Bioinformatics Engineer · Johns Hopkins School of Medicine

Avinash Karkada Ashok

Computational biology, NGS analysis, and reproducible pipelines.

See the work Download CV

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  • HA1
  • HA2
Fig. 1 Full-length H3 hemagglutinin trimer, modelled by homology modelling, threading with AlphaFold and optimization with simulated annealing. Drawn as a C-alpha trace. Model file.
01

About

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.

02

Selected work

Immune profiling at scale

Johns Hopkins School of Medicine · Larman Lab · 2024–present

The PhIP-Seq platform

Develop and maintain the production PhIP-Seq pipeline and codespace on the JHU Rockfish HPC system, including phipmake2, an R library for post-alignment summarisation across multi-library screens.

When a run finishes, the reads and the metadata that says which library they belong to go through alignment, library splitting, beads-only background modelling, hit calling, annotation, and taxon-level aggregation. Which partition each step runs on is a judgment call rather than a fixed recipe.

  • R
  • Bash
  • SLURM
  • HPC

From sequencing run to shared results

Fig. 2 The platform end to end. Select a stage to read what it does.

Johns Hopkins School of Medicine · Larman Lab · 2024–present

PhIP-Seq antibody profiling across colorectal cancer cohorts

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.

Differential reactivity is analysed at peptide, protein, pathway, and genus and species levels.

Developed CALIPER, a groupwise differential method for PhIP-Seq, and benchmarked it against existing tools using Boston Birth Cohort MMR vaccine data as ground truth. Contributed to developing and evaluating genus- and species-level aggregate reactivity scoring methods.

  • PhIP-Seq
  • R
  • Bash
  • SLURM

Differential reactivity at two levels

  • passes 5% FDR
  • does not
  • planted signal

Fig. 3 Why a cohort is analysed at more than one level. In this simulated cohort, cases are more often exposed to three species, which lifts reactivity a little across each of their peptides. Tested peptide by peptide, most of that signal fails false-discovery control. Counted per species, it is clear.

Infinity Bio, Inc. · 2025

EpitopeFindeR 2 and structural epitope mapping

Contributed to EpitopeFindeR 2, a pipeline integrating iterative sequence alignment and FoldDisco-based structural mapping to identify continuous and discontinuous epitopes from MIPSA (Molecular Indexing of Proteins by Self-Assembly) protein libraries.

Built Latch-based analysis workflows and a sequence-space visualization dashboard for exploring peptide and epitope embeddings.

  • Python
  • FoldDisco
  • AlphaFold
  • Latch

Why epitopes have to be mapped on the structure

Fig. 4 The same H3 model as Fig. 1, one protomer highlighted. A continuous epitope is one run of sequence; a discontinuous one is built from segments that meet only once the chain folds, which is why mapping is done against the structure. Distances measured from the model.

Functional antibody profiling

Johns Hopkins School of Medicine · Larman Lab · 2024–present

HAScan

A PhIP-Seq library of overlapping peptide tiles covering hemagglutinin across essentially all known influenza A and B strains. It asks where on HA a person’s antibodies bind, and which strains they recognise.

Every HA is aligned to a shared coordinate system before tiling, so the same position is comparable from one strain to the next and reactivity can be read as strain-specific or conserved. It pairs with InFlux: one assay says where antibodies bind, the other whether they block infection.

  • PhIP-Seq
  • Influenza
  • Serology

Which strains a serum reacts to

Fig. 5 What the assay reads out, for one simulated serum sample: binding at each position along HA, for every strain in the panel. Stem positions are conserved and react across the whole panel. Head positions are strain-specific and react only on strains close to what that donor has met. Switch donors and the head pattern moves while the stem band stays.

Johns Hopkins School of Medicine · Larman Lab · 2024–present

InFlux neutralization pipeline

Contributed to the development of InFlux, a novel multiplexed NGS-based influenza neutralization assay, and built its analysis workflow.

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

  • Python
  • Snakemake
  • SLURM
Repository

Workflow rule graph

Select a rule

Each box is a Snakemake rule. Arrows show which rule feeds which.


                

              

              
Fig. 6 Rule graph of the public InFlux workflow, reduced to direct dependencies. The replay animates rule order; it is not a live job.

            


            

              
Four-parameter logistic fit

              

                
                

                  
                  
                  
                

              

              

              

                

              

              
Fig. 7 A four-parameter logistic curve fitted to simulated neutralization data. Drag any point and the curve refits; the marker follows the IC50, the dilution at which half the virus is neutralized, with an approximate 95% interval.

