A Novel Algorithm for Active Module Aggregation Based on the Earth Mover's Distance Liu, J.1, Xu, M. PhD2, Xing J., PhD1,1 - Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA., 2 - Department of Statistics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA Gene-gene interaction networks play a central role in -omics analysis. These networks can be combined with transcriptomic data to better understand how candidate genes i

Integrating Genetic and Clinical Data for Childhood Cancer and Birth Defects Taha Mohseni Ahooyi(1); Benjamin Stear(1); Dave D. Hill(1); Ryan Corbett(2); J. Alan Simmons(3); Rebecca Kaufman(1); Shiping Zhang(1); Aditya Lahiri(1); Yuanchao Zhang(1); Asif Chinwalla(1); Christopher Nemarich(1); Adam Resnick(1); Sarah Tasian(1,4); Kristina Cole(1); Jonathan Silverstein(3); Elizabeth Goldmuntz(1,4); Jo Lynne Rokita(2); Sharon Diskin(1,4); Deanne M. Taylor(1,4) Affiliations: (1)

Enhancing Bulk RNA-Seq Deconvolution Using Atlas-Level Deep Learning Embeddings Ali Oku, Rui Fu, Heather Geiger, Will Liao, Nicolas Robine New York Genome Center Cell type deconvolution estimates the relative abundances of cell types in bulk RNA-seq data, allowing researchers to infer tissue composition when single-cell RNA sequencing (scRNA-seq) is not feasible. However, conventional tools are often sensitive to batch effects and reference biases. To overcome these limitati

MOSAIC (Multi-scale Ontology-driven Semantic Analysis and Inference over Contexts): An Optimal Knowledge Graph Embedding Framework Taha Mohseni Ahooyi(1); Benjamin Stear(1); Dave D. Hill(1); Ryan Corbett(2); J. Alan Simmons(3); Aditya Lahiri(1); Yuanchao Zhang(1); Shiping Zhang(1); James Terry(4); Rebecca Kaufman(1); Asif Chinwalla(1); Christopher Nemarich(1); Adam Resnick(1); Sarah Tasian(1,5); Kristina Cole(1); Jonathan Silverstein(3); Elizabeth Goldmuntz(1,5); Jo Lynne Rok

Elucidating the shared genetic architecture of hypercholesterolemia and endometriosis through a mediation framework Ananya Rajagopalan1 BS, Lindsay Guare1 BS, Aude Ikuzwe1 BS, Lanna Caruth1 BS, Craig Teerlink2 PhD, Danielle Candelieri2 ScD, MPH, Penn Medicine BioBank, Regeneron Genetics Center, Marijana Vujković 3 PhD, Julie Lynch4 RN, PhD, MBA, Shefali Setia-Verma1 PhD 1Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA, United

Using novel c/μ method to predict adaptive mutations in Respiratory Syncytial Virus A Marco DiGialleonardo 1 Chun Wu, Ph.D. 1,2 1 Department of Biological and Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA 2 Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA Respiratory Syncytial Virus A (RSV-A) is a leading cause of respiratory infections in infants, young children, and elderly. While there has been progress in developi

Optimizing Clinical LLM Agents: Design Choices for FHIR and Rare Disease Diagnosis Workflows Youssef Mokssit, MS; Cong Liu, PhD; Junyoung Kim, MS; Mengshu Nie, MS Affiliation: Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA This project aims to systematically evaluate the architectural choices that most impact the effectiveness of large language model (LLM)-based clinical agents in genomics and rare disease workflow

Evaluating LLM Agents for Insurance Coverage Workflow Automation/Translational Bioinformatics , MA, Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Youssef Mokssit, MS, Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Mengshu Nie, MA, Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Cong Liu, PhD,

Pangenome-Guided Recovery of Human DNA Missed by the Linear Reference in Cancer PDX Genomes Brydon P. G. Wall, MS Student - Virginia Commonwealth University My Nguyen, PhD Candidate - Virginia commonwealth University Stella Castro, BS/MS Student - Virginia Commonwealth University Shasmeen Azhar, BS/MS Student - Virginia Commonwealth University Nina Dashti-Gibson, MD/PhD Student - Virginia Commonwealth University J. Chuck Harrell, PhD - Virginia Commonwealth University

The Stability of Epigenetic Cell Identity in Cancer Cameron Cloud, BS Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA Benjamin Steinberg, BS Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel Tzachi Reizel, PhD Department of Biotechnology and Food Engineering, Technion -

Prioritizing NICU Patients for Genetics Referral and Rapid Exome/Genome Sequencing via EHR-Based Machine Learning Models Cong Liu, PhD; Department of Pediatrics; Division of Genetics and Genomics; Boston Children's Hospital Rapid exome/genome sequencing (rES/rGS) can critically inform care in the neonatal intensive care unit (NICU) but is resource-intensive and under-utilized. We investigated whether machine learning (ML) models applied to electronic health records (EHRs) can

