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Items: 1 to 20 of 76

1.

HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data.

Zhou X, Batzoglou S, Sidow A, Zhang L.

BMC Genomics. 2018 Jun 18;19(1):467. doi: 10.1186/s12864-018-4867-7.

2.

Genome-wide reconstruction of complex structural variants using read clouds.

Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou S, Sidow A.

Nat Methods. 2017 Sep;14(9):915-920. doi: 10.1038/nmeth.4366. Epub 2017 Jul 17.

3.

Extensive sequencing of seven human genomes to characterize benchmark reference materials.

Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M.

Sci Data. 2016 Jun 7;3:160025. doi: 10.1038/sdata.2016.25.

4.

A research roadmap for next-generation sequencing informatics.

Altman RB, Prabhu S, Sidow A, Zook JM, Goldfeder R, Litwack D, Ashley E, Asimenos G, Bustamante CD, Donigan K, Giacomini KM, Johansen E, Khuri N, Lee E, Liang XS, Salit M, Serang O, Tezak Z, Wall DP, Mansfield E, Kass-Hout T.

Sci Transl Med. 2016 Apr 20;8(335):335ps10. doi: 10.1126/scitranslmed.aaf7314. Review.

5.

Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells.

Soucie EL, Weng Z, Geirsdóttir L, Molawi K, Maurizio J, Fenouil R, Mossadegh-Keller N, Gimenez G, VanHille L, Beniazza M, Favret J, Berruyer C, Perrin P, Hacohen N, Andrau JC, Ferrier P, Dubreuil P, Sidow A, Sieweke MH.

Science. 2016 Feb 12;351(6274):aad5510. doi: 10.1126/science.aad5510. Epub 2016 Jan 21.

6.

svviz: a read viewer for validating structural variants.

Spies N, Zook JM, Salit M, Sidow A.

Bioinformatics. 2015 Dec 15;31(24):3994-6. doi: 10.1093/bioinformatics/btv478. Epub 2015 Aug 18.

PMID:
26286809
7.

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.

8.

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.

9.

Constraint and divergence of global gene expression in the mammalian embryo.

Spies N, Smith CL, Rodriguez JM, Baker JC, Batzoglou S, Sidow A.

Elife. 2015 Apr 14;4:e05538. doi: 10.7554/eLife.05538.

10.

Concepts in solid tumor evolution.

Sidow A, Spies N.

Trends Genet. 2015 Apr;31(4):208-14. doi: 10.1016/j.tig.2015.02.001. Epub 2015 Feb 27. Review.

11.

The future of sequencing: convergence of intelligent design and market Darwinism.

Greenleaf WJ, Sidow A.

Genome Biol. 2014 Mar 25;15(3):303. doi: 10.1186/gb4168.

12.

Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta.

Finn EH, Smith CL, Rodriguez J, Sidow A, Baker JC.

Dev Biol. 2014 Jun 1;390(1):80-92. doi: 10.1016/j.ydbio.2014.02.020. Epub 2014 Mar 2.

13.

Discovery of recurrent structural variants in nasopharyngeal carcinoma.

Valouev A, Weng Z, Sweeney RT, Varma S, Le QT, Kong C, Sidow A, West RB.

Genome Res. 2014 Feb;24(2):300-9. doi: 10.1101/gr.156224.113. Epub 2013 Nov 8.

14.

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.

15.
16.

Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses.

Kenzelmann Broz D, Spano Mello S, Bieging KT, Jiang D, Dusek RL, Brady CA, Sidow A, Attardi LD.

Genes Dev. 2013 May 1;27(9):1016-31. doi: 10.1101/gad.212282.112.

17.

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.

18.

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.

Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J; 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G.

Genome Res. 2013 May;23(5):749-61. doi: 10.1101/gr.148718.112. Epub 2013 Mar 11.

19.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

20.

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.

Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A.

Genome Res. 2012 Sep;22(9):1735-47. doi: 10.1101/gr.136366.111.

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