Shraddha Puntambekar

Bioinformatics Scientist

Enabling data-driven drug discovery through bioinformatics, multi-omics, and scientific workflows

Industry Projects

Selected consulting and biotech engagements, framed as concise case studies so you can scan each in under a minute. Each section is divided into Problem · Approach · Outcome · Technologies — .

Pharma R&D Lab Digital Maturity Assessment

Employer: Cognizant · Role: Lab Informatics Scientific SME (Senior Associate)

Problem

A global pharmaceutical company needed an objective assessment of how digitally mature their R&D laboratories were across multiple sites, to understand the current state, benchmark against industry peers, and prioritize digitalization investments.

Approach

  • Defined and owned the maturity assessment framework (strategic areas, levels, baseline criteria) and designed mapped survey and interview questions to enable accurate stakeholder engagement and heatmap scoring.
  • Established assessment areas for pharma benchmarking, adopted by the team for comparative analysis; created structured forms and ran internal interviews to assess maturity across labs.
  • Stakeholder engagement: customized interview questions per stakeholder lab; co-conducted 16+ interviews; documented transcripts and meeting minutes for leadership alignment.
  • Led interviews with internal instrument-connectivity experts to capture connectivity requirements and data types.
  • Translated leadership requirements into actionable steps for the team; contributed to weekly leadership presentations; owned and developed the organizational chart.

Outcome

  • A scoring heatmap and benchmarking framework the client used to prioritize digital investments.
  • Post-submission contributions to dashboard and instrument-connectivity proposals.

Technologies & methods

Digital maturity assessment, Pharma benchmarking, Stakeholder interviews, Structured surveys, Heatmap scoring, Instrument connectivity, Strategic leadership artifacts

Bioinformatics Pipeline Validation & Documentation

Employer: Cognizant · Role: Bioinformatics Expert / SME

Problem

A British vaccine major was building a cloud-native bioinformatics analysis platform. They had 17 omics Nextflow pipelines (genomics and transcriptomics) needing independent validation, and proteomics/metabolomics pipelines being engineered. They needed centralized error triage, a comprehensive developer documentation suite covering the full pipeline lifecycle, and architecture documentation capturing the as-is (on-prem) and to-be (on-cloud) states.

Approach

  • Tested and validated 17 omics Nextflow pipelines (genomics, transcriptomics) by executing them through Google Cloud Workflows, Seqera/Nextflow Tower, and locally.
  • Triaged observed errors with engineering teams; documented root causes; maintained a troubleshooting knowledgebase.
  • Authored comprehensive developer documentation covering:
    • Nextflow pipeline development: coding standards, modular design, testing
    • Pipeline publishing via Azure DevOps
    • Pipeline publishing via GitHub Actions
    • Pipeline execution via Google Cloud Workflows and Seqera/Nextflow Tower
    • FAQs and runbooks for common operational scenarios
  • Captured and documented as-is (on-prem) and to-be (on-cloud) architectures of proteomics and metabolomics analysis pipelines, gathering details from engineering teams.

Outcome

  • 17 omics pipelines validated and triaged, with a documented error knowledgebase used by engineering teams.
  • A developer documentation suite covering the full pipeline lifecycle (build → publish → execute).
  • As-is / to-be architecture artifacts for proteomics and metabolomics workflows, used as the basis for cloud-migration planning.

Technologies

Nextflow, nf-core, Google Cloud Workflows, Seqera/Nextflow Tower, Azure DevOps, GitHub Actions, Genomics & transcriptomics pipelines, Proteomics & metabolomics analysis

Pre-Sales & RFP Support — Life Sciences Practice

Employer: Cognizant · Role: Bioinformatics SME contributor

Problem

Cognizant’s life sciences consulting practice receives multiple client opportunities that need rapid responses combining bioinformatics depth with consulting framing — RFP responses, capability presentations, project plans, and resource/loading estimates. Each requires translating ambiguous client needs into a defensible scientific and technical approach.

Approach

  • Contributed bioinformatics-domain content to RFP responses aligned with client requirements.
  • Presented technical approach and capability directly to prospective clients.
  • Built project plans and resource/loading (R/L) estimates mapped to delivery timelines.
  • Translated client requirements into structured scopes of work and team compositions.

Outcome

  • Strengthened proposal quality across multiple opportunities by adding bioinformatics-domain credibility.
  • Direct client presentations as a subject-matter contributor.

Technologies & methods

Proposal writing, Capability presentations, Project planning, Resource/loading estimation, Scope definition, Client communication

Cancer Biomarker & Target Discovery

Employer: NonExomics LLP · Role: Head of Computational Biology (2021–2023)

Problem

NonExomics, an early-stage biotech startup, needed to identify novel cancer biomarkers and therapeutic targets at startup pace from proprietary and publicly available WGS and RNA-seq data, while building the bioinformatics function from scratch and managing a fully remote 3-person team across time zones.

Approach

  • Implemented and maintained nf-core RNA-seq and WGS Nextflow pipelines on AWS.
  • Processed and analyzed proprietary and publicly available DNA and RNA expression datasets to identify novel cancer target candidates.
  • Designed siRNAs and qPCR primers for bioinformatically predicted targets.
  • Managed a fully remote 3-person team across time zones in a startup environment; defined delivery cadence and quality standards.
  • Represented NonExomics at the startup meetup organized by VCR Park, Vizag, India.

Outcome

  • Candidate cancer biomarkers and therapeutic targets identified and experimentally validated by the wet-lab team.
  • On-time delivery across geographies; established the company’s bioinformatics function and team.

Technologies

Nextflow · nf-core · AWS (EC2, S3) · WGS · RNA-seq · siRNA & qPCR primer design · Remote team management