Acta Computationis Biologicae

Supplementary Information

S3. Laboratory notebook

Dated entries. Ruled as a bench book.

Kovalchuk Laboratory and earlier benches. Each entry is a day in the book, not a card on a wall. Healthcare work is described without patient detail.

All healthcare-related experience is described at a professional, non-identifying level. No confidential patient data, documents, or PHI are referenced or published on this site, consistent with HIPAA and organizational privacy requirements.

Graduated 2019 · education

Bachelor's in Science (Biology, Biotechnology & Bioinformatics)

Bangalore University, India

Foundational training across biology, biotechnology, and bioinformatics ahead of graduate specialization.

2020 - 2022 · education

Master's Degree, Applied Genetics & Bioinformatics

Bangalore University, India

In-silico screening of anti-arthritic phytochemicals against rheumatoid arthritis drug targets for the master's thesis.

Jan 2022 - Present · research

Bioinformatics Intern

ArrayGene, Bangalore, India

RNA-seq and microarray differential expression analysis, alongside CRISPR guide design, for client genomics projects.

Jan 2022 - Present · industry

Medical Reviewer / Coder

Omega Healthcare Management Pvt. Ltd., Bangalore, India

Reviews and codes oncology (NSCLC) patient records for accuracy and coding compliance.

Aug 2022 - Jan 2023 · industry

Data Science Intern

DataMites, Bangalore, India

Led end-to-end machine learning projects spanning classification, regression, and computer vision.

Jun 2023 - Nov 2023 · industry

Data Scientist

SirpiData Science, Bangalore, India

Applied machine learning and geospatial analytics to urban growth and environmental risk on the IUDX project.

Jan 2024 - Present · research

PhD Researcher, Bioinformatics

University of Lethbridge, Alberta, Canada

Multi-omics biomarker discovery in rheumatoid arthritis, supervised by Dr. Igor Kovalchuk.

2024 - Present · mentorship

Teaching Assistant & Research Mentor

Kovalchuk Lab, University of Lethbridge

Mentoring independent-study, research assistant, and Honours students across bioinformatics and computational biology.

Mar 2026 - Apr 2026 · ai

Bioinformatics Expert (AI Model Evaluation)

Mercor (Remote)

Designed and reviewed bioinformatics and genomics benchmark tasks for AI model evaluation.

Mar 2026 - Present · ai

Biology Coding Expert (Human-in-the-Loop AI Workflows)

Mercor (Remote)

Built reproducible Jupyter notebook workflows across transcriptomics, genomics, and epigenomics for AI research.

S3.1 Industry and applied posts

Mar 2026 - Apr 2026 · Remote

Bioinformatics Expert (AI Model Evaluation), Mercor

Designed and reviewed bioinformatics and genomics benchmark tasks used to evaluate AI model performance, defining rubrics for what counts as a correct, high-quality solution.

  • Designed and reviewed bioinformatics/genomics tasks for AI model evaluation, defining clear rubrics and evaluation criteria.
  • Assessed model-generated analyses and explanations against these rubrics, providing structured written feedback on analytical rigor, clarity, and adherence to best practices.
  • Applied CRISPR-Cas9 guide-design domain knowledge to evaluate model outputs on functional-genomics tasks.
  • Collaborated with a distributed team to maintain consistent evaluation quality across task batches.

Mar 2026 - Present · Remote

Biology Coding Expert (Human-in-the-Loop AI Workflows), Mercor

Built reproducible Jupyter notebook workflows spanning transcriptomics, genomics, and epigenomics to support AI research and model evaluation at a leading AI lab.

  • Designed and solved benchmark bioinformatics tasks used for AI model evaluation and training-data quality assurance.
  • Developed reproducible Jupyter notebook workflows for transcriptomics, genomics, and epigenomics use cases.
  • Performed annotation quality review and data quality assurance on research-oriented, human-in-the-loop AI workflows.
  • Collaborated with a diverse, distributed team to resolve product and workflow issues under fast-paced delivery cycles.

Jun 2023 - Nov 2023 · Bangalore, India

Data Scientist, SirpiData Science

Applied machine learning and geospatial analytics to environmental and urban-planning problems, including the IUDX urban-infrastructure initiative.

  • Applied Google Earth Engine to process satellite imagery for urban growth and environmental-risk analysis, cutting data-preparation time by roughly 30%.
  • Conducted water-quality analysis of urban lakes using NDWI, EVI, turbidity, and chlorophyll indices to flag pollution hotspots and trends.
  • Built geospatial data pipelines integrating multiple datasets into environmental and urban-analysis reports.
  • Delivered interactive maps and dashboards communicating water-quality and urban-growth findings to stakeholders.

