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2024	Cracking the black box of deep sequence-based protein–protein interaction prediction Briefings in Bioinformatics Judith Bernett, David B Blumenthal, Markus List
2024	iAFPs-Mv-BiTCN: Predicting antifungal peptides using self-attention transformer embedding and transform evolutionary based multi-view features with bidirectional temporal convolutional networks Artificial Intelligence in Medicine Shahid Akbar, Quan Zou, Ali Raza, Fawaz Khaled Alarfaj
2024	MGPPI: multiscale graph neural networks for explainable protein–protein interaction prediction Frontiers in Genetics Shiwei Zhao, Zhenyu Cui, Gonglei Zhang, Yanlong Gong, Lingtao Su
2024	Funnel graph neural networks with multi-granularity cascaded fusing for protein–protein interaction prediction Expert Systems with Applications Weicheng Sun, Jinsheng Xu, Weihan Zhang, Xuelian Li, Yongbin Zeng, Ping Zhang
2024	Lecture Notes in Computer Science Matteo Tolloso, Silvia Giulia Galfrè, Arianna Pavone, Marco Podda, Alina Sîrbu, Corrado Priami
2024	Prediction of interactions between cell surface proteins by machine learning Proteins: Structure, Function, and Bioinformatics Zhaoqian Su, Brian Griffin, Scott Emmons, Yinghao Wu
2024	Guiding questions to avoid data leakage in biological machine learning applications Nature Methods Judith Bernett, David B. Blumenthal, Dominik G. Grimm, Florian Haselbeck, Roman Joeres, Olga V. Kalinina, Markus List
2024	Machine Learning Empowering Drug Discovery: Applications, Opportunities and Challenges Molecules Xin Qi, Yuanchun Zhao, Zhuang Qi, Siyu Hou, Jiajia Chen
2024	SpatialPPI: Three-dimensional space protein-protein interaction prediction with AlphaFold Multimer Computational and Structural Biotechnology Journal Wenxing Hu, Masahito Ohue
2024	AttABseq: an attention-based deep learning prediction method for antigen–antibody binding affinity changes based on protein sequences Briefings in Bioinformatics Ruofan Jin, Qing Ye, Jike Wang, Zheng Cao, Dejun Jiang, Tianyue Wang, Yu Kang, Wanting Xu, Chang-Yu Hsieh, Tingjun Hou
2024	Improving protein-protein interaction prediction using protein language model and protein network features Analytical Biochemistry Jun Hu, Zhe Li, Bing Rao, Maha A. Thafar, Muhammad Arif
2024	How natural language processing derived techniques are used on biological data: a systematic review Network Modeling Analysis in Health Informatics and Bioinformatics Emmanouil D. Oikonomou, Petros Karvelis, Nikolaos Giannakeas, Aristidis Vrachatis, Evripidis Glavas, Alexandros T. Tzallas
2024	Prediction of Protein–Protein Interactions Based on Integrating Deep Learning and Feature Fusion International Journal of Molecular Sciences Hoai-Nhan Tran, Phuc-Xuan-Quynh Nguyen, Fei Guo, Jianxin Wang
2024	Co-training based prediction of multi-label protein–protein interactions Computers in Biology and Medicine Tao Tang, Xiaocai Zhang, Weizhuo Li, Qing Wang, Yuansheng Liu, Xiaofeng Cao
2024	Informatic challenges and advances in illuminating the druggable proteome Drug Discovery Today Rahil Taujale, Nathan Gravel, Zhongliang Zhou, Wayland Yeung, Krystof Kochut, Natarajan Kannan
2024	Computational Approaches to Predict Protein–Protein Interactions in Crowded Cellular Environments Chemical Reviews Greta Grassmann, Mattia Miotto, Fausta Desantis, Lorenzo Di Rienzo, Gian Gaetano Tartaglia, Annalisa Pastore, Giancarlo Ruocco, Michele Monti, Edoardo Milanetti
2023	Machine learning on protein–protein interaction prediction: models, challenges and trends Briefings in Bioinformatics Tao Tang, Xiaocai Zhang, Yuansheng Liu, Hui Peng, Binshuang Zheng, Yanlin Yin, Xiangxiang Zeng
2023	Growing ecosystem of deep learning methods for modeling protein–protein interactions Protein Engineering, Design and Selection Julia R Rogers, Gergő Nikolényi, Mohammed AlQuraishi
2023	HNSPPI: a hybrid computational model combing network and sequence information for predicting protein–protein interaction Briefings in Bioinformatics Shijie Xie, Xiaojun Xie, Xin Zhao, Fei Liu, Yiming Wang, Jihui Ping, Zhiwei Ji
2023	Studies in Computational Intelligence Nicolás López-Rozo, Jorge Finke, Camilo Rocha
