gaussian mixture distributions
- Jason Westra, Nicholas Hartman, Bethany Lake, Gregory Shearer, Nathan Tintle;
Pacific Symposium on Biocomputing 23:496-506(2018)
- Session Introduction
- Yves A. Lussier†, Joanne Berghout, Francesca Vitali, Kenneth S. Ramos, Maricel Kann, Jason H. Moore;
Pacific Symposium on Biocomputing 23:507-511(2018)
- Pan-cancer analysis of expressed somatic nucleotide variants in long intergenic non-coding RNA
- Travers Ching, Lana X. Garmire;
Pacific Symposium on Biocomputing 23:512-523(2018)
- Convergent downstream candidate mechanisms of independent intergenic polymorphisms
between co-classified diseases implicate epistasis among noncoding elements
- Jiali Han, Jianrong Li, Ikbel Achour, Lorenzo Pesce, Ian Foster, Haiquan Li, Yves A. Lussier;
Pacific Symposium on Biocomputing 23:524-535(2018)
- Network analysis of pseudogene-gene relationships: from pseudogene evolution
to their functional potentials
- Travis S. Johnson, Sihong Li, Jonathan R. Kho, Kun Huang, Yan Zhang;
Pacific Symposium on Biocomputing 23:536-547(2018)
- Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in
Type 2 Diabetes GWAS
- Elisabetta Manduchi, Alessandra Chesi, Molly A. Hall, Struan F. A. Grant, Jason H. Moore;
Pacific Symposium on Biocomputing 23:548-558(2018)
- Session Introduction
- Graciela Gonzalez-Hernandez, Abeed Sarker, Karen O’Connor, Casey Greene, Hongfang Liu;
Pacific Symposium on Biocomputing 23:559-565(2018)
- Improving precision in concept normalization
- Mayla Boguslav, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence E. Hunter;
Pacific Symposium on Biocomputing 23:566-577(2018)
- VisAGE: Integrating external knowledge into electronic medical record visualization
- Edward W. Huang, Sheng Wang, ChengXiang Zhai;
Pacific Symposium on Biocomputing 23:578-589(2018)
- GeneDive: A gene interaction search and visualization tool to facilitate precision
medicine
- Paul Previde, Brook Thomas, Mike Wong, Emily K. Mallory, Dragutin Petkovic, Russ B. Altman,
Anagha Kulkarni;
Pacific Symposium on Biocomputing 23:590-601(2018)
- Annotating gene sets by mining large literature collections with protein networks
- Sheng Wang, Jianzhu Ma, Michael Ku Yu, Fan Zheng, Edward W. Huang, Jiawei Han, Jian Peng, Trey Ideker;
Pacific Symposium on Biocomputing 23:601-613(2018)
- The diversity and disparity in biomedical informatics (DDBI) workshop
- William Southerland, S. Joshua Swamidass, Philip R. O. Payne, Laura Wiley, ClarLynda Williams-DeVane;
Pacific Symposium on Biocomputing 23:614-617(2018)
- Integrating community-level data resources for precision medicine research
- William S. Bush, Dana C. Crawford, Farren Briggs, Darcy Freedman, Chantel Sloan;
Pacific Symposium on Biocomputing 23:618-622(2018)
- Machine learning and deep analytics for biocomputing: Call for better explainability
- Dragutin Petkovic, Lester Kobzik, Christopher Re;
Pacific Symposium on Biocomputing 23:623-627(2018)
- Methods for examining data quality in healthcare integrated data repositories
- Vojtech Huser, Michael G. Kahn, Jeffrey S. Brown, Ramkiran Gouripeddi;
Pacific Symposium on Biocomputing 23:628-633(2018)
- ERRATUM: Identifying mutation specific cancer pathways using a structurally resolved protein
interaction network
- H. Billur Engin, Matan Hofree, Hannah Carter
Pacific Symposium on Biocomputing 23:634(2018)
Funding for this conference was made possible (in part) by Grant # 5 R13 LM006766
from the National Library of Medicine. The views expressed in written conference materials
or publications, and by speakers and moderators, does not necessarily reflect the official
policies of the Department of Health and Human Services; nor does mention by trade names,
commercial practices, or organizations imply endorsement by the U.S. Government.
