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Rafiya Jan, Ahsan Hussain, Assif Assad, Basharat Bhat

Ziqi Zhang, Guanqing Yu, Zhaohong Deng, Chenxi Luo, Cheng Cai, Wei Zhang, Fuping Hu, Kup-Sze Choi, Zhisheng Wei, Lei Wang, Jing Wu

Jiashan Li, Xi Chen, He Huang, Mingliang Zeng, Jingcheng Yu, Xinqi Gong, Qiwei Ye

Dingyi Rong, Bozitao Zhong, Wenzhuo Zheng, Liang Hong, Ning Liu

Neha Tripathi, Joan Hérisson, Jean-Loup Faulon

Abderrahim Mechache, Hamamache Kheddouci

Minglei Li, Yurui Hou, Shuqin Wang, Jinmao Wei, Jian Liu

JiangYi Shao, JunJie Chen, Bin Liu

Yi Li, Yahui Liu, Jiangchun Hou, Xiaohui Liu

Prabha Singh, Sudhakar Tripathi, Anand Bihari

Gregor Wirnsberger, Iva Pritišanac, Gustav Oberdorfer, Karl Gruber

Milad Rayka, Ali Mohammad Latifi, Morteza Mirzaei, Gholamreza Farnoosh, Zeinab Khosravi

David Harding-Larsen, Jonathan Funk, Niklas Gesmar Madsen, Hani Gharabli, Carlos G. Acevedo-Rocha, Stanislav Mazurenko, Ditte Hededam Welner

Chang Li, Yixuan Luo, Yibo Xie, Zaifeng Zhang, Ye Liu, Lihui Zou, Fei Xiao

Ailun Sun, Hongfei Li, Guanghui Dong, Yuming Zhao, Dandan Zhang

Yuji Takiguchi, Daisuke Nakane, Takashiro Akitsu

Jianrong Zhang, Hehe Fan, Yi Yang

Jie Zhuang, Adam C. Midgley, Yonghua Wei, Qiqi Liu, Deling Kong, Xinglu Huang

Thanh-Hoang Nguyen-Vo, Paul Teesdale-Spittle, Joanne E. Harvey, Binh P. Nguyen

Chinju John, Jayakrushna Sahoo, Manu Madhavan, Oommen K. Mathew

Pedro Sousa Sampaio, Pedro Fernandes

Dmitrij Rappoport, Adrian Jinich

Lucrecia L. Chaillou, Valeria Boeris, Darío Spelzini, Mónica A. Nazareno

Ziqi Gao, Chenran Jiang, Jiawen Zhang, Xiaosen Jiang, Lanqing Li, Peilin Zhao, Huanming Yang, Yong Huang, Jia Li

Ana Marta Sequeira, Ivan Gomes, Miguel Rocha

Petr Kouba, Pavel Kohout, Faraneh Haddadi, Anton Bushuiev, Raman Samusevich, Jiri Sedlar, Jiri Damborsky, Tomas Pluskal, Josef Sivic, Stanislav Mazurenko

Arnold Kazadi, Ming Zhang, Jingbo Zhou

Khaled Boulahrouf, Salah Eddine Aliouane, Hamza Chehili, Mohamed Skander Daas, Adel Belbekri, Mohamed Abdelhafid Hamidechi

Hehe Fan, Linchao Zhu, Yi Yang, Mohan Kankanhalli

Hongshuai Wang, Lujie Jin, Jie Feng, Zhihao Dong, Weiqiao Deng, Youyong Li

Saurabh Agrawal, Dilip Singh Sisodia, Naresh Kumar Nagwani

Ana Marta Sequeira, Miguel Rocha

Marcel Wittmund, Frederic Cadet, Mehdi D. Davari

Xiaosheng Zhao, Yi Mao, Cheng Cheng, Benjamin D. Wandelt

Jiahao Shen, Qiang Tong, Zhanqi Cui, Zanqiang Dong, Xiulei Liu

Glen Williams, Nicholas A. Meisel, Timothy W. Simpson, Christopher McComb

Nathan Jariwala, Matiss Ozols, Mike Bell, Eleanor Bradley, Andrew Gilmore, Laurent Debelle, Michael J. Sherratt

