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Bioinformatics: Software

Date: Monday, January 14, 2013
Time: 7:00 AM-10:00 PM
Room: Grand Exhibit Hall
Biological Computing Using the iPlant Discovery Environment
Joshua Stein, Cold Spring Harbor Laboratory; Jerry Lu, Cold Spring Harbor Laboratory; Christos Noutsos, Cold Spring Harbor Laboratory; Liya Wang, Cold Spring Harbor Laboratory; Roger A. Barthelson, University of Arizona, iPlant Collaborative; Fusheng Wei, University of Arizona, iPlant Collaborative; Naim Matasci, University of Arizona, iPlant Collaborative; Eric Lyons, University of Arizona; Nicole Hopkins, University of Arizona, iPlant Collaborative; Andrew Lenards, University of Arizona, iPlant Collaborative; Sheldon McKay, Dolan DNA Learning Center, Cold Spring Harbor Laboratory; Matt Vaughn, Texas Advances Computing Ctr, University of Texas; Dan Stanzione, Texas Advances Computing Ctr, University of Texas; Stephen A. Goff, University of Arizona, iPlant Collaborative; Doreen Ware, Cold Spring Harbor Laboratory; The iPlant Collaborative, University of Arizona, iPlant Collaborative

iPlant Collaborator: BioExtract
Carol Lushbough, University of South Dakota

Gene Finding Platform for Large Plant and Animal Genomes
Alexandre Lomsadze, Georgia institute of Technology; Mark Borodovsky, Georgia Institute of Technology

Web-Portal for the SAGE and EST Analysis Pipeline
Theo Crouch, California State University San Marcos

WebApollo: A Web-based Sequence Annotation Editor for Distributed Community Annotation
Ed Lee, Lawrence Berkeley National Laboratory; Gregg A Helt, Lawrence Berkeley National Laboratory; Monica C. Munoz-Torres, Lawrence Berkeley National Laboratory; Suzanna E. Lewis, Lawrence Berkeley National Laboratory; Justin Reese, Division of Animal Sciences, University of Missouri; Christopher Childers, Division of Animal Sciences, University of Missouri; Christine G. Elsik, Division of Animal Sciences, University of Missouri; Robert Buels, University of California, Berkeley; Ian Holmes, University of California, Berkeley

Three New Tools to Dramatically Improve Draft Genome Assemblies
Kim C. Worley, Baylor College of Medicine; Jiaxin Qu, Baylor College of Medicine; Yue Liu, Baylor College of Medicine; Adam C. English, Baylor College of Medicine; Huaiyang Jiang, Baylor College of Medicine; Xiang Qin, Baylor College of Medicine; Yi Han, Baylor College of Medicine; Min Wang, Baylor College of Medicine; Donna M. Muzny, Baylor College of Medicine; Jeffrey G. Reid, Baylor College of Medicine; Stephen Richards, Baylor College of Medicine; Richard A. Gibbs, Baylor College of Medicine

A Biologist-Oriented Sequencing Data Analytic Platform for Easy Collaboration and Data Sharing
Patricia Chan, Maverix Biomics; Todd Lowe, University of California Santa Cruz; Dan Kearns, Maverix Biomics

An Integrated Bioinformatics Framework for Genomic Variants Discovery from Next Generation Sequencing Data
Daniel Cruz, International Center for Tropical Agriculture; Jorge A. Duitama Castellanos, International Center for Tropical Agriculture – CIAT; Juan Camilo Quintero, International Center for Tropical Agriculture; Joe Tohme, CIAT

Optimisation of SNP and Alternative Splicing Discovery using the Tablet NGS Viewer
Iain Milne, The James Hutton Institute; Gordon Stephen, The James Hutton Institute; Micha Bayer, The James Hutton Institute; Linda Cardle, The James Hutton Institute; Paul Shaw, The James Hutton Institute; David Marshall, The James Hutton Institute

