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9 Article(s) on File
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High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource
Seaver SM,
Gerdes S,
Frelin O,
Lerma-Ortiz C,
Bradbury LM,
Zallot R,
Hasnain G,
Niehaus TD,
El Yacoubi B,
Pasternak S,
Olson R,
Pusch G,
Overbeek R,
Stevens R,
de Crecy-Lagard V,
Ware D,
Hanson AD,
Henry CS

Proc Natl Acad Sci U S A
  111 (26): 9645-9650; Jun 9 2014   NLM
[Abstract]
[DOI] [Full Text]

Gramene 2013: comparative plant genomics resources
Monaco MK,
Stein J,
Naithani S,
Wei S,
Dharmawardhana P,
Kumari S,
Amarasinghe V,
Youens-Clark K,
Thomason J,
Preece J,
Pasternak S,
Olson A,
Jiao Y,
Lu Z,
Bolser D,
Kerhornou A,
Staines D,
Walts B,
Wu G,
DEustachio P,
Haw R,
Croft D,
Kersey PJ,
Stein L,
Jaiswal P,
Ware D

Nucleic Acids Research
  42 (0): D1193-9; Jan 2014   NLM
[Abstract]
[DOI] [Full Text]

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor
Luo MC,
Gu YQ,
You FM,
Deal KR,
Ma Y,
Hu Y,
Huo N,
Wang Y,
Wang J,
Chen S,
Jorgensen CM,
Zhang Y,
McGuire PE,
Pasternak S,
Stein JC,
Ware D,
Kramer M,
McCombie WR,
Kianian SF,
Martis MM,
Mayer KF,
Sehgal SK,
Li W,
Gill BS,
Bevan MW,
Šimková H,
Doležel J,
Weining S,
Lazo GR,
Anderson OD,
Dvorak J

Proceedings of the National Academy of Sciences of the United States of America
  110 (19): 7940-7945; May 7 2013  
[DOI] [Full Text]

