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Bioinformatics: Databases

Date: Monday, January 14, 2013
Time: 7:00 AM-10:00 PM
Room: Grand Exhibit Hall
dbSNP and dbVar: The NCBI Databases of Simple and Structural Variation
Lon Phan, NIH/NLM/NCBI; Ming Ward, NIH/NLM/NCBI; Hua Zhang, NIH/NLM/NCBI; Mike Kholodov, NIH/NLM/NCBI; David Shao, NIH/NLM/NCBI; Eugene Shekhtman, NIH/NLM/NCBI; Rama Maiti, NIH/NLM/NCBI; Qiang Wang, NCBI/NLM/NIH; Adrienne Kitts, NCBI/NLM/NIH; John Lopez, NIH/NLM/NCBI; Tim Hefferon, NIH/NLM/NCBI; John Garner, NIH/NLM/NCBI; Deanna M. Church, NCBI/NLM/NIH

Using Ensembl to Understand Variation Data
Laura Clarke, European Molecular Biology Laboratory; Fiona Cunningham, EBI; William McLaren, EBI; Graham Ritchie, EBI; Laurent Gil, EBI; Anja Thormann, EBI; Sarah Hunt, EBI

Entrez Probe - A Resource for Nucleic Acid Reagents Used in Genomics
Brian Smith-White, NCBI/NLM/NIH; Michael Baxter, NCBI/NLM/NIH; Dakshesh Darji, NCBI/NLM/NIH, Bethesda, MD; Svetlana Iazvovskaia, NCBI/NLM/NIH; Kirill Rotmistrovsky, NCBI/NLM/NIH; Ilene Mizrachi, NCBI/NLM/NIH; Tatiana Tatusova, NCBI/NLM/NIH

Sequence the Genome once, use any time: Web Based System for Real Time, in silico Genotyping and Visualization of High Throughput Sequence Data
Ted Kalbfleisch, University of Louisville; Michael P. Heaton, USDA, ARS, U.S. Meat Animal Research Center (USMARC)

A Model Organism Database for Phytozome
Joseph W Carlson, US DOE Joint Genome Institute; Shengqiang Shu, DOE Joint Genome Institute; Richard Hayes, US DOE Joint Genome Institute, Walnut Creek, CA; Daniel S. Rokhsar, DOE Joint Genome Institute; David M. Goodstein, US DOE Joint Genome Institute, Walnut Creek, CA

The Plant Metabolic Network - from Arabidopsis thaliana to Zea mays: 11 Metabolic Pathway Databases Power Research in Plant Metabolism
Kate A. Dreher, Carnegie Institution for Science; Peifen Zhang, Carnegie Institution for Science; Lee Chae, Carnegie Institution for Science; Ricardo Nilo-Poyanco, Universidad Andres Bello; Robert Muller, Carnegie Institution for Science; Seung Yon Rhee, Carnegie Institution for Science

Plant Reactome: Metabolic and Regulatory Networks for Plants
Palitha Dharmawardhana, Oregon State University; Justin Preece, Dept. of Botany & Plant Pathology, Oregon State University; Vindya Amarasinghe, Dept. of Botany & Plant Pathology, Oregon State University; Guanming Wu, Ontario Institute for Cancer Research; Dylan Beorchia, Oregon State University; Kindra Amoss, Oregon State University; Sushma Naithani, Oregon State University; Peter D'Eustachio, NYU School of Medicine; Hardeep Nahal, University of Toronto; Marcela Karey Monaco, Cold Spring Harbor Laboratory; David Croft, European Bioinformatics Institute; Robin Haw, Ontario Institute for Cancer Research; Nick Provart, University of Toronto; Henning Hermjakob, European Bioinformatics Institute; Lincoln Stein, Ontario Institute for Cancer Research; Doreen Ware, Cold Spring Harbor Laboratory; Pankaj Jaiswal, Dept. of Botany & Plant Pathology, Oregon State University

SRGPs: An Online Resource for Comparative Analysis of Stress Responsive Genes in Plants
Mychal W. Ivancich, Michigan Technological University; Rafi Shaik, Dept.of Biological Sciences, Michigan Tech; Ramakrishna Wusirika, Michigan Technological University

Function Prediction in Plant Genomes from Large Scale Phylogenomics Analyses
Valentin Guignon, Bioversity International; Jean-François Dufayard, CIRAD - UMR AGAP; Sebastien Briois, Syngenta Seeds; Matthieu G. Conte, Syngenta Seeds; Mathieu Rouard, Bioversity International

