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15 Article(s) on File
Page 1 of 1
Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes
Fortunato SA,
Adamski M,
Ramos OM,
Leininger S,
Liu J,
Ferrier DE,
Adamska M

Nature
  514 (7524): 620-623; Oct 30 2014   NLM
[DOI] [Full Text]

Systematic evaluation of spliced alignment programs for RNA-seq data
Engström PG,
Steijger T,
Sipos B,
Grant GR,
Kahles A,
Rätsch G,
Goldman N,
Hubbard TJ,
Harrow J,
Guigó R,
Bertone P,
Alioto T,
Behr J,
Bohnert R,
Campagna D,
Davis CA,
Dobin A,
Gingeras TR,
Jean G,
Kosarev P,
Li S,
Liu J,
Mason CE,
Molodtsov V,
Ning Z,
Ponstingl H,
Prins JF,
Ribeca P,
Seledtsov I,
Solovyev V,
Valle G,
Vitulo N,
Wang K,
Wu TD,
Zeller G

Nature Methods
  10 (12): 1185-1191; Dec 2013  
[Abstract]
[DOI] [Full Text]

Gentrepid V2.0: a web server for candidate disease gene prediction
Ballouz S,
Liu JY,
George RA,
Bains N,
Liu A,
Oti M,
Gaeta B,
Fatkin D,
Wouters MA

BMC Bioinformatics
  14 (0): Aug 16 2013   NLM
[DOI] [Full Text]

The central cell plays a critical role in pollen tube guidance in Arabidopsis
Chen YH,
Li HJ,
Shi DQ,
Yuan L,
Liu J,
Sreenivasan R,
Baskar R,
Grossniklaus U,
Yang WC

Plant Cell
  19 (11): 3563-3577; Nov 2007  
[Abstract]
[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]

A role for the P-body component GW182 in microRNA function
Liu JD,
Rivas FV,
Wohlschlegel J,
Yates JR,
Parker R,
Hannon GJ

Nature Cell Biology
  7 (12): 1261-1266; Dec 2005  
[Abstract]
[DOI] [Full Text]

The map-based sequence of the rice genome
Matsumoto T,
Wu JZ,
Kanamori H,
Katayose Y,
Fujisawa M,
Namiki N,
Mizuno H,
Yamamoto K,
Antonio BA,
Baba T,
Sakata K,
Nagamura Y,
Aoki H,
Arikawa K,
Arita K,
Bito T,
Chiden Y,
Fujitsuka N,
Fukunaka R,
Hamada M,
Harada C,
Hayashi A,
Hijishita S,
Honda M,
Hosokawa S,
Ichikawa Y,
Idonuma A,
Iijima M,
Ikeda M,
Ikeno M,
Ito K,
Ito S,
Ito T,
Ito Y,
Iwabuchi A,
Kamiya K,
Karasawa W,
Kurita K,
Katagiri S,
Kikuta A,
Kobayashi H,
Kobayashi N,
Machita K,
Maehara T,
Masukawa M,
Mizubayashi T,
Mukai Y,
Nagasaki H,
Nagata Y,
Naito S,
Nakashima M,
Nakama Y,
Nakamichi Y,
Nakamura M,
Meguro A,
Negishi M,
Ohta I,
Ohta T,
Okamoto M,
Ono N,
Saji S,
Sakaguchi M,
Sakai K,
Shibata M,
Shimokawa T,
Song JY,
Takazaki Y,
Terasawa K,
Tsugane M,
Tsuji K,
Ueda S,
Waki K,
Yamagata H,
Yamamoto M,
Yamamoto S,
Yamane H,
Yoshiki S,
Yoshihara R,
Yukawa K,
Zhong HS,
Yano M,
Sasaki T,
Yuan QP,
Shu OT,
Liu J,
Jones KM,
Gansberger K,
Moffat K,
Hill J,
Bera J,
Fadrosh D,
Jin SH,
Johri S,
Kim M,
Overton L,
Reardon M,
Tsitrin T,
Vuong H,
Weaver B,
Ciecko A,
Tallon L,
Jackson J,
Pai G,
Van Aken S,
Utterback T,
Reidmuller S,
Feldblyum T,
Hsiao J,
Zismann V,
Iobst S,
de Vazeille AR,
Buell CR,
Ying K,
Li Y,
Lu TT,
Huang YC,
Zhao Q,
Feng Q,
Zhang L,
Zhu JJ,
Weng QJ,
Mu J,
Lu YQ,
Fan DL,
Liu YL,
Guan JP,
Zhang YJ,
Yu SL,
Liu XH,
Zhang Y,
Hong GF,
Han B,
Choisne N,
Demange N,
Orjeda G,
Samain S,
Cattolico L,
Pelletier E,
Couloux A,
Segurens B,
Wincker P,
DHont A,
Scarpelli C,
Weissenbach J,
Salanoubat M,
Quetier F,
Yu Y,
Kim HR,
Rambo T,
Currie J,
Collura K,
Luo MZ,
Yang TJ,
Ammiraju JS,
Engler F,
Soderlund C,
Wing RA,
Palmer LE,
de la Bastide M,
Spiegel L,
Nascimento L,
Zutavern T,
OShaughnessy A,
Dike S,
Dedhia N,
Preston R,
Balija V,
McCombie WR,
Chow TY,
Chen HH,
Chung MC,
Chen CS,
Shaw JF,
Wu HP,
Hsiao KJ,
Chao YT,
Chu MK,
Cheng CH,
Hour AL,
Lee PF,
Lin SJ,
Lin YC,
Liou JY,
Liu SM,
Hsing YI,
Raghuvanshi S,
Mohanty A,
Bharti AK,
Gaur A,
Gupta V,
Kumar D,
Ravi V,
Vij S,
Kapur A,
Khurana P,
Khurana JP,
Tyagi AK,
Gaikwad K,
Singh A,
Dalal V,
Srivastava S,
Dixit A,
Pal AK,
Ghazi IA,
Yadav M,
Pandit A,
Bhargava A,
Sureshbabu K,
Batra K,
Sharma TR,
Mohapatra T,
Singh NK,
Messing J,
Nelson AB,
Fuks G,
Kavchok S,
Keizer G,
Llaca EL,
Song RT,
Tanyolac B,
Young S,
Il KH,
Hahn JH,
Sangsakoo G,
Vanavichit A,
de Mattos LA,
Zimmer PD,
Malone G,
Dellagostin O,
de Oliveira AC,
Bevan M,
Bancroft I,
Minx P,
Cordum H,
Wilson R,
Cheng ZK,
Jin WW,
Jiang JM,
Leong SA,
Iwama H,
Gojobori T,
Itoh T,
Niimura Y,
Fujii Y,
Habara T,
Sakai H,
Sato Y,
Wilson G,
Kumar K,
McCouch S,
Juretic N,
Hoen D,
Wright S,
Bruskiewich R,
Bureau T,
Miyao A,
Hirochika H,
Nishikawa T

