Computational Gene Discovery

New sequencing technologies have transformed the whole landscape of biological research. Computational gene discovery on a big data scale has to address problems of NGS read assembly along with building pipelines of genome annotation and interpretation concordant with multiple layers of OMICs data. The task of annotation of protein-coding and RNA genes in large eukaryotic genomes still presents a bottleneck in obtaining biological knowledge from sequence information. The Workshop talks will describe the latest advances in all components of computational gene discovery. The speakers represent leading research groups developing state-of-the-art algorithms and methods of structural and functional annotation integrating different types of OMICs data (genomic, RNA, protein, proteomics data, etc.).
Date: Sunday, January 11, 2015
Time: 10:30 AM-12:40 PM
Room: Pacific Salon 3
Mark Borodovsky
10:30 AM
Chromosome-Scale Scaffolding of de novo Genome Assemblies Using Hi-C
Joshua N. Burton, University of Washington - Department of Genome Sciences; Ivan Liachko, University of Washington - Department of Genome Sciences

10:50 AM
Annotation of Protein Coding Genes for Non-Model de-novo Sequenced Organisms
Anna Vlasova, Center for Genomic Regulation; Francisco Câmara Ferreira, Center for Genomic Regulation; Didac Santesmasses Ruiz, Center for Genomic Regulation; Mariotti Marco, Center for Genomic Regulation; Roderic Guigo, Center for Genomic Regulation

11:10 AM
Complexity of Gene Landscape Beyond Model Organisms
Stephane Rombauts, Ghent University; Yves Van de Peer, VIB - Ghent University

11:30 AM
Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and Augustus
Simone Lange, University of Greifswald; Katharina Hoff, University of Greifswald; Alexandre Lomsadze, Georgia Institute of Technology; Mark Borodovsky, Georgia Institute of Technology; Mario Stanke, University of Greifswald

11:50 AM
Integration of ab initio Gene Finding with Mapping of Homologous Proteins
Alexandre Lomsadze, Georgia Institute of Technology

12:10 PM
Automated Interpretation of Metabolic Capacity from Complete Genomes Using KEGG Modules
Minoru Kanehisa, Institute for Chemical Research, Kyoto University

12:30 PM
Proteogenomics of Cancer: Peptides to Events
Seong W Cha, University of California San Diego

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