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19 Article(s) on File
Page 1 of 1
A promoter-level mammalian expression atlas
Forest AR,
Kawaji H,
Rehli M,
Baillie JK,
De Hoon MJ,
Haberle V,
Lassmann T,
Kulakovskiy IV,
Lizio M,
Itoh M,
Andersson R,
Mungall CJ,
Meehan TF,
Schmeier S,
Bertin N,
Jørgensen M,
Dimont E,
Arner E,
Schmidl C,
Schaefer U,
Medvedeva YA,
Plessy C,
Vitezic M,
Severin J,
Semple CA,
Ishizu Y,
Young RS,
Francescatto M,
Altschuler IA,
Albanese D,
Altschule GM,
Arakawa T,
Archer JA,
Arner P,
Babina M,
Rennie S,
Balwierz PJ,
Beckhouse AG,
Pradhan-Bhatt S,
Blake JA,
Blumenthal A,
Bodega B,
Bonetti A,
Briggs J,
Brombacher F,
Burroughs AM,
Califano A,
Cannistraci CV,
Carbajo D,
Chen Y,
Chierici M,
Ciani Y,
Clevers HC,
Dalla E,
Davis CA,
Detmar M,
Diehl AD,
Dohi T,
Drabløs F,
Edge AS,
Edinger M,
Ekwall K,
Endoh M,
Enomoto H,
Fagiolini M,
Fairbairn L,
Fang H,
Farach-Carson MC,
Faulkner GJ,
Favorov AV,
Fisher ME,
Frith MC,
Fujita R,
Fukuda S,
Furlanello C,
Furuno M,
Furusawa JI,
Geijtenbeek TB,
Gibson AP,
Gingeras T,
Goldowitz D,
Gough J,
Guhl S,
Guler R,
Gustincich S,
Ha TJ,
Hamaguchi M,
Hara M,
Harbers M,
Harshbarger J,
Hasegawa A,
Hasegawa Y,
Hashimoto T,
Herlyn M,
Hitchens KJ,
Sui SJ,
Hofmann OM,
Hoof I,
Hori F,
Huminiecki L,
Iida K,
Ikawa T,
Jankovic BR,
Jia H,
Joshi A,
Jurman G,
Kaczkowski B,
Kai C,
Kaida K,
Kaiho A,
Kajiyama K,
Kanamori-Katayama M,
Kasianov AS,
Kasukawa T,
Katayama S,
Kato S,
Kawaguchi S,
Kawamoto H,
Kawamura YI,
Kawashima T,
Kempfle JS,
Kenna TJ,
Kere J,
Khachigian LM,
Kitamura T,
Klinken SP,
Knox AJ,
Kojima M,
Kojima S,
Kondo N,
Koseki H,
Koyasu S,
Krampitz S,
Kubosaki A,
Kwon AT,
Laros JF,
Lee W,
Lennartsson A,
Li K,
Lilje B,
Lipovich L,
Mackay-sim A,
Manabe RI,
Mar JC,
Marchand B,
Mathelier A,
Mejhert N,
Meynert A,
Mizuno Y,
De Morais DA,
Morikawa H,
Morimoto M,
Moro K,
Motakis E,
Motohashi H,
Mummery CL,
Murata M,
Nagao-Sato S,
Nakachi Y,
Nakahara F,
Nakamura T,
Nakamura Y,
Nakazato K,
Van Nimwegen E,
Ninomiya N,
Nishiyori H,
Noma S,
Nozaki T,
Ogishima S,
Ohkura N,
Ohmiya H,
Ohno H,
Ohshima M,
Okada-Hatakeyama M,
Okazaki Y,
Orlando V,
Ovchinnikov DA,
Pain A,
Passier R,
Patrikakis M,
Persson H,
Piazza S,
Prendergast JG,
Rackham OJ,
Ramilowski JA,
Rashid M,
Ravasi T,
Rizzu P,
Roncador M,
Roy S,
Rye MB,
Saijyo E,
Sajantila A,
Saka A,
Sakaguchi S,
Sakai M,
Sato H,
Satoh H,
Savvi S,
Saxena A,
Schneider C,
Schultes EA,
Schulze-Tanzil GG,
Schwegmann A,
Sengstag T,
Sheng G,
Shimoji H,
Shimoni Y,
Shin JW,
Simon C,
Sugiyama D,
Sugiyama T,
Suzuki M,
Suzuki N,
Swoboda RK,
T Hoen PA,
Tagami M,
Tagami NT,
Takai J,
Tanaka H,
Tatsukawa H,
Tatum Z,
Thompson M,
Toyoda H,
Toyoda T,
Valen E,
Van De Wetering M,
Van Den Berg LM,
Verardo R,
Vijayan D,
Vorontsov IE,
Wasserman WW,
Watanabe S,
Wells CA,
Winteringham LN,
Wolvetang E,
Wood EJ,
Yamaguchi Y,
Yamamoto M,
Yoneda M,
Yonekura Y,
Yoshida S,
Zabierowski SE,
Zhang PG,
Zhao X,
Zucchelli S,
Summers KM,
Suzuki H,
Daub CO,
Kawai J,
Heutink P,
Hide W,
Freeman TC,
Lenhard B,
Bajic LV,
Taylor MS,
Makeev VJ,
Sandelin A,
Hume DA,
Carninci P,
Hayashizaki Y

