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30 Article(s) on File
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Whole-genome sequencing in an autism multiplex family
Shi L,
Zhang X,
Golhar R,
Otieno FG,
He M,
Hou C,
Kim C,
Keating B,
Lyon GJ,
Wang K,
Hakonarson H

Mol Autism
  4 (1): 8; Apr 18 2013   Nlm
[Abstract]
[DOI] [Full Text]

An integrated encyclopedia of DNA elements in the human genome
Dunham I,
Kundaje A,
Aldred SF,
Collins PJ,
Davis C,
Doyle F,
Epstein CB,
Frietze S,
Harrow J,
Kaul R,
Khatun J,
Lajoie BR,
Landt SG,
Lee BK,
Pauli F,
Rosenbloom KR,
Sabo P,
Safi A,
Sanyal A,
Shoresh N,
Simon JM,
Song L,
Trinklein ND,
Altshuler RC,
Birney E,
Brown JB,
Cheng C,
Djebali S,
Dong XJ,
Ernst J,
Furey TS,
Gerstein M,
Giardine B,
Greven M,
Hardison RC,
Harris RS,
Herrero J,
Hoffman MM,
Iyer S,
Kellis M,
Kheradpour P,
Lassmann T,
Li QH,
Lin X,
Marinov GK,
Merkel A,
Mortazavi A,
Parker SC,
Reddy TE,
Rozowsky J,
Schlesinger F,
Thurman RE,
Wang J,
Ward LD,
Whitfield TW,
Wilder SP,
Wu W,
Xi HL,
Yip KY,
Zhuang JL,
Bernstein BE,
Green ED,
Gunter C,
Snyder M,
Pazin MJ,
Lowdon RF,
Dillon LA,
Adams LB,
Kelly CJ,
Zhang J,
Wexler JR,
Good PJ,
Feingold EA,
Crawford GE,
Dekker J,
Elnitski L,
Farnham PJ,
Giddings MC,
Gingeras TR,
Guigo R,
Hubbard TJ,
Kent WJ,
Lieb JD,
Margulies EH,
Myers RM,
Stamatoyannopoulos JA,
Tenenbaum SA,
Weng ZP,
White KP,
Wold B,
Yu Y,
Wrobel J,
Risk BA,
Gunawardena HP,
Kuiper HC,
Maier CW,
Xie L,
Chen X,
Mikkelsen TS,
Gillespie S,
Goren A,
Ram O,
Zhang XL,
Wang L,
Issner R,
Coyne MJ,
Durham T,
Ku M,
Truong T,
Eaton ML,
Davis CA,
Dobin A,
Tanzer A,
Lagarde J,
Lin W,
Xue CH,
Williams BA,
Zaleski C,
Roeder M,
Kokocinski F,
Abdelhamid RF,
Alioto T,
Antoshechkin I,
Baer MT,
Batut P,
Bell I,
Bell K,
Chakrabortty S,
Chrast J,
Curado J,
Derrien T,
Drenkow J,
Dumais E,
Dumais J,
Duttagupta R,
Fastuca M,
Fejes-Toth K,
Ferreira P,
Foissac S,
Fullwood MJ,
Gao H,
Gonzalez D,
Gordon A,
Howald C,
Jha S,
Johnson R,
Kapranov P,
King B,
Kingswood C,
Li GL,
Luo OJ,
Park E,
Preall JB,
Presaud K,
Ribeca P,
Robyr D,
Ruan XA,
Sammeth M,
Sandhu KS,
Schaeffer L,
See LH,
Shahab A,
Skancke J,
Suzuki AM,
Takahashi H,
Tilgner H,
Trout D,
Walters N,
Wang HE,
Yu YB,
Hayashizaki Y,
Reymond A,
Antonarakis SE,
Hannon GJ,
Ruan YJ,
Carninci P,
Sloan CA,
Learned K,
Malladi VS,
Wong MC,
Barber G,
Cline MS,
Dreszer TR,
Heitner SG,
Karolchik D,
Kirkup VM,
Meyer LR,
Long JC,
Maddren M,
Raney BJ,
Song LY,
Grasfeder LL,
Giresi PG,
Battenhouse A,
Sheffield NC,
Showers KA,
London D,
Bhinge AA,
Shestak C,
Schaner MR,
Kim SK,
Zhang ZZ,
Mieczkowski PA,
Mieczkowska JO,
Liu Z,
McDaniell RM,
Ni YY,