Development of a Unified Phenotype Dataset for Plants
Eva Huala, Carnegie Institution for Science; Steven B. Cannon, USDA-ARS-CICGRU; Laurel Cooper, Dept. of Botany & Plant Pathology, Oregon State University; George Gkoutos, University of Aberystwyth; Lisa C Harper, USDA-ARS; Pankaj Jaiswal, Dept. of Botany & Plant Pathology, Oregon State University; Carolyn J. Lawrence, USDA ARS Iowa State University; Johnny Lloyd, Michigan State University; David Meinke, Oklahoma State University; Naama Menda, Boyce Thompson Institute for Plant Research; Laura Moore, Oregon State University; Lukas Mueller, Boyce Thompson Institute for Plant Research; Rex T. Nelson, USDA-ARS-CICGRU; Ramona Walls, University of Arizona

GnpSeq NGS: a New Tool to Manage NGS Data in URGI's Information System (GnpIS)
Célia Michotey, INRA; Nacer Mohellibi, INRA - URGI; Hadi Quesneville, INRA - URGI; Delphine Steinbach, INRA - URGI

PLAIN – A Computational API for Plant Genomic Data
Robert Muller, Carnegie Institution for Science; David K. Huang, Carnegie Institution for Science; Cynthia Lee, Carnegie Institution for Science; Eva Huala, Carnegie Institution for Science

Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics
Laurel Cooper, Dept. of Botany & Plant Pathology, Oregon State University; Laura Moore, Oregon State University; Elizabeth Arnaud, Bioversity International; Rex T. Nelson, USDA-ARS-CICGRU; Naama Menda, Boyce Thompson Institute for Plant Research; Rosemary Shrestha, CIMMYT; David Grant, USDA-ARS-CICGRU and Iowa State University; Luca Matteis, Bioversity International; Christopher Mungall, Berkeley Bioinformatics Open-Source Projects; Lukas Mueller, Boyce Thompson Institute for Plant Research; Ruth Bastow, GARNet; Graham McLaren, Generation Challenge Programme; Pankaj Jaiswal, Dept. of Botany & Plant Pathology, Oregon State University

The Species-Specific Crop Ontology (Generation Challenge Programme): Application and Integration into the Reference Plant Trait Ontology to Enable Data Mining on Phenotypes
Elizabeth Arnaud, Bioversity International; Rosemary Shrestha, CIMMYT; Peter Kulakow, International Institute of Tropical Agriculture (IITA); Moshood Bakare, IITA; Antonio Lopez-Montes, IITA; Sam Ofodile, IITA; Praveen Reddy T., ICRISAT; Peteti Prasad, ICRISAT; Trushar Shah, ICRISAT; Charles Thomas Hash, ICRISAT; Eva Weltzien-Rattunde, ICRISAT; Ibrahima Sissoko, ICRISAT; Alberto Fabio Guerrero, CIAT; Reinhard Simon, CIP; Nikki Frances Borja Borja, IRRI; Mauleon Ramil, IRRI; Luca Matteis, Bioversity International; Milko Skofic, Bioversity International; Tom Hazekamp, Bioversity International; Graham McLaren, GCP; Laurel Cooper, Dept. of Botany & Plant Pathology, Oregon State University; Pankaj Jaiswal, Dept. of Botany & Plant Pathology, Oregon State University; Naama Menda, Boyce Thompson Institute for Plant Research; Rex Nelson, USDA-ARS CICGRU; David Grant, USDA-ARS-CICGRU and Iowa State University; Ruth Bastow, GARNet; Lukas Mueller, Boyce Thompson Institute for Plant Research; Jean-Francois Rami, CIRAD

Ontological Descriptions of Phenotypes, with a Case Study in Maize
Ramona Walls, The iPlant Collaborative; Lisa C Harper, USDA-ARS; Mary Schaeffer, USDA ARS and University of Missouri; Carolyn J. Lawrence, USDA ARS Iowa State University; Eva Huala, Carnegie Institution for Science

The transPLANT Consortium - Special Focus on Triticeae Genome Resources
Manuel Spannagl, MIPS/IBIS, Helmholtz Center Munich; Klaus Mayer, Helmholtz Center Munich, IBIS/MIPS; Paul J. Kersey, EMBL - The European Bioninformatics Institute; Dan Bolser, EMBL-EBI; Delphine Steinbach, INRA - URGI; Hadi Quesneville, INRA URGI; on Behalf Of The transPLANT consortium, European Union FP7

