Cell-Type-Resolved Placental Epigenomics Identifies Clinically Distinct Subtypes of Preeclampsia Yuheng Du, Ph.D. Student, Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Paula A. Benny, Research Scientist, Department of Obstetrics and Gynecology, University of Hawaii, Honolulu, HI, USA; Fadhl M. AlAkwaa, Assistant Research Scientist, Department of Neurology, University of Michigan, Ann Arbor, MI, USA; Cameron B. Lassite

Interpretable Multimodal Interaction-aware Mixture-of-Experts Jiayi Xin, BS, PhD Student, University of Pennsylvania, PA, USA Sukwon Yun, MS, PhD Student, University of North Carolina at Chapel Hill, NC, USA Jie Peng, BS, PhD Student, University of Science and Technology of China, Anhui, China Inyoung Choi, BS, PhD Student, University of Pennsylvania, PA, USA Jenna L. Ballard, BS, PhD Student, University of Pennsylvania, PA, USA Tianlong Chen, PhD, University o

Tumor subtype and clinical factors mediate the impact of tumor PPARɣ expression on outcomes in patients with primary breast cancer. Aditya Shah1,2, Katie Liu1,3, Ryan Liu1, 4, Gautham Ramshankar1, Curtis J. Perry MD, Ph.D.5,6, and Rachel J. Perry Ph.D1* 1Departments of Cellular & Molecular Physiology, Internal Medicine (Endocrinology), and Comparative Medicine, Yale University, New Haven, CT, United States 2Woodbridge Academy Magnet School, Woodbridge, NJ, United States

Single Cell Analysis based Identification of Unique Markers and Metastasis Mechanism in Triple Negative Breast Cancer Aashi Dixit Triple-negative breast cancer (TNBC) is a subtype of breast cancer which has none of the known unique biomarkers of the other subtypes. There is no established targeted treatment for TNBC and rare early diagnosis, which is also metastatic in 46% of cases, leading to poor survival rates in patients. Single-cell analysis maps the genomic information

KnowYourCG: Enabling CpG-centric Interpretation of Sparse DNA Methylomes Hongxiang Fu1,* David C Goldberg1,* Daniel Atkins1, Ethan Moyer1, Chin Nien Lee2, Yanxiang Deng2, Wanding Zhou1 1Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA, 19104, USA, 2Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA *Authors contributed equally. Decoding DNA methylomes for biological insights i

Proteomic Characterization of Porcine Brain Parenchyma in Acute and Sustained Models of Hydrocephalus Davis, LM1; Haddad, S1; Curtin, K1; Fazelinia, H2,3; Roof, J2; Brown, EM2; Spruce, LA2; Kilbaugh, T1; Hwang, M1,4. Affiliations: 1 Radiology Department, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 2 Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA 19104 3 Department of Biomedical and Health Informatics, Children's Hosp

Ancestry-Specific Pangenome Graphs Enable the Study of Population-Specific Genomic Variation and Structural Complexity Brydon P. G. Wall, MS, Department of Biostatistics, SOPH, VCU Bei Zhang, PhD, Department of Biostatistics, SOPH, VCU My Nguyen, BS, Department of Biostatistics, SOPH, VCU Stella Castro, School of Life Sciences and Sustainability, CHS, VCU; The Honors College, VCU Shasmeen Azhar, School of Life Sciences and Sustainability, CHS, VCU; The Honors College, VCU

Promoting Data Sharing and Compliance for Biomedical Data: Introducing the CHOP Dataverse Allison Olsen, MA, MS; Nicole Feldman, MSIS; Julianna Pakstis, MI; Jennae Luecke, MSLS, Ene Belleh, MBA, MLIS In response to the NIH Data Management and Sharing (DMS) Policy, which took effect in January 2023 requires researchers to plan for and share scientific data generated from NIH-funded research. The Arcus Library Science Team at Children's Hospital of Philadelphia (CHOP) launched

Broad immunophenotyping panel with supervised immune cell classification reveals age-dependent differences between mitochondrial disease subjects and healthy controls Matei Ionita1,2, Richard Schretzenmair1, Derek Jones1, Kelsey Keith3#, Matthew Sullenberger4, Benjamin R. Fischer4, Hakon Hakonarson3,5, Jonni Moore1, Marni J. Falk4,5* 1Penn Cytomics & Cell Sorting Shared Resource Laboratory, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 2Institute

A Closed-Form Estimator of Selection Strength from Substitution-Mutation Ratios: Theory and a SARS-CoV-2 Case Study Paradis, N., PhD Candidate, Dept. of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, 08028. Wu, C., Associate Professor, Dept. of Chemistry and Biochemistry, Dept. of Molecular & Cellular Biosciences, Rowan University, Glassboro, NJ, 08028. Classical fixation probability (Pfix) formulations are central to population genetics but are analytically no

Mitochondrial clone tracing within spatially intact human tissues. Sydney A. Bracht 1†, Jiazhen Rong 2†, Rodrigo A. Gier 1,10, Maureen DeMarshall 4, Hailey Golden 5, Diya Dhakal 5,Jayne C. McDevitt 7,8, Feiyan Mo 7,8, Emma E. Furth 3,9, Alexandra Strauss Starling 4, Amanda B. Muir 6, Gary W. Falk 4, Bryson W. Katona 4, Ben Z. Stanger 7,8,9, Nancy R. Zhang 6*, Sydney M. Shaffer 1,3,8* 1 Department of Bioengineering, School of Engineering and Applied Science, University of

