Category: 2022

Experimental and in silico analysis of TEM beta lactamase adaptive evolution E
By December 9, 2022

Standley M, Blay V, Beleva Guthrie B, Kim J, Lyman A, Moya A, Karchin R, Camps M. (2022) Experimental and in silico analysis of TEM beta lactamase adaptive evolution”. ACS Infectious Diseases 8(12):2451-63

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Evidence-based calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for clinical use of PP3/BP4 criteria E
By December 1, 2022

Pejaver V,Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O-Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS, Biesecker LG, Radivojac P, Brenner SE (2022) Evidence-based calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for clinical use of PP3/BP4 criteria. Am J Hum Genet Dec 1,109(12):2163-2177.

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Gene-mediated Tumor Immunogenicity and Immune Evasion Mol Cancer G
By August 5, 2022

Gong X, Karchin R. (2022) Pan-cancer HLA Gene-mediated Tumor Immunogenicity and Immune Evasion Mol Cancer Res. 2022 May 9:molcanres.MCR-21-0886-A.2021.doi: 10.1158/1541-7786.MCR-21-0886.

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Sex-specific differences in immunogenic features of response to immune checkpoint blockade S
By August 3, 2022

Scott SC, Shao XM, Niknafs N, Balan A, Pereira G, Marrone KA, Lam VK, Murray JC, Feliciano JL, Levy BP, Ettinger DS, Hann CL, Brahmer JR, Forde PM, Karchin R, Naidoo J, Anagnostou V. (2022) Sex-specific differences in immunogenic features of response to immune checkpoint blockade Front Oncol. 2022 Aug;12:945798.

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Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors E
By August 2, 2022

Zheng L, Niknafs N, Wood LD, Karchin R, Scharpf RB. Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors. Bioinformatics. 2022 Aug 2;38(15):3677-3683. doi: 10.1093/bioinformatics/btac367. PMID: 35642899; PMCID: PMC9344857.

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HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade H
By July 10, 2022

Shao XM, Huang J, Niknafs N, Balan A, Cherry C, White J, Velculescu VE, Anagnostou V, Karchin R. HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade. Ann Oncol. 2022 Jul;33(7):728-738. doi: 10.1016/j.annonc.2022.03.013. Epub 2022 Mar 23. Erratum in: Ann Oncol. 2023 Jul;34(7):634. PMID: 35339648; PMCID: PMC10621650.

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