The tomato genome sequence provides insights into fleshy fruit evolution
Sato S,
Tabata S,
Hirakawa H,
Asamizu E,
Shirasawa K,
Isobe S,
Kaneko T,
Nakamura Y,
Shibata D,
Aoki K,
Egholm M,
Knight J,
Bogden R,
Li CB,
Shuang Y,
Xu X,
Pan SK,
Cheng SF,
Liu X,
Ren YY,
Wang J,
Albiero A,
Dal Pero F,
Todesco S,
Van Eck J,
Buels RM,
Bombarely A,
Gosselin JR,
Huang MY,
Leto JA,
Menda N,
Strickler S,
Mao LY,
Gao S,
Tecle IY,
York T,
Zheng Y,
Vrebalov JT,
Lee J,
Zhong SL,
Mueller LA,
Stiekema WJ,
Ribeca P,
Alioto T,
Yang WC,
Huang SW,
Du YC,
Zhang ZH,
Gao JC,
Guo YM,
Wang XX,
Li Y,
He J,
Li CY,
Cheng ZK,
Zuo JR,
Ren JF,
Zhao JH,
Yan LH,
Jiang HL,
Wang B,
Li HS,
Li ZJ,
Fu FY,
Chen BT,
Han B,
Feng Q,
Fan DL,
Wang Y,
Ling HQ,
Xue YB,
Ware D,
McCombie WR,
Lippman ZB,
Chia JM,
Jiang K,
Pasternak S,
Gelley L,
Kramer M,
Anderson LK,
Chang SB,
Royer SM,
Shearer LA,
Stack SM,
Rose JK,
Xu YM,
Eannetta N,
Matas AJ,
McQuinn R,
Tanksley SD,
Camara F,
Guigo R,
Rombauts S,
Fawcett J,
Van de Peer Y,
Zamir D,
Liang CB,
Spannagl M,
Gundlach H,
Bruggmann R,
Mayer K,
Jia ZQ,
Zhang JH,
Ye ZB,
Bishop GJ,
Butcher S,
Lopez-Cobollo R,
Buchan D,
Filippis I,
Abbott J,
Dixit R,
Singh M,
Singh A,
Pal JK,
Pandit A,
Singh PK,
Mahato AK,
Dogra V,
Gaikwad K,
Sharma TR,
Mohapatra T,
Singh NK,
Causse M,
Rothan C,
Schiex T,
Noirot C,
Bellec A,
Klopp C,
Delalande C,
Berges H,
Mariette J,
Frasse P,
Vautrin S,
Zouine M,
Latche A,
Rousseau C,
Regad F,
Pech JC,
Philippot M,
Bouzayen M,
Pericard P,
Osorio S,
del Carmen AF,
Monforte A,
Granell A,
Fernandez-Munoz R,
Conte M,
Lichtenstein G,
Carrari F,
De Bellis G,
Fuligni F,
Peano C,
Grandillo S,
Termolino P,
Pietrella M,
Fantini E,
Falcone G,
Fiore A,
Giuliano G,
Lopez L,
Facella P,
Perrotta G,
Daddiego L,
Bryan G,
Orozco M,
Pastor X,
Torrents D,
van Schriek K,
Feron RM,
van Oeveren J,
de Heer P,
daPonte L,
Jacobs-Oomen S,
Cariaso M,
Prins M,
van Eijk MJ,
Janssen A,
van Haaren MJ,
Jo SH,
Kim J,
Kwon SY,
Kim S,
Koo DH,
Lee S,
Hur CG,
Clouser C,
Rico A,
Hallab A,
Gebhardt C,
Klee K,
Jocker A,
Warfsmann J,
Gobel U,
Kawamura S,
Yano K,
Sherman JD,
Fukuoka H,
Negoro S,
Bhutty S,
Chowdhury P,
Chattopadhyay D,
Datema E,
Smit S,
Schijlen EW,
van de Belt J,
van Haarst JC,
Peters SA,
van Staveren MJ,
Henkens MH,
Mooyman PJ,
Hesselink T,
van Ham R,
Jiang GY,
Droege M,
Choi D,
Kang BC,
Kim BD,
Park M,
Yeom SI,
Lee YH,
Choi YD,
Li GC,
Gao JW,
Liu YS,
Huang SX,
Fernandez-Pedrosa V,
Collado C,
Zuniga S,
Wang GP,
Cade R,
Dietrich RA,
Rogers J,
Knapp S,
Fei ZJ,
White RA,
Thannhauser TW,
Giovannoni JJ,
Botella MA,
Gilbert L,
Gonzalez R,
Goicoechea JL,
Yu Y,
Kudrna D,
Collura K,
Wissotski M,
Wing R,
Schoof H,
Meyers BC,
Gurazada AB,
Green PJ,
Mathur S,
Vyas S,
Solanke AU,
Kumar R,
Gupta V,
Sharma AK,
Khurana P,
Khurana JP,
Tyagi AK,
Dalmay T,
Mohorianu I,
Walts B,
Chamala S,
Barbazuk WB,
Li JP,
Guo H,
Lee TH,
Wang YP,
Zhang D,
Paterson AH,
Wang XY,
Tang HB,
Barone A,
Chiusano ML,
Ercolano MR,
DAgostino N,
Di Filippo M,
Traini A,
Sanseverino W,
Frusciante L,
Seymour GB,
Elharam M,
Fu Y,
Hua A,
Kenton S,
Lewis J,
Lin SP,
Najar F,
Lai HS,
Qin BF,
Qu CM,
Shi RH,
White D,
White J,
Xing YB,
Yang KQ,
Yi J,
Yao ZY,
Zhou LP,
Roe BA,
Vezzi A,
DAngelo M,
Zimbello R,
Schiavon R,
Caniato E,
Rigobello C,
Campagna D,
Vitulo N,
Valle G,
Nelson DR,
De Paoli E,
Szinay D,
de Jong HH,
Bai YL,
Visser RG,
Lankhorst RM,
Beasley H,
McLaren K,
Nicholson C,
Riddle C,
Gianese G

Nature
  485 (7400): 635-641; May 2012  
[Abstract]
[DOI] [Full Text]

The iPlant Collaborative: Cyberinfrastructure for Plant Biology
Goff SA,
Vaughn M,
McKay ,
Lyons E,
Stapleton AE,
Gessler D,
Matasci N,
Wang L,
Hanlon M,
Lenards A,
Muir A,
Merchant N,
Lowry S,
Mock S,
Helmke M,
Kubach A,
Narro M,
Hopkins N,
Micklos D,
Hilgert U,
Gonzales M,
Jordan C,
Skidmore ,
Dooley R,
Cazes J,
McLay R,
Lu Z,
Pasternak S,
Koesterke L,
Piel WH,
Grene R,
Noutsos C,
Gendler K,
Feng X,
Tang C,
Lent M,
Kim SJ,
Kvilekval K,
Manjunath B,
Tannen V,
Stamatakis ,
Sanderson MJ,
Welch SM,
Cranston K,
Soltis P,
Soltis ,
OMeara B,
Ane C,
Brutnell T,
Kleibenstein DJ,
White JW,
Leebens-Mack J,
Donoghue MJ,
Spalding EP,
Vision TJ,
Myers R,
Lowenthal D,
Enquist BJ,
Boyle B,
Akoglu A,
Andrews G,
Ram S,
Ware D,
Stein L,
Stanzione D

