Structure-based protein folding type classification and folding rate prediction. - Balachandran Manavalan; Kunihiro Kuwajima; InSuk Joung; Jooyoung Lee 002 (BIBM, 2015)

SVMQA: support-vector-machine-based protein single-model quality assessment. - Balachandran Manavalan; Jooyoung Lee (Bioinform., 2017)

mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation. - Balachandran Manavalan; Shaherin Basith; Tae Hwan Shin; Leyi Wei; Gwang Lee (Bioinform., 2019)

Iterative feature representations improve N4-methylcytosine site prediction. - Leyi Wei; Ran Su; Shasha Luan; Zhijun Liao; Balachandran Manavalan; Quan Zou 001; Xiaolong Shi (Bioinform., 2019)

Protein-Carbohydrate Interactions. - Adeel Malik; Mohammad H. Baig; Balachandran Manavalan (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Empirical comparison and analysis of web-based cell-penetrating peptide prediction tools. - Ran Su; Jie Hu; Quan Zou 001; Balachandran Manavalan; Leyi Wei (Briefings Bioinform., 2020)

HLPpred-Fuse: improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation. - Md. Mehedi Hasan 002; Nalini Schaduangrat; Shaherin Basith; Gwang Lee; Watshara Shoombuatong; Balachandran Manavalan (Bioinform., 2020)

NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning. - Md. Mehedi Hasan 002; Md. Ashad Alam; Watshara Shoombuatong; Hong-Wen Deng; Balachandran Manavalan; Hiroyuki Kurata (Briefings Bioinform., 2021)

Integrative machine learning framework for the identification of cell-specific enhancers from the human genome. - Shaherin Basith; Md. Mehedi Hasan 002; Gwang Lee; Leyi Wei; Balachandran Manavalan (Briefings Bioinform., 2021)

StackIL6: a stacking ensemble model for improving the prediction of IL-6 inducing peptides. - Phasit Charoenkwan; Wararat Chiangjong; Chanin Nantasenamat; Md. Mehedi Hasan 002; Balachandran Manavalan; Watshara Shoombuatong (Briefings Bioinform., 2021)

Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework. - Md. Mehedi Hasan 002; Shaherin Basith; Mst. Shamima Khatun; Gwang Lee; Balachandran Manavalan; Hiroyuki Kurata (Briefings Bioinform., 2021)

Computational prediction and interpretation of cell-specific replication origin sites from multiple eukaryotes by exploiting stacking framework. - Leyi Wei; Wenjia He; Adeel Malik; Ran Su; Lizhen Cui; Balachandran Manavalan (Briefings Bioinform., 2021)

BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides. - Phasit Charoenkwan; Chanin Nantasenamat; Md. Mehedi Hasan 002; Balachandran Manavalan; Watshara Shoombuatong (Bioinform., 2021)

STALLION: a stacking-based ensemble learning framework for prokaryotic lysine acetylation site prediction. - Shaherin Basith; Gwang Lee; Balachandran Manavalan (Briefings Bioinform., 2022)

Accelerating bioactive peptide discovery via mutual information-based meta-learning. - Wenjia He; Yi Jiang; Junru Jin; Zhongshen Li; Jiaojiao Zhao; Balachandran Manavalan; Ran Su; Xin Gao 001; Leyi Wei (Briefings Bioinform., 2022)

TACOS: a novel approach for accurate prediction of cell-specific long noncoding RNAs subcellular localization. - Young-Jun Jeon; Md. Mehedi Hasan 002; Hyun Woo Park; Ki Wook Lee; Balachandran Manavalan (Briefings Bioinform., 2022)

iACVP: markedly enhanced identification of anti-coronavirus peptides using a dataset-specific word2vec model. - Hiroyuki Kurata; Sho Tsukiyama; Balachandran Manavalan (Briefings Bioinform., 2022)

Comparative analysis of machine learning-based approaches for identifying therapeutic peptides targeting SARS-CoV-2. - Balachandran Manavalan; Shaherin Basith; Gwang Lee (Briefings Bioinform., 2022)

