36
Bioinformatics: Software

Date: Monday, January 13, 2014
Time: 7:00 AM-10:00 PM
Room: Grand Exhibit Hall
iPlant: Tools for Large Scale Assembly and Annotation of Plant Genomes
Joshua Stein, Cold Spring Harbor Laboratory; The iPlant Collaborative, University of Arizona, iPlant Collaborative; Roger A. Barthelson, University of Arizona, iPlant Collaborative

Sequencing, Assembling, and Annotating a Mid-Sized Genome
Viraj Deshpande, University of California at San Diego; Vineet Bafna, University of California at San Diego

VCF Miner: A Platform and Tools for Collaborative Information Mining from Next-Generation Sequence Variant Data
Zhiliang Hu, Iowa State University; James Koltes, Department of Animal Science, Iowa State University; Eric Fritz-Waters, Department of Animal Science, Iowa State University; James M. Reecy, Iowa State University

Plant Resources at the DOE KBase Project
Samuel M. D. Seaver, Argonne National Laboratory; Doreen Ware, Cold Spring Harbor Laboratory/USDA-ARS; 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; Sunita Kumari, Cold Spring Harbor Laboratory; Shiran Pasternak, Cold Spring Harbor Lab; 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; Dave Weston, Oak Ridge National Laboratory; Priya Ranjan, Oak Ridge National Laboratory; Mustafa Syed, Oak Ridge National Laboratory; Miriam Land, Oak Ridge National Laboratory; Adam Arkin, Lawrence Berkeley National Laboratory

GMOD in the Cloud and GMOD in a Box
Scott Cain, Ontario Institute for Cancer Research; Robert Buels, Boyce Thompson Institute for Plant Research; Stephen P. Ficklin, Washington State University; Ed Lee, Lawrence Berkeley National Laboratory; Lacey-Anne Sanderson, University of Saskatchewan; Amelia Ireland, University of California, Berkeley; Lincoln Stein, Ontario Institute of Cancer Research

Crop> pedia
Jesse Munkvold, Keygene Inc.; Rudi van Bavel, Keygene; Lian Perebolte, Keygene; Evert-Jan Blom, Keygene; Mark van Haaren, Keygene; Uwe Thissen, KeyGene

Geneious R7: A Bioinformatics Platform for Biologists
Christian Olsen, Biomatters; Kashef Qaadri, Biomatters

Genome Annotation in the Cloud through xGDBvm Virtual Server Instances Deployed at iPlant
Jon Duvick, Iowa State University; Daniel Standage, Indiana University; Nirav Merchant, iPlant Collaborative/University of Arizona; Volker Brendel, Indiana University

Genome Annotation with Maker - How Much Evidence Is Enough?  How Much Evidence Is Too Much?
Kevin L. Childs, Michigan State University; Megan J Bowman, Michigan State University

ORCAE: Online Resource for Community Annotation of Eukaryotes
Lieven Sterck, VIB Ghent University; Thomas Abeel, VIB Ghent University; Stephane Rombauts, VIB Department of Plant Systems Biology, Ghent University; Yao-Cheng Lin, VIB Department of Plant Systems Biology, Ghent University; Pierre RouzÚ, VIB Ghent University, Department of Plant Biotechnology and Bioinformatics; Yves Van de Peer, VIB - Ghent University

PlantGenIE - the Plant Genome Integrative Explorer
David Sundell, Umeň Plant Science Center; Sergiu Netotea, Umeň Plant Science Centre, Umeň University; Chanaka Mannapperuma, Umeň Plant Science Centre, Umeň University; Nicolas Delhomme, Umeň Plant Science Center, Umeň University; Torgeir R. Hvidsten, Norwegian University of Life Sciences; Nathaniel R. Street, Umeň Plant Science Center, Umeň University

An Improved Method for Clustering Fragmented Protein and Coding Sequences
Theodore R. Gibbons, University of Maryland; Charles F. Delwiche, University of Maryland

Improving Genomes Using Long Reads and PBJelly 2
Kim C. Worley, Baylor College of Medicine; Adam C. English, Baylor College of Medicine; Stephen Richards, Baylor College of Medicine; Jeffrey Ross-Ibarra, Baylor College of Medicine; Yi Han, Baylor College of Medicine; Daniel Hughes, Baylor College of Medicine; David Rio Deiros, Baylor College of Medicine; Vanessa Vee, Baylor College of Medicine; Min Wang, Baylor College of Medicine; Eric Boerwinkle, University of Texas Health Science Center; Donna M. Muzny, Baylor College of Medicine; Jeffrey G. Reid, Baylor College of Medicine; Richard A. Gibbs, Baylor College of Medicine