2023	MARPPI: boosting prediction of protein–protein interactions with multi-scale architecture residual network Briefings in Bioinformatics Xue Li, Peifu Han, Wenqi Chen, Changnan Gao, Shuang Wang, Tao Song, Muyuan Niu, Alfonso Rodriguez-Patón
2023	Sequence-based prediction of protein–protein interaction using auto-feature engineering of RNN-based model Research on Biomedical Engineering Bhawna Mewara, Soniya Lalwani
2023	DeepSG2PPI: A Protein-Protein Interaction Prediction Method Based on Deep Learning IEEE/ACM Transactions on Computational Biology and Bioinformatics Fan Zhang, Yawei Zhang, Xiaoke Zhu, Xiaopan Chen, Fuhao Lu, Xinhong Zhang
2023	AIPs-SnTCN: Predicting Anti-Inflammatory Peptides Using fastText and Transformer Encoder-Based Hybrid Word Embedding with Self-Normalized Temporal Convolutional Networks Journal of Chemical Information and Modeling Ali Raza, Jamal Uddin, Abdullah Almuhaimeed, Shahid Akbar, Quan Zou, Ashfaq Ahmad
2023	Protein–protein interaction and site prediction using transfer learning Briefings in Bioinformatics Tuoyu Liu, Han Gao, Xiaopu Ren, Guoshun Xu, Bo Liu, Ningfeng Wu, Huiying Luo, Yuan Wang, Tao Tu, Bin Yao, Feifei Guan, Yue Teng, Huoqing Huang, Jian Tian
2023	State‐of‐the‐art computational methods to predict protein–protein interactions with high accuracy and coverage PROTEOMICS Neal Kewalramani, Andrew Emili, Mark Crovella
2023	Lecture Notes in Computer Science Sarwan Ali, Prakash Chourasia, Murray Patterson
2023	Peptides of a Feather: How Computation Is Taking Peptide Therapeutics under Its Wing Genes Thomas David Daniel Kazmirchuk, Calvin Bradbury-Jost, Taylor Ann Withey, Tadesse Gessese, Taha Azad, Bahram Samanfar, Frank Dehne, Ashkan Golshani
2023	DeepCF-PPI: improved prediction of protein-protein interactions by combining learned and handcrafted features based on attention mechanisms Applied Intelligence Hoai-Nhan Tran, Quynh Nguyen Phuc Xuan, Tuong-Tri Nguyen
2022	Struct2Graph: a graph attention network for structure based predictions of protein–protein interactions BMC Bioinformatics Mayank Baranwal, Abram Magner, Jacob Saldinger, Emine S. Turali-Emre, Paolo Elvati, Shivani Kozarekar, J. Scott VanEpps, Nicholas A. Kotov, Angela Violi, Alfred O. Hero
2022	Multi-TransDTI: Transformer for Drug–Target Interaction Prediction Based on Simple Universal Dictionaries with Multi-View Strategy Biomolecules Gan Wang, Xudong Zhang, Zheng Pan, Alfonso Rodríguez Patón, Shuang Wang, Tao Song, Yuanqiang Gu
2022	SDNN-PPI: self-attention with deep neural network effect on protein-protein interaction prediction BMC Genomics Xue Li, Peifu Han, Gan Wang, Wenqi Chen, Shuang Wang, Tao Song
2022	Compact Genetic Algorithm-Based Feature Selection for Sequence-Based Prediction of Dengue–Human Protein Interactions IEEE/ACM Transactions on Computational Biology and Bioinformatics Lopamudra Dey, Anirban Mukhopadhyay
2022	InfersentPPI: Prediction of Protein-Protein Interaction Using Protein Sentence Embedding With Gene Ontology Information Frontiers in Genetics Meijing Li, Yingying Jiang, Keun Ho Ryu
2022	Recent developments of sequence-based prediction of protein–protein interactions Biophysical Reviews Yoichi Murakami, Kenji Mizuguchi
2022	Protein‐protein interaction networks as miners of biological discovery PROTEOMICS Steven Wang, Runxin Wu, Jiaqi Lu, Yijia Jiang, Tao Huang, Yu‐Dong Cai
2022	ADH-PPI: An attention-based deep hybrid model for protein-protein interaction prediction iScience Muhammad Nabeel Asim, Muhammad Ali Ibrahim, Muhammad Imran Malik, Andreas Dengel, Sheraz Ahmed
2022	Deep learning frameworks for protein–protein interaction prediction Computational and Structural Biotechnology Journal Xiaotian Hu, Cong Feng, Tianyi Ling, Ming Chen
2022	A Novel Ensemble Learning-Based Computational Method to Predict Protein-Protein Interactions from Protein Primary Sequences Biology Jie Pan, Shiwei Wang, Changqing Yu, Liping Li, Zhuhong You, Yanmei Sun
2022	ProteinPrompt: a webserver for predicting protein–protein interactions Bioinformatics Advances Sebastian Canzler, Markus Fischer, David Ulbricht, Nikola Ristic, Peter W Hildebrand, René Staritzbichler
