Papers since 2011

Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou S, Sidow A.
Genome-wide reconstruction of complex structural variants using read clouds.
Nat Methods. 2017 Sep;14(9):915-920. doi: 10.1038/nmeth.4366.
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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.
Extensive sequencing of seven human genomes to characterize benchmark reference materials.
Sci Data. 2016 Jun 7;3:160025. doi: 10.1038/sdata.2016.25.
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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.
A research roadmap for next-generation sequencing informatics.
Sci Transl Med. 2016 Apr 20;8(335):335ps10. DOI: 10.1126/scitranslmed.aaf7314.
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Soucie EL, Weng Z, Geirsdóttir L, Molawi K, Maurizio J, Fenouil R, Mossadegh-Keller N, Gimenez G, VanHille L, Beniazza M, Favret J, Perrin P, Hacohen N, Andrau J-C, Ferrier P, Dubreuil P, Sidow A, Sieweke MH.
Activation of Self-Renewal Gene Network on a Macrophage-Specific Enhancer Platform.
Science 351 2016 Feb 21; DOI: 10.1126/science.aad5510.
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Bishara A, Liu Y, Weng Z, Kashef-Haghighi D, Newburger DE, West R, Sidow A, Batzoglou S.
Read clouds uncover variation in complex regions of the human genome.
Genome Res. 2015 Oct;25(10):1570-80.
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Sidow A, Spies N.
Concepts in solid tumor evolution.
Trends Genet. 2015 Apr;31(4):208-214.
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Weng Z, Spies N, Zhu SX, Newburger DE, Kashef-Haghighi D, Batzoglou S, Sidow A, West RB.
Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia.
Genome Med. 2015 Apr 9;7(1):28.
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Spies N, Smith CL, Rodriguez JM, Baker JC, Batzoglou S, Sidow A.
Constraint and divergence of global gene expression in the mammalian embryo.
eLife. 2015 Apr 14;4.
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Finn EH, Smith CL, Rodriguez J, Sidow A, Baker JC.
Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta.
Dev Biol. 2014 Jun 1;390(1):80-92.
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Valouev A, Weng Z, Sweeney RT, Varma S, Le QT, Kong C, Sidow A, West RB.
Discovery of recurrent structural variants in nasopharyngeal carcinoma.
Genome Res. 2014 Feb;24(2):300-9.
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Salari R, Saleh SS, Kashef-Haghighi D, Khavari D, Newburger DE, West RB, Sidow A, Batzoglou S.
Inference of tumor phylogenies with improved somatic mutation discovery.
J Comput Biol. 2013 Nov;20(11):933-44.
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Foley JW, Sidow A.
Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines.
BMC Genomics. 2013 Oct 20;14:720.
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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 evolution during progression to breast cancer.
Genome Res. 2013 Jul;23(7):1097-108.
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Kenzelmann Broz D, Spano Mello S, Bieging KT, Jiang D, Dusek RL, Brady CA, Sidow A, Attardi LD.
Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses.
Genes Dev. 2013 May 1;27(9):1016-31.
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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.
The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.
Genome Res. 2013 May;23(5):749-61.
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Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A.
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.
Genome Res. 2012 Sep;22(9):1735-47.
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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 J, 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.
Architecture of the human regulatory network derived from ENCODE data.
Nature. 2012 Sep 6;489(7414):91-100.
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ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M.
An integrated encyclopedia of DNA elements in the human genome.
Nature. 2012 Sep 6;489(7414):57-74.
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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.
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Genome Res. 2012 Sep;22(9):1813-31.
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Valouev A, Johnson SM, Boyd S, Smith C, Fire AZ, Sidow A.
Determinants of nucleosome organization in primary human cells.
Nature 2011 May 22;474(7352):516-520.
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