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Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor.
Islam SMA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, Alexandrov LB. Islam SMA, et al. Among authors: zhang t, zhang j. Cell Genom. 2022 Nov 9;2(11):None. doi: 10.1016/j.xgen.2022.100179. Cell Genom. 2022. PMID: 36388765 Free PMC article.
The genomic and epigenomic evolutionary history of papillary renal cell carcinomas.
Zhu B, Poeta ML, Costantini M, Zhang T, Shi J, Sentinelli S, Zhao W, Pompeo V, Cardelli M, Alexandrov BS, Otlu B, Hua X, Jones K, Brodie S, Dabrowska ME, Toro JR, Yeager M, Wang M, Hicks B, Alexandrov LB, Brown KM, Wedge DC, Chanock S, Fazio VM, Gallucci M, Landi MT. Zhu B, et al. Among authors: zhang t. Nat Commun. 2020 Jun 18;11(1):3096. doi: 10.1038/s41467-020-16546-5. Nat Commun. 2020. PMID: 32555180 Free PMC article.
Tracing Lung Cancer Risk Factors Through Mutational Signatures in Never-Smokers.
Landi MT, Synnott NC, Rosenbaum J, Zhang T, Zhu B, Shi J, Zhao W, Kebede M, Sang J, Choi J, Mendoza L, Pacheco M, Hicks B, Caporaso NE, Abubakar M, Gordenin DA, Wedge DC, Alexandrov LB, Rothman N, Lan Q, Garcia-Closas M, Chanock SJ. Landi MT, et al. Among authors: zhang t. Am J Epidemiol. 2021 Jun 1;190(6):962-976. doi: 10.1093/aje/kwaa234. Am J Epidemiol. 2021. PMID: 33712835 Free PMC article.
Genomic and evolutionary classification of lung cancer in never smokers.
Zhang T, Joubert P, Ansari-Pour N, Zhao W, Hoang PH, Lokanga R, Moye AL, Rosenbaum J, Gonzalez-Perez A, Martínez-Jiménez F, Castro A, Muscarella LA, Hofman P, Consonni D, Pesatori AC, Kebede M, Li M, Gould Rothberg BE, Peneva I, Schabath MB, Poeta ML, Costantini M, Hirsch D, Heselmeyer-Haddad K, Hutchinson A, Olanich M, Lawrence SM, Lenz P, Duggan M, Bhawsar PMS, Sang J, Kim J, Mendoza L, Saini N, Klimczak LJ, Islam SMA, Otlu B, Khandekar A, Cole N, Stewart DR, Choi J, Brown KM, Caporaso NE, Wilson SH, Pommier Y, Lan Q, Rothman N, Almeida JS, Carter H, Ried T, Kim CF, Lopez-Bigas N, Garcia-Closas M, Shi J, Bossé Y, Zhu B, Gordenin DA, Alexandrov LB, Chanock SJ, Wedge DC, Landi MT. Zhang T, et al. Nat Genet. 2021 Sep;53(9):1348-1359. doi: 10.1038/s41588-021-00920-0. Epub 2021 Sep 6. Nat Genet. 2021. PMID: 34493867 Free PMC article.
Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA.
Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischel PS, Harris RS, Alexandrov LB. Bergstrom EN, et al. Among authors: zhang t. Nature. 2022 Feb;602(7897):510-517. doi: 10.1038/s41586-022-04398-6. Epub 2022 Feb 9. Nature. 2022. PMID: 35140399 Free PMC article.
Defining novel causal SNPs and linked phenotypes at melanoma-associated loci.
Castaneda-Garcia C, Iyer V, Nsengimana J, Trower A, Droop A, Brown KM, Choi J, Zhang T, Harland M, Newton-Bishop JA, Bishop DT, Adams DJ, Iles MM, Robles-Espinoza CD. Castaneda-Garcia C, et al. Among authors: zhang t. Hum Mol Genet. 2022 Aug 25;31(17):2845-2856. doi: 10.1093/hmg/ddac074. Hum Mol Genet. 2022. PMID: 35357426 Free PMC article.
Tumor Mutational Burden by Whole-Genome Sequencing in Resected NSCLC of Never Smokers.
Ruel LJ, Li Z, Gaudreault N, Henry C, Saavedra Armero V, Boudreau DK, Zhang T, Landi MT, Labbé C, Couture C, Desmeules P, Joubert P, Bossé Y. Ruel LJ, et al. Among authors: zhang t. Cancer Epidemiol Biomarkers Prev. 2022 Dec 5;31(12):2219-2227. doi: 10.1158/1055-9965.EPI-22-0630. Cancer Epidemiol Biomarkers Prev. 2022. PMID: 36126278 Free PMC article.
Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers.
Stueve TR, Li WQ, Shi J, Marconett CN, Zhang T, Yang C, Mullen D, Yan C, Wheeler W, Hua X, Zhou B, Borok Z, Caporaso NE, Pesatori AC, Duan J, Laird-Offringa IA, Landi MT. Stueve TR, et al. Among authors: zhang t. Hum Mol Genet. 2017 Aug 1;26(15):3014-3027. doi: 10.1093/hmg/ddx188. Hum Mol Genet. 2017. PMID: 28854564 Free PMC article.
Cell-type-specific meQTLs extend melanoma GWAS annotation beyond eQTLs and inform melanocyte gene-regulatory mechanisms.
Zhang T, Choi J, Dilshat R, Einarsdóttir BÓ, Kovacs MA, Xu M, Malasky M, Chowdhury S, Jones K, Bishop DT, Goldstein AM, Iles MM, Landi MT, Law MH, Shi J, Steingrímsson E, Brown KM. Zhang T, et al. Am J Hum Genet. 2021 Sep 2;108(9):1631-1646. doi: 10.1016/j.ajhg.2021.06.018. Epub 2021 Jul 21. Am J Hum Genet. 2021. PMID: 34293285 Free PMC article.
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