A Gene Discovery Method from Large-Scale Gene Expression Data with Next-Generation Sequencing Technology
Kentaro Yano, School of Agri., Meiji University; Hiroko Tsuchida, Meiji University; Taiki Kuchiki, Meiji University; Koji Yokoyama, School of Agri., Meiji University; Yuuki Yoshida, School of Agri., Meiji University; Kayoko Kikue, Meiji University; Hiroshi Chiba, TOHOKU CHEMICAL CO., LTD.; Yoshifumi Tada, TOHOKU CHEMICAL CO., LTD.; Akifumi Shimizu, The University of Shiga Prefecture

Yabi: A Cross -Omics Internet-Based Platform for Bioinformatics Workflows
Matthew Bellgard, Centre for Comparative Genomics, Murdoch University; Paula Moolhuijzen, Centre for Comparative Genomics, Murdoch University; Andrew Macgregor, Centre for Comparative Genomics, Murdoch University; Adam Hunter, Centre for Comparative Genomics, Murdoch University

Visualizing Genetic Transmission Patterns in Plant Pedigrees
Paul Shaw, The James Hutton Institute; Bill Thomas, The James Hutton Institute; Luke Ramsay, The James Hutton Institute; Robbie Waugh, The James Hutton Institute; Jordi Comadran, The James Hutton Institute; Gordon Stephen, The James Hutton Institute; Iain Milne, The James Hutton Institute; Martin Graham, Edinburgh Napier University; Jessie Kennedy, Edinburgh Napier University; David Marshall, The James Hutton Institute

PlantTFcat: An Online Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool
Xinbin Dai, The Samuel Roberts Noble Foundation; Senjuti Sinharoy, The Samuel Roberts Noble Foundation; Michael K. Udvardi, The Samuel Roberts Noble Foundation; Patrick Xuechun Zhao, The Samuel Roberts Noble Foundation

Detecting Secreted Peptides in Plants Using SPADA (Secreted Peptide Alignment Discovery Algorithm)
Peng Zhou, Department of Plant Pathology, University of Minnesota; Kevin A. T. Silverstein, Supercomputing Institute, University of Minnesota; Liangliang Gao, Department of Plant Pathology, University of Minnesota; Sumitha Nallu, Dept. of Ecology and Evolution, University of Chicago; Joseph Guhlin, Department of Plant Pathology, University of Minnesota; Nevin Young, Department of Plant Pathology, University of Minnesota

GRNCASE: A High Performance Gene Regulatory Network Construction and Functional Module Discovery and Analysis Web Server
Jun Li, The Samuel Roberts Noble Foundation; Tingsong Liu, The Samuel Roberts Noble Foundation; Patrick Xuechun Zhao, The Samuel Roberts Noble Foundation

Load Your Own: Loading and Sharing Private Genomes in CoGe
Matthew Bomhoff, Plant Sciences, University of Arizona; Eric Lyons, Plant Sciences, University of Arizona

QTL IciMapping: Integrated Software for Building Linkage Maps and Mapping Quantitative Trait Genes
Jiankang Wang, Chinese Academy of Agricultural Science and CIMMYT

QTLNetMiner - Candidate Gene Discovery in Plant and Animal Knowledge Networks
Keywan Hassani-Pak, Rothamsted Research; Minja Zorc, Rothamsted Research; Jan Taubert, Rothamsted Research; Christopher Rawlings, Rothamsted Research

