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USD 40 /hr

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Hire Dr. Prashanth S J.

India

USD 40 /hr

AI-Driven Multi-Omics Expert | Biomarker Discovery in Cancer & Inflammation via NGS, ML & MD and Scientific writing

Profile Summary

A highly accomplished PhD Candidate in Bioinformatics and Molecular Systems Biology with proven expertise in accelerating drug and biomarker discovery Specializing in the integrative analysis of multi-omics data using advanced computational and machine learning methodologies . I translate complex in silico predictions into actionable, validated translational insights for clients in the cancer and inflammatory disease sectors. Specialized Writing and Communication Services : 1. Scientific and Medical Writing: Creating comprehensive scientific reports, study protocols, literature reviews, and evidence summaries. 2. Grant Proposal Support: Assisting in drafting the technical and methodological sections of grant applications, leveraging expertise in cutting-edge techniques like scRNA-seq and AI/ML. 3. Data Visualization and Presentation: Generating high-quality figures and presentations from complex data using tools like ggplot2, matplotlib, and Plotly. 4. I offer specialized services to translate complex research outcomes into clear, publication-ready documents, accelerating your R&D communication goals. 5. Research Paper and Manuscript Drafting: Expert in structuring, writing, and editing peer-reviewed research articles for submission to high-impact journals, with a strong publication record in areas like ulcerative colitis, colorectal cancer, and senotherapeutics. High-Value Skills & Deliverables: 1.AI/ML for Precision Medicine: Developing and deploying robust Machine Learning (ML) pipelines (using Python, R, TensorFlow, PyTorch) for predictive biomarker discovery and target classification from large-scale biological datasets. 2. Next-Generation Sequencing (NGS) Analysis: Expertise in processing and analyzing complex sequencing data, including both bulk RNA-seq and high-resolution single-cell RNA-seq (scRNA-seq). 3. Computational Drug Discovery: Utilizing Molecular Dynamics (MD) simulations (GROMACS, AMBER) and molecular docking (AutoDock Vina, Schrödinger Glide) for lead optimization, target validation, and calculating binding free energy (MM/PBSA, MM/GBSA). 4. Systems Biology & Network Analysis: Employing Network Pharmacology, WGCNA, and pathway enrichment (KEGG, Reactome, STRING) to identify novel therapeutic targets and understand disease mechanisms at a systems level. 5. Translational Pipeline Development: Skilled in building automated, reproducible workflows (Snakemake, Nextflow, Docker) in Linux/HPC/Cloud environments (AWS, Azure). Project Experience and Achievements 1. PhD Research (VIT): Integrated multi-omics, network pharmacology, and ML to identify the therapeutic targets of Embelin in ulcerative colitis and colorectal cancer. 2. Anti-Malarial Drug Design (DST Project): Performed structural modeling, docking, and MD simulations on Plasmodium falciparum enzymes to identify potent inhibitors, contributing to international therapeutic design efforts. 3. Precision Oncology Support (Internship): Applied bioinformatics pipelines for lung fusion gene analysis using the NanoString platform, supporting key molecular profiling in cancer research. Awards: Recipient of the Best Research Paper Award (ICGEC 2024) and multiple Raman Research Awards.

Subject Matter Expertise

• ★ Computational Biology
• ★ Omics
• ★ Gene Expression Analysis
• ☆ Molecular Biology
• ☆ Biomarkers
• ☆ Microarrays
• ☆ Transcriptomics
• ☆ Proteomics
• ☆ Metabolomics
• ☆ Genomics
• ☆ PCR
• ☆ Next Generation Sequencing (NGS)
• ☆ ATAC-Seq
• ☆ Exome Sequencing
• ☆ RNA Sequencing
• ☆ DNA Damage & Repair
• ☆ ChIP-Seq
• ☆ Kinases
• ☆ Blotting
• ☆ R
• ☆ Drug Discovery
• ☆ Drug Design
• ☆ Medical Genetics
• ☆ Traditional Medicine

Services

• Writing

Writing Medical Writing, Technical Writing

Work Experience

Ph.D. Research Scholar

Vellore Institute of Technology University

- Present

Teaching cum Research Assistant

Vellore Institute of Technology

December 2021 - June 2025

Junior Research Fellow DST Indo Taiwan Project

Alagappa University

December 2020 - June 2021

Intern

Theracuse Innovation Private Limited

November 2017 - March 2018

Education

Computational Biology

Vellore Institute of Technology

December 2021 - Present

Masters in Biomedical genetics (School of Bioscience and technology )

Vellore Institute of Technology University

2018 - 2020

B.Sc.

