PSB 2022 Online Proceedings

<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <title>PSB 2022 Online Proceedings</title> <meta name="description" content="PSB 2022 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 2022 Online Proceedings</h1></div> <div style="flex: 0 1 auto"> <a href="http://psb.stanford.Edu/">PSB 2022</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 2022 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="#ai-driven">AI-driven Advances in Modeling of Protein Structure</a></li> <li><a href="#bigdata">Big Data Imaging Genomics</a></li> <li><a href="#human">Human Intrigue: Meta Analysis Approaches for Big Questions with Big Data</a></li> <li><a href="#pm">Precision Medicine: Using Artificial Intelligence to Improve Diagnostics and Healthcare</a></li> </ul> <hr> <a href="preface.pdf">Preface</a> <h3 id="ai-driven">AI-driven Advances in Modeling of Protein Structure</h3> <dl> <dt><a href='intro_aidriven.pdf'>Session Introduction</a></dt> <dd><i>Krzysztof Fidelis, Sergei Grudinin</i>;Pacific Symposium on Biocomputing 27:1-9(2022)</dd> <dt><a href='derry.pdf'>Training data composition affects performance of protein structure analysis algorithms</a></dt> <dd><i>Alexander Derry, Kristy A. Carpenter, Russ B. Altman</i>; Pacific Symposium on Biocomputing 27:10-21(2022)</dd> <dt><a href="koehl.pdf">Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions</a></dt> <dd><i>Antoine Koehl, Milind Jagota, Dan D. Erdmann-Pham, Alexander Fung, Yun S. Song</i>; Pacific Symposium on Biocomputing 27:22-33(2022)</dd> <dt><a href="bhattacharya.pdf">Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention</a></dt> <dd><i>Nicholas Bhattacharya, Neil Thomas, Roshan Rao, Justas Dauparas, Peter K. Koo, David Baker, Yun S. Song, Sergey Ovchinnikov</i>; Pacific Symposium on Biocomputing 27:34-45(2022)</dd> <dt><a href="jindal.pdf">Side Chain Packing Using SE(3)-Transformer</a></dt> <dd><i>Akhil Jindal, Yimin Zhu, Sergey Kotelnikov, Rezaul Chowdhury, Sandor Vajda, Dzmitry Padhorny, Dima Kozakov</i>; Pacific Symposium on Biocomputing 27:46-55(2022)</dd> <dt><a href="quintana.pdf">DeepVASP-E: A Flexible Analysis of Electrostatic Isopotentials for Finding and Explaining Mechanisms that Control Binding Specificity</a></dt> <dd><i>Felix M. Quintana, Zhaoming Kong, Lifang He, Brian Y. Chen</i>; Pacific Symposium on Biocomputing 27:56-67(2022)</dd> </dl> <h3 id="bigdata">Big Data Imaging Genomics</h3> <dl> <dt><a href="intro_bigdata.pdf">Session Introduction</a></dt> <dd><i>Peter Kochunov, Li Shen, John Darrell van Horn, Paul M. Thompson</i>;Pacific Symposium on Biocomputing 27:68-72(2022)</dd> <dt><a href="mo.pdf">A new Mendelian Randomization method to estimate causal effects of multivariable brain imaging exposures</a></dt> <dd><i>Chen Mo, Zhenyao Ye, Hongjie Ke, Tong Lu, Travis Canida, Song Liu, Qiong Wu, Zhiwei Zhao, Yizhou Ma, L. Elliot Hong, Peter Kochunov, Tianzhou Ma, Shuo Chen</i>; Pacific Symposium on Biocomputing 27:73-84(2022)</dd> <dt><a href="yamamoto.pdf">Efficient Differentially Private Methods for a Transmission