Raphael, Benjamin J.

Mutational landscape and significance across 12 major cancer types

Kandoth, C., McLellan, M. D., Vandin, F., Ye, K., Niu, B., Lu, C., Xie, M., Zhang, Q., McMichael, J. F., Wyczalkowski, M. A., et al. (2013) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 4,419

The repertoire of mutational signatures in human cancer

Alexandrov, L. B., Kim, J., Haradhvala, N. J., Huang, M. N., Tian Ng, A. W., Wu, Y., Boot, A., Covington, K. R., Gordenin, D. A., Bergstrom, E. N., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,496

Pan-cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,064

The mutational landscape of lethal castration-resistant prostate cancer

Grasso, C. S., Wu, Y.-M., Robinson, D. R., Cao, X., Dhanasekaran, S. M., Khan, A. P., Quist, M. J., Jing, X., Lonigro, R. J., Brenner, J. C., et al. (2012) · Nature

Prostate Cancer Treatment and ResearchCancer Genomics and Diagnostics

Cited by 2,517

Integrated genomic characterization of pancreatic ductal adenocarcinoma

Raphael, B. J., Hruban, R. H., Aguirre, A. J., Moffitt, R. A., Yeh, J. J., Stewart, C., Robertson, A. G., Cherniack, A. D., Gupta, M., Getz, G., et al. (2017) · Cancer Cell

Pancreatic and Hepatic Oncology ResearchCancer Genomics and Diagnostics

Cited by 2,019

Eleven grand challenges in single-cell data science

Lähnemann, D., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., Vallejos, C. A., Campbell, K. R., Beerenwinkel, N., Mahfouz, A., et al. (2020) · Genome Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,327

Patterns of somatic structural variation in human cancer genomes

Li, Y., Roberts, N. D., Wala, J. A., Shapira, O., Schumacher, S. E., Kumar, K., Khurana, E., Waszak, S., Korbel, J. O., Haber, J. E., et al. (2020) · Nature

Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

Cited by 867

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Cortés-Ciriano, I., Lee, J. J.-K., Xi, R., Jain, D., Jung, Y. L., Yang, L., Gordenin, D., Klimczak, L. J., Zhang, C.-Z., Pellman, D. S., et al. (2020) · Nature Genetics

Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

Cited by 712

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

Dentro, S. C., Leshchiner, I., Haase, K., Tarabichi, M., Wintersinger, J., Deshwar, A. G., Yu, K., Rubanova, Y., Macintyre, G., Demeulemeester, J., et al. (2021) · Cell

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 533

Spatial epigenome–transcriptome co-profiling of mammalian tissues

Zhang, D., Deng, Y., Kukanja, P., Agirre, E., Bartosovic, M., Dong, M., Ma, C., Ma, S., Su, G., Bao, S., et al. (2023) · Nature

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 483

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Rodriguez-Martin, B., Alvarez, E. G., Baez-Ortega, A., Zamora, J., Supek, F., Demeulemeester, J., Santamarina, M., Ju, Y. S., Temes, J., Garcia-Souto, D., et al. (2020) · Nature Genetics

Genomic variations and chromosomal abnormalitiesCancer Genomics and Diagnostics

Cited by 451

Alignment and integration of spatial transcriptomics data

Zeira, R., Land, M., Strzalkowski, A., & Raphael, B. J. (2022) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 298

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Akdemir, K. C., Le, V. T., Chandran, S., Li, Y., Verhaak, R. G., Beroukhim, R., Campbell, P. J., Chin, L., Dixon, J. R., Futreal, P. A., et al. (2020) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 283

Visible Machine Learning for Biomedicine

Yu, M. K., Ma, J., Fisher, J., Kreisberg, J. F., Raphael, B. J., & Ideker, T. (2018) · Cell

Machine Learning in HealthcareExplainable Artificial Intelligence (XAI)

Cited by 162

A weighted exact test for mutually exclusive mutations in cancer

Leiserson, M. D., Reyna, M. A., & Raphael, B. J. (2016) · Bioinformatics

Cancer Genomics and DiagnosticsGenomics and Phylogenetic Studies

Cited by 56

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

Rajan, S., Zaccaria, S., Cannon, M. V., Cam, M., Gross, A. C., Raphael, B. J., & Roberts, R. D. (2021) · Cancer Research Communications

Cancer Genomics and DiagnosticsSarcoma Diagnosis and Treatment

Cited by 33

Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics

Ma, C., Chitra, U., Zhang, S., & Raphael, B. J. (2022) · Cell Systems

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 27