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Correction to: Recommendations for performance optimizations when using GATK3.8 and GATK4.
Heldenbrand JR, Baheti S, Bockol MA, Drucker TM, Hart SN, Hudson ME, Iyer RK, Kalmbach MT, Kendig KI, Klee EW, Mattson NR, Wieben ED, Wiepert M, Wildman DE, Mainzer LS. Heldenbrand JR, et al. Among authors: mainzer ls. BMC Bioinformatics. 2019 Dec 17;20(1):722. doi: 10.1186/s12859-019-3277-4. BMC Bioinformatics. 2019. PMID: 31847808 Free PMC article.
Recommendations for performance optimizations when using GATK3.8 and GATK4.
Heldenbrand JR, Baheti S, Bockol MA, Drucker TM, Hart SN, Hudson ME, Iyer RK, Kalmbach MT, Kendig KI, Klee EW, Mattson NR, Wieben ED, Wiepert M, Wildman DE, Mainzer LS. Heldenbrand JR, et al. Among authors: mainzer ls. BMC Bioinformatics. 2019 Nov 8;20(1):557. doi: 10.1186/s12859-019-3169-7. BMC Bioinformatics. 2019. PMID: 31703611 Free PMC article.
Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy.
Kendig KI, Baheti S, Bockol MA, Drucker TM, Hart SN, Heldenbrand JR, Hernaez M, Hudson ME, Kalmbach MT, Klee EW, Mattson NR, Ross CA, Taschuk M, Wieben ED, Wiepert M, Wildman DE, Mainzer LS. Kendig KI, et al. Among authors: mainzer ls. Front Genet. 2019 Aug 20;10:736. doi: 10.3389/fgene.2019.00736. eCollection 2019. Front Genet. 2019. PMID: 31481971 Free PMC article.
Design considerations for workflow management systems use in production genomics research and the clinic.
Ahmed AE, Allen JM, Bhat T, Burra P, Fliege CE, Hart SN, Heldenbrand JR, Hudson ME, Istanto DD, Kalmbach MT, Kapraun GD, Kendig KI, Kendzior MC, Klee EW, Mattson N, Ross CA, Sharif SM, Venkatakrishnan R, Fadlelmola FM, Mainzer LS. Ahmed AE, et al. Among authors: mainzer ls. Sci Rep. 2021 Nov 4;11(1):21680. doi: 10.1038/s41598-021-99288-8. Sci Rep. 2021. PMID: 34737383 Free PMC article.
Identification of missing variants by combining multiple analytic pipelines.
Ren Y, Reddy JS, Pottier C, Sarangi V, Tian S, Sinnwell JP, McDonnell SK, Biernacka JM, Carrasquillo MM, Ross OA, Ertekin-Taner N, Rademakers R, Hudson M, Mainzer LS, Asmann YW. Ren Y, et al. Among authors: mainzer ls. BMC Bioinformatics. 2018 Apr 16;19(1):139. doi: 10.1186/s12859-018-2151-0. BMC Bioinformatics. 2018. PMID: 29661148 Free PMC article.
Managing genomic variant calling workflows with Swift/T.
Ahmed AE, Heldenbrand J, Asmann Y, Fadlelmola FM, Katz DS, Kendig K, Kendzior MC, Li T, Ren Y, Rodriguez E, Weber MR, Wozniak JM, Zermeno J, Mainzer LS. Ahmed AE, et al. Among authors: mainzer ls. PLoS One. 2019 Jul 9;14(7):e0211608. doi: 10.1371/journal.pone.0211608. eCollection 2019. PLoS One. 2019. PMID: 31287816 Free PMC article.
Impact of variant-level batch effects on identification of genetic risk factors in large sequencing studies.
Wickland DP, Ren Y, Sinnwell JP, Reddy JS, Pottier C, Sarangi V, Carrasquillo MM, Ross OA, Younkin SG, Ertekin-Taner N, Rademakers R, Hudson ME, Mainzer LS, Biernacka JM, Asmann YW. Wickland DP, et al. Among authors: mainzer ls. PLoS One. 2021 Apr 16;16(4):e0249305. doi: 10.1371/journal.pone.0249305. eCollection 2021. PLoS One. 2021. PMID: 33861770 Free PMC article.
Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics.
Baichoo S, Souilmi Y, Panji S, Botha G, Meintjes A, Hazelhurst S, Bendou H, Beste E, Mpangase PT, Souiai O, Alghali M, Yi L, O'Connor BD, Crusoe M, Armstrong D, Aron S, Joubert F, Ahmed AE, Mbiyavanga M, Heusden PV, Magosi LE, Zermeno J, Mainzer LS, Fadlelmola FM, Jongeneel CV, Mulder N. Baichoo S, et al. Among authors: mainzer ls. BMC Bioinformatics. 2018 Nov 29;19(1):457. doi: 10.1186/s12859-018-2446-1. BMC Bioinformatics. 2018. PMID: 30486782 Free PMC article.
GABAC: an arithmetic coding solution for genomic data.
Voges J, Paridaens T, Müntefering F, Mainzer LS, Bliss B, Yang M, Ochoa I, Fostier J, Ostermann J, Hernaez M. Voges J, et al. Among authors: mainzer ls. Bioinformatics. 2020 Apr 1;36(7):2275-2277. doi: 10.1093/bioinformatics/btz922. Bioinformatics. 2020. PMID: 31830243 Free PMC article.
17 results