Deep Generative Modeling of Isoform Aware RNA Velocity in Long-read Single-cell RNA-seq Shizhuo Mu1,2, Zhuoran Xu1,2, Joe Chan2, Haoran Zhang1, Quan Ma1, Qin Li1, Kai Wang1,2; 1University of Pennsylvania, Philadelphia, PA, 2Children's Hospital of Philadelphia, Philadelphia, PA RNA velocity measures the temporal dynamics of gene expression by modeling the splicing dynamics from unspliced to spliced mRNA. However, current RNA velocity methods are developed for short-read data,

DeepU-PRS: Integrating Uncertainty-Aware Deep-ensemble SNP Heritability Estimation to Improve PRS / Bioinformatics methods development. Junhyeong Lee, MS¹,²; Dokyoon Kim, PhD²; Seunggeun Lee, PhD¹ Affiliations ¹ Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea ² Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA To enhance the predictive performance

Improving prediction of 3D chromatin structures (Topologically Associating Domains) My Nguyen, BS, Department of Biostatistics, SOPH, VCU Shaojun Tang, , PhD, Department of Biostatistics, SOPH, VCU J. Chuck Harrell, PhD, Department of Pathology, SOM, VCU Mikhail G. Dozmorov, PhD, Department of Biostatistics, SOPH, VCU The human genome can be divided into different 3D topologically associating domains (TADs). DNA regions within a TAD interact with each other more often t

Benchmarking Statistical Dimension Reduction Frameworks for Integrative Multi-Omics Analysis with Missing Modalities Busra Coskun; University of Pennsylvania Qi Long, PhD; University of Pennsylvania Konstantinos Tsingas, MS; University of Pennsylvania Multi-omics studies, which integrate data sources from distinct biological scales such as transcriptomics, proteomics, and metabolomics, have the potential to reveal mechanisms that underlie disease. However, these studies oft

An Agentic System for Automated Data Curation and Analysis in Large-Scale Biobanks Chang-Uk Jeong, BS, University of Pennsylvania Jaesik Kim, MS, University of Pennsylvania Jaehyun Joo, PhD, University of Pennsylvania Byounghan Lee, MS, Ajou University Yang-Gyun Kim, MD, PhD, Kyunghee University Dokyoon Kim, PhD, University of Pennsylvania The translation of clinical and lifestyle concepts into computable phenotypes is a critical yet manually intensive bottleneck in leve

Visium Spatial Transcriptomics Reveals Localized Host Responses to Bacterial Exposure in Vaginal Epithelium Miranda Brown, BS¹; Mallory Cunningham, BS²; Chris Oldfield, PhD²; Megan Williams, PhD²; Myrna Serrano, PhD²; Kimberly Jefferson, PhD²; Gregory Buck, PhD²,³,⁴; Katarzyna M. Tyc, PhD¹,⁵ Affiliations: ¹ Department of Biostatistics, School of Public Health, Virginia Commonwealth University, Richmond, VA ² Department of Microbiology and Immunology, School of Medicine,

Scalable Computational Approaches for Genome-Wide Epistatic Variance Component Approximation Ziyan Zhang, BS, Carnegie Mellon University Martin Zhang , PhD, Carnegie Mellon University Richard Border, PhD, Carnegie Mellon University Epistatic variance arising from interactions between genes across loci represents a poorly characterized aspect of broad-sense heritability across many complex traits in humans. Accurate estimation of epistatic variance can help address missing

Pan-Cancer Analysis of Transposable Element Expression Reveals Cancer Type-Specific Patterns Mammedova A, MS 1; Calendo G, MS 1; Issa, JPJ, MD 1 Affiliations: 1 Coriell Institute for Medical Research, Camden, NJ, USA Transposable elements (TEs) comprise nearly half of the human genome and are normally silenced in healthy cells through DNA methylation and other epigenetic mechanisms. Recent evidence suggests that epigenetic dysregulation of TEs during tumorigenesis not only dr

Pediatric metadata collection in the Developmental Genotype Expression Project enhances developmental comparison Patrick Van Hoose (National Disease Research Interchange), Raquel G. Hernandez (Johns Hopkins All Children’s Hospital), Melissa Faith (Johns Hopkins All Children’s Hospital), Simone Guambana (Johns Hopkins All Children’s Hospital), Thomas G. Blanchard (University of Maryland School of Medicine), Deanne M. Taylor (Children’s Hospital of Philadelphia), Rebecca L. Lin

Identifying Adaptive Mutations in Rubella Virus Using the c/μ Method Vaughn Flippen, B.S. Candidate, Biological Sciences, Rowan University; Chun Wu, Ph.D., Department of Chemistry and Biochemistry & Department of Biological and Biomedical Sciences, Glassboro, NJ 08028, USA Rubella Virus (RV) is a positive-sense RNA virus (+ssRNA) belonging to the Matonaviridae family. It typically causes mild fever and rashes in children and adults but poses a severe risk to pregnant women, w

