LIGHTNING ROUND PRESENTERS

These top posters (in pink) received the highest rankings in the poster review and scoring and will be presented during the Lightning Round at 11:15 AM on Friday October 7, 2022. Attendees will vote for the best poster presentation and 3 will receive $250 Trainee Awards at the close of the conference day.

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Causal impact of Mobile Elements (MEs) on neurodevelopmental disorders

Sammy Hansali, Anthony Wong, Anbo Zhou, Xiaolong Cao, Vaidhyanathan Mahaganapathy, Marco Azaro, Christine Gwin, Sherri Wilson, Steven Buyske, Christopher W. Bartlett, Judy F. Flax, Linda M. Brzustowicz, and Jinchuan Xing

 

Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease

Hongbo Liu1,2,3, Tomohito Doke1,2,3, Dong Guo4, Xin Sheng1,2,3, Ziyuan Ma1,2,3, Joseph Park1,3,5, Ha My T. Vy6,7, Girish N. Nadkarni6,7,8,9, Amin Abedini1,2,3, Zhen Miao1,2,3, Matthew Palmer10, Benjamin F. Voight2,3,11,12, Hongzhe Li13, Christopher D. Brown3, Marylyn D. Ritchie3,5, Yan Shu4 and Katalin Susztak1,2,3    1Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, PA, USA; 2Institute of Diabetes Obesity and Metabolism, University of Pennsylvania, Philadelphia, PA, USA; 3Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA; 4Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, Baltimore, MD, USA; 5Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; 6Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 7The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 8The Hasso Plattner Institute of Digital Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 9The Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 10Pathology and Laboratory Medicine at the Hospital of the University of Pennsylvania, Philadelphia, , USA; 11Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; 12Institute of Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA; 13Department of Biostatistics, Epidemiology, and Informatics, and Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 

 

Diagnostic gene fusion detection in cancer by adaptation of short-read CHOP Fusion Panel to Oxford Nanopore long-read sequencing

Karleena Rybacki, BS, 1,2   Li Fang, PhD, 2  Feng Xu, PhD, 3   Yu Hu, PhD, 2  Mian Umair Ahsan, MS, 2  Marilyn Li, MD, 3  Kai Wang, PhD, 1,2    1 University of Pennsylvania   2 Children's Hospital of Philadelphia (CHOP)  3 Division of Genomic Diagnostics at Children's Hospital of Philadelphia (CHOP)

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Predicting embryonic aneuploidy rate and identifying candidate genes in IVF patients using synonymous variants

Jason Liu  Siqi Sun  Jinchuan Xing Rutgers University

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A combined polygenic risk score provides a data-driven biomarker for metabolic syndrome

Leiby, Jacob S.; Choe, Eun Kyung; Kim, Dokyoon University of Pennsylvania School of Medicine

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Is common genetic risk for psychiatric disorders associated with traumatic experiences in youth?

Alison K. Merikangas PhD, MPH (1,2,3), Laura M. Schultz PhD (2,3), Zoe Rapisardo-Drigot (1,4), PNC Collaborators (3,5), Laura Almasy PhD (1,2,3)    1. Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA    2. Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA    3. Lifespan Brain Institute of the Children's Hospital of Philadelphia and the University of Pennsylvania, Philadelphia, PA    4. Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO    5. Department of Psychiatry, Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 

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Investigation of Cell-Free DNA Methylation as a Biomarker of Malignant vs. Benign Lung Nodules

Jennifer Guo1; Jacob E. Till, MD, PhD1; Thrusha Puttaraju1; Aseel Abdalla1; Zhouyang Wang1; Danielle Shoshany1; Wanding Zhou, PhD2; Jeffrey Thompson, MD3*; Erica L. Carpenter, MBA, PhD1*;    1Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania; 2Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia; 3Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania; *Co-Senior Author 

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All posters will be on display in the Roberts Center lobbies.

Please visit the authors in the main lobby and the level B lobby. 

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Seamless integrative pipeline for QTL datasets enhance the discovery of putative causal variants for Alzheimer's Disease.

