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Bioinformatics: Algorithms

Date: Monday, January 14, 2013
Time: 7:00 AM-10:00 PM
Room: Grand Exhibit Hall
Statistical Methods for VINOtyping on Affymetrix® Axiom® Arrays
Teresa A. Webster, Affymetrix, Inc.; Ali Pirani, Affymetrix, Inc.; Mei-mei Shen, Affymetrix; Laurent R. Bellon, Affymetrix Inc.; Hong Gao, Affymetrix Inc.

Allo-Polyploid Genotyping Algorithm on Affymetrix® Axiom® Arrays
Hong Gao, Affymetrix Inc.; Ali Pirani, Affymetrix, Inc.; Laurent R. Bellon, Affymetrix Inc.; Teresa A. Webster, Affymetrix, Inc.

Best Practices for Genotyping Analysis of Plant and Animal Genomes with Affymetrix® Axiom® Arrays
Ali Pirani, Affymetrix, Inc.; Hong Gao, Affymetrix Inc.; Laurent R. Bellon, Affymetrix Inc.; Teresa A. Webster, Affymetrix, Inc.

Towards Finished Genome Assemblies using SMRT® Sequencing
Jenny Gu, Pacific Biosciences; Lawrence Hon, Pacific Biosciences; Jason Chin, Pacific Biosciences; David Alexander, Pacific Biosciences; Aaron Klammer, Pacific Biosciences

epiSNP_cc: A Cloud Computing GWAS Software for Epistasis Testing
Hakizumwami Birali Runesha, The University of Chicago; Shengwen Wang, Department of Animal Science, University of Minnesota; Yang Da, Department of Animal Science, University of Minnesota

Protein Function Prediction and Human Readable Descriptions
Heiko Schoof, University of Bonn, INRES Crop Bioinformatics; Asis Hallab, Max Planck Institute for Plant Breeding Research; Kathrin Klee, University of Bonn, INRES Crop Bioinformatics

Using Cluster-Unique Sequences in Proteomes to Enhance Confidence in Identifications from Shotgun Proteomics Studies of Organisms with Complex Genomes
Rachel M Adams, University of Tennessee; Richard J. Giannone, Oak Ridge National Laboratory; Paul E. Abraham, University of Tennessee; Robert L. Hettich, BioEnergy Science Center, Oak Ridge National Laboratory

Inclusive Composite Interval Mapping (ICIM) of Quantitative Trait Genes
Jiankang Wang, Chinese Academy of Agricultural Science and CIMMYT

Chargaff's “Grammar of Biology”: New Fractal-like Rules
Michel E Beleza Yamagishi, Embrapa Agriculture Informatics; Roberto H. Herai, University of California San Diego

Joint Genomic Prediction and Estimation of Variance Components of Additive and Dominance Effects using SNP Markers
Yang Da, Department of Animal Science, University of Minnesota; Shengwen Wang, Department of Animal Science, University of Minnesota

Evaluation of Three Methods for Genomic Additive and Dominance Relationships using SNP Markers
Guo Hu, Department of Animal Science, University of Minnesota; Shengwen Wang, Department of Animal Science, University of Minnesota; Yang Da, Department of Animal Science, University of Minnesota

Finding Genes in Compositionally Heterogeneous Plants
Mark Borodovsky, Georgia Institute of Technology; Alexandre Lomsadze, Georgia institute of Technology

Sample Variability Tracking in Population-Scale Studies as a Methodology for Reference Genome Characterization
Roberto Alonso, Institute for Genomcis and Computational Medicine, CIPF; Jose Carbonell, Institute for Genomcis and Computational Medicine, CIPF; Ana Conesa, 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

TrueSight-ES: Machine Learning Approach to Detecting Splice Junctions in RNA-Seq Data
Paul D. Burns, Georgia Institute of Technology; Yang Li, University of Illinois at Urbana-Champaign; Jian Ma, University of Illinois at Urbana-Champaign; Mark Borodovsky, Georgia Institute of Technology

Estimation of Variation within Transcriptome de novo Assemblies, co-assemblies of Paralogs, Heterozygosity or Polyploidy Possibly Accumulated Within the Isotigs of a Newbler Assembly
Ram Podicheti, School of Informatics and Computing, Indiana University; Mehmet Dalkilic, Indiana University; Keithanne Mockaitis, Indiana University

An Algorithm for Estimating Contig Copy Number for Polyploid Genomes
Gabriel R.A. Margarido, Microsoft Research; Bob Davidson, Microsoft Research; David Heckerman, Microsoft

Normalization of Batch Effect in Large Scale DNA Methylation Profiling
Jo Ling Liao, Academia Sinica; Marco Morselli, University of California, Los Angeles; Liudmilla Rubbi, University of California, Los Angeles; Luz Orozco, University of California, Los Angeles; Matteo Pellegrini, University of California, Los Angeles; Pao-Yang Chen, University of California, Los Angeles

Coverage-based Consensus Calling (CbCC) Method for Identification of SNPs in Crop Species Without a Reference Genome
Sarwar Azam, ICRISAT; Vivek Thakur, IRRI; Pradeep Ruperao, University of Queensland; Trushar Shah, ICRISAT; Jayashree Balaji, ICRISAT; BhanuPrakash Amindala, ICRISAT; Andrew Farmer, National Center for Genome Resources; David J Studholme, University of Exeter; Gregory D. May, National Center for Genome Resources; David Edwards, University of Queensland; Jonathan Jones, The Sainsbury Laboratory; Rajeev Varshney, ICRISAT

Time Course Lesion Tracking for Maize Phenotype Images
Chi-Ren Shyu, University of Missouri; Jason Green, University of Missouri; Peter Balint-Kurti, North Carolina State University; Gurmukh S Johal, Purdue University

Genomic Prediction of Trait Segregation in Progeny Populations: Examples in Japanese Pear and Rice
Hiroyoshi Iwata, The University of Tokyo; Norio Takada, NARO Institute of Fruit Tree Science; Shingo Terakami, NARO Institute of Fruit Tree Science; Toshihiro Saito, NARO Institute of Fruit Tree Science; Toshiya Yamamoto, NARO Institute of Fruit Tree Science; Takuma Yoshioka, Kobe University; Masanori Yamasaki, Kobe University; Kaworu Ebana, National Institute of Agrobiological Sciences; Takeshi Hayashi, NARO Agricultural Research Center (NARC)

SNP Calling in the Zebrafish Mutation Project
Richard White, Wellcome Trust Sanger Institute; Ian Sealy, Wellcome Trust Sanger Institute; Ross Kettleborough, Wellcome Trust Sanger Institute; Elisabeth Busch-Nentwich, Wellcome Trust Sanger Institute; Colin Herd, Wellcome Trust Sanger Institute; Amanda Hall, Wellcome Trust Sanger Institute; Derek Stemple, Wellcome Trust Sanger Institute

BigPlant v2: Fully Automated Construction of a High Resolution Seed Plant Phylogeny
Kranthi K Varala, New York University; Ernest K Lee, American Museum of Natural History; Tamara Tershakovec, New York University; W. Richard McCombie, Cold Spring Harbor Laboratory; Dennis Shasha, New York University; Dennis Wm. Stevenson, New York Botanical Garden; Rob Martienssen, HHMI-GBMF Cold Spring Harbor Laboratory; Rob DeSalle, American Museum of Natural History; Gloria Coruzzi, New York University

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