Benjamin J. Raphael

68.3k total citations · 3 hit papers
127 papers, 8.9k citations indexed

About

Benjamin J. Raphael is a scholar working on Molecular Biology, Cancer Research and Genetics. According to data from OpenAlex, Benjamin J. Raphael has authored 127 papers receiving a total of 8.9k indexed citations (citations by other indexed papers that have themselves been cited), including 94 papers in Molecular Biology, 60 papers in Cancer Research and 55 papers in Genetics. Recurrent topics in Benjamin J. Raphael's work include Cancer Genomics and Diagnostics (58 papers), Genomics and Phylogenetic Studies (33 papers) and Genomic variations and chromosomal abnormalities (29 papers). Benjamin J. Raphael is often cited by papers focused on Cancer Genomics and Diagnostics (58 papers), Genomics and Phylogenetic Studies (33 papers) and Genomic variations and chromosomal abnormalities (29 papers). Benjamin J. Raphael collaborates with scholars based in United States, United Kingdom and Israel. Benjamin J. Raphael's co-authors include Fabio Vandin, Mark D.M. Leiserson, Li Ding, Eli Upfal, Michael C. Wendl, Beifang Niu, Joshua F. McMichael, Michael D. McLellan, Layla Oesper and Matthew A. Wyczalkowski and has published in prestigious journals such as Nature, Cell and Proceedings of the National Academy of Sciences.

In The Last Decade

Benjamin J. Raphael

123 papers receiving 8.8k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

Mutational landscape and significance across 12 major cancer types

2013 3.1k citations Benjamin J. Raphael, Li Ding et al. profile →
Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

2014 588 citations Hsin-Ta Wu, Li Ding et al. Nature Genetics profile →
Network propagation: a universal amplifier of genetic associations

2017 400 citations Benjamin J. Raphael et al. profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
Benjamin J. Raphael United States	40	6.5k	3.5k	1.8k	1.5k	840	127	8.9k
Núria López-Bigas Spain	52	7.4k 1.1×	3.6k 1.0×	1.8k 1.0×	1.6k 1.0×	827 1.0×	125	10.5k
Matthew J. Marton United States	18	7.5k 1.1×	2.8k 0.8×	1.4k 0.8×	2.5k 1.6×	532 0.6×	45	10.6k
Yudong D. He United States	27	6.8k 1.0×	3.2k 0.9×	1.3k 0.7×	2.8k 1.8×	576 0.7×	49	10.6k
Hongyue Dai United States	34	9.3k 1.4×	4.4k 1.3×	1.5k 0.8×	3.4k 2.2×	806 1.0×	66	14.2k
Eivind Hovig Norway	46	6.0k 0.9×	2.3k 0.7×	1.1k 0.6×	2.2k 1.4×	568 0.7×	218	8.9k
Joshua M. Stuart United States	40	9.8k 1.5×	3.5k 1.0×	1.3k 0.8×	1.7k 1.1×	544 0.6×	108	13.6k
Sally Bamford United Kingdom	12	5.6k 0.9×	3.1k 0.9×	1.3k 0.7×	2.1k 1.3×	1.1k 1.3×	19	8.1k
Abel González-Pérez Spain	31	4.5k 0.7×	3.0k 0.8×	1.3k 0.7×	1.1k 0.7×	686 0.8×	71	6.5k
Chai Yin Kok United Kingdom	10	4.4k 0.7×	2.4k 0.7×	972 0.6×	1.6k 1.0×	787 0.9×	14	6.5k
Richard Wooster United Kingdom	36	6.4k 1.0×	2.9k 0.8×	2.9k 1.6×	2.6k 1.7×	1.6k 1.9×	62	9.6k

Countries citing papers authored by Benjamin J. Raphael

Since Specialization

Citations

This map shows the geographic impact of Benjamin J. Raphael's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Benjamin J. Raphael with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Benjamin J. Raphael more than expected).

Fields of papers citing papers by Benjamin J. Raphael

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Benjamin J. Raphael. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Benjamin J. Raphael. The network helps show where Benjamin J. Raphael may publish in the future.