            

          

        


        
        

          

            
Johns Hopkins School of Medicine · Larman Lab

            
Influenza antigenic cartography

            
Built the multidimensional-scaling antigenic cartography placing PhIP-Seq reactivity and measured neutralization titres in a shared two-dimensional space over influenza sequence diversity.

            

              
  • Python
  • Bash
  • MDS

              Repository
            

          

          

            
Sequence-based antigenic map

            

              
            

            

            

              
    
                
  • season 156
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  • panel strain
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Fig. 8 A sequence-based antigenic map of a simulated lineage. Each point is one antigenic-site sequence; pairwise BLOSUM62 distances are laid out in two dimensions by multidimensional scaling, so drift shows up as a path across the map. Triangles mark a panel of strains spread through time. Scramble the map, or drag a strain, and watch it relax. The pipeline uses classical MDS; this figure uses an iterative variant so the relaxation is visible.

          

        


        
        
Molecular and structural interpretation


        

          

            
Public repository · 2026

            
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.

            

              
  • Python
  • Docking
  • CLI + GUI

              Repository
            

          

          

            
Quickstart, from the README

              
            

            
# 0. Prepare the receptor (PDB or mmCIF), and check what came out
drydock prep-receptor -i 2OVX.cif -o receptor
drydock check-receptor receptor.pdbqt

# 1. Look at the library before committing to it
drydock survey library.sdf

# 2. Prepare it (streams; never loads the whole file into memory)
drydock prep-ligands --input library.sdf --out ligands/ --ph 7.4

# 3. Define the search box from the residues lining your site
drydock box --receptor receptor.pdbqt --residues 187,188,401,405,411,420,421,423

# 4. Screen
drydock screen --receptor receptor.pdbqt --ligands ligands/ --run runs/mmp9 \
               --residues 187,188,401,405,411,420,421,423

# progress, from anywhere, while it runs
drydock status runs/mmp9

          

        


        
        

          

            
Kesavardhana Lab, IISc · DRP Lab, SIT · 2021–2024

            
Molecular dynamics and free-energy landscapes

            
In the Kesavardhana Lab at the Indian Institute of Science, modelled hemagglutinin and neuraminidase variants embedded in a lipid bilayer and ran the simulations on them, looking at how hemagglutinin glycosylation patterns and neuraminidase stalk length affect sialic acid binding.

            
Earlier, in the DRP Lab at SIT, 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.

            

              
  • GROMACS
  • Membrane systems
  • PCA
  • Free energy

              PCA-FEL
              GROMACS-COLAB
            

          

          

            
Free-energy landscape from sampling

            

              
              
              

                
                
                
              

            

            

            

              
              

            

            
Fig. 9 A free-energy landscape building up as walkers sample a two-dimensional potential, F = −kT ln P. In a real analysis the axes are the first two principal components of an MD trajectory.

          

        

      

    


    
    

      

        
03
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.


        

          

            
            
            
            
            
          

          

        


        
    
          
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    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.
    
            
    PythonRepository
    
          
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    PhIP-Seq analysis pipeline
    
            
    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 · SLURMLarman Lab · not public
    
          
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    CALIPER
    
            
    A groupwise differential method for PhIP-Seq, benchmarked against existing tools using Boston Birth Cohort MMR vaccine data as ground truth.
    
            
    RLarman Lab · not public
    
          
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    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.
    
            
    RPrivate repository
    
          
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    InFlux pipeline
    
            
    Snakemake and SLURM workflow for the InFlux influenza neutralization assay, covering read processing, QC, quantification, titration modeling, and neutralization curves.
    
            
    Python · SnakemakeRepository
    
          
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    Influenza Antigenic Cartography
    
            
    Antigenic cartography mapping for H1N1 and H3N2 by multidimensional scaling over hemagglutinin sequence diversity.
    
            
    PythonRepository
    
          
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    PhIP-Seq-Pipeline-Installer
    
            
    Shell scripts that reproduce the PhIP-Seq pipeline's dependency stack on a clean machine.
    
            
    ShellRepository
    
          
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    GROMACS-COLAB
    
            
    Jupyter notebooks for running GROMACS molecular dynamics simulations in Colab.
    