Automated RNA-Seq Analysis for Non-Model Organisms on the Cloud
Lu Zhang, Seven Bridges Genomics; Brian Haas, The Broad Institute; Sebastian Wernicke, Seven Bridges Genomics

A GUI Application "CA Plot Viewer" for Large-Scale Gene Expression Analysis with Next-Generation Sequencing Technology
Kentaro Yano, School of Agri., Meiji University; Tomoyuki Takano, School of Agri., Meiji University; Shin Terashima, School of Agri., Meiji University; Hayato Matsumura, School of Agri., Meiji University; Maasa Kanno, School of Agri., Meiji University; Kyoko Morimoto, School of Agri., Meiji University; Koji Yokoyama, School of Agri., Meiji University; Yuuki Yoshida, School of Agri., Meiji University; Yoshifumi Tada, TOHOKU CHEMICAL CO., LTD.; Hiroshi Chiba, TOHOKU CHEMICAL CO., LTD.; Hajime Ohyanagi, School of Agri., Meiji University; Masaaki Kobayashi, School of Agri., Meiji University

Graphical Applications for Visualization and Analysis of Genotype Data Sets
Iain Milne, The James Hutton Institute; Gordon Stephen, The James Hutton Institute; Micha Bayer, The James Hutton Institute; Paul Shaw, The James Hutton Institute; Sebastian Raubach, The James Hutton Institute; Sarah Hearne, CIMMYT; Sukhwinder Singh, CIMMYT- International Maize and Wheat Improvement Centre; Peter Wenzl, CIMMYT - International Maize and Wheat Improvement Centre; David Marshall, The James Hutton Institute

Defining haplotypes in genic and non-genic regions using user specified window size
BhanuPrakash Amindala, ICRISAT; Punna Ramu, ICRISAT; Santosh Deshpande, ICRISAT; C Tom Hash, ICRISAT; Stefania Grando, ICRISAT; Trushar Shah, ICRISAT

VIGoR: Software for Variational Inference for Genome-Wide Regression
Akio Onogi, The University of Tokyo; Benjamin Galliot, The University of Tokyo; Hiroyoshi Iwata, The University of Tokyo

Oligoreef - Generation of Primers for Complex Polymerase Chain Reactions
Petra Kellers, Max Planck Institute for Biophysical Chemistry; ┼sa S÷derberg, Uppsala University, Section of Chemistry; Peter Lindblad, Uppsala University, Section of Chemistry; Dirk-Jan de Koning, Swedish University of Agricultural Sciences; Fernando Lopes Pinto, Swedish University of Agricultural Sciences

RepeatExplorer: Collection of Tools for Mining of Repetitive Elements from NGS Data
Petr Novak, Biology Centre ASCR, Institute of Plant Molecular Biology; Jiri Macas, Biology Centre ASCR, Institute of Plant Molecular Biology; Pavel Neumann, Biology Centre ASCR, Institute of Plant Molecular Biology

Multi-Omic Data Integration and Pathway Analysis to Develop Insights and Hypotheses for Subsequent Verification
Shweta Shukradas, Strand Scientific Intelligence; Antoni Wandycz, Agilent Technologies; Dipa Roy Choudhury, Strand Scientific Intelligence

iTAK – Identification and Classification of Plant Transcription Factors and Protein Kinases
Yi Zheng, Boyce Thompson Institute for Plant Research; Zhangjun Fei, Boyce Thompson Institute for Plant Research, Cornell University

The SGN VIGS Tool: User-Friendly Software to Optimize Virus-Induced Gene Silencing (VIGS) Constructs for Functional Genomics
Noe Fernandez-Pozo, Boyce Thompson Institute for Plant Research; Hernan G. Rosli, Boyce Thompson Institute for Plant Research; Greg B Martin, Boyce Thompson Institute for Plant Research; Lukas Mueller, Boyce Thompson Institute for Plant Research

Detecting Small Plant Peptides Using Spada (Small Peptide Alignment Discovery Application)
Peng Zhou, Department of Plant Pathology, University of Minnesota; Kevin AT Silverstein, Supercomputing Institute, University of Minnesota; Liangliang Gao, Department of Plant Pathology, University of Minnesota; Jonathan Walton, Michigan State University; 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