Nature
  507 (7493): 462-470; Mar 27 2014   NLM
[DOI] [Full Text]

Identification of Driver Genes in Hepatocellular Carcinoma by Exome Sequencing
Cleary SP,
Jeck WR,
Zhao XB,
Chen K,
Selitsky SR,
Savich GL,
Tan TX,
Wu MC,
Getz G,
Lawrence MS,
Parker JS,
Li JY,
Powers S,
Kim H,
Fischer S,
Guindi M,
Ghanekar A,
Chiang DY

Hepatology
  58 (5): 1693-1702; Nov 2013   NLM
[Abstract]
[DOI] [Full Text]

Dissociation of rugose-dependent short-term memory component from memory consolidation in Drosophila
Zhao J,
Lu Y,
Zhao X,
Yao X,
Shuai Y,
Huang C,
Wang L,
Jeong SH,
Zhong Y

Genes, Brain and Behavior
  12 (6): 626-632; Aug 2013   Elsevier
[DOI] [Full Text]

Identification of driver genes in hepatocellular carcinoma by exome sequencing
Cleary SP,
Jeck WR,
Zhao XB,
Selitsky SR,
Savich GL,
Tan TX,
Wu MC,
Getz G,
Lawrence MS,
Parker JS,
Li JY,
Powers S,
Kim H,
Fischer SE,
Guindi M,
Ghanekar A,
Chiang DY

Cancer Research
  73 (8): 4598; Apr 2013  
[Abstract]
[DOI] [Full Text]

Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder
Vacic V,
Markwick PR,
Oldfield CJ,
Zhao X,
Haynes C,
Uversky VN,
Iakoucheva LM

PLoS Computational Biology
  8 (10): Oct 4 2012  
[DOI] [Full Text]

Mutant p53 disrupts mammary tissue architecture via the mevalonate pathway
Freed-Pastor WA,
Mizuno H,
Zhao X,
Langerød A,
Moon SH,
Rodriguez-Barrueco R,
Barsotti A,
Chicas A,
Li W,
Polotskaia A,
Bissell MJ,
Osborne TF,
Tian B,
Lowe SW,
Silva JM,
Børresen-Dale AL,
Levine AJ,
Bargonetti J,
Prives C

Cell
  148 (1): 244-258; Jan 2012  
[Abstract]
[DOI] [Full Text]

Methylation detection oligonucleotide microarray analysis: a high-resolution method for detection of CpG island methylation
Kamalakaran S,
Kendall JT,
Zhao X,
Tang C,
Khan S,
Ravi K,
Auletta T,
Riggs M,
Wang Y,
Helland A,
Naume B,
Dimitrova N,
Borresen-Dale AL,
Hicks JB,
Lucito R

