Vishal Kumar Sahu
Research Fellow & Computational Biologist
Vishal Kumar Sahu
Technical Lead Engineer · NextEra-AI · EIQDigital
About
Computational biologist with a decade of experience bridging cancer research and software engineering. Work spans computational drug discovery, miRNA structural biology and bioinformatics pipeline development. Author of 5+ open-source scientific tools, with platforms serving 17,000+ users.
Tools
Highlights
SieveAI
ResearchAutomated drug discovery pipeline — months to hours
ExoLoger
AI/MLML-based exosomal miRNA prediction tool
miRvim
Bioinformatics3D miRNA structure database (2,693+ entries)
GMXvg
ScientificGROMACS analysis and visualization tool
UtilityLib
PythonPyPI Python library — 200+ reusable functions
TheBiomics
PlatformBioinformatics platform — 17K+ users, 10 years
Professional Experience
Industry and research roles
Technical Lead Engineer
NextEra-AI · EIQDigital
Pune, India
- Lead AWS cloud infrastructure for bioinformatics and data pipelines — EC2, S3, Cognito, CodeCommit, CI/CD.
- Design and maintain automated deployment pipelines, environment orchestration, and production debugging.
- Manage relational and NoSQL databases (MySQL, MongoDB) supporting research and application workloads.
- Build RPA and scraping pipelines (Playwright) for large-scale scientific data extraction and processing.
- Apply cloud-native tooling to accelerate research workflows, from data ingestion to model deployment.
Senior Research Fellow (CSIR-SRF)
Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Pune
Pune, India
- Led computational drug discovery — molecular docking (AutoDock Vina, 1,950+ complexes) and MD simulations (GROMACS, up to 300 ns).
- Developed SieveAI, an automated drug discovery pipeline reducing months of manual screening to hours.
- Built ExoLoger (exosomal miRNA prediction) and GMXvg (GROMACS visualization) — published open-source tools.
- Performed protein structure prediction (AlphaFold2, SwissModel, I-TASSER, Rosetta) and MMPBSA binding free-energy analysis.
- Mentored students and internship trainees in pipeline development, automation, and data processing.
Junior Research Fellow (CSIR-JRF)
Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Pune
Pune, India
- Conducted in silico and in vitro cancer research — protein–ligand docking, MD simulation, and cell-based assays.
- Performed genomics and transcriptomics analysis (GEO, TCGA) and differential gene expression studies.
- Validated computational predictions with wet-lab assays (MTT, colony formation, Western blot, qPCR).
- Contributed to peer-reviewed publications on drug synergy, PPAR modulation, and miRNA structural biology.
Programming & Database — Freelance
Self-employed
India
- Built full-stack applications (React, PHP, Python) and managed relational databases (MySQL, SQLite).
- Developed management systems for schools and coaching institutes — attendance, admissions, fees, certificates.
§Research Interests
Core areas of research focus and methodological expertise
Computational Drug Discovery
Structure-based drug design using molecular docking (AutoDock Vina), MD simulations (GROMACS), and in vitro validation — identifying therapeutic candidates for cancer targets.
miRNA & ncRNA Structural Biology
Three-dimensional miRNA structure analysis, database development (miRVim), and functional characterization of non-coding RNAs in cancer regulation.
Protein–Ligand Interactions & MD Simulations
Molecular dynamics simulations of protein–ligand and protein–membrane systems, binding free energy calculations, and transmembrane protein characterization.
Bioinformatics Pipeline Development
Development of automated computational pipelines (SieveAI, ExoLoger) for drug screening, miRNA prediction, and genomics data mining from public databases.
Cancer Biology & Pharmacology
In vitro and in silico studies on cancer targets — cell-based assays (MTT, colony formation, apoptosis), drug synergy analysis, and PPAR receptor modulation.
Research Output
Academic publications, reviews, and scholarly contributions
Articles
6Synergistic combination of ritonavir and cisplatin as an efficacious therapy in human cervical cancer cells: a computational drug discovery and in vitro insight
Dayanand Swami, Priyanka Mudaliar, Yash Shrinivas Bichu, Vishal Kumar Sahu, Shine Devarajan, Soumya Basu, Jyotirmoi Aich · Journal of Biomolecular Structure and Dynamics
Investigated synergistic drug combination of ritonavir and cisplatin for cervical cancer through computational docking and in vitro validation, demonstrating enhanced therapeutic efficacy.
