🇬🇧 Curriculum vitae (CV)

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Contact

Education

  • PhD Candidate (2023–current), Stellenbosch University, Division of Molecular Biology and Human Genetics, Bioinformatics Research Unit.
    Supervisor: Prof. Gian van der Spuy.
  • Masters in Data Science (2020–2021), Liverpool John Moores University, UK.
  • Post-graduate diploma in Data Science (2019–2020), International Institute of Information Technology – Bengaluru.
  • Bachelors in Information Technology (2012–2016), Delhi Technological University, India.

Experience

  • GENPATH Africa consortium (2024–current) — Bioinformatician
    Performed bioinformatic analysis, pipeline and SOP implementation, data management, and training development in computer science and bioinformatics.
  • National Council for Scientific and Technological Development (CNPq), Brazil (2024–current), REVIGET and GEMIBRA Consortiums — Bioinformatician and Capacity Building Mentor
    Performed bioinformatic analysis, pipeline and SOP implementation, data management, and training development in computer science and bioinformatics.
  • TORCH Consortium (2022–2024) — Software Development (Nextflow pipeline)
    MAGMA pipeline development and maintenance.
  • Telethon Kids Institute (2023–2024) — Senior Data Scientist
    Facilitated omics analysis for research groups across clinical trials.
  • Seqera Labs (2020–2022) — Nextflow Specialist and Customer Success
    Helped top biopharma companies optimize analysis environments (AWS/Azure) and debug pipelines.
  • Biosharp OĂś (2020–2023) — Principal Data Scientist
    Provided data science and data engineering services to multiple clients and conducted international capacity-building workshops.
  • Pxoximity Labs (2020) — Senior Full Stack Software Engineer
    Worked on upgrading the frontend into a performant progressive web app (PWA), focused on UX, performance, and caching.
  • Devnagri (2017–2019) — Chief Technology Officer
    Led a team of 15 software engineers to build the digital platform, including NLP translation engine, CLI tooling, web scrapers, and data transformation services.

Grant awards

  1. NRF Scholarship for PhD, South Africa (2024–2026)
  2. Oracle Research Cloud Credits (2023–2026)
  3. Google Cloud Research Credits (2024)
  4. SAMRC registration bursary (2023)

Human languages (proficiency)

  • English
  • Hindi
  • Portuguese

Main skills

Cloud computing

  • AWS
  • Azure
  • Google Cloud
  • Oracle Cloud

Programming languages

  • Nextflow
  • Python
  • R
  • Clojure(Script)
  • Powershell
  • Java

Databases

  • MySQL
  • Sqlite3
  • DuckDB
  • Datomic
  • Oracle database

Project management

  • Clicks
  • RedCap

Published/accepted peer-reviewed articles

  1. Heupinkin, Verboven, Sharma* et al. The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples (1st author). https://doi.org/10.1371/journal.pcbi.1011648
  2. Sharma* et al. Tuberculosis drug resistance profiling based on machine learning: A literature review (1st author). https://doi.org/10.1016/j.bjid.2022.102332
  3. (Accepted) A Near-complete Genome of the Uncultured Staphylococcus aureus Phage COMBAT-CF_PAR1, Isolated from the Lungs of an Infant with Cystic Fibrosis.
  4. A Genome-Focused Investigation Reveals the Emergence of a Mycobacterium tuberculosis Strain Related to Multidrug-Resistant Tuberculosis in the Amazon Region of Brazil. https://doi.org/10.3390/microorganisms12091817
  5. Description of new species of Mycobacterium terrae complex isolated from sewage at the SĂŁo Paulo zoological park foundation in Brazil. https://doi.org/10.3389/fmicb.2024.1335985
  6. Whole-Genome Sequencing of Alcaligenes faecalis HZ01, with Potential to Inhibit Nontuberculous Mycobacterial Growth. https://doi.org/10.1128/mra.00521-21
  7. Molecular epidemiology of Mycobacterium tuberculosis in Brazil before the whole genome sequencing era: A literature review. https://doi.org/10.1590/0074-0276020517
  8. Genomic Diversity of the Rarely Observed Genotype of the Mycobacterium tuberculosis Central Asian (CAS) Lineage 3 from North Brazil. https://doi.org/10.3390/microorganisms11010132
  9. Analysis of potential household transmission events of tuberculosis in the city of Belem, Brazil. https://doi.org/10.1016/j.tube.2018.09.011
  10. Characterization of Mycobacterium tuberculosis var. africanum isolated from a patient with pulmonary tuberculosis in Brazil. https://doi.org/10.1016/j.meegid.2020.104550
  11. Evaluation of drug susceptibility profile of Mycobacterium tuberculosis Lineage 1 from Brazil based on whole genome sequencing and phenotypic methods. https://doi.org/10.1590/0074-02760200520

Articles under peer-review

  1. Marcon, Sharma et al. Genomic surveillance reveals transmission profiles of the first extensively drug-resistant tuberculosis cases in Pará, Brazil (1st author). Frontiers in Microbiology, Oct 2024.
  2. Virome Assembly Reveals Draft Genomes of Native Pseudomonas Phages isolated from a Paediatric Bronchoalveolar Lavage Sample. Microbiology Resource Announcements, Sep 2024.

Articles in-submission

  1. Sharma* et al. MTBseq-nf: Enabling Scalable Tuberculosis Genomics “Big Data” Analysis through a User-Friendly Nextflow Wrapper for MTBseq pipeline (1st author). Intended journal: PEERJ.
  2. Sharma* et al. CholeraSeq: a comprehensive genomic automated pipeline for cholera surveillance and near real-time outbreak investigation (1st author). Intended journal: Oxford Bioinformatics.
  3. Sharma# et al. Ten simple rules to build sustainable bioinformatics capacity using Nextflow and nf-core with a focus on early-mid career researchers: The Kids Institute case report (#Senior author). Intended journal: PLOS One Bioinformatics.
  4. Leveraging the State of Whole Genome Sequencing for Precision Public Health in a High-Burden Tuberculosis Setting using the GEMIBRA Platform. Intended journal: Discovery Public Health.

International collaboration network

  1. South Africa: Stellenbosch University Research Groups (TB Genomics – Rob Warren, CERI – Tulio de Oliveira, Host Genetics – Marlo Moller, Africa Microbiome Institute – Kristine Nel van Zyl), University of the Western Cape (UWC) – Alan Christoffels, University of Limpopo – Ivy Rukasha, and DIPLOMICS – Mhlekazi Molatoli.
  2. Brazil: Instituto Evandro Chagas (Karla Lima), Fiocruz-IOC (Philip Suffys), Fiocruz-INI (Cristina Lourenço), UNIFESP (Cristina Viana), UNIPEX (Patricia Reis), USP (Ana Marcia Guimaraes), UFC (Cristiane Frota).
  3. Zambia: Tropical Disease Research Center (TDRC), Ndola (Kabengele Keith).
  4. Belgium: Antwerp University (Annelies van Rie) and University Hospital Ghent (Tom Sante).
  5. Australia: The Kids Institute and University of Western Australia (Patricia Agudelo-Romero).
  6. Spain: nf-core and Nextflow communities (Seqera Labs) – Ambassador.
  7. United Kingdom: LSHTM (Jody Phelan).