Curriculum Vitae

AllenKalampukattussery

QC & Bioinformatics  —  Wet Lab to Pipeline

Quality control professional with over two years of experience in cGMP-regulated pharmaceutical and biotech laboratories. M.S. in Bioinformatics from San Jose State University, with hands-on experience spanning molecular diagnostics, genome assembly, and machine learning.

San Jose, CA · · 781-325-6568 · LinkedIn · GitHub
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Experience
Quality Control Supervisor Sep 2021 – Jan 2023
Lucira Health · San Jose, CA
  • Maintained cGMP-compliant QC operations for single-use molecular COVID-19 diagnostic devices in a BSL-2, ISO 13485-regulated medical device laboratory, working directly with SARS-CoV-2 positive clinical samples.
  • Performed and supervised routine product testing and data review, verifying accuracy, completeness, and compliance with specifications.
  • Wrote new SOPs and updated existing procedures, technical reports, and quality documentation to reflect current cGMP requirements.
  • Reviewed batch records and QC data packages; performed complex data analysis and calculations to verify test results prior to disposition.
  • Supported regulatory audit readiness and helped establish QC lab operations during production ramp-up, including product transfers and new testing workflows.
  • Maintained and calibrated laboratory instrumentation per established schedules; troubleshot analytical method issues and escalated as needed.
  • Trained staff on quality procedures, analytical methods, documentation standards, and safety protocols.
Research Associate Jan 2023 – Jul 2023
Genista Biosciences Inc · San Jose, CA
  • Performed pathogen detection testing using DNA/RNA extraction, PCR, and gel electrophoresis with strict adherence to SOPs and data integrity standards.
  • Operated custom-programmed automated liquid handlers for high-throughput sample preparation; maintained calibration records and verified instrument performance.
  • Prepared media, buffers, and reagents per written procedures for daily molecular and microbiological testing workflows.
  • Performed microbiological testing via plating, streaking, culturing, and isolation techniques in support of daily laboratory workflows.
  • Maintained detailed laboratory records, identified sources of variability, and refined workflows to improve reproducibility and data quality.
Undergraduate Researcher Jun 2020 – May 2021
Bennett Lab · UC Merced, Merced, CA
  • Performed RNAi experiments in planthoppers, including RNA extraction, DNA extraction, and PCR for gene knockdown studies.
  • Quantified nucleic acid concentration and purity using Qubit fluorometry.
  • Performed gel electrophoresis for verification of PCR products and nucleic acid quality assessment.
  • Assembled and curated three bacterial endosymbiont genomes from raw sequencing data, performing data quality assessment at each stage of the bioinformatics pipeline.
  • Conducted pairwise evolutionary divergence analysis using codeML and R to identify biologically meaningful variation across species.
  • Applied statistical and computational methods in R and Python for data analysis, visualization, and technical reporting.
  • Maintained live planthopper colonies and host plant cultures, monitoring health and ensuring consistent experimental conditions.
  • Designed and developed containment enclosures for insect rearing and experimental housing.
Projects
Gel Image Segmentation via CNN–ViT Hybrid
SJSU M.S. Bioinformatics · 2025

Developed a deep learning pipeline combining a convolutional neural network with a Vision Transformer (ViT) architecture in PyTorch to perform automated segmentation of gel electrophoresis images. Trained, validated, and evaluated model performance on annotated gel image datasets.

PyTorch CNN Vision Transformer Image Segmentation Python
Long-Read Sequencing Artifact Detection Pipeline
SJSU M.S. Bioinformatics · 2025

Built a reproducible Nextflow pipeline for detecting and characterizing sequencing artifacts in long-read human genomic data. Pipeline covered quality control, alignment, artifact identification, and summary reporting across configurable reference inputs.

Nextflow Long-Read Sequencing Bioinformatics Pipeline Development Linux
Education
M.S. in Bioinformatics
San Jose State University
Dec 2025
B.S. in Human Biology
University of California, Merced
May 2021
Skills
Quality & cGMP
cGMP Compliance QC Testing SOP Authorship Data Review Batch Record Review Analytical Methods EHS Compliance Audit Readiness CAPA Support Deviation Management
Laboratory
DNA/RNA Extraction PCR Gel Electrophoresis Qubit Fluorometry RNAi BSL-2 Aseptic Technique Microbiological Methods Plating & Culturing Media Preparation Instrument Calibration Liquid Handling
Data & Software
Python R SQL PyTorch NumPy Pandas Nextflow Microsoft Office AI/LLM Tools
Professional
Technical Writing Staff Training Cross-Functional Collab Independent Work Oral Communication
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