Analyzes biobank, electronic health record, RNA-seq and single-cell RNA-seq data with integrative genomics methods. Uses polygenic scoring and transcriptome-wide association studies for precision health.
114 papers since 2024
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Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms
Science, 2024
Temporally distinct 3D multi-omic dynamics in the developing human brain
Nature, 2024
Evaluating Performance and Agreement of Coronary Heart Disease Polygenic Risk Scores
“We are recruiting kind and motivated quantitatively oriented trainees at all levels (undergraduate, graduate and postdoctoral); contact Bogdan for details.”
Develops AI and bioinformatics methods for EHR, whole-genome/exome, PacBio, Oxford Nanopore and single-cell long-read RNA-seq data. Targets rare-disease diagnosis, genome reinterpretation and precision genomic medicine.
Uses machine learning on EHR data, genetic markers, environmental factors and clinical indicators. Builds prediction models for women’s health, including endometriosis and glaucoma.
10 papers since 2024
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TRACE: A FINE-TUNED BIOMEDICAL LANGUAGE MODEL FOR DIRECTIONALLY INFORMED DRUG REPURPOSING FROM TRANSCRIPTOME-WIDE ASSOCIATION STUDIES
medRxiv, 2026
Integrating Imaging-Derived Clinical Endotypes with Plasma Proteomics and External Polygenic Risk Scores Enhances Coronary Microvascular Disease Risk Prediction †
medRxiv, 2025
Social Determinants of Health and Lifestyle Risk Factors Modulate Genetic Susceptibility for Women’s Health Outcomes
Funded by National Institute of Child Health and Human Development (NICHD)
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National Institute of Child Health and Human Development (NICHD), Comprehensive Predictive Modeling for Endometriosis Using Genetic and Non-Genetic Risk Factors · active
““Funded by the National Institute of Child Health and Human Development (NICHD), this project aims to develop an advanced predictive model for endometriosis.””
Studies Alzheimer’s genetics using genetic fine-mapping, single-cell DNA sequencing, bulk long-read DNA sequencing and genome engineering in cellular models. Develops computational diagnostics for neurogenetic conditions.
11 papers since 2024
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Polygenic burden of short tandem repeat expansions promotes risk for Alzheimer’s disease
Nature Communications, 2025
Disparities in Genetic Testing for Neurologic Disorders
Neurology, 2024
Ischemic stroke associated with amyloid‐related imaging abnormalities in a patient treated with lecanemab
Uses statistical and computational methods on scRNA-seq, CITE-seq and spatial transcriptomics data. Studies cellular heterogeneity, cell state transition and disease susceptibility genes for clinical translation.
43 papers since 2024
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Inferring super-resolution tissue architecture by integrating spatial transcriptomics with histology
Nature Biotechnology, 2024
Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues
Cell, 2024
High-Dimensional Single-Cell Multimodal Landscape of Human Carotid Atherosclerosis
Arteriosclerosis Thrombosis and Vascular Biology, 2024
Analyzes biobank/EHR, CT/MRI, echocardiography, cardiac MRI, ECG, GWAS and exome-wide data. Uses Penn Medicine BioBank and other biobanks for genetic-risk prediction and clinical AI.
59 papers since 2024
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Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
Science, 2025
Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program
Science, 2024
A deep catalogue of protein-coding variation in 983,578 individuals
Provides genetic testing and counseling by telephone or video conferencing. Serves patients nationwide, community settings without genetic services, and large clinical trials.
52 papers since 2024
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Clinical management of TP53 mosaic variants found on germline genetic testing
Cancer Genetics, 2024
The ENGAGE study: a 3-arm randomized hybrid type 1 effectiveness and implementation study of an in-home, collaborative PCP model of remote telegenetic services to increase uptake of cancer genetic services in childhood cancer survivors
BMC Health Services Research, 2024
Test-takers’ perspectives on consumer genetic testing for hereditary cancer risk
Develops informatics, computing and data science methods for genetics, omics, imaging, biomarker, outcome and EHR data. Applies advanced AI to biobank and health datasets.
