Publications
Germline structural variation globally impacts the cancer transcriptome including disease-relevant genes. Cell Rep Med. 2024 ;5(3):101446.
. Gene Expression Profiles in Cancers and Their Therapeutic Implications. Cancer J. 2023 ;29(1):9-14.
. Global impact of somatic structural variation on the cancer proteome. Nat Commun. 2023 ;14(1):5637.
. Pan-cancer molecular subtypes of metastasis reveal distinct and evolving transcriptional programs. Cell Rep Med. 2023 ;4(2):100932.
. Using cancer proteomics data to identify gene candidates for therapeutic targeting. Oncotarget. 2023 ;14:399-412.
. EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants. Nucleic Acids Res. 2022 ;50(12):e70.
. HSPA6 and its role in cancers and other diseases. Mol Biol Rep. 2022 ;49(11):10565-10577.
. Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways. Nat Commun. 2022 ;13(1):2669.
. Searching thousands of genomes to classify somatic and novel structural variants using STIX. Nat Methods. 2022 ;19(4):445-448.
. A Validation Framework for Somatic Copy Number Detection in Targeted Sequencing Panels. J Mol Diagn. 2022 ;24(7):760-774.
. COVID-19 disease and malignant cancers: The impact for the gene expression in susceptibility to SARS-CoV-2. Int J Biol Sci. 2021 ;17(14):3954-3967.
. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biol. 2021 ;22(1):109.
. The Exceptional Responders Initiative: Feasibility of a National Cancer Institute Pilot Study. J Natl Cancer Inst. 2021 ;113(1):27-37.
. High resolution copy number inference in cancer using short-molecule nanopore sequencing. Nucleic Acids Res. 2021 ;49(21):e124.
. Mass-spectrometry-based proteomic correlates of grade and stage reveal pathways and kinases associated with aggressive human cancers. Oncogene. 2021 ;40(11):2081-2095.
. Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment. Cancer Cell. 2021 ;39(1):38-53.e7.
. Portals for Exploring Noncoding Variants in Pediatric Cancer. Trends Genet. 2021 ;37(4):297-298.
. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 ;578(7793):102-111.
. Ancestry-specific predisposing germline variants in cancer. Genome Med. 2020 ;12(1):51.
. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun. 2020 ;11(1):736.
. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2020 ;11(1):729.
. The repertoire of mutational signatures in human cancer. Nature. 2020 ;578(7793):94-101.
. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020 ;11(1):4748.
. Variant Classification Concordance using the ACMG-AMP Variant Interpretation Guidelines across Nine Genomic Implementation Research Studies. Am J Hum Genet. 2020 ;107(5):932-941.
. Framework for microRNA variant annotation and prioritization using human population and disease datasets. Hum Mutat. 2019 ;40(1):73-89.
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