pLMSNOSite: an ensemble-based approach for predicting protein S-nitrosylation sites by integrating supervised word embedding and embedding from pre-trained protein language model
Pratyush, Pawel, Pokharel, Suresh, Saigo, Hiroto, Kc, Dukka B
Published in BMC bioinformatics (08.02.2023)
Published in BMC bioinformatics (08.02.2023)
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Journal Article
DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction
Thapa, Niraj, Chaudhari, Meenal, McManus, Sean, Roy, Kaushik, Newman, Robert H, Saigo, Hiroto, Kc, Dukka B
Published in BMC bioinformatics (23.04.2020)
Published in BMC bioinformatics (23.04.2020)
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Journal Article
Deep Learning-Based Advances in Protein Structure Prediction
Pakhrin, Subash C., Shrestha, Bikash, Adhikari, Badri, KC, Dukka B.
Published in International journal of molecular sciences (24.05.2021)
Published in International journal of molecular sciences (24.05.2021)
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Journal Article
Improving protein succinylation sites prediction using embeddings from protein language model
Pokharel, Suresh, Pratyush, Pawel, Heinzinger, Michael, Newman, Robert H., KC, Dukka B.
Published in Scientific reports (08.10.2022)
Published in Scientific reports (08.10.2022)
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Journal Article
RF-GlutarySite: a random forest based predictor for glutarylation sites
AL-barakati, Hussam J, Saigo, Hiroto, Newman, Robert H, KC, Dukka B
Published in Molecular omics (01.06.2019)
Published in Molecular omics (01.06.2019)
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Journal Article
DFT-aided machine learning-based discovery of magnetism in Fe-based bimetallic chalcogenides
Pant, Dharmendra, Pokharel, Suresh, Mandal, Subhasish, KC, Dukka B., Pati, Ranjit
Published in Scientific reports (25.02.2023)
Published in Scientific reports (25.02.2023)
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Journal Article
Comparison of Machine Learning and Deep Learning Models for Network Intrusion Detection Systems
Thapa, Niraj, Liu, Zhipeng, KC, Dukka B., Gokaraju, Balakrishna, Roy, Kaushik
Published in Future internet (01.10.2020)
Published in Future internet (01.10.2020)
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Journal Article
A deep learning based approach for prediction of Chlamydomonas reinhardtii phosphorylation sites
Thapa, Niraj, Chaudhari, Meenal, Iannetta, Anthony A., White, Clarence, Roy, Kaushik, Newman, Robert H., Hicks, Leslie M., KC, Dukka B.
Published in Scientific reports (15.06.2021)
Published in Scientific reports (15.06.2021)
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Journal Article
CNN-BLPred: a Convolutional neural network based predictor for β-Lactamases (BL) and their classes
White, Clarence, Ismail, Hamid D, Saigo, Hiroto, Kc, Dukka B
Published in BMC bioinformatics (28.12.2017)
Published in BMC bioinformatics (28.12.2017)
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Journal Article
Hydrogen peroxide-dependent oxidation of ERK2 within its D-recruitment site alters its substrate selection
Postiglione, Anthony E., Adams, Laquaundra L., Ekhator, Ese S., Odelade, Anuoluwapo E., Patwardhan, Supriya, Chaudhari, Meenal, Pardue, Avery S., Kumari, Anjali, LeFever, William A., Tornow, Olivia P., Kaoud, Tamer S., Neiswinger, Johnathan, Jeong, Jun Seop, Parsonage, Derek, Nelson, Kimberly J., Kc, Dukka B., Furdui, Cristina M., Zhu, Heng, Wommack, Andrew J., Dalby, Kevin N., Dong, Ming, Poole, Leslie B., Keyes, Jeremiah D., Newman, Robert H.
Published in iScience (20.10.2023)
Published in iScience (20.10.2023)
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Journal Article
SVM-SulfoSite: A support vector machine based predictor for sulfenylation sites
AL-barakati, Hussam J., McConnell, Evan W., Hicks, Leslie M., Poole, Leslie B., Newman, Robert H., KC, Dukka B.
Published in Scientific reports (26.07.2018)
Published in Scientific reports (26.07.2018)
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Journal Article
RF-Phos: A Novel General Phosphorylation Site Prediction Tool Based on Random Forest
Newman, Robert H., Kim, Jung H., Jones, Ahoi, Ismail, Hamid D., KC, Dukka B.
Published in BioMed research international (01.01.2016)
Published in BioMed research international (01.01.2016)
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Journal Article
The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches
Khan, Ishita K, Wei, Qing, Chapman, Samuel, Kc, Dukka B, Kihara, Daisuke
Published in Gigascience (14.09.2015)
Published in Gigascience (14.09.2015)
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Journal Article
DTL-DephosSite: Deep Transfer Learning Based Approach to Predict Dephosphorylation Sites
Chaudhari, Meenal, Thapa, Niraj, Ismail, Hamid, Chopade, Sandhya, Caragea, Doina, Köhn, Maja, Newman, Robert H., KC, Dukka B.
Published in Frontiers in cell and developmental biology (24.06.2021)
Published in Frontiers in cell and developmental biology (24.06.2021)
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