Evaluating the Cost and Feasibility of LLM-Based HPO Term Extraction in Clinical Genomics Cong Liu PhD, Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital Human Phenotype Ontology (HPO) terms are essential for variant interpretation in whole-exome and whole-genome sequencing (WES/WGS) analysis and reanalysis. Natural language processing (NLP) tools have been widely used to extract HPO terms from clinical notes in electronic health records

PREDICTION OF BINDING AFFINITIES FOR PROTEIN-PEPTIDE SYSTEMS USING SE(3) EQUIVARIANT NEURAL NETWORKS Aditya Birla (PhD Candidate- Rutgers University), Guillaume Lamoureux (Associate Professor- Rutgers University) Protein-peptide interactions are fundamental to biology but difficult to predict due to peptide flexibility and limited structural data. We present a deep learning framework based on SE(3)-equivariant convolutional neural networks that estimates binding affinity dir

Resolution of Selection Versus Adaptation in Cellular Evolution Xinyi E. Chen1,6,7,†, Kevin Z. Lin2,†, Dylan Schaff3,4†, Robert Vander Velde5, Christopher Cote5, Sijia Huang6, Andy J. Minn7,8,9,10, Sydney M. Shaffer3,5,∗, Nancy R. Zhang8,10,11, * 1Graduate Program in Genomics and Computational Biology, University of Pennsylvania 2Department of Biostatistics, University of Washington 3Department of Bioengineering, University of Pennsylvania 4Merck & Co, Incorporated 5Dep

Harnessing Computational and Statistical Techniques for Insights into Liver MPS RNA-Seq Data Rima Zinjuwadia (Northeastern University, Novo Nordisk), Dan Sazer (Novo Nordisk), Dennis McDuffie (Novo Nordisk), Nate Sorensen (Novo Nordisk), Sara Toftegaard Hjuler (Novo Nordisk), Rachelle Prantil Baun (Novo Nordisk), Aditya Misra (Novo Nordisk), and Alex Drong (Novo Nordisk) Metabolic disorders, particularly insulin resistance, affect millions worldwide, significantly elevating t

Emergent patterns of methylation across early life associated with carotid intima-media thickness in young adults Eve Schoeffler a+, Lisa M. Schneper a+, Yinan Zheng b, Mindy Szeto b, Shantelle Little a, Ayanava Ganguly a, Hongyan Ning b, Colter Mitchell e, Boriana P. Pratt d, Jun Wang b,f, Claudia Korcarz c, Kristin Hansen c, Nicole Katchur a, Elisabeth Tawa a, Lifang Hou b,f, Jim Stein c, Norrina Bai Allen b, Noreen Goldman d, Donald M. Lloyd-Jones b,g+, Daniel A. Notterman

Adapting a Probabilistic Alignment Method for Multi-Mapping Rescue in Ribo-Seq Data Katie Barfield, Clemson University Ishika Verma, The Pennsylvania State University Shaun Mahony, PhD, The Pennsylvania State University Multi-mapping is a persistent challenge in short-read sequencing, particularly in ribosome profiling (Ribo-Seq). The repetitive nature and limited length of reads (20-38nt) often lead to ambiguous alignments. This reduces the number of usable reads available

Identifying maternal risk and protective genes for egg aneuploidy Weijun Zeng, Karen Schindler, Jinchuan Xing Egg aneuploidy is a major cause of female infertility, but how intrinsic oocyte aging interacts with the genetic risk of egg aneuploidy is still not well understood. Whole-exome sequencing (WES) data from IVF patients with higher or lower than normal age-adjusted aneuploidy rates is used to identify hundreds of candidate genes that may affect meiotic function. To plac

Enhanced EEG-Enabled Auditory Attention Detection Based on Multi-Modal Contrastive Learning with Graph Structure Hua Lin - Student Researcher, Roslyn High School, Roslyn, NY, USA Xianzhang Zeng, Ph.D. - Research Mentor, South China University of Technology As life expectancy increases, hearing impairments have become an increasing health concern that affects millions of people. Conventional hearing aids face limitations in isolating target sounds in noisy environments, signif

Single-nucleus multiomic analysis of Beckwith-Wiedemann syndrome liver reveals PPARA signaling enrichment and metabolic dysfunction Snehal Nirgude, PhD1; Elisia D. Tichy, PhD1; Sanam L. Kavari1; Rose D. Pradieu1; Michael Xie1, PhD; Jennifer M. Kalish, MD PhD1,2 1Children's Hospital of Philadelphia, Philadelphia, USA. 2Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA Beckwith-Wiedemann Syndrome (BWS) is an epigenetic overgrowth syndrome caused b