Jeffrey Cifello(1), Pavel P Kuksa(1), Li-San Wang(1), Yuk Yee Leung(1)  1 Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania

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Cladebreaker: Using proteomic novelty to test clonality in outbreaks and epidemics

A Feder1, AM Moustafa2,3, PJ Planet1,3  1- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA  2- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA  3- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA

 

Single-cell Genomics Study of Fontan-associated Liver Disease

Po Hu, B.S., Juanjuan Zhao, Ph.D., Wenbao Yu, Ph.D., Benjamin Wilkins, M.D., Ph.D., Aidan Bauer, B.S., Kai Tan, Ph.D., Jack Rychik, M.D., Liming Pei, Ph.D.

 

Genetic Heterogeneity of Four Deep Learning-derived MCI/AD Dimensions via Genome-wide Tiling Associations

Jiong Chen1,2,3, Junhao Wen, PhD1,2, Zhijian Yang1,2, Yuhan Cui1,2, Jingxuan Bao4, Brian N Lee2, Guray Erus, PhD1,2, Sarah Wait Zaranek, PhD5, Alexander Wait Zaranek, PhD5, Yong Fan, PhD1,2, Andrew J. Saykin, MS, PsyD6, Paul M. Thompson, PhD7, Li Shen, PhD4, Haochang Shou, PhD1,8, Ilya M. Nasrallah, MD, PhD1,2, Christos Davatzikos, PhD1,2,9,10    1Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA  2Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA  3Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, USA  4Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, USA  5Curii Corporation, Somerville, MA, USA  6Center for Neuroimaging, Department of Radiology and Imaging Sciences, and the Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, USA  7Keck School of Medicine, University of Southern California, Los Angeles, CA, USA  8Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA  9For the Alzheimer's Disease Neuroimaging Initiative  10For the AI4AD consortium   

 

Translational Bioinformatics for Heterogenous Longitudinal Data in Pre-Clinical Models of Neurological Injury: From Collection to Therapeutic Target Discovery

Hunter A. Gaudio1,2, Viveknarayanan Padmanabhan3, Gerard Laurent4, Ryan W. Morgan1,2, Julia Slovis1,2, Frank Mi3, Helen Shi3, Luiz Eduardo Silva3, Wesley B. Baker2,4, Fuchiang Tsui3, Todd J. Kilbaugh1,2, Tiffany S. Ko1,2    1 Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, Philadelphia, PA  2 The Resuscitation Science Center, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA  3 Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA  4 Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 

 

Using combinatorial hash-joins to identify SARS-CoV-2 variants.

S Haag1, A Feder2, AM Moustafa3,4, PJ Planet2,4  1-Arcus, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA  2- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA  3- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA  4- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA

 

SNAF: Comprehensive prediction of splicing neoantigens for targeted cancer immunotherapy

Guangyuan Li, BS, Cincinnati Children's Hospital Medical Center  2. Anukana Bhattacharjee, PhD, Cincinnati Children's Hospital Medical Center  3. Gloria M. Sheynkman, PhD, University of Virginia  4. Nathan Salomonis, PhD, Cincinnati Children's Hospital Medical Center 

 

Deep Learning of Videourodynamics to Classify Bladder Dysfunction Severity

Weaver JK, Martin-olenski M, Logan J, Broms R, Antony M, Van Batavia J, Weiss D, Long CJ, Smith AL, Zderic SA, Yong F, Tasian GE

 

A 3D Anatomical and Molecular Map of Cardiac Vagal Motor Neurons

Hornung E, Robbins S, Srivastava A, Achanta S, Schwaber J, and Vadigepalli R

 

Best Practices for COVID-19 Dashboards

Malkani, Dillon, Bullis School; Malkani, Melina, Bullis School; Singh, Neel, Landon School; Madan, Eesha, BASIS Independent School McLean

 

Single cell long read sequencing and perturbation analysis reveals splicing heterogeneity and logic

Yuntian Fu:Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA    Heonseok Kim,  Susan M. Grimes, Billy T. Lau, Anuja Sathe,:Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA

 

rMATS-turbo: An efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data

Yuanyuan Wang 1,2,†, Zhijie Xie 2,†, Eric Kutschera 2, Jenea I. Adams 2,3, Kathryn E.  Kadash-Edmondson 2, Yi Xing 2,4,5,*    1. Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los  Angeles, CA 90095, USA  2. Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia,  Philadelphia, PA, 19104, USA  3. Genomics and Computational Biology Graduate Program, University of Pennsylvania,  Philadelphia, PA, 19104, USA  4. Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia,  PA, 19104, USA  5. Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia,  Philadelphia, PA, 19104, USA  *Corresponding author. Phone: (215) 590-0280  †These authors contributed equally to this work   

 

Modules of genotypic variance reflect heterogeneity across TDP-43 proteinopathies

Barbara E Spencer, PhD; David J. Irwin, MD; Vivianna M Van Deerlin, MD, PhD; Eddie B Lee, MD, PhD; Lauren Elman, MD; Colin Quinn, MD; Murray Grossman, MD, EdD; David A. Wolk, MD and Corey T McMillan, PhD    University of Pennsylvania, Philadelphia, PA, USA

 

The Codon Statistics Database: a Database of Codon Usage Bias

Krishnamurthy Subramanian1,2,‡, Bryan Payne1,‡, Felix Feyertag1 and David Alvarez-Ponce1    1 Biology Department, University of Nevada, Reno, Reno, NV, 89557.   2 Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854

 

LongReadSum: A fast and flexible quality control tool for long-read sequencing data

[1] Jonathan Elliot Perdomo, BA. Children's Hospital of Philadelphia.    [2] Mian Umair Ahsan, MS. Children's Hospital of Philadelphia.    [3] Qian Liu, Ph.D. Children's Hospital of Philadelphia.    [4] Li Fang, Ph.D. Children's Hospital of Philadelphia.    [5] Kai Wang, Ph.D. Children's Hospital of Philadelphia.

 

Detecting Coupled-Gene Clusters In scRNA-Seq Data Using Deep Learning

Alicia Petrany, Yong Chen PhD.

 

Functional Impact of Copy Number Variants in Autism Probands

Rohan Alibutud, Vaidhyanathan Mahaganapathy, Xiaolong Cao, Marco Azaro, Christine Gwin, Sherri Wilson, Steven Buyske, Christopher W. Bartlett, Judy F. Flax, Linda M. Brzustowicz, Jinchuan Xing

 

Analysis of variation in epigenetic age prediction in Domestic dog samples (Canis lupus familiaris)

Nirali Desai1,2, Matteo Pellegrini2    1College of Science, Northeastern University, Boston, MA    25000D Terasaki Life Sciences Building, Molecular, Cell & Developmental Biology Department, University of California, Los Angeles, California    Corresponding Author    Matteo Pellegrini    5000D Terasaki Life Sciences Building, Molecular, Cell & Developmental Biology Department, University of California, Los Angeles, California 

 

Medulloblastoma subtype single sample predictor built on multiple gene expression platforms

Steven M. Foltz, PhD 1,2,  Casey S. Greene, PhD 1,3, Jaclyn N. Taroni, PhD 2    1 Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA  2 Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Wynnewood, PA, USA  3 Center for Health AI, University of Colorado School of Medicine, Aurora, CO, USA

 

Distinct cellular trajectories diverge between cancerous and non-cancerous pathologies in the murine esophageal epithelium

Adam Karami, MS(1); Mohammed Faujul Kabir, PhD(1); Alena Klochkova, MS(1); Anbin Mu(1); Yinfei Tan, PhD(2); Andres Klein-Szanto, MD, PhD(2); Kelly A. Whelan, PhD(1)    (1)Fels Cancer Institute for Personalized Medicine, Temple University, Philadelphia, PA  (2)Department of Pathology and Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 

 

JOnTAD: joint hierarchical TAD caller for high resolution, single cell and bulk cell Hi-C data

Qiuhai Zeng, BS, Pennsylvania State University; Guanjue Xiang, PhD, CAMP4 Therapeutics; Yu Zhang, PhD, Two Sigma; Qunhua Li, PhD, Pennsylvania State University

 

Linkreg: a Bayesian framework for linking candidate cis-regulatory elements to target genes

