Long-Read Whole-Transcriptome Sequencing Uncovers Gene Fusions and Structural Rearrangements in Fusion Panel-Negative Gliomas Karleena Rybacki (MS) 1,2 Feng Xu (BS) 2,3 Joe Chan (BS) 2 Hannah Deutsch (BS) 4 Eloise Gaudet (BSE) 1, 5 Mian Umair Ahsan (MS) 2,6 Zizhuo Liang (BS) 2 Yuanquan Song (Ph.D) 2,4,7 Marilyn Li (MD, MS) 2,3,7 Kai Wang (Ph.D) 1,2,7 1. Department of Bioengineering, University of Pennsylvania, Gene fusion (GF) detection in cancer diagnosis labs pr

Biomarker Discovery in Tourette's Disorder Subramanian Krishnamurthy¹,², Jay A. Tischfield¹,², Gary A. Heiman¹,², Jinchuan Xing¹,² ¹Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA ²Human Genome Institute of New Jersey, Rutgers, The State University of New Jersey Tourette's disorder (TD) is a childhood onset neuro-developmental disorder (NDD), Characterized by Motor and Vocal tics. It has a large genetic component. A variety of

Lasting mitochondrial and epigenetic disruption after prenatal hypoxia in glutamatergic neurons DaSilva, Sabrina, MS (1,2), Cassidy, Margaret M., BA (1), Gadra, Ethan, BS (1), Smith, Maddie, BA (1), Cristancho, Ana G., MD, PhD (1,3) (1) Division of Child Neurology, Departments of Pediatrics and Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA (2) Medical Scientist Training Program, Perelman School of Medicine at the University of Pennsylvania, Phila

From Phenome to Casuality: A Multilayered Analysis of Age at Natural Menopause and its Health-Related Consequences Stephanie Mohammed, Ph.D 1, Lindsay Guare 2, Tess Cherlin 1, Penn Medicine Biobank, Regeneron Genetics Center, Marylyn D. Ritchie, Molly A. Hall, Shefali S. Verma Ph.D 1,2,3  1 Department of Pathology and Laboratory Medicine, University of Pennsylvania 2 Institute for Biomedical Informatics, University of Pennsylvania 3 Department of Biostatistics, Ep

tatDB/tarDB: cancer use cases and machine learning Sathyanarayanan Vaidhyanathan, Adesupo Adetowubo, Sarthak Chandervanshi, Hameed Sanusi, and Andrey Grigoriev* Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA Ribosomal RNA-derived fragments (rRFs) and transfer RNA-derived fragments (tRFs) are often neglected as noise while analyzing experimental data like CLASH and CLIP, which capture RNA-RNA interactions lo

AI-driven discovery of GPNMB CAR T cells as a pan-cancer therapy Daniel J. Baker1,2,3*, Leon Frommer4, Ugur Uslu1,2, Nils W. Engel1,2, Daniel Zhu1,2, Samuel I. Kim1,2, Lisa Sun1,2, Kisha K. Patel1,2, James M. George5, Christopher Roselle1,2, Philipp C. Rommel1,2, Regina M. Young1,2, Jonathan A. Epstein3,6,7,8, Sikander Hayat4*, Zoltan Arany3,6*, Carl H. June1,2,9* Affiliations: 1Center for Cellular Immunotherapies, University of Pennsylvania Perelman School of Medicine,

Comparative Performance of Machine Learning Models for Genomic-Based Survival Prediction in Breast, Lung, and Liver Cancers: A Network Meta-Analysis Sunmin Kim, Undergraduate Student, Johns Hopkins University Purpose: Accurate survival prediction is fundamental in oncology, supporting therapeutic stratification, clinical trial design, and personalized treatment. With the growing integration of high-dimensional genomic data into clinical care, machine learning (ML) methods pro

Domain-Specific Evolution of Influenza A H3N2 Hemagglutinin Revealed by c/µ and Molecular Clock Analyses Akanksha Alampally, Rowan University Dr.Chun Wu Department of Chemistry and Biochemistry & Department of Biological & Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA Influenza A H3N2 is a major driver of seasonal epidemics, causing millions of severe cases and up to 650,000 global deaths annually. Despite yearly vaccinations, rapid antigenic drift often r

Uncovering how YY1 knockout alters B-cell lineage using single-cell and 3D genomics Nasreen Bano1, Sulagna Sanyal1, Sarah Naiyer1, Suchita Hodawadekar1, Michael L. Atchison1* 1Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA *Principal Investigator Yin Yang 1 (YY1) is a multifunctional transcription factor that regulates gene expression by recruiting chromatin remodelers, modifying histones, and facilitating

