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Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes
Law M,
Childs KL,
Campbell MS,
Stein JC,
Olson AJ,
Holt C,
Panchy N,
Lei J,
Jiao D,
Andorf CM,
Lawrence CJ,
Ware D,
Shiu SH,
Sun Y,
Jiang N,
Yandell M

Plant Physiol
  167 (1): 25-39; Jan 2015   Nlm
[Abstract]
[DOI] [Full Text]

An Arabidopsis gene regulatory network for secondary cell wall synthesis
Taylor-Teeples M,
Lin L,
de Lucas M,
Turco G,
Toal TW,
Gaudinier A,
Young NF,
Trabucco GM,
Veling MT,
Lamothe R,
Handakumbura PP,
Xiong G,
Wang C,
Corwin J,
Tsoukalas A,
Zhang L,
Ware D,
Pauly M,
Kliebenstein DJ,
Dehesh K,
Tagkopoulos I,
Breton G,
Pruneda-Paz JL,
Ahnert SE,
Kay SA,
Hazen SP,
Brady SM

Nature
  (0): Dec 24 2014   Nlm
[Abstract]
[DOI] [Full Text]

Automated update, revision and quality control of the Zea mays genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes
Law M,
Childs KL,
Campbell MS,
Stein JC,
Holt C,
Panchy N,
Lei J,
Jao D,
Andorf CM,
Lawrence CJ,
Ware D,
Shiu SH,
Sun Y,
Jiang N,
Yandell M

Plant Physiology
  (0): Nov 10 2014   Nlm
[Abstract]
[DOI] [Full Text]

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3
Zwickl DJ,
Stein JC,
Wing RA,
Ware D,
Sanderson MJ

Systematic biology
  63 (5): 645-59; Sep 2014   Nlm
[Abstract]
[DOI] [Full Text]

Expanding and Vetting Sorghum bicolor Gene Annotations through Transcriptome and Methylome Sequencing
Olson A,
Klein RR,
Dugas DV,
Lu ZY,
Regulski M,
Klein PE,
Ware D

Plant Genome
  7 (2): 20; Jul 2014   Thomson Reuters
[Abstract]
[DOI] [Full Text]

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]

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations
Campbell MS,
Law M,
Holt C,
Stein JC,
Moghe GD,
Hufnagel DE,
Lei J,
Achawanantakun R,
Jiao D,
Lawrence CJ,
Ware D,
Shiu SH,
Childs KL,
Sun Y,
Jiang N,
Yandell M

Plant Physiol
  164 (2): 513-24; Feb 2014   Nlm
[Abstract]
[DOI] [Full Text]

Regulatory modules controlling maize inflorescence architecture
Eveland AL,
Goldshmidt A,
Pautler M,
Morohashi K,
Liseron-Monfils C,
Lewis MW,
Kumari S,
Hiraga S,
Yang F,
Unger-Wallace E,
Olson A,
Hake S,
Vollbrecht E,
Grotewold E,
Ware D,
Jackson D

Genome Research
  24 (3): 431-443; 2014   Nlm
[Abstract]
[DOI] [Full Text]

Ensembl Genomes 2013: scaling up access to genome-wide data
Kersey PJ,
Allen JE,
Christensen M,
Davis P,
Falin LJ,
Grabmueller C,
Hughes DS,
Humphrey J,
Kerhornou A,
Khobova J,
Langridge N,
McDowall MD,
Maheswari U,
Maslen G,
Nuhn M,
Ong CK,
Paulini M,
Pedro H,
Toneva I,
Tuli MA,
Walts B,
Williams G,
Wilson D,
Youens-Clark K,
Monaco MK,
Stein J,
Wei X,
Ware D,
Bolser DM,
Howe KL,
Kulesha E,
Lawson D,
Staines DM

Nucleic Acids Research
  42 (0): D546-52; Jan 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]

Genome-Wide Computational Prediction and Analysis of Core Promoter Elements across Plant Monocots and Dicots
Kumari S,
Ware D

PLoS ONE
  8 (10): Art no. e79011; Oct 29 2013   NLM
[Abstract]
[DOI] [Full Text]

Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between arabidopsis and poplar
Wang D,
Pan E,
Fang G,
Kumari S,
He F,
Ware D,
Maslov S,
Gerstein M

2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
  689-690; Sep 22-Sep 25 2013   Elsevier
[Abstract]
[DOI] [Full Text]

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
Regulski M,
Lu Z,
Kendall J,
Donoghue MT,
Reinders J,
Llaca V,
Deschamps S,
Smith A,
Levy D,
McCombie WR,
Tingey S,
Rafalski A,
Hicks J,
Ware D,
Martienssen R

Genome Res
  (0): Jun 5 2013   NLM
[Abstract]
[DOI] [Full Text]

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress
Dharmawardhana P,
Ren L,
Amarasinghe V,
Monaco M,
Thomason J,
Ravenscroft D,
McCouch S,
Ware D,
Jaiswal P

Rice
  6 (1): 1-15; May 29 2013   Elsevier
[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]

Maize Metabolic Network Construction and Transcriptome Analysis
Monaco MK,
Sen TZ,
Dharmawardhana PD,
Ren L,
Schaeffer M,
Naithani S,
Amarasinghe V,
Thomason J,
Harper L,
Gardiner J,
Cannon EK,
Lawrence CJ,
Ware D,
Jaiswal P

Plant Genome
  6 (1): Mar 2013   Thomson-Reuters
[Abstract]
[DOI] [Full Text]

ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize
Hung HY,
Shannon LM,
Tian F,
Bradbury PJ,
Chen C,
Flint-Garcia SA,
McMullen MD,
Ware D,
Buckler ES,
Doebley JF,
Holland JB

Proceedings of the National Academy of Sciences of the United States of America
  109 (28): E1913-E1921; Jul 10 2012  
[Abstract]
[DOI] [Full Text]

Comparative population genomics of maize domestication and improvement
Hufford MB,
Xu X,
van Heerwaarden J,
Pyhajarvi T,
Chia JM,
Cartwright RA,
Elshire RJ,
Glaubitz JC,
Guill KE,
Kaeppler SM,
Lai JS,
Morrell PL,
Shannon LM,
Song C,
Springer NM,
Swanson-Wagner RA,
Tiffin P,
Wang J,
Zhang GY,
Doebley J,
McMullen MD,
Ware D,
Buckler ES,
Yang S,
Ross-Ibarra J

Nature Genetics
  44 (7): 808-811; Jul 2012  
[Abstract]
[DOI] [Full Text]

Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays
Liu ZJ,
Kumari S,
Zhang LF,
Zheng YL,
Ware D

PLoS ONE
  7 (6): e39786; Jun 29 2012  
[Abstract]
[DOI] [Full Text]

Maize HapMap2 identifies extant variation from a genome in flux
Chia JM,
Song C,
Bradbury PJ,
Costich D,
de Leon N,
Doebley J,
Elshire RJ,
Gaut B,
Geller L,
Glaubitz JC,
Gore M,
Guill KE,
Holland J,
Hufford MB,
Lai J,
Li M,
Liu X,
Lu Y,
McCombie R,
Nelson R,
Poland J,
Prasanna BM,
Pyhajarvi T,
Rong T,
Sekhon RS,
Sun Q,
Tenaillon MI,
Tian F,
Wang J,
Xu X,
Zhang Z,
Kaeppler SM,
Ross-Ibarra J,
McMullen MD,
Buckler ES,
Zhang G,
Xu Y,
Ware D

Nat Genet
  44 (7): 803-U238; Jun 3 2012   NLM
[Abstract]
[DOI] [Full Text]

Taking the Next Step: Building an Arabidopsis Information Portal
Baerenfaller K,
Bastow R,
Beynon J,
Brady S,
Brendel V,
Donaldson S,
Dooley R,
Forster M,
Friesner J,
Gifford D,
Grotewold E,
Gutierrez R,
Huala E,
Jaiswal P,
Joshi H,
Kersey P,
Liu L,
Loraine A,
Lyons E,
May S,
Mayer K,
MacLean D,
Meyers B,
Mueller L,
Muller R,
Muller HM,
Ouellette F,
Pires JC,
Provart N,
Staiger D,
Stanzione D,
Taylor J,
Taylor C,
Town C,
Toyoda T,
Vaughn M,
Walsh S,
Ware D,
Weckwerth W,
Int Arabidopsis I

Plant Cell
  24 (6): 2248-2256; Jun 2012  
[Abstract]
[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]

GrameneMart: the BioMart data portal for the Gramene project
Spooner W,
Youens-Clark K,
Staines D,
Ware D

Database (Oxford)
  2012 (0): bar056; Feb 28 2012   NLM
[Abstract]
[DOI] [Full Text]

