Ayushman Mallick

Ayushman Mallick

Senior Research Fellow — Plant Molecular Physiology Lab
ICAR–Indian Agricultural Research Institute, New Delhi

Molecular Dynamics GROMACS Genome Editing Root Nodule Symbiosis Python · HPC · SLURM Structural Bioinformatics

Decoding Plants at the
Molecular Scale

I am a plant biologist specialising in molecular genetics, molecular dynamics, abiotic stress signalling, and plant–microbe interactions. Currently working as a Senior Research Fellow at the Plant Molecular Physiology Lab, ICAR–IARI, on an ICAR-funded project — “Enhancing Climate Resilience and Ensuring Food Security with Genome Editing Tools” — under the guidance of Dr. Shivani Nagar.

My work sits at the intersection of experimental biology and computation: I run all-atom molecular dynamics simulations of rice signalling proteins under ABA-mediated abiotic stress using GROMACS on HPC clusters (Linux/SLURM), while driving wet-lab goals through Python-based sequencing pipelines, CRISPR editing, metagenomics, and protein–protein interaction assays. The broader aim is to decode the molecular architecture of stress-resilient traits and translate those insights into climate-smart rice for sustainable agriculture in India.

I completed my BS–MS Dual Degree in Biology at IISER Tirupati. My master’s thesis — supervised by Dr. Swarup Roy Choudhury — characterised the transcription factor CYCLOPS in Arachis hypogaea (groundnut) and mapped its downstream interactors in root nodule symbiosis signalling, combining site-directed mutagenesis, RNAi mutant generation in groundnut, molecular docking, and structural modelling.

✓ GATE 2025 Qualified · Life Sciences (XL) ✓ CSIR–NET Qualified · Dec 2025 · Category 3

// Wet Lab

Molecular Cloning & Gene Expression
BiFC & Y1H Interaction Assays
Hairy Root Transformation
Tobacco Infiltration & Microscopy
CRISPR–Cas Editing Strategies
Biochemical & Bacterial Assays

// Computational

GROMACS · Molecular Dynamics
Python · Biopython · R
Linux · HPC · SLURM
RNA-seq Pipelines & WGA
PyMOL · Chimera · Discovery Studio
Molecular Docking & PPI Analysis

Areas of Investigation

Current Work GROMACS PYL6–ABA–PP2C51 Rice HPC · SLURM

Molecular Dynamics of the PYL6–ABA–PP2C51 Complex in Oryza sativa

All-atom molecular dynamics simulations of the rice ABA receptor complex PYL6–PP2C51 under abscisic acid (ABA)-mediated abiotic stress, performed using GROMACS on HPC clusters (Linux/SLURM). This work probes the conformational dynamics and binding interfaces of a key stress-signalling gate in rice — providing structural insights to drive climate-adaptive crop improvement and inform genome-editing targets for drought and heat tolerance in India’s staple cereal.

ICAR–IARI · Plant Molecular Physiology Lab · 2024–present

CRISPR-MD genome editing — molecular dynamics guided target

Genome Editing · MD Target

PPI Assay

Sequencing Pipeline

Current Work CRISPR Rice Food Security

Genome Editing for Climate Resilience in Rice

Computational and molecular biology contributions to an ICAR-funded project engineering climate-resilient rice using CRISPR-based genome editing, under Dr. Shivani Nagar. Integrates Python sequencing pipelines, metagenomics, protein–protein interaction assays, and MD-derived structural insights to identify and validate editing targets for sustainable food security in India.

ICAR–IARI · Dr. Shivani Nagar · 2026–present

Confocal microscopy (FM 4-64) — fragmented vacuole in groundnut root cross-section under high calcium stress

Confocal · FM 4-64

Confocal · Brightfield

Compound Microscope

Electron Microscopy

Root Nodule Symbiosis Groundnut CYCLOPS MS Dissertation

CYCLOPS & Root Nodule Symbiosis in Arachis hypogaea

MS dissertation at IISER Tirupati — characterised the transcription factor CYCLOPS and its downstream interactors in root nodule symbiosis (RNS) signalling in groundnut. Combined site-directed mutagenesis, RNAi mutant generation, hairy root transformation, confocal and electron microscopy, molecular docking, and in-silico structural analyses to map the CCaMK–CYCLOPS signalling axis.

IISER Tirupati · Dr. Swarup Roy Choudhury · 2023–2025

Motif Scanner

Co-expression Network

Sequence Logo & Clustering

Current Work Coming Soon Bioinformatics Python PyQt5

Cis-GS: Cis-regulatory Element Genome Scanner

A standalone desktop application for genome-wide identification and functional characterisation of cis-regulatory elements (CREs) and transcription factor binding sites (TFBS). Runs an eight-step bioinformatics pipeline: live NCBI genome & annotation fetching, promoter extraction, IUPAC motif scanning against PlantTFDB, AnimalTFDB, JASPAR 2024 and HOCOMOCO v11, publication-ready sequence logo generation, RNA-seq expression integration, co-expression network analysis (Pearson / Spearman / WGCNA-style, Louvain & hierarchical clustering), K-means temporal clustering, and KEGG pathway enrichment (hypergeometric ORA + Benjamini–Hochberg FDR across 11,700+ organisms via live REST queries). Full CLI included for server and pipeline use.

🥈 2nd Best Poster Award — APEI 2026 · 🔒 Public release coming soon on GitHub.

