Computational Gene Discovery

Summary: THE TIDE OF SEQUENCE DATA. Majority of sequenced genomes to date are short prokaryotic genomes. Fungal genomes (with length below 100MB)constitute the largest group among sequenced eukaryotes. In 2010 the number of completely sequenced eukaryotic genomes longer than 100MB just exceeded 20; now about 60 completed genomes are longer than 500MB - the tide of eukaryotic genomes is rising. THE WORKSHOP MISSION. The task of annotation of protein-coding and RNA genes in large eukaryotic genomes is a bottleneck in extracting biological knowledge from sequence information. The Workshop focus is on the latest advances in computational gene prediction. Speakers represent leading research groups developing state-of-the-art algorithms of genome annotation integrating different types of sequence information from given species as well as from other species (genomic DNA, RNA-seq, protein sequences).
Date: Sunday, January 12, 2014
Time: 10:30 AM-12:40 PM
Room: Pacific Salon 3
Mark Borodovsky
10:30 AM
Sequencing, Assembling, and Annotating a Mid-Sized Genome
Viraj Deshpande, University of California at San Diego; Vineet Bafna, University of California at San Diego

10:50 AM
Simultaneous Gene Finding in Several Aligned Genomes
Mario Stanke, University of Greifswald

11:10 AM
The StringTie Approach to Reconstructing the Transcriptome from RNA-Seq Data
Mihaela Pertea, McKusick-Nathans Institute of Genetic Medicine, JHU

11:50 AM
RNA-Seq-based Genome Annotation using mGene.ngs and MiTie
Gunnar Rätsch, Memorial Sloan-Kettering Cancer Center

12:10 PM
Gene Finding with Semi-Supervised Training: Integration of RNA-Seq and Protein Data
Alexandre Lomsadze, Georgia Institute of Technology; Mark Borodovsky, Georgia Institute of Technology

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