Benjamin J. Raphael

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 5%percentile

0.396Author DataRank

Indexed papers

4in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 4 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction

Nature Biotechnology(2024)10.1038/s41587-024-02250-y

Top 46%

0.396DataRank

Top 46%13 citations

Maxime Tarabichi, Alex Buchanan, Shadrielle M. G. Espiritu, Hongjiu Zhang, Kaiyi Zhu +83 more

Papers

Driven by 42 papers — median percentile 54. Top paper: “De novo discovery of mutated driver pathways in cancer”.

De novo discovery of mutated driver pathways in cancer

Genome Research(2012)10.1101/gr.120477.111

N/A

12.0DataRank · unranked

459 citations

Eli Upfal, Benjamin J. Raphael, Fabio Vandin

Simultaneous Identification of Multiple Driver Pathways in Cancer

PLoS Computational Biology(2013)10.1371/journal.pcbi.1003054

N/A

8.7DataRank · unranked

255 citations

Dima Blokh, Roded Sharan, Benjamin J. Raphael, Mark D. M. Leiserson

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

Cell(2021)10.1016/j.cell.2021.03.009

N/A

7.3DataRank · unranked

560 citations

Ignaty Leshchiner, Kerstin Haase, Maxime Tarabichi, Jeff Wintersinger, Amit G. Deshwar +64 more

Spatial epigenome–transcriptome co-profiling of mammalian tissues

Nature(2023)10.1038/s41586-023-05795-1

N/A

7.1DataRank · unranked

452 citations

Yanxiang Deng, Petra Kukanja, Eneritz Agirre, Marek Bartošovič, Mingze Dong +18 more

netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis

Genome Research(2020)10.1101/gr.251603.119

N/A

3.5DataRank · unranked

121 citations

Bianca Dumitrascu, Barbara E. Engelhardt, Benjamin J. Raphael, Rebecca Elyanow

Current and future directions in network biology

Bioinformatics Advances(2024)10.1093/bioadv/vbae099

N/A

1.6DataRank · unranked

100 citations

Michelle M. Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Krishnan, Arjun +32 more

The mutational landscape of lethal castration-resistant prostate cancer

Nature(2012)10.1038/nature11125

N/A

1.2DataRank · unranked

2601 citations

Yi-Mi Wu, Dan R. Robinson, Xuhong Cao, Saravana M. Dhanasekaran, Amjad P. Khan +22 more

Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway

Cell Reports(2021)10.1016/j.celrep.2021.108707

N/A

1.1DataRank · unranked

32 citations

Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S. Damrauer, Tiago C. Silva +77 more

The evolutionary history of 2,658 cancers

Nature(2020)10.1038/s41586-019-1907-7

N/A

1.1DataRank · unranked

1106 citations

Clemency Jolly, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Daniel Rosebrock +59 more

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

Nature Methods(2024)10.1038/s41592-024-02438-9

N/A

1.0DataRank · unranked

29 citations

Metin Balaban, Jingxian Liu, Siqi Chen, Michael J. Wilson, Christopher H. Sun +3 more

Epigenetic regulation during cancer transitions across 11 tumour types

Nature(2023)10.1038/s41586-023-06682-5

N/A

0.803DataRank · unranked

211 citations

Alla Y. Karpova, Wen-Wei Liang, Alexander Strzalkowski, Siqi Chen, Yize Li +39 more

Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data

Nature Communications(2020)10.1038/s41467-020-17967-y

N/A

0.740DataRank · unranked

138 citations

Benjamin J. Raphael, Simone Zaccaria

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

Cancer Cell(2022)10.1016/j.ccell.2022.09.017

N/A

0.633DataRank · unranked

67 citations

Margarida Barroso, Milan G. Chheda, Hans Clevers, Élena Elez, Salma Kaochar +21 more

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

Cancer Research Communications(2023)10.1158/2767-9764.crc-22-0348

N/A

0.524DataRank · unranked

32 citations

Simone Zaccaria, Matthew V. Cannon, Maren Cam, Amy C. Gross, Benjamin J. Raphael +2 more

Co-evolution of AR gene copy number and structural complexity in endocrine therapy resistant prostate cancer

NAR Cancer(2023)10.1093/narcan/zcad045

N/A

0.510DataRank · unranked

29 citations

Jeffrey T. Miller, Sarah A. Munro, Todd P. Knutson, Yingming Li, Courtney N. Passow +12 more

The Evolutionary Forest of Pancreatic Cancer

Cancer Discovery(2024)10.1158/2159-8290.cd-23-1541

N/A

0.494DataRank · unranked

26 citations

Jungeui Hong, Marc A. Attiyeh, Akimasa Hayashi, Hitomi Sakamoto, Zachary A. Kohutek +14 more

Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.08.30.458268

N/A

0.406DataRank · unranked

7 citations

Simone Zaccaria, Matthew V. Cannon, Maren Cam, Amy C. Gross, Benjamin J. Raphael +2 more

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

Genome biology(2025)10.1186/s13059-025-03649-9

N/A

0.396DataRank · unranked

13 citations

Uyen Mai, Henri Schmidt, Benjamin J. Raphael, Gillian Chu

Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction

Nature Biotechnology(2024)10.1038/s41587-024-02250-y

Top 46%

0.396DataRank

Top 46%13 citations

Maxime Tarabichi, Alex Buchanan, Shadrielle M. G. Espiritu, Hongjiu Zhang, Kaiyi Zhu +83 more

