Shafna (V s) A.

LLM Trainer/Evaluator

Abu Dhabi, United Arab Emirates

Experience

Jul 2025 - Nov 2025
5 months

LLM Trainer/Evaluator

Turing

  • Developed advanced, multi-layered AI-breaking prompts specifically designed to challenge and test the limits of large language models within the domain of molecular biology and genetics.
  • Conducted rigorous evaluations of AI-generated responses to ensure accuracy, depth, and reliability in biomedical and scientific contexts, identifying failure points and areas for improvement.
  • Collaborated in refining AI training datasets by labeling complex biomedical questions and answers, enhancing model performance in specialized scientific knowledge areas.
  • Provided expert biological insights to interpret nuanced domain-specific outputs, aligning model behavior with cutting-edge research and scientific standards.
Aug 2024 - Present
1 year 5 months
Abu Dhabi, United Arab Emirates

Bioinformatics Scientist

Prepaire Lab

  • Designed and implemented advanced computational pipelines for multi-omic data analysis, including RNA-Seq, DNA-Seq, and microbiome sequencing.
  • Performed variant discovery, annotation, and functional impact analysis using cutting-edge tools such as GATK, DeepVariant, ANNOVAR, and PolyPhen-2.
  • Conducted transcriptomic and differential expression analyses with DESeq2, edgeR, and StringTie to elucidate key molecular changes.
  • Analyzed microbiome datasets using QIIME2, DADA2, and HUMAnN to derive taxonomic and functional insights.
  • Integrated genomic, transcriptomic, and microbiome data to support precision medicine through biomarker identification and biomedical knowledge graph development in Neo4j.
Jan 2013 - Dec 2014
2 years
United Arab Emirates

Research Assistant in Bioinformatics

UAE University

  • Created a therapeutic pathway for Type II Diabetes targeting several natural chemicals under Prof. Ranjith Vijayan.
  • Identified and validated multiple biological targets to enhance therapeutic strategies employing natural compounds.
Jan 2009 - Dec 2012
4 years
Coimbatore, India

Assistant Professor

Dr G R Damodaran College of Science

  • Conducted classes for postgraduate students in Bioinformatics, Biochemistry, and Biotechnology.
  • Managed departmental examinations as the department controller.
  • Provided guidance and counseling to students as a student counselor.
  • Demonstrated strong organizational skills and proficiency in communication.

Summary

A highly motivated bioinformatics scientist with a PhD specializing in computational transcriptomic analysis, I am eager to contribute my expertise in NGS data analysis, variant calling, and multi-omics integration to cutting-edge biomedical research.

With a strong emphasis on identifying disease mechanisms, especially in diabetic retinopathy, I am an expert at creating and refining computational pipelines utilising Python and R. I have expertise in creating knowledge graphs for biological data, functional annotation, and differential gene expression analysis.

Through cooperative research, creative problem-solving, and ongoing education, I am committed to enhancing precision medicine. I'm committed to mentorship and scientific achievement, and I want to help fund important studies that enhance patient outcomes.

Skills

  • Develop and optimize bioinformatics pipelines for high-throughput genomic data
  • Expertise in NGS (Next Generation Sequencing) analysis
  • Structural Bioinformatics
  • Programming in Python and R
  • Passionate in teaching and research
  • Performed variant calling pipelines using FastQC, TrimGalore, BWA-MEM, GATK HaplotypeCaller, DeepVariant, bcftools, and SnpEff for variant annotation
  • Conducted microbiome analysis with QIIME 2, DADA2, MetaPhlAn 3, Kraken 2, and HUMAnN 3 for taxonomic and functional profiling
  • Used STAR and Salmon for RNA-Seq alignment and quantification; analyzed differential expression with DESeq2
  • Visualized molecular structures with PyMOL, ChimeraX, VMD, and Swiss PDB Viewer
  • Carried out molecular docking using AutoDock Vina and SwissDock
  • Accessed biological databases such as NCBI, OMIM, PDB, EMBL-EBI, UniProt, and Pfam for sequence and functional data
  • Utilized sequence alignment and analysis tools including BLAST, Clustal Omega, MAFFT, and EMBOSS
  • Developed reproducible workflows using Nextflow, Snakemake, and nf-core pipelines
  • Skilled in scripting with Python and R for data analysis and automation

Languages

Malayalam
Native
Tamil
Native
English
Advanced

Education

Oct 2017 - Jun 2024

Bharathiar University

PhD in Bioinformatics · Bioinformatics · Coimbatore, India

Oct 2007 - Jun 2009
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Masters in Bioinformatics · Bioinformatics

Oct 2004 - Jun 2007
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Bachelors in Biochemistry · Biochemistry

Certifications & licenses

Machine Learning through FOSS

International center for free and open source software (ICFOSS), Government of kerala, Trivandrum

R Language

Department of Statistics, Bharathiar university

Next Generation Sequencing and Analysis

University of Kerala, Trivandrum

Clinical Biochemistry

United Diagnostic Lab, Coimbatore

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