Venkatesh (Venki) is a Genome Informatics professional with GCP-certification. He has a degree in Veterinary Medicine and postgraduate degree in Biosystems & Informatics.
I work as Bioinformatician in Prostate cancer genomics group at the Department of Medical Epidemiology & Biostatistics (MEB) Karolinska Institute.
I am also a doctoral student at MEB. My doctoral research focuses on Cancer Genomics - Liquid Biopsy profiling of prostate cancer.
My research interests include developing computational pipelines for analysis of sequencing data. I am also interested in employing ML and AI tools for mining and integrating x-omics data to get better insight into high penetrance cancers. I focus on cancer genomics and transcriptomics. My current work revolves around building pipelines for analysis of liquid biopsy data from prostate cancers and integration of cancer transcriptome profiles with mutation profiles.
At KI, I work in Johan Lindberg's group on translational projects that involve genomics at the interface of clinical research and laboratory tests to diagnose and optimize treatment options for cancers. Along with the bioinformaticians in my group, I maintain the Autoseq Informatics framework for analysis of cancer NGS data.
I develop and maintain NGS data analysis pipelines to identify significant structural variants and SNVs in targeted cell-free & circulating-tumour DNA-based liquid biopsy samples from prostate cancer. Along with my team, one of the main projects of focus for me is the ProBio Clinical Trial which looks at biomarker-based liquid biopsies for treatment of prostate cancer. To know more about ProBio Trial please visit www.probiotrial.org
I am also involved in bioinformatics work for other clinical trials like ALASCCA, CITCCA, iPCM, CRC-Reflex and PSFF.
I collaborate with bioinformaticians at Scilifelab across the road for improving the pipelines for clinical grade reports and user-friendliness. I am an active contributor to the Bioinformatics OSS community.
Tags: cancer genome interpretation, clinical genomics, targeted resequencing, NGS data analysis, prostate cancer, PIK3CA, PTEN, genome informatics, ML for genomics, AI for genomics, nextflow for genomics, cancer transcriptome, liquid biopsy
2006 - Bachelor of Veterinary Sciences & Animal Husbandry, Pondicherry, India
2010 - Master of Science in Biosystems & Informatics, Liverpool, UK
2021 - present - Doctoral Student (Medical Sciences) - Cancer Genomics, Liquid Biopsy Profiling of Prostate Cancer