Rashid NU,
Kim MJ,
Adar S,
Zhang ZC,
Wang TY,
Winter D,
Keefe D,
Iyer VR,
Zheng MZ,
Wang P,
Gertz J,
Vielmetter J,
Partridge EC,
Varley KE,
Gasper C,
Bansal A,
Pepke S,
Jain P,
Amrhein H,
Bowling KM,
Anaya M,
Cross MK,
Muratet MA,
Newberry KM,
McCue K,
Nesmith AS,
Fisher-Aylor KI,
Pusey B,
DeSalvo G,
Parker SL,
Balasubramanian S,
Davis NS,
Meadows SK,
Eggleston T,
Newberry JS,
Levy SE,
Absher DM,
Wong WH,
Blow MJ,
Visel A,
Pennachio LA,
Petrykowska HM,
Abyzov A,
Aken B,
Barrell D,
Barson G,
Berry A,
Bignell A,
Boychenko V,
Bussotti G,
Davidson C,
Despacio-Reyes G,
Diekhans M,
Ezkurdia I,
Frankish A,
Gilbert J,
Gonzalez JM,
Griffiths E,
Harte R,
Hendrix DA,
Hunt T,
Jungreis I,
Kay M,
Khurana E,
Leng J,
Lin MF,
Loveland J,
Lu Z,
Manthravadi D,
Mariotti M,
Mudge J,
Mukherjee G,
Notredame C,
Pei BK,
Rodriguez JM,
Saunders G,
Sboner A,
Searle S,
Sisu C,
Snow C,
Steward C,
Tapanari E,
Tress ML,
van Baren MJ,
Washietl S,
Wilming L,
Zadissa A,
Zhang ZD,
Brent M,
Haussler D,
Valencia A,
Addleman N,
Alexander RP,
Auerbach RK,
Bettinger K,
Bhardwaj N,
Boyle AP,
Cao AR,
Cayting P,
Charos A,
Cheng Y,
Eastman C,
Euskirchen G,
Fleming JD,
Grubert F,
Habegger L,
Hariharan M,
Harmanci A,
Iyengar S,
Jin VX,
Karczewski KJ,
Kasowski M,
Lacroute P,
Lam H,
Lamarre-Vincent N,
Lian J,
Lindahl-Allen M,
Min RQ,
Miotto B,
Monahan H,
Moqtaderi Z,
Mu XM,
OGeen H,
Ouyang ZQ,
Patacsil D,
Raha D,
Ramirez L,
Reed B,
Shi MY,
Slifer T,
Witt H,
Wu LF,
Xu XQ,
Yan KK,
Yang XQ,
Struhl K,
Weissman SM,
Penalva LO,
Karmakar S,
Bhanvadia RR,
Choudhury A,
Domanus M,
Ma LJ,
Moran J,
Victorsen A,
Auer T,
Centanin L,
Eichenlaub M,
Gruhl F,
Heermann S,
Hoeckendorf B,
Inoue D,
Kellner T,
Kirchmaier S,
Mueller C,
Reinhardt R,
Schertel L,
Schneider S,
Sinn R,
Wittbrodt B,
Wittbrodt J,
Jain G,
Balasundaram G,
Bates DL,
Byron R,
Canfield TK,
Diegel MJ,
Dunn D,
Ebersol AK,
Frum T,
Garg K,
Gist E,
Hansen RS,
Boatman L,
Haugen E,
Humbert R,
Johnson AK,
Johnson EM,
Kutyavin TV,
Lee K,
Lotakis D,
Maurano MT,
Neph SJ,
Neri FV,
Nguyen ED,
Qu HZ,
Reynolds AP,
Roach V,
Rynes E,
Sanchez ME,
Sandstrom RS,
Shafer AO,
Stergachis AB,
Thomas S,
Vernot B,
Vierstra J,
Vong S,
Wang H,
Weaver MA,
Yan YQ,
Zhang MH,
Akey JM,
Bender M,
Dorschner MO,
Groudine M,
MacCoss MJ,
Navas P,
Stamatoyannopoulos G,
Beal K,
Brazma A,
Flicek P,
Johnson N,
Lukk M,
Luscombe NM,
Sobral D,
Vaquerizas JM,
Batzoglou S,
Sidow A,
Hussami N,
Kyriazopoulou-Panagi S,
Libbrecht MW,
Schaub MA,
Miller W,
Bickel PJ,
Banfai B,
Boley NP,
Huang HY,
Li JJ,
Noble WS,
Bilmes JA,
Buske OJ,
Sahu AD,
Kharchenko PV,
Park PJ,
Baker D,
Taylor J,
Lin XY,
Lochovsky L,
Min R,
Encode Project Conso