Nature
  436 (7052): 793-800; Aug 2005  
[Abstract]
[DOI] [Full Text] [PDF]

Purified Argonaute2 and an siRNA form recombinant human RISC
Rivas FV,
Tolia NH,
Song JJ,
Aragon JP,
Liu J,
Hannon GJ,
Joshua-Tor L

Nat Struct Mol Biol
  12 (4): 340-9; Apr 2005   NLM
[Abstract]
[DOI] [Full Text]

The transcriptional landscape of the mammalian genome
Carninci P,
Kasukawa T,
Katayama S,
Gough J,
Frith MC,
Maeda N,
Oyama R,
Ravasi T,
Lenhard B,
Wells C,
Kodzius R,
Shimokawa K,
Bajic VB,
Brenner SE,
Batalov S,
Forrest AR,
Zavolan M,
Davis MJ,
Wilming LG,
Aidinis V,
Allen JE,
Ambesi-Impiombato A,
Apweiler R,
Aturaliya RN,
Bailey TL,
Bansal M,
Baxter L,
Beisel KW,
Bersano T,
Bono H,
Chalk AM,
Chiu KP,
Choudhary V,
Christoffels A,
Clutterbuck DR,
Crowe ML,
Dalla E,
Dalrymple BP,
de Bono B,
della Gatta G,
di Bernardo D,
Down T,
Engstrom P,
Fagiolini M,
Faulkner G,
Fletcher CF,
Fukushima T,
Furuno M,
Futaki S,
Gariboldi M,
Georgii-Hemming P,
Gingeras TR,
Gojobori T,
Green RE,
Gustincich S,
Harbers M,
Hayashi Y,
Hensch TK,
Hirokawa N,
Hill D,
Huminiecki L,
Iacono M,
Ikeo K,
Iwama A,
Ishikawa T,
Jakt M,
Kanapin A,
Katoh M,
Kawasawa Y,
Kelso J,
Kitamura H,
Kitano H,
Kollias G,
Krishnan SP,
Kruger AF,
Kummerfeld SK,
Kurochkin IV,
Lareau LF,
Lazarevic D,
Lipovich L,
Liu J,
Liuni S,
McWilliam S,
Madan Babu M,
Madera M,
Marchionni L,
Matsuda H,
Matsuzawa S,
Miki H,
Mignone F,
Miyake S,
Morris K,
Mottagui-Tabar S,
Mulder N,
Nakano N,
Nakauchi H,
Ng P,
Nilsson R,
Nishiguchi S,
Nishikawa S,
Nori F,
Ohara O,
Okazaki Y,
Orlando V,
Pang KC,
Pavan WJ,
Pavesi G,
Pesole G,
Petrovsky N,
Piazza S,
Reed J,
Reid JF,
Ring BZ,
Ringwald M,
Rost B,
Ruan Y,
Salzberg SL,
Sandelin A,
Schneider C,
Schönbach C,
Sekiguchi K,
Semple CA,
Seno S,
Sessa L,
Sheng Y,
Shibata Y,
Shimada H,
Shimada K,
Silva D,
Sinclair B,
Sperling S,
Stupka E,
Sugiura K,
Sultana R,
Takenaka Y,
Taki K,
Tammoja K,
Tan SL,
Tang S,
Taylor MS,
Tegner J,
Teichmann SA,
Ueda HR,
van Nimwegene E,
Verardo R,
Wei CL,
Yagi K,
Yamanishi H,
Zabarovsky E,
Zhu S,
Zimmer A,
Hide W,
Bult C,
Grimmond SM,
Teasdale RD,
Liu ET,
Brusic V,
Quackenbush J,
Wahlestedt C,
Mattick JS,
Hume DA,
Kai C,
Sasaki D,
Tomaru Y,
Fukuda S,
Kanamori-Katayama M,
Suzuki M,
Aoki J,
Arakawa T,
Iida J,
Imamura K,
Itoh M,
Kato T,
Kawaji H,
Kawagashira N,
Kawashima T,
Kojima M,
Kondo S,
Konno H,
Nakano K,
Ninomiya N,
Nishio T,
Okada M,
Plessy C,
Shibata K,
Shiraki T,
Suzuki S,
Tagami M,
Waki K,
Watahiki A,
Okamura-Oho Y,
Suzuki H,
Kawai J,
Hayashizaki Y

