Benjamin J. Raphael

Princeton University — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

81h-index63.3kcitations452works6.12yr avg
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Research Topics

Cancer Genomics and Diagnostics(210), Single-cell and spatial transcriptomics(68), Genomics and Phylogenetic Studies(56), Gene expression and cancer classification(52), Genomic variations and chromosomal abnormalities(51)

Publications396 total

Riemannian Metric Learning for Alignment of Spatial Multiomics
2025Open Access
Inferring cell differentiation maps from lineage tracing data
Nature Methods·2025Open Access
Abstract B013: Chromosomal rearrangements at the YAP/TAZ pathway genes are associated with heterogeneity and stem cell-like castration-resistant prostate cancer
Cancer Research·2025
Spatial patterning of transcriptional and regulatory programs in the primate subcortex
2025Open Access
Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
Genome Research·2025· 1 citedOpen Access
Spatial metabolic gradients in the liver and small intestine
Nature·2025· 4 citedOpen Access
Generative AI for Biosciences: Emerging Threats and Roadmap to Biosecurity
arXiv (Cornell University)·2025Open Access
A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints
Nature Communications·2025· 1 citedOpen Access
Deriving longitudinal tumor phylogenies from single-cell sequencing data
2025Open Access
Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAML
Genome biology·2025· 6 citedOpen Access
Informatics at the Frontier of Cancer Research
Cancer Research·2025Open Access
Genomic alterations in the YAP/TAZ pathway are associated with stem cell-like castration-resistant prostate cancer
2025Open Access
Anomaly detection in spatial transcriptomics via spatially localized density comparison
Bioinformatics·2025· 1 citedOpen Access
Fast tumor phylogeny regression via tree-structured dual dynamic programming
Bioinformatics·2025Open Access
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts
Bioinformatics·2025Open Access
Between Cluster Analysis: Supervised Dimensionality Reduction for Trajectory Inference
Bioinformatics·2025Open Access
Spatial metabolic gradients in the liver and small intestine
2025Open Access
Abstract 2385: Discovery of non-coding somatic driver mutations in single-cell chromatin accessibility data
Cancer Research·2025
Abstract 3883: Evolution of genomic and epigenomic heterogeneity in prostate cancer from tissue and liquid biopsies
Cancer Research·2025· 1 cited
Hierarchical Refinement: Optimal Transport to Infinity and Beyond
arXiv (Cornell University)·2025Open Access
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Frequent Co-authors

Gad Getz(11), Mark D.M. Leiserson(10), Michael D. McLellan(9), Fabio Vandin(9), Andrew D. Cherniack(9), David A. Wheeler(8), Michael S. Lawrence(8), Rehan Akbani(8), Michael C. Wendl(7), Li Ding(7), Katherine A. Hoadley(7), Paul C. Boutros(7), Layla Oesper(7), Marcin Imieliński(6), Rameen Beroukhim(6), Matthew Meyerson(6), Steven E. Schumacher(6), Seungchan Kim(6), Stacey Gabriel(5), Cyriac Kandoth(5)