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About Me

I am a computational biologist with an M.S. in Bioinformatics at Johns Hopkins University with a passion for working at the intersection of biology, data, and software engineering. I have experience in bioinformatics and omics analytics (NGS and immune profiling), biostatistics/visualization, as well as ML-driven discovery with a strong focus on reproducibility using git, Linux/HPC and cloud environments. I also have a background in drug discovery and structural biology/molecular modeling/molecular dynamics simulations, providing a computational chemistry perspective where appropriate. I have contributed across academic and industry settings, collaborate well with cross-functional teams, and care deeply about rigorous, biologically grounded analysis, from experimental context to interpretation and communication of results. I am also a published researcher and reviewer.

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Education

Master of Science, Johns Hopkins University

Bioinformatics • 2024 - Present

Bachelor of Engineering, Siddaganga Institute of Technology

Biotechnology Engineering • 2019 - 2023

Works

JOHNS HOPKINS SCHOOL OF MEDICINE

Bioinformatics Engineer • 09/2024 - Present

I'm currently working on a project involving profiling humoral immunity against Influenza A using InFlux, a highly multiplexed neutralization assay. My role is to handle the computational aspects of the project, designing and implementing a pipeline for analyzing the generated data. I also lead a PhIP-Seq antibody-profiling project investigating influence of microbial dysbiosis on humoral immunityin early-onset, late-onset colorectal cancer, and polyp/healthy control cohorts.

INFINITY BIO, INC.

Summer Bioinformatics Intern • 06/2025 - 08/2025

Based in Baltimore, USA, I contributed to EpitopeFindeR 2, a reproducible pipeline to align and cluster library peptide sequences to identify continuous and discontinuous epitopes, integrating FoldDisco-based structural mapping to localize antibody binding sites on 3D antigen structures. I developed Latch Bio-based analysis pipelines to improve customer experience, including a UMAP-based sequence-space analyzer and visualization module for EpitopeFindeR 2. I also benchmarked and optimized NGS-based MIPSA analysis pipelines by comparing alignment strategies, improving alignment quality and I/O handling while reducing overall runtime and resource usage.

INDIAN INSTITUTE OF SCIENCE

Junior Research Fellow • 11/2023 - 08/2024

I have worked on various computational biology projects, including the study “Decoding Non-Human Mammalian Adaptive Signatures of 2.3.4.4b H5N1 to Assess its Human Adaptive Potential” , which provided a quantitative assessment of adaptive signatures in non-human mammals to evaluate the zoonotic potential of the 2.3.4.4b H5N1 influenza virus. Another project, “Bat RNA Viruses Employ Viral RHIMs to Orchestrate Species-Specific Cell Death Programs Linked to Z-RNA Sensing and ZBP1-RIPK3 Signaling” , explored how bat RNA viruses utilize viral RHIMs to regulate species-specific cell death pathways via Z-RNA sensing and ZBP1-RIPK3 signaling. Additionally, I contributed to a molecular dynamics study that elucidated how glycosylation patterns and stalk length affect the structural dynamics and functional properties of influenza neuraminidase.

DRP LAB, SIT, TUMKUR, INDIA

Project intern • 11/2021 - 08/2023

Structural insights of SAICAR synthase in the presence of Mg2+ ions through Molecular Dynamics Simulations. Structural insights on the deformations induced by various mutations on cholesteryl ester transfer protein.

SCIOMICS Pvt. Lmt., OOTY, INDIA

Project intern • 05/2020 - 09/2023

Worked as a research associate on molecular dynamics simulations, virtual screening, and genome informatics. Wrote Python programs, bash scripts, and GUI tools for simpler research workflows. My work includes Modeller GUI, GROMACS bash scripts, XVG-to-RMS graph plotters, and average SDF calculators.

PRISTINE ORGANICS, BANGALORE, INDIA

Summer research intern • 05/2021 - 10/2021

Worked in R&D with a focus on dietary management for patients with inborn errors of metabolic disorders.

Skills

Programming and Platforms

Python R Bash SQL Java Git GitHub Linux Unix HPC SLURM AWS EC2 S3 Docker Singularity Conda Mamba Jupyter R Markdown Quarto Shiny VS Code RStudio

Bioinformatics, NGS, and Omics

PhIP-seq RNA-seq scRNA-seq ChIP-seq WGS Biopython Bioconductor SAMtools BCFtools BEDTools Bowtie Bowtie2 BWA Minimap2 Kallisto Salmon STAR HISAT2 Cutadapt Trimmomatic FastQC GATK IGV SRA Toolkit BLAST Clustal Omega MAFFT EMBOSS CD-HIT HMMER edgeR DESeq2 limma Seurat Scanpy MEGA IQ-TREE Comparative genomics Genome informatics Epitope mapping

Computational Biology and Data Science

pandas NumPy SciPy scikit-learn XGBoost matplotlib plotly ggplot2 dplyr tidyr randomForest SVM LASSO PCA UMAP t-SNE Clustering Differential expression Enrichment analysis Pathway analysis Network analysis Statistical data analysis Sequence-space analysis

Workflow and Reproducibility

Snakemake Latch Docker Singularity

Structural Biology, Docking, and Molecular Modeling

PyMOL UCSF ChimeraX Chimera VMD MODELLER AlphaFold ESMFold Rosetta HADDOCK AutoDock AutoDock Vina GROMACS AMBER gmx_MMPBSA FoldX Maestro Schrödinger CP2K Gaussian ORCA RDKit Open Babel Molecular dynamics Protein structure prediction Structural mapping Virtual screening Free energy analysis MM/PBSA ADMET Protein-protein docking Protein-ligand docking Protein-DNA docking Nucleic acid docking Binder design