Qiuhai Zeng, BS, Pennsylvania State University; Guanjue Xiang, PhD, CAMP4 Therapeutics; Ross Hardison, PhD, Pennsylvania State University; Xiang Zhu, PhD, Pennsylvania State University; Qunhua Li, PhD, Pennsylvania State University

 

Identifying and Validating Recurrent Structural Variants Affecting Tumor Genomes using GROM and VN

Syeda Aiman Nadeem [1]  James J. Kelley, MS [1,2],   Andrey Grigoriev, PhD [1,2]    1. Dept of Biology, Rutgers University, Camden, NJ  2. Center of Computational and Integrative Biology, Rutgers University, Camden, NJ

 

RNA-seq reveals condition-dependent global transcriptional effects of the msf gene in Haemophilus influenzae biofilms

Evangeline Williams, BA; Laura Anastor-Walters, MS; Bhaswati Sen, PhD; Steven Lang, BS; Sergey Balashov, PhD; Rachel L. Ehrlich, MS; Garth D. Ehrlich, PhD; Benjamin Janto, PhD; Joshua Chang Mell PhD    AFFILIATIONS: Drexel University College of Medicine, Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease 

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Network-based cross-phenotype risk scoring models for compositing multiple disease risks using biobank-scaled PheWAS data

Yonghyun Nam 1, Vivek Sriram 1, Sang-Hyuk Jung 1,2, Brenda Xiao 1, Manu Shivakumar 1, Anurag Verma 3*, Dokyoon Kim 1,4*    1Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA    2Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul 06351, Republic of Korea    3Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA    4Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
 

Mapping PTBP splicing in human brain identifies targets for therapeutic splice switching including SYNGAP1

Jennine M. Dawicki-McKenna, PhD 1*  Alex J. Felix, PhD 1*  Elisa A. Waxman, PhD 2  Congsheng Cheng, PhD 2  Defne A. Amado, MD, PhD 2  Paul T. Ranum, PhD 2  Alexey Bogush, PhD 1  Lea V. Dungan 2  Elizabeth A. Heller, PhD 3  Deborah L. French, PhD 2,4  Beverly L. Davidson, PhD 2,4  Benjamin L. Prosser, PhD 1  * These authors contributed equally to the work.  1 - Department of Physiology, Pennsylvania Muscle Institute, University of Pennsylvania Perelman School of Medicine  2 - Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia  3 - Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine  4 - Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine 

 

A Novel Genetic Correlation Disease-Disease Network for the Improved Identification of Associated Phenotypes

Jakob Woerner(1,2), Vivek Sriram(1,2), Yonghyun Nam(2), Dokyoon Kim(2,3)    1Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA  2Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA  3Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA 

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Repairing the neutral set in codon evolutionary models

Hannah Verdonk (1), Sergei L. Kosakovsky Pond, PhD (1), and Jody Hey, PhD (2)    1. Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, Pennsylvania, USA  2. Center for Computational Genetics and Genomics, Department of Biology, Temple University, Philadelphia, Pennsylvania, USA

 

The Single-cell Pediatric Cancer Atlas: Open-source data and tools for single-cell transcriptomics of pediatric tumors

Allegra G. Hawkins, PhD. Alex's Lemonade Stand Foundation.  Joshua A. Shapiro, PhD. Alex's Lemonade Stand Foundation.  Chante Bethell, BS. Alex's Lemonade Stand Foundation.  David S. Mejia. HSD. Alex's Lemonade Stand Foundation.  Deepa Prasad, MS. Alex's Lemonade Stand Foundation.  Nozomi Ichihara, AS. Alex's Lemonade Stand Foundation.  Arkadii Yakovets, MS. Alex's Lemonade Stand Foundation.  Kurt Wheeler, BS. Alex's Lemonade Stand Foundation (former); Reify Health (current).  Steven Foltz PhD. Alex's Lemonade Stand Foundation; University of Pennsylvania.  Jennifer O'Malley, MA.  Alex's Lemonade Stand Foundation.  Stephanie J. Spielman, PhD.  Alex's Lemonade Stand Foundation.  Jaclyn N. Taroni, PhD. Alex's Lemonade Stand Foundation. 

