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Items: 15

1.

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.

Nat Biotechnol. 2018 Nov;36(10):983-987. doi: 10.1038/nbt.4235. Epub 2018 Sep 24.

PMID:
30247488
2.

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.

Genome Res. 2015 Oct;25(10):1570-80. doi: 10.1101/gr.191189.115. Epub 2015 Aug 18.

3.

Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia.

Weng Z, Spies N, Zhu SX, Newburger DE, Kashef-Haghighi D, Batzoglou S, Sidow A, West RB.

Genome Med. 2015 Apr 9;7(1):28. doi: 10.1186/s13073-015-0146-2. eCollection 2015.

4.

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.

J Comput Biol. 2013 Nov;20(11):933-44. doi: 10.1089/cmb.2013.0106.

5.

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.

Genome Res. 2013 Jul;23(7):1097-108. doi: 10.1101/gr.151670.112. Epub 2013 Apr 8.

6.

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome.

Newburger DE, Natsoulis G, Grimes S, Bell JM, Davis RW, Batzoglou S, Ji HP.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1137-43. doi: 10.1093/nar/gkr973. Epub 2011 Nov 18.

7.

A cross-sample statistical model for SNP detection in short-read sequencing data.

Muralidharan O, Natsoulis G, Bell J, Newburger D, Xu H, Kela I, Ji H, Zhang N.

Nucleic Acids Res. 2012 Jan;40(1):e5. doi: 10.1093/nar/gkr851. Epub 2011 Nov 7.

8.

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.

PLoS One. 2011;6(6):e21088. doi: 10.1371/journal.pone.0021088. Epub 2011 Jun 30.

9.

A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors.

Grove CA, De Masi F, Barrasa MI, Newburger DE, Alkema MJ, Bulyk ML, Walhout AJ.

Cell. 2009 Jul 23;138(2):314-27. doi: 10.1016/j.cell.2009.04.058.

10.

Diversity and complexity in DNA recognition by transcription factors.

Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML.

Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.

11.

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.

Genome Res. 2009 Apr;19(4):556-66. doi: 10.1101/gr.090233.108. Epub 2009 Jan 21.

12.

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions.

Newburger DE, Bulyk ML.

Nucleic Acids Res. 2009 Jan;37(Database issue):D77-82. doi: 10.1093/nar/gkn660. Epub 2008 Oct 8.

13.

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR.

Cell. 2008 Jun 27;133(7):1266-76. doi: 10.1016/j.cell.2008.05.024.

14.

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.

Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB.

Genome Res. 2007 Jun;17(6):732-45.

15.

Heterogeneity of nemaline myopathy cases with skeletal muscle alpha-actin gene mutations.

Agrawal PB, Strickland CD, Midgett C, Morales A, Newburger DE, Poulos MA, Tomczak KK, Ryan MM, Iannaccone ST, Crawford TO, Laing NG, Beggs AH.

Ann Neurol. 2004 Jul;56(1):86-96.

PMID:
15236405

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