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Items: 1 to 50 of 79

1.

Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations.

Lal A, Ramazzotti D, Weng Z, Liu K, Ford JM, Sidow A.

BMC Med Genomics. 2019 Jun 10;12(1):84. doi: 10.1186/s12920-019-0545-0.

2.

Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival.

Ramazzotti D, Lal A, Wang B, Batzoglou S, Sidow A.

Nat Commun. 2018 Oct 26;9(1):4453. doi: 10.1038/s41467-018-06921-8.

3.

High-quality genome sequences of uncultured microbes by assembly of read clouds.

Bishara A, Moss EL, Kolmogorov M, Parada AE, Weng Z, Sidow A, Dekas AE, Batzoglou S, Bhatt AS.

Nat Biotechnol. 2018 Oct 15. doi: 10.1038/nbt.4266. [Epub ahead of print]

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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
10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.
19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

25.

A cell cycle phosphoproteome of the yeast centrosome.

Keck JM, Jones MH, Wong CC, Binkley J, Chen D, Jaspersen SL, Holinger EP, Xu T, Niepel M, Rout MP, Vogel J, Sidow A, Yates JR 3rd, Winey M.

Science. 2011 Jun 24;332(6037):1557-61. doi: 10.1126/science.1205193.

26.

Determinants of nucleosome organization in primary human cells.

Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A.

Nature. 2011 May 22;474(7352):516-20. doi: 10.1038/nature10002.

27.

Identifying a high fraction of the human genome to be under selective constraint using GERP++.

Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S.

PLoS Comput Biol. 2010 Dec 2;6(12):e1001025. doi: 10.1371/journal.pcbi.1001025.

28.

An in vitro-identified high-affinity nucleosome-positioning signal is capable of transiently positioning a nucleosome in vivo.

Gracey LE, Chen ZY, Maniar JM, Valouev A, Sidow A, Kay MA, Fire AZ.

Epigenetics Chromatin. 2010 Jul 1;3(1):13. doi: 10.1186/1756-8935-3-13.

29.

Functional analyses of variants reveal a significant role for dominant negative and common alleles in oligogenic Bardet-Biedl syndrome.

Zaghloul NA, Liu Y, Gerdes JM, Gascue C, Oh EC, Leitch CC, Bromberg Y, Binkley J, Leibel RL, Sidow A, Badano JL, Katsanis N.

Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10602-7. doi: 10.1073/pnas.1000219107. Epub 2010 May 24.

30.

Single-nucleotide evolutionary constraint scores highlight disease-causing mutations.

Cooper GM, Goode DL, Ng SB, Sidow A, Bamshad MJ, Shendure J, Nickerson DA.

Nat Methods. 2010 Apr;7(4):250-1. doi: 10.1038/nmeth0410-250. No abstract available.

31.

3'-end sequencing for expression quantification (3SEQ) from archival tumor samples.

Beck AH, Weng Z, Witten DM, Zhu S, Foley JW, Lacroute P, Smith CL, Tibshirani R, van de Rijn M, Sidow A, West RB.

PLoS One. 2010 Jan 19;5(1):e8768. doi: 10.1371/journal.pone.0008768.

32.

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes.

Goode DL, Cooper GM, Schmutz J, Dickson M, Gonzales E, Tsai M, Karra K, Davydov E, Batzoglou S, Myers RM, Sidow A.

Genome Res. 2010 Mar;20(3):301-10. doi: 10.1101/gr.102210.109. Epub 2010 Jan 12.

33.

Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells.

Peng JC, Valouev A, Swigut T, Zhang J, Zhao Y, Sidow A, Wysocka J.

Cell. 2009 Dec 24;139(7):1290-302. doi: 10.1016/j.cell.2009.12.002.

34.

ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses.

Binkley J, Karra K, Kirby A, Hosobuchi M, Stone EA, Sidow A.

Genome Res. 2010 Jan;20(1):142-54. doi: 10.1101/gr.097121.109. Epub 2009 Oct 21.

35.

SHRiMP: accurate mapping of short color-space reads.

Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M.

PLoS Comput Biol. 2009 May;5(5):e1000386. doi: 10.1371/journal.pcbi.1000386. Epub 2009 May 22.

36.

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data.

Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A.

Nat Methods. 2008 Sep;5(9):829-34. doi: 10.1038/nmeth.1246.

37.

The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution.

Hill MM, Broman KW, Stupka E, Smith WC, Jiang D, Sidow A.

Genome Res. 2008 Aug;18(8):1369-79. doi: 10.1101/gr.078576.108. Epub 2008 Jun 2.

38.

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.

Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM.

Genome Res. 2008 Jul;18(7):1051-63. doi: 10.1101/gr.076463.108. Epub 2008 May 13.

39.

Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members.

Hughes I, Binkley J, Hurle B, Green ED; NISC Comparative Sequencing Program, Sidow A, Ornitz DM.

BMC Evol Biol. 2008 Feb 6;8:41. doi: 10.1186/1471-2148-8-41.

40.

Fruit fly family fun.

Sidow A, Lacroute P.

Cell. 2007 Dec 28;131(7):1222-3.

41.

Functional architecture and evolution of transcriptional elements that drive gene coexpression.

Brown CD, Johnson DS, Sidow A.

Science. 2007 Sep 14;317(5844):1557-60.

42.

Mammalian comparative sequence analysis of the Agrp locus.

Kaelin CB, Cooper GM, Sidow A, Barsh GS.

PLoS One. 2007 Aug 8;2(8):e702.

43.
44.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

45.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A.

Genome Res. 2007 Jun;17(6):760-74.

46.
47.

Extreme genomic variation in a natural population.

Small KS, Brudno M, Hill MM, Sidow A.

Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5698-703. Epub 2007 Mar 19.

48.

Structural and molecular evolutionary analysis of Agouti and Agouti-related proteins.

Jackson PJ, Douglas NR, Chai B, Binkley J, Sidow A, Barsh GS, Millhauser GL.

Chem Biol. 2006 Dec;13(12):1297-305.

49.

De novo discovery of a tissue-specific gene regulatory module in a chordate.

Johnson DS, Zhou Q, Yagi K, Satoh N, Wong W, Sidow A.

Genome Res. 2005 Oct;15(10):1315-24. Epub 2005 Sep 16.

50.

Trade-offs in detecting evolutionarily constrained sequence by comparative genomics.

Stone EA, Cooper GM, Sidow A.

Annu Rev Genomics Hum Genet. 2005;6:143-64. Review.

PMID:
16124857

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