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Bioinformatics: Databases

Date: Monday, January 13, 2014
Time: 7:00 AM-10:00 PM
Room: Grand Exhibit Hall
Genome-wide prediction of highly specific guide RNA spacers for the CRISPR-Cas9 mediated genome editing in model plants and major crops
Kabin Xie, Pennsylvania State University; Jianwei Zhang, Arizona Genomics Institute; Yinong Yang, Pennsylvania State University

Data Collection, Processing and Integration for Systems Biology Research on Drought Tolerance
Aneta Sawikowska, Institute of Plant Genetics, Polish Academy of Science; Hanna Cwiek, Institute of Plant Genetics, Polish Academy of Science; Wojciech Frohmberg, Institute of Plant Genetics, Polish Academy of Science; Zygmunt Kaczmarek, Institute of Plant Genetics, Polish Academy of Science; Pawel Krajewski, Institute of Plant Genetics PAS; Consortium Polapgen, POLAPGEN Consortium for Applied Genetics and Genomics

Plant Reactome
Vindya Amarasinghe, Dept. of Botany & Plant Pathology, Oregon State University; Justin Preece, Department of Botany & Plant Pathology, Oregon State University; Palitha Dharmawardhana, Department of Botany & Plant Pathology, Oregon State University; Guanming Wu, Ontario Institute for Cancer Research; Sushma Naithani, Department of Botany & Plant Pathology, Oregon State University; Peter D'Eustachio, NYU School of Medicine; Marcela Karey Tello-Ruiz, Cold Spring Harbor Laboratory; Dylan Beorchia, Oregon State University; Alex Roos, Oregon State University; Kindra Amoss, Oregon State University; David Croft, European Bioinformatics Institute; Robin Haw, Ontario Institute for Cancer Research; Henning Hermjakob, European Bioinformatics Institute; Lincoln Stein, Ontario Institute of Cancer Research; Doreen Ware, Cold Spring Harbor Laboratory, Cold Spring Harbor; Pankaj Jaiswal, Department of Botany & Plant Pathology, Oregon State University

Crop Ontology, a Resource for Enabling Access to Breeders' Data
Elizabeth Arnaud, Bioversity International; Luca Matteis, Bioversity International; Marie-Angelique Laporte, Bioversity International; Herlin R. Espinosa Gutierrez, International Center for Tropical Agriculture (CIAT); Glenn Hyman, International Center for Tropical Agriculture (CIAT); Rosemary Shrestha, Genetic Resources Prog.,CIMMYT; Arllet Portugal, Integrated Breeding Platform; Pierre-Yves Chibon, UR Plant Breeding, Wageningen Univ.; Medha Devare, CGIAR Consortium Office; Akinnola N. Akintunde, International Black Sea University (IBSU); Jeffrey W. White, USDA-ARS; Mark D. Wilkinson, CBGP, Univ. Politécnica de Madrid; Caterina Caracciolo, Food and Agriculture Organization (FAO); Fabrizio Celli, Food and Agriculture Organization (FAO); Graham McLaren, Integrated Breeding Platform

Ensembl Plants - an Integrative Resource for Plant Genome Data
Paul J. Kersey, EMBL - The European Bioinformatics Institute

Plant Genome Database Japan (PGDBj), a Comprehensive Database Covering Information of Plant Genome-Related Databases in Japan
Erika Asamizu, Kazusa DNA Research Institute; Hisako Ichihara, Kazusa DNA Research Institute; Akihiro Nakaya, Niigata University; Yasukazu Nakamura, Kazusa DNA Research Institute; Hideki Hirakawa, Kazusa DNA Research Institute; Satoshi Tabata, Kazusa DNA Research Institute