            
    Jupyter NotebookRepository
    
          
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Smaller tools

        
    
          
  • Immune-cell trial dashboardmodels longitudinal immune-cell frequencies from a clinical-trial dataset and serves responder comparisons through an interactive dashboard.
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  • MSA-Gap-Analyzergenerates and optimizes multiple sequence alignments by gap profile.
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  • MODELLER-GUITkinter front end that simplifies MODELLER homology-modeling workflows.
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  • pdbqt_makerconverts SDF, PDB, and MOL2 files to PDBQT for docking.
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  • RMSD/RMSF graph plotterGUI for plotting RMSD and RMSF directly from GROMACS .xvg output.
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  • PCA-FELprincipal component analysis and free-energy landscape plots from MD trajectories.
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04
Experience


        

          

          

            
              Johns Hopkins School of MedicineBioinformatics Engineer
              
              
            
            

              
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 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
              
              
            
            

              
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 ScienceJunior Research Fellow
              
              
            
            

              
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 hemagglutinin 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, IndiaProject intern
              
              
            
            

              
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, IndiaSummer research intern
              
              
            
            

              
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, IndiaResearch Associate
              
              
            
            

              
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, IndiaSummer research intern
              
              
            
            

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

            

          

        

      

    


    
    

      

        
05
Publications


        

          
          

            
            
            
            
            
            
          

          

        


        
    
          
  1. 
            2026
            
    
              
    Virologic determinants promoting the emergence of highly pathogenic clade 2.3.4.4b A(H5N1) viruses
    
              
    Ranjana Nataraj, Ahmed Kandeil, Avinash Karkada Ashok, Konstantin Andreev, Anantika Chandra, Richard J Webby, Sannula Kesavardhana
    
              
    The EMBO Journal · In press
    
            
    
          
    2. 
          
  2. 
            2026
            
          
    3. 
          
  3. 
            2025
            
    
              
    Decoding non-human mammalian adaptive signatures of 2.3.4.4b H5N1 to assess its human adaptive potential
    
              
    Ranjana Nataraj, Avinash Karkada Ashok, Ayushi Amin Dey, Sannula Kesavardhana
    
              
    Microbiology Spectrum
    
            
    
          
    4. 
          
  4. 
            2025
            
    
              
    Computational-driven discovery of AI-2 quorum sensing inhibitor targeting the 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) to combat drug-resistant Helicobacter pylori
    
              
    Manish Kumar, Avinash Karkada Ashok, Thejaswi Bhat, Krishnakumar Ballamoole, Pavan Gollapalli
    
              
    Computers in Biology and Medicine
    
            
    
          
    5. 
          
  5. 
            2025
            
    
              
    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
    
              
    Ambar Iqbal, Wasim Abbas, Samina Ejaz, Naheed Riaz, Avinash Karkada Ashok, Muhammad Munawar Hayat, Muhammad Ashraf
    
              
    International Journal of Biological Macromolecules
    
            
    
          
    6. 
          
  6. 
            2025
            
    
              
    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
    
              
    Ambar Iqbal, Muhammad Ashraf, Avinash Karkada Ashok, Farah Chafika Kaouche, Bushra Bashir, Abdul Qadir, Naheed Riaz
    
              
    Journal of Molecular Structure
    
            
    
          
    7. 
          
  7. 
            2025
            
    
              
    Exploring Antiurease Activity of Antibiotics: Insights From In Vitro, SAR, In Silico, DNA Docking, and MD Simulation Studies
    
              
    Sara Mujtaba, Misbah Aslam, Ambar Iqbal, Naheed Riaz, Avinash Karkada Ashok, Muhammad Munawar Hayat, Muhammad Ashraf
    
              
    ChemistrySelect
    
            
    
          
    8. 
          
  8. 
            2024
            
    
              
    Bat RNA viruses employ viral RHIMs orchestrating species-specific cell death programs linked to Z-RNA sensing and ZBP1-RIPK3 signaling
    
              
    Sanchita Mishra, Disha Jain, Ayushi Amin Dey, Sahana Nagaraja, Mansi Srivastava, Oyahida Khatun, Keerthana Balamurugan, Micky Anand, Avinash Karkada Ashok, Shashank Tripathi, Mahipal Ganji, Sannula Kesavardhana
    
              
    iScience
    
            
    
          
    9. 
          
  9. 
            2024
            
    
              
    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
    
              
    Avinash Karkada Ashok, Tamizh Selvan Gnanasekaran, Hulikal Shivashankara Santosh Kumar, Koigoora Srikanth, Nayana Prakash, Pavan Gollapalli
    
              
    Journal of Biomolecular Structure and Dynamics
    
            
    
          
    10. 
          
