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21 Article(s) on File
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Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing
Le Thomas A,
Stuwe E,
Li S,
Du J,
Marinov G,
Rozhkov N,
Chen YC,
Luo Y,
Sachidanandam R,
Toth KF,
Patel D,
Aravin AA

Genes Development
  28 (15): 1667-80; Aug 1 2014   Nlm
[Abstract]
[DOI] [Full Text]

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
Delaneau O,
Marchini J,
McVeanh GA,
Donnelly P,
Lunter G,
Marchini JL,
Myers S,
Gupta-Hinch A,
Iqbal Z,
Mathieson I,
Rimmer A,
Xifara DK,
Kerasidou A,
Churchhouse C,
Altshuler DM,
Gabriel SB,
Lander ES,
Gupta N,
Daly MJ,
DePristo MA,
Banks E,
Bhatia G,
Carneiro MO,
Del Angel G,
Genovese G,
Handsaker RE,
Hartl C,
McCarroll SA,
Nemesh JC,
Poplin RE,
Schaffner SF,
Shakir K,
Sabeti PC,
Grossman SR,
Tabrizi S,
Tariyal R,
Li H,
Reich D,
Durbin RM,
Hurles ME,
Balasubramaniam S,
Burton J,
Danecek P,
Keane TM,
Kolb-Kokocinski A,
McCarthy S,
Stalker J,
Quail M,
Ayub Q,
Chen Y,
Coffey AJ,
Colonna V,
Huang N,
Jostins L,
Scally A,
Walter K,
Xue Y,
Zhang Y,
Blackburne B,
Lindsay SJ,
Ning Z,
Frankish A,
Harrow J,
Chris TS,
Abecasis GR,
Kang HM,
Anderson P,
Blackwell T,
Busonero F,
Fuchsberger C,
Jun G,
Maschio A,
Porcu E,
Sidore C,
Tan A,
Trost MK,
Bentley DR,
Grocock R,
Humphray S,
James T,
Kingsbury Z,
Bauer M,
Cheetham RK,
Cox T,
Eberle M,
Murray L,
Shaw R,
Chakravarti A,
Clark AG,
Keinan A,
Rodriguez-Flores JL,
De LaVega FM,
Degenhardt J,
Eichler EE,
Flicek P,
Clarke L,
Leinonen R,
Smith RE,
Zheng-Bradley X,
Beal K,
Cunningham F,
Herrero J,
McLaren WM,
Ritchie GR,
Barker J,
Kelman G,
Kulesha E,
Radhakrishnan R,
Roa A,
Smirnov D,
Streeter I,
Toneva I,
Gibbs RA,
Dinh H,
Kovar C,
Lee S,
Lewis L,
Muzny D,
Reid J,
Wang M,
Yu F,
Bainbridge M,
Challis D,
Evani US,
Lu J,
Nagaswamy U,
Sabo A,
Wang Y,
Yu J,
Fowler G,
Hale W,
Kalra D,
Green ED,
Knoppers BM,
Korbel JO,
Rausch T,
Sttz AM,
Lee C,
Griffin L,
Hsieh CH,
Mills RE,
Von Grotthuss M,
Zhang C,
Shi X,
Lehrach H,
Sudbrak R,
Amstislavskiy VS,
Lienhard M,
Mertes F,
Sultan M,
Timmermann B,
Yaspo ML,
Herwig SR,
Mardis ER,
Wilson RK,
Fulton L,
Fulton R,
Weinstock GM,
Chinwalla A,
Ding L,
Dooling D,
Koboldt DC,
McLellan MD,
Wallis JW,
Wendl MC,
Zhang Q,
Marth GT,
Garrison EP,
Kural D,
Lee WP,
Leong WF,
Ward AN,
Wu J,
Zhang M,
Nickerson DA,
Alkan C,
Hormozdiari F,
Ko A,
Sudmant PH,
Schmidt JP,
Davies CJ,
Gollub J,
Webster T,
Wong B,
Zhan Y,
Sherry ST,
Xiao C,
Church D,
Ananiev V,
Belaia Z,
Beloslyudtsev D,
Bouk N,
Chen C,
Cohen R,
Cook C,
Garner J,
Hefferon T,
Kimelman M,
Liu C,
Lopez J,
Meric P,
Ostapchuk Y,
Phan L,
Ponomarov S,
Schneider V,
Shekhtman E,
Sirotkin K,
Slotta D,
Zhang H,
Wang J,
Fang X,
Guo X,
Jian M,
Jiang H,
Jin X,
Li G,
Li J,
Li Y,
Liu X,
Lu Y,
Ma X,
Tai S,
Tang M,
Wang B,
Wang G,
Wu H,
Wu R,
Yin Y,
Zhang W,
Zhao J,
Zhao M,
Zheng X,
Lachlan H,
Fang L,
Li Q,
Li Z,
Lin H,
Liu B,
Luo R,
Shao H,
Xie Y,
Ye C,
Yu C,
Zheng H,
Zhu H,
Cai H,
Cao H,
Su Y,
Tian Z,
Yang H,
Yang L,
Zhu J,
Cai Z,
Albrecht MW,
Borodina TA,
Auton A,
Yoon SC,
Lihm J,
Makarov V,
Jin H,
Kim W,
Kim KC,
Gottipati S,
Jones D,
Cooper DN,
Ball EV,
Stenson PD,
Barnes B,
Kahn S,
Ye K,
Batzer MA,
Konkel MK,
Walker JA,
MacArthur DG,
Lek M,
Shriver MD,
Bustamante CD,
Gravel S,
Kenny EE,
Kidd JM,
Lacroute P,
Maples BK,
Moreno-Estrada A,
Zakharia F,
Henn B,
Sandoval K,
Byrnes JK,
Halperin E,
Baran Y,
Craig DW,
Christoforides A,
Izatt T,
Kurdoglu AA,
Sinari SA,
Homer N,
Squire K,
Sebat J,
Bafna V,
Burchard EG,
Hernandez RD,
Gignoux CR,
Haussler D,
Katzman SJ,
Kent WJ,
Howie B,
Ruiz-Linares A,
Dermitzakis ET,
Lappalainen T,
Devine SE,
Maroo A,
Tallon LJ,
Rosenfeld JA,
Michelson LP,
Angius A,
Cucca F,
Sanna S,
Bigham A,
Jones C,
Reinier F,
Lyons R,
Schlessinger D,
Awadalla P,
Hodgkinson A,
Oleksyk TK,
Martinez-Cruzado JC,
Fu Y,
Xiong M,
Jorde L,
Witherspoon D,
Xing J,
Browning BL,
Hajirasouliha I,
Chen K,
Albers CA,
Gerstein MB,
Abyzov A,
Chen J,
Habegger L,
Harmanci AO,
Mu XJ,
Sisu C,
Balasubramanian S,
Jin M,
Khurana E,
Clarke D,
Michaelson JJ,
Osullivan C,
Barnes KC,
Gharani N,
Toji LH,
Gerry N,
Kaye JS,
Kent A,
Mathias R,
Ossorio PN,
Parker M,
Rotimi CN,
Royal CD,
Tishkoff S,
Via M,
Bodmer W,
Bedoya G,
Yang G,
You CJ,
Garcia-Montero A,
Orfao A,
Dutil J,
Brooks LD,
Felsenfeld AL

Nature Communications
  5 (0): Jun 13 2014   Elsevier
[Abstract]
[DOI] [Full Text]

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]

