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Benjamin J. Raphael

princeton

79H-index
445Paper Count
6.8WCitation Count
Published Papers 73
Publication Date
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The tree labeling polytope: A unified approach to ancestral reconstruction problems
errCell Systems
IF7.7
err2026-06-01
err0
PREAI
errHenri Schmidt; Benjamin J. Raphael
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Inferring cell differentiation maps from lineage tracing data
errNature Methods
IF32.1
err2025-12-08
err0
errOAAI
errPalash Sashittal; Richard Y. Zhang; Benjamin K. Law; Henri Schmidt; Alexander Strzalkowski; Adriano Bolondi; Michelle M. Chan; Benjamin J. Raphael
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errSave
Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
errGENOME RESEARCH
IF5.5
err2025-12-01
err1
PREAI
errZheng, Hongyu; Sarkar, Hirak; Raphael, Benjamin J.
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errSave
Spatial metabolic gradients in the liver and small intestine
errNature
IF48.5
err2025-10-15
err0
errOAAI
errLaith Z. Samarah; Clover Zheng; Xi Xing; Won Dong Lee; Amichay Afriat; Uthsav Chitra; Michael R. MacArthur; Wenyun Lu; Connor S. R. Jankowski; Cong Ma; Craig J. Hunter; Michael Neinast; Daniel R. Weilandt; Benjamin J. Raphael; Joshua D. Rabinowitz
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errSave
A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints
errNature Communications
IF15.7
err2025-08-28
err0
errOAAI
errKiril Kuzmin; Henri Schmidt; Maryam Kafi Kang; Sagi Snir; Benjamin J. Raphael; Pavel Skums
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errSave
Anomaly detection in spatial transcriptomics via spatially localized density comparison
errBIOINFORMATICS
IF5.4
err2025-07-01
err0
errOAAI
errHu, Gary; Gold, Julian; Chitra, Uthsav; Joshi, Sunay; Raphael, Benjamin J.
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errSave
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts
errBIOINFORMATICS
IF5.4
err2025-07-01
err0
errOAAI
errChitra, Uthsav; Dan, Shu; Krienen, Fenna; Raphael, Benjamin J.
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errSave
Fast tumor phylogeny regression via tree-structured dual dynamic programming
errBIOINFORMATICS
IF5.4
err2025-07-01
err0
errOAAI
errSchmidt, Henri; Qi, Yuanyuan; Raphael, Benjamin J.; El-Kebir, Mohammed
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DeST-OT: Alignment of spatiotemporal transcriptomics data
errCELL SYSTEMS
IF7.7
err2025-02-01
err0
PREAI
errHalmos, Peter; Liu, Xinhao; Gold, Julian; Chen, Feng; Ding, Li; Raphael, Benjamin J.
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errSave
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
errNATURE METHODS
IF32.1
err2024-10-30
err0
errOAAI
errMa, Cong; Balaban, Metin; Liu, Jingxian; Chen, Siqi; Wilson, Michael J.; Sun, Christopher H.; Ding, Li; Raphael, Benjamin J.
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errSave
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data
errGENOME BIOLOGY
IF9.4
err2024-05-21
err1
errOAAI
errMyers, Matthew A.; Arnold, Brian J.; Bansal, Vineet; Balaban, Metin; Mullen, Katelyn M.; Zaccaria, Simone; Raphael, Benjamin J.
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errSave
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
errCANCER RESEARCH
IF16.6
err2024-03-22
err0
PREAI
errMa, Cong; Balaban, Metin; Liu, Jingxian; Chen, Siqi; Ding, Li; Raphael, Benjamin J.
errShare
errSave
A refined view of pancreatic cancer genomic evolution through single-nucleus DNA sequencing
errCANCER RESEARCH
IF16.6
err2024-03-22
err0
PREAI
errZhang, Haochen; Sashittal, Palash; Karnoub, Elias-Ramzey; Jakatdar, Akhil; Umeda, Shigeaki; Lecomte, Nicolas; Hong, Jungeui; Mullen, Katelyn; Hayashi, Akimasa; McIntyre, Caitlin A.; Raphael, Benjamin J.; Iacobuzio-Donahue, Christine A.
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errSave
Genomic evolution of pancreatic cancer at single-cell resolution
errCANCER RESEARCH
IF16.6
err2024-01-16
err0
PREAI
errZhang, Haochen; Sashittal, Palash; Karnoub, Elias-Ramzey; Umeda, Shigeaki; Lecomte, Nicolas; Hong, Jungeui; Jakatdar, Akhil; Mullen, Katelyn; Hayashi, Akimasa; McIntyre, Caitlin A.; Raphael, Benjamin J.; Iacobuzio-Donahue, Christine A.
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errSave
Startle: A star homoplasy approach for CRISPR-Cas9 lineage tracing
errCELL SYSTEMS
IF7.7
err2023-12-01
err6
errOAAI
errSashittal, Palash; Schmidt, Henri; Chan, Michelle; Raphael, Benjamin J.
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errSave
ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model
errGENOME BIOLOGY
IF9.4
err2023-11-30
err3
errOAAI
errSashittal, Palash; Zhang, Haochen; Iacobuzio-Donahue, Christine A.; Raphael, Benjamin J.
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errSave
Co-evolution of AR gene copy number and structural complexity in endocrine therapy resistant prostate cancer
errNAR CANCER
IF3.2
err2023-08-24
err12
errOAAI
errZivanovic, Andrej; Miller, Jeffrey T.; Munro, Sarah A.; Knutson, Todd P.; Li, Yingming; Passow, Courtney N.; Simonaitis, Pijus; Lynch, Molly; Oseth, Leann; Zhao, Shuang G.; Feng, Felix Y.; Wikstrom, Pernilla; Corey, Eva; Morrissey, Colm; Henzler, Christine; Raphael, Benjamin J.; Dehm, Scott M.
errShare
errSave
Genomic evolution of pancreatic cancer at single-cell resolution
errCANCER RESEARCH
IF16.6
err2023-04-04
err0
PREAI
errZhang, Haochen; Sashittal, Palash; Karnoub, Elias-Ramzey; Raphael, Benjamin J.; Iacobuzio-Donahue, Christine A.
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errSave
Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics
errCELL SYSTEMS
IF7.7
err2022-10-01
err7
errOAAI
errMa, Cong; Chitra, Uthsav; Zhang, Shirley; Raphael, Benjamin J.
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errSave
Convergent evolution and multi-wave clonal invasion in H3 K27-altered diffuse midline gliomas treated with a PDGFR inhibitor
errACTA NEUROPATHOLOGICA COMMUNICATIONS
IF5.7
err2022-05-31
err6
errOAAI
errArunachalam, Sasi; Szlachta, Karol; Brady, Samuel W.; Ma, Xiaotu; Ju, Bensheng; Shaner, Bridget; Mulder, Heather L.; Easton, John; Raphael, Benjamin J.; Myers, Matthew; Tinkle, Christopher; Allen, Sariah J.; Orr, Brent A.; Wetmore, Cynthia J.; Baker, Suzanne J.; Zhang, Jinghui
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errSave

Research Directions

No research directions
Co-authors
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