  10. 
            2024
            
    
              
    A combined in vitro and molecular dynamics simulation studies unveil the molecular basis of the anticancer potential of piperine targeting AKT1 against prostate cancer
    
              
    Prakash Nayana, Hanumanthappa Manjunatha, Pavan Gollapalli, Avinash Karkada Ashok, Preema Karal Andrade, Vijayalaksmi V
    
              
    Journal of Biomolecular Structure and Dynamics
    
            
    
          
    11. 
          
  11. 
            2024
            
    
              
    System-level protein interaction network analysis and molecular dynamics study reveal interaction of ferulic acid with PTGS2 as a natural radioprotector
    
              
    Pavan Gollapalli, Avinash Karkada Ashok, Tamizh Selvan G
    
              
    Journal of Biomolecular Structure and Dynamics
    
            
    
          
    12. 
          
  12. 
            2024
            
    
              
    Antiurease Activity of Antibiotics: In Vitro, In Silico, Structure Activity Relationship, and MD Simulations of Cephalosporins and Fluoroquinolones
    
              
    Misbah Aslam, Jameel Rahman, Ambar Iqbal, Sara Mujtaba, Avinash Karkada Ashok, Farah Chafika Kaouche, Muhammad Munawar Hayat, Mouqadus-Un Nisa, Muhammad Ashraf
    
              
    ACS Omega
    
            
    
          
    13. 
          
  13. 
            2024
            
    
              
    Anti-enzymatic and DNA docking studies of montelukast: A multifaceted molecular scaffold with in vitro investigations, molecular expression analysis and molecular dynamics simulations
    
              
    Shawana Abdullah, Ambar Iqbal, Avinash Karkada Ashok, Farah Chafika Kaouche, Misbah Aslam, Safdar Hussain, Jameel Rahman, Muhammad Munawar Hayat, Muhammad Ashraf
    
              
    Heliyon
    
            
    
          
    14. 
          
  14. 
            2024
            
    
              
    Glutamic acid-catalyzed synthesis of dihydroquinazolinone: anticancer activity, electrochemical behavior, molecular docking, dynamics, simulations and drug-likeness studies
    
              
    Radhika Mane, Deepak A. Yaraguppi, Avinash Karkada Ashok, Bhavya Gangadharappa, K. B. Chandrakala, Kantharaju Kamanna
    
              
    Research on Chemical Intermediates
    
            
    
          
    15. 
          
  15. 
            2023
            
    
              
    Nrf2-regulated antioxidant response ameliorating ionizing radiation-induced damages explored through in vitro and molecular dynamics simulations
    
              
    Tamizh Selvan G, Avinash Karkada Ashok, Aditya Rao S. J, Pavan Gollapalli, Vishakh R, Suchetha Kumari N, Nabo K. Chaudhury
    
              
    Journal of Biomolecular Structure and Dynamics
    
            
    
          
    16. 
        

        
      

    


    
    

      

        
06
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

          

        

        
      

    


    
    

      

        
07
Education & recognition

        

          

            
Education

            
    
              
  • Master of Science, Johns Hopkins UniversityBioinformatics
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  • Bachelor of Engineering, Visvesvaraya Technological UniversityBiotechnology, First Class with Distinction
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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.
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  • Paper presentation, Immunology 2025 (AAI Annual Meeting).
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  • Best Paper Presentation, JAIVIK 2022.
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  • Best Undergraduate Thesis for work on SAICAR synthase molecular dynamics.
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  • Mentoring students in practical bioinformatics, molecular dynamics, and NGS analysis.
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          Certificates11
          
    
            
  • Epigenetic Control of Gene ExpressionUniversity of Melbourne
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  • SARS-CoV-2 Protein Modeling and Drug DockingCoursera Project Network
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  • Algorithms for DNA SequencingJohns Hopkins University
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  • Drug DiscoveryUC San Diego
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  • Python for Genomic Data ScienceJohns Hopkins University
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  • Introduction to Genomic TechnologiesJohns Hopkins University
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  • Introduction to the Biology of CancerJohns Hopkins University
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  • Summer School on Machine Learning in BioinformaticsHSE University
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  • Antibody PurificationSiddaganga Institute of Technology
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  • Artificial Intelligence in Drug DiscoveryCSIR-NEIST
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  • Technical Hands-On Workshop, Molecular DockingBDG Lifesciences
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          Relevant Courses22
          
  • 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

        

      

    


    
    

      

        
08
Get in touch

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

        

          avikarkada@gmail.com
          
        

        
      

    

  


  

  
  
    

      
      
      
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