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Yuji Takiguchi, Daisuke Nakane, Takashiro Akitsu

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

Gregor Wirnsberger, Iva Pritišanac, Gustav Oberdorfer, Karl Gruber

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

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

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

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

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

Pedro Sousa Sampaio, Pedro Fernandes

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

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

Arnold Kazadi, Ming Zhang, Jingbo Zhou

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

Hehe Fan, Linchao Zhu, Yi Yang, Mohan Kankanhalli

Ana Marta Sequeira, Ivan Gomes, Miguel Rocha

Dmitrij Rappoport, Adrian Jinich

Saurabh Agrawal, Dilip Singh Sisodia, Naresh Kumar Nagwani

Ana Marta Sequeira, Miguel Rocha

Marcel Wittmund, Frederic Cadet, Mehdi D. Davari

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

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

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

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

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

Jintae Kim, Sera Park, Dongbo Min, Wankyu Kim

H. Erdinç KOCER, Kerim Kürşat ÇEVİK

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

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

Stanislav Mazurenko, Zbynek Prokop, Jiri Damborsky

Jocelyn Sunseri, David R. Koes

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

Kanchan Jha, Sriparna Saha, Matloob Khushi

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

Sergi Roda, Gerard Santiago, Victor Guallar

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

Zhiyu Tao, Benzhi Dong, Zhixia Teng, Yuming Zhao

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

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

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

Sebastian Spänig, Dominik Heider

Nguyen Quoc Khanh Le, Van-Nui Nguyen

Riccardo Concu, M. Natália D. S. Cordeiro

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

Isidro Cortés-Ciriano, Andreas Bender

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

2024	The prediction of single-molecule magnet properties via deep learning IUCrJ Yuji Takiguchi, Daisuke Nakane, Takashiro Akitsu
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	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	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	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
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	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
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	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	Advanced Pharmacy Lucrecia L. Chaillou, Valeria Boeris, Darío Spelzini, Mónica A. Nazareno
2023	2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Arnold Kazadi, Ming Zhang, Jingbo Zhou
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/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Hehe Fan, Linchao Zhu, Yi Yang, Mohan Kankanhalli
2023	2023 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) Ana Marta Sequeira, Ivan Gomes, Miguel Rocha
2023	Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves Journal of Chemical Information and Modeling Dmitrij Rappoport, Adrian Jinich
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	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	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	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	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	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	Comprehensive Survey of Recent Drug Discovery Using Deep Learning International Journal of Molecular Sciences Jintae Kim, Sera Park, Dongbo Min, Wankyu Kim
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	Deep neural networks based wrist print region segmentation and classification MANAS Journal of Engineering H. Erdinç KOCER, Kerim Kürşat ÇEVİK
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	Lecture Notes in Computer Science Dimitrios Vlachakis
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	Machine Learning in Enzyme Engineering ACS Catalysis Stanislav Mazurenko, Zbynek Prokop, Jiri Damborsky
2020	libmolgrid: Graphics Processing Unit Accelerated Molecular Gridding for Deep Learning Applications Journal of Chemical Information and Modeling Jocelyn Sunseri, David R. Koes
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	Communications in Computer and Information Science Kanchan Jha, Sriparna Saha, Matloob Khushi
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 Protein Chemistry and Structural Biology Sergi Roda, Gerard Santiago, Victor Guallar
2020	Advances in Experimental Medicine and Biology Louis Papageorgiou, Eleni Papakonstantinou, Constantinos Salis, Eleytheria Polychronidou, Marianna Hagidimitriou, Dimitris Maroulis, Elias Eliopoulos, Dimitrios Vlachakis
2020	The Classification of Enzymes by Deep Learning IEEE Access Zhiyu Tao, Benzhi Dong, Zhixia Teng, Yuming Zhao
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
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	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	Encodings and models for antimicrobial peptide classification for multi-resistant pathogens BioData Mining Sebastian Spänig, Dominik Heider
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	Alignment-Free Method to Predict Enzyme Classes and Subclasses International Journal of Molecular Sciences Riccardo Concu, M. Natália D. S. Cordeiro
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	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
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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