 

RNA-seq with and without rRNA depletion and varying library prep protocol parameters

Thomas G Brooks 1  Nicholas F Lahens 1  Antonijo Mrčela 1  Shaon Sengupta 1, 2  Peter S Choi 3  Gregory R Grant 1, 4    1. Institute for Translational Medicine and Therapeutics, University of Pennsylvania  2. Division of Neonatology, Children's Hospital of Philadelphia  3.  Division of Cancer Pathobiology, Children's Hospital of Philadelphia  4. Department of Genetics, University of Pennsylvania 

 

Comparing Metabolic Pathway Fluxes of Ground-Bound and Space-Flown Mice Using Single-cell RNA-sequencing and a Constraint-based Metabolic Model

Shubha Vasisht (1), Yuanchao Zhang (1), Deanne Taylor (1,2)  1. Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia   2. Perelman School of Medicine, University of Pennsylvania 

 

Niche differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

Kaishu Mason, Nancy Zhang, University of Pennsylvania, Professor of Statistics  Anuja Sathe, Stanford University, Postdoctoral Fellow  

 

Using Decision Trees to Predict the Clinical Isolation Source of Haemophilus influenzae Based on Pan-Genomic Diversity

Koser, K(2345), Ehrlich, R. L(1234)., Hammond, J.(1234), Czerski, S.(1234), Mell, J. C.(12345), Earl, J. P.(1234), Ahmed, A.(1234), Ehrlich, G. D.(12345)    Affiliations:  1Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia PA 19102  2Institute for Molecular Medicine & Infectious Disease, Drexel University College of Medicine, Philadelphia, PA 19102  3Center for Advanced Microbial Processing, Drexel University College of Medicine, Philadelphia, PA, 19102  4Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, PA, 19102  5Molecular & Cellular Biology & Genetics Graduate Program, Drexel University College of Medicine, Philadelphia PA 19102 

 

Integrating common and rare variants into a genetic risk score for Alzheimer's disease risk prediction

Erica H Suh1, Garam Lee1, Sang-Hyuk Jung2, Zixuan Wen1, Jingxuan Bao1, Li Shen1,3, Dokyoon Kim1,3*     1Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA  2Department of Digital Health, SAIHST, Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea  3Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA 

 

Intuitive intracellular communication deconvolution and ranking for improved discovery of context-dependent signaling via TrokaChat

Michael E. Troka, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.    Michael V. Gonzalez, Center for Cytokine Storm Treatment & Laboratory, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.    Dana T. Graves, Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

 

Gene Signature Reveals Decreased SOX10 Activity in Malignant Cells from Immunotherapy-Resistant Cutaneous Melanoma Tumors

Timothy J. Purwin1, 2, Claudia Capparelli1, Ahmet Sacan2 and Andrew E. Aplin1, 3  1 Department of Pharmacology, Physiology, and Cancer Biology, 3 Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA. 2 School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, USA. 

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Gene-environment interaction of coffee with body mass index in multiple populations

Manu Shivakumar1, Dokyoon Kim1§, Eun Kyung Choe1,2§    1 Department of Biostatistics, Epidemiology & Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA  2 Department of Surgery, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea 
 

Quantification of 3′ UTR isoform expression from scRNA-seq reveals substantial changes in differentiation

Mervin M. Fansler (1,2), Gang Zhen, PhD (2), and Christine Mayr, MD, PhD (1,2).    (1) Tri-Institutional Training Program in Computational Biology and Medicine, Weill-Cornell Graduate College, New York, NY 10021, USA  (2) Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 

 

What Can Bioinformatics Scientists Learn from Librarians? Using Library and Archival Methodologies to Preserve and Reuse Omics Data

Ene Belleh, Children's Hospital of Philadelphia; Jennae Luecke, Children's Hospital of Philadelphia; Allison Olsen, Children's Hospital of Philadelphia; Julianna Pakstis, Children's Hospital of Philadelphia 

 

Understanding Interferon-γ-Induced Esophageal Epithelial Barrier Dysfunction and Apoptosis using Integrative Analysis of In Vivo and Model Gene Expression