Nature
  489 (7414): 57-74; Sep 6 2012  
[Abstract]
[DOI] [Full Text]

Punctate vascular expression1 is a novel maize gene required for leaf pattern formation that functions downstream of the trans-acting small interfering RNA pathway
Zhang X,
Douglas RN,
Strable J,
Lee M,
Buckner B,
Janick-Buckner D,
Schnable PS,
Timmermans MC,
Scanlon MJ

Plant Physiology
  159 (4): 1453-1462; Aug 2012  
[DOI] [Full Text]

Functional analysis of the protein phosphatase activity of PTEN
Zhang XC,
Piccini A,
Myers MP,
Van Aelst L,
Tonks NK

Biochem J
  444 (3): 457-64; Jun 15 2012   NLM
[Abstract]
[DOI] [Full Text]

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
Melnikov A,
Murugan A,
Zhang X,
Tesileanu T,
Wang L,
Rogov P,
Feizi S,
Gnirke A,
Callan Jr CG,
Kinney JB,
Kellis M,
Lander ES,
Mikkelsen TS

Nature Biotechnology
  30 (3): 271-277; Mar 2012  
[Abstract]
[DOI] [Full Text]

A Users Guide to the Encyclopedia of DNA Elements (ENCODE)
Myers RM,
Stamatoyannopoulos J,
Snyder M,
Dunham I,
Hardison RC,
Bernstein BE,
Gingeras TR,
Kent WJ,
Birney E,
Wold B,
Crawford GE,
Epstein CB,
Shoresh N,
Ernst J,
Mikkelsen TS,
Kheradpour P,
Zhang XL,
Wang L,
Issner R,
Coyne MJ,
Durham T,
Ku MC,
Truong T,
Ward LD,
Altshuler RC,
Lin MF,
Kellis M,
Davis CA,
Kapranov P,
Dobin A,
Zaleski C,
Schlesinger F,
Batut P,
Chakrabortty S,
Jha S,
Lin W,
Drenkow J,
Wang HE,
Bell KG,
Gao H,
Bell I,
Dumais E,
Dumais J,
Antonarakis SE,
Ucla C,
Borel C,
Guigo R,
Djebali S,
Lagarde J,
Kingswood C,
Ribeca P,
Sammeth M,
Alioto T,
Merkel A,
Tilgner H,
Carninci P,
Hayashizaki Y,
Lassmann T,
Takahashi H,
Abdelhamid RF,
Hannon G,
Fejes-Toth K,
Preall J,
Gordon A,
Sotirova V,
Reymond A,
Howald C,
Graison EA,
Chrast J,
Ruan YJ,
Ruan XA,
Shahab A,
Poh WT,
Wei CL,
Furey TS,
Boyle AP,
Sheffield NC,
Song LY,
Shibata Y,
Vales T,
Winter D,
Zhang ZC,
London D,
Wang TY,
Keefe D,
Iyer VR,
Lee BK,
McDaniell RM,
Liu Z,
Battenhouse A,
Bhinge AA,
Lieb JD,
Grasfeder LL,
Showers KA,
Giresi PG,
Kim SK,
Shestak C,
Pauli F,
Reddy TE,
Gertz J,
Partridge EC,
Jain P,
Sprouse RO,
Bansal A,
Pusey B,
Muratet MA,
Varley KE,
Bowling KM,
Newberry KM,
Nesmith AS,
Dilocker JA,
Parker SL,
Waite LL,
Thibeault K,
Roberts K,
Absher DM,
Mortazavi A,
Williams B,
Marinov G,
Trout D,
Pepke S,
King B,
McCue K,
Kirilusha A,
DeSalvo G,
Fisher-Aylor K,
Amrhein H,
Vielmetter J,
Sherlock G,
Sidow A,
Batzoglou S,
Rauch R,
Kundaje A,
Libbrecht M,
Margulies EH,
Parker SC,
Elnitski L,
Green ED,
Hubbard T,
Harrow J,
Searle S,
Kokocinski F,
Aken B,
Frankish A,
Hunt T,
Despacio-Reyes G,
Kay M,
Mukherjee G,
Bignell A,
Saunders G,
