Ben Raphael

Professor

Princeton University

United States

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Ben Raphael is a Professor at Princeton University in the United States. His research areas encompass spatial transcriptomics, tumor phylogeny, and higher-order epistasis, as demonstrated in his recent publications. His work includes innovative approaches to anomaly detection, phylogenetic reconstruction, and spatial gene expression analysis, contributing significantly to the understanding of cancer genomics.

Articles (20)

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2025

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2022

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2022

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2022

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2022

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2021

Collaborators (9)

Suzanne Baker

Professor

St. Jude Children's Research Hospital

UNITED STATES

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Sai Ma

Mount Sinai Hospital

UNITED STATES

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Yuval Kluger

Yale University

UNITED STATES

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Yang Liu

Assistant Professor

Yale University

UNITED STATES

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Uthsav Chitra

Assistant Professor

Johns Hopkins University

UNITED STATES

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Paul Robson

Professor

Jackson Laboratory - Farmington

UNITED STATES

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Eneritz Agirre

Karolinska Institutet

SWEDEN

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Yang Xiao

Assistant Professor

University of Michigan

UNITED STATES

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Mohammed El-Kebir

Assistant Professor

University of Illinois at Urbana-Champaign

UNITED STATES

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Ben Raphael

Research Interests

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About

Articles (20)

Anomaly detection in spatial transcriptomics via spatially localized density comparison

Fast tumor phylogeny regression via tree-structured dual dynamic programming

GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts

Resolving discrepancies between chimeric and multiplicative measures of higher-order epistasis

DeST-OT: Alignment of spatiotemporal transcriptomics data

Mapping the topography of spatial gene expression with interpretable deep learning

A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors

Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics

A count-based model for delineating cell–cell interactions in spatial transcriptomics data

HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data

Spatial epigenome–transcriptome co-profiling of mammalian tissues

Partial alignment of multislice spatially resolved transcriptomics data

Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

A path to translation: How 3D patient tumor avatars enable next generation precision oncology

NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks

Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics.

Alignment and integration of spatial transcriptomics data

Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor.

SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types.

DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution.

Collaborators (9)

Suzanne Baker

Sai Ma

Yuval Kluger

Yang Liu

Uthsav Chitra

Paul Robson

Eneritz Agirre

Yang Xiao

Mohammed El-Kebir

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