Venkatesh Chellappa Patel

Venkatesh Chellappa Patel

Bioinformatician | Phd Student
Visiting address: Nobels väg 12a, 17165 Solna
Postal address: C8 Medicinsk epidemiologi och biostatistik, C8 MEB Grönberg Lindberg, 171 77 Stockholm
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About me

  • Venkatesh (Venki) is a GCP-certified Genome Informatics (Bioinformatics) professional.

    Qualifications: Bachelors in Vet. Medicine, Masters in Biosystems &
  • Informatics. Currently Doktorand in Medical Sciences at KI.

    Interests: Workflow Management, Reproducible Research, Cloud Computing, ML (Deep Learning, LLM), Bioinformatics Training &
  • Education, OSS, Cybersecurity, Blockchain, Ui/UX, Research Informatics, Lab Informatics

    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 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

Research

  • 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 am the Product Owner for our apps ecosystem. 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 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 [1]

    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 [2] for improving the pipelines and with Molecular Pathologists at Karolinska Hospital [3] 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, docker, singularity, machine learning/
    [1] https://www.probiotrial.org/
    [2] https://www.scilifelab.se/
    [3] https://www.karolinska.se/en/karolinska-university-hospital/

Teaching

  • Clinical Cancer Genomics course at MEB, KI.

Articles

Employments

  • Bioinformatician, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 2018-
  • Phd Student, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 2021-2025

Degrees and Education

  • Bachelor of Veterinary Sciences & Animal Husbandry, Veterinary Medicine & Surgery, Epidemiological Report of Trypanosomosis in Captive Wild Animals of India, Pondicherry Veterinary College, Pondicherry University, 2006

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