Characterizing Transcriptional Landscape in Gliomas with Oxford Nanopore Long-Read Sequencing/Translational Bioinformatics Eloise Gaudet(BSE)1,2 Karleena Rybacki(MS)1,3 Joe Chan(BS)3 Yuanquan Song(Ph.D)3,4,5 Marilyn Li(MD, MS)3,5,6 Kai Wang(Ph.D)1,3,5 1. Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA 2. Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, USA 3. Raymond G. Perelman Center for

Clinically Characterizing Monogenic Variants in Pediatric Kidney Stone Disease Tanisha Johri1, Rishi Suresh1, Jing Karchin PhD1, Thomas A. Reynolds3, Nikhil Lavu1, Laura Perez1, Gregory Tasian MD, MSc, MSCE 1,2 1Division of Pediatric Urology, The Children's Hospital of Philadelphia, Philadelphia PA 2Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 3The Richard D. Wood Jr. Center for Fetal Diagnosis & Treatment, Children's Hospital of Philadelphia,

Cell type proportions rather than DNA methylation in the cord blood show statistically significant associations with severe preeclampsia Xiaotong Yang1✝, Wenting Liu1✝, Zhixin Mao1, Yuheng Du1, Cameron Lassiter2, Fadhl M. AlAkwaa1, Paula A Benny2, Lana X Garmire1* 1. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 2. University of Hawaii Cancer Center, Epidemiology, Honolulu, HI 3. Department of Neurology, University of M

Uncovering Divergent Viral DNA polymerase B Variants Using Protein Language Model Embeddings. Zaina T.A. Punter, Zachary D. Schreiber, Barbra D. Ferrell, K. Eric Wommack, Shawn W. Polson There are 10^30 bacteriophages (phages)-viruses that infect bacteria-in the world's oceans, making them the most abundant biological entity on Earth. Phage maintain a singular central function of genome replication through lytic or lysogenic infection of their bacterial host, and the outcomes

Machine Learning Approaches to Prioritize Variants of Uncertain Significance in the Regulatory Domains of ABCA4 Davis, Z. University of Delaware, Center for Bioinformatics and Computational Biology Biswas, S. University of Delaware, Department of Medical and Molecular Sciences, College of Health Sciences Biswas-Fiss, E. University of Delaware, Department of Medical and Molecular Sciences, College of Health Sciences This study leverages supervised machine learning to cla

Evolution of the HIV Envelope Protein and Its Connection to HIV Reservoir Dynamics: Longitudinal Analysis Over 13 Years April E. Boyd LaMont Cannon, Ph.D. Evolution of the HIV Envelope Protein and Its Connection to HIV Reservoir Dynamics: Longitudinal Analysis Over 13 Years April E. Boyd1 and Dr. LaMont Cannon1 1School of Life Sciences and Sustainability, VCU Life Sciences Background: HIV-related mortality has significantly declined due to the use of combination anti

Large-scale Phylogenetic Analysis of Intra-tumor Genetic Heterogeneity Dynamics in Pediatric Brain and CNS Tumor Minh A. Nguyen (1) Pablo G. Cámara, PhD (1) (1) Department of Genetics, Perelman School of Medicine, University of Pennsylvania Brain and central nervous system (CNS) tumors are the second most common cancers in children and adolescents and remain the leading cause of disease-related death in these populations. Despite their clinical impact, therapeutic development

Revealing the hidden landscape of selection: detecting divergent, soft, and background signatures in diverse human genomes Christopher J. Sottolano, PhD [1], Grace Tzun-Wen Shaw, PhD [1], Timothy L. Mosbruger, PhD [1], Yuncheng Duan, PhD [3], Andrew S. Allen [3], Dimitri S. Monos, PhD [1,2], Tristan J. Hayeck, PhD [1,2] 1. Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia 2. Department of Pathology and Lab

Investigating pediatric cancer through deep learning-enabled genomics and phenomics Fahimeh Palizban, Frank Mentch, Michael March, Xiang Wang, Deborah Watson, Joseph Glessner, Hakon Hakonarson. Background: Pediatric cancers differ fundamentally from adult malignancies, often arising during development and characterized by rare germline variants, low mutational burden, and heterogeneous clinical outcomes. Conventional GWAS and PheWAS approaches struggle to capture pleiotropy,

Evaluation of Multi-Agent LLMs in Multidisciplinary Team Decision-Making for Challenging Cancer Cases Jaesik Kim1, Byounghan Lee2, Kyung-Ah Sohn2, DokyoonKim3, Young Chan Lee4 1Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA 2Department of Artificial Intelligence, Ajou University, Suwon, Republic of Korea 3Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA 4Department of Pathology,

