Ben Raphael

Ben Raphael is a Professor in the Department of Computer Science at Princeton University, with affiliations at the Lewis-Sigler Institute for Integrative Genomics, Omenn-Darling Bioengineering Institute, and Center for Statistics and Machine Learning. He is also an Affiliate Faculty member at the Rutgers Cancer Institute of New Jersey, Irving Institute for Cancer Dynamics at Columbia University, and New York Genome Center. His research focuses on computational methods for analyzing large-scale biological data, emphasizing cancer evolution, network/pathway analysis, and structural variation in genomes.

Research Trends: His recent work spans cancer lineage trees, spatial transcriptomics, optimal transport for developmental models, and network analysis of mutations. Articles highlight applications in prostate cancer, pancreatic cancer, and single-cell genomics.

Scientific Awards:

• 2024 ACM Fellow
• 2023 RECOMB Test of Time Award
• 2022 RECOMB Test of Time Runner-Up
• 2021 ISCB Innovator Award
• 2021 RECOMB Best Paper Runner-Up
• 2020 ISCB Fellow
• 2020 AACR Team Science Award
• 2011 NSF CAREER Award
• 2013 RECOMB Best Paper
• 2010-2012 Sloan Research Fellowship

Advising: He has mentored numerous Ph.D. students and postdoctoral fellows, many of whom have transitioned to academic and industry roles. Current advisees include Uthsav Chitra, Gillian Chu, and Alexander Strzalkowski.

Labs & Teams: Raphael leads the Raphael Lab at Princeton, developing tools like HotNet2, CHISEL, and HATCHet for cancer genomics and network analysis.