Unraveling the Intricacies of HIV-1 Evolution through a Novel Near-Neutral UnBalanced Selection Theory Approach Annie Tran, MS, Pharmaceutical Science (tranan85@rowan.edu), Department of Chemistry and Biochemistry & Department of Biological & Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA Nicholas Paradis, PhD, Pharmaceutical Science, (paradi84@rowan.edu), Department of Chemistry and Biochemistry & Department of Biological & Biomedical Sciences, Rowa

AI-driven 3D Digital Pathology of Immune Follicular Structures in Human Zhu, Irina Y., MS (Department of Bioengineering, University of Pennsylvania; Oldridge Lab, Children's Hospital of Philadelphia, Philadelphia, PA, USA) Dubensky, Sam B., BS (Immunology Graduate Group, University of Pennsylvania; Oldridge Lab, Children's Hospital of Philadelphia, Philadelphia, PA, USA) Carter, Ashley, MS (Oldridge Lab, Children's Hospital of Philadelphia, Philadelphia, PA, USA) Cabrera,

Ontology‑Aware Integration of Kids First and dGTEx data for Pediatric Anatomy Deanne Taylor PhD (CHOP/UPenn), Adam C Resnick PhD (CHOP/UPenn), Thomas Bell PhD (NDRI), Kristin Ardlie PhD (Broad Institute), Rebecca Linn MD (CHOP/UPenn), Raquel Hernandez MD, MPH (JHU), Melissa VonDran PhD (NDRI) Emilie Hattrell (NDRI), Patrick Van Hoose (NDRI), Thomas Blanchard PhD (U. Maryland), Brady Walker (Broad Institute), Jared Nedzel PhD (Broad Institute), Nenad Sestan MD PhD (Yale)

Identifying Risk Genes Associated with Neural Progenitor Cell (NPC) Hyperproliferation Lodi, M.K., Millonig, J., Xing, J. Due to genetic heterogeneity, Autism Spectrum Disorder (ASD) exhibits comorbidity with other neurodevelopmental phenotypes, such as macrocephaly. Macrocephaly is found in ~20% of ASD individuals, with ASD patients exhibiting statistically larger head circumference and brain volume. One possible mechanism to explain the enlarged brain associated with macroc

Multiomics Analysis of Impact of Increased FOXD3 Expression in BRAF-Mutant Melanoma Colette E. Trouillot, M.S.[1,2]; Will Madden, B.S.[1]; Glenn Mersky, M.S.[1]; Dan A. Erkes, PhD [1]; Scott Varney, PhD [1]; Timothy J. Purwin, PhD [1]; and Andrew E. Aplin [1,3] 1Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19017, USA 2 School of Biomedical Engineering, Science & Health Systems, Drexel University, Philadelphia, P

Evaluating Low-Pass Whole Genome Sequencing as a Cost-Effective Alternative to SNP Genotyping Arrays for Copy Number Variant Detection Lionel Sequeira, BSc (1,2); Yue Xing, PhD (2); Jay A Tischfield, PhD (1,2); Gary A Heiman, PhD (1,2); Jinchuan Xing, PhD (1,2) 1 Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA 2 Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA Copy number vari

Using the substitution-mutation rate ratio test (c/µ) and the Near Neutral Balanced Selectionist Theory (NNBST) to Analyze the Mutational Spectrum of Monkeypox Virus Deosaran, I., & Wu, C. Department of Chemistry and Biochemistry & Department of Biological & Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA Monkeypox virus (MPXV) is a zoonotic orthopoxvirus closely related to the variola virus, which causes smallpox. Monkeypox has emerged as a significant public

A toolkit for the analysis of contiguous regions of hydrophobicity in a protein sequence Lindsey Riggs[1], Connor Pitman[1], Ezry Santiago-McRae[1], Ruchi Lohia[2], Ryan Lamb[1], Kaitlin Bassi[1], Thomas T. Joseph[3], Matthew E.B. Hansen[4], and Grace Brannigan[1,5]* [1]Center for Computational and Integrative Biology, Rutgers University-Camden, 201 Broadway, 08103, NJ, USA [2]Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civi

Untangling the role of contiguous hydrophobicity and specialty hydrophobic interactions in residue coevolution Connor Pitman[1], Anthony Geneva[1,2] Matthew E. B. Hansen[4], Grace Brannigan[1,3] [1] Center for Computational and Integrative Biology, Rutgers-Camden, NJ, 08102 [2] Department of Biology, Rutgers-Camden, NJ, 08102 [3] Department of Physics, Rutgers-Camden, NJ, 08102 [4] Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadel

Spatial Profiling of the Tumor Immune Microenvironment in Higher-Grade Meningioma Ijeoma C. Meremikwu, Mingshuang Wang, Emily Ling-Lin Pai, Amy E. Baxter, Christina Jackson, Derek A. Oldridge Meningiomas are the most common central nervous system tumors, with higher-grade meningiomas (HGM) being more aggressive and faster growing than lower grades. Additionally, HGMs can invade brain tissue, which poses greater challenges for treatment. The gold standard of treatment is a com