Mar 2024 - Oct 2024 · Bangalore, India

Data Science Engineer, SirpiData Science

Built and tuned machine learning models for a project affiliated with the Indian Institute of Science (IISc) Bangalore.

  • Built, tested, and hyperparameter-tuned multiple machine learning models (MinMax/Standard scaling) for an IISc Bangalore-affiliated project.
  • Researched problem statements to inform project direction and modelling approach.
  • Presented data stories to clients through a web application, translating model output into decision-ready insight.
  • Collaborated with a cross-functional engineering team on solution design and technical documentation.

2022 · Bangalore, India

Bioinformatics Intern, ArrayGene

Contributed to analysis of genomics datasets and supported ongoing bioinformatics research projects.

  • Applied differential gene expression analysis using DESeq2 and edgeR in R to identify key genes across experimental conditions.
  • Performed preprocessing and quality control of high-throughput sequencing data with samtools ahead of downstream analysis.
  • Conducted functional enrichment and pathway analysis (clusterProfiler/KEGG) to interpret the biological significance of identified genes.
  • Designed CRISPR-Cas9 guides with on-target/off-target scoring, and created heatmap, volcano-plot, and PCA visualizations to summarize results.

Aug 2022 - Jan 2023 · Bangalore, India

Data Science Intern, DataMites

Led end-to-end applied machine learning projects spanning classification, regression, and computer vision, achieving A+ project grades.

  • Directed development of classification and regression models (logistic regression, random forest, XGBoost, KNN, SVM, gradient boosting), reaching 90-92% test accuracy on a lung-cancer prediction task.
  • Built a CNN-based image classification model for a rice-leaf computer-vision project, achieving 88-90% accuracy.
  • Addressed class imbalance with SMOTE and applied systematic hyperparameter tuning, cross-validation, and ensemble methods.
  • Led a team through three major end-to-end projects, from data collection to model evaluation and reporting.

Jan 2022 - Present · Bangalore, India

Medical Reviewer / Coder, Omega Healthcare Management Pvt. Ltd.

Reviews and codes oncology patient records for accuracy and coding compliance in a healthcare documentation setting with strict privacy requirements.

  • Reviews and analyzes non-small cell lung cancer (NSCLC) patient records - clinical notes, lab results, imaging, and treatment plans - for completeness and accuracy.
  • Assigns ICD-10 codes in accordance with medical coding standards to support billing, clinical reporting, and research use.
  • Reviews roughly 50 NSCLC patient records weekly, applying coding knowledge to support oncology research and decision-making.
  • Maintains strict compliance with HIPAA, PHI, and confidentiality standards throughout all record handling.

S3.2 Teaching and mentorship

2025 - Present

Independent Study Student Supervision

University of Lethbridge, Department of Biological Sciences

  • Supervising approximately 7 independent-study students, designing individualized research problems in bioinformatics, machine learning, and applied AI.
  • Guide students from problem formulation through analysis, covering multi-omics data handling, statistical reasoning, and reproducible R/Python workflows.
  • Provide structured, recurring feedback on project progress and support academic and professional development beyond the technical scope of each project.

2024 - Present

Research Assistant (RA) Mentoring

Kovalchuk Lab, University of Lethbridge

  • Mentor research assistants on transcriptomic and methylomic data-processing pipelines, from raw GEO data retrieval through differential expression analysis.
  • Review analysis code and results for statistical soundness before findings are incorporated into shared lab research.

2024 - Present

HYRS Student Mentoring

Honours / Year-Round Research Students, University of Lethbridge

  • Mentored Honours and year-round research students on bioinformatics research design, dataset selection, and computational methods.
  • Helped translate open biological questions into tractable, well-scoped computational research projects.

2024 - Present

Teaching Assistant (TA) Responsibilities

University of Lethbridge, Biological Sciences

  • Supported course delivery and grading for graduate and undergraduate biology courses.
  • Held office hours and lab sessions to help students build practical R and bioinformatics skills.

Course design with Dr. Igor Kovalchuk. Contributed to the design and delivery of graduate and undergraduate coursework in the Kovalchuk lab, helping translate active bioinformatics research methods into structured, teachable curricula. Graduate Topics in Biological Sciences, Undergraduate Biological Sciences, Advanced Graduate Seminar.

I believe computational biology is best learned by doing: reproducibly, transparently, and on real data. With every student, I make three things visible: the biological question, the statistical assumptions behind the method, and the code that connects them. I favour structured, recurring check-ins over one-off feedback, because research skill builds through iteration, not a single corrected mistake. My goal is to leave students with more than a finished project: a framework they can bring to the next open question on their own.