Reis-Filho, Jorge S.

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 evolutionary history of 2,658 cancers

Gerstung, M., Jolly, C., Leshchiner, I., Dentro, S. C., Gonzalez, S., Rosebrock, D., Mitchell, T. J., Rubanova, Y., Anur, P., Yu, K., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 1,057

Resistance to therapy caused by intragenic deletion in BRCA2

Edwards, S. L., Brough, R., Lord, C. J., Natrajan, R., Vatcheva, R., Levine, D. A., Boyd, J., Reis-Filho, J. S., & Ashworth, A. (2008) · Nature

PARP inhibition in cancer therapyBRCA gene mutations in cancer

Cited by 1,011

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

ESMO recommendations on the use of circulating tumour DNA assays for patients with cancer: A report from the ESMO Precision Medicine Working Group

Pascual, J., Attard, G., Bidard, F.-C., Curigliano, G., De Mattos-Arruda, L., Diehn, M., Italiano, A., Lindberg, J., Merker, J. D., Montagut, C., et al. (2022) · Annals of Oncology

Cancer Genomics and DiagnosticsBRCA gene mutations in cancer

Cited by 783

Pathogenesis of Triple-Negative Breast Cancer

Derakhshan, F., & Reis-Filho, J. S. (2022) · Annual Review of Pathology: Mechanisms of Disease

Breast Cancer Treatment StudiesBreast Lesions and Carcinomas

Cited by 714

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

Loss of the FAT1 Tumor Suppressor Promotes Resistance to CDK4/6 Inhibitors via the Hippo Pathway

Li, Z., Razavi, P., Li, Q., Toy, W., Liu, B., Ping, C., Hsieh, W., Sanchez-Vega, F., Brown, D. N., Da Cruz Paula, A. F., et al. (2018) · Cancer Cell

Advanced Breast Cancer TherapiesHippo pathway signaling and YAP/TAZ

Cited by 508

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

Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer

Boehm, K. M., Aherne, E. A., Ellenson, L., Nikolovski, I., Alghamdi, M., Vázquez-García, I., Zamarin, D., Long Roche, K., Liu, Y., Patel, D., et al. (2022) · Nature Cancer

Ovarian cancer diagnosis and treatmentRadiomics and Machine Learning in Medical Imaging

Cited by 357

Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis

Li, J., Duran, M. A., Dhanota, N., Chatila, W. K., Bettigole, S. E., Kwon, J., Sriram, R. K., Humphries, M. P., Salto-Tellez, M., James, J. A., et al. (2021) · Cancer Discovery

Adenosine and Purinergic SignalingCancer Immunotherapy and Biomarkers

Cited by 312

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

Mutations in BRCA1 and BRCA2 differentially affect the tumor microenvironment and response to checkpoint blockade immunotherapy

Samstein, R. M., Krishna, C., Ma, X., Pei, X., Lee, K.-W., Makarov, V., Kuo, F., Chung, J., Srivastava, R. M., Purohit, T. A., et al. (2020) · Nature Cancer

Cancer Immunotherapy and BiomarkersBRCA gene mutations in cancer

Cited by 219

Synthetic lethality of PARP inhibition in cancers lacking BRCA1 and BRCA2 mutations

Dedes, K. J., Wilkerson, P. M., Wetterskog, D., Weigelt, B., Ashworth, A., & Reis-Filho, J. S. (2011) · Cell Cycle

PARP inhibition in cancer therapyBRCA gene mutations in cancer

Cited by 191

Automated Real-World Data Integration Improves Cancer Outcome Prediction

Jee, J., Fong, C., Pichotta, K., Tran, T. N., Luthra, A., Waters, M., Fu, C., Altoe, M., Liu, S.-Y., Maron, S. B., et al. (2024) · Nature

Machine Learning in HealthcareCancer Genomics and Diagnostics

Cited by 188

An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer

Xue, Y., Martelotto, L., Baslan, T., Vides, A., Solomon, M., Mai, T. T., Chaudhary, N., Riely, G. J., Li, B. T., Scott, K., et al. (2017) · Nature Medicine

Melanoma and MAPK PathwaysCancer Genomics and Diagnostics

Cited by 174

Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer

Yaeger, R., Mezzadra, R., Sinopoli, J., Bian, Y., Marasco, M., Kaplun, E., Gao, Y., Zhao, H., Paula, A. D. C., Zhu, Y., et al. (2023) · Cancer Discovery

Colorectal Cancer Treatments and StudiesLung Cancer Treatments and Mutations

Cited by 144

FOXA1 mutations reveal distinct chromatin profiles and influence therapeutic response in breast cancer

Arruabarrena-Aristorena, A., Maag, J. L. V., Kittane, S., Cai, Y., Karthaus, W. R., Ladewig, E., Park, J., Kannan, S., Ferrando, L., Cocco, E., et al. (2020) · Cancer Cell

Estrogen and related hormone effectsChromatin Remodeling and Cancer

Cited by 130

The landscape of somatic genetic alterations in breast cancers from ATM germline mutation carriers

Weigelt, B., Bi, R., Kumar, R., Blecua, P., Mandelker, D. L., Geyer, F. C., Pareja, F., James, P. A., kConFab Investigators, Couch, F. J., et al. (2018) · JNCI: Journal of the National Cancer Institute

BRCA gene mutations in cancerCancer Genomics and Diagnostics

Cited by 128

Clinical Validation of Artificial Intelligence–Augmented Pathology Diagnosis Demonstrates Significant Gains in Diagnostic Accuracy in Prostate Cancer Detection

Raciti, P., Sue, J., Retamero, J. A., Ceballos, R., Godrich, R., Kunz, J. D., Casson, A., Thiagarajan, D., Ebrahimzadeh, Z., Viret, J., et al. (2023) · Archives of Pathology & Laboratory Medicine

AI in cancer detectionArtificial Intelligence in Healthcare and Education

Cited by 119

Regression-based Deep-Learning predicts molecular biomarkers from pathology slides

El Nahhas, O. S. M., Loeffler, C. M. L., Carrero, Z. I., van Treeck, M., Kolbinger, F. R., Hewitt, K. J., Muti, H. S., Graziani, M., Zeng, Q., Calderaro, J., et al. (2024) · Nature Communications

AI in cancer detectionRadiomics and Machine Learning in Medical Imaging

Cited by 108

Large language models should be used as scientific reasoning engines, not knowledge databases

Truhn, D., Reis-Filho, J. S., & Kather, J. N. (2023) · Nature Medicine

Artificial Intelligence in Healthcare and EducationMultimodal Machine Learning Applications

Cited by 102

Overcoming the challenges to implementation of artificial intelligence in pathology

Reis-Filho, J. S., & Kather, J. N. (2023) · JNCI: Journal of the National Cancer Institute

AI in cancer detectionArtificial Intelligence in Healthcare and Education

Cited by 79