Elana J. Fertig

Elana J. Fertig, PhD is Professor of Oncology and Director of the Convergence Institute at Johns Hopkins University School of Medicine, where she leads a research program integrating computational mathematics, machine learning, and multi-omics biology to understand cancer progression and treatment resistance. Dr. Fertig is best known for developing CoGAPS (Coordinated Gene Activity in Pattern Sets), a Bayesian non-negative matrix factorization algorithm that decomposes multi-omics datasets (bulk RNA-seq, scRNA-seq, ATAC-seq, spatial transcriptomics) into biologically interpretable transcriptional programs, widely used to identify cancer-associated gene activity patterns across patient cohorts and single cells. Her ProjectR framework enables transfer learning of NMF-derived patterns across datasets and modalities, allowing computational transfer of biological programs from training cohorts to new datasets, enabling cross-study generalization of cancer molecular signatures. Dr. Fertig's laboratory has made major contributions to understanding treatment resistance in head and neck, colorectal, and pancreatic cancers using multi-omics single-cell approaches, identifying transcriptional programs that emerge under therapeutic selection. She co-directs the JHU Convergence Institute for Cancer Informatics and leads multi-institutional computational oncology consortia integrating multi-omics data from clinical trials. Dr. Fertig is a computational biologist whose mathematical foundations and cross-disciplinary training make her work uniquely rigorous at the interface of AI, genomics, and cancer biology.