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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: drucker tm. 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: drucker tm. 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: drucker tm. Front Genet. 2019 Aug 20;10:736. doi: 10.3389/fgene.2019.00736. eCollection 2019. Front Genet. 2019. PMID: 31481971 Free PMC article.
Integrated Genomic Analysis of Pancreatic Ductal Adenocarcinomas Reveals Genomic Rearrangement Events as Significant Drivers of Disease.
Murphy SJ, Hart SN, Halling GC, Johnson SH, Smadbeck JB, Drucker T, Lima JF, Rohakhtar FR, Harris FR, Kosari F, Subramanian S, Petersen GM, Wiltshire TD, Kipp BR, Truty MJ, McWilliams RR, Couch FJ, Vasmatzis G. Murphy SJ, et al. Cancer Res. 2016 Feb 1;76(3):749-61. doi: 10.1158/0008-5472.CAN-15-2198. Epub 2015 Dec 16. Cancer Res. 2016. PMID: 26676757 Free PMC article.
A simple method for gene phasing using mate pair sequencing.
Cradic KW, Murphy SJ, Drucker TM, Sikkink RA, Eberhardt NL, Neuhauser C, Vasmatzis G, Grebe SK. Cradic KW, et al. Among authors: drucker tm. BMC Med Genet. 2014 Feb 6;15:19. doi: 10.1186/1471-2350-15-19. BMC Med Genet. 2014. PMID: 24502676 Free PMC article.
BIMA V3: an aligner customized for mate pair library sequencing.
Drucker TM, Johnson SH, Murphy SJ, Cradic KW, Therneau TM, Vasmatzis G. Drucker TM, et al. Bioinformatics. 2014 Jun 1;30(11):1627-9. doi: 10.1093/bioinformatics/btu078. Epub 2014 Feb 12. Bioinformatics. 2014. PMID: 24526710
Identification of independent primary tumors and intrapulmonary metastases using DNA rearrangements in non-small-cell lung cancer.
Murphy SJ, Aubry MC, Harris FR, Halling GC, Johnson SH, Terra S, Drucker TM, Asiedu MK, Kipp BR, Yi ES, Peikert T, Yang P, Vasmatzis G, Wigle DA. Murphy SJ, et al. Among authors: drucker tm. J Clin Oncol. 2014 Dec 20;32(36):4050-8. doi: 10.1200/JCO.2014.56.7644. Epub 2014 Nov 10. J Clin Oncol. 2014. PMID: 25385739 Free PMC article.
SVAtools for junction detection of genome-wide chromosomal rearrangements by mate-pair sequencing (MPseq).
Johnson SH, Smadbeck JB, Smoley SA, Gaitatzes A, Murphy SJ, Harris FR, Drucker TM, Zenka RM, Pitel BA, Rowsey RA, Hoppman NL, Aypar U, Sukov WR, Jenkins RB, Feldman AL, Kearney HM, Vasmatzis G. Johnson SH, et al. Among authors: drucker tm. Cancer Genet. 2018 Feb;221:1-18. doi: 10.1016/j.cancergen.2017.11.009. Epub 2017 Dec 2. Cancer Genet. 2018. PMID: 29405991
Copy number variant analysis using genome-wide mate-pair sequencing.
Smadbeck JB, Johnson SH, Smoley SA, Gaitatzes A, Drucker TM, Zenka RM, Kosari F, Murphy SJ, Hoppman N, Aypar U, Sukov WR, Jenkins RB, Kearney HM, Feldman AL, Vasmatzis G. Smadbeck JB, et al. Among authors: drucker tm. Genes Chromosomes Cancer. 2018 Sep;57(9):459-470. doi: 10.1002/gcc.5. Epub 2018 Jul 30. Genes Chromosomes Cancer. 2018. PMID: 29726617 Free PMC article.