Herbert A. Simon Professor of Computer Science
Ray and Stephanie Lane Computational Biology Department
Affiliate Faculty, Machine Learning Department
Director, Center for Machine Learning in Health
Director, Center for Innovation in Health
Co-Director, Joint CMU-Univ Pittsburgh Ph.D. Program in Computational Biology
Room 7719, Gates-Hillman Complex
Carnegie Mellon University
5000 Forbes Ave
Pittsburgh, PA 15213
My research group is interested in advancing computer science and machine learning methodologies to extract insight from biological data. We currently focus on the following classes of problems:
- Genomics & genome assembly: RNA-seq expression quantification; genome assembly; large-scale sequence search, sketching, etc. This work is currently supported by NIH grant 1R01HG012470. It was previously supported by NIH grant 1R21HG006913, NSF grant CCF-1319998, a Data-Driven Investigator grant from the Gordon and Betty Moore Foundation NIH grant R01GM122935, and an award from The Shurl and Kay Curci foundation.
- Pan-genomics and genome graphs: Storing, searching, and using large collections of genomes and transcriptomes from many individuals. This work is supported by NSF grant III-2232121.
- Automatically learning algorithms and wetlab protocols: Scheduling automated experimentation, hyperparameter optimization, autoML, and automated algorithm design. Supported by an award from Schmidt Sciences.
Previous research interests include:
- Chromatin structure and function: Algorithms for determining the spatial organization of eukaryotic genomes from Chromosome Conformation Capture data. Previously supported by NIH grant R01HG007104.
- Viral evolution: Reassortment in the influenza genome. This work was supported by NIH grant 1R21AI085376.
- Protein interactions and networks: Evolution of interactions; protein function prediction; clustering within networks; protein structure prediction. This work was supported by NSF grant EF-0849899 and by NSF grant CCF-1053918/CCF-1256087 (CAREER award).
Disclosure: I am a co-founder of Ocean Genomics, Inc.