AJ

Ashish Kumar Jaiswal

Also known as: Ashish Kumar Jaiswal

Research areas: Medicine · Cardiology and Cardiovascular Medicine · Genomics and Phylogenetic Studies · Protist diversity and phylogeny · Energy Efficient Wireless Sensor Networks

ORCID iD 0000-0002-6193-1824
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About

Computational biologist working at the intersection of AI, structural biology and laboratory automation at NYU Abu Dhabi's A2S2 Lab, with two decades in bioinformatics — protein design and structure prediction, genomics, and the research computing that runs them.

My research centres on computational protein design and structure prediction. I build and operate production pipelines for AlphaFold 3, Boltz-2 and BoltzGen across RTX A6000 workstations, Blackwell-class DGX systems and institutional GPU clusters, applying them to genome-scale problems — protein–protein interaction prediction, interactome screening for collaborators, and dark-proteome mapping across microalgal genomes. I am currently representing the lab in the Anthropic × Adaptyv Bio international protein design competition.

On the AI/ML side I work with deep learning and generative protein language models (LA4SR, published in Patterns, and AlgaGPT), PyTorch model training and fine-tuning, interpretable ML for structural analysis, and agentic AI workflows. I also contribute to ALG-ALL-CODE, one of the largest single-lab algal genome collections — 229 assembled genomes and 250+ curated Pathway/Genome Databases — alongside NGS assembly and annotation across Illumina, PacBio HiFi and Oxford Nanopore.

I serve as the lab's systems administrator and research-computing lead, running a multi-node Linux GPU fleet — dual-A6000 workstations, an RTX 5090 node and ARM64 DGX systems — covering CUDA stacks, containerised and conda environments, interconnects, storage and backup architecture, and security hardening with university IT, plus work on NYUAD's Jubail and NYU's Torch clusters. I also maintain the lab's full-stack website and hosting, its interactive 229-genome explorer, and FAIR data stewardship across NCBI, Zenodo, ModelArchive and Hugging Face.

As Lab Manager I lead laboratory operations and infrastructure: new lab build-out, specification and commissioning of research equipment — including FrankenLab-OS, the lab's AI-and-robotics automation platform — safety and EHS compliance, and oversight of procurement and research budgets. I mentor student and visiting researchers.

Fourteen years at NYUAD; earlier posts at ICMR and ICAR. ~25 peer-reviewed publications in journals including Patterns, Molecular Plant, Cell Host & Microbe, eLife and Science Advances.

Focus: AI & data science · protein design · structural prediction · AlphaFold 3 · Boltz-2 · protein language models · PyTorch · genomics · NGS · HPC & GPU systems · Linux administration · research software · lab operations

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