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2023 1
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Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets.
Ellrott K, Wong CK, Yau C, Castro MAA, Lee JA, Karlberg BJ, Grewal JK, Lagani V, Tercan B, Friedl V, Hinoue T, Uzunangelov V, Westlake L, Loinaz X, Felau I, Wang PI, Kemal A, Caesar-Johnson SJ, Shmulevich I, Lazar AJ, Tsamardinos I, Hoadley KA; Cancer Genome Atlas Analysis Network; Robertson AG, Knijnenburg TA, Benz CC, Stuart JM, Zenklusen JC, Cherniack AD, Laird PW. Ellrott K, et al. Cancer Cell. 2025 Feb 10;43(2):195-212.e11. doi: 10.1016/j.ccell.2024.12.002. Epub 2025 Jan 2. Cancer Cell. 2025. PMID: 39753139 Free PMC article.
Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.
Salcedo A, Tarabichi M, Buchanan A, Espiritu SMG, Zhang H, Zhu K, Ou Yang TH, Leshchiner I, Anastassiou D, Guan Y, Jang GH, Mootor MFE, Haase K, Deshwar AG, Zou W, Umar I, Dentro S, Wintersinger JA, Chiotti K, Demeulemeester J, Jolly C, Sycza L, Ko M; PCAWG Evolution and Heterogeneity Working Group; SMC-Het Participants; Wedge DC, Morris QD, Ellrott K, Van Loo P, Boutros PC. Salcedo A, et al. Nat Biotechnol. 2025 Apr;43(4):581-592. doi: 10.1038/s41587-024-02250-y. Epub 2024 Jun 11. Nat Biotechnol. 2025. PMID: 38862616 Free PMC article.
AI-readiness for Biomedical Data: Bridge2AI Recommendations.
Clark T, Caufield H, Parker JA, Al Manir S, Amorim E, Eddy J, Gim N, Gow B, Goar W, Haendel M, Hansen JN, Harris N, Hermjakob H, Joachimiak M, Jordan G, Lee IH, McWeeney SK, Nebeker C, Nikolov M, Shaffer J, Sheffield N, Sheynkman G, Stevenson J, Chen JY, Mungall C, Wagner A, Kong SW, Ghosh SS, Patel B, Williams A, Munoz-Torres MC. Clark T, et al. bioRxiv [Preprint]. 2024 Nov 24:2024.10.23.619844. doi: 10.1101/2024.10.23.619844. bioRxiv. 2024. PMID: 39484409 Free PMC article. Preprint.
NFTest: automated testing of Nextflow pipelines.
Patel Y, Zhu C, Yamaguchi TN, Bugh YZ, Tian M, Holmes A, Fitz-Gibbon ST, Boutros PC. Patel Y, et al. Bioinformatics. 2024 Feb 1;40(2):btae081. doi: 10.1093/bioinformatics/btae081. Bioinformatics. 2024. PMID: 38341660 Free PMC article.
PipeVal: light-weight extensible tool for file validation.
Patel Y, Beshlikyan A, Jordan M, Kim G, Holmes A, Yamaguchi TN, Boutros PC. Patel Y, et al. Bioinformatics. 2024 Feb 1;40(2):btae079. doi: 10.1093/bioinformatics/btae079. Bioinformatics. 2024. PMID: 38341658 Free PMC article.
Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?
Afiaz A, Ivanov AA, Chamberlin J, Hanauer D, Savonen CL, Goldman MJ, Morgan M, Reich M, Getka A, Holmes A, Pati S, Knight D, Boutros PC, Bakas S, Caporaso JG, Del Fiol G, Hochheiser H, Haas B, Schloss PD, Eddy JA, Albrecht J, Fedorov A, Waldron L, Hoffman AM, Bradshaw RL, Leek JT, Wright C. Afiaz A, et al. ArXiv [Preprint]. 2023 Jun 5:arXiv:2306.03255v1. ArXiv. 2023. PMID: 37332562 Free PMC article. Preprint.
Best practices to evaluate the impact of biomedical research software-metric collection beyond citations.
Afiaz A, Ivanov AA, Chamberlin J, Hanauer D, Savonen CL, Goldman MJ, Morgan M, Reich M, Getka A, Holmes A, Pati S, Knight D, Boutros PC, Bakas S, Caporaso JG, Del Fiol G, Hochheiser H, Haas B, Schloss PD, Eddy JA, Albrecht J, Fedorov A, Waldron L, Hoffman AM, Bradshaw RL, Leek JT, Wright C. Afiaz A, et al. Bioinformatics. 2024 Aug 2;40(8):btae469. doi: 10.1093/bioinformatics/btae469. Bioinformatics. 2024. PMID: 39067017 Free PMC article.
Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline.
Patel Y, Zhu C, Yamaguchi TN, Wang NK, Wiltsie N, Zeltser N, Gonzalez AE, Winata HK, Pan Y, Mootor MFE, Sanders T, Fitz-Gibbon ST, Kandoth C, Livingstone J, Liu LY, Carlin B, Holmes A, Oh J, Sahrmann J, Tao S, Eng S, Hugh-White R, Pashminehazar K, Park A, Beshlikyan A, Jordan M, Wu S, Tian M, Arbet J, Neilsen B, Haas R, Bugh YZ, Kim G, Salmingo J, Zhang W, Anand A, Hwang E, Neiman-Golden A, Steinberg P, Zhao W, Anand P, Agrawal R, Tsai BL, Boutros PC. Patel Y, et al. bioRxiv [Preprint]. 2025 Apr 25:2024.09.04.611267. doi: 10.1101/2024.09.04.611267. bioRxiv. 2025. PMID: 39282325 Free PMC article. Preprint.
13 results