Genetic structure and domestication history of the grape
Myles S,
Boyko AR,
Owens CL,
Brown PJ,
Grassi F,
Aradhya MK,
Prins B,
Reynolds A,
Chia JM,
Ware DH,
Bustamante CD,
Buckler ES

Proceedings of the National Academy of Sciences of the United States of America
  108 (9): 3530-3535; Mar 2011   Elsevier PMC3048109
[Abstract]
[DOI]

Sequencing for the cream of the crop
Chia JM,
Ware DH

Nature Biotechnology
  29 (2): 138-9; Feb 2011  
[DOI]

Gramene database in 2010: Updates and extensions
Youens-Clark K,
Buckler E,
Casstevens T,
Chen C,
DeClerck G,
Derwent P,
Dharmawardhana P,
Jaiswal P,
Kersey P,
Karthikeyan AS,
Lu J,
McCouch SR,
Ren L,
Spooner W,
Stein JC,
Thomason J,
Wei S,
Ware DH

Nucleic Acids Research
  39 (0): Jan 2011   PMCID: PMC3013721
[Abstract]
[DOI] [Full Text] [PDF]

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]

Enhanced Y1H assays for Arabidopsis
Gaudinier A,
Zhang L,
Reece-Hoyes JS,
Taylor-Teeples M,
Pu L,
Liu Z,
Breton G,
Pruneda-Paz JL,
Kim D,
Kay SA,
Walhout AJ,
Ware D,
Brady SM

Nature Methods
  (0): 2011  
[Abstract]
[DOI] [Full Text]

A stele-enriched gene regulatory network in the Arabidopsis root
Brady SM,
Zhang L,
Megraw M,
Martinez NJ,
Jiang E,
Yi CS,
Liu W,
Zeng A,
Taylor-Teeples M,
Kim D,
Ahnert S,
Ohler U,
Ware DH,
Walhout AJ,
Benfey PN

Molecular Systems Biology
  7 (0): 2011   PMC3049412
[Abstract]
[DOI] [Full Text] [PDF]

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
Swanson-Wagner RA,
Eichten SR,
Kumari S,
Tiffin P,
Stein JC,
Ware DH,
Springer NM

Genome Research
  20 (12): 1689-1699; Dec 2010   PMCID: PMC2989995
[Abstract]
[DOI]

Digital Gene Expression Signatures for Maize Development
Eveland AL,
Satoh-Nagasawa N,
Goldschmidt A,
Meyer S,
Beatty M,
Sakai H,
Ware DH,
Jackson DP

Plant Physiol
  (0): Sep 10 2010   PMCID: PMC2971585
[Abstract]
[DOI] [Full Text] [PDF]

Rapid Genomic Characterization of the Genus Vitis
Myles S,
Chia JM,
Hurwitz BL,
Simon C,
Zhong GY,
Buckler E,
Ware DH

PLoS ONE
  5 (1): Jan 13 2010   PMCID: PMC2805708
[Abstract]
[DOI] [Full Text] [PDF]

Comprehensive data infrastructure for plant bioinformatics
Jordan C,
Stanzione D,
Ware DH,
Lu J,
Noutsos C

  2010  
[Abstract]
[Full Text]

Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents
Gill N,
SanMiguel P,
Dhillon BD,
Abernathy B,
Kim H,
Stein LD,
Ware DH,
Wing R,
Jackson SA

Rice
  (0): 1-19; 2010  
[Abstract]
[DOI] [Full Text]

The Oryza BAC resource: A genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives
Ammiraju JS,
Song X,
Luo M,
Sisneros N,
Angelova A,
Kudrna D,
Kim H,
Yu Y,
Goicoechea JL,
Lorieux M,
Kurata N,
Brar D,
Ware DH,
Jackson S,
Wing RA

Breeding Science
  60 (5): 536-543; 2010   Elsevier
[Abstract]
[DOI]

Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae)
Cranston KA,
Hurwitz BL,
Sanderson MJ,
Ware DH,
Wing RA,
Stein LD

Systematic Botany
  35 (3): 512-523; 2010  
[Abstract]
[DOI] [Full Text]

Rice structural variation: A comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza
Hurwitz BL,
Kudrna D,
Yu Y,
Sebastian A,
Zuccolo A,
Jackson SA,
Ware DH,
Wing RA,
Stein LD

Plant Journal
  63 (6): 990-1003; 2010  
[Abstract]
[DOI] [Full Text] [PDF]

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,
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PLoS genetics
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PLoS Genet
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PLoS Genet
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Systematic Biology
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PLoS Genet
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