Megha Lal, PhD1, Ravi Gautam, PhD1, Zoe Mrozek, BS1, Yusen Zhou, PhD3, Jarad Beers, MS1, Margaret C. Carroll, MS1, Melanie A. Ruffner, MD, PhD1,2.    1Division of Allergy and Immunology, Children's Hospital of Philadelphia  2Department of Pediatrics, Perelman School of Medicine at University of Pennsylvania  3Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia  

 

Identification of genetic loci associated with the risk of aneuploidy with maternal origin using PGT-A sequences

Siqi Sun1 , Aishee Bag1 , Daniel Ariad2 , Mary Haywood3 , Mandy Katz-Jaffe3 , Rajiv McCoy2 , Karen Schindler1, 4, Jinchuan Xing1, 4    1Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA. 2Department of Biology, Johns Hopkins University, Baltimore, MD, USA.   3CCRM Genetics, Lone Tree, CO, USA.   4Human Genetic Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.  

 

Evaluating the frequency and the impact of pharmacogenetic variants in an ancestrally diverse Biobank population

Karl Keat1*, Shefali S. Verma2*, Binglan Li3, Glenda Hoffecker4, Marjorie Risman5, Regeneron Genetics Center, Katrin Sangkuhl3, Michelle Whirl-Carrillo3, Scott Dudek5, Anurag Verma4, Teri E. Klein3,6, Marylyn D. Ritchie5*, Sony Tuteja4*    1Genomics & Computational Biology PhD Program, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA  2Department of Pathology & Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA  3Department of Biomedical Data Science, Stanford University, Stanford, California, USA  4Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA  5Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA  6Department of Biomedical Data Science and Medicine (BMIR), Stanford University,  Stanford, California, USA 

 

Susceptibility of human glycogenes to functional variations

Taha Mohseni Ahooyi (1)  Benjamin Stear (1)  Deanne Taylor (1,2)  (1) Department of Biomedical and Health Informatics (DBHi), The Children's Hospital of Philadelphia, Philadelphia, PA  (2) Perelman School of Medicine, University of Pennsylvania 

 

ADE: an integrated bioinformatics web server for neurodegenerative  disease exploration, omics data analysis, and drug discovery

Jiannan Liu (1), Huanmei Wu (2,1), Daniel H. Robertson (3), Kun Huang (4), Jie Zhang (5)    1. Dept of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN, USA.   2. Dept of Health Services Administration & Policy, Temple University College of Public Health, Philadelphia, PA, USA.   3. Indiana Biosciences Research Institute, Indianapolis, IN, USA.   4. Dept of Biostatistics & Health Data Science, Indiana University School of   Medicine, Indianapolis, IN, USA.   5. Dept of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA. 
 

Petagraph: A biomedical knowledge graph built into the UMLS

Ben Stear (1), MS; Taha Mohseni Ahooyi (1), PhD;  Shubha Vasisht (1);  Jonathan Silverstein (3,4), MD, MS, FACS, FACMI; Tiffany Callahan (5), PhD; Deanne Taylor (1,2), PhD.    1. Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia  2. Perelman School of Medicine, University of Pennsylvania  3. Health Sciences and Institute for Precision Medicine, University of Pittsburgh  4. Department of Biomedical Informatics, University of Pittsburgh  5. Anschutz Medical Campus, University of Colorado Denver

 

Improving Genomic Data Diversity Using Few-shot Generative Domain Adaptation

Chen Song, Computer and Information Science Department, Temple University    Emily Thyrum, Computer and Information Science Department, Temple University    Dr. Xinghua Shi, Computer and Information Science Department, Temple University 

 

Leveraging Graph Neural Networks for Interpretable Prediction of Pathological Stages in Prostate Cancer

Wenkang Zhan, Department of Computer & Information Science, Temple University  Chen Song, Department of Computer & Information Science, Temple University  Xinghua Shi, PhD, Department of Computer & Information Science, Temple University

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Cardiovascular Events Associated with PCOS Diagnosis in Large Longitudinal Cohort

Cherlin T , PhD (1), Morse C, PT, DPT, MSA (2), Lee ITL , MD (3), Dokras A, MD, PhD (3), Verma SS, PhD (1)       1. Dept. of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA  2.         Penn Medicine Biobank, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA  3.      Perelman School of Medicine, Division of Reproductive Endocrinology and Infertility, University of Pennsylvania, Philadelphia, PA  