Topological Characterization of Protein-Protein Interaction Networks Using Graph Theory Maryam Ramazani, Dr. Imtiaz Ahmed, PhD. Industrial & Management Systems Engineering, West Virginia University, Morgantown, WV, USA Protein-protein interaction (PPI) networks are central to understanding cellular function and disease mechanisms. In this project, we construct a PPI graph using a curated subset of high-confidence interactions and analyze its topological structure using class

Development of Highly Specific Aptamers Against Carbendazim Using Machine Learning-Guided Computational Strategies Ajay Yadav1 and Hariprasad P.1* 1 Environmental Biotechnology Lab Centre for Rural Development and Technology Indian Institute of Technology Delhi Hauz Khas, New Delhi 110016, India Aptamers are short, single-stranded oligonucleotides that can selectively recognize diverse targets, including small molecules, proteins, toxins, hormones, and even entire micro

A Diagnostic Blind Spot: Deep Intronic SVA_E Insertion Identified as the Most Common Pathogenic Variant Associated with Canavan Disease Carlos A. Dominguez Gonzalez1,*, Katrina M. Bell2,3,*, Ramakrishnan Rajagopalan4,5, Michelle G. de Silva2,3, Aída Lemes6, Cristina Zabala6, Florencia Pérez7, Alfredo Cerisola6,7, Arastoo Vossough8,9, Matthew T. Whitehead8,9, Chloe Cunningham2,3,10, Natasha J. Brown2,3,10, Rebecca Quin3,11, Cas Simons12,13, Thomas Conway2, Eloise Uebergang2, R

3D Computational Gut Cell Characterization Across Animal Models Rachelle Saint-Fort, Khai C. Ang, Mee S. Ngu, Daniel J. Vanselow & Keith C. Cheng Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey PA Emerging computational tools are revolutionizing 3D anatomical image analysis, enabling high-throughput pipelines for faster, more accurate diagnoses and reducing clinical biases. However, identifying cellular mo

Decoding the Genetic Architecture of Pregnancy Loss and Adverse Outcomes: Insights into Rare, Common, and Structural Variants from Large-Scale Biobanks Aude Benigne Ikuzwe Sindikubwabo1, Lannawill Caruth1, Lindsay Guare1,Pauline Gachanja1,Craig Teerlink2, Julie Lynch5, Maja Bucan3, Ziyue Gao3, Courtney Schrieber4, Regeneron Genetics Center, Penn Medicine BioBank, Shefali S. Verma1 1Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelp

Clinically Aligned Multi-Modal Image-Text Model for Pan-Cancer Prognosis Prediction J onghyun Lee, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA • Jacob S. Leiby, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA • Lina Takemaru, Department of Biostatistics, Epidemiology and Informatics, Perelma

Unsupervised quantitative comparison of subcellular proteome organization in morphologically complex cells Robert Hu, Pablo Camara Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA 19104, USA Understanding how proteins are spatially organized within cells is essential for decoding cellular function. While large-scale imaging assays based on immunofluorescence and en

Integrating Imaging-Derived Clinical Endotypes with Plasma Proteomics and External Polygenic Risk Scores Enhances Coronary Microvascular Disease Risk Prediction Rasika Venkatesh (1,), Tess Cherlin (2), Penn Medicine BioBank (3), Marylyn D. Ritchie (4), Marie A. Guerraty (5), Shefali Setia-Verma (2) (1) Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA (2) Department of Pathology and Laboratory Medicine, University of Pennsy

Beyond PRS: Geno2Vec Learns Rich SNP Embeddings to Predict Endometriosis Risk Lindsay Guare, Rachit Kumar, Jagyashila Das, Anurag Verma, Shefali Setia-Verma Polygenic risk scores (PRSs) remain limited in clinical utility for most complex traits due to modest predictiveness and poor transferability across ancestries. We focused on endometriosis (endo), a women's health condition characterized by painful endometrial lesions growing outside of the uterus. While genomic studies h

1          Lindsay Guare            University of Pennsylvania                           Beyond PRS: Geno2Vec Learns Rich SNP Embeddings to Predict Endometriosis Risk   2       Haedong Kim, PhD          Children's Hospital of Philadelphia Exome-Wide Copy Number Variation in 142,357 Individuals from Autism Spectrum Families in the Simons SPARK Cohort   3        Fahimeh Palizban, PhD          Children's Hospital of Philadelphia                Investigating pediatric cancer thro