Understanding the role of LINE-1 expression in Hematopoietic Stem Cell development using targeted long-read RNA sequencing Krystal Kuang1, Dewan Shrestha2, Jinchuan Xing1,3, Yong Cheng2 1 Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA 2 Department of Hematology, St. Jude's Children's Research Hospital, Memphis, TN, USA 3 Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA Long

Training Breast Cancer Genetic Association Models using biobank scale data for effective risk prediction. Lannawill Caruth1,2, Roukiatou Sore3, Sarah Ehsan3, Penn Medicine BioBank, Regeneron Genetics Center, Anne Marie McCarthy3*, Shefali Setia-Verma1,2*​​ 1.Perelman Sch. of Med. Inst. of BioMed. Informatics, Philadelphia, PA 2. Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia,​​ PA, United States 3. Perelman Sch. of Med. Dept.

Contribution of de novo retroelements to birth defects and childhood cancers in 3244 trios Chu, Chong, PhD¹,²; Tran, Antuan¹; Ljungström, Viktor, PhD¹,³; Sexton, Corinne¹; Jin, Hu, PhD¹; Hamilton, Kayla V., MD⁴; Kamihara, Junne, MD, PhD⁴; Ting, David T., MD⁵; Park, Peter J., PhD¹* ¹ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA ² The Wistar Institute, Philadelphia, PA, USA ³ Department of Immunology, Genetics and Pathology, Uppsala Univers

Exome-Wide Copy Number Variation in 142,357 Individuals from Autism Spectrum Families in the Simons SPARK Cohort Haedong Kim,1,2 Grace Tzun-Wen Shaw,1 Jeffrey K. Ng,3 Timothy L. Mosbruger,1 Ramakrishnan Rajagopalan,1,2 Tychele N. Turner*,3,4 Tristan J. Hayeck*,1,2 (*Co-Senior Authors. 1. Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA. 2. Department of Pathology and Laboratory Medicine, P

PipeVar: Reproducible pipeline to prioritize pathogenic variants in undiagnosed, rare disease patients for short-read sequencing and long-read sequencing. Beoung Hun Lee1,2, Elizabeth Bhoj1,3, Rebecca Ahrens-Nicklas1,3, Kai Wang1,2 1. University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA 2. Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA 3. Division of Human Genetics, Ch

Leveraging Open-Source Large Language Models to Identify Undiagnosed Patients with Rare Genetic Aortopathies Pankhuri Singhal, PhD1*, Zilinghan Li, MS2*, Ze Yang, MS3*, Tarak Nandi, PhD2, Colleen Morse, PT1, Zachary Rodriguez, PhD1, Alex Rodriguez, PhD2, Volodymyr Kindratenko, DSc3,4, Giorgio Sirugo, MD, PhD1, Reed E. Pyeritz, MD, PhD1, Theodore Drivas, MD1, Ravi Madduri, MS2,5+, and Anurag Verma, PhD1+ 1Department of Medicine, Division of Translational Medicine and Human Ge

Comprehensive computational and evidence-based epitope profiling of Bordetella pertussis Thalía Silvestre, MSc¹&, Jennifer Z. Almeyda-Tejada, BSc¹&, Sheyla Carmen, BSc¹&, David Tachiquerín, MSc¹, Luis Tataje-Lavanda, PhD²˒³, David Requena, PhD¹* 1 Bioinformatics Group in Multiomics and Immunology. New York, NY, 10016, USA 2 Laboratorios de Investigación y Desarrollo, FARVET. Chincha Alta, Ica, Perú 3 Escuela Profesional de Medicina Humana, Universidad Privada San Juan Ba

Unraveling SMARCA1's Role in Cancer Progression, Drug Resistance, and Muscle Differentiation Through EMT-Related Signaling, the TGF-β Pathway, and Key Transcription Factors SNAI1 and EGR1 Ashwaq K. Aljabri¹² Yuliya Kriga³ Juan Manuel Caravaca³ Jyoti Shetty³ Bao Tran³ Matthew Geisler⁴ Judith K. Davie² Marielle E. Yohe¹ 1. Laboratory of Cell and Developmental Signaling, National Cancer Institute, National Institutes of Health, Frederick, MD, USA 2. Department of Bioc

Evaluating Current Single-Cell Annotation Methods in Pediatric Populations Knight, Montana Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA Svirydava2, Maryia Division of Allergy and Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA Campos, Jose S. Division of Allergy and Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA

Butyrate Modulates Intestinal Microbiome and Epithelial Function to Attenuate Irinotecan-induced GI Toxicity (Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, 23298, USA:)Stanley M Cheatham , Zayd Rehman , Mahshid Arastonejad , Yuesheng Zhang , David A Gewirtz , Hamid I Akbarali , Hisashi Harada:(Department of Oral and Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond) , Natalie Luffman :Department of Oral and