Constructing an Integrated DNA Polymorphism Database and an Analytical Workflow for Plants and Bacteria
Takako Mochizuki, Genome Informatics Laboratory, NIG, ROIS; Takatomo Fujisawa, Genome Informatics Laboratory, NIG, ROIS; Yasuhiro Tanizawa, Genome Informatics Laboratory, NIG, ROIS; Hideki Nagasaki, Genome Informatics Laboratory, NIG, ROIS; Eli Kaminuma, Genome Informatics Laboratory, NIG, ROIS, JAPAN; Tokurou Shimizu, Okitsu group, NIFTS, JAPAN; Atsushi Toyoda, Comparative Genomics laboratory, NIG, ROIS, JAPAN; Asao Fujiyama, Comparative Genomics laboratory, NIG, ROIS; Nori Kurata, Plant Genetics Laboratory, NIG, ROIS; Naruo Nikoh, Liberal Arts, OUJ; Yasukazu Nakamura, Genome Informatics Laboratory, NIG, ROIS

ODG: A Graph Database Generator for Omics Data
Joseph Guhlin, Department of Plant Pathology, University of Minnesota; Kevin AT Silverstein, Supercomputing Institute, University of Minnesota; Peng Zhou, Department of Plant Pathology, University of Minnesota; Shaun Curtin, University of Minnesota; Roxanne Denny, Department of Plant Pathology, University of Minnesota; Trevor Wennblom, Supercomputing Institute, University of Minnesota; Nevin D. Young, Department of Plant Pathology, University of Minnesota

ATGC Transcriptomics: An Application to Explore and Analyze de novo Transcriptomic Data
Maximo Lisandro Rivarola, National Institute of Agronomic Technologies

Differential and Coherent Processing of Small RNA-Seq Data
Jan Gorodkin, Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen

The South Green Bioinformatics Platform
Mathieu Rouard, Bioversity International; Alexis Dereeper, IRD, UMR RPB; Gaetan Droc, CIRAD, UMR AGAP; Gautier Sarah, INRA, UMR AGAP; Jean-François Dufayard, CIRAD, UMR AGAP; Valentin Guignon, Bioversity International; Chantal Hamelin, CIRAD, UMR AGAP; Felix Homa, CIRAD, UMR AGAP; Fred de Lamotte, INRA, UMR AGAP; Pierre Larmande, IRD, UMR DIADE, Institut de Biologie Computationnelle; Delphine Lariviere, CIRAD, UMR AGAP; François Sabot, UMR DIADE; Guilhem Sempéré, CIRAD, UMR Intertryp; Marilyne Summo, CIRAD; Bertrand Pitollat, CIRAD; Stephanie Pointet, CIRAD, UMR AGAP; Dominique This, Montpellier SupAgro; Stéphanie Bocs, CIRAD, UMR AGAP; Manuel Ruiz, CIRAD, UMR AGAP

Common Reference Ontologies for Plant Biology: A Platform for Integrative Plant Genomics
Laurel Cooper, Department of Botany & Plant Pathology, Oregon State University; Justin L. Elser, Department of Botany & Plant Pathology, Oregon State University; Justin Preece, Department of Botany & Plant Pathology, Oregon State University; Elizabeth Arnaud, Bioversity International; Dennis Wm. Stevenson, New York Botanical Garden; Sinisa Todorovic, Oregon State University; Eugene Zhang, Oregon State University; Christopher Mungall, Berkeley Bioinformatics Open-Source Projects; Barry Smith, University at Buffalo; Pankaj Jaiswal, Department of Botany & Plant Pathology, Oregon State University

GigaDB: Helping Users Get Credit for Data By Citation
Christopher I Hunter, BGI-Hong Kong/GigaScience; Tam P Sneddon, ex-BGI Hong Kong/Gigascience; Xiao Si Zhe, BGI-Hong Kong/GigaScience; Peter Li, BGI-Hong Kong/GigaScience; Scott C Edmunds, BGI-Hong Kong/GigaScience; Laurie Goodman, GigaScience BGI/BMC

