Publications
Global impact of somatic structural variation on the DNA methylome of human cancers. Genome Biol. 2019 ;20(1):209.
. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Rep. 2019 ;28(5):1370-1384.e5.
. Molecular Correlates of Metastasis by Systematic Pan-Cancer Analysis Across The Cancer Genome Atlas. Mol Cancer Res. 2019 ;17(2):476-487.
. . Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 ;173(2):371-385.e18.
. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 ;23(1):239-254.e6.
. A Landscape of Metabolic Variation across Tumor Types. Cell Syst. 2018 ;6(3):301-313.e3.
. Making Use of Cancer Genomic Databases. Curr Protoc Mol Biol. 2018 ;121:19.14.1-19.14.13.
. A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases. Cell Rep. 2018 ;24(2):515-527.
. Pan-Cancer Molecular Classes Transcending Tumor Lineage Across 32 Cancer Types, Multiple Data Platforms, and over 10,000 Cases. Clin Cancer Res. 2018 ;24(9):2182-2193.
. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 2018 ;173(2):305-320.e10.
. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst. 2018 ;6(3):271-281.e7.
. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell. 2017 ;31(6):820-832.e3.
. Recommended Guidelines for Validation, Quality Control, and Reporting of Variants in Clinical Practice. Cancer Res. 2017 ;77(6):1250-1260.
. Target and Agent Prioritization for the Children's Oncology Group-National Cancer Institute Pediatric MATCH Trial. J Natl Cancer Inst. 2017 ;109(5).
. UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses. Neoplasia. 2017 ;19(8):649-658.
. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data. Genome Biol. 2016 ;17(1):178.
. Is Whole-Exome Sequencing an Ethically Disruptive Technology? Perspectives of Pediatric Oncologists and Parents of Pediatric Patients With Solid Tumors. Pediatr Blood Cancer. 2016 ;63(3):511-5.
. DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage. Science. 2015 ;349(6249):742-7.
. Identifying gene disruptions in novel balanced de novo constitutional translocations in childhood cancer patients by whole-genome sequencing. Genet Med. 2015 ;17(10):831-5.
. Pediatric Cancer Genetics Research and an Evolving Preventive Ethics Approach for Return of Results after Death of the Subject. J Law Med Ethics. 2015 ;43(3):529-37.
. Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms. BMC Bioinformatics. 2014 ;15 Suppl 17(Suppl 17):I1.
. Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. Nat Commun. 2014 ;5:5274.
. Effects of TP53 mutational status on gene expression patterns across 10 human cancer types. J Pathol. 2014 ;232(5):522-33.
. Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication. Genome Res. 2014 ;24(11):1740-50.
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