156 papers since 2024
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Frequency and Clinical Outcomes Associated With Tau Positron Emission Tomography Positivity
JAMA, 2025
The genetic architecture of multimodal human brain age
Nature Communications, 2024
Gene-SGAN: discovering disease subtypes with imaging and genetic signatures via multi-view weakly-supervised deep clustering
Machine learning, Deep learning, Natural language processing, Large language models, Knowledge graphs, Genome-wide association studies, Structured sparse canonical correlation analysis, SPHARM shape modeling
Studies African populations with genomic, proteomic, epigenetic, transcriptomic, metabolomic, microbiome and single-cell RNA and ATAC data. Research targets adaptation, disease risk and immune variation.
14 papers since 2024
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Sequencing in over 50,000 cases identifies coding and structural variation underlying atrial fibrillation risk
Nature Genetics, 2025
A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies
Nature Computational Science, 2025
Deciphering the impact of genomic variation on function
Studies BRCA1/2 gene mutations in basic, clinical and translational cancer research. Focuses on cancer interception, early detection and care for mutation carriers.
Funded by Gray Foundation, Basser Center for BRCA +1 more
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Basser Center for BRCA, Internal Research Grant Program · 2026
“Funding begins on July 1, 2026.”
Basser Center for BRCA, External Research Grant Program · 2026
“The 2026 Basser Center external grant program is temporarily delayed until later in 2026.”
Gray Foundation, Gray Foundation Grants · active
“Basser Center founding donors, Mindy and Jon Gray, have established the Gray Foundation.”
Runs 10X Chromium, Illumina and PacBio sequencing, genotyping, and biorepository services. Studies pediatric rare and complex disorders to develop diagnostics and therapies.
155 papers since 2024
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Selection, optimization and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse US populations
Nature Medicine, 2024
Dependency-aware deep generative models for multitasking analysis of spatial omics data
Nature Methods, 2024
Exome sequencing of 20,979 individuals with epilepsy reveals shared and distinct ultra-rare genetic risk across disorder subtypes
Funded by National Institutes of Health, Children’s Hospital of Philadelphia
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National Institutes of Health · active
“The Center for Applied Genomics (CAG) at Children's Hospital of Philadelphia is one of 10 sites that receives funds from the National Institutes of Health”
Children’s Hospital of Philadelphia · active
“He leads a $40 million commitment from Children’s Hospital of Philadelphia to genomically characterize approximately 100,000 children”
Uses Capture C, Hi-C, ATAC-seq, ChIP-seq and RNA-seq with CRISPR/Cas9 in iPSC-derived neurons and cerebral organoids. Maps variants to genes in neurodegenerative disorders.
41 papers since 2024
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White Matter Abnormalities and Cognition in Aging and Alzheimer Disease
JAMA Neurology, 2025
Polygenic prediction of body mass index and obesity through the life course and across ancestries
Nature Medicine, 2025
Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3′ UTR of FAIM2
Analyzes EHR-linked genotyping arrays and exome sequencing from medical biobanks, then validates findings in cell models. Focuses on primary-cilium disorders and human disease mechanisms.
35 papers since 2024
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Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
Science, 2025
A deep catalogue of protein-coding variation in 983,578 individuals
Nature, 2024
Evaluating Performance and Agreement of Coronary Heart Disease Polygenic Risk Scores
Trains students in computational and experimental genomics using long-read RNA sequencing, spatial transcriptomics and electronic health records. Studies human disease, evolution and biomedical research.
Funded by National Science Foundation, National Institutes of Health
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National Science Foundation · active
“applicants are encouraged to apply for scholarships from prestigious funding sources such as the National Science Foundation and the National Institutes of Health.”
National Institutes of Health · active
“applicants are encouraged to apply for scholarships from prestigious funding sources such as the National Science Foundation and the National Institutes of Health.”
Develops statistical methods for biomedical data, including imaging and genetic studies. Trains investigators in clinical trials, cohort studies and statistical computing.
Funded by Individual Research Fellowships (Students), Individual Research Fellowships (Students)
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Individual Research Fellowships (Students), 1-F31-AG-091981-01A1; Genetic and Environmental Sources of Heterogeneity in Alzheimer's Disease: A Pathway Specific Approach · active
“[name] - 1-F31-AG-091981-01A1: Genetic and Environmental Sources of Heterogeneity in Alzheimer's Disease: A Pathway Specific Approach”
Individual Research Fellowships (Students), 5-F31-LM-014282-03; Addressing Algorithmic Unreliability and Dataset Shift in EHR-based Risk Prediction Models · active
“Likhitha Kolla - 5-F31-LM-014282-03: Addressing Algorithmic Unreliability and Dataset Shift in EHR-based Risk Prediction Models”
Studies cancer immunotherapy using flow cytometry, transcriptional approaches and spatial transcriptomics. Examines checkpoint blockade responses in melanoma, Merkel cell carcinoma and renal cell carcinoma.