Amyotrophic lateral sclerosis disease-related mutations disrupt the dimerization of superoxide dismutase 1 - A comparative molecular dynamics simulation study. - Shaherin Basith; Balachandran Manavalan; Gwang Lee (Comput. Biol. Medicine, 2022)

NEPTUNE: A novel computational approach for accurate and large-scale identification of tumor homing peptides. - Phasit Charoenkwan; Nalini Schaduangrat; Pietro Lio'; Mohammad Ali Moni; Balachandran Manavalan; Watshara Shoombuatong (Comput. Biol. Medicine, 2022)

SAPPHIRE: A stacking-based ensemble learning framework for accurate prediction of thermophilic proteins. - Phasit Charoenkwan; Nalini Schaduangrat; Mohammad Ali Moni; Pietro Lio'; Balachandran Manavalan; Watshara Shoombuatong (Comput. Biol. Medicine, 2022)

FRTpred: A novel approach for accurate prediction of protein folding rate and type. - Balachandran Manavalan; Jooyoung Lee (Comput. Biol. Medicine, 2022)

SER-Fuse: An Emotion Recognition Application Utilizing Multi-Modal, Multi-Lingual, and Multi-Feature Fusion. - Nhat Truong Pham; Le Thi Phan; Duc Ngoc Minh Dang; Balachandran Manavalan (SoICT, 2023)

SiameseCPP: a sequence-based Siamese network to predict cell-penetrating peptides by contrastive learning. - Xin Zhang; Lesong Wei; Xiucai Ye; Kai Zhang; Saisai Teng; Zhongshen Li; Junru Jin; Min Jae Kim; Tetsuya Sakurai; Lizhen Cui; Balachandran Manavalan; Leyi Wei (Briefings Bioinform., 2023)

Computational prediction of protein folding rate using structural parameters and network centrality measures. - Saraswathy Nithiyanandam; Vinoth Kumar Sangaraju; Balachandran Manavalan; Gwang Lee (Comput. Biol. Medicine, 2023)

MonkeyNet: A robust deep convolutional neural network for monkeypox disease detection and classification. - Diponkor Bala; Md Shamim Hossain; Mohammad Alamgir Hossain; Md. Ibrahim Abdullah; Md. Mizanur Rahman; Balachandran Manavalan; Naijie Gu; Mohammad S. Islam; Zhangjin Huang (Neural Networks, 2023)

VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing. - Kijin Kim; Kyungmin Park; Seonghyeon Lee; Seung-Hwan Baek; Tae-Hun Lim; Jongwoo Kim; Balachandran Manavalan; Jin-Won Song; Won-Keun Kim (Bioinform., 2023)

PSRQSP: An effective approach for the interpretable prediction of quorum sensing peptide using propensity score representation learning. - Phasit Charoenkwan; Pramote Chumnanpuen; Nalini Schaduangrat; Changmin Oh; Balachandran Manavalan; Watshara Shoombuatong (Comput. Biol. Medicine, 2023)

DrugormerDTI: Drug Graphormer for drug-target interaction prediction. - Jiayue Hu; Yu Wang; Chao Pang; Junru Jin; Nhat Truong Pham; Balachandran Manavalan; Leyi Wei (Comput. Biol. Medicine, 2023)

Ensemble feature selection using Bonferroni, OWA and Induced OWA aggregation operators. - K. Janani; S. S. Mohanrasu; Chee Peng Lim; Balachandran Manavalan; R. Rakkiyappan (Appl. Soft Comput., 2023)

Identification of SH2 domain-containing proteins and motifs prediction by a deep learning method. - Duanzhi Wu; Xin Fang; Kai Luan; Qijin Xu; Shiqi Lin; Shiying Sun; Jiaying Yang; Bingying Dong; Balachandran Manavalan; Zhijun Liao (Comput. Biol. Medicine, 2023)

ADP-Fuse: A novel two-layer machine learning predictor to identify antidiabetic peptides and diabetes types using multiview information. - Shaherin Basith; Nhat Truong Pham; Minkyung Song; Gwang Lee; Balachandran Manavalan (Comput. Biol. Medicine, 2023)