Science
  309 (5740): 1559-1563; 2005  
[Abstract]
[Full Text]

Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model
Neuwald AF,
Liu JS

BMC Bioinformatics
  5 (0): 157; Oct 25 2004  
[Abstract]
[DOI] [Full Text]

Argonaute2 is the catalytic engine of mammalian RNAi
Liu J,
Carmell MA,
Rivas FV,
Marsden CG,
Thomson JM,
Song JJ,
Hammond SM,
Joshua-Tor L,
Hannon GJ

Science
  305 (5689): 1437-41; Sep 3 2004   NLM
[Abstract]
[DOI] [Full Text]

The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes
Song JJ,
Liu J,
Tolia NH,
Schneiderman J,
Smith SK,
Martienssen RA,
Hannon GJ,
Joshua-Tor L

Nat Struct Biol
  10 (12): 1026-32; Dec 2003   NLM
[Abstract]
[DOI] [Full Text]

In-depth view of structure, activity, and evolution of rice chromosome 10
Yu YS,
Rambo T,
Currie J,
Saski C,
Kim HR,
Collura K,
Thompson S,
Simmons J,
Yang TJ,
Nah G,
Patel AJ,
Thurmond S,
Henry D,
Oates R,
Palmer M,
Pries G,
Gibson J,
Anderson H,
Paradkar M,
Crane L,
Dale J,
Carver MB,
Wood T,
Frisch D,
Engler F,
Soderlund C,
Palmer LE,
Tetylman L,
Nascimento L,
de la Bastide M,
Spiegel L,
Ware D,
OShaughnessy A,
Dike S,
Dedhia N,
Preston R,
Huang E,
Ferraro K,
Kuit K,
Miller B,
Zutavern T,
Katzenberger F,
Muller S,
Balija V,
Martienssen RA,
Stein L,
Minx P,
Johnson D,
Cordum H,
Mardis E,
Cheng ZK,
Jiang JM,
Wilson R,
McCombie WR,
Wing RA,
Yuan QP,
Shu OY,
Liu J,
Jones KM,
Gansberger K,
Moffat K,
Hill J,
Tsitrin T,
Overton L,
Bera J,
Kim M,
Jin SH,
Tallon L,
Ciecko A,
Pai G,
Van Aken S,
Utterback T,
Reidmuller S,
Bormann J,
Feldblyum T,
Hsiao J,
Zismann V,
Blunt S,
de Vazeilles A,
Shaffer T,
Koo H,
Suh B,
Yang Q,
Haas B,
Peterson J,
Pertea M,
Volfovsky N,
Wortman J,
White O,
Salzberg SL,
Fraser CM,
Buell CR,
Messing J,
Song RT,
Fuks G,
Llaca V,
Kovchak S,
Young S,
Bowers JE,
Paterson AH,
Johns MA,
Mao L,
Pan HQ,
Dean RA,
Rice Chromosome 10 S

Science
  300 (5625): 1566-1569; Jun 6 2003  
[Abstract]
[Full Text]

Rans C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases
Neuwald AF,
Kannan N,
Poleksic A,
Hata N,
Liu JS

Genome Research
  13 (4): 673-692; Apr 2003  
[Abstract]
[Full Text]

Identification of the cell cycle regulator VCP (p97/CDC48) as a substrate of the band 4.1-related protein-tyrosine phosphatase PTPH1
Zhang SH,
Liu J,
Kobayashi R,
Tonks NK

J Biol Chem
  274 (25): 17806-12; Jun 18 1999  
[Abstract]
[Full Text]


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