Boychenko V,
Brent M,
Van Baren MJ,
Brown RH,
Gerstein M,
Khurana E,
Balasubramanian S,
Zhang ZD,
Lam H,
Cayting P,
Robilotto R,
Lu Z,
Derrien T,
Tanzer A,
Knowles DG,
Mariotti M,
Haussler D,
Harte R,
Diekhans M,
Lin M,
Valencia A,
Tress M,
Rodriguez JM,
Landt SG,
Raha D,
Shi MY,
Euskirchen G,
Grubert F,
Kasowski M,
Lian J,
Lacroute P,
Xu YH,
Monahan H,
Patacsil D,
Slifer T,
Yang XQ,
Charos A,
Reed B,
Wu LF,
Auerbach RK,
Habegger L,
Hariharan M,
Rozowsky J,
Abyzov A,
Weissman SM,
Struhl K,
Lamarre-Vincent N,
Lindahl-Allen M,
Miotto B,
Moqtaderi Z,
Fleming JD,
Newburger P,
Farnham PJ,
Frietze S,
OGeen H,
Xu XQ,
Blahnik KR,
Cao AR,
Iyengar S,
Stamatoyannopoulos JA,
Kaul R,
Thurman RE,
Wang H,
Navas PA,
Sandstrom R,
Sabo PJ,
Weaver M,
Canfield T,
Lee K,
Neph S,
Roach V,
Reynolds A,
Johnson A,
Rynes E,
Giste E,
Vong S,
Neri J,
Frum T,
Johnson EM,
Nguyen ED,
Ebersol AK,
Sanchez ME,
Sheffer HH,
Lotakis D,
Haugen E,
Humbert R,
Kutyavin T,
Shafer T,
Dekker J,
Lajoie BR,
Sanyal A,
Rosenbloom KR,
Dreszer TR,
Raney BJ,
Barber GP,
Meyer LR,
Sloan CA,
Malladi VS,
Cline MS,
Learned K,
Swing VK,
Zweig AS,
Rhead B,
Fujita PA,
Roskin K,
Karolchik D,
Kuhn RM,
Wilder SP,
Sobral D,
Herrero J,
Beal K,
Lukk M,
Brazma A,
Vaquerizas JM,
Luscombe NM,
Bickel PJ,
Boley N,
Brown JB,
Li QH,
Huang HY,
Sboner A,
Yip KY,
Cheng C,
Yan KK,
Bhardwaj N,
Wang J,
Lochovsky L,
Jee J,
Gibson T,
Leng J,
Du J,
Harris RS,
Song G,
Miller W,
Suh B,
Wang T,
Paten B,
Noble WS,
Hoffman MM,
Buske OJ,
Weng ZP,
Dong XJ,
Xi HL,
Tenenbaum SA,
Doyle F,
Penalva LO,
Chittur S,
Tullius TD,
White KP,
Karmakar S,
Victorsen A,
Jameel N,
Bild N,
Grossman RL,
Whitfield TW,
Collins PJ,
Trinklein ND,
Giddings MC,
Chen X,
Khatun J,
Maier C,
Yu YB,
Gunawardena H,
Risk B,
Feingold EA,
Lowdon RF,
Dillon LA,
Good PJ,
Encode Project Conso

Plos Biology
  9 (4): Apr 2011   PMCID: PMC3079585
[Abstract]
[DOI] [Full Text]

MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer
Png KJ,
Yoshida M,
Zhang XH,
Shu W,
Lee H,
Rimner A,
Chan TA,
Comen E,
Andrade VP,
Kim SW,
King TA,
Hudis CA,
Norton L,
Hicks JB,
Massagué J,
Tavazoie SF

Genes and Development
  25 (3): 226-231; Feb 1 2011   Elsevier PMC3034897
[Abstract]
[DOI]

Sensitivity of Cancer Cells to Plk1 Inhibitor GSK461364A Is Associated with Loss of p53 Function and Chromosome Instability
Degenhardt Y,
Greshock J,
Laquerre S,
Gilmartin AG,
Jing J,
Richter M,
Zhang X,
Bleam M,
Halsey W,
Hughes A,
Moy C,
Liu-Sullivan N,
Powers S,
Bachman K,
Jackson J,
Weber B,
Wooster R

Mol Cancer Ther
  (0): July 2010  
[Abstract]
[DOI] [Full Text] [PDF]

Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis
Dalloul RA,
Long JA,
Zimin AV,
Aslam L,
Beal K,
Blomberg LA,
Bouffard P,
Burt DW,
Crasta O,
Crooijmans RP,
Cooper K,
Coulombe RA,
De S,
Delany ME,
Dodgson JB,
Dong JJ,
Evans C,
Frederickson KM,
Flicek P,
Florea L,
Folkerts O,
Groenen MA,
Harkins TT,
Herrero J,
Hoffmann S,
Megens HJ,
Jiang A,
de Jong P,
Kaiser P,
Kim H,
Kim KW,
Kim S,
Langenberger D,
Lee MK,
Lee T,
Mane S,
Marcais G,
Marz M,
McElroy AP,
Modise T,
Nefedov M,
Notredame C,
Paton IR,
Payne WS,
Pertea G,
Prickett D,
Puiu D,
Qioa D,
Raineri E,
Ruffier M,
Salzberg SL,
Schatz MC,
Scheuring C,
Schmidt CJ,
Schroeder S,
Searle SM,
Smith EJ,
Smith J,
Sonstegard TS,
Stadler PF,
Tafer H,
Tu Z,
van Tassell CP,
Vilella AJ,
Williams KP,
Yorke JA,
Zhang L,
Zhang HB,
Zhang X,
Zhang Y,
Reed KM

Plos Biology
  8 (9): 2010  
[Abstract]
[DOI] [Full Text]

Microdissection of shoot meristem functional domains
Brooks L,
Strable J,
Zhang X,
Ohtsu K,
Zhou R,
Sarkar A,
Hargreaves S,
Elshire RJ,
Eudy D,
Pawlowska T,
Ware DH,
Janick-Buckner D,
Buckner B,
Timmermans MC,
Schnable PS,
Nettleton D,
Scanlon MJ

PLoS Genet
  5 (5): e1000476; May 2009   PMCID: PMC2673047
[Abstract]
[DOI] [Full Text] [PDF]

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster
Zhang X,
Lian Z,
Padden C,
Gerstein MB,
Rozowsky J,
Snyder M,
Gingeras TR,
Kapranov P,
Weissman SM,
Newburger PE

Blood
  113 (11): 2526-34; Mar 12 2009  
[Abstract]
[DOI] [Full Text] [PDF]

Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development
Li T,
Huang J,
Jiang Y,
Zeng Y,
He F,
Zhang MQ,
Han Z,
Zhang X

Genomics
  93 (3): 235-242; Mar 2009   PMCID: PMC2995988
[Abstract]
[DOI] [Full Text] [PDF]

The seventh Asia Pacific bioinformatics conference (APBC2009)
Zhang MQ,
Waterman MS,
Zhang X

BMC Bioinformatics
  10 (0): Jan 30 2009   PMCID: PMC2648764
[DOI] [Full Text] [PDF]

Histone methylation marks play important roles in predicting the methylation status of CpG islands
Fan S,
Zhang MQ,
Zhang X

Biochemical and Biophysical Research Communications
  374 (3): 559-564; Sep 2008  
[Abstract]
[DOI] [Full Text] [PDF]

Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure
Maulik U,
Mukhopadhyay A,
Bandyopadhyay S,
Zhang MQ,
Zhang X

2008 IEEE Congress on Evolutionary Computation, CEC 2008
  1536-1543; Jun 2008  
[Abstract]
[DOI] [Full Text]

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
Johnson DS,
Li W,
Gordon DB,
Bhattacharjee A,
Curry B,
Ghosh J,
Brizuela L,
Carroll JS,
Brown M,
Flicek P,
Koch CM,
Dunham I,
Bieda M,
Xu X,
Farnham PJ,
Kapranov P,
Nix DA,
Gingeras TR,
Zhang X,
Holster H,
Jiang N,
Green RD,
Song JS,
McCuine SA,
Anton E,
Nguyen L,
Trinklein ND,
Ye Z,
Ching K,
Hawkins D,
Ren B,
Scacheri PC,
Rozowsky J,
Karpikov A,
Euskirchen G,
Weissman S,
Gerstein M,
Snyder M,
Yang A,
Moqtaderi Z,
Hirsch H,
Shulha HP,
Fu Y,
Weng Z,
Struhl K,
Myers RM,
Lieb JD,
Liu XS

Genome Research
  18 (3): 393-403; 2008