Benjamin J. Raphael

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• Spatial Mapping of the Precancer-to-Cancer Transition in Breast and Prostate

  Cancer Discovery · 2026-04-17

• Riemannian Metric Learning for Alignment of Spatial Multiomics

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-11

• Inferring cell differentiation maps from lineage tracing data

  Nature Methods · 2025-12-08 · 4 citations

• Abstract B013: Chromosomal rearrangements at the YAP/TAZ pathway genes are associated with heterogeneity and stem cell-like castration-resistant prostate cancer

  Cancer Research · 2025-12-04

• Spatial patterning of transcriptional and regulatory programs in the primate subcortexPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-24

• Joint imputation and deconvolution of gene expression across spatial transcriptomics platformsPreprint

  Genome Research · 2025-11-17 · 1 citations

• Spatial metabolic gradients in the liver and small intestine

  Nature · 2025-10-15 · 20 citations

• Generative AI for Biosciences: Emerging Threats and Roadmap to BiosecurityPreprint

  ArXiv.org · 2025-10-13

• A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints

  Nature Communications · 2025-08-28 · 2 citations

• Deriving longitudinal tumor phylogenies from single-cell sequencing dataPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-09

• Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAML

  Genome biology · 2025-07-02 · 10 citations

• Informatics at the Frontier of Cancer Research

  Cancer Research · 2025-07-02

• Genomic alterations in the YAP/TAZ pathway are associated with stem cell-like castration-resistant prostate cancerPreprint

  medRxiv · 2025-07-02

• Fast tumor phylogeny regression via tree-structured dual dynamic programming

  Bioinformatics · 2025-07-01 · 1 citations

• Anomaly detection in spatial transcriptomics via spatially localized density comparison

  Bioinformatics · 2025-07-01 · 1 citations

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

  Bioinformatics · 2025-07-01

• Between Cluster Analysis: Supervised Dimensionality Reduction for Trajectory Inference

  Bioinformatics · 2025-06-05

• Spatial metabolic gradients in the liver and small intestinePreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-02

• Abstract 2385: Discovery of non-coding somatic driver mutations in single-cell chromatin accessibility data

  Cancer Research · 2025-04-21

• Abstract 3883: Evolution of genomic and epigenomic heterogeneity in prostate cancer from tissue and liquid biopsies

  Cancer Research · 2025-04-21 · 1 citations