Publications

Featured & recent work.

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Recent

New

2026

Cross-cohort Mamography: Representation-dependent domain adaptation for cross-cohort generalization of mammography diagnostic models

Ankesh Kumar Pandey, Shandar Ahmad · Biorxiv

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New

2026

Methods and applications of artificial intelligence in tuberculosis diagnostics: advances, opportunities, and challenges

Waseem Ali · Shivangi Prandiyal · Anwar Alam · Mohd. Shariq · Nasreen Z. Ehtesham · Seyed E. Hasnain · Shandar Ahmad · Molecular Medicine

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New

2026

Tracing the regulatory atlas of non-coding RNA in human labour

Murali Aadhitya Magateshvaren Saras, Shandar Ahmad, Roger Smith, Mithun K Mitra, Sonika Tyagi · Biorxiv

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New

2026

Identification of Moonlighting Proteins from Published Literature Using Natural Language Processing and AI

Dana Mary Varghese, Vishwas Kukreti, Ajay Kumar Verma, Anirban Chakraborti, Shandar Ahmad · The Protein Journal

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New

2026

QXRNet: a hybrid CNN–QNN model with resolution-conditioned feature extraction and variational quantum circuit

Neha Vinayak, Shandar Ahmad · Quantum Machine Intelligence

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New

2026

A comprehensive benchmark of publicly available image foundation models for their usability to predict gene expression from whole slide images

Arfa Jabin, Shandar Ahmad · bioRxiv

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New

2026

Direct pathway enrichment prediction from histopathological whole slide images and comparison with gene expression mediated models

Arfa Jabin, Shandar Ahmad · bioRxiv

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New

2026

Transcriptome-based lead generation, ligand- and structure-based prioritization and experimental validation of TLR5-activating molecules

Anuja Jain, Hungyo Hungharla, Naidu Subbarao, Vibha Tandon, Shandar Ahmad · BioRxiv

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New

2026

MPGEM: A harmonized and transcriptome-complete resource for large-scale reuse of legacy human microarray data

Shruti Gupta, Ajay Kumar Verma, Sougata Jana, Shandar Ahmad · bioRxiv

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New

2026

Protein-DNA interactions in disease and drug discovery

Richa Mishra, Shandar Ahmad* · Chemical Communications

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Earlier — methods & reviews

2025

AI-based methods for modelling whole-slide imaging data in cancer diagnosis and transcriptome profile prediction

Arfa Jabin, Jyoti Singh Kirar, Shandar Ahmad · BMC Artificial Intelligence 1(1):16

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2025

A Survey of Biological Function Prediction Methods with Focus on NLP and Large Language Models (LLM)

Dana Mary Varghese, T. Athulya, Vikash K. Mohani, Shandar Ahmad · Methods in Molecular Biology, vol 2941 (Humana / Springer)

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2024

Low-dimension medical images and generative deep-learning models can help reduce X-ray radiation exposure of patients

Neha Vinayak, Divyansh Pandey, Shandar Ahmad · International Journal of Computer

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2022

Predictive modeling of moonlighting DNA-binding proteins

Dana M. Varghese, Ruth Nussinov, Shandar Ahmad · NAR Genomics and Bioinformatics

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2022

Host–pathogen protein–nucleic acid interactions: a comprehensive review

A. Jain, S. Mittal, L. P. Tripathi, R. Nussinov, S. Ahmad · Computational and Structural Biotechnology Journal

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2022

Unravelling molecular mechanisms of head and neck cancer

P. Parashar, H. Hungyo, A. Jain, S. Ahmad, V. Tandon · Critical Reviews in Oncology / Hematology

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2021

MycoVarP: Mycobacterium variant and drug-resistance prediction pipeline for whole-genome sequence data

S. Swargam et al., S. E. Hasnain, Shandar Ahmad · Frontiers in Bioinformatics

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2020

Feature selection for topological proximity prediction of single-cell transcriptomic profiles in Drosophila embryo using a genetic algorithm

Shruti Gupta, Ajay Kumar Verma, Shandar Ahmad · Genes 12(1):28

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