H. Erdinç KOCER, Kerim Kürşat ÇEVİK

Yanqiang Han, Imran Ali, Zhilong Wang, Junfei Cai, Sicheng Wu, Jiequn Tang, Lin Zhang, Jiahao Ren, Rui Xiao, Qianqian Lu, Lei Hang, Hongyuan Luo, Jinjin Li

Christopher E. Lawson, Jose Manuel Martí, Tijana Radivojevic, Sai Vamshi R. Jonnalagadda, Reinhard Gentz, Nathan J. Hillson, Sean Peisert, Joonhoon Kim, Blake A. Simmons, Christopher J. Petzold, Steven W. Singer, Aindrila Mukhopadhyay, Deepti Tanjore, Joshua G. Dunn, Hector Garcia Martin

Qiang Shi, Weiya Chen, Siqi Huang, Yan Wang, Zhidong Xue

Apichat Suratanee, Kitiporn Plaimas

Vladimir Gligorijević, P. Douglas Renfrew, Tomasz Kosciolek, Julia Koehler Leman, Daniel Berenberg, Tommi Vatanen, Chris Chandler, Bryn C. Taylor, Ian M. Fisk, Hera Vlamakis, Ramnik J. Xavier, Rob Knight, Kyunghyun Cho, Richard Bonneau

Zhiyu Tao, Benzhi Dong, Zhixia Teng, Yuming Zhao

Kanchan Jha, Sriparna Saha, Matloob Khushi

Louis Papageorgiou, Eleni Papakonstantinou, Constantinos Salis, Eleytheria Polychronidou, Marianna Hagidimitriou, Dimitris Maroulis, Elias Eliopoulos, Dimitrios Vlachakis

Mojtaba Haghighatlari, Jie Li, Farnaz Heidar-Zadeh, Yuchen Liu, Xingyi Guan, Teresa Head-Gordon

Jocelyn Sunseri, David R. Koes

Stanislav Mazurenko, Zbynek Prokop, Jiri Damborsky

Satya P. Singh, Lipo Wang, Sukrit Gupta, Haveesh Goli, Parasuraman Padmanabhan, Balázs Gulyás

Louis Papageorgiou, Dimitris Maroulis, George P. Chrousos, Elias Eliopoulos, Dimitrios Vlachakis

Constantinos Salis, Louis Papageorgiou, Eleni Papakonstantinou, Marianna Hagidimitriou, Dimitrios Vlachakis

Kanchan Jha, Sriparna Saha

Pablo Carbonell, Rosalind Le Feuvre, Eriko Takano, Nigel S Scrutton

Ruibo Gao, Mengmeng Wang, Jiaoyan Zhou, Yuhang Fu, Meng Liang, Dongliang Guo, Junlan Nie

Isidro Cortés-Ciriano, Andreas Bender

Daniel C. Elton, Zois Boukouvalas, Mark D. Fuge, Peter W. Chung

Nguyen Quoc Khanh Le, Van-Nui Nguyen

Sebastian Spänig, Dominik Heider

Shuai Liu, Jie Li, Kochise C. Bennett, Brad Ganoe, Tim Stauch, Martin Head-Gordon, Alexander Hexemer, Daniela Ushizima, Teresa Head-Gordon

Riccardo Concu, M. Natália D. S. Cordeiro

Alperen Dalkiran, Ahmet Sureyya Rifaioglu, Maria Jesus Martin, Rengul Cetin-Atalay, Volkan Atalay, Tunca Doğan