2022	cACP-DeepGram: Classification of anticancer peptides via deep neural network and skip-gram-based word embedding model Artificial Intelligence in Medicine Shahid Akbar, Maqsood Hayat, Muhammad Tahir, Salman Khan, Fawaz Khaled Alarfaj
2022	2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Hoai-Nhan Tran, Phuc-Xuan-Quynh Nguyen, Xiaoqing Peng, Jianxin Wang
2022	ProteinGLUE multi-task benchmark suite for self-supervised protein modeling Scientific Reports Henriette Capel, Robin Weiler, Maurits Dijkstra, Reinier Vleugels, Peter Bloem, K. Anton Feenstra
2022	Recent advances in predicting protein–protein interactions with the aid of artificial intelligence algorithms Current Opinion in Structural Biology Shiwei Li, Sanan Wu, Lin Wang, Fenglei Li, Hualiang Jiang, Fang Bai
2022	DeepTrio: a ternary prediction system for protein–protein interaction using mask multiple parallel convolutional neural networks Bioinformatics Xiaotian Hu, Cong Feng, Yincong Zhou, Andrew Harrison, Ming Chen
2022	Assessing sequence-based protein–protein interaction predictors for use in therapeutic peptide engineering Scientific Reports François Charih, Kyle K. Biggar, James R. Green
2022	Proceedings of the 2022 6th International Conference on Computational Biology and Bioinformatics Jihong Wang, Xiaodan Wang,, Junwei Wu
2022	Deep Neural Network and Extreme Gradient Boosting Based Hybrid Classifier for Improved Prediction of Protein-Protein Interaction IEEE/ACM Transactions on Computational Biology and Bioinformatics Satyajit Mahapatra, Vivek Raj Gupta, Sitanshu Sekhar Sahu, Ganapati Panda
2022	Protein–protein interaction prediction with deep learning: A comprehensive review Computational and Structural Biotechnology Journal Farzan Soleymani, Eric Paquet, Herna Viktor, Wojtek Michalowski, Davide Spinello
2022	Lecture Notes in Networks and Systems Bhawna Mewara, Soniya Lalwani
2021	Using Chou’s 5-Step Rule to Predict DNA-Protein Binding with Multi-scale Complementary Feature Journal of Proteome Research Xiuquan Du, Jiajia Hu, Shuo Li
2021	Predicting Protein–Protein Interactions Using Symmetric Logistic Matrix Factorization Journal of Chemical Information and Modeling Fen Pei, Qingya Shi, Haotian Zhang, Ivet Bahar
2021	Text mining for modeling of protein complexes enhanced by machine learning Bioinformatics Varsha D Badal, Petras J Kundrotas, Ilya A Vakser
2021	Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification Briefings in Bioinformatics Pieter Moris, Joey De Pauw, Anna Postovskaya, Sofie Gielis, Nicolas De Neuter, Wout Bittremieux, Benson Ogunjimi, Kris Laukens, Pieter Meysman
2021	Predicting Protein–Protein Interactions via Gated Graph Attention Signed Network Biomolecules Zhijie Xiang, Weijia Gong, Zehui Li, Xue Yang, Jihua Wang, Hong Wang
2021	Epigenetics: Roles and therapeutic implications of non-coding RNA modifications in human cancers Molecular Therapy - Nucleic Acids Dawei Rong, Guangshun Sun, Fan Wu, Ye Cheng, Guoqiang Sun, Wei Jiang, Xiao Li, Yi Zhong, Liangliang Wu, Chuanyong Zhang, Weiwei Tang, Xuehao Wang
2021	Benchmark Evaluation of Protein–Protein Interaction Prediction Algorithms Molecules Brandan Dunham, Madhavi K. Ganapathiraju
2021	Improved prediction of protein–protein interaction using a hybrid of functional-link Siamese neural network and gradient boosting machines Briefings in Bioinformatics Satyajit Mahapatra, Sitanshu Sekhar Sahu
2020	Prediction of Protein-Protein Interactions with Local Weight-Sharing Mechanism in Deep Learning BioMed Research International Lei Yang, Yukun Han, Huixue Zhang, Wenlong Li, Yu Dai
2020	Identifying Enhancers and Their Strength by the Integration of Word Embedding and Convolution Neural Network IEEE Access Jhabindra Khanal, Hilal Tayara, Kil To Chong
2020	Combining sequence and network information to enhance protein–protein interaction prediction BMC Bioinformatics Leilei Liu, Xianglei Zhu, Yi Ma, Haiyin Piao, Yaodong Yang, Xiaotian Hao, Yue Fu, Li Wang, Jiajie Peng
2020	Protein–Protein Interaction Methods and Protein Phase Separation Annual Review of Biomedical Data Science Castrense Savojardo, Pier Luigi Martelli, Rita Casadio
2019	2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Leilei Liu, Yi Ma, Xianglei Zhu, Yaodong Yang, Xiaotian Hao, Li Wang, Jiajie Peng
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