I am a Bioinformatician|
I work at the intersection of biological science, computational pipelines, and high-throughput genomic data. Specialized in end-to-end RNA-seq transcriptomics workflows (HISAT-2, featureCounts, DESeq2 in R) and molecular oncology data interpretation, with a distinction-grade foundation in Plant Biotechnology.
VASANTH NARAYANAN E
Where Computational Logic Meets Molecular Biology
Bridging dry-lab high-performance algorithms with wet-lab experimental understanding.
Integrated Life Science & Informatics Perspective
I am a postgraduate in Bioinformatics (M.Sc., First Class, Bharathiar University) with an undergraduate degree in Plant Biology and Plant Biotechnology (B.Sc., First Class with Distinction, 86%, University of Madras).
Because of my formal laboratory background in molecular biology, plant genetics, and microbial techniques, I understand the real cellular mechanisms behind sequencing data—enabling rigorous quality filtering, biologically grounded hypothesis testing, and accurate pathway interpretation.
Multi-Sector Practical Exposure
- Cancer Institute (WIA), Adyar: 5-month observership in Molecular Oncology analyzing patient RNA-seq datasets.
- Indica Seeds & Crop Care: 1-month Data Analyst Intern collating, cleaning, and evaluating agricultural trial metrics.
- Dr. Agarwal's Eye Hospital: 1-month clinical laboratory diagnostic training and hospital MLT standards.
Proven Execution
M.Sc. Dissertation Score (193/200, Grade 'O')
Wet-Lab Microbial & Phytochemical Practical (Grade 'O')
Transcriptomic Analysis of Cisplatin Resistance in Cervical Cancer
Next-Generation Sequencing Pipeline, Statistical Differential Expression & TCGA Clinical Cohort Validation
The Clinical Challenge
Concurrent Chemoradiotherapy (CCRT) with platinum-based cisplatin is standard for advanced cervical cancer, but chemoresistance causes high recurrence. This project established a computational RNA-seq workflow to uncover predictive transcriptomic biomarkers and dysregulated cellular bypass pathways.
The Computational Solution
Engineered an end-to-end RNA-seq analytical pipeline for paired-end sequencing datasets comparing CCRT non-responders vs durable responders. Quantified expression, modeled overdispersed count data via negative binomial distributions (DESeq2 in R), mapped dysregulated pathways via GSEA, and clinically verified candidates on TCGA-CESC.
Pipeline Architecture
Quality Control
FastQC evaluation of per-base Phred scores ($Q > 30$) and adapter checks on paired-end FASTQ reads.
FastQCSplice Alignment
Splice-aware read mapping against Human Reference Genome (GRCh38) using hierarchical FM-indexing.
HISAT-2 / SAMtoolsQuantification
Exon-level read summarization and gene-level count matrix generation across biological replicates.
featureCountsDifferential Expression
Negative Binomial GLMs in R, dispersion estimation, Wald test, and Benjamini-Hochberg FDR correction.
DESeq2 in RPathway Enrichment
GSEA mapping DNA damage repair, autophagy, and cellular stress response bypass mechanisms.
GSEA / clusterProfilerTCGA Validation
Candidate biomarker verification (ATG9B, HSPA1) across independent TCGA-CESC patient cohort data.
TCGA-CESC / GDCExplore Research Visualizations in Real-Time
Interactive representations of downstream exploratory data analysis and transcriptomic statistical models.
Volcano Plot Interpretation
Plots statistical significance against magnitude of expression change.
Key Candidate Signatures:
Principal Component Analysis (PCA)
PCA projects high-dimensional transcript counts onto orthogonal axes to inspect sample variance structure.
- PC1 (43.6% Variance): Clearly separates Non-Responders from Durable Responders.
- PC2 (22.8% Variance): Captures inter-patient biological heterogeneity.
- Sample Concordance: Biological replicate clustering confirms high pipeline reproducibility.
Hierarchical Clustering
Visualizes relative gene expression across samples using Euclidean distance and Ward's linkage method.
Verified Skills & Evidence Matrix
Classified rigorously according to demonstrated project, practical internship, and academic achievements. Click any card to inspect verified evidence.
RNA-seq Transcriptomics
End-to-end pipeline execution from raw FASTQ to biological pathway enrichment (FastQC, HISAT-2, featureCounts, DESeq2).
Differential Gene Expression (DGE)
Statistical modeling of count data using Negative Binomial GLMs, Wald testing, and Benjamini-Hochberg FDR correction in R.
Clinical Data Validation
Independent cohort validation of candidate biomarker signatures against public repositories including TCGA-CESC and NCBI GEO.
R Statistical Programming
Bioconductor core packages, DESeq2, ggplot2, pheatmap, EnhancedVolcano, PCA, dispersion estimation, and reproducible R Markdown.
Python for Life Sciences
Scripting for genomic data manipulation, FASTA/FASTQ parsing, Pandas dataframes, NumPy arrays, and Biopython fundamentals.
Linux Command Line & Bash
Bioinformatics pipeline orchestration, high-throughput batch script execution, BAM/SAM indexing, and command-line automation.
Agricultural Data Analytics
Field trial dataset collation, phenotypic variation analysis, crop performance evaluation, and structured trial reporting.
Microbial & Phytochemical Assays
Microbial isolation, bacterial staining, phytochemical extraction, and qualitative biochemical screening assays.
Plant Biotechnology & Tissue Culture
Plant tissue culture, explant sterilization, media preparation, callus induction, organogenesis, and plant physiology.
Research Exposure & Industry Internships
Research Observer – Department of Molecular Oncology
Cancer Institute (WIA), Adyar, Chennai
Carried out a 5-month research observership in translational cancer genomics. Handled clinical oncology datasets, performed computational differential expression analysis of cervical cancer RNA-seq data, and participated in departmental multidisciplinary research reviews.
Data Analyst Intern
Indica Seeds and Crop Care
Collected, validated, and analyzed agricultural trial datasets. Performed on-site field visits across crop plots to evaluate phenotypic traits, seed performance, and yield metrics for management trial reporting.
Medical Laboratory Technology (MLT) Intern
Dr. Agarwal’s Eye Hospital Ltd., Chennai
Trained in clinical diagnostic laboratory workflows, specimen processing protocols, laboratory safety assurance, and clinical data logging.
Education & Recognitions
Master of Science (M.Sc.) in Bioinformatics
Department of Bioinformatics, Bharathiar University, Coimbatore
Dissertation: Transcriptomic Analysis of Cisplatin Resistance in Cervical Cancer using NGS Data (Awarded Grade 'O' / 193 out of 200 marks).
Bachelor of Science (B.Sc.) in Plant Biology & Plant Biotechnology
Guru Nanak College, University of Madras, Chennai
Awarded Certificate of Proficiency in Academics (2021–2022) for academic rank in core plant biotechnology.
Best Presentation Award
MOTIF 2023 • Department of Bioinformatics, Bharathiar University
Awarded 1st Prize for outstanding scientific paper presentation and defense in computational biology.
Certificate of Proficiency in Academics
Guru Nanak College (Academic Year 2021–2022)
Conferred for outstanding academic merit and subject leadership in Plant Biology and Biotechnology.