2026	Cancer Interactome: An in-silico Novel Approach for Elucidating Cancer Protein-Protein Interactions (CPPIs) Using Structural Graph Learning Augmented with Attention Journal of Computational Biophysics and Chemistry Rafiya Jan, Ahsan Hussain, Assif Assad, Basharat Bhat
2025	SEFP: Structure-Based Enzyme Function Prediction IEEE Transactions on Computational Biology and Bioinformatics Ziqi Zhang, Guanqing Yu, Zhaohong Deng, Chenxi Luo, Cheng Cai, Wei Zhang, Fuping Hu, Kup-Sze Choi, Zhisheng Wei, Lei Wang, Jing Wu
2025	$\mathcal{S}$ able: bridging the gap in protein structure understanding with an empowering and versatile pre-training paradigm Briefings in Bioinformatics Jiashan Li, Xi Chen, He Huang, Mingliang Zeng, Jingcheng Yu, Xinqi Gong, Qiwei Ye
2025	Autoregressive enzyme function prediction with multi-scale multi-modality fusion Briefings in Bioinformatics Dingyi Rong, Bozitao Zhong, Wenzhuo Zheng, Liang Hong, Ning Liu
2025	Machine learning in predictive biocatalysis: A comparative review of methods and applications Biotechnology Advances Neha Tripathi, Joan Hérisson, Jean-Loup Faulon
2025	Lecture Notes in Computer Science Abderrahim Mechache, Hamamache Kheddouci
2025	PCLT-PPI: Predicting Multi-Type Interactions Between Proteins Based on Point Cloud Structure and Local Topology Preservation IEEE Journal of Biomedical and Health Informatics Minglei Li, Yurui Hou, Shuqin Wang, Jinmao Wei, Jian Liu
2025	ProFun-SOM: Protein Function Prediction for Specific Ontology Based on Multiple Sequence Alignment Reconstruction IEEE Transactions on Neural Networks and Learning Systems JiangYi Shao, JunJie Chen, Bin Liu
2025	A center-anchored adaptive hierarchical graph neural network with application in structure-aware recognition of enzyme catalytic specificity Neurocomputing Yi Li, Yahui Liu, Jiangchun Hou, Xiaohui Liu
2025	Exploration of Computational Approaches in Enzyme Classification: Problems and Recent Development—A Critical Review Archives of Computational Methods in Engineering Prabha Singh, Sudhakar Tripathi, Anand Bihari
2024	Flattening the curve—How to get better results with small deep‐mutational‐scanning datasets Proteins: Structure, Function, and Bioinformatics Gregor Wirnsberger, Iva Pritišanac, Gustav Oberdorfer, Karl Gruber
2024	ADDZYME: A software to predict effect of additives on enzyme activity Journal of Chemical Sciences Milad Rayka, Ali Mohammad Latifi, Morteza Mirzaei, Gholamreza Farnoosh, Zeinab Khosravi
2024	Protein representations: Encoding biological information for machine learning in biocatalysis Biotechnology Advances David Harding-Larsen, Jonathan Funk, Niklas Gesmar Madsen, Hani Gharabli, Carlos G. Acevedo-Rocha, Stanislav Mazurenko, Ditte Hededam Welner
2024	Structural and functional prediction, evaluation, and validation in the post-sequencing era Computational and Structural Biotechnology Journal Chang Li, Yixuan Luo, Yibo Xie, Zaifeng Zhang, Ye Liu, Lihui Zou, Fei Xiao
2024	DBPboost:A method of classification of DNA-binding proteins based on improved differential evolution algorithm and feature extraction Methods Ailun Sun, Hongfei Li, Guanghui Dong, Yuming Zhao, Dandan Zhang
2024	The prediction of single-molecule magnet properties via deep learning IUCrJ Yuji Takiguchi, Daisuke Nakane, Takashiro Akitsu
2024	Protein Captioning: Bridging the Gap between Protein Sequences and Natural Languages ACM Transactions on Multimedia Computing, Communications, and Applications Jianrong Zhang, Hehe Fan, Yi Yang
2024	Machine‐Learning‐Assisted Nanozyme Design: Lessons from Materials and Engineered Enzymes Advanced Materials Jie Zhuang, Adam C. Midgley, Yonghua Wei, Qiqi Liu, Deling Kong, Xinglu Huang
2024	Molecular representations in bio-cheminformatics Memetic Computing Thanh-Hoang Nguyen-Vo, Paul Teesdale-Spittle, Joanne E. Harvey, Binh P. Nguyen
2023	Convolutional Neural Networks: A Promising Deep Learning Architecture for Biological Sequence Analysis Current Bioinformatics Chinju John, Jayakrushna Sahoo, Manu Madhavan, Oommen K. Mathew