Disequilibrium Test in Genome Wide Association Studies</a></dt> <dd><i>Akito Yamamoto, Tetsuo Shibuya</i>; Pacific Symposium on Biocomputing 27:85-96(2022)</dd> <dt><a href="bao_morphometricity.pdf">Identifying imaging genetic associations via regional morphometricity estimation</a></dt> <dd><i>Jingxuan Bao, Zixuan Wen, Mansu Kim, Andrew J. Saykin, Paul M. Thompson, Yize Zhao, Li Shen, for the Alzheimer's Disease Neuroimaging Initiative</i>; Pacific Symposium on Biocomputing 27:97-108(2022)</dd> <dt><a href="bao_heritable.pdf">Identifying highly heritable brain amyloid phenotypes through mining Alzheimer's imaging and sequencing biobank data</a></dt> <dd><i>Jingxuan Bao, Zixuan Wen, Mansu Kim, Xiwen Zhao, Brian N. Lee, Sang-Hyuk Jung, Christos Davatzikos, Andrew J. Saykin, Paul M. Thompson, Dokyoon Kim, Yize Zhao, Li Shen, for the Alzheimer鈥檚 Disease Neuroimaging Initiative</i>; Pacific Symposium on Biocomputing 27:109-120(2022)</dd> <dt><a href="nir.pdf">Effects of ApoE4 and ApoE2 genotypes on subcortical magnetic susceptibility and microstructure in 27,535 participants from the UK Biobank</a></dt> <dd><i>Talia M. Nir, Alyssa H. Zhu, Iyad Ba Gari, Daniel Dixon, Tasfiya Islam, Julio E. Villalon-Reina, Sarah E. Medland, Paul M. Thompson, Neda Jahanshad</i>; Pacific Symposium on Biocomputing 27:121-132(2022)</dd> <dt><a href="kochunov_v2.pdf">Separating Clinical and Subclinical Depression by Big Data Informed Structural Vulnerability Index and Its impact on Cognition: ENIGMA Dot Product</a></dt> <dd><i>Peter Kochunov, Yizhou Ma, Kathryn S. Hatch, Si Gao, Lianne Schmaal, Neda Jahanshad, Paul M. Thompson, Bhim M. Adhikari, Heather Bruce, Joshua Chiappelli, Andrew Van der vaart, Eric L. Goldwaser, Aris Sotiras, Tianzhou Ma, Shuo Chen, Thomas E. Nichols, L. Elliot Hong</i>; Pacific Symposium on Biocomputing 27:133-143(2022)</dd> <dt><a href="chao.pdf">Generalizing Few-Shot Classification of Whole-Genome Doubling Across Cancer Types</a></dt> <dd><i>Sherry Chao, David Belanger</i>; Pacific Symposium on Biocomputing 27:144-155(2022)</dd> </dl> <h3 id="human">Human Intrigue: Meta Analysis Approaches for Big Questions with Big Data</h3> <dl> <dt><a href="intro_human.pdf">Session Introduction</a></dt> <dd><i>Carly A. Bobak, Meghan E. Muse, Kristine A. Giffin, Derek A. Williamson, Casey S. Greene, Jason H. Moore, Dennis P. Wall</i>;Pacific Symposium on Biocomputing 27:156-162(2022)</dd> <dt><a href="nouira.pdf">Multitask group Lasso for Genome Wide association Studies in diverse populations</a></dt> <dd><i>Asma Nouira, Chlo茅-Agathe Azencottt</i>; Pacific Symposium on Biocomputing 27:163-174(2022)</dd> <dt><a href="levy.pdf">Mixed Effects Machine Learning Models for Colon Cancer Metastasis Prediction using Spatially Localized Immuno-Oncology Markers</a></dt> <dd><i>Joshua J. Levy, Carly A. Bobak, Mustafa Nasir-Moin, Eren M. Veziroglu, Scott M. Palisoul, Rachael E. Barney, Lucas A. Salas, Brock C. Christensen, Gregory J. Tsongalis, Louis J. Vaickus</i>; Pacific Symposium on Biocomputing 27:175-186(2022)</dd> <dt><a href="romano.pdf">Improving QSAR Modeling for