Cold Spring Harbor Library  CSHL: Home
   Home       Services       Archives       About Us   
 
CSHL Publication List
CSHL Authors Publications
Go back to Search Mode

          
Sort by   in order
37 Article(s) on File
Page 1 of 1
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]

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,
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]

A first-generation haplotype map of maize
Gore MA,
Chia JM,
Elshire RJ,
Sun Q,
Ersoz ES,
Hurwitz BL,
Peiffer JA,
McMullen MD,
Grills GS,
Ross-Ibarra J,
Ware DH,
Buckler ES

Science
  326 (5956): 1115-1117; Nov 20 2009  
[Abstract]
[DOI] [Full Text] [PDF]

CMap 1.01: A comparative mapping application for the Internet
Youens-Clark K,
Faga BP,
Yap IV,
Stein LD,
Ware DH

Bioinformatics
  25 (22): 3040-3042; Nov 15 2009   PMCID: PMC2773250
[Abstract]
[DOI] [Full Text] [PDF]

A Genome-Wide Characterization of MicroRNA Genes in Maize
Zhang L,
Chia JM,
Kumari S,
Stein JC,
Liu Z,
Narechania A,
Maher CA,
Guill K,
McMullen MD,
Ware DH

PLoS Genet
  5 (11): e1000716; Nov 2009   PMCID:PMC2773440
[Abstract]
[DOI] [Full Text] [PDF]

The physical and genetic framework of the maize b73 genome
Wei F,
Zhang J,
Zhou S,
He R,
Schaeffer M,
Collura K,
Kudrna D,
Faga BP,
Wissotski M,
Golser W,
Rock SM,
Graves TA,
Fulton RS,
Coe E,
Schnable PS,
Schwartz DC,
Ware DH,
Clifton SW,
Wilson RK,
Wing RA

PLoS Genet
  5 (11): e1000715; Nov 2009   PMCID: PMC2774505
[Abstract]
[DOI] [Full Text] [PDF]

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]

Evidence-based gene predictions in plant genomes
Liang C,
Mao L,
Ware DH,
Stein LD

Genome Res
  19 (10): 1912-1923 ; Oct 2009   PMCID: PMC 2765265
[Abstract]
[DOI] [Full Text] [PDF]

Species Trees from Highly Incongruent Gene Trees in Rice
Cranston KA,
Hurwitz BL,
Ware DH,
Stein LD,
Wing RA

Systematic Biology
  58 (5): 489-500; Oct 2009  
[Abstract]
[Full Text]

The genetic architecture of maize flowering time
Buckler ES,
Holland JB,
Bradbury PJ,
Acharya CB,
Brown PJ,
Browne C,
Ersoz E,
Flint-Garcia S,
Garcia A,
Glaubitz JC,
Goodman MM,
Harjes C,
Guill K,
Kroon DE,
Larsson S,
Lepak NK,
Li H,
Mitchell SE,
Pressoir G,
Peiffer JA,
Rosas MO,
Rocheford TR,
Romay MC,
Romero S,
Salvo S,
Sanchez Villeda H,
da Silva HS,
Sun Q,
Tian F,
Upadyayula N,
Ware DH,
Yates H,
Yu J,
Zhang Z,
Kresovich S,
McMullen MD

Science
  325 (5941): 714-8; Aug 7 2009  
[Abstract]
[DOI] [Full Text] [PDF]

Genetic Properties of the Maize Nested Association Mapping Population
McMullen MD,
Kresovich S,
Villeda HS,
Bradbury PJ,
Li H,
Sun Q,
Flint-Garcia S,
Thornsberry J,
Acharya CB,
Bottoms C,
Brown PJ,
Browne C,
Eller M,
Guill K,
Harjes C,
Kroon DE,
Lepak N,
Mitchell SE,
Peterson B,
Pressoir G,
Romero S,
Rosas MO,
Salvo S,
Yates H,
Hanson M,
Jones EG,
Smith S,
Glaubitz JC,
Goodman MM,
Ware DH,
Holland JB,
Buckler ES

Science
  325 (5941): 737-740; Aug 7 2009  
[Abstract]
[DOI] [Full Text] [PDF]

Gramene QTL database: development, content and applications
Ni J,
Pujar A,
Youens-Clark K,
Yap IV,
Jaiswal P,
Tecle I,
Tung C,
Ren L,
Spooner W,
Wei X,
Avraham S,
Ware DH,
Stein LD,
McCouch S

Database
  2009 (0): bap005; May 12 2009   PMC2790302
[Abstract]
[DOI] [Full Text] [PDF]

Microdissection of shoot meristem functional domains
Brooks L,
Strable J,
Zhang X,
Ohtsu K,
Zhou R,
Sarkar A,
Hargreaves S,
Elshire RJ,
Eudy D,
Pawlowska T,
Ware DH,
Janick-Buckner D,
Buckner B,
Timmermans MC,
Schnable PS,
Nettleton D,
Scanlon MJ

PLoS Genet
  5 (5): e1000476; May 2009   PMCID: PMC2673047
[Abstract]
[DOI] [Full Text] [PDF]

The Sorghum bicolor genome and the diversification of grasses
Paterson AH,
Bowers JE,
Bruggmann R,
Dubchak I,
Grimwood J,
Gundlach H,
Haberer G,
Hellsten U,
Mitros T,
Poliakov A,
Schmutz J,
Spannagl M,
Tang H,
Wang X,
Wicker T,
Bharti AK,
Chapman J,
Feltus FA,
Gowik U,
Grigoriev IV,
Lyons E,
Maher CA,
Martis M,
Narechania A,
Otillar RP,
Penning BW,
Salamov AA,
Wang Y,
Zhang L,
Carpita NC,
Freeling M,
Gingle AR,
Hash CT,
Keller B,
Klein P,
Kresovich S,
McCann MC,
Ming R,
Peterson DG,
Mehboob ur R,
Ware DH,
Westhoff P,
Mayer KF,
Messing J,
Rokhsar DS

Nature
  457 (7229): 551-556; Jan 29 2009  
[Abstract]
[DOI] [Full Text] [PDF]

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats
Wicker T,
Narechania A,
Sabot F,
Stein JC,
Vu GT,
Graner A,
Ware DH,
Stein N

BMC Genomics
  9 (0): 518; Oct 31 2008   PMCID: PMC2584661
[Abstract]
[DOI] [Full Text] [PDF]

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes
Kurtz S,
Narechania A,
Stein JC,
Ware DH

BMC Genomics
  9 (0): 517; Oct 31 2008   PMCID: PMC2613927
[Abstract]
[DOI] [Full Text] [PDF]

Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)
Lu C,
Jeong DH,
Kulkarni K,
Pillay M,
Nobuta K,
German R,
Thatcher SR,
Maher C,
Zhang L,
Ware DH,
Liu B,
Cao X,
Meyers BC,
Green PJ

Proc Natl Acad Sci U S A
  105 (12): 4951-4956; Mar 2008   PMCID: PMC2290808
[Abstract]
[DOI] [Full Text] [PDF]

Construction, alignment and analysis of 12 framework physical maps that represent the 10 genome types of the genus Oryza
Kim HR,
Hurwitz BL,
Yu Y,
Collura K,
Gill N,
SanMiguel P,
Mullikin JC,
Maher C,
Nelson W,
Wissotski M,
Braidotti M,
Kudrna D,
Goigochia JL,
Stein LD,
Ware DH,
Jackson S,
Soderlund C,
Wing R

Genome Biology
  9 (2): R45; Feb 27 2008   PMCID: PMC2374706
[Abstract]
[DOI] [Full Text] [PDF]

Gramene: a growing plant comparative genomics resource
Liang C,
Jaiswal P,
Hebbard C,
Avraham S,
Buckler ES,
Casstevens T,
Hurwitz BL,
McCouch S,
Ni J,
Pujar A,
Ravenscroft D,
Ren L,
Spooner W,
Tecle I,
Thomason J,
Tung CW,
Wei X,
Yap I,
Youens-Clark K,
Ware DH,
Stein LD

Nucleic Acids Res
  36 (0): D947-53; Jan 2008   PMCID: PMC2238951
[Abstract]
[DOI] [Full Text] [PDF]

Panzea: an update on new content and features
Canaran P,
Buckler ES,
Glaubitz JC,
Stein LD,
Sun Q,
Zhao W,
Ware DH

Nucleic Acids Res
  36 (0): D1041-3; Jan 2008   PMCID: PMC2238995
[Abstract]
[DOI] [Full Text] [PDF]

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
Avraham S,
Tung CW,
Ilic K,
Jaiswal P,
Kellogg EA,
McCouch S,
Pujar A,
Reiser L,
Rhee SY,
Sachs MM,
Schaeffer M,
Stein LD,
Stevens P,
Vincent L,
Zapata F,
Ware DH

Nucleic Acids Res
  36 (0): D449-54; Jan 2008   PMCID: PMC2238838
[Abstract]
[DOI] [Full Text] [PDF]

Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci
Hufford KM,
Canaran P,
Ware DH,
McMullen MD,
Gaut BS

Plant Physiology
  144 (3): 1642-1653; Jul 2007  
[Abstract]
[DOI] [Full Text] [PDF]

The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
Ilic K,
Kellogg EA,
Jaiswal P,
Zapata F,
Stevens PF,
Vincent LP,
Avraham S,
Reiser L,
Pujar A,
Sachs MM,
Whitman NT,
McCouch SR,
Schaeffer ML,
Ware DH,
Stein LD,
Rhee SY

Plant Physiology
  143 (2): 587-599; Feb 2007  
[DOI] [Full Text] [PDF]

Gramene
Ware DH

Methods Mol Biol
  406 (0): 315-29; 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Panzea: a database and resource for molecular and functional diversity in the maize genome
Zhao W,
Canaran P,
Jurkuta R,
Fulton T,
Glaubitz J,
Buckler E,
Doebley J,
Gaut B,
Goodman M,
Holland J,
Kresovich S,
McMullen MD,
Stein LD,
Ware DH

Nucleic Acids Res
  34 (0): D752-7; Jan 1 2006  
[Abstract]
[DOI] [Full Text] [PDF]

Gramene, a tool for grass Genomics
Ware DH,
Jaiswal PJ,
Ni JJ,
Yap I,
Pan XK,
Clark KY,
Teytelman L,
Schmidt SC,
Zhao W,
Chang K,
Cartinhour S,
Stein LD,
McCouch SR

Plant Physiology
  130 (4): 1606-1613; Dec 2002  
[Abstract]
[DOI] [Full Text]


Page 1 of 1

Go back to Search Mode


Last Updated: November, 2017
Most Recent Publications: Jan 13, 2015

© 2012   CSHL Library and Archives   1 Bungtown Rd.   Cold Spring Harbor, NY 11724   Library Information 516-367-6872
CSHL Home Intranet