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A universal SNP and small-indel variant caller using deep neural networks.
Poplin R, Chang PC, Alexander D, Schwartz S, Colthurst T, Ku A, Newburger D, Dijamco J, Nguyen N, Afshar PT, Gross SS, Dorfman L, McLean CY, DePristo MA. Poplin R, et al. Among authors: newburger d. Nat Biotechnol. 2018 Nov;36(10):983-987. doi: 10.1038/nbt.4235. Epub 2018 Sep 24. Nat Biotechnol. 2018. PMID: 30247488
Inference of tumor phylogenies with improved somatic mutation discovery.
Salari R, Saleh SS, Kashef-Haghighi D, Khavari D, Newburger DE, West RB, Sidow A, Batzoglou S. Salari R, et al. Among authors: newburger de. J Comput Biol. 2013 Nov;20(11):933-44. doi: 10.1089/cmb.2013.0106. J Comput Biol. 2013. PMID: 24195709 Free PMC article.
Genome evolution during progression to breast cancer.
Newburger DE, Kashef-Haghighi D, Weng Z, Salari R, Sweeney RT, Brunner AL, Zhu SX, Guo X, Varma S, Troxell ML, West RB, Batzoglou S, Sidow A. Newburger DE, et al. Genome Res. 2013 Jul;23(7):1097-108. doi: 10.1101/gr.151670.112. Epub 2013 Apr 8. Genome Res. 2013. PMID: 23568837 Free PMC article.
Read clouds uncover variation in complex regions of the human genome.
Bishara A, Liu Y, Weng Z, Kashef-Haghighi D, Newburger DE, West R, Sidow A, Batzoglou S. Bishara A, et al. Among authors: newburger de. Genome Res. 2015 Oct;25(10):1570-80. doi: 10.1101/gr.191189.115. Epub 2015 Aug 18. Genome Res. 2015. PMID: 26286554 Free PMC article.
A flexible approach for highly multiplexed candidate gene targeted resequencing.
Natsoulis G, Bell JM, Xu H, Buenrostro JD, Ordonez H, Grimes S, Newburger D, Jensen M, Zahn JM, Zhang N, Ji HP. Natsoulis G, et al. Among authors: newburger d. PLoS One. 2011;6(6):e21088. doi: 10.1371/journal.pone.0021088. Epub 2011 Jun 30. PLoS One. 2011. PMID: 21738606 Free PMC article.
High-resolution DNA-binding specificity analysis of yeast transcription factors.
Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, Bulyk ML. Zhu C, et al. Genome Res. 2009 Apr;19(4):556-66. doi: 10.1101/gr.090233.108. Epub 2009 Jan 21. Genome Res. 2009. PMID: 19158363 Free PMC article.
15 results