Co-authorship network of co-authors of Benjamin J. Raphael

This figure shows the co-authorship network connecting the top 25 collaborators of Benjamin J. Raphael. A scholar is included among the top collaborators of Benjamin J. Raphael based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Benjamin J. Raphael. Benjamin J. Raphael is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

Liu, Xinhao, et al.. (2025). DeST-OT: Alignment of spatiotemporal transcriptomics data. Cell Systems. 16(2). 101160–101160. 4 indexed citations

Schmidt, Henri, et al.. (2025). Fast tumor phylogeny regression via tree-structured dual dynamic programming. Bioinformatics. 41(Supplement_1). i170–i179.

Gold, Julian, et al.. (2024). A count-based model for delineating cell–cell interactions in spatial transcriptomics data. Bioinformatics. 40(Supplement_1). i481–i489. 1 indexed citations

Ma, Cong, Metin Balaban, Jingxian Liu, et al.. (2024). Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics. Nature Methods. 21(12). 2239–2247. 6 indexed citations

Schmidt, Henri & Benjamin J. Raphael. (2024). A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors. PLoS Computational Biology. 20(12). e1012631–e1012631. 2 indexed citations

Schmidt, Henri, et al.. (2023). Startle: A star homoplasy approach for CRISPR-Cas9 lineage tracing. Cell Systems. 14(12). 1113–1121.e9. 14 indexed citations

Zaccaria, Simone, Matthew V. Cannon, Maren Cam, et al.. (2023). Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time. Cancer Research Communications. 3(4). 564–575. 17 indexed citations

Schmidt, Henri, et al.. (2023). A zero-agnostic model for copy number evolution in cancer. PLoS Computational Biology. 19(11). e1011590–e1011590. 6 indexed citations

Park, Tae Yoon, et al.. (2022). NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks. Journal of Computational Biology. 29(12). 1305–1323. 3 indexed citations

10.

Zeira, Ron, et al.. (2021). Genome Halving and Aliquoting Under the Copy Number Distance. DROPS (Schloss Dagstuhl – Leibniz Center for Informatics). 25. 2 indexed citations

11.

Aganezov, Sergey & Benjamin J. Raphael. (2020). Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples. Genome Research. 30(9). 1274–1290. 8 indexed citations

12.

Zaccaria, Simone & Benjamin J. Raphael. (2020). Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. Nature Communications. 11(1). 4301–4301. 53 indexed citations

13.

Elyanow, Rebecca, Ron Zeira, Max Land, & Benjamin J. Raphael. (2020). STARCH: copy number and clone inference from spatial transcriptomics data. Physical Biology. 18(3). 35001–35001. 26 indexed citations

14.

Myers, Matthew, Simone Zaccaria, & Benjamin J. Raphael. (2020). Identifying tumor clones in sparse single-cell mutation data. Bioinformatics. 36(Supplement_1). i186–i193. 14 indexed citations

15.

El-Kebir, Mohammed, Gryte Satas, & Benjamin J. Raphael. (2018). Inferring parsimonious migration histories for metastatic cancers. Nature Genetics. 50(5). 718–726. 2 indexed citations

16.

Nakka, Priyanka, Natalie P. Archer, Heng Xu, et al.. (2017). Novel Gene and Network Associations Found for Acute Lymphoblastic Leukemia Using Case–Control and Family-Based Studies in Multiethnic Populations. Cancer Epidemiology Biomarkers & Prevention. 26(10). 1531–1539. 4 indexed citations

17.

Oesper, Layla, Simone Dantas, & Benjamin J. Raphael. (2017). Identifying simultaneous rearrangements in cancer genomes. Bioinformatics. 34(2). 346–352. 4 indexed citations

18.

Elyanow, Rebecca, Hsin-Ta Wu, & Benjamin J. Raphael. (2017). Identifying structural variants using linked-read sequencing data. Bioinformatics. 34(2). 353–360. 51 indexed citations

19.

Raphael, Benjamin J., et al.. (2012). Algorithms in Bioinformatics. Lecture notes in computer science. 7 indexed citations

20.

Raphael, Benjamin J. & Pavel A. Pevzner. (2004). Reconstructing tumor amplisomes. Bioinformatics. 20(suppl_1). i265–i273. 23 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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