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Benjamin J. Raphael

Princeton University · US
Area of research
Cancer Research · Molecular Biology
Research interest
Research interests include Cancer Genomics and Diagnostics, Single-cell and spatial transcriptomics, Genomic variations and chromosomal abnormalities, and Gene expression and cancer classification.
h-index
79
citations
71,500
works
448
NIH funding
primary concept
Biology
email

Recent publications

Spatial patterning of transcriptional and regulatory programs in the primate subcortex
bioRxiv (Cold Spring Harbor Laboratory) 2025cited by 0position: middledoi
Tumour evolution and microenvironment interactions in 2D and 3D space
Nature 2024cited by 136position: middledoi
Current and future directions in network biology
Bioinformatics Advances 2024cited by 92position: middledoi
Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers
Science 2024cited by 41position: middledoi
Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction
Nature Biotechnology 2024cited by 9position: middledoi
Spatial epigenome–transcriptome co-profiling of mammalian tissues
Nature 2023cited by 405position: middledoi
Epigenetic regulation during cancer transitions across 11 tumour types
Nature 2023cited by 191position: middledoi
Co-evolution of <i>AR</i> gene copy number and structural complexity in endocrine therapy resistant prostate cancer
NAR Cancer 2023cited by 26position: middledoi
Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Nature 2023cited by 12position: middledoi
Author Correction: The evolutionary history of 2,658 cancers
Nature 2023cited by 5position: middledoi
A path to translation: How 3D patient tumor avatars enable next generation precision oncology
Cancer Cell 2022cited by 61position: middledoi
Author Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
Communications Biology 2022cited by 3position: middledoi
Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower
Nature Communications 2022cited by 0position: middledoi
Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
Nature Communications 2022cited by 0position: middledoi
Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
Cell 2021cited by 550position: middledoi
Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway
Cell Reports 2021cited by 32position: middledoi
Spatially interacting phosphorylation sites and mutations in cancer
Nature Communications 2021cited by 26position: middledoi
Eleven grand challenges in single-cell data science
Genome biology 2020cited by 1,402position: middledoi
The evolutionary history of 2,658 cancers
Nature 2020cited by 1,117position: middledoi
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
Communications Biology 2020cited by 189position: middledoi
Combined burden and functional impact tests for cancer driver discovery using DriverPower
Nature Communications 2020cited by 63position: middledoi
Inferring structural variant cancer cell fraction
Nature Communications 2020cited by 56position: middledoi
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig
Nature Communications 2020cited by 50position: middledoi
Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia
Blood 2019cited by 299position: middledoi
12 Grand Challenges in Single-Cell Data Science
2019cited by 7position: middledoi
12 Grand challenges in single-cell data science
2019cited by 5position: middledoi
12 Grand challenges in single-cell data science
2019cited by 2position: middledoi
12 Grand Challenges in Single-Cell Data Science
2019cited by 1position: middledoi
Genetic Mechanisms of Immune Evasion in Colorectal Cancer
Cancer Discovery 2018cited by 548position: middledoi
The Integrated Genomic Landscape of Thymic Epithelial Tumors
Cancer Cell 2018cited by 381position: middledoi

Grants

CAREER: Algorithms for Next-Generation Genomics
NSF1724784$292,1012016–2019PIRePORTER
CAREER: Algorithms for Next-Generation Genomics
NSF1053753$461,7902011–2017PIRePORTER
III: Small: Algorithmic Approaches for Pathway and Gene Group Analysis in Genetic Studies
NSF1016648$527,6272010–2015PIRePORTER

Frequent collaborators

Li Ding · South China Institute of Collaborative Innovation3 papers (2013–2021)Michael C. Wendl · Centre for Genomic Regulation2 papers (2013–2021)Núria López-Bigas · Institució Catalana de Recerca i Estudis Avançats2 papers (2014–2015)Fabio Vandin · University of Padua2 papers (2013–2014)Abel González-Pérez · Institute of Science and Technology2 papers (2014–2015)Mark D.M. Leiserson · Brown University2 papers (2013–2014)Trey Ideker · UC San Diego Health System2 papers (2017–2018)Michael D. McLellan · James S. McDonnell Foundation2 papers (2013–2014)Beifang Niu · Chinese Academy of Sciences2 papers (2013–2014)Matthew A. Wyczalkowski · James S. McDonnell Foundation2 papers (2013–2021)Kelly V. Ruggles · NYU Langone Health1 papers (2021–2021)Todd P. Knutson · University of Minnesota, Twin Cities1 papers (2023–2023)Lenore Cowen · Tufts University1 papers (2017–2017)B. F. Francis Ouellette · Montreal Clinical Research Institute1 papers (2015–2015)LeAnn Oseth · University of Minnesota, Twin Cities1 papers (2023–2023)Joshua M. Stuart · National Cancer Institute1 papers (2015–2015)Christine Henzler · University of California, Santa Barbara1 papers (2023–2023)Kai Ye · Wannan Medical College1 papers (2013–2013)Kuan‐lin Huang · Center for Genomic Science1 papers (2021–2021) · 1 papers (2023–2023)