University of Agricultural Sciences, Bangalore - India

June 2014 - June 2018

Certifications

• Reverse and complement nucleic acid sequences (DNA, RNA) using R

  coursera

  https://coursera.org/verify/RM28XWKHJ3A4

  July 2020 - Present

• Introduction to Genomic Technologies

  coursera

  https://www.coursera.org/account/accomplishments/verify/WKV66LW6RQX8

  June 2020 - Present

• Drug Discovery

  coursera

  https://www.coursera.org/account/accomplishments/verify/SDACSVFCPTKG

  June 2020 - Present

• Python for Genomic Data Science

  coursera

  https://www.coursera.org/account/accomplishments/verify/7HVX788Q4JLQ

  June 2019 - Present

Publications

CONFERENCE PAPER

Javali, P.S., Thirumurugan, K.(2025). Comprehensive Analysis to Understand the Potential of Embelin in Ulcerative Colitis: An Integrated Approach of Weighted Gene Expression Analysis and Random Forest Algorithm . Lecture Notes in Electrical Engineering. 1321 LNEE. p. 13-23.

BOOK CHAPTER

Javali, P.S., Kumar, A., Sarkar, S., Sree Varshini, R., Jose Mathew, D., Thirumurugan, K.(2025). Next-gen senotherapeutics: AI/ML-driven strategies for aging and age-related disorders . Advances in Pharmacology. 104. p. 87-119.

JOURNAL ARTICLE

Javali, P.S., Thirumurugan, K.(2025). Structural characterization of Aurora kinase B modulation by Epigallocatechin gallate: Insights from docking and dynamics simulations . Journal of Molecular Graphics and Modelling. 136.

Javali, P.S., Thirumurugan, K.(2024). Embelin targets PI3K/AKT and MAPK in age-related ulcerative colitis: an integrated approach of microarray analysis, network pharmacology, molecular docking, and molecular dynamics . Journal of Biomolecular Structure and Dynamics. 42. (19). p. 10114-10128.

Prashanth S. Javali, Mouliganesh Sekar, Ashish Kumar, Kavitha Thirumurugan (2023). Dynamics of redox signaling in aging via autophagy, inflammation, and senescence . Biogerontology.

Prashanth S. Javali, Kavitha Thirumurugan (2023). Embelin targets PI3K/AKT and MAPK in age-related ulcerative colitis: an integrated approach of microarray analysis, network pharmacology, molecular docking, and molecular dynamics . Journal of Biomolecular Structure and Dynamics.

Javali, P.S., Sekar, M., Kumar, A., Thirumurugan, K.(2023). Dynamics of redox signaling in aging via autophagy, inflammation, and senescence . Biogerontology. 24. (5). p. 663-678.

Murugan, N.A., Javali, P.S., Pandianb, C.J., Ali, M.A., Srivastava, V., Jeyaraman, J.(2022). Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7 . Physical Chemistry Chemical Physics. 24. (34). p. 20371-20380.

N. Arul Murugan, Prashanth S. Javali, Chitra Jeyaraj Pandianb, Muhammad Akhtar Ali, Vaibhav Srivastava, Jeyakanthan Jeyaraman (2022). Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7 . Physical Chemistry Chemical Physics.

Murugan, N.A., Javali, P.S., Pandianb, C.J., Ali, M.A., Srivastava, V., Jeyaraman, J.(2022). Erratum: Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7 (Phys. Chem. Chem. Phys. (2022) 24 (20371–20380) DOI: 10.1039/D2CP00469K) . Physical Chemistry Chemical Physics. 24. (42). p. 26316.

PREPRINT

S Prashanth Javali, J Jeyakanthan, Chun-Jung Chen, Mohanapriya Arumugam (2023). An integrated bioinformatics approach to identify candidate biomarkers and the evaluation of drugs for pheochromocytoma .

OTHER

Murugan, N.A., Javali, P.S., Pandian, C.J., Akhtar Ali, M., Srivastava, V., Jeyaraman, J.(2021). Computational investigation of increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7 . Biorxiv.