Jones, Steven J. M.

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

Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution

Chan-Seng-Yue, M., Kim, J. C., Wilson, G. W., Ng, K., Figueroa, E. F., O’Kane, G. M., Connor, A. A., Denroche, R. E., Grant, R. C., McLeod, J., et al. (2020) · Nature Genetics

Pancreatic and Hepatic Oncology ResearchCancer Genomics and Diagnostics

Cited by 669

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

Zheng, S., Cherniack, A. D., Dewal, N., Moffitt, R. A., Danilova, L., Murray, B. A., Lerario, A. M., Else, T., Knijnenburg, T. A., Ciriello, G., et al. (2016) · Cancer Cell

Adrenal and Paraganglionic TumorsChromatin Remodeling and Cancer

Cited by 657

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

Griffith, M., Spies, N. C., Krysiak, K., McMichael, J. F., Coffman, A. C., Danos, A. M., Ainscough, B. J., Ramirez, C. A., Rieke, D. T., Kujan, L., et al. (2017) · Nature Genetics

Genomics and Rare DiseasesCancer Genomics and Diagnostics

Cited by 628

Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Hmeljak, J., Sanchez-Vega, F., Hoadley, K. A., Shih, J., Stewart, C., Heiman, D., Tarpey, P., Danilova, L., Drill, E., Gibb, E. A., et al. (2018) · Cancer Discovery

Occupational and environmental lung diseasesIntraperitoneal and Appendiceal Malignancies

Cited by 618

Comprehensive Characterization of Cancer Driver Genes and Mutations

Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 552

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

Karimi, M. M., Goyal, P., Maksakova, I. A., Bilenky, M., Leung, D., Tang, J. X., Shinkai, Y., Mager, D. L., Jones, S., Hirst, M., et al. (2011) · Cell Stem Cell

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 535

Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer

Wang, Y., Xu, X., Maglic, D., Dill, M. T., Mojumdar, K., Ng, P. K.-S., Jeong, K. J., Tsang, Y. H., Moreno, D., Bhavana, V. H., et al. (2018) · Cell Reports

Hippo pathway signaling and YAP/TAZCancer-related molecular mechanisms research

Cited by 500

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

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Schaub, F. X., Dhankani, V., Berger, A. C., Trivedi, M., Richardson, A. B., Shaw, R., Zhao, W., Zhang, X., Ventura, A., Liu, Y., et al. (2018) · Cell Systems

Cancer Genomics and DiagnosticsCancer-related Molecular Pathways

Cited by 431

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

Ding, L., Bailey, M. H., Porta-Pardo, E., Thorsson, V., Colaprico, A., Bertrand, D., Gibbs, D. L., Weerasinghe, A., Huang, K.-L., Tokheim, C., et al. (2018) · Cell

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 399

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

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

Fejes, A. P., Robertson, G., Bilenky, M., Varhol, R., Bainbridge, M., & Jones, S. J. M. (2008) · Bioinformatics

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 272

Phosphorylated Caveolin-1 Regulates Rho/ROCK-Dependent Focal Adhesion Dynamics and Tumor Cell Migration and Invasion

Joshi, B., Strugnell, S. S., Goetz, J. G., Kojic, L. D., Cox, M. E., Griffith, O. L., Chan, S. K., Jones, S. J., Leung, S.-P., Masoudi, H., et al. (2008) · Cancer Research

Caveolin-1 and cellular processesProtein Kinase Regulation and GTPase Signaling

Cited by 256

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach

Bainbridge, M. N., Warren, R. L., Hirst, M., Romanuik, T., Zeng, T., Go, A., Delaney, A., Griffith, M., Hickenbotham, M., Magrini, V., et al. (2006) · BMC Genomics

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 222

A SAGE Approach to Discovery of Genes Involved in Autophagic Cell Death

Gorski, S. M., Chittaranjan, S., Pleasance, E. D., Freeman, J. D., Anderson, C. L., Varhol, R. J., Coughlin, S. M., Zuyderduyn, S. D., Jones, S. J. M., & Marra, M. A. (2003) · Current Biology

Autophagy in Disease and TherapyCell death mechanisms and regulation

Cited by 213

CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer

Lever, J., Zhao, E. Y., Grewal, J., Jones, M. R., & Jones, S. J. M. (2019) · Nature Methods

Biomedical Text Mining and OntologiesCancer Genomics and Diagnostics

Cited by 205

Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts

D’Souza, C. A., Kronstad, J. W., Taylor, G., Warren, R., Yuen, M., Hu, G., Jung, W. H., Sham, A., Kidd, S. E., Tangen, K., et al. (2011) · mBio

Fungal Infections and StudiesPlant Pathogens and Fungal Diseases

Cited by 202

ORegAnno 3.0: a community-driven resource for curated regulatory annotation

Lesurf, R., Cotto, K. C., Wang, G., Griffith, M., Kasaian, K., Jones, S. J. M., Montgomery, S. B., Griffith, O. L., & The Open Regulatory Annotation Consortium (2016) · Nucleic Acids Research

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 201

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

Robertson, A. G., Bilenky, M., Tam, A., Zhao, Y., Zeng, T., Thiessen, N., Cezard, T., Fejes, A. P., Wederell, E. D., Cullum, R., et al. (2008) · Genome Research

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 182

Comprehensive pan-genomic characterization of adrenocortical carcinoma

Zheng, S., Cherniack, A. D., Dewal, N., Moffitt, R. A., Danilova, L., Murray, B. A., Lerario, A. M., Else, T., Knijnenburg, T. A., Ciriello, G., et al. (2016) · Cancer Cell

Adrenal and Paraganglionic TumorsChromatin Remodeling and Cancer

Cited by 165

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

Wederell, E. D., Bilenky, M., Cullum, R., Thiessen, N., Dagpinar, M., Delaney, A., Varhol, R., Zhao, Y., Zeng, T., Bernier, B., et al. (2008) · Nucleic Acids Research

Genomics and Chromatin DynamicsLiver physiology and pathology

Cited by 150

Cryptococcus neoformans Gene Expression during Experimental Cryptococcal Meningitis

Steen, B. R., Zuyderduyn, S., Toffaletti, D. L., Marra, M., Jones, S. J. M., Perfect, J. R., & Kronstad, J. (2003) · Eukaryotic Cell

Fungal Infections and StudiesFungal and yeast genetics research

Cited by 123

A mouse atlas of gene expression: Large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells

Siddiqui, A. S., Khattra, J., Delaney, A. D., Zhao, Y., Astell, C., Asano, J., Babakaiff, R., Barber, S., Beland, J., Bohacec, S., et al. (2005) · Proceedings of the National Academy of Sciences

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 116