Protein Side-chain Packing Problem: A Maximum Edge-weight Clique Algorithmic Approach. - Dukka Bahadur; Tatsuya Akutsu; Etsuji Tomita; Tomokazu Seki (APBC, 2004)

Clique-based algorithms for protein threading with profiles and constraints. - Dukka Bahadur; Etsuji Tomita; Jun'ichi Suzuki; Katsuhisa Horimoto; Tatsuya Akutsu (APBC, 2005)

Protein Side-chain Packing Problem: a Maximum Edge-weight Clique Algorithmic Approach. - K. C. Dukka Bahadur; Etsuji Tomita; Jun'ichi Suzuki; Tatsuya Akutsu (J. Bioinform. Comput. Biol., 2005)

Dynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints. - Tatsuya Akutsu; Morihiro Hayashida; Dukka Bahadur; Etsuji Tomita; Jun'ichi Suzuki; Katsuhisa Horimoto (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2006)

Protein Threading with Profiles and Distance Constraints Using Clique Based Algorithms. - K. C. Dukka Bahadur; Etsuji Tomita; Jun'ichi Suzuki; Katsuhisa Horimoto; Tatsuya Akutsu (J. Bioinform. Comput. Biol., 2006)

Clique-based algorithms for protein structure prediction. - Dukka Bahadur (2006)

Improving position-specific predictions of protein functional sites using phylogenetic motifs. - K. C. Dukka Bahadur; Dennis R. Livesay (Bioinform., 2008)

Topology Improves Phylogenetic Motif Functional Site Predictions. - K. C. Dukka Bahadur; Dennis R. Livesay (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Hierarchical multi-label gene function prediction using adaptive mutation in crowding niching. - Mina Moradi Kordmahalleh; Abdollah Homaifar; K. C. Dukka Bahadur (BIBE, 2013)

Time-series forecasting with evolvable partially connected artificial neural network. - Mina Moradi Kordmahalleh; Mohammad Gorji Sefidmazgi; Abdollah Homaifar; K. C. Dukka Bahadur; Anthony Guiseppi-Elie (GECCO (Companion), 2014)

RF-Phos: Random forest-based prediction of phosphorylation sites. - Ahoi Jones; Hamid D. Ismail; Jung H. Kim; Robert H. Newman; K. C. Dukka B. (BIBM, 2015)

Phosphorylation sites prediction using Random Forest. - Hamid D. Ismail; Ahoi Jones; Jung H. Kim; Robert H. Newman; K. C. Dukka B. (ICCABS, 2015)

Recent advances in sequence-based protein structure prediction. - K. C. Dukka B. (Briefings Bioinform., 2017)

CNN-BLPred: a Convolutional neural network based predictor for β-Lactamases (BL) and their classes. - Clarence White; Hamid D. Ismail; Hiroto Saigo; K. C. Dukka B. (BMC Bioinform., 2017)

RF-NR: Random Forest Based Approach for Improved Classification of Nuclear Receptors. - Hamid D. Ismail; Hiroto Saigo; K. C. Dukka B. (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Comparison of Machine Learning and Deep Learning Models for Network Intrusion Detection Systems. - Niraj Thapa; Zhipeng Liu; Dukka B. KC; Balakrishna Gokaraju; Kaushik Roy 003 (Future Internet, 2020)

DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction. - Niraj Thapa; Meenal Chaudhari; Sean McManus; Kaushik Roy 003; Robert H. Newman; Hiroto Saigo; Dukka B. KC (BMC Bioinform., 2020)

GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool. - Elijah A. MacCarthy; Chengxin Zhang; Yang Zhang 040; Dukka B. KC (Bioinform., 2022)

Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction. - Niraj Thapa; Meenal Chaudhari; Sean McManus; Kaushik Roy 003; Robert H. Newman; Hiroto Saigo; K. C. Dukka B. (BMC Bioinform., 2022)

Experimental Study: Deep Learning-Based Fall Monitoring among Older Adults with Skin-Wearable Electronics. - Yongkuk Lee; Suresh Pokharel; Asra Al Muslim; Dukka B. KC; Kyoung Hag Lee; Woon-Hong Yeo (Sensors, 2023)

pLMSNOSite: an ensemble-based approach for predicting protein S-nitrosylation sites by integrating supervised word embedding and embedding from pre-trained protein language model. - Pawel Pratyush; Suresh Pokharel; Hiroto Saigo; Dukka B. KC (BMC Bioinform., 2023)

Benchmarking a Wide Range of Unsupervised Learning Methods for Detecting Anomaly in Blast Furnace. - Kendai Itakura; Dukka Bahadur; Hiroto Saigo (ICPRAM, 2024)

PLM-DBPs: enhancing plant DNA-binding protein prediction by integrating sequence-based and structure-aware protein language models. - Suresh Pokharel; Kepha Barasa; Pawel Pratyush; Dukka B. KC (Briefings Bioinform., 2025)