2023	Machine Learning: A Suitable Method for Biocatalysis Catalysts Pedro Sousa Sampaio, Pedro Fernandes
2023	Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves Journal of Chemical Information and Modeling Dmitrij Rappoport, Adrian Jinich
2023	Advanced Pharmacy Lucrecia L. Chaillou, Valeria Boeris, Darío Spelzini, Mónica A. Nazareno
2023	Hierarchical graph learning for protein–protein interaction Nature Communications Ziqi Gao, Chenran Jiang, Jiawen Zhang, Xiaosen Jiang, Lanqing Li, Peilin Zhao, Huanming Yang, Yong Huang, Jia Li
2023	2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) Ana Marta Sequeira, Ivan Gomes, Miguel Rocha
2023	Machine Learning-Guided Protein Engineering ACS Catalysis Petr Kouba, Pavel Kohout, Faraneh Haddadi, Anton Bushuiev, Raman Samusevich, Jiri Sedlar, Jiri Damborsky, Tomas Pluskal, Josef Sivic, Stanislav Mazurenko
2023	2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Arnold Kazadi, Ming Zhang, Jingbo Zhou
2023	EZYDeep: A Deep Learning Tool for Enzyme Function Prediction based on Sequence Information The Open Bioinformatics Journal Khaled Boulahrouf, Salah Eddine Aliouane, Hamza Chehili, Mohamed Skander Daas, Adel Belbekri, Mohamed Abdelhafid Hamidechi
2023	2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Hehe Fan, Linchao Zhu, Yi Yang, Mohan Kankanhalli
2023	Molecular represention in AI-assisted synthesis chemistry: from sequence to graph SCIENTIA SINICA Chimica Hongshuai Wang, Lujie Jin, Jie Feng, Zhihao Dong, Weiqiao Deng, Youyong Li
2022	Long short term memory based functional characterization model for unknown protein sequences using ensemble of shallow and deep features Neural Computing and Applications Saurabh Agrawal, Dilip Singh Sisodia, Naresh Kumar Nagwani
2022	Lecture Notes in Networks and Systems Ana Marta Sequeira, Miguel Rocha
2022	Learning Epistasis and Residue Coevolution Patterns: Current Trends and Future Perspectives for Advancing Enzyme Engineering ACS Catalysis Marcel Wittmund, Frederic Cadet, Mehdi D. Davari
2022	Simulation-based Inference of Reionization Parameters from 3D Tomographic 21 cm Light-cone Images The Astrophysical Journal Xiaosheng Zhao, Yi Mao, Cheng Cheng, Benjamin D. Wandelt
2022	2022 15th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI) Jiahao Shen, Qiang Tong, Zhanqi Cui, Zanqiang Dong, Xiulei Liu
2022	Design for Artificial Intelligence: Proposing a Conceptual Framework Grounded in Data Wrangling Journal of Computing and Information Science in Engineering Glen Williams, Nicholas A. Meisel, Timothy W. Simpson, Christopher McComb
2022	Matrikines as mediators of tissue remodelling Advanced Drug Delivery Reviews Nathan Jariwala, Matiss Ozols, Mike Bell, Eleanor Bradley, Andrew Gilmore, Laurent Debelle, Michael J. Sherratt
2021	Deep neural networks based wrist print region segmentation and classification MANAS Journal of Engineering H. Erdinç KOCER, Kerim Kürşat ÇEVİK
2021	Protein–Protein Interface Topology as a Predictor of Secondary Structure and Molecular Function Using Convolutional Deep Learning Journal of Chemical Information and Modeling Benjamin Bouvier
2021	Machine learning accelerates quantum mechanics predictions of molecular crystals Physics Reports Yanqiang Han, Imran Ali, Zhilong Wang, Junfei Cai, Sicheng Wu, Jiequn Tang, Lin Zhang, Jiahao Ren, Rui Xiao, Qianqian Lu, Lei Hang, Hongyuan Luo, Jinjin Li
2021	Machine learning for metabolic engineering: A review Metabolic Engineering Christopher E. Lawson, Jose Manuel Martí, Tijana Radivojevic, Sai Vamshi R. Jonnalagadda, Reinhard Gentz, Nathan J. Hillson, Sean Peisert, Joonhoon Kim, Blake A. Simmons, Christopher J. Petzold, Steven W. Singer, Aindrila Mukhopadhyay, Deepti Tanjore, Joshua G. Dunn, Hector Garcia Martin
2021	Deep learning for mining protein data Briefings in Bioinformatics Qiang Shi, Weiya Chen, Siqi Huang, Yan Wang, Zhidong Xue