 

Identifying longitudinal disease trajectories and their clinical associations in 146,000 individuals with hypertension from Penn Medicine Electronic Health Records

Pankhuri Singhal1 (BS), Lindsay Guare1 (BS), Anastasia Lucas1,2 (BS), Colleen Morse1 (DPT), Marta Byrska-Bishop3 (PhD), Marie A. Guerraty1 (MD), Dokyoon Kim1 (PhD), Anurag Verma1,2 (PhD) , and Marylyn D. Ritchie1 (PhD),    1 University of Pennsylvania Perelman School of Medicine, Philadelphia, PA  2Corporal Michael Crescenz VA Medical Center, Philadelphia, PA  3New York Genome Center, New York, NY  

 

MultiNEP: disease-specific Multi-omics Network Enhancement for Prioritizing disease genes and metabolites

Zhuoran Xu, Brian Lee, Luigi Marchionni, Shuang Wang 

 

Benchmark study of similarity measures from query phenotypic abnormalities to diseases based on the human phenotype ontology

Yu Hu, PhD 1, Joe Chan, MS 1, Kai Wang, PhD 1,2    1: Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA  2: Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA 

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Prioritizing de novo variants using phenotype selection and an annotated data knowledge graph

Erin Nesmith(1),   Michelle Gong(1), Deanne Taylor (1,2)    DBHI, CHOP  Dept Pediatrics,  UPenn  Perelman School of Medicine

 

Accepted abstracts not being presented at live poster session.

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Sensitive and Efficient Pangenome Construction through Alignment-Free Residue Pangenome Analysis (ARPA)

Arnav Lal 1, Andries Feder 2, Ahmed Moustafa 3,4, and Paul J. Planet 2,3,5  1 School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104,  USA  2 Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia,  Philadelphia, PA 19104, USA  3 Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania,  Philadelphia, PA 19104, USA  4 Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of  Philadelphia, Philadelphia, PA 19104, USA  5 Institute for Comparative Genomics, American Museum of Natural History,  New York, NY 10024, USA

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Understanding common and distinct information in paired multiomic data with Tilted-CCA

Dr. Kevin Lin*, Dr. Nancy R. Zhang*    *Wharton Statistics and Data Science, University of Pennsylvania

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A unified framework for realistic in silico data generation and statistical model inference in single-cell and spatial omics

Dongyuan Song, PhD candidate in Bioinformatics, UCLA  Qingyang Wang, PhD student in Statistics, UCLA  Guanao Yan, PhD candidate in Statistics, UCLA  Tianyang Liu, Master of Applied Statistics, UCLA  Jingyi Jessica Li, Associate Professor in the Department of Statistics, Department of Human Genetics, Department of Computational Medicine and Department of Biostatistics, UCLA

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Structuring information via an immune-focused ontology enables the construction of a high-quality knowledge graph for the study of autoimmune diseases

Van Q. Truong1-5, Joseph D. Romano2, Allison R. Greenplate4-6, Scott M. Dudek2,3, E. John Wherry4-6, Marylyn D. Ritchie2,3,7  1 Graduate Group in Genomics & Computational Biology, Perelman School of Medicine, University of Pennsylvania  2 Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania   3 Biomedical and Translational Informatics Laboratory, Perelman School of Medicine, University of Pennsylvania  4 Immune Health Project, Perelman School of Medicine, University of Pennsylvania  5 Institute for Immunology, Perelman School of Medicine, University of Pennsylvania  6 Department of Pharmacology & Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania  7 Department of Genetics, Perelman School of Medicine, University of Pennsylvania 

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Multi-modal single cell analysis of Multiple myeloma patient bone marrow over time reveal mechanisms

Wesley V Wilson (1), Fei Miao, Alfred L Garfall (2), Adam D Cohen(2), Michael C.Milone (1) 1 - Center for Cellular Immunotherapies, Perelman School of Medicine At the Univ. of Pennsylvania, Philadelphia, PA 2 - Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA