Doreen Ware

Doreen Ware

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Doreen Ware

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Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing.

Front Genet 2019 26;10:384. Epub 2019 Apr 26.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States.

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http://dx.doi.org/10.3389/fgene.2019.00384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498185PMC
April 2019

Predicting gene structure changes resulting from genetic variants via exon definition features.

Bioinformatics 2018 11;34(21):3616-3623

Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198862PMC
November 2018

SciApps: a cloud-based platform for reproducible bioinformatics workflows.

Bioinformatics 2018 11;34(22):3917-3920

Cold Spring Harbor Laboratories, Cold Spring Harbor, Ithaca, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty439DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6223375PMC
November 2018

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes.

Nat Genet 2018 09 30;50(9):1289-1295. Epub 2018 Jul 30.

State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.

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http://dx.doi.org/10.1038/s41588-018-0182-0DOI Listing
September 2018

Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure.

Curr Protoc Bioinformatics 2018 09 31;63(1):e53. Epub 2018 Aug 31.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

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http://doi.wiley.com/10.1002/cpbi.53
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http://dx.doi.org/10.1002/cpbi.53DOI Listing
September 2018

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Nat Biotechnol 2018 07;36(7):566-569

Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA.

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http://dx.doi.org/10.1038/nbt.4163DOI Listing
July 2018

A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing.

Genome Res 2018 06 30;28(6):921-932. Epub 2018 Apr 30.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gr.227462.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991521PMC
June 2018

MSD1 regulates pedicellate spikelet fertility in sorghum through the jasmonic acid pathway.

Nat Commun 2018 02 26;9(1):822. Epub 2018 Feb 26.

U.S. Department of Agriculture-Agricultural Research Service, Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, Lubbock, TX, 79415, USA.

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http://www.nature.com/articles/s41467-018-03238-4
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http://dx.doi.org/10.1038/s41467-018-03238-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5826930PMC
February 2018

Efficient Identification of Causal Mutations through Sequencing of Bulked F from Two Allelic Bloomless Mutants of .

Front Plant Sci 2017 12;8:2267. Epub 2018 Jan 12.

Cropping Systems Research Laboratory, Agricultural Research Service (USDA), Lubbock, TX, United States.

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http://dx.doi.org/10.3389/fpls.2017.02267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5771210PMC
January 2018

The Plastid and Mitochondrial Peptidase Network in : A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis.

Plant Cell 2017 Nov 25;29(11):2687-2710. Epub 2017 Sep 25.

School for Integrative Plant Sciences, Section Plant Biology, Cornell University, Ithaca, New York 14853

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http://dx.doi.org/10.1105/tpc.17.00481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5728138PMC
November 2017

A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses.

Plant Cell 2016 07 27;28(7):1551-62. Epub 2016 Jun 27.

Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415

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http://dx.doi.org/10.1105/tpc.16.00373DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981137PMC
July 2016

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.

Plant J 2016 06;86(6):472-80

Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA.

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http://dx.doi.org/10.1111/tpj.13175DOI Listing
June 2016

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.

Nat Commun 2016 06 24;7:11708. Epub 2016 Jun 24.

Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/ncomms11708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4931018PMC
June 2016

Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.

Methods Mol Biol 2016 ;1374:141-63

Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA.

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http://dx.doi.org/10.1007/978-1-4939-3167-5_7DOI Listing
May 2016

Metabolomic Profiling of the Nectars of Aquilegia pubescens and A. Canadensis.

PLoS One 2015 1;10(5):e0124501. Epub 2015 May 1.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America; USDA-ARS-NAA, Robert W. Holley Center, Ithaca, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124501PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416886PMC
January 2016

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences.

PLoS Biol 2016 Jan 11;14(1):e1002342. Epub 2016 Jan 11.

The University of Arizona, Tucson, Arizona, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4709069PMC
January 2016

An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize.

BMC Genomics 2015 Dec 21;16:1078. Epub 2015 Dec 21.

Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130, Chengdu, China.

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http://dx.doi.org/10.1186/s12864-015-2242-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687334PMC
December 2015

The BioMart community portal: an innovative alternative to large, centralized data repositories.

Authors:
Damian Smedley Syed Haider Steffen Durinck Luca Pandini Paolo Provero James Allen Olivier Arnaiz Mohammad Hamza Awedh Richard Baldock Giulia Barbiera Philippe Bardou Tim Beck Andrew Blake Merideth Bonierbale Anthony J Brookes Gabriele Bucci Iwan Buetti Sarah Burge Cédric Cabau Joseph W Carlson Claude Chelala Charalambos Chrysostomou Davide Cittaro Olivier Collin Raul Cordova Rosalind J Cutts Erik Dassi Alex Di Genova Anis Djari Anthony Esposito Heather Estrella Eduardo Eyras Julio Fernandez-Banet Simon Forbes Robert C Free Takatomo Fujisawa Emanuela Gadaleta Jose M Garcia-Manteiga David Goodstein Kristian Gray José Afonso Guerra-Assunção Bernard Haggarty Dong-Jin Han Byung Woo Han Todd Harris Jayson Harshbarger Robert K Hastings Richard D Hayes Claire Hoede Shen Hu Zhi-Liang Hu Lucie Hutchins Zhengyan Kan Hideya Kawaji Aminah Keliet Arnaud Kerhornou Sunghoon Kim Rhoda Kinsella Christophe Klopp Lei Kong Daniel Lawson Dejan Lazarevic Ji-Hyun Lee Thomas Letellier Chuan-Yun Li Pietro Lio Chu-Jun Liu Jie Luo Alejandro Maass Jerome Mariette Thomas Maurel Stefania Merella Azza Mostafa Mohamed Francois Moreews Ibounyamine Nabihoudine Nelson Ndegwa Céline Noirot Cristian Perez-Llamas Michael Primig Alessandro Quattrone Hadi Quesneville Davide Rambaldi James Reecy Michela Riba Steven Rosanoff Amna Ali Saddiq Elisa Salas Olivier Sallou Rebecca Shepherd Reinhard Simon Linda Sperling William Spooner Daniel M Staines Delphine Steinbach Kevin Stone Elia Stupka Jon W Teague Abu Z Dayem Ullah Jun Wang Doreen Ware Marie Wong-Erasmus Ken Youens-Clark Amonida Zadissa Shi-Jian Zhang Arek Kasprzyk

Nucleic Acids Res 2015 Jul 20;43(W1):W589-98. Epub 2015 Apr 20.

Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia

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http://dx.doi.org/10.1093/nar/gkv350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489294PMC
July 2015

Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots.

PLoS One 2013 29;8(10):e79011. Epub 2013 Oct 29.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0079011PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812177PMC
February 2015

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.

Plant Physiol 2015 Jan 10;167(1):25-39. Epub 2014 Nov 10.

The Jackson Laboratory, Bar Harbor, Maine 04609 (M.L.);Eccles Institute of Human Genetics (M.L., M.S.C., M.Y.), Department of Biomedical Informatics (M.L.), and USTAR Center for Genetic Discovery (C.H., M.Y.), University of Utah, Salt Lake City, Utah 84112;Genetics Program (N.P., S.-H.S., N.J.), Department of Plant Biology (K.L.C., S.-H.S.), Department of Computer Science and Engineering (J.L., Y.S.), and Department of Horticulture (N.J.), Michigan State University, East Lansing, Michigan 48824;iPlant Collaborative, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (J.C.S., A.J.O., D.W.);Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 1L7 (C.H.);Texas Advanced Computing Center, University of Texas, Austin, Texas 78758 (D.J.);Department of Genetics, Development, and Cell Biology and Department of Agronomy (C.J.L.), and United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research (C.M.A.), Iowa State University, Ames, Iowa 50011; andUnited States Department of Agriculture-Agricultural Research Service Northeast Area, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853 (D.W.)

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http://dx.doi.org/10.1104/pp.114.245027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280997PMC
January 2015

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

Syst Biol 2014 Sep 9;63(5):645-59. Epub 2014 Apr 9.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA, and Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1093/sysbio/syu027DOI Listing
September 2014

Ensembl Genomes 2013: scaling up access to genome-wide data.

Nucleic Acids Res 2014 Jan 25;42(Database issue):D546-52. Epub 2013 Oct 25.

The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK, Wellcome Trust Sanger Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK, Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA and USDA-ARS, Cornell University, Ithaca, NY, 14853, USA.

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http://dx.doi.org/10.1093/nar/gkt979DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965094PMC
January 2014

Gramene 2013: comparative plant genomics resources.

Nucleic Acids Res 2014 Jan 11;42(Database issue):D1193-9. Epub 2013 Nov 11.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada, Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA and NAA Plant, Soil & Nutrition Laboratory Research Unit, USDA-ARS, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1093/nar/gkt1110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964986PMC
January 2014

Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays.

PLoS One 2012 29;7(6):e39786. Epub 2012 Jun 29.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039786PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3387268PMC
November 2012

GrameneMart: the BioMart data portal for the Gramene project.

Database (Oxford) 2012 28;2012:bar056. Epub 2012 Feb 28.

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1093/database/bar056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289142PMC
June 2012

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid.

BMC Genomics 2011 Oct 18;12:514. Epub 2011 Oct 18.

Department of Horticulture, Texas A&M University, College Station, TX 77843, USA.

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http://dx.doi.org/10.1186/1471-2164-12-514DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219791PMC
October 2011

Enhanced Y1H assays for Arabidopsis.

Nat Methods 2011 Oct 30;8(12):1053-5. Epub 2011 Oct 30.

Department of Plant Biology and Genome Center, University of California Davis, Davis, California, USA.

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http://dx.doi.org/10.1038/nmeth.1750DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821074PMC
October 2011

Sequencing for the cream of the crop.

Nat Biotechnol 2011 Feb;29(2):138-9

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http://dx.doi.org/10.1038/nbt.1756DOI Listing
February 2011

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor.

Genome Res 2010 Dec 29;20(12):1689-99. Epub 2010 Oct 29.

Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA.

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http://dx.doi.org/10.1101/gr.109165.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989995PMC
December 2010

Rapid genomic characterization of the genus vitis.

PLoS One 2010 Jan 13;5(1):e8219. Epub 2010 Jan 13.

Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008219PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805708PMC
January 2010

CMap 1.01: a comparative mapping application for the Internet.

Bioinformatics 2009 Nov 30;25(22):3040-2. Epub 2009 Jul 30.

Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773250PMC
November 2009

A genome-wide characterization of microRNA genes in maize.

PLoS Genet 2009 Nov 20;5(11):e1000716. Epub 2009 Nov 20.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773440PMC
November 2009

The physical and genetic framework of the maize B73 genome.

PLoS Genet 2009 Nov 20;5(11):e1000715. Epub 2009 Nov 20.

Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000715DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774505PMC
November 2009

A single molecule scaffold for the maize genome.

PLoS Genet 2009 Nov 20;5(11):e1000711. Epub 2009 Nov 20.

Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774507PMC
November 2009

The B73 maize genome: complexity, diversity, and dynamics.

Authors:
Patrick S Schnable Doreen Ware Robert S Fulton Joshua C Stein Fusheng Wei Shiran Pasternak Chengzhi Liang Jianwei Zhang Lucinda Fulton Tina A Graves Patrick Minx Amy Denise Reily Laura Courtney Scott S Kruchowski Chad Tomlinson Cindy Strong Kim Delehaunty Catrina Fronick Bill Courtney Susan M Rock Eddie Belter Feiyu Du Kyung Kim Rachel M Abbott Marc Cotton Andy Levy Pamela Marchetto Kerri Ochoa Stephanie M Jackson Barbara Gillam Weizu Chen Le Yan Jamey Higginbotham Marco Cardenas Jason Waligorski Elizabeth Applebaum Lindsey Phelps Jason Falcone Krishna Kanchi Thynn Thane Adam Scimone Nay Thane Jessica Henke Tom Wang Jessica Ruppert Neha Shah Kelsi Rotter Jennifer Hodges Elizabeth Ingenthron Matt Cordes Sara Kohlberg Jennifer Sgro Brandon Delgado Kelly Mead Asif Chinwalla Shawn Leonard Kevin Crouse Kristi Collura Dave Kudrna Jennifer Currie Ruifeng He Angelina Angelova Shanmugam Rajasekar Teri Mueller Rene Lomeli Gabriel Scara Ara Ko Krista Delaney Marina Wissotski Georgina Lopez David Campos Michele Braidotti Elizabeth Ashley Wolfgang Golser HyeRan Kim Seunghee Lee Jinke Lin Zeljko Dujmic Woojin Kim Jayson Talag Andrea Zuccolo Chuanzhu Fan Aswathy Sebastian Melissa Kramer Lori Spiegel Lidia Nascimento Theresa Zutavern Beth Miller Claude Ambroise Stephanie Muller Will Spooner Apurva Narechania Liya Ren Sharon Wei Sunita Kumari Ben Faga Michael J Levy Linda McMahan Peter Van Buren Matthew W Vaughn Kai Ying Cheng-Ting Yeh Scott J Emrich Yi Jia Ananth Kalyanaraman An-Ping Hsia W Brad Barbazuk Regina S Baucom Thomas P Brutnell Nicholas C Carpita Cristian Chaparro Jer-Ming Chia Jean-Marc Deragon James C Estill Yan Fu Jeffrey A Jeddeloh Yujun Han Hyeran Lee Pinghua Li Damon R Lisch Sanzhen Liu Zhijie Liu Dawn Holligan Nagel Maureen C McCann Phillip SanMiguel Alan M Myers Dan Nettleton John Nguyen Bryan W Penning Lalit Ponnala Kevin L Schneider David C Schwartz Anupma Sharma Carol Soderlund Nathan M Springer Qi Sun Hao Wang Michael Waterman Richard Westerman Thomas K Wolfgruber Lixing Yang Yeisoo Yu Lifang Zhang Shiguo Zhou Qihui Zhu Jeffrey L Bennetzen R Kelly Dawe Jiming Jiang Ning Jiang Gernot G Presting Susan R Wessler Srinivas Aluru Robert A Martienssen Sandra W Clifton W Richard McCombie Rod A Wing Richard K Wilson

Science 2009 Nov;326(5956):1112-5

Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.

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http://www.dawelab.org/wp-content/uploads/2011/03/schnable-2
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http://www.sciencemag.org/cgi/doi/10.1126/science.1178534
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http://dx.doi.org/10.1126/science.1178534DOI Listing
November 2009

Evidence-based gene predictions in plant genomes.

Genome Res 2009 Oct 18;19(10):1912-23. Epub 2009 Jun 18.

Cold Spring Harbor Laboratory, New York 11724, USA.

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http://dx.doi.org/10.1101/gr.088997.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765265PMC
October 2009

Species trees from highly incongruent gene trees in rice.

Syst Biol 2009 Oct 21;58(5):489-500. Epub 2009 Sep 21.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.

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https://academic.oup.com/sysbio/article/58/5/489/1637458
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http://dx.doi.org/10.1093/sysbio/syp054DOI Listing
October 2009

Gramene QTL database: development, content and applications.

Database (Oxford) 2009 8;2009:bap005. Epub 2009 May 8.

Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853-1901, USA and Cold Spring Harbor Labs, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1093/database/bap005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790302PMC
May 2009

Gramene.

Authors:
Doreen Ware

Methods Mol Biol 2007 ;406:315-29

Gramene, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1007/978-1-59745-535-0_15DOI Listing
January 2009

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.

BMC Genomics 2008 Oct 31;9:517. Epub 2008 Oct 31.

Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany.

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http://dx.doi.org/10.1186/1471-2164-9-517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613927PMC
October 2008

Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs).

Proc Natl Acad Sci U S A 2008 Mar 19;105(12):4951-6. Epub 2008 Mar 19.

Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.

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http://dx.doi.org/10.1073/pnas.0708743105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2290808PMC
March 2008

Panzea: an update on new content and features.

Nucleic Acids Res 2008 Jan 19;36(Database issue):D1041-3. Epub 2007 Nov 19.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1093/nar/gkm1022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238995PMC
January 2008

Patterns of selection and tissue-specific expression among maize domestication and crop improvement loci.

Plant Physiol 2007 Jul 11;144(3):1642-53. Epub 2007 May 11.

Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1104/pp.107.098988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1914116PMC
July 2007

Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support.

Bioinformatics 2006 Apr 10;22(7):885-6. Epub 2006 Feb 10.

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl028DOI Listing
April 2006

Evolution of Arabidopsis microRNA families through duplication events.

Genome Res 2006 Apr 6;16(4):510-9. Epub 2006 Mar 6.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gr.4680506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1457037PMC
April 2006

Maintaining collections of mutants for plant functional genomics.

Methods Mol Biol 2003 ;236:311-26

Department of Plant Biology, The Ohio State University, Columbus, OH, USA.

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http://dx.doi.org/10.1385/1-59259-413-1:311DOI Listing
February 2004

Comparison of genes among cereals.

Curr Opin Plant Biol 2003 Apr;6(2):121-7

Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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April 2003