KBase: Plant Science
David Weston, Oak Ridge National Laboratory; Doreen Ware, Cold Spring Harbor Laboratory; Priya Ranjan, University of Tennessee, Knoxville; Mustafa Syed, Oak Ridge National Laboratory; Miriam Land, Oak Ridge National Laboratory; Sergei Maslov, Brookhaven National Laboratory; Shinjae Yoo, Brookhaven National Laboratory; Dantong Yu, Brookhaven National Laboratory; Michael Schatz, Cold Spring Harbor Laboratory; James Gurtowski, Cold Spring Harbor Laboratory; Matt Titmus, Cold Spring Harbor Laboratory; Jer-Ming Chia, Cold Spring Harbor Labs; Sunita Kumari, Cold Spring Harbor Laboratory; Andrew Olson, Cold Spring Harbor Laboratory; Shiran Pasternak, Cold Spring Harbor Laboratory; Jim Thomason, Cold Spring Harbor Laboratory; Mark Gerstein, Yale University; Gang Fang, Yale University; Darryl Reeves, Yale University; Pamela Ronald, Joint BioEnergy Institute (JBEI); TaeYun Oh, University of California, Davis; Christopher Henry, Argonne National Laboratory; Samuel M. D. Seaver, Argonne National Laboratory; Adam Arkin, Lawrence Berkeley National Laboratory

GDHDF5 - A Genetic Diversity Database Server
Jaroslaw Pillardy, Cornell University; Qi Sun, Cornell University

AISO: Annotation of Image Segments using Ontologies
Nikhil Lingutla, Oregon State University; Justin Preece, Dept. of Botany & Plant Pathology, Oregon State University; Sinisa Todorovic, Oregon State University; Pankaj Jaiswal, Dept. of Botany & Plant Pathology, Oregon State University

Using GMOD to Annotate and Distribute Data in the Cloud
Scott Cain, Ontario Institute for Cancer Research; Amelia Ireland, University of California, Berkeley

GenSAS: Genome Sequence Annotation Server, a Tool for Online Annotation and Curation
Dorrie Main, Washington State University; Taein Lee, Washington State University; Ping Zheng, Washington State University; Sook Jung, Washington State University; Stephen P. Ficklin, Washington State University; Jodi Humann, Washington State University; Jill Wegrzyn, University of California, Davis; David Neale, University of California, Davis

CLASS and ASprofile: Resources for Alternative Splicing Annotation from RNA-seq Data
Liliana Florea, Johns Hopkins University School of Medicine; Li Song, Johns Hopkins University

Using Plasmode Datasets to Compare Statistical Methods for RNA-seq Analysis
Pablo Daniel Reeb, Michigan State University; Juan P. Steibel, Department of Animal Science, Michigan State University

Tools Enabling Biology Lab-Driven Genome Annotation
Daniel Standage, Iowa State University

Discovery of Genetic Interactions Across Diverse Oryza sativa Sequencing Data Sets: a Workflow-Based Approach
Benjamin J. Adamczyk, Genedata; Tamas Rujan, Genedata AG; Jens Hoefkens, Genedata USA Inc.

Blueprint for RosMASS: A Web-based Rosaceae Marker-assisted Seedling Selection Decision Support Tool
Sushan Ru, Washington State University; Daniel Anthony Edge-Garza, Washington State University; Cameron Peace, Washington State University; Katherine M. Evans, Washington State University; Patrick A. Carter, Washington State University; Sook Jung, Washington State University; Dorrie Main, Washington State University

CartograTree: Connecting Forest Tree Genomes, Phenotypes, and Environment
Hans Vasquez-Gross, University of California Davis; Ben Figueroa, University of California, Davis; John Yu, University of California, Davis; Damian Gessler, University of Arizona; David Neale, University of California, Davis; Jill Wegrzyn, University of California, Davis

Pathway Modeling for Citrus Variation
Jose Carbonell, Institute for Genomcis and Computational Medicine, CIPF; Nicolas Desoignies, Institute for Genomcis and Computational Medicine, CIPF; Roberto Alonso, Institute for Genomcis and Computational Medicine, CIPF; Javier Terol, Centro de Genomica, IVIA; Manuel Talon, Centro de Genómica, IVIA; Joaquin Dopazo, Institute for Genomcis and Computational Medicine, CIPF; Ana Conesa, Institute for Genomcis and Computational Medicine, CIPF

Mapping Cattle Copy Number Variations in Water Buffalo
George Liu, USDA-ARS-BFGL; Derek Bickhart, USDA-ARS-AIPL

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