Evaluation of methods for modeling transcription factor sequence specificity
Weirauch MT,
Cote A,
Norel R,
Annala M,
Zhao Y,
Riley TR,
Saez-Rodriguez J,
Cokelaer T,
Vedenko A,
Talukder S,
Bussemaker HJ,
Quaid MD,
Bulyk ML,
Stolovitzky G,
Hughes TR,
Agius P,
Arvey A,
Bucher P,
Callan Jr CG,
Chang CW,
Chen CY,
Chen YS,
Chu YW,
Grau J,
Grosse I,
Jagannathan V,
Keilwagen J,
Kiebasa SM,
Kinney JB,
Klein H,
Kursa MB,
Lähdesmäki H,
Laurila K,
Lei C,
Leslie C,
Linhart C,
Murugan A,
Myšičková A,
Noble WS,
Nykter M,
Orenstein Y,
Posch S,
Ruan J,
Rudnicki WR,
Schmid CD,
Shamir R,
Sung WK,
Vingron M,
Zhang Z

Nature Biotechnology
  31 (2): 126-134; Feb 2013  
[Abstract]
[DOI] [Full Text]

A Hybrid Likelihood Model for Sequence-Based Disease Association Studies
Chen YC,
Carter H,
Parla J,
Kramer M,
Goes FS,
Pirooznia M,
Zandi PP,
McCombie WR,
Potash JB,
Karchin R

PLoS Genetics
  9 (1): Jan 2013  
[Abstract]
[DOI] [Full Text]

