Venkatesh Chellappa

About me

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 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 sequencing data from various cancers.

Research description

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. My main responsibility as lead Bioinformatician is modernization and maintenance of core technology infrastructure.

Along with my team, I maintain our github repos and informatics framework including our codebase, VMs, servers, computational pipelines. This involves an automated continuous integration and continuous deployment (CI/CD) pipeline comprising of development, testing, production, and monitoring phases. I am also responsible for housekeeping of bioinformatics tools, apps, pipelines, on-prem and cloud computing environments.

I develop and maintain NGS data analysis pipelines to analyse 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 one of the responsible people for the bioinformatics work for other clinical trials like ALASCCA, CITCCA, iPCM, CRC-Reflex and PSFF. 

I collaborate with bioinformaticians at Scilifelab for improving the pipelines and with Molecular Pathologists at Karolinska Hospital for clinical grade reports. 

Tags: cancer genome interpretation, clinical genomics, targeted resequencing, NGS data analysis, prostate cancer, ctDNA, cfDNA, genome informatics, ML for genomics, AI for genomics, snakemake, nextflow, cancer transcriptome, liquid biopsy

Education

2021 - present - Doctoral Student (Medical Sciences) - Cancer Genomics, Liquid Biopsy Profiling of Prostate Cancer, KI, Stockholm, Sweden

2010 - Master of Science in Biosystems & Informatics, Liverpool, UK

2006 - Bachelor of Veterinary Sciences & Animal Husbandry, Pondicherry, India