PSB 2021 Online Proceedings

<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <title>PSB 2021 Online Proceedings</title> <meta name="description" content="PSB 2021 Online Proceedings"> <meta name="viewport" content="width=device-width, initial-scale=1"> <link rel="stylesheet" href="/css/normalize.css"> <link rel="stylesheet" href="/css/main.css"> <link rel="stylesheet" href="/css/bootstrap.min.css"> <script src="/js/vendor/modernizr-2.6.2.min.js"></script> <style> dd { margin-left: 2em; } </style> </head> <body> <div class="container"> <div style="display: flex"> <div style="flex: 1 0 auto"><h1>PSB 2021 Online Proceedings</h1></div> <div style="flex: 0 1 auto"> <a href="http://psb.stanford.Edu/">PSB 2021</a> <img alt="PSB logo" src="/images/nucleosome_psbweb.gif"> </div> </div> <p> <a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/80x15.png" /></a> PSB 2021 proceedings are published as Open Access chapters by World Scientific Publishing Company and distributed under the terms of the <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution (CC BY) 4.0 License</a>. </p> <p><strong><a href="http://psb.stanford.edu/psb-online/">PSB Proceedings for All Years</a></strong></p> <hr>  <H3>Contents</H3> <ul> <li><a href="#trustworthy">Achieving Trustworthy Biomedical Data</a></li> <li><a href="#women">Advanced Methods for Big Data Analytics in Women's Health</a></li> <li><a href="#ai">Biocomputing and AI for infectious disease modelling and therapeutics</a></li> <li><a href="#pm">Computational Challenges and Artificial Intelligence in Precision Medicine</a></li> <li><a href="#pattern">Pattern Recognition in Biomedical Data for Discovery</a></li> <li><a href="#environment">What about the environment? Leveraging multi-omic datasets to characterize the environment鈥檚 role in human health</a></li> <li><a href="#workshops">Workshops</a></li> </ul> <hr> <a href="preface.pdf">Preface</a> <h3 id="trustworthy">Achieving Trustworthy Biomedical Data</h3> <dl> <dt><a href="intro-trustworthy.pdf">Session Introduction</a></dt> <dd><i>Peter Washington, Serena Yeung, Bethany Percha, Nicholas Tatonetti, Jan Liphardt, Dennis P. Wall</i>; Pacific Symposium on Biocomputing 26:1-13(2021)</dd> <dt><a href="washington.pdf">Selection of Trustworthy Crowd Workers for Telemedical Diagnosis of Pediatric Autism Spectrum Disorder</a></dt> <dd><i>Peter Washington, Emilie Leblanc, Kaitlyn Dunlap, Yordan Penev, Maya Varma, Jae-Yoon Jung, Brianna Chrisman, Min Woo Sun, Nathaniel Stockham, Kelley Marie Paskov, Haik Kalantarian, Catalin Voss, Nick Haber, Dennis P. Wall</i>;Pacific Symposium on Biocomputing 26:14-25(2021)</dd> <dt><a href="chen_j.pdf">Differential Privacy Protection Against Membership Inference Attack on Machine Learning for Genomic Data</a></dt> <dd><i>Junjie Chen, Wendy Hui Wang, Xinghua Shi</i>; Pacific Symposium on Biocomputing 26:26-37(2021)</dd> <dt><a href="greenbaum.pdf">Making Compassionate Use More Useful: Using Real-World Data, Real-World Evidence and Digital Twins to Supplement or Supplant Randomized Controlled Trials</a></dt> <dd><i>Dov Greenbaum</i>; Pacific Symposium on Biocomputing 26:38-49(2021)</dd> </dl> <h3 id="women">Advanced Methods for Big Data Analytics in Women's Health</h3> <dl> <dt><a href="intro-big_data.pdf">Session Introduction</a></dt> <dd><i>Mary Regina Boland, Karin Verspoor, Maricel G Kann, Su Golder, Lisa Levine, Karen O'Conner, Natalia Villanueva-Rosales, Graciela Gonzalez-Hernandez</i>; Pacific Symposium on Biocomputing 26:50-54(2021)</dd> <dt><a href="chen_i.pdf">Intimate Partner Violence and Injury Prediction from Radiology Reports</a></dt> <dd><i>Irene Y. Chen, Emily Alsentzer, Hyesun Park, Richard Thomas, Babina Gosangi, Rahul Gujrathi, and Bharti Khurana</i>; Pacific Symposium on Biocomputing 26:55-66(2021)</dd> <dt><a href="canelon.pdf">Not All C-sections Are the Same: Investigating Emergency vs. Elective C-section deliveries as an Adverse Pregnancy Outcome</a></dt> <dd><i>Silvia P. Canel贸n, Mary Regina Boland</i>; Pacific Symposium on Biocomputing 26:67-78(2021)</dd> <dt><a href="hac谋aliefendioglu.pdf">Co-occurrence Patterns of Intimate Partner Violence</a></dt> <dd><i>Ahmet Hacialiefendioglu, Serhan Yilmaz, Mehmet Koyuturk, Gunnur Karakurt</i>; Pacific Symposium on Biocomputing 26:79-90(2021)</dd> </dl> <h3 id="ai">Biocomputing and AI for infectious disease modelling and therapeutics</h3> <dl> <dt><a href="intro-biocomp_ai.pdf">Session Introduction</a></dt> <dd><i>Gil Alterovitz, Wei-Lun Alterovitz, Gail H. Cassell, Lixin Zhang, A. Keith Dunker</i>; Pacific Symposium on Biocomputing 26:(2021)91-94</dd> <dt><a href="sullivan.pdf">Characterization of Anonymous Physician Perspectives on COVID-19 Using Social Media Data</a></dt> <dd><i>Katherine J. Sullivan, Marisha Burden, Angela Keniston, Juan M. Banda, Lawrence E. Hunter</i>; Pacific Symposium on Biocomputing 26:95-106(2021)</dd> <dt><a href="dinakar.pdf">Semantic Changepoint Detection for Finding Potentially Novel Research Publications</a></dt> <dd><i>Bhavish Dinakar, Mayla R. Boguslav, Carsten G枚rg, Deendayal Dinakarpandian</i>; Pacific Symposium on Biocomputing 26:107-118(2021)</dd> <dt><a href="sledzieski.pdf">TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference</a></dt> <dd><i>Samuel Sledzieski, Chengchen Zhang, Ion Mandoiu, Mukul S. Bansal</i>; Pacific Symposium on Biocomputing 26:(2021)119-130</dd> <dt><a href="mudide.pdf">SARS-CoV-2 Drug Discovery based on Intrinsically Disordered Regions</a></dt> <dd><i>Anish Mudide, Gil Alterovitz</i>; Pacific Symposium on Biocomputing 26:131-142(2021)</dd> <dt><a href="goh.pdf">Feasibility of the Vaccine Development for SARS-CoV-2 and Other Viruses Using the Shell Disorder Analysis</a></dt> <dd><i>Gerard Kian-Meng Goh, A. Keith Dunker, James A. Foster, Vladimir N. Uversky</i>; Pacific Symposium on Biocomputing 26:143-153(2021)</dd> <dt><a href="kshirsagar.pdf">Protein Sequence Models for Prediction and Comparative Analysis of the SARS-CoV-2鈭扝uman Interactome</a></dt> <dd><i>Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman, Judith Klein-Seetharaman</i>; Pacific Symposium on Biocomputing 26:154-165(2021)</dd> </dl> <h3 id="pm">Computational Challenges and Artificial Intelligence in Precision Medicine</h3> <dl> <dt><a href="intro-precision_med.pdf">Session Introduction</a></dt> <dd><i>Olga Afanasiev, Joanne Berghout, Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jonathan H. Chen, Roxana Daneshjou, 艁ukasz Kidzi艅ski</i>; Pacific Symposium on Biocomputing 26:166-171(2021)</dd> <dt><a href="dong.pdf">AeQTL: eQTL Analysis Using Region-Based Aggregation of Rare Genomic Variants</a></dt> <dd><i>Guanlan Dong, Michael C. Wendl, Bin Zhang, Li Ding, Kuan-lin Huang</i>; Pacific Symposium on Biocomputing 26:172-183(2021)</dd> <dt><a href="mcinnes.pdf">Drug Response Pharmacogenetics for 200,000 UK Biobank Participants</a></dt> <dd><i>Gregory McInnes, Russ B. Altman</i>; Pacific Symposium on Biocomputing 26:184-195(2021)</dd> <dt><a href="aoki.pdf">ParKCa: Causal Inference with Partially Known Causes</a></dt> <dd><i>Raquel Aoki, Martin Ester</i>; Pacific Symposium on Biocomputing 26:196-207(2021)</dd> <dt><a href="mayhew.pdf">Optimization of Genomic Classifiers for Clinical Deployment: Evaluation of Bayesian Optimization to Select Predictive Models of Acute Infection and In-Hospital Mortality</a></dt> <dd><i>Michael B. Mayhew, Elizabeth Tran, Kirindi Choi, Uros Midic, Roland Luethy, Nandita Damaraju, Ljubomir Buturovic</i>; Pacific Symposium on Biocomputing 26:208-219(2021)</dd> <dt><a href="vodrahalli.pdf">TrueImage: A Machine Learning Algorithm to Improve the Quality of Telehealth Photo</a></dt> <dd><i>Kailas Vodrahalli, Roxana Daneshjou, Roberto A. Novoa, Albert Chiou, Justin M. Ko, James Zou</i>; Pacific Symposium on Biocomputing 26:220-231(2021)</dd> <dt><a href="seyyed-kalantari.pdf">CheXclusion: Fairness Gaps in Deep Chest X-ray Classifiers</a></dt> <dd><i>Laleh Seyyed-Kalantari, Guanxiong Liu, Matthew McDermott, Irene Y. Chen, Marzyeh Ghassemi</i>; Pacific Symposium on Biocomputing 26:232-243(2021)</dd> <dt><a href="singh_a.pdf">Incorporation of DNA Methylation into eQTL Mapping in African Americans</a></dt> <dd><i>Anmol Singh, Yizhen Zhong, Layan Nahlawi, C. Sehwan Park, Tanima De, Cristina Alarcon, and Minoli A. Perera</i>; Pacific Symposium on Biocomputing 26:244-255(2021)</dd> </dl> <h3 id="pattern">Pattern Recognition in Biomedical Data for Discovery</h3> <dl> <dt><a href="intro-pattern_rec.pdf">Session Introduction</a></dt> <dd><i>Brett Beaulieu-Jones, Christian Darabos, Dokyoon Kim, Anurag Verma, Shilpa Nadimpalli Kobren</i>; Pacific Symposium on Biocomputing 26:256-260(2021)</dd> <dt><a href="durmaz.pdf">Frequent Subgraph Mining of Functional Interaction Patterns Across Multiple Cancers</a></dt> <dd><i>Arda Durmaz, Tim A. D. Henderson, Gurkan Bebek</i>; Pacific Symposium on Biocomputing 26:261-272(2021)</dd> <dt><a href="finlayson.pdf">Cross-modal Representation Alignment of Molecular Structure and Perturbation-Induced Transcriptional Profiles</a></dt> <dd><i>Samuel G. Finlayson, Matthew B.A. McDermott, Alex V. Pickering, Scott L. Lipnick, Isaac S. Kohane</i>; Pacific Symposium on Biocomputing 26:273-284(2021)</dd> <dt><a href="levy_j.pdf">Topological Feature Extraction and Visualization of Whole Slide Images Using Graph Neural Networks</a></dt> <dd><i>Joshua Levy, Christian Haudenschild, Clark Barwick, Brock Christensen, Louis Vaickus</i>; Pacific Symposium on Biocomputing 26:285-296(2021)</dd> <dt><a href="scott.pdf">A Multi-Scale Integrated Analysis Identifies KRT8 as a Pan-Cancer Early Biomarker</a></dt> <dd><i>Madeleine K. D. Scott, Michael G. Ozawa, Pauline Chu, Maneesha Limaye, Viswam S. Nair, Steven Schaffert, Albert C. Koong, Robert West, Purvesh Khatri</i>; Pacific Symposium on Biocomputing 26:297-308(2021)</dd> </dl> <h3 id="environment">What about the environment? Leveraging multi-omic datasets to characterize the environment鈥檚 role in human health</h3> <dl> <dt><a href="intro-environment.pdf">Session Introduction</a></dt> <dd><i>Kristin Passero, Shefali Setia-Verma, Kimberly McAllister, Arjun Manrai, Chirag Patel, Molly Hall</i>; Pacific Symposium on Biocomputing 26:309-315(2021)</dd> <dt><a href="aguilar.pdf">Semi-automated NMR Pipeline for Environmental Exposures: New Insights on the Metabolomics of Smokers versus Non-smokers</a></dt> <dd><i>Morris A. Aguilar, John McGuigan, Molly A. Hall</i>; Pacific Symposium on Biocomputing 26:316-327(2021)</dd> <dt><a href="makridis.pdf">How Much Does the (Social) Environment Matter? Using Artificial Intelligence to Predict COVID-19 Outcomes with Socio-demographic Data</a></dt> <dd><i>Christos A. Makridis, Anish Mudide, Gil Alterovitz</i>; Pacific Symposium on Biocomputing 26:328-335(2021)</dd> </dl> <h3 id="workshops">Workshops</h3> <dl> <dt><a href="wksp_bioinfo_of_coral.pdf">Bioinformatics of Corals</a></dt> <dd><i>Lenore J. Cowen, Judith Klein-Seetharaman, Hollie Putnam</i>; Pacific Symposium on Biocomputing 26:336-340(2021)</dd> <dt><a href="wksp_rel_algo.pdf">Establishing the Reliability of Algorithms in Biomedical Informatics</a></dt> <dd><i>Lara Mangravite, Sean D. Mooney, Iddo Friedberg, Justin Guinney</i>; Pacific Symposium on Biocomputing 26:341-345(2021)</dd> <dt><a href="wksp_making_tools.pdf">Making Tools that People Will Use: User-Centered Design in Computational Biology Research</a></dt> <dd><i>Mary Goldman, Nils Gehlenborg</i>; Pacific Symposium on Biocomputing 26:346-350(2021)</dd> <dt><a href="wksp_stake.pdf">Raising the Stakeholders: Improving Patient Outcomes Through Interprofessional Collaborations in AI for Healthcare</a></dt> <dd><i>Carly A. Bobak, Marek Svoboda, Kristine A. Giffin, Dennis P. Wall, Jason Moore</i>; Pacific Symposium on Biocomputing 26:351-355(2021)</dd> <dt><a href="wksp_trans_bioinfo.pdf">Translational Bioinformatics</a></dt> <dd><i>Dokyoon Kim, Ju Han Kim, Jason H. Moore</i>; Pacific Symposium on Biocomputing 26:356-359(2021)</dd> </dl> <p><em> Funding for this conference was made possible (in part) by R13LM006766 from the National Library of Medicine. The views expressed in written conference materials or publications and by speakers and moderators do 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. </em></p> <div class="row" style="margin: 5em 0"> <div class="col-md-6"><a href="/index.html">Back to the Main PSB Page</a></div> <div class="col-md-6 text-right">Updated: December 4, 2020</div> </div> </div> </body> </html>

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PSB 2021 Online Proceedings