CaLMPhosKAN: prediction of general phosphorylation sites in proteins via fusion of codon aware embeddings with amino acid aware embeddings and wavelet-based Kolmogorov–Arnold network. Pawel Pratyush, Callen Carrier, Suresh Pokharel, Hamid D Ismail, Meenal Chaudhary, and Dukka B. KC. Bioinformatics, (2025). journal

Crowd-sourced machine learning prediction of long COVID using data from the National COVID Cohort Collaborative. T. Bergquist, J. Loomba, E. Pfaff, F. Xia, Z. Zhao, Y. Zhu, E. Mitchell, et al. EBioMedicine 108 (2024). journal

LMPTMSite: A Platform for PTM Site Prediction in Proteins Leveraging Transformer-Based Protein Language Models. Pawel Pratyush, Suresh Pokharel, Hamid D Ismail, Soufia Bahmani, and Dukka B KC Prediction of Protein Secondary Structure, Springer Nature, Vol:2867, PP: 261–297 book chapter

LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model Pawel Pratyush, Soufia Bahmani, Suresh Pokharel, Hamid D Ismail, and Dukka B. KC. Bioinformatics, (2024). journal

Integrating Embeddings from Multiple Protein Language Models to Improve Protein O-GlcNAc Site Prediction . Suresh Pokharel, Pawel Pratyush, Hamid D Ismail, Junfeng Ma, and Dukka B. KC. International Journal of Molecular Sciences (IJMS), (2023). journal

LMPhosSite: A Deep Learning-Based Approach for General Protein Phosphorylation Site Prediction Using Embeddings from the Local Window Sequence and Pretrained Protein Language Model. Subash C. Pakhrin, Suresh Pokharel, Pawel Pratyush, Meenal Chaudhari, Hamid D Ismail, and Dukka B. KC. Journal of Proteome Research, (2023). journal

LMNglyPred: prediction of human N-linked glycosylation sites using embeddings from a pre-trained protein language model. Pakhrin Subash C., Pokharel Suresh, F Kiyoko, Beck Moriah R., Dam Tarun K., Caragea Doina, and Dukka B. KC. Glycobiology, (2023). journal

Experimental Study: Deep Learning-Based Fall Monitoring among Older Adults with Skin-Wearable Electronics. Lee, Yongkuk, Suresh Pokharel, Asra Al Muslim, Dukka KC, Kyoung Hag Lee, and Woon-Hong Yeo. Sensors 2023, 23, 3983. journal

DFT-aided machine learning-based discovery of magnetism in Fe-based bimetallic chalcogenides. Dharmendra Pant, Suresh Pokharel, Subhasish Mandal, Dukka B. KC, Ranjit Pati. Scientific Reports 13.1 (2023): 3277. journal

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 bioinformatics 24.1 (2023): 41. journal

NLP-based Encoding Techniques for Prediction of Post-translational Modification Sites and Protein Functions. Suresh Pokharel, Evgenii Sidorov, Doina Caragea, Dukka B KC. 2022 Computational Methods for Predicting Post-Translational Modification Sites, Springer Nature, Vol:2499, PP: 285–322 book chapter

Improving Protein Succinylation Sites Prediction Using Embeddings from Protein Language Model. Suresh Pokharel, Pawel Pratyush, Michael Heinzinger, Robert Newman, KC Dukka. Scientific Reports 12.1 (2022): 16933. journal

Image Quality Assessment by Integration of Low-level & High-level Features: Threshold Similarity Index. Jatin Chaudhary, Dibakar Raj Pant, Suresh Pokharel, Jukka-Pekka Skön, Jukka Heikkonen, Rajeev Kanth. 2022 IEEE 31st International Symposium on Industrial Electronics (ISIE) conference

Deep Learning–Based Advances In Protein Posttranslational Modification Site and Protein Cleavage Prediction. Subash C Pakhrin ^#, Suresh Pokharel ^# , Hiroto Saigo, Dukka KC. 2022 Computational Methods for Predicting Post-Translational Modification Sites, Springer Nature, Vol:2499, PP: 285–322 book chapter ( ^#Equally contributing first authors)

Performance Evaluation of Convolutional Neural Network Using Synthetic Medical Data Augmentation Generated by GAN. Ramesh Adhikari and Suresh Pokharel . 2021 International Journal of Image and Graphics, 2350002 journal

Deep learning based handwritten signature recognition. Suresh Pokharel, Santosh Giri, Subarna Shakya . 2020 NCE JOURNAL OF SCIENCE AND ENGINEERING (NJSE)" journal