Prof. Shandar Ahmad Research Group · SCIS, JNU New Delhi
SciWhyLab builds data-driven algorithms for biology — from protein–DNA recognition and DNA shape dynamics to multi-omics and AI for human health. Scientific query for human health and happiness.
About the lab
We are based at the School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi — a young school whose thrust areas are bioinformatics, complex systems and big-data analytics.
SciWhyLab stands for scientific query for human health and happiness — a quiet pun on the Japanese 幸い (saiwai), the happiness we hope to derive from our work.
We develop machine-learning methods for biological data, building on our work in sequence- and structure-based analysis of protein–DNA and other biomolecular interactions. Our interests sit in machine learning, big-data analytics, and novel architectures for deep neural networks.
Principal Investigator
Principal Investigator
Trained as a physicist, working in bioinformatics since 2002. His contributions include first-generation sequence-based prediction of DNA-binding sites and proteins, free-energy and conserved-residue analyses of protein–DNA complexes, and the classification of conformational change on complex formation.
“Science, poetry and pretentious thinking are all my passions — of which I chose the first as a profession.”
News
Announcement 
Announcement 
Announcement ICMR has selected the proposed Collaborating Centre of Excellence (CCoE) on Artificial Intelligence and Data-driven Biomedical Discovery, led by Prof. Shandar Ahmad.
Read →Talks
Research
Sequence- and structure-based prediction of binding sites and the energetics of complex formation.
Learn more →Genome-wide dictionaries of DNA conformation — twist, roll, slide, groove width — for indirect-readout models of recognition.
Learn more →Novel architectures and training strategies, including language-model encodings, purpose-built for biological problems.
Learn more →Integrating expression, phosphoproteomics and toxicogenomics to translate signals across species toward drug discovery.
Learn more →Deep learning on whole-slide images and RNA-Seq for cancer diagnostics and early detection.
Learn more →AI/ML modelling of antimicrobial resistance and host–pathogen interactions, with a focus on tuberculosis.
Learn more →Projects
A genome-wide analysis of the conformational dynamics of transcription-factor targets, building shape-based models of transcriptional recognition.
A machine-learning method to identify previously unannotated DNA-binding proteins by integrating sequence and expression evidence.
Linking documented genetic diversity across sequenced bacterial and viral genomes to phenotype, including therapeutic-target discovery.
Publications
Ankesh Kumar Pandey, Shandar Ahmad · Biorxiv
Read →Waseem Ali · Shivangi Prandiyal · Anwar Alam · Mohd. Shariq · Nasreen Z. Ehtesham · Seyed E. Hasnain · Shandar Ahmad · Molecular Medicine
Read →Murali Aadhitya Magateshvaren Saras, Shandar Ahmad, Roger Smith, Mithun K Mitra, Sonika Tyagi · Biorxiv
Read →People
Collaborations
Partners overseas, across India, and within JNU.
Funding
Our current research is funded in part by the following agencies and organizations.
Some work shown on this site was funded in the past by:
Blog & Poetry
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