Plant Omics Data Center: The Integrated Web Repository for Intra- and Interspecies Gene Expression Networks
Hajime Ohyanagi, School of Agriculture, Meiji University, CREST, JST; Masaaki Kobayashi, School of Agri., Meiji University, CREST, JST; Tomoyuki Takano, School of Agriculture, Meiji University; Shin Terashima, School of Agriculture, Meiji University; Hayato Matsumura, School of Agriculture, Meiji University; Hiromi Toyoshima, School of Agriculture, Meiji University, JST, CREST; Kyoko Morimoto, School of Agriculture, Meiji University; Maasa Kanno, School of Agriculture, Meiji University; Yohei Sasaki, School of Agriculture, Meiji University; Takayuki Suzuki, School of Agriculture, Meiji University; Koji Yokoyama, School of Agriculture, Meiji University; Kentaro Yano, School of Agriculture, Meiji University

K-GCAK: K-mer-based Genome Composition Analysis Knowledgebase
Dapeng Wang, Beijing Institute of Genomics, CAS; Jiayue Xu, Beijing Institute of Genomics, CAS, Beijing, China; Jun Yu, Beijing Institute of Genomics, CAS, Beijing, China

Soybean Knowledge Base (SoyKB)
Trupti Joshi, University of Missouri; Shiyuan Chen, University of Missouri; Yang Liu, University of Missouri-Columbia; Hongxin Zhang, University of Missouri-Columbia; Gary Stacey, University of Missouri; Henry T. Nguyen, University of Missouri; Dong Xu, University of Missouri

Intermine Webservices for Phytozome
Joseph W. Carlson, DOE Joint Genome Institute; Richard D Hayes, DOE Joint Genome Institute; David M. Goodstein, DOE Joint Genome Institute; Daniel S. Rokhsar, DOE Joint Genome Institute

Plant Gene Families in Phytozome v10
Jeremy L. Phillips, DOE Joint Genome Institute; Sajeev Batra, DOE Joint Genome Institute; Joseph W. Carlson, DOE Joint Genome Institute; Raf Podowski, DOE Joint Genome Institute; David M. Goodstein, DOE Joint Genome Institute; Daniel S. Rokhsar, DOE Joint Genome Institute

Gramene: A Comparative Resource for Plants
Ken Youens-Clark, Cold Spring Harbor Laboratory; Vindya Amarasinghe, Dept. of Botany & Plant Pathology, Oregon State University; Palitha Dharmawardhana, Department of Botany & Plant Pathology, Oregon State University; Pankaj Jaiswal, Department of Botany & Plant Pathology, Oregon State University; Sunita Kumari, Cold Spring Harbor Laboratory; Marcela Karey Tello-Ruiz, Cold Spring Harbor Laboratory; Sushma Naithani, Department of Botany & Plant Pathology, Oregon State University; Shiran Pasternak, Cold Spring Harbor Lab; Justin Preece, Department of Botany & Plant Pathology, Oregon State University; Joshua Stein, Cold Spring Harbor Laboratory; Jim Thomason, Cold Spring Harbor Laboratory; Sharon Wei, Cold Spring Harbor Laboratory; Doreen Ware, Cold Spring Harbor Laboratory/USDA-ARS; Paul J. Kersey, EMBL - The European Bioinformatics Institute; Helen Parkinson, EMBL-EBI

Browsing and Comparing Genomes Using the Gramene Ensembl Browser
Joshua Stein, Cold Spring Harbor Laboratory; Sharon Wei, Cold Spring Harbor Laboratory; Marcela Karey Tello-Ruiz, Cold Spring Harbor Laboratory; Ken Youens-Clark, Cold Spring Harbor Laboratory; Andrew Olson, Cold Spring Harbor Laboratory; Sunita Kumari, Cold Spring Harbor Laboratory; Jerry Lu, Cold Spring Harbor Laboratory; Jim Thomason, Cold Spring Harbor Laboratory; Dan Bolser, EMBL - The European Bioinformatics Institute; Arnaud Kerhornou, EMBL-The European Bioinformatics Institute; Paul J. Kersey, EMBL - The European Bioinformatics Institute; Doreen Ware, USDA ARS NAA Robert W. Holley Center

Oryzabase: Utilization of Solr to Provide Search Services
Kyohei Matsuno, National Institute of Genetics; Shunsuke Maeda, National Institute of Genetics; Gaku Kimura, National Institute of Genetics; Rie Tsuchiya, National Institute of Genetics; Yukiko Yamazaki, National Institute of Genetics

