Gene expression patterns of the developing human face at single cell resolution reveal cell type contributions to normal facial variation and disease risk. Alexandra Manchel 1, Nagham Khouri-Farah 2, Emma Wentworth Winchester 2, Brian M. Schilder 3,4, Kelsey Robinson 5, Sarah W. Curtis 5, Nathan G. Skene 3,4, Elizabeth J. Leslie-Clarkson 5, Justin Cotney 1,6 Affiliations: 1 Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 2 Graduate Program in

A robust machine learning approach for genotyping the 17q21.31 inversion polymorphism across diverse ancestral populations. Schultz, L.M. (PhD), Quinto-Cortés, C.D. (PhD), Montserrat, D.M. (PhD), Ioannidis, A. (PhD), Lanzagorta, N. (MS), Bustamante, C.D. (PhD), Jacquémont, S. (MD), Nicolini, H. (MD, PhD), Glahn, D.C. (PhD), and Almasy, L. (PhD) Inversions are relatively understudied structural variants that are increasingly recognized for their contributions to human phenotyp

Integrative Visual Analytics of Sociodemographic and Financial Literacy Data to Identify High-Risk Veteran Populations Ramona Raya, MD, Department of Medicine, University of Virginia School of Medicine; Harman Sabharwal, Langley High School, McLean, VA Background: Veteran health insurance programs aim to reduce financial toxicity-the destabilizing impact of healthcare costs-yet housing and financial instability continue to rise. Using a bioinformatics-inspired stratification

PhenoGPT2: A Multimodal Fine-tuned Large Language Models for Phenotype Extraction and Normalization from Clinical Text and Facial Images. Quan M. Nguyen, Bachelor 1,2, Umair M. Ahsan, MS 1, Zhanliang Wang, MS 1, Kai Wang, Ph.D. 1,3* 1 Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; 2 Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA; 3 Department of Pathology and

Relationship Classification in SNOMED CT Using Domain-Specific BERT Models T M Rubaith Bashar¹, James Geller² ¹ PhD Student, Department of Data Science, New Jersey Institute of Technology ² PhD, Professor and Chair, Department of Data Science, New Jersey Institute of Technology SNOMED CT is an important, large, and constantly evolving medical ontology organized around a good number of relationships among the medical concepts. Keeping its relationship correct is onerous an

Isoform-Resolved Single-Cell Transcriptomics with Microfluidics-Free Barcoding and Long-Read Sequencing Avi Srivastava, PhD, The Wistar Institute Calen Nichols, BS, The Wistar Institute Rajeev Ramisetti, PhD, The Wistar Institute Jamie Bregman, MS, The Wistar Institute Alternative splicing creates the functional diversity of the human transcriptome through the production of multiple distinct mRNA transcripts from a single gene. Despite this fact, most single-cell RNA-sequ

Design of a Lightweight Algorithm for Robust Mass Spectrometry Peak Detection Jo, Serin, Roslyn High School, Roslyn Heights, NY, USA Li, Guangyuan, Ph.D., Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA Mass spectrometry-based proteomics remains the predominant approach for identifying and quantifying proteins and peptides across a wide range of applications. The preprocessing of raw MS data is an important step for accurate downstream analysis. One challen

Characterizing Cellular Heterogeneity and Spatial Organization in Lung Adenocarcinoma with Visium HD Sameen S. Hossain, School of Life Sciences and Sustainability, CHS, VCU; The Honors College, VCU Katarzyna M. Tyc, PhD, Department of Biostatistics, SOPH, VCU; Massey BISR Spatial transcriptomics is an emerging technology that enables the profiling of gene expression while preserving the spatial context of cells within intact tissue sections. This approach offers unprecedente

Characterizing Regulatory Regions of Key Cardiac Transcription Factors Using Lentiviral Based Massively Parallel Reporter Assays Pooja Sonawane1,2, Justin Cotney2,3 Affiliations 1 University of Connecticut Health Center, Farmington, CT 2 Department of Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 3 Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA Congenital Heart Defects (CHDs) are the most prevalent form of structural birth defec