Predictive Toxicology using Publicly Aggregated Semantic Graph Data and Graph Neural Networks</a></dt> <dd><i>Joseph D. Romano, Yun Hao, Jason H. Moore</i>; Pacific Symposium on Biocomputing 27:187-198(2022)</dd> <dt><a href="schiebout.pdf">CAMML: Multi-Label Immune Cell-Typing and Stemness Analysis for Single-Cell RNA-sequencing</a></dt> <dd><i>Courtney Schiebout, H. Robert Frost</i>; Pacific Symposium on Biocomputing 27:199-210(2022)</dd> <dt><a href="rubel.pdf">Reconciling Signaling Pathway Databases with Network Topologies</a></dt> <dd><i>Tobias Rubel, Pramesh Singh, Anna Ritz</i>; Pacific Symposium on Biocomputing 27:211-222(2022)</dd> </dl> <h3 id="pm">Precision Medicine: Using Artificial Intelligence to Improve Diagnostics and Healthcare</h3> <dl> <dt><a href="intro_pm.pdf">Session Introduction</a></dt> <dd><i>Roxana Daneshjou, Steven E Brenner, Jonathan H Chen, Dana C Crawford, Samuel G Finlayson, 艁ukasz Kidzi艅ski, Martha L Bulyk</i>;Pacific Symposium on Biocomputing 27:223-230(2022)</dd> <dt><a href="duffy.pdf">Interpretable Deep Learning Prediction of 3D Assessment of Cardiac Function</a></dt> <dd><i>Grant Duffy, Ishan Jain, Bryan He, David Ouyang</i>; Pacific Symposium on Biocomputing 27:231-241(2022)</dd> <dt><a href="vodrahalli.pdf">Predicting Visuo-Motor Diseases from Eye Tracking Data</a></dt> <dd><i>Kailas Vodrahalli, Maciej Filipkowski, Tiffany Chen, James Zou, Yaping Joyce Liao</i>; Pacific Symposium on Biocomputing 27:242-253(2022)</dd> <dt><a href="chao_s.pdf">Identifying Cell Type-Specific Chemokine Correlates with Hierarchical Signal Extraction from Single-Cell Transcriptomes</a></dt> <dd><i>Sherry Chao, Michael P. Brenner, Nir Hacohen</i>; Pacific Symposium on Biocomputing 27:254-265(2022)</dd> <dt><a href="cui.pdf">Hierarchical Gaussian Processes and Mixtures of Experts to Model COVID-19 Patient Trajectories</a></dt> <dd><i>Sunny Cui, Elizabeth C. Yoo, Didong Li, Krzysztof Laudanski, Barbara E. Engelhardt</i>; Pacific Symposium on Biocomputing 27:266-277(2022)</dd> <dt><a href="ren.pdf">De novo Prediction of Cell-Drug Sensitivities Using Deep Learning-based Graph Regularized Matrix Factorization</a></dt> <dd><i>Shuangxia Ren, Yifeng Tao, Ke Yu, Yifan Xue, Russell Schwartz, Xinghua Lu</i>; Pacific Symposium on Biocomputing 27:278-289(2022)</dd> <dt><a href="noshad.pdf">Clinical Recommender Algorithms to Simulate Digital Specialty Consultations</a></dt> <dd><i>Morteza Noshad, Ivana Jankovic, Jonathan H. Chen</i>; Pacific Symposium on Biocomputing 27:290-300(2022)</dd> <dt><a href="poorawala-lohani.pdf">A Novel Approach for Time Series Forecasting of Influenza-like Illness Using a Regression Chain Method</a></dt> <dd><i>Nooriyah Poorawala-Lohani, Patricia Riddle, Mehnaz Adnan, J枚rg Wicker</i>; Pacific Symposium on Biocomputing 27:301-312(2022)</dd> <dt><a href="chrisman.pdf">A Method for Localizing Non-Reference Sequences to the Human Genome</a></dt> <dd><i>Brianna Sierra Chrisman, Kelley M Paskov, Chloe He, Jae-Yoon Jung, Nate Stockham, Peter Yigitcan Washington, Dennis Paul Wall</i>; Pacific Symposium on Biocomputing 27:313-324(2022)</dd> <dt><a href="nam.pdf">netCRS: Network-based comorbidity risk score for prediction of myocardial infarction using biobank-scaled PheWAS data</a></dt> <dd><i>Yonghyun Nam, Sang-Hyuk Jung, Anurag Verma, Vivek Sriram, Hong-Hee Won, Jae-Seung Yun, Regeneron Genetics Center, Dokyoon Kim</i>; Pacific Symposium on Biocomputing 27:325-336(2022)</dd> <dt><a href="he.pdf">CloudPred: Predicting Patient Phenotypes From Single-cell RNA-seq</a></dt> <dd><i>Bryan He, Matthew Thomson, Meena Subramaniam, Richard Perez, Chun Jimmie Ye, James Zou</i>; Pacific Symposium on Biocomputing 27:337-348(2022)</dd> <dt><a href="slim.pdf">Nonlinear post-selection inference for genome-wide association studies</a></dt> <dd><i>Lotfi Slim, Cl茅ment Chatelain, Chlo茅-Agathe Azencott</i>; Pacific Symposium on Biocomputing 27:349-360(2022)</dd> <dt><a href="mahoney.pdf">Evaluation of Sex-Aware PrediXcan Models for Predicting Gene Expression</a></dt> <dd><i>Emily Mahoney, Vaibhav Janve, Timothy J. Hohman, Logan Dumitrescu</i>; Pacific Symposium on Biocomputing 27:361-372(2022)</dd> <dt><a href="kaczmarek.pdf">Multi-Omic Graph Transformers for Cancer Classification and Interpretation</a></dt> <dd><i>Emily Kaczmarek, Amoon Jamzad, Tashifa Imtiaz, Jina Nanayakkara, Neil Renwick, Parvin Mousavi</i>; Pacific Symposium on Biocomputing 27:373-384(2022)</dd> <dt><a href="li.pdf">An Investigation of the Knowledge Overlap between Pharmacogenomics and Disease Genetics</a></dt> <dd><i>Binglan Li, Michelle Whirl-Carrillo, Matt W. Wright, Larry Babb, Heidi L. Rehm, Teri E. Klein</i>; Pacific Symposium on Biocomputing 27:385-396(2022)</dd> </dl> <h3 id="">Workshops</h3> <dl> <dt><a href="wkshop_emerging.pdf"> Emerging Topics in Cancer Evolution </a></dt> <dd><i>Mohammed El-Kebir, Quaid Morris, Layla Oesper, S. Cenk Sahinalp</i>;Pacific Symposium on Biocomputing 27:397-401(2022)</dd> <dt><a href="wkshop_synbio.pdf">Genomic and Synthetic Biology Digital Biosecurity </a></dt> <dd><i>Corey M. Hudson, Nicholas D. Pattengale, Ravishankar K. Iyer, Zbigniew T. Kalbarczyk, Nina Alli</i>; Pacific Symposium on Biocomputing 27:402-406(2022)</dd> <dt><a href="wkshop_image.pdf">Image-based profiling: a powerful and challenging new data type</a></dt> <dd><i> Gregory P. Way, Hannah Spitzer, Philip Burnham, Arjun Raj, Fabian Theis, Shantanu Singh, Anne E. Carpenter</i>; Pacific Symposium on Biocomputing 27:407-411(2022)</dd> <dt><a href="wkshop_packaging.pdf">Packaging Biocomputing Software to Maximize Distribution and Reuse</a></dt> <dd><i>William S. Bush, Nicholas Wheeler, Christian Darabos, Brett Beaulieu-Jones</i>; Pacific Symposium on Biocomputing 27:412-416(2022)</dd> <dt><a href="wkshop_social.pdf">Social, Technical, and Ethical Challenges in Biomedical Data Privacy</a></dt> <dd><i>Gamze Gursoy, Bradley Malin, Steven E. Brenner</i>; Pacific Symposium on Biocomputing 27:417-418(2022)</dd> </dl> <hr> <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: October 15, 2022</div> </div> </body> </html>

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PSB 2022 Online Proceedings