An integrated map of genetic variation from 1,092 human genomes
Altshuler DM,
Durbin RM,
Abecasis GR,
Bentley DR,
Chakravarti A,
Clark AG,
Donnelly P,
Eichler EE,
Flicek P,
Gabriel SB,
Gibbs RA,
Green ED,
Hurles ME,
Knoppers BM,
Korbel JO,
Lander ES,
Lee C,
Lehrach H,
Mardis ER,
Marth GT,
McVean GA,
Nickerson DA,
Schmidt JP,
Sherry ST,
Wang J,
Wilson RK,
Dinh H,
Kovar C,
Lee S,
Lewis L,
Muzny D,
Reid J,
Wang M,
Fang XD,
Guo XS,
Jian M,
Jiang H,
Jin X,
Li GQ,
Li JX,
Li YR,
Li Z,
Liu X,
Lu Y,
Ma XD,
Su Z,
Tai SS,
Tang MF,
Wang B,
Wang GB,
Wu HL,
Wu RH,
Yin Y,
Zhang WW,
Zhao J,
Zhao MR,
Zheng XL,
Zhou Y,
Gupta N,
Clarke L,
Leinonen R,
Smith RE,
Zheng-Bradley X,
Grocock R,
Humphray S,
James T,
Kingsbury Z,
Sudbrak R,
Albrecht MW,
Amstislavskiy VS,
Borodina TA,
Lienhard M,
Mertes F,
Sultan M,
Timmermann B,
Yaspo ML,
Fulton L,
Fulton R,
Weinstock GM,
Balasubramaniam S,
Burton J,
Danecek P,
Keane TM,
Kolb-Kokocinski A,
McCarthy S,
Stalker J,
Quail M,
Davies CJ,
Gollub J,
Webster T,
Wong B,
Zhan YP,
Auton A,
Yu F,
Bainbridge M,
Challis D,
Evani US,
Lu J,
Nagaswamy U,
Sabo A,
Wang Y,
Yu J,
Coin LJ,
Fang L,
Li QB,
Li ZY,
Lin HX,
Liu BH,
Luo RB,
Qin N,
Shao HJ,
Wang BQ,
Xie YL,
Ye C,
Yu C,
Zhang F,
Zheng HC,
Zhu HM,
Garrison EP,
Kural D,
Lee WP,
Leong WF,
Ward AN,
Wu JT,
Zhang MY,
Griffin L,
Hsieh CH,
Mills RE,
Shi XH,
von Grotthuss M,
Zhang CS,
Daly MJ,
DePristo MA,
Banks E,
Bhatia G,
Carneiro MO,
del Angel G,
Genovese G,
Handsaker RE,
Hartl C,
McCarroll SA,
Nemesh JC,
Poplin RE,
Schaffner SF,
Shakir K,
Yoon SC,
Lihm J,
Makarov V,
Jin HJ,
Kim W,
Kim KC,
Rausch T,
Beal K,
Cunningham F,
Herrero J,
McLaren WM,
Ritchie GR,
Gottipati S,
Keinan A,
Rodriguez-Flores JL,
Sabeti PC,
Grossman SR,
Tabrizi S,
Tariyal R,
Cooper DN,
Ball EV,
Stenson PD,
Barnes B,
Bauer M,
Cheetham RK,
Cox T,
Eberle M,
Kahn S,
Murray L,
Peden J,
Shaw R,
Ye K,
Batzer MA,
Konkel MK,
Walker JA,
MacArthur DG,
Lek M,
Herwig R,
Shriver MD,
Bustamante CD,
Byrnes JK,
De la Vega FM,
Gravel S,
Kenny EE,
Kidd JM,
Lacroute P,
Maples BK,
Moreno-Estrada A,
Zakharia F,
Halperin E,
Baran Y,
Craig DW,