Plant Signaling Lab · IISER Tirupati · 2024–present

Pipeline Overview

Live Web App

Live & Published Python Package Structural Biology Boltz-2 Open Source

A preprocessing-file generator for ternary Protein 1 + Ligand + Protein 2 binding prediction with Boltz-2. Accepts two CIF files (holo Protein 1–Ligand complex + Protein 1–Protein 2 reference), auto-detects chains and ligand identity, computes CA-to-ligand pocket contacts, and emits a ready-to-run Boltz-2 v1 YAML — with affinity prediction and pocket constraints — in seconds. Runs entirely in the browser (no uploads, no server) or via a zero-dependency CLI.

ICAR–IARI · May 2026 · DOI: 10.5281/zenodo.20399843

Web App GitHub PyPI Zenodo DOI

v2 Architecture

Boltz-2 Pipeline

Live & Published Web Engine N-body Cofolding Boltz-2 API Open Source

v2.0

A major evolution of BoltzYML into a zero-install, browser-based engine that builds, cleans, and submits hosted Boltz-2 API predictions — binary, ternary, or arbitrary N-body molecular complexes — directly from the browser. Repairs template CIF/PDB metadata that breaks parsers (drops phantom chains, strips waters/HETATM, fixes modified residues), constructs the API payload, and submits with your own API key via an open-source stateless proxy — the key never leaves your browser tab. Streams back full server output: structures, confidence (ipTM/pTM/pLDDT), PAE/PDE matrices, and binding affinity.

ICAR–IARI · Jun 2026 · DOI: 10.5281/zenodo.20440141

Web App GitHub Zenodo DOI

ampliscan — sort sequencing reads into per-sample bins

Overview

Workflow

Live & Published Python Package Amplicon Sequencing Demultiplexing Open Source

ampliscan v1.1.0

An open-source tool for demultiplexing amplicon sequencing reads by custom primer barcodes. Sequencing facilities handle standard i5/i7 indexing, but many amplicon workflows add a second inner layer of short barcodes built into custom PCR primers — separating pooled samples by these is left to the researcher. ampliscan locates a constant anchor sequence next to each barcode and matches them together; this combined anchor+barcode matching (Hamming / Levenshtein) is far more error-tolerant than matching the barcode alone, so fewer reads are lost or misassigned to sequencing noise. Ships with a full desktop GUI — no terminal, no coding — plus a CLI/Python API, per-sample FASTQ/FASTA bins, and a QC heatmap.

ICAR–IARI · 2026 · DOI: 10.5281/zenodo.21505581

GitHub PyPI Zenodo DOI

Scientific Contributions

All publications, preprints, and datasets are archived on ORCID and kept up to date.
ORCID iD: 0009-0004-5774-450X

View Full Publication List ↗

Mallick, A.

BoltzYML: a preprocessing-file generator for Boltz-2 ternary (Protein 1 + Ligand + Protein 2) binding prediction.

Zenodo · v1.0.0 · May 2026 · DOI: 10.5281/zenodo.20399843 ↗ · Software

Mallick, A.

BoltzYML v2.0: A Zero-Install, Browser-Based Engine for Template Repair, Payload Construction, and Submission of N-body Cofolding and Binding-Affinity Predictions to the Boltz-2 API.

Zenodo · v2.0.0 · Jun 2026 · DOI: 10.5281/zenodo.20440141 ↗ · Software

Mallick, A.

ampliscan: anchor-based demultiplexing of amplicon sequencing reads into per-sample bins by custom primer barcodes.

Zenodo · v1.1.0 · 2026 · DOI: 10.5281/zenodo.21505581 ↗ · Software

Das, A., Pal, M., Price, A. H., Taria, S., Mallick, A., Sharma, M., Kumar, S., Ellur, R. K., Krishnan, S. G., Sathee, L., Jain, P. K., Dalal, M., Anandan, A., Panda, S., Kumari, A., Agarwal, M., & Chinnusamy, V.

Haplotype-based multi-locus genome-wide association study reveals genomic regions associated with reproductive stage high temperature stress tolerance in rice.

Plant Molecular Biology · Vol. 116, 56 · 2026 · DOI: 10.1007/s11103-026-01716-8 ↗

Mallick, A., Ramesh, R., Chinnusamy, V., Pandey, R., & Nagar, S.

Artificial Intelligence-Guided Genome Editing: Shaping the Future of Next-Generation Crop Improvement.

Indian Journal of Agricultural Sciences · Accepted — DOI pending

Tools & Expertise

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// Wet Lab & Experimental

CRISPR–Cas Cloning Hairy Root Transformation Mutant Generation Confocal Microscopy Scanning Electron Microscopy EDX Analysis Y1H Experiments BiFC Experiments Tobacco Infiltration Biochemical Assays Bacterial Culturing Gene Expression & Protein Work

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// Computational & Bioinformatics

GROMACS · MD Simulations Python & Biopython RNA-seq Analysis Whole Genome Analysis PyMOL · Chimera · Discovery Studio MEGA (Phylogenetics) ArcGIS R (Preliminary) Linux · HPC · SLURM Molecular Docking & PPI

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// Other & Creative

Biological Molecular Animation (Blender) Digital Art & Animation Guitar Poster Presentation Rodent Skeletal & Dental ID Club Coordinator & Leadership

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// Languages

Bengali Native English Professional Hindi Bilingual Japanese Elementary

Where can you find me?

Click a pin to find out my current whereabouts.

Tirupati, India

Kolkata, India

New Delhi, India