PSB 2018 Online Proceedings

PSB 2018
CC BY: 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.

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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.

Back to the Main PSB Page Updated: December 1, 2017