64 papers since 2024
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Combined JAK inhibition and PD-1 immunotherapy for non–small cell lung cancer patients
Science, 2024
Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8+ T cells
Cancer Cell, 2024
LAG-3 sustains TOX expression and regulates the CD94/NKG2-Qa-1b axis to govern exhausted CD8 T cell NK receptor expression and cytotoxicity
Develops AI, machine-learning, NLP and data-integration methods for EHRs, imaging, omics and wearable-sensor data. Applies them to precision medicine, population health and clinical care.
156 papers since 2024
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Frequency and Clinical Outcomes Associated With Tau Positron Emission Tomography Positivity
JAMA, 2025
The genetic architecture of multimodal human brain age
Nature Communications, 2024
Gene-SGAN: discovering disease subtypes with imaging and genetic signatures via multi-view weakly-supervised deep clustering
electronic health records (EHRs), health claims, imaging data, single-cell genomics, metagenomics, wearable sensors, patient-generated platforms
Techniques
artificial intelligence and machine learning, natural language processing, causal inference, genome-wide association studies, polygenic risk scores, clinical decision support systems
Develops AI, machine-learning and NLP infrastructure for EHR, TriNetX, Epic Cosmos and Epic Clarity data. Serves Penn Medicine clinical, translational and basic research.
59 papers since 2024
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Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
Science, 2025
Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program
Science, 2024
A deep catalogue of protein-coding variation in 983,578 individuals
Integrates multi-omics, imaging and EHR phenotype data with machine learning and deep learning. Uses these methods for precision medicine and translational informatics.
62 papers since 2024
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Addressing biomedical data challenges and opportunities to inform a large-scale data lifecycle for enhanced data sharing, interoperability, analysis, and collaboration across stakeholders
Scientific Reports, 2025
Harnessing Artificial Intelligence in Multimodal Omics Data Integration: Paving the Path for the Next Frontier in Precision Medicine
Annual Review of Biomedical Data Science, 2024
Effect of virtual reality-based biofeedback for depressive and anxiety symptoms: Randomized controlled study
Develops statistical methodologies for single-cell CRISPR screens and single-cell multi-omics data. Uses them to study enhancer–gene regulation and human disease.
11 papers since 2024
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Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection
Genome biology, 2024
Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling
Nature Biotechnology, 2024
GWAS-Informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density
Uses human genetics and bioinformatics to identify therapeutic targets and predict cardiovascular risk. Builds polygenic risk scores in deeply phenotyped biobank and clinical cohorts.
190 papers since 2024
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Exploring the role of large language models in the scientific method: from hypothesis to discovery
npj Artificial Intelligence, 2025
AI is a viable alternative to high throughput screening: a 318-target study
Scientific Reports, 2024
Collective intelligence: A unifying concept for integrating biology across scales and substrates
Studies BRCA1/2 and TP53 cancers using EM-seq, single-cell RNA sequencing, organoids and biobank data. Targets early detection and prostate-cancer genetics in Penn and VA cohorts.
141 papers since 2024
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Update on Cancer Screening Recommendations for Individuals with Li–Fraumeni Syndrome
Clinical Cancer Research, 2025
BRCA1, BRCA2 , and Associated Cancer Risks and Management for Male Patients
JAMA Oncology, 2024
Update on Pediatric Cancer Surveillance Recommendations for Patients with Neurofibromatosis Type 1, Noonan Syndrome, CBL Syndrome, Costello Syndrome, and Related RASopathies
Enzymatic methylation-sequencing (EM-seq), Single-cell RNA sequencing, Amplicon-based DNA sequencing, Bulk RNA sequencing, Targeted DNA sequencing, Whole-genome sequencing, SNP genotyping
Techniques
In vitro modeling, In vivo modeling, Organoid development, Patient-derived prostate organoid models, Western blot, RT-qPCR, Immunofluorescence, Organoid transfection
Combines Penn patient samples with clinical, genetic and survey data, including whole-exome sequencing and genotyping-chip data. Supports precision medicine and disease research with Penn investigators.
