Prediction of Thyroid Cancer Genes Using an Ensemble of Post Translational Modification, Semantic and Structural Similarity Based Clustering Results. - Anup Kumar Halder; Pritha Dutta; Mahantapas Kundu; Mita Nasipuri; Subhadip Basu (PReMI, 2017)

Bio-inspired cryptosystem with DNA cryptography and neural networks. - Sayantani Basu; Marimuthu Karuppiah; Mita Nasipuri; Anup Kumar Halder; Niranchana Radhakrishnan (J. Syst. Archit., 2019)

3gClust: Human Protein Cluster Analysis. - Anup Kumar Halder; Piyali Chatterjee; Mita Nasipuri; Dariusz Plewczynski; Subhadip Basu (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Computational modeling of Human-nCoV protein-protein interaction network. - Sovan Saha; Anup Kumar Halder; Soumyendu Sekhar Bandyopadhyay; Piyali Chatterjee; Mita Nasipuri; Subhadip Basu (CoRR, 2020)

JUPPI: A Multi-Level Feature Based Method for PPI Prediction and a Refined Strategy for Performance Assessment. - Anup Kumar Halder; Soumyendu Sekhar Bandyopadhyay; Piyali Chatterjee; Mita Nasipuri; Dariusz Plewczynski; Subhadip Basu (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

ccLoopER: Deep Prediction of CTCF and cohesin Mediated Chromatin looping Using DNA Transformer Model. - Anup Kumar Halder; Abhishek Agarwal; Sevastianos Korsak; Karolina Jodkowska; Dariusz Plewczynski (PReMI, 2023)

Prediction of chromatin looping using deep hybrid learning (DHL). - Mateusz Chilinski; Anup Kumar Halder; Dariusz Plewczynski (Quant. Biol., 2023)

RUBic: rapid unsupervised biclustering. - Brijesh Kumar Sriwastava; Anup Kumar Halder; Subhadip Basu; Tapabrata Chakraborti (BMC Bioinform., 2023)

FuzzyPPI: Large-Scale Interaction of Human Proteome at Fuzzy Semantic Space. - Anup Kumar Halder; Soumyendu Sekhar Bandyopadhyay; Witold Jedrzejewski; Subhadip Basu; Jacek Sroka (IEEE Trans. Big Data, 2025)