Identification of novel PPAR-β/δ agonists from Kaempferol, Quercetin, and Resveratrol derivatives by targeting cancer: An integrative molecular docking and dynamics simulation approach
Sangeeta Ballav, Kiran Bharat Lokhande, Vishal Kumar Sahu, Rohit Singh Yadav, K. Venkateswara Swamy, Soumya Basu · Letters in Drug Design & Discovery
Identified novel PPAR-β/δ agonists from natural flavonoid derivatives using molecular docking and MD simulations, proposing therapeutic candidates for cancer targeting.
miRVim: Three-dimensional miRNA Structure Database
Vishal Kumar Sahu, Ankita Subhadarsani Parida, Amit Ranjan, Harishkumar Madhyastha, Soumya Basu · MicroRNA
Developed miRVim, a comprehensive database of three-dimensional miRNA structures sourced from miRBase, PDB, and homology modeling, enabling structural analysis of miRNA–target interactions.
Role of the transmembrane polar residues on CD151 in cholesterol binding
Vishal Kumar Sahu, Kiran Bharat Lokhande, Venkateswar K. Swamy, Soumya Basu, Amit Ranjan · Journal of Biomolecular Structure and Dynamics
Elucidated the role of transmembrane polar residues of CD151 in cholesterol binding through computational modeling and molecular dynamics, contributing to understanding of tetraspanin–lipid interactions.
Unveiling theranostic potential: Insights into cell-free microRNA-protein interactions
Vishal Kumar Sahu, Subhayan Sur, Sanjana Agarwal, Harishkumar Madhyastha, Amit Ranjan, Soumya Basu · Biophysical Chemistry
Examined the theranostic potential of cell-free microRNA-protein interactions, characterising circulating miRNA-protein complexes relevant to cancer detection.
Pratenol B, Eriodictyol, Losbanine, and Isookanin, as potential EGFR and HRAS inhibitors in oral squamous cell carcinoma
Shubha Behara, Uday Yadav, Vishal Kumar Sahu, Shuchi Nagar, Soumya Basu, Samir Gupta, B. M. Rudagi, Supriya Kheur, Dimple Davray, Subhayan Sur · Scientific Reports
Identified Pratenol B, Eriodictyol, Losbanine, and Isookanin as potential EGFR and HRAS inhibitors in oral squamous cell carcinoma through integrated computational and experimental analysis.
Reviews
2PPAR-γ Partial Agonists in Disease-Fate Decision with Special Reference to Cancer
Sangeeta Ballav, Bini Biswas, Vishal Kumar Sahu, Amit Ranjan, Soumya Basu · Cells
Comprehensive review of PPAR-γ partial agonists and their dual role in disease-fate decisions, with special focus on cancer therapeutics and the mechanisms distinguishing partial from full agonists.
Dietary flavonoids as modulators of non-coding RNAs in hormone-associated cancer
Saurabh Dey, Bini Biswas, Sangeeta Ballav, Vishal Kumar Sahu, Amit Ranjan, Soumya Basu · Food Chemistry Advances
Reviewed the role of dietary flavonoids as modulators of non-coding RNAs in hormone-associated cancers, bridging nutritional biochemistry and epigenetic regulation.
Book Chapters
5AI Techniques and IoT Applications Transforming the Future of Healthcare
Book chapter exploring the intersection of artificial intelligence and IoT in healthcare transformation.
Image processing: an early detection tool for Alzheimer's disease
Book chapter on image processing techniques for early detection of Alzheimer's disease.
Microfluidics-enabled aptamer-based sensing devices — the aptafluidics microdevices
Book chapter on microfluidics-enabled aptamer-based sensing devices and aptafluidics technology.
In Vivo Testing of Biomaterials in Animal Models
Book chapter on in vivo biomaterial testing methodology in animal models.
Computational tools for mining microbial genomes and metabolites
Book chapter surveying computational tools and pipelines for mining microbial genomes and metabolites.
Software & Tools
5ExoLoger
Prediction of unidentified exosomal microRNAs using machine learning — trained on exosome proteomics data to predict novel miRNA candidates
SieveAI
An automated drug discovery pipeline integrating AutoDock Vina, SwissADME, and custom scoring functions — reducing months of manual screening to hours
GMXvg
GROMACS visualization tool for automated analysis of molecular dynamics trajectories — RMSD, RMSF, Rg, and energy plots from .xvg files
UtilityLib
Unified Python utility library with 200+ reusable functions for file I/O, string manipulation, data structures, and system operations — published on PyPI
Education
MSc Biotechnology
T M Bhagalpur University, Bhagalpur
BSc Biotechnology
CSJM University, Kanpur
Intermediate (Class XII)
JNV, Kanpur Nagar
National Level Exams
Public Profiles
Connect with me on various academic and professional platforms