Christoforides A,
Homer N,
Izatt T,
Kurdoglu AA,
Sinari SA,
Squire K,
Xiao CL,
Sebat J,
Bafna V,
Burchard EG,
Hernandez RD,
Gignoux CR,
Haussler D,
Katzman SJ,
Kent WJ,
Howie B,
Ruiz-Linares A,
Dermitzakis ET,
Lappalainen T,
Devine SE,
Liu XY,
Maroo A,
Tallon LJ,
Rosenfeld JA,
Michelson LP,
Kang HM,
Anderson P,
Angius A,
Bigham A,
Blackwell T,
Busonero F,
Cucca F,
Fuchsberger C,
Jones C,
Jun G,
Li Y,
Lyons R,
Maschio A,
Porcu E,
Reinier F,
Sanna S,
Schlessinger D,
Sidore C,
Tan A,
Trost MK,
Awadalla P,
Hodgkinson A,
Lunter G,
Marchini JL,
Myers S,
Churchhouse C,
Delaneau O,
Gupta-Hinch A,
Iqbal Z,
Mathieson I,
Rimmer A,
Xifara DK,
Oleksyk TK,
Fu YX,
Liu XM,
Xiong MM,
Jorde L,
Witherspoon D,
Xing JC,
Browning BL,
Alkan C,
Hajirasouliha I,
Hormozdiari F,
Ko A,
Sudmant PH,
Chen K,
Chinwalla A,
Ding L,
Dooling D,
Koboldt DC,
McLellan MD,
Wallis JW,
Wendl MC,
Zhang QY,
Tyler-Smith C,
Albers CA,
Ayub Q,
Chen Y,
Coffey AJ,
Colonna V,
Huang N,
Jostins L,
Li H,
Scally A,
Walter K,
Xue YL,
Zhang YJ,
Gerstein MB,
Abyzov A,
Balasubramanian S,
Chen JM,
Clarke D,
Fu Y,
Habegger L,
Harmanci AO,
Jin MK,
Khurana E,
Mu XJ,
Sisu C,
Degenhardt J,
Stutz AM,
Church D,
Michaelson JJ,
Ben B,
Lindsay SJ,
Ning ZM,
Yu FL,
Frankish A,
Harrow J,
Fowler G,
Hale W,
Kalra D,
Guo X,
Li G,
Zheng X,
Barker J,
Kelman G,
Kulesha E,
Radhakrishnan R,
Roa A,
Smirnov D,
Streeter I,
Toneva I,
Vaughan B,
Ananiev V,
Belaia Z,
Beloslyudtsev D,
Bouk N,
Chen C,
Cohen R,
Cook C,
Garner J,
Hefferon T,
Kimelman M,
Liu C,
Lopez J,
Meric P,
OSullivan C,
Ostapchuk Y,
Phan L,
Ponomarov S,
Schneider V,
Shekhtman E,
Sirotkin K,
Slotta D,
Zhang H,
Barnes KC,
Beiswanger C,
Cai HY,
Cao HZ,
Gharani N,
Henn B,
Jones D,
Kaye JS,
Kent A,
Kerasidou A,
Mathias R,
Ossorio PN,
Parker M,
Reich D,
Rotimi CN,
Royal CD,
Sandoval K,
Su YY,
Tian ZM,
Tishkoff S,
Toji LH,
Via M,
Wang YH,
Yang HM,
Yang L,
Zhu JY,
Bodmer W,
Bedoya G,
Ming CZ,
Yang G,
You CJ,
Peltonen L,
Garcia-Montero A,
Orfao A,
Dutil J,
Martinez-Cruzado JC,
Brooks LD,
Felsenfeld AL,
McEwen JE,
Clemm NC,
Duncanson A,
Dunn M,
Guyer MS,
Peterson JL,
Genomes Project C