11 platforms and techniques
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Works with
whole-exome sequencing, genome-wide SNP arrays, genotype imputation, longitudinal electronic health records, CT scans
Techniques
polygenic risk scores, bioinformatics, deep learning, genome-first approach, phenome-wide association study, genome-wide association study
Builds graph machine-learning models from electronic health records, biobanks, multi-omics datasets and Penn Medicine BioBank data. Studies disease mechanisms, women’s health and toxicology.
35 papers since 2024
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Comparing Recent Pulsar Timing Array Results on the Nanohertz Stochastic Gravitational-wave Background
The Astrophysical Journal, 2024
Erratum: “The NANOGrav 15 yr Data Set: Search for Signals from New Physics” (2023, ApJL 951 L11)
The Astrophysical Journal Letters, 2024
Characterizing gravitational wave detector networks: from A ♯ to cosmic explorer
NSF, 2500339: SCH: An intraoral device for multimodal data integration and risk modification connects the oral microbiome to systemic health · 2025-2029
“NSF [2500339]: SCH: An intraoral device for multimodal data integration and risk modification connects the oral microbiome to systemic health (2025-2029).”
NIH, OT2-OD040373: Genomic and exposomic factors in the cause and rise of autism · 2025-2028
“NIH [OT2-OD040373]: Genomic and exposomic factors in the cause and rise of autism (2025-2028).”
NIH/NLM, K99/R00-LM013646: Discovering clinical endpoints of toxicity via graph machine learning and semantic data analysis · 2021-2025
“NIH/NLM [K99/R00-LM013646]: Discovering clinical endpoints of toxicity via graph machine learning and semantic data analysis (2021-2025).”
electronic health records, Penn Medicine BioBank, dbSNP, NCBI Human Gene, Omics Pred, GTEx, Open Targets
Techniques
graph neural networks, QSAR modeling, knowledge graph construction, multimodal data integration, natural language processing, link prediction, protein and drug representation learning, differential gene expression analysis
Analyzes GWAS and electronic health-record data with computational biology and clinical epidemiology. Studies cardiometabolic and liver disease for precision risk assessment and drug repurposing.
51 papers since 2024
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Genetic drivers of heterogeneity in type 2 diabetes pathophysiology
Nature, 2024
Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis
Nature Genetics, 2024
A genome-first approach to variants in MLXIPL and their association with hepatic steatosis and plasma lipids
Develops computational and experimental methods for RNA processing using long-read RNA-seq, short-read RNA-seq and nanopore sequencing. Applies them to human genetics, diagnostics and cancer immunotherapy.
104 papers since 2024
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Research progress and future prospects of chemical utilization of CO2
Chemical Engineering Journal, 2025
rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data
Nature Protocols, 2024
Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues
Integrates human genetics with human pluripotent stem cells and animal models. Studies developmental brain disorders, neurodegeneration and treatments.
27 papers since 2024
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Targeted therapy improves cellular dysfunction, ataxia, and seizure susceptibility in a model of a progressive myoclonus epilepsy
Cell Reports Medicine, 2024
KOLF2.1J iPSCs carry CNVs associated with neurodevelopmental disorders
Cell stem cell, 2024
Altered lipid homeostasis is associated with cerebellar neurodegeneration in SNX14 deficiency
CRISPR base editing, Adenine base editors, Genome-edited cardiomyocytes, hiPSCs and derived hepatocyte-like cells, Exome-wide association studies
Techniques
CRISPR-Cas9 base editing, Prime editing, Adult stem-cell cardiomyocyte modeling, In vivo therapeutic gene editing, hiPSCs and hepatocyte-like cells, Mouse and monkey models
Studies pharmacogenomics with EHR-linked DNA, Penn Medicine Biobank and Million Veteran Program data. Integrates pharmacogenetic testing into care and studies multiomic predictors of drug response.
23 papers since 2024
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A Guide for Implementing DPYD Genotyping for Systemic Fluoropyrimidines into Clinical Practice
Clinical Pharmacology & Therapeutics, 2025
CYP2C19 Genetic Testing for Oral P2Y12 Inhibitor Therapy: A Scientific Statement From the American Heart Association
Circulation, 2024
The Pharmacogenomics Global Research Network Implementation Working Group: global collaboration to advance pharmacogenetic implementation