The transPLANT Variation Data Management System
Paul J. Kersey, EMBL - The European Bioninformatics Institute; Christoph Grabmueller, EMBL-EBI; Dan Bolser, EMBL-EBI

Gramene Build 36: A Resource for Comparative Plant Genomics
Ken Youens-Clark, Cold Spring Harbor Laboratory; Vindya Amarasinghe, Dept. of Botany & Plant Pathology, Oregon State University; Palitha Dharmawardhana, Oregon State University; Pankaj Jaiswal, Dept. of Botany & Plant Pathology, Oregon State University; Sunita Kumari, Cold Spring Harbor Laboratory; Marcela Karey Monaco, Cold Spring Harbor Laboratory; Sushma Naithani, Oregon State University; Shiran Pasternak, Cold Spring Harbor Laboratory; Justin Preece, Dept. 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; Paul J. Kersey, EMBL - The European Bioninformatics Institute; Helen Parkinson, EMBL-EBI

Towards Efficient Use of Image Resources in Oryzabase
Yukiko Yamazaki, National Institute of Genetics; Gaku Kimura, National Institute of Genetics; Rie Tsuchiya, National Institute of Genetics

Pathways at MaizeGDB – Strategies for Curation and Data Sharing
Mary Schaeffer, USDA ARS and University of Missouri; Taner Z Sen, USDA ARS and Iowa State University; Jack Gardiner, Iowa State University; Ethalinda Cannon, Iowa State University; Scott M Birkett, Iowa State University; Jesse R. Walsh, Iowa State University; Lisa C Harper, USDA-ARS; Julie Dickerson, Iowa State University; Carolyn J. Lawrence, USDA ARS and Iowa State University

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

The RosBREED Pedigree-Based Breeding Information Management System
Sook Jung, Washington State University; Taein Lee, Washington State University; Sushan Ru, Washington State University; Dorrie Main, Washington State University; Amy Iezzoni, Michigan State University; Cameron Peace, Washington State University; Gennaro Fazio, USDA, ARS/ Cornell University

VitisCyc: A Species-Specific Metabolic Pathway Database for Grape (Vitis vinifera)
Sushma Naithani, Oregon State University; Rajani Raja, Dept. of Botany & Plant Pathology, Oregon State University; Justin L. Elser, Dept. of Botany & Plant Pathology, Oregon State University; Palitha Dharmawardhana, Oregon State University; Daniel Petty, Dept. of Horticulture, Oregon State University; Laurent G. Deluc, Dept. of Horticulture, Oregon State University; Pankaj Jaiswal, Dept. of Botany & Plant Pathology, Oregon State University

Bioinformatic Solutions in Forest Genomics: Accessing the TreeGenes Database
Jill Wegrzyn, University of California, Davis; Ben Figueroa, University of California, Davis; John Yu, University of California, Davis; Hans Vasquez-Gross, University of California Davis; John Liechty, University of California, Davis; Brian Lin, University of California, Davis; Jacob Zieve, University of California, Davis; Jason Ip, University of California, Davis; David Neale, University of California, Davis

The Soybean Genome Database (SoyGD): A Genomic Interactome Viewer Based On Cultivar Forrest
David A. Lightfoot, Southern Illinois University; Naresh Pola, SIUC; Pavan Kasarla, SIUC

LegumeIP 2.0: An Integrative Platform to Study Gene Function and Genome Evolution in Legumes
Jun Li, The Samuel Roberts Noble Foundation; Patrick Xuechun Zhao, The Samuel Roberts Noble Foundation

The Legume Information System 2013
Steven B. Cannon, USDA-ARS-CICGRU; Andrew Farmer, National Center for Genome Resources; Ken A. Seal, The National Center for Genome Resources; Arvind K. Bharti, National Center for Genome Resources (NCGR); Alex G. Rice, National Center for Genome Resources (NCGR); Nathan Weeks, USDA-ARS-CICGRU; Benjamin Deonovic, University of Iowa; Scott Kalberer, USDA-ARS-CICGRU; Rex T. Nelson, USDA-ARS-CICGRU; David Grant, USDA-ARS-CICGRU and Iowa State University; Randy C. Shoemaker, USDA-ARS-CICGRU

