CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction X Cui, Z Lu, S Wang, J Jing-Yan Wang, X Gao Bioinformatics 32 (12), i332-i340, 2016 | 58 | 2016 |
DNN-DTIs: Improved drug-target interactions prediction using XGBoost feature selection and deep neural network C Chen, H Shi, Z Jiang, A Salhi, R Chen, X Cui, B Yu Computers in Biology and Medicine 136, 104676, 2021 | 57 | 2021 |
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind H Kuwahara, M Alazmi, X Cui, X Gao Nucleic acids research 44 (W1), W217-W225, 2016 | 57 | 2016 |
SHREC 2020: Classification in cryo-electron tomograms I Gubins, ML Chaillet, G van Der Schot, RC Veltkamp, F Förster, Y Hao, ... Computers & Graphics 91, 279-289, 2020 | 54 | 2020 |
Homology search for genes X Cui, T Vinař, B Brejová, D Shasha, M Li Bioinformatics 23 (13), i97-i103, 2007 | 25 | 2007 |
A Flexible Domain-Domain Hinge Promotes an Induced-fit Dominant Mechanism for the Loading of Guide-DNA into Argonaute Protein in Thermus thermophilus L Zhu, H Jiang, FK Sheong, X Cui, X Gao, Y Wang, X Huang The Journal of Physical Chemistry B 120 (10), 2709-2720, 2016 | 22 | 2016 |
Ontology-aware deep learning enables ultrafast and interpretable source tracking among sub-million microbial community samples from hundreds of niches Y Zha, H Chong, H Qiu, K Kang, Y Dun, Z Chen, X Cui, K Ning Genome medicine 14 (1), 43, 2022 | 17 | 2022 |
Finding optimal interaction interface alignments between biological complexes X Cui, H Naveed, X Gao Bioinformatics 31 (12), i133-i141, 2015 | 15 | 2015 |
Fingerprinting protein structures effectively and efficiently X Cui, SC Li, L He, M Li Bioinformatics 30 (7), 949-955, 2014 | 15 | 2014 |
Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes L Zhu, H Jiang, FK Sheong, X Cui, Y Wang, X Gao, X Huang Progress in biophysics and molecular biology 128, 39-46, 2017 | 13 | 2017 |
VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms Y Hao, X Wan, R Yan, Z Liu, J Li, S Zhang, X Cui, F Zhang Computer Methods and Programs in Biomedicine 221, 106871, 2022 | 11 | 2022 |
Coatgin: Marrying convolution and attention for graph-based molecule property prediction X Zhang, C Chen, Z Meng, Z Yang, H Jiang, X Cui 2022 IEEE international conference on bioinformatics and biomedicine (BIBM …, 2022 | 9 | 2022 |
Structure-based protein-drug affinity prediction with spatial attention mechanisms Y Wang, Z Qiu, Q Jiao