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Benjamin J Raphael

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2018-2023
Publications (10 Years): 32

Top Venues

bioRxiv : the preprint server for biology

Nature communications

Genome research

Journal of computational biology : a journal of computational molecular cell biology

Princeton University

University of California San Diego (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Princeton University Sep 1o 2016

United States

Professor :: Computer Science

Education History

University of California San Diego

United States

PHD :: Mathematics

Publications

Uthsav Chitra, Brian J Arnold, Hirak Sarkar, Cong Ma, Sereno Lopez-Darwin, Kohei Sanno, Benjamin J Raphael
Mapping the topography of spatial gene expression with interpretable deep learning. bioRxiv : the preprint server for biology (2023)
Palash Sashittal, Haochen Zhang, Christine A Iacobuzio-Donahue, Benjamin J Raphael
ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model. bioRxiv : the preprint server for biology (2023)
Henri Schmidt, Palash Sashittal, Benjamin J Raphael
A zero-agnostic model for copy number evolution in cancer. bioRxiv : the preprint server for biology (2023)
Henri Schmidt, Palash Sashittal, Benjamin J Raphael
A zero-agnostic model for copy number evolution in cancer. bioRxiv : the preprint server for biology (2023)
Xinhao Liu, Ron Zeira, Benjamin J Raphael
Partial alignment of multislice spatially resolved transcriptomics data. Genome research (2023)
Matthew A Myers, Brian J Arnold, Vineet Bansal, Katelyn M Mullen, Simone Zaccaria, Benjamin J Raphael
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data. bioRxiv : the preprint server for biology (2023)
Di Zhang, Yanxiang Deng, Petra Kukanja, Eneritz Agirre, Marek Bartosovic, Mingze Dong, Cong Ma, Sai Ma, Graham Su, Shuozhen Bao, Yang Liu, Yang Xiao, Gorazd B Rosoklija, Andrew J Dwork, Robyn S Klein, Kam W Leong, Maura Boldrini, Liya Wang, Maximilian Haeussler, Benjamin J Raphael, Yuval Kluger, Gonçalo Castelo-Branco, Rong Fan
Spatial epigenome-transcriptome co-profiling of mammalian tissues. Nature (2023)
Xinhao Liu, Ron Zeira, Benjamin J Raphael
PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data. bioRxiv : the preprint server for biology (2023)
Henri Schmidt, Palash Sashittal, Benjamin J Raphael
A zero-agnostic model for copy number evolution in cancer. PLoS computational biology 19 (11) (2023)
Nadezhda V Terekhanova, Alla Karpova, Wen-Wei Liang, Alexander Strzalkowski, Siqi Chen, Yize Li, Austin N Southard-Smith, Michael D Iglesia, Michael C Wendl, Reyka G Jayasinghe, Jingxian Liu, Yizhe Song, Song Cao, Andrew Houston, Xiuting Liu, Matthew A Wyczalkowski, Rita Jui-Hsien Lu, Wagma Caravan, Andrew Shinkle, Nataly Naser Al Deen, John M Herndon, Jacqueline Mudd, Cong Ma, Hirak Sarkar, Kazuhito Sato, Omar M Ibrahim, Chia-Kuei Mo, Sara E Chasnoff, Eduard Porta-Pardo, Jason M Held, Russell Pachynski, Julie K Schwarz, William E Gillanders, Albert H Kim, Ravi Vij, John F Dipersio, Sidharth V Puram, Milan G Chheda, Katherine C Fuh, David G DeNardo, Ryan C Fields, Feng Chen, Benjamin J Raphael, Li Ding
Epigenetic regulation during cancer transitions across 11 tumour types. Nature (2023)
Palash Sashittal, Haochen Zhang, Christine A Iacobuzio-Donahue, Benjamin J Raphael
ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model. bioRxiv : the preprint server for biology (2023)
Palash Sashittal, Haochen Zhang, Christine A Iacobuzio-Donahue, Benjamin J Raphael
ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model. bioRxiv : the preprint server for biology (2023)
Henri Schmidt, Palash Sashittal, Benjamin J Raphael
A zero-agnostic model for copy number evolution in cancer. bioRxiv : the preprint server for biology (2023)
Sanjana Rajan, Simone Zaccaria, Matthew V Cannon, Maren Cam, Amy C Gross, Benjamin J Raphael, Ryan D Roberts
Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time. Cancer research communications 3 (4) (2023)
Xinhao Liu, Ron Zeira, Benjamin J Raphael
PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data. bioRxiv : the preprint server for biology (2023)
Henri Schmidt, Palash Sashittal, Benjamin J Raphael
A zero-agnostic model for copy number evolution in cancer. bioRxiv : the preprint server for biology (2023)
Palash Sashittal, Haochen Zhang, Christine A Iacobuzio-Donahue, Benjamin J Raphael
ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model. Genome biology 24 (1) (2023)
Xinhao Liu, Ron Zeira, Benjamin J Raphael
PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data. bioRxiv : the preprint server for biology (2023)
Ron Zeira, Max Land, Alexander Strzalkowski, Benjamin J Raphael
Alignment and integration of spatial transcriptomics data. Nature methods 19 (5) (2022)