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

Genome biology(2024)10.1186/s13059-024-03267-x

N/A

0.373DataRank · unranked

11 citations

Brian J. Arnold, Vineet Bansal, Metin Balaban, Katelyn M. Mullen, Simone Zaccaria +2 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.09.584244

N/A

0.262DataRank · unranked

3 citations

Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael +1 more

DeST-OT: Alignment of Spatiotemporal Transcriptomics Data

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.05.583575

N/A

0.241DataRank · unranked

4 citations

Xinhao Liu, Julian Gold, Feng Chen, Li Ding, Benjamin J. Raphael +1 more

Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data

Bioinformatics(2024)10.1093/bioinformatics/btae231

N/A

0.208DataRank · unranked

3 citations

V W Chen, Amey P. Pasarkar, Benjamin J. Raphael, Palash Sashittal

Current and future directions in network biology

arXiv (Cornell University)(2023)10.48550/arxiv.2309.08478

N/A

0.208DataRank · unranked

3 citations

Michelle M. Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Krishnan, Arjun +32 more

NetMix: A network-structured mixture model for reduced-bias estimation of altered subnetworks

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.18.911438

N/A

0DataRank · unranked

6 citations

Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael, Matthew A. Reyna

Inferring cell differentiation maps from lineage tracing data

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.09.611835

N/A

0DataRank · unranked

8 citations

Richard Zhang, Benjamin K. Law, Alexander Strzalkowski, Henri Schmidt, Adriano Bolondi +3 more

A latent variable model for evaluating mutual exclusivity and co-occurrence between driver mutations in cancer

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.24.590995

N/A

0DataRank · unranked

1 citations

Uthsav Chitra, Benjamin J. Raphael, Ahmed Shuaibi

DeST-OT: Alignment of spatiotemporal transcriptomics data

Cell Systems(2025)10.1016/j.cels.2024.12.001

N/A

0DataRank · unranked

17 citations

Xinhao Liu, Julian Gold, Feng Chen, Li Ding, Benjamin J. Raphael +1 more

Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.02.14.638351

N/A

0DataRank · unranked

2 citations

Julian Gold, Xinhao Liu, Benjamin J. Raphael, Peter Halmos

Informatics at the Frontier of Cancer Research

Cancer Research(2025)10.1158/0008-5472.can-24-2829

N/A

0DataRank · unranked

0 citations

Taxiarchis Botsis, Pablo G. Cámara, Lauren Ciotti, Lee Cooper, Jeremy Goecks +19 more

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

medRxiv(2025)10.1101/2025.07.01.25330467

N/A

0DataRank · unranked

0 citations

Alexander Martinez‐Fundichely, Sandra Cohen, Metin Balaban, Chen Khuan Wong, Weiling Li +26 more

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples

Genome Research(2020)10.1101/gr.256701.119

N/A

0DataRank · unranked

20 citations

Benjamin J. Raphael, Sergey Aganezov

Copy number evolution with weighted aberrations in cancer

Bioinformatics(2020)10.1093/bioinformatics/btaa470

N/A

0DataRank · unranked

21 citations

Benjamin J. Raphael, Ron Zeira

The Integrated Genomic Landscape of Thymic Epithelial Tumors

UNC Libraries(2021)10.17615/v61n-cs39

N/A

0DataRank · unranked

0 citations

Mirella Marino, Jiabin Huang, Ming-Sound Tsao, J. Zhang, Hyun Jung Jo +43 more

SCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses

Cell Systems(2020)10.1016/j.cels.2020.04.001

N/A

0DataRank · unranked

113 citations

Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael, Gryte Satas

Startle: A star homoplasy approach for CRISPR-Cas9 lineage tracing

Cell Systems(2023)10.1016/j.cels.2023.11.005

N/A

0DataRank · unranked

38 citations

Henri Schmidt, Michelle M. Chan, Benjamin J. Raphael, Palash Sashittal

ConDoR: tumor phylogeny inference with a copy-number constrained mutation loss model

Genome biology(2023)10.1186/s13059-023-03106-5

N/A

0DataRank · unranked

29 citations

Haochen Zhang, Christine A. Iacobuzio–Donahue, Benjamin J. Raphael, Palash Sashittal

DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution

Cell Systems(2021)10.1016/j.cels.2021.07.006

N/A

0DataRank · unranked

39 citations

Simone Zaccaria, Mohammed El-Kebir, Benjamin J. Raphael, Gryte Satas

ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.05.522408

N/A

0DataRank · unranked

6 citations

Haochen Zhang, Christine A. Iacobuzio–Donahue, Benjamin J. Raphael, Palash Sashittal

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.13.548855

N/A

0DataRank · unranked

6 citations

Brian J. Arnold, Vineet Bansal, Katelyn M. Mullen, Simone Zaccaria, Benjamin J. Raphael +1 more

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

(2023)10.1158/2767-9764.c.6551261.v2

N/A

0DataRank · unranked

0 citations

Simone Zaccaria, Matthew V. Cannon, Maren Cam, Amy C. Gross, Benjamin J. Raphael +2 more

Integrating genetic dependencies and genomic alterations across pathways and cancer types

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.13.184697

N/A

0DataRank · unranked

0 citations

Mark D.M. Leiserson, Gunnar W. Klau, Benjamin J. Raphael, Tae Yoon Park

Benjamin J. Raphael

Indexed papers

Top data-sharing exemplar

Papers