Venkatesh Chellappa Patel

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 snakemake and nextflow pipelines for analysis of liquid biopsy sequencing data from various cancers.

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

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.

I manage the software development projects following Rapid Learning Cycles Agile Framework. 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 cancer. 

/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, docker, singularity, machine learning/

Lab assitant - Clinical Cancer Genomics course at MEB, KI.