Advancing the accuracy of SARS-CoV-2 phosphorylation site detection via meta-learning approach. - Nhat Truong Pham; Le Thi Phan; Jimin Seo; Yeonwoo Kim; Minkyung Song; Sukchan Lee; Young-Jun Jeon; Balachandran Manavalan (Briefings Bioinform., 2023)

Hybrid data augmentation and deep attention-based dilated convolutional-recurrent neural networks for speech emotion recognition. - Nhat Truong Pham; Duc Ngoc Minh Dang; Ngoc Duy Nguyen; Thanh Nguyen 004; Hai Nguyen; Balachandran Manavalan; Chee Peng Lim; Sy Dzung Nguyen (Expert Syst. Appl., 2023)

H2Opred: a robust and efficient hybrid deep learning model for predicting 2'-O-methylation sites in human RNA. - Nhat Truong Pham; Rajan Rakkiyapan; Jongsun Park 002; Adeel Malik; Balachandran Manavalan (Briefings Bioinform., 2024)

mHPpred: Accurate identification of peptide hormones using multi-view feature learning. - Shaherin Basith; Vinoth Kumar Sangaraju; Balachandran Manavalan; Gwang Lee (Comput. Biol. Medicine, 2024)

CODENET: A deep learning model for COVID-19 detection. - Hong Ju; Yanyan Cui; Qiaosen Su; Liran Juan; Balachandran Manavalan (Comput. Biol. Medicine, 2024)

HOTGpred: Enhancing human O-linked threonine glycosylation prediction using integrated pretrained protein language model-based features and multi-stage feature selection approach. - Nhat Truong Pham; Ying Zhang; Rajan Rakkiyappan; Balachandran Manavalan (Comput. Biol. Medicine, 2024)

Unveiling local and global conformational changes and allosteric communications in SOD1 systems using molecular dynamics simulation and network analyses. - Shaherin Basith; Balachandran Manavalan; Gwang Lee (Comput. Biol. Medicine, 2024)

Stack-DHUpred: Advancing the accuracy of dihydrouridine modification sites detection via stacking approach. - Md. Harun-Or-Roshid; Kazuhiro Maeda; Le Thi Phan; Balachandran Manavalan; Hiroyuki Kurata (Comput. Biol. Medicine, 2024)

Leveraging deep transfer learning and explainable AI for accurate COVID-19 diagnosis: Insights from a multi-national chest CT scan study. - Nhat Truong Pham; Jinsol Ko; Masaud Shah; Rajan Rakkiyappan; Hyun Goo Woo; Balachandran Manavalan (Comput. Biol. Medicine, 2025)

REMED-T2D: A robust ensemble learning model for early detection of type 2 diabetes using healthcare dataset. - Le Thi Phan; Rajan Rakkiyappan; Balachandran Manavalan (Comput. Biol. Medicine, 2025)

M3S-ALG: Improved and robust prediction of allergenicity of chemical compounds by using a novel multi-step stacking strategy. - Phasit Charoenkwan; Nalini Schaduangrat; Le Thi Phan; Balachandran Manavalan; Watshara Shoombuatong (Future Gener. Comput. Syst., 2025)

Decision making based ensemble feature selection approach through a new score function in q-rung orthopair hesitant fuzzy environment. - Kavitha S.; Kendra N.; Satheeshkumar J.; T. Amudha; Balachandran Manavalan (Math. Comput. Simul., 2025)

XMolCap: Advancing Molecular Captioning Through Multimodal Fusion and Explainable Graph Neural Networks. - Duong Thanh Tran; Nguyen Doan Hieu Nguyen; Nhat Truong Pham; Rajan Rakkiyappan; Rajendra Karki; Balachandran Manavalan (IEEE J. Biomed. Health Informatics, 2025)

xBitterT5: an explainable transformer-based framework with multimodal inputs for identifying bitter-taste peptides. - Nguyen Doan Hieu Nguyen; Nhat Truong Pham; Duong Thanh Tran; Leyi Wei; Adeel Malik; Balachandran Manavalan (J. Cheminformatics, 2025)