Genetic Ancestry Inference in PDX Models: Benchmarking WGS and RNA-seq Approaches Brydon P. G. Wall, MS, Department of Biostatistics, SOPH, VCU Katarzyna M. Tyc, PhD, Department of Biostatistics, SOPH, VCU; Massey BISR Amy L. Olex, PhD, Wright Center for Clinical and Translational Research, VCU My Nguyen, BS, Department of Biostatistics, SOPH, VCU Jinze Liu, PhD, Department of Biostatistics, SOPH, VCU; Massey BISR J. Chuck Harrell, PhD, Department of Pathology, SOM, VCU;

Multimodal analysis resolves GNG4 as a distinguishing feature of activated germinal center-resident Tfh in humans Barnett Dubensky S, BS 1,2, Gallagher M, MS 3†, Kumashie KG, PhD 3, Lu T, MS 4, Zhu Y, MS 5, Tedesco J, BA 3, De Luna N, BS 2, Premo K, BS 2, Qi Y, MSE 5, Rachimi S, BS 2, Cruz Cabrera E, MS 6, Fulmer F, BS 2, Meremikwu IC, BS 7, Carter A, MS 9,10, Henrickson SE, MD, PhD 4,6,8, Romberg N, MD 6,8, Baxter AE, PhD 8‡, Oldridge DA, MD, PhD 9,10* & Vella LA, MD, PhD 3,

Neonatal Microglia Replacement: Monocyte-Derived Cells Rescue Seizure Phenotypes While Embryonic Microglia Exacerbate Them Sangeeta Shukla1, Carleigh A. O'Brien2, Samuelle A. S. Delcy3, Eli M. Levitt2, Akiva S. Cohen4,5, Mariko L. Bennett6, Frederick C. Bennett2,6 1 The Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia PA, USA, 19104. 2 Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, P

Towards a Unified Pediatric Cancer Resource: Integrating Clinical Trials, Molecular Targets, and Therapeutic Databases Aditya Lahiri [1], Sangeeta Shukla [1], Eric Wafula [1], Kelsey Keith [1], Yuanchao Zhang [1], Dave Hill [1], Krutika S. Gaonkar [1,2,3], Run Jin [2,3], Komal S. Rathi [1,2], Yuankun Zhu [2,3], Bailey K. Farrow [2,3], Daniel P. Miller [2,3], Adam A. Kraya [2,3], Xiaoyan Huang [2,3], Bo Zhang [2,3], Zhuangzhuang Geng [2,3], Brian M. Ennis [2,3], Ryan J. Corbet

Genetic variants regulating immune cell-cell interactions are key drivers for autoimmune disease risk Avantika R. Diwadkar (1,2), Lida Wang (2), Havell Markus (1,3), Natashia J. Benjamin (1,2), Jeniece M. Regan (4), Paige E. Bond (4), Bibo Jiang (2), Laura Carrel (1,4), Dajiang J. Liu (1,2,3) 1. Bioinformatics and Genomics PhD Program; Pennsylvania State University College of Medicine; Hershey, Pennsylvania, 17033; USA. 2. Department of Public Health Sciences; Pennsylvani

MarginDetect reveals distinct clonal dynamics and its interactions within the microenvironment near the tumor margins in rare subtypes of Bladder Cancer Luisa Quezada Ziesse, PhD student, Rutgers Cancer Institute of New Jersey Antara Biswas, PhD, Rutgers Cancer Institute of New Jersey Saum Ghodoussipour, MD, Rutgers Cancer Institute of New Jersey Subhajyoti De, PhD, Rutgers Cancer Institute of New Jersey Rare subtypes of bladder carcinoma have a different prognosis compare

Billion-level TCR clustering analysis with GIANAplus Yizhou Tracy Wang (PhD Student, University of Pennsylvania Perelman School of Medicine), David Chen (High School Student, Tower Hill School), Bo Li (PhD, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine) T cells play a critical role in adaptive immunity, while T cell receptors (TCRs) determine their specificity to antigens in the form of peptide-MHC (pMHC). TCRs are highly dive

THE IMPACT OF CELL-FREE DNA FRAGMENTATION AND BASE-CALLING ON LIQUID BIOPSY SENSITIVITY Akshaya V. Selvarajan (1), Subhajyoti De (1) (1) Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA Liquid biopsy based on tumor-derived cell-free circulating DNA offers a non-invasive approach to monitor minimal residual disease (MRD), evaluate treatment response, and guide patient prognostication. Cell-free circulating DNA (cfDNA) in blood is subject to f

A Patient Data-driven Graph Approach to Understand Genetic Drivers of Disease. Yunjun Kang, BS, University of Pennsylvania Bioengineering Graduate Group, Perelman School of Medicine Division of Translational Medicine and Human Genetics Theodore G. Drivas, University of Pennsylvania Perelman School of Medicine Division of Translational Medicine and Human Genetics Despite advances in genomic association studies, understanding disease mechanisms from genetic correlations remain