Professor
Cincinnati Children’s Hospital Medical Center
Cincinnati, Ohio, United States
I am a trained computational and experimental biologist who develops approaches to understand the interplay
between diverse modes of gene regulation, including transcription, alternative splicing, genetics, and
epigenetics that underlie disease interaction networks. I have co-authored over 130 peer-reviewed manuscripts
related to computational genomics and have over 25 years of experience directing the development of highly
used software applications for computational experts and biologists alike. Our focus is on understanding the
role of unique mRNA isoforms in lineage specification and mis-splicing in disease. To achieve these goals, my
lab has developed dozens of computational approaches (>5,000 collective citations), with an emphasis on
multimodal single cell integration, alternative splicing analysis and functional inference. These approaches
include game theory and machine learning to integrate measurements and clustering across diverse modalities
(scTriangulate), unsupervised methods to identify novel disease subtypes from single-cell datasets (UDON),
and machine learning approaches to predict the functional consequences of alternative splicing in diverse
contexts (AltAnalyze). Over the last decade, we have used these approaches to reveal novel isoforms
regulating stem cell differentiation, splicing factor-mediated disease mechanisms, new disease subtypes and
metastable transitional cell states. In last few years, our team created a series of analytical tools that leverage
deep learning and Bayesian modeling to define splicing events that give rise to new peptides for therapy
(SNAF, BayesTS, DeepImmuno, RNA-SPRINT). In addition to developing new analytical approaches, I lead
the LungMAP Data Coordination Center and participate in multiple cell atlas initiatives, including the HCA and HuBMAP.
Disclosure information not submitted.
"ML/AI-Informed Tumor Profiling and Neoantigen Analysis from Bulk and Single-Cell Long-Read RNA-Seq
Saturday, November 15, 2025
3:30 PM - 4:00 PM EST