2021	Hybrid Deep Learning Based on a Heterogeneous Network Profile for Functional Annotations of Plasmodium falciparum Genes International Journal of Molecular Sciences Apichat Suratanee, Kitiporn Plaimas
2021	Structure-based protein function prediction using graph convolutional networks Nature Communications Vladimir Gligorijević, P. Douglas Renfrew, Tomasz Kosciolek, Julia Koehler Leman, Daniel Berenberg, Tommi Vatanen, Chris Chandler, Bryn C. Taylor, Ian M. Fisk, Hera Vlamakis, Ramnik J. Xavier, Rob Knight, Kyunghyun Cho, Richard Bonneau
2020	The Classification of Enzymes by Deep Learning IEEE Access Zhiyu Tao, Benzhi Dong, Zhixia Teng, Yuming Zhao
2020	Communications in Computer and Information Science Kanchan Jha, Sriparna Saha, Matloob Khushi
2020	Advances in Experimental Medicine and Biology Louis Papageorgiou, Eleni Papakonstantinou, Constantinos Salis, Eleytheria Polychronidou, Marianna Hagidimitriou, Dimitris Maroulis, Elias Eliopoulos, Dimitrios Vlachakis
2020	Learning to Make Chemical Predictions: The Interplay of Feature Representation, Data, and Machine Learning Methods Chem Mojtaba Haghighatlari, Jie Li, Farnaz Heidar-Zadeh, Yuchen Liu, Xingyi Guan, Teresa Head-Gordon
2020	libmolgrid: Graphics Processing Unit Accelerated Molecular Gridding for Deep Learning Applications Journal of Chemical Information and Modeling Jocelyn Sunseri, David R. Koes
2020	Machine Learning in Enzyme Engineering ACS Catalysis Stanislav Mazurenko, Zbynek Prokop, Jiri Damborsky
2020	3D Deep Learning on Medical Images: A Review Sensors Satya P. Singh, Lipo Wang, Sukrit Gupta, Haveesh Goli, Parasuraman Padmanabhan, Balázs Gulyás
2020	Advances in Experimental Medicine and Biology Louis Papageorgiou, Dimitris Maroulis, George P. Chrousos, Elias Eliopoulos, Dimitrios Vlachakis
2020	Advances in Experimental Medicine and Biology Constantinos Salis, Louis Papageorgiou, Eleni Papakonstantinou, Marianna Hagidimitriou, Dimitrios Vlachakis
2020	Amalgamation of 3D structure and sequence information for protein–protein interaction prediction Scientific Reports Kanchan Jha, Sriparna Saha
2020	In silico design and automated learning to boost next-generation smart biomanufacturing Synthetic Biology Pablo Carbonell, Rosalind Le Feuvre, Eriko Takano, Nigel S Scrutton
2020	Lecture Notes in Computer Science Dimitrios Vlachakis
2020	Advances in Protein Chemistry and Structural Biology
2019	Prediction of Enzyme Function Based on Three Parallel Deep CNN and Amino Acid Mutation International Journal of Molecular Sciences Ruibo Gao, Mengmeng Wang, Jiaoyan Zhou, Yuhang Fu, Meng Liang, Dongliang Guo, Junlan Nie
2019	KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images Journal of Cheminformatics Isidro Cortés-Ciriano, Andreas Bender
2019	Deep learning for molecular design—a review of the state of the art Molecular Systems Design & Engineering Daniel C. Elton, Zois Boukouvalas, Mark D. Fuge, Peter W. Chung
2019	SNARE-CNN: a 2D convolutional neural network architecture to identify SNARE proteins from high-throughput sequencing data PeerJ Computer Science Nguyen Quoc Khanh Le, Van-Nui Nguyen
2019	Encodings and models for antimicrobial peptide classification for multi-resistant pathogens BioData Mining Sebastian Spänig, Dominik Heider
2019	Multiresolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography The Journal of Physical Chemistry Letters Shuai Liu, Jie Li, Kochise C. Bennett, Brad Ganoe, Tim Stauch, Martin Head-Gordon, Alexander Hexemer, Daniela Ushizima, Teresa Head-Gordon
2019	Alignment-Free Method to Predict Enzyme Classes and Subclasses International Journal of Molecular Sciences Riccardo Concu, M. Natália D. S. Cordeiro
2018	ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature BMC Bioinformatics Alperen Dalkiran, Ahmet Sureyya Rifaioglu, Maria Jesus Martin, Rengul Cetin-Atalay, Volkan Atalay, Tunca Doğan
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