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About Me

I am a computational biologist with an M.S. in Bioinformatics from 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.

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Education

Master of Science, Johns Hopkins University

Bioinformatics • Aug 2024 - May 2026

Bachelor of Engineering, Visvesvaraya Technological University

Biotechnology, First Class with Distinction • Jun 2019 - Jul 2023

Works

JOHNS HOPKINS SCHOOL OF MEDICINE

Bioinformatics Engineer • 09/2024 - Present

I lead the computational analysis for an R01-funded PhIP-Seq antibody-profiling project in Dr. Benjamin H. Larman's lab, across early-onset colorectal cancer, late-onset colorectal cancer, polyp, and healthy control cohorts, owning the analysis strategy, QC, statistics, and interpretation. I am developing an interpretable machine learning framework based on stability selection to recover reproducible cancer-associated antibody-reactivity signatures from sparse, high-dimensional PhIP-Seq data. I also design and maintain the computational workflows for InFlux, a U01-funded highly multiplexed NGS-based influenza A neutralization assay, including cohort-level QC, validation logic, and reproducible reporting.

INFINITY BIO, INC.

Summer Bioinformatics Intern • 06/2025 - 08/2025

Based in Baltimore, USA, I benchmarked and optimized NGS-based MIPSA analysis pipelines on AWS EC2 by evaluating aligners and improving I/O handling, reducing runtime from approximately 24 hours to 6 hours and lowering compute cost by approximately 75%. I contributed to EpitopeFindeR 2, a reproducible peptide-sequence pipeline that uses FoldDisco-based structural mapping to identify continuous and discontinuous epitopes and localize antibody binding sites on antigen structures. I also built Latch Bio workflows and a sequence-space visualization module so that client-facing epitope mapping analyses could be run and inspected without engineering support.

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. I also helped show that neuraminidase stalk length and haemagglutinin glycosylation patterns can bias segment pairing and promote reassortment routes linked to the emergence of highly pathogenic clade 2.3.4.4b A(H5N1).

DRP LAB, SIT, TUMKUR, INDIA

Project intern • 11/2021 - 08/2023

Performed molecular dynamics simulations of SAICAR synthase comparing Mg2+-bound and apo states, revealing ion-dependent conformational changes; the project received Best Undergraduate Thesis recognition. I also assisted molecular dynamics and free-energy analyses of CETP mutants, showing structural distortions associated with reduced neutral lipid transfer efficiency.

NITTE UNIVERSITY, MANGALORE, INDIA

Summer research intern • 08/2022 - 11/2022

Performed virtual screening of natural product libraries against LuxS, followed by docking, ADMET, and MD/MM-PBSA validation to nominate hits that could disrupt AI-2 signaling in Helicobacter pylori.

INSILICOMICS Pvt. Ltd., OOTY, INDIA

Research Associate • 05/2020 - 08/2023

Worked on molecular dynamics simulations, virtual screening, genome informatics, and statistical data analysis while building Python scripts, Bash workflows, and GUI tools for research use. I also supported practical bioinformatics training programs and mentored students through hands-on computational biology workflows.

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.

Software

Pipelines and research tools I have built or maintain. Production pipelines developed inside the Larman Lab are described here but are not publicly released.

drydock

Reproducible high-throughput virtual screening on Linux, with a CLI and a GUI. Prepares receptors and ligand libraries and docks them across four engines. Screens run detached and resume after interruption; pinned dependencies and per-run manifests make results reproducible on another machine.

Repository Python

PhIP-Seq analysis pipeline Larman Lab · not public

Production PhIP-Seq pipeline, which I run and maintain. Takes demultiplexed sequencing reads through alignment, QC, enrichment testing, hit calling, and reactivity scoring.

R · Bash · SLURM

PhIPmake2

A memory-bounded R rewrite of the PhIP-Seq pipeline's summarisation step. Collapses peptide-level counts to proteins and joins annotations; a drop-in replacement for the original.

Repository R

InFlux pipeline

Snakemake and SLURM workflow for the InFlux influenza neutralization assay, covering read processing, QC, quantification, titration modeling, and neutralization curves.

Repository Python · Snakemake

ARscape (groupwise)

Extension of the PhIP-Seq pipeline's reactivity scoring, which scores whole organisms or peptide groups rather than single peptides, with support for groupwise comparisons.

Repository R

Influenza Antigenic Cartography

Python and Bash pipeline that builds 2D antigenic maps for H1N1 and H3N2 from neutralization data using multidimensional scaling.

Repository Python

Immune-cell trial dashboard

Models longitudinal immune-cell frequencies from a clinical-trial dataset in a SQLite schema and serves responder comparisons through an interactive dashboard.

Repository Python · SQLite

PhIP-Seq-Pipeline-Installer

Shell scripts that reproduce the PhIP-Seq pipeline's dependency stack on a clean machine.

Repository Shell

GROMACS-COLAB

Jupyter notebooks for running GROMACS molecular dynamics simulations in Colab.

Repository Jupyter Notebook

Smaller tools

  • MSA-Gap-Analyzer — generates and optimizes multiple sequence alignments by gap profile.
  • MODELLER-GUI — Tkinter front end that simplifies MODELLER homology-modeling workflows.
  • pdbqt_maker — converts SDF, PDB, and MOL2 files to PDBQT for docking.
  • RMSD/RMSF graph plotter — GUI for plotting RMSD and RMSF directly from GROMACS .xvg output.
  • PCA-FEL — principal component analysis and free-energy landscape plots from MD trajectories.

Skills

Programming and Platforms

Python R Bash SQL Java Git GitHub Linux Unix HPC SLURM AWS EC2 S3 Conda Mamba Jupyter

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 dplyr tidyr randomForest SVM LASSO PCA UMAP t-SNE Clustering Differential expression Enrichment analysis Pathway analysis Network 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 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

Awards & Service

  • Peer reviewer for Nature Communications, Journal of Crohn's and Colitis, Journal of Biomolecular Structure and Dynamics, and International Journal of Biological Macromolecules.
  • Paper presentation, Immunology 2025 (AAI Annual Meeting).
  • Best Paper Presentation, JAIVIK 2022.
  • Best Undergraduate Thesis for work on SAICAR synthase molecular dynamics.
  • Mentoring students in practical bioinformatics, molecular dynamics, and NGS analysis.

Get in touch

Happy to hear about new projects, roles, or collaborations. Email is the best way to reach me.

avikarkada@gmail.com