Nucl. Acids Res.
  37 (12): e89; Jul 2009   PMCID: PMC2709589
[Abstract]
[DOI] [Full Text] [PDF]

High-resolution human core-promoter prediction with CoreBoost_HM
Wang X,
Xuan Z,
Zhao X,
Li Y,
Zhang MQ

Genome Res
  19 (2): 266-75; Feb 2009   PMCID: PMC2652208
[Abstract]
[DOI] [Full Text] [PDF]

Classification method for microarray probe selection using sequence, thermodynamics and secondary structure parameters
Gupta L,
Kumar S,
Singh R,
Shaik R,
Dimitrova N,
Gorthi A,
Lakshmi B,
Pai D,
Kamalakaran S,
Zhao X,
Wigler MH

2008 19th International Conference on Pattern Recognition
  1; Dec 2008  
[Abstract]
[DOI] [Full Text]

CHD8 associates with human Staf and contributes to efficient U6 RNA polymerase III transcription
Yuan CC,
Zhao X,
Florens L,
Swanson SK,
Washburn MP,
Hernandez N

Mol Cell Biol
  27 (24): 8729-8738; Dec 2007   PMCID: PMC2169411
[Abstract]
[DOI] [Full Text] [PDF]

A unified genetic theory for sporadic and inherited autism
Zhao X,
Leotta A,
Kustanovich V,
Lajonchere C,
Geschwind DH,
Law K,
Law P,
Qiu S,
Lord C,
Sebat J,
Ye K,
Wigler MH

Proc Natl Acad Sci U S A
  104 (31): 12831-12836; Jul 31 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Boosting with stumps for predicting transcription start sites
Zhao X,
Xuan ZY,
Zhang MQ

Genome Biol
  8 (2): R17; Feb 2 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
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,
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,
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,
Hoon Kim T,
Wang K,
Qu C,
Hon G,
Luna R,
Glass CK,
Rosenfeld MG,
Aldred SF,
Cooper SJ,
Halees A,
Lin JM,
Shulha HP,
Xu M,
Haidar JN,
Yu 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
  447 (7146): 799-816; 2007  
[Abstract]
[DOI] [Full Text]

Mutational analysis of BTAF1-TBP interaction: BTAF1 can rescue DNA-binding defective TBP mutants
Klejman MP,
Zhao XM,
van Schaik FM,
Herr W,
Timmers HT

Nucleic Acids Research
  33 (17): 5426-5436; 2005  
[Abstract]
[Full Text]

Role of the inhibitory DNA-binding surface of human TATA-binding protein in recruitment of human TFIIB family members
Zhao X,
Herr W

Mol Cell Biol
  23 (22): 8152-60; Nov 2003  
[Abstract]
[Full Text]

Survival of DNA damage in yeast directly depends on increased dNTP levels allowed by relaxed feedback inhibition of ribonucleotide reductase
Chabes A,
Georgieva B,
Domkin V,
Zhao XL,
Rothstein R,
Thelander L

Cell
  112 (3): 391-401; Feb 2003  
[Abstract]
[Full Text]

A shared surface of TBP directs RNA polymerase II and III transcription via association with different TFIIB family members
Zhao XM,
Schramm L,
Hernandez N,
Herr W

Molecular Cell
  11 (1): 151-161; Jan 2003  
[Abstract]
[DOI] [Full Text]

A regulated two-step mechanism of TBP binding to DNA: A solvent-exposed surface of TBP inhibits TATA box recognition
Zhao XM,
Herr W

Cell
  108 (5): 615-627; Mar 2002  
[Full Text]

A positioned nucleosome on the human U6 promoter allows recruitment of SNAP(c) by the Oct-1 POU domain
Zhao XY,
Pendergrast PS,
Hernandez N

Molecular Cell
  7 (3): 539-549; Mar 2001  
[Abstract]
[DOI] [Full Text]


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