Visualization and Reporting

ggplot2 plotly GraphPad Prism Excel PowerPoint BioRender LaTeX R Markdown Quarto Shiny Dash Cytoscape UCSC Genome Browser Ensembl Genome Browser

Wet Lab Techniques

Bacterial cell culture Agarose gel electrophoresis PCR SDS-PAGE Western blot Sample handling and QC Basic ELISA handling

Certificates

Certificates

Epigenetic Control of Gene ExpressionUniversity of Melbourne
SARS-CoV-2 Protein Modeling and Drug DockingCoursera Project Network
Algorithms for DNA SequencingJohns Hopkins University
Drug DiscoveryUC San Diego
Python for Genomic Data ScienceJohns Hopkins University
Introduction to Genomic TechnologiesJohns Hopkins University
Introduction to the Biology of CancerJohns Hopkins University
Summer School on Machine Learning in BioinformaticsHSE University
Antibody PurificationSiddaganga Institute of Technology
Artificial Intelligence in Drug DiscoveryCSIR-NEIST
Technical Hands-On Workshop, Molecular DockingBDG Lifesciences

Relevant Courses

Introduction to Bioinformatics Algorithms for Bioinformatics Applied Machine Learning Artificial Intelligence Gene Expression Data Analysis and Visualization Protein Bioinformatics Practical Computer Concepts for Bioinformatics Molecular Basis of Pharmacology Molecular Biology Epigenetics, Gene Organization and Expression Genomic and Personalized Medicine Biostatistics and Biomodelling Biochemistry Microbiology Genetics and Genetic Engineering Immunology and Immunotechnology Biomolecular Simulations Programming with Python Genomics and Proteomics Data Analytics Enzyme Technology Clinical Trials and Data Management Biopharmaceuticals and Regulatory Affairs

Publications

Decoding non-human mammalian adaptive signatures of 2.3.4.4b H5N1 to assess its human adaptive potential

Microbiology Spectrum

DOI: https://doi.org/10.1128/spectrum.00948-25

Bat RNA viruses employ viral RHIMs orchestrating species-specific cell death programs linked to Z-RNA sensing and ZBP1-RIPK3 signaling

Cell iScience

DOI: https://doi.org/10.1016/j.isci.2024.111444

Computational-driven discovery of AI-2 quorum sensing inhibitor targeting the 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) to combat drug-resistant Helicobacter pylori

Computers in Biology and Medicine

PMID: 39536388 | DOI: https://doi.org/10.1016/j.compbiomed.2024.109409

Anti-enzymatic and DNA docking studies of montelukast: A multifaceted molecular scaffold with in vitro investigations, molecular expression analysis and molecular dynamics simulations

Cell Heliyon

PMID: 38298631 | DOI: https://doi.org/10.1016/j.heliyon.2024.e24470

Antiurease Activity of Antibiotics: In Vitro, In Silico, Structure Activity Relationship, and MD Simulations of Cephalosporins and Fluoroquinolones

ACS Omega

PMID: 38559955 | DOI: https://doi.org/10.1021/acsomega.3c09355

Nrf2-regulated antioxidant response ameliorating ionizing radiation-induced damages explored through in vitro and molecular dynamics simulations

Journal of Biomolecular Structure and Dynamics

PMID: 36307909 | DOI: https://doi.org/10.1080/07391102.2022.2137245

System-level protein interaction network analysis and molecular dynamics study reveal interaction of ferulic acid with PTGS2 as a natural radioprotector

Journal of Biomolecular Structure and Dynamics

PMID: 37144749 | DOI: https://doi.org/10.1080/07391102.2023.2208224

High-throughput screening and molecular dynamics simulations of natural products targeting LuxS/AI-2 system as a novel antibacterial strategy for antibiotic resistance in Helicobacter pylori

Journal of Biomolecular Structure and Dynamics

PMID: 37160706 | DOI: https://doi.org/10.1080/07391102.2023.2210674

A combined in vitro and molecular dynamics simulation studies unveil the molecular basis of the anticancer potential of piperine targeting AKT1 against prostate cancer

Journal of Biomolecular Structure and Dynamics

PMID: 37272194 | DOI: https://doi.org/10.1080/07391102.2023.2220045

Exploration of 4-tolyl-5-(p-tolyloxymethyl)-4H-1,2,4-triazole thioethers as potent 15-LOX inhibitors supported by in vitro, in silico, MD simulation and DNA binding studies

Journal of Molecular Structure

DOI: https://doi.org/10.1016/j.molstruc.2024.139963

Glutamic acid-catalyzed synthesis of dihydroquinazolinone: anticancer activity, electrochemical behavior, molecular docking, dynamics, simulations and drug-likeness studies

Research on Chemical Intermediates

DOI: https://doi.org/10.1007/s11164-024-05305-6

Multimodal evaluation of lipoxygenase-targeting NSAIDs using integrated in vitro, SAR, in silico, cytotoxicity towards MCF-7 cell line, DNA docking and MD simulation approaches

International Journal of Biological Macromolecules

PMID: 40316117 | DOI: https://doi.org/10.1016/j.ijbiomac.2025.143665