Interview – Brian Haas Manager of Genome Annotation, Outreach, Bioinformatics and Analysis Broad Institute

Brian Haas speaks to Izzy Scott Moncrieff in the run up to the  upcoming RNA-Seq 2013 Summit, 18th–20th June 2013, Boston, MA

Brian has been based at the Broad Institute since 2007. His main areas of focus include gene discovery and genome annotation, and he was part of a  collective effort to write the Trinity software for RNA-Seq de novo assembly.

What initially attracted you to RNA-Seq?

Much of my work over the years has involved developing software for leveraging transcript data to annotate genomes and resolve gene structures. I initially started at the Institute for Genomic Research in 1999 and moved to the Broad Institute in 2007. During that time I’ve worked on a large number of genome projects, many of which involved eukaryotes with complex genomes. One of the primary tasks was to identify all genes before we could do more in-depth analysis. The earliest work involved using EST sequences and full-length cDNAs. Those were sequenced using the earlier Sanger sequencing technology, which was rather expensive. With today’s technology, RNA-Seq, we can sample the transcriptome cheaply and more comprehensively, so it’s a very attractive way of capturing the same types of data to help with annotating gene structures. This was what originally attracted me to the technology, as I wanted to find a way to use these short RNA-Seq reads to identify transcripts in the genome and use them like I would ESTs or other cDNA sequences.

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