Hua Sun, Song Cao, R Jay Mashl, Chia-Kuei Mo, Simone Zaccaria, Michael C Wendl, Sherri R Davies, Matthew H Bailey, Tina M Primeau, Jeremy Hoog, Jacqueline L Mudd, Dennis A Dean, Rajesh Patidar, Li Chen, Matthew A Wyczalkowski, Reyka G Jayasinghe, Fernanda Martins Rodrigues, Nadezhda V Terekhanova, Yize Li, Kian-Huat Lim, Andrea Wang-Gillam, Brian Andrew Van Tine, Cynthia X Ma, Rebecca Aft, Katherine C Fuh, Julie K Schwarz, Jose P Zevallos, Sidharth V Puram, John F Dipersio, null null, Brandi Davis-Dusenbery, Matthew J Ellis, Michael T Lewis, Michael A Davies, Meenhard Herlyn, Bingliang Fang, Jack A Roth, Alana L Welm, Bryan E Welm, Funda Meric-Bernstam, Feng Chen, Ryan C Fields, Shunqiang Li, Ramaswamy Govindan, James H Doroshow, Jeffrey A Moscow, Yvonne A Evrard, Jeffrey H Chuang, Benjamin J Raphael, Li Ding
Author Correction: Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment. Nature communications 13 (1) (2022)
Uthsav Chitra, Tae Yoon Park, Benjamin J Raphael
NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks. Journal of computational biology : a journal of computational molecular cell biology 29 (12) (2022)
Uthsav Chitra, Tae Yoon Park, Benjamin J Raphael
NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks. Journal of computational biology : a journal of computational molecular cell biology 29 (12) (2022)
Matthew A Reyna, David Haan, Marta Paczkowska, Lieven P C Verbeke, Miguel Vazquez, Alexandre Thiéry, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad A Getz, Michael S Lawrence, Jakob Skou Pedersen, Mark A Rubin, David A Wheeler, Søren Brunak, Jose M G Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S Cenk Sahinalp, Alfonso Valencia, null null, Jüri Reimand, Joshua M Stuart, Benjamin J Raphael, null null
Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes. Nature communications 13 (1) (2022)
Uthsav Chitra, Tae Yoon Park, Benjamin J Raphael
NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks. Journal of computational biology : a journal of computational molecular cell biology 29 (12) (2022)
Hua Sun, Song Cao, R Jay Mashl, Chia-Kuei Mo, Simone Zaccaria, Michael C Wendl, Sherri R Davies, Matthew H Bailey, Tina M Primeau, Jeremy Hoog, Jacqueline L Mudd, Dennis A Dean, Rajesh Patidar, Li Chen, Matthew A Wyczalkowski, Reyka G Jayasinghe, Fernanda Martins Rodrigues, Nadezhda V Terekhanova, Yize Li, Kian-Huat Lim, Andrea Wang-Gillam, Brian Andrew Van Tine, Cynthia X Ma, Rebecca Aft, Katherine C Fuh, Julie K Schwarz, Jose P Zevallos, Sidharth V Puram, John F Dipersio, null null, Brandi Davis-Dusenbery, Matthew J Ellis, Michael T Lewis, Michael A Davies, Meenhard Herlyn, Bingliang Fang, Jack A Roth, Alana L Welm, Bryan E Welm, Funda Meric-Bernstam, Feng Chen, Ryan C Fields, Shunqiang Li, Ramaswamy Govindan, James H Doroshow, Jeffrey A Moscow, Yvonne A Evrard, Jeffrey H Chuang, Benjamin J Raphael, Li Ding
Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. Nature communications 12 (1) (2021)
Rebecca Elyanow, Bianca Dumitrascu, Barbara Elizabeth Engelhardt, Benjamin J Raphael
netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysis. Genome research 30 (2) (2020)
Sergey Aganezov, Benjamin J Raphael
Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples. Genome research 30 (9) (2020)
Simone Zaccaria, Benjamin J Raphael
Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL. Nature biotechnology 39 (2) (2020)
Simone Zaccaria, Benjamin J Raphael
Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. Nature communications 11 (1) (2020)
Matthew A Reyna, David Haan, Marta Paczkowska, Lieven P C Verbeke, Miguel Vazquez, Alexandre Thiéry, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad A Getz, Michael S Lawrence, Jakob Skou Pedersen, Mark A Rubin, David A Wheeler, Søren Brunak, Jose M G Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S Cenk Sahinalp, Alfonso Valencia, null null, Jüri Reimand, Joshua M Stuart, Benjamin J Raphael, null null
Pathway and network analysis of more than 2500 whole cancer genomes. Nature communications 11 (1) (2020)
Samuel W Brady, Xiaotu Ma, Armita Bahrami, Gryte Satas, Gang Wu, Scott Newman, Michael C Rusch, Daniel K Putnam, Heather L Mulder, Donald A Yergeau, Michael N Edmonson, John Easton, Ludmil B Alexandrov, Xiang Chen, Elaine R Mardis, Richard K Wilson, James R Downing, Alberto S Pappo, Benjamin J Raphael, Michael A Dyer, Jinghui Zhang
The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment. Molecular cancer research : MCR 17 (4) (2019)
Mohammed El-Kebir, Gryte Satas, Benjamin J Raphael
Inferring parsimonious migration histories for metastatic cancers. Nature genetics 50 (5) (2018)

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Publication Activity (10 Years)

Top Topics

Top Venues

Benjamin J Raphael