Nature
  491 (7422): 56-65; Nov 1 2012  
[Abstract]
[DOI] [Full Text]

Nonrigid Registration of 2-D and 3-D Dynamic Cell Nuclei Images for Improved Classification of Subcellular Particle Motion
Kim IH,
Chen YC,
Spector DL,
Eils R,
Rohr K

Ieee Transactions on Image Processing
  20 (4): 1011-1022; Apr 2011   ISI
[Abstract]
[DOI] [Full Text]

Drosophila PQBP1 Regulates Learning Acquisition at Projection Neurons in Aversive Olfactory Conditioning
Tamura T,
Horiuchi D,
Chen YC,
Sone M,
Miyashita T,
Saitoe M,
Yoshimura N,
Chiang AS,
Okazawa H

J Neurosci
  30 (42): 14091-14101; Oct 20 2010  
[Abstract]
[DOI] [Full Text] [PDF]

Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera
Cornman SR,
Schatz MC,
Johnston SJ,
Chen Y,
Pettis J,
Hunt G,
Bourgeois L,
Elsik C,
Anderson D,
Grozinger CM,
Evans JD

BMC Genomics
  11 (1): 2010  
[Abstract]
[DOI] [Full Text]

Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees
Cornman RS,
Chen YP,
Schatz MC,
Street C,
Zhao Y,
Desany B,
Egholm M,
Hutchison S,
Pettis JS,
Lipkin WI,
Evans JD

Plos Pathogens
  5 (6): 2009  
[Abstract]
[DOI] [Full Text]

53BP1 promotes non-homologous end joining of telomeres by increasing chromatin mobility
Dimitrova N,
Chen YC,
Spector DL,
de Lange T

Nature
  456 (7221): 524-528; Nov 27 2008  
[Abstract]
[DOI] [Full Text] [PDF]

Live Cell Dynamics of PML Nuclear Bodies upon Entry into and Exit from Mitosis
Chen YC,
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Mol Biol Cell
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Genome analysis of the platypus reveals unique signatures of evolution
Warren WC,
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Nature
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Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5 terminal nucleotide
Mi SJ,
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Cell
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FEBS Journal
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Specific requirement of NMDA receptors for long-term memory consolidation in Drosophila ellipsoid body
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Nat Neurosci
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The central cell plays a critical role in pollen tube guidance in Arabidopsis
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Plant Cell
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A map of olfactory representation in the Drosophila mushroom body
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Cell
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DR5 knockout mice are compromised in radiation-induced apoptosis
Finnberg N,
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Molecular and Cellular Biology
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FOG-1 recruits the NuRD repressor complex to mediate transcriptional repression by GATA-1
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Embo Journal
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radish encodes a phospholipase-A2 and defines a neural circuit involved in anesthesia-resistant memory
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Current Biology
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