Frontiers in Plant Science
  2 (0): Jan 2011  
[Abstract]
[DOI] [Full Text]

The B73 Maize Genome: Complexity, Diversity, and Dynamics
Schnable PS,
Ware DH,
Fulton RS,
Stein JC,
Wei FS,
Pasternak S,
Liang CZ,
Zhang JW,
Fulton L,
Graves TA,
Minx P,
Reily AD,
Courtney L,
Kruchowski SS,
Tomlinson C,
Strong C,
Delehaunty K,
Fronick C,
Courtney B,
Rock SM,
Belter E,
Du FY,
Kim K,
Abbott RM,
Cotton M,
Levy A,
Marchetto P,
Ochoa K,
Jackson SM,
Gillam B,
Chen WZ,
Yan L,
Higginbotham J,
Cardenas M,
Waligorski J,
Applebaum E,
Phelps L,
Falcone J,
Kanchi K,
Thane T,
Scimone A,
Thane N,
Henke J,
Wang T,
Ruppert J,
Shah N,
Rotter K,
Hodges J,
Ingenthron E,
Cordes M,
Kohlberg S,
Sgro J,
Delgado B,
Mead K,
Chinwalla A,
Leonard S,
Crouse K,
Collura K,
Kudrna D,
Currie J,
He RF,
Angelova A,
Rajasekar S,
Mueller T,
Lomeli R,
Scara G,
Ko A,
Delaney K,
Wissotski M,
Lopez G,
Campos D,
Braidotti M,
Ashley E,
Golser W,
Kim H,
Lee S,
Lin JK,
Dujmic Z,
Kim W,
Talag J,
Zuccolo A,
Fan C,
Sebastian A,
Kramer MR,
Spiegel L,
Nascimento L,
Zutavern T,
Miller B,
Ambroise C,
Muller S,
Spooner W,
Narechania A,
Ren LY,
Wei S,
Kumari S,
Faga BP,
Levy MJ,
McMahan L,
Van Buren P,
Vaughn MW,
Ying K,
Yeh CT,
Emrich SJ,
Jia Y,
Kalyanaraman A,
Hsia AP,
Barbazuk WB,
Baucom RS,
Brutnell TP,
Carpita NC,
Chaparro C,
Chia JM,
Deragon JM,
Estill JC,
Fu Y,
Jeddeloh JA,
Han YJ,
Lee H,
Li PH,
Lisch DR,
Liu SZ,
Liu ZJ,
Nagel DH,
McCann MC,
SanMiguel P,
Myers AM,
Nettleton D,
Nguyen J,
Penning BW,
Ponnala L,
Schneider KL,
Schwartz DC,
Sharma A,
Soderlund C,
Springer NM,
Sun Q,
Wang H,
Waterman M,
Westerman R,
Wolfgruber TK,
Yang LX,
Yu Y,
Zhang LF,
Zhou SG,
Zhu Q,
Bennetzen JL,
Dawe RK,
Jiang JM,
Jiang N,
Presting GG,
Wessler SR,
Aluru S,
Martienssen RA,
Clifton SW,
McCombie WR,
Wing RA,
Wilson RK

Science
  326 (5956): 1112-1115; Nov 20 2009  
[Abstract]
[DOI] [Full Text] [PDF]

Detailed analysis of a contiguous 22-Mb region of the maize genome
Wei F,
Stein JC,
Liang C,
Zhang J,
Fulton RS,
Baucom RS,
De Paoli E,
Zhou S,
Yang L,
Han Y,
Pasternak S,
Narechania A,
Zhang L,
Yeh CT,
Ying K,
Nagel DH,
Collura K,
Kudrna D,
Currie J,
Lin J,
Kim H,
Angelova A,
Scara G,
Wissotski M,
Golser W,
Courtney L,
Kruchowski S,
Graves TA,
Rock SM,
Adams S,
Fulton LA,
Fronick C,
Courtney W,
Kramer M,
Spiegel L,
Nascimento L,
Kalyanaraman A,
Chaparro C,
Deragon JM,
Miguel PS,
Jiang N,
Wessler SR,
Green PJ,
Yu Y,
Schwartz DC,
Meyers BC,
Bennetzen JL,
Martienssen RA,
McCombie WR,
Aluru S,
Clifton SW,
Schnable PS,
Ware D,
Wilson RK,
Wing RA