Predicting Genes with AUGUSTUS and RNA-Seq Data
Katharina Hoff, University of Greifswald; Mario Stanke, University of Greifswald

Cartogratree: Enabling Forest Tree Genomics through Association Studies
Jacob Zieve, University of California, Davis; Hans Vasquez-Gross, University of California Davis; Damian Gessler, University of Arizona; David Neale, Dept. Plant Sciences University of California Davis; Jill Wegrzyn, University of Connecticut

Integrative System for Gene Family Gathering and Analysis in a Context of Crops’ Stress Response Study
Delphine LariviŔre, Cirad, UMR AGAP; Jean-Franšois Dufayard, CIRAD, UMR AGAP; StÚphanie Bocs, CIRAD; Dominique This, CIRAD - Montpellier SupAgro

RNA-Seq Mapping Software Evaluation on Non-Model Genetic Organism Gallus gallus for Differential Expression Analysis and Novel Single Nucleotide Polymorphisms (SNPs) Discovery
John Hsieh, Iowa State University; Damarius Fleming, Iowa State University; Derrick J. Coble, Iowa State University; Susan J. Lamont, Iowa State University

Tissue‐Specific Alternative Splicing in Rainbow Trout
Rafet Al-Tobasei, Middle Tennessee State University

Comparison of Variant Calling Pipelines for Whole Genome Sequencing Data in Dairy Cattle
Christine F. Baes, Bern University of Applied Sciences; Marlies A. Dolezal, UniversitÓ degli Studi di Milano; Eric Fritz-Waters, Department of Animal Science, Iowa State University; James Koltes, Department of Animal Science, Iowa State University; Beat Bapst, Qualitas AG; Christine Flury, Bern University of Applied Sciences; Heidi Signer-Hasler, Bern University of Applied Sciences; Christian Stricker, agn-genetics; Rohan L. Fernando, Iowa State University; James M. Reecy, Iowa State University; Dorian J. Garrick, Department of Animal Science, Iowa State University; Fritz Schmitz-Hsu, swissgenetics; Ruedi Fries, Chair of Animal Breeding - Technische Universitńt MŘnchen; Birgit Gredler, Qualitas AG

Synergy: A Web Resource for Exploring Gene Expression in Synechocystis sp. PCC6803
Niklas Mńhler, Norwegian University of Life Sciences; Sergiu Netotea, Umeň University; Torgeir R. Hvidsten, Norwegian University of Life Sciences

spliceR: Detecting and Quantifying Allele-Specific-Expression from RNA-Seq Data
Shreyartha Mukherjee, The Samuel Roberts Noble Foundation; Paul Scott, Iowa State University; Richard Johnson, University of Illinois, Urbana; Andrew D. Farmer, National Center for Genome Resources (NCGR); Gregory D. May, Pioneer HiBred; William Beavis, Iowa State University

A Computational Framework for High-throughput Virus Detection and Pathogen Discovery
Mark Wamalwa, BecA-ILRI Hub; Francesca Stomeo, BecA-ILRI Hub; Jagger Harvey, BecA-ILRI Hub; Miano Douglas, University of Nairobi; Neil Boonham, Food and Environment Research Agency (FERA); Ian Adams; Dora Kilalo, University of Nairobi; Appolinaire Djikeng, BecA-ILRI Hub

Using LTC Software Package for Wheat Physical Mapping: Increasing Contig Lengths and MTP Quality
Zeev M. Frenkel, Institute of Evolution, University of Haifa; Vladimir A. Glikson, MultiQTL Ltd.; Dina Raats, Institute of Evolution, University of Haifa; Bujie Zhan, Norwegian University of Life Sciences; Tatiana Belova, Norwegian University of Life Sciences; Etienne Paux, INRA GDEC; Tzion Fahima, Institute of Evolution, University of Haifa; Catherine Feuillet, INRA GDEC; Odd-Arne Olsen, Hedmark University College; Simen R°d Sandve, Norwegian University of Life Sciences; Abraham B. Korol, Institute of Evolution, University of Haifa

A Fast Algorithm and Software for  Building Ultra-Dense Genetic Maps in the Presence of Genotyping Errors and Missing Data
Yefim I. Ronin, Institute of Evolution, University of Haifa; Dina M. Minkov, MultiQTL Ltd.; David I. Mester, Institute of Evolution, University of Haifa; Abraham B. Korol, Institute of Evolution, University of Haifa

See more of: Poster Categories