Germinate: Wheat and Maize Databases for the Seeds of Discovery Project
Paul Shaw, The James Hutton Institute; Sebastian Raubach, The James Hutton Institute; Iain Milne, The James Hutton Institute; Gordon Stephen, The James Hutton Institute; Peter Wenzl, CIMMYT - International Maize and Wheat Improvement Centre; Sarah Hearne, CIMMYT; Sukhwinder Singh, CIMMYT- International Maize and Wheat Improvement Centre; David Marshall, The James Hutton Institute

The Transplant Consortium – Tools and Resources for the Complex Genomes of Wheat and Barley
Manuel Spannagl, Helmholtz Center Munich - Plant Genome and Systems Biology; Kai C. Bader, Helmholtz Center Munich, IBIS/MIPS; Klaus Mayer, Institute of Bioinformatics & Systems Biology, MIPS; Paul J. Kersey, EMBL - The European Bioinformatics Institute; Dan Bolser, EMBL-EBI; Arnaud Kerhornou, EMBL-The European Bioinformatics Institute; Michael Alaux, INRA - URGI; Delphine Steinbach, INRA - URGI; Hadi Quesneville, INRA - URGI

The Triticeae Toolbox (T3): Improvements in Crop Phenotyping, Data Visualization, and  Analysis Tools
Clay Birkett, USDA-ARS; David E. Matthews, USDA ARS; Jean-Luc Jannink, USDA, Cornell University; Victoria Carollo Blake, USDA ARS WRRC

The Triticeae Toolbox:  Separating the Grain from the Chaff for Small Grains Breeders
Victoria Carollo Blake, USDA ARS WRRC; David E. Matthews, USDA ARS; Clay Birkett, USDA-ARS; David Hane, University of California / USDA-ARS-WRRC; Peter Bradbury, USDA ARS-Cornell University; Jean-Luc Jannink, USDA, Cornell University

Next Generation Resequencing of 108 Soybean Germplasm for Trait Discovery
Trupti Joshi, University of Missouri; Babu Valliyodan, University of Missouri & National Center for Soybean Biotechnology; Saad M. Khan, University of Missouri-Columbia; Yang Liu, University of Missouri-Columbia; Joao V. Maldonado dos Santos, University of Missouri-Columbia; Yongqing Jiao, University of Missouri-Columbia; Dong Xu, University of Missouri; Henry T. Nguyen, University of Missouri-Columbia

The Legume Information System 2014
Steven B. Cannon, USDA-ARS-CICGRU; Andrew D. Farmer, National Center for Genome Resources (NCGR); Alex G. Rice, National Center for Genome Resources (NCGR); Pooja E. Umale, National Center for Genome Resources (NCGR); Alan Cleary, Montana State University; Nathan T. Weeks, USDA-ARS-CICGRU; Scott R. Kalberer, USDA-ARS-CICGRU; Ethalinda Cannon, Iowa State University; Sudhansu Dash, Virtual Reality Application Center; Rex Nelson, USDA-ARS-CICGRU; David Grant, USDA-ARS

solGS: A Bioinformatics Solution for Genomic Selection
Isaak Y. Tecle, Boyce Thompson Institute for Plant Research; Naama Menda, Boyce Thompson Institute for Plant Research; Jeremy D. Edwards, Boyce Thompson Institute for Plant Research; Lukas Mueller, Boyce Thompson Institute for Plant Research

Accessing SGN Genomes through Tools
Susan R. Strickler, Boyce Thompson Institute for Plant Research

Bioinformatic Solutions in Forest Genomics: Accessing the Treegenes Database
Jill Wegrzyn, University of Connecticut; Jacob Zieve, University of California, Davis; Hans Vasquez-Gross, University of California Davis; Derek Lin, University of California, Davis; James Zheng, University of California, Davis; David Neale, Dept. Plant Sciences University of California Davis

Building a Sustainable Database Resource for Arabidopsis and Plant Research
Donghui Li, Carnegie Institution for Science; Tanya Z. Berardini, Phoenix Bioinformatics; Robert Muller, Carnegie Institution for Science; David Huang, Carnegie Institution for Science; Eva Huala, Carnegie Institution for Science

HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Hormone Signaling and Regulatory Networks
Tingsong Liu, The Samuel Roberts Noble Foundation; Xinbin Dai, The Samuel Roberts Noble Foundation; Jun Li, The Samuel Roberts Noble Foundation; Patrick Xuechun Zhao, The Samuel Roberts Noble Foundation

Liverwort Genome Analysis Using DDBJ Pipeline and Construction of the Database Annotated By the Research Communities
Hideki Nagasaki, Genome Informatics Laboratory, NIG, ROIS; Kimitsune Ishizaki, Kobe University, Graduate School of Science; Katsuyuki T. Yamato, Kinki University, B.O.S.T.; Takayuki Kohchi, Kyoto University, Graduate School of Biostudies; Yasukazu Nakamura, Genome Informatics Laboratory, NIG, ROIS

Parasitic Plant Genome Database: A Resource for Parasitic Orobanchaceae Transcritptomes
Eric Kenneth Wafula, Penn State University; Loren Honaas, Penn State University; Paula Ralph, Penn State University; Yeting Zhang, Penn State University; Zhenzhen Yang, Penn State University; Lena Sheaffer, Penn State University; Norman Wickett, Chicago Botanical Garden; Kan Huang, University of Virginia; Yongde Bao, University of Virginia; Monica Fernandez-Aparicio, Virginia Tech University; Malay Das, Presidency University; Pradeepa Bandaranayake, Department of Crop Science, University of Peradeniya; Biao Wu, University of California-Davis; Michael P. Timko, University of Virginia; John Yoder, University of California-Davis; James H. Westwood, Virginia Tech University; Claude dePamphilis, Penn State University

Hymenoptera Genome Database: 2014 Update
Colin Diesh, Division of Animal Sciences, University of Missouri; Darren E. Hagen, Division of Animal Sciences, University of Missouri; Christopher P. Childers, Division of Animal Sciences, University of Missouri; Jay D. Evans, USDA ARS Bee Research Lab; Christine G. Elsik, delete

Bovine Genome Database: Resources for Re-Annotating the Bos taurus Genome
Darren E. Hagen, Division of Animal Sciences, University of Missouri; Christopher P. Childers, Division of Animal Sciences, University of Missouri; Colin Diesh, Division of Animal Sciences, University of Missouri; Christine G. Elsik, delete

The NextGen Project: Whole Genome Data to Optimize Methods to Maintain Farm Animal Biodiversity
Laura Clarke, European Molecular Biology Laboratory; Ian Streeter, European Molecular Biology Laboratory; Holly Zheng-Bradley, European Molecular Biology Laboratory; David Richardson, European Molecular Biology Laboratory; Avik Datta, European Molecular Biology Laboratory; Paul Flicek, European Molecular Biology Laboratory; The NextGen Consortium, European Molecular Biology Laboratory

The National Avian Research Facility Genomic Database
Richard Kuo, Roslin Institute, University of Edinburgh; Lel Arpad Eory, Roslin Institute University of Edinburgh; David Burt, Roslin Institute Univ of Edinburgh; Almas A. Gheyas, The Roslin Institute, University of Edinburgh; Clarissa Boschiero, University of São Paulo/ESALQ; Alan Hart, Roslin Institute; Pete Kaiser, The Roslin Institute, University of Edinburgh; Mark Fife, Pirbright Institute

ELMA: A Platform for Transcriptional and Epigenetic Microarray Studies of Livestock Embryos
Jason R. Grant, University of Alberta; Eric Fournier, Université Laval; Prudencio Tossou, Université Laval; Adriano S. Arantes, University of Alberta; Claude Robert, Université Laval; Marc-André Sirard, Université Laval; Walter T. Dixon, University of Alberta; Michael Dyck, University of Alberta; George Foxcroft, University of Alberta; Paul Stothard, University of Alberta

Introduction to the Gramene Website
Ken Youens-Clark, Cold Spring Harbor Laboratory

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