PLoS genetics
  5 (11): e1000728; Nov 2009  
[Abstract]
[DOI] [Full Text]

A single molecule scaffold for the maize genome
Zhou S,
Wei F,
Nguyen J,
Bechner M,
Potamousis K,
Goldstein S,
Pape L,
Mehan MR,
Churas C,
Pasternak S,
Forrest DK,
Wise R,
Ware DH,
Wing RA,
Waterman MS,
Livny M,
Schwartz DC

PLoS Genet
  5 (11): e1000711; Nov 2009   PMCID: PMC2774507
[Abstract]
[DOI] [Full Text] [PDF]

A second generation human haplotype map of over 3.1 million SNPs
Frazer KA,
Ballinger DG,
Cox DR,
Hinds DA,
Stuve LL,
Gibbs RA,
Belmont JW,
Boudreau A,
Hardenbol P,
Leal SM,
Pasternak S,
Wheeler DA,
Willis TD,
Yu FL,
Yang HM,
Zeng CQ,
Gao Y,
Hu HR,
Hu WT,
Li CH,
Lin W,
Liu SQ,
Pan H,
Tang XL,
Wang J,
Wang W,
Yu J,
Zhang B,
Zhang QR,
Zhao HB,
Zhao H,
Zhou J,
Gabriel SB,
Barry R,
Blumenstiel B,
Camargo A,
Defelice M,
Faggart M,
Goyette M,
Gupta S,
Moore J,
Nguyen H,
Onofrio RC,
Parkin M,
Roy J,
Stahl E,
Winchester E,
Ziaugra L,
Altshuler D,
Shen Y,
Yao ZJ,
Huang W,
Chu X,
He YG,
Jin L,
Liu YF,
Shen YY,
Sun WW,
Wang HF,
Wang Y,
Xiong XY,
Xu L,
Waye MM,
Tsui SK,
Wong JT,
Galver LM,
Fan JB,
Gunderson K,
Murray SS,
Oliphant AR,
Chee MS,
Montpetit A,
Chagnon F,
Ferretti V,
Leboeuf M,
Olivier JF,
Phillips MS,
Roumy S,
Sallee C,
Verner A,
Hudson TJ,
Kwok PY,
Cai DM,
Koboldt DC,
Miller RD,
Pawlikowska L,
Taillon-Miller P,
Xiao M,
Tsui LC,
Mak W,
Song YQ,
Tam PK,
Nakamura Y,
Kawaguchi T,
Kitamoto T,
Morizono T,
Nagashima A,
Ohnishi Y,
Sekine A,
Tanaka T,
Tsunoda T,
Deloukas P,
Bird CP,
Delgado M,
Dermitzakis ET,
Gwilliam R,
Hunt S,
Morrison J,
Powell D,
Stranger BE,
Whittaker P,
Bentley DR,
Daly MJ,
de Bakker PI,
Barrett J,
Chretien YR,
Maller J,
McCarroll S,
Patterson N,
Peer I,
Price A,
Purcell S,
Richter DJ,
Sabeti P,
Saxena R,
Schaffner SF,
Sham PC,
Varilly P,
Stein LD,
Krishnan L,
Smith AV,
Tello-Ruiz MK,
Thorisson GA,
Chakravarti A,
Chen PE,
Cutler DJ,
Kashuk CS,
Lin S,
Abecasis GR,
Guan WH,
Li Y,
Munro HM,
Qin ZH,
Thomas DJ,
McVean G,
Auton A,
Bottolo L,
Cardin N,
Eyheramendy S,
Freeman C,
Marchini J,
Myers S,
Spencer C,
Stephens M,
Donnelly P,
Cardon LR,
Clarke G,
Evans DM,
Morris AP,
Weir BS,
Johnson TA,
Mullikin JC

Nature
  449 (7164): 851-U3; Oct 2007  
[Abstract]
[DOI] [Full Text] [PDF]


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