Project Description

Dr Harsha Gowda

QIMR Berghofer Medical Research Institute

Proteogenomics for accurate assembly and annotation of genomes

Next generation sequencing & bioinformatics

Monday 2 July 2018

Dr Harsha Gowda did his PhD at the Institute of Bioinformatics, Bangalore. During his PhD, he worked in Dr Akhilesh Pandey’s laboratory at Johns Hopkins University, USA on proteomic profiling of pancreatic cancers where his work involved proteomic approaches to study signaling pathways activated in pancreatic cancers and identification of novel biomarkers. In addition, he has worked as a visiting scientist in Dr Gary Siuzdak‚Äôs laboratory at Scripps Center for Metabolomics and Mass Spectrometry, USA. He is a recipient of Wellcome Trust-DBT fellowship which is awarded for the most promising young researchers in India. He moved to QIMR Berghofer Medical Research Institute in January 2018 as a group leader. He is a recipient of career development fellowship from NHMRC, Australia. His group employs cutting-edge technologies including genomics and proteomics to investigate cancer biomarkers and therapeutic targets.

One of the major goals of genome sequencing efforts is to provide an accurate assembly and annotation of all the genomic features including protein coding genes. Annotation of protein coding genes has been largely carried out using a combination of transcriptome data and gene prediction programs. However, our studies using proteogenomics has revealed inherent limitations of these widely used approaches. Proteogenomics uses mass spectrometry based proteomics data to directly identify protein coding regions in the genome and transcriptome. Using this approach, we have identified novel protein coding regions in annotated genomes of both prokaryotic and eukaryotic organisms. We have also demonstrated that some of the annotated pseudogenes and non-coding RNAs code for proteins thus challenging the conventional ways in which these annotations are carried out. These observations make a compelling case for employing proteomics to annotate genomes and identify novel proteins that have not been discovered till date.