CottonGen: An Integrated Web-Database for Cotton Genomics, Genetics and Breeding Research
Jing Yu, Washington State University; Sook Jung, Washington State University; Chun-Huai Cheng, Washington State University; Stephen P. Ficklin, Washington State University; Taein Lee, Washington State University; Ping Zheng, Washington State University; Don C. Jones, Cotton Incorporated; Richard G. Percy, USDA-ARS, Southern Plains Agricultural Research Center; Dorrie Main, Washington State University

Liverwort Genome Analysis using DDBJ Pipeline and Construction of the Genome Annotation Database
Hideki Nagasaki, Genome Informatics Laboratory, NIG, ROIS; Takatomo Fujisawa, Genome Informatics Laboratory, NIG, ROIS, JAPAN; Takako Mochizuki, Genome Informatics Laboratory, NIG, ROIS, JAPAN; Satoshi Saruhashi, Genome Informatics Laboratory, NIG, ROIS, JAPAN; Eli Kaminuma, Genome Informatics Laboratory, NIG, ROIS, JAPAN; Kimitsune Ishizaki, Kyoto University, Graduate School of Biostudies; Katsuyuki T. Yamato, Kinki University, B.O.S.T.; Takayuki Kohchi, Kyoto University, Graduate School of Biostudies; Yasukazu Nakamura, Genome Informatics Laboratory, NIG, ROIS, JAPAN

All Animals Are Not Equal: Some Genomes Are More Equal Than Others
Elspeth Bruford, EMBL-EBI; Ruth Seal, EMBL-EBI; Matt Wright, EMBL-EBI

The NextGen Project, Next Generation Methods to Preserve Farm Animal Diversity
Laura Clarke, European Molecular Biology Laboratory; Ian Streeter, EMBL-EBI; Holly Zheng-Bradley, EMBL-EBI; David Richardson, European Bioinformatics Institute (EMBL-EBI); Paul Flicek, European Bioinformatics Institute (EMBL-EBI); The NextGen Consortium, EMBL-EBI

Annotation of Livestock and Aquaculture species in Ensembl
Steve M. J. Searle, Wellcome Trust Sanger Institute; Daniel Barrell, Wellcome Trust Sanger Institute; Carlos Garcia-Giron, Wellcome Trust Sanger Institute; Andreas Kahari, Wellcome Trust Sanger Institute; Thibaut Hourlier, Wellcome Trust Sanger Institute; Rishi Nag, Wellcome Trust Sanger Institute; Simon White, Wellcome Trust Sanger Institute; Amonida Zadissa, Wellcome Trust Sanger Institute; Bronwen Aken, Wellcome Trust Sanger Institute; Paul Flicek, European Bioinformatics Institute (EMBL-EBI); Tim Hubbard, Wellcome Trust Sanger Institute

SNP Identification in Ovine APOM, BAT2 and G6B Genes in the MHC Class III Region and Phylogenetic Analysis in 10 Mammalian Species
Samuel A. Amusan, Federal University of Agriculture, Abeokuta; Mufliat A. Adefenwa, University of Lagos; Brilliant O. Agaviezor, University of Port Harcourt; Mathew Wheto, Federal University of Agriculture; Oyeyemi O. Ajayi, Federal University of Agriculture; Christian O.N. Ikeobi, Federal University of Agriculture; Moses Okpeku, Niger Delta University, Bayelsa State, Nigeria; S.O. Peters, Cornell University; Marcos De Donato, Cornell University; Ikhide G. Imumorin, Cornell University

Bovine Genome Database: Working Towards an Improved Bovine Gene Set Using Community-provided RNA-Seq Data
Darren E. Hagen, Division of Animal Sciences, University of Missouri; Christopher P. Childers, Division of Animal Sciences, University of Missouri; Justin T. Reese, Division of Animal Sciences, University of Missouri; Christine G. Elsik, Division of Animal Sciences, University of Missouri

CorrDB: A Livestock Animal Genetic/Phenotypic Trait Correlation Database
Zhiliang Hu, Department of Animal Science, Iowa State University; Dinesh Kumar, Centre for Agricultural Bioinformatics, IASRI; James M. Reecy, Department of Animal Science, Iowa State University

Hymenoptera Genome Database: Resources for Annotating and Comparing Hymenopteran Insect Genomes
Justin T. Reese, Division of Animal Sciences, University of Missouri; Christopher P. Childers, Division of Animal Sciences, University of Missouri; Anna K. Bennett, Biology Department, Georgetown University; Darren E. Hagen, Division of Animal Sciences, University of Missouri; Christine G. Elsik, Division of Animal Sciences, University of Missouri; Monica C. Munoz-Torres, Lawrence Berkeley National Laboratory

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