GeneGrad: Geometric Gradient-Based Biomarker Discovery in Single-Cell Transcriptomics Shupeng Luxu, MS candidate, Department of Biostatistics, Harvard T.H. Chan School of Public Health; Rong Ma, PhD, Department of Biostatistics, Harvard T.H. Chan School of Public Health Single-cell technologies have enabled the characterization of gene expression at cellular resolution, providing critical insights into both static cellular heterogeneity and dynamic biological processes such

Unraveling Dengue Virus Adaptation: Insights from Near-Neutral Balanced Selectionist Theory (NNBST) and Evolutionary Model Comparison Md Nazmul Hasan, Department of Chemistry & Biochemistry, Rowan University, USA Dr. Chun Wu,  Department of Chemistry and Biochemistry & Department of Biological & Biomedical Sciences, Rowan University, USA Dengue virus serotype 1 (DENV1), a mosquito-borne flavivirus, causes severe disease due to antibody-dependent enhancement (ADE), limited

Identifying Adaptive Mutations in HPV 16 Using Novel c/µ Method Caitlyn Johnson, Wu Chun* *Department of Chemistry and Biochemistry & Department of Biological & Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA Human papillomavirus (HPV) is responsible for approximately 70% of cervical cancer cases worldwide, with HPV16 alone accounting for nearly half of cases. Cervical cancer is the 4th most common cancer among women, with an estimated 348,709 deaths worldwid

FSLearning: A Collaborative Deep Learning Framework for Efficient and Private Disease Prediction Bin Li, M.S., Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA Xiaoqian Jiang, Ph.D., D. Bradley McWilliams School of Biomedical Informatics, UTHealth Houston, Houston, TX, USA Yu-Chun Hsu, Ph.D., D. Bradley McWilliams School of Biomedical Informatics, UTHealth Houston, Houston, TX, USA Arif O. Harmanci, Ph.D., D. Bradley McWilliams Scho

Prenatal Hypoxia Reprograms Alternative Splicing Landscapes in the Developing Cortex Gupta, Shikhar. (Undergraduate Researcher), University of Pennsylvania, Philadelphia, PA, USA. Cassidy, Maggie. (BA), Cell & Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. Cristancho, Ana. (MD/PhD), Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA. Prenatal hypoxia is a leading cause of

Interpreting congenital heart disorders by comprehensive analysis of cell type-specific gene regulatory program in the developing human heart. Sungryong Oh1, Kevin Child2, Pooja Sonawane2, and Justin Cotney1 1. Dep. of Plastic Surgery, Children's Hospital of Philadelphia, Philadelphia 19104, USA 2. Dep. of Genetics and Genome Science, University of Connecticut Health Center, Farmington 06030, USA Congenital heart diseases (CHD) are among the most common defects found in new

Harnessing Longitudinal Claims Data to Reveal Predictive Signals for Clinical Event Forecasting Lai, E., Chen, J., & Dubrawski, A. Ellyse Lai, Student/Research Intern, CMU Auton Lab Jieshi Chen, Researcher, CMU Auton Lab Artur Dubrawski, Professor, CMU Auton Lab Introduction: Large administrative health datasets are a powerful resource for public health surveillance, but their utility is often hindered by recording complexities, such as change of diagnostic coding systems.

GATES: a lightweight, automated tool making whole-exome sequencing analysis accessible to scientists with limited computational backgrounds. Nicholas E. Bambach, MS1, Julio C. Ricarte-Filho, PhD1, Erin R. Reichenberger, PhD2, Aime T. Franco, PhD1,3 1Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States 2Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia,

Population genomic analysis of H. majoris and its host the blue tit (Cyanistes caeruleus) over a quarter of a century Esther Weyer, BS Center for Bioinformatics and Computational Biology & Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA Diana Ekman, PhD Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Sweden Vincenzo A. Ellis, PhD Depa

Evaluation of potential ligand-receptor interactions between mechanically stressed human visceral smooth muscle cells and other cell types in the human bowel Sharon M. Wolfson (MD)1,2, Katherine Beigel (MS)3, Sierra E. Anderson (MS)1, Brooke Deal (PhD)1, Molly Weiner1,4, Se-Hwan Lee (PhD)6, Deanne Taylor (PhD)1,2,3, Su Chin Heo (PhD)4,5,6,7,8, Robert O. Heuckeroth (MD, PhD)1,2**, Sohaib K. Hashmi (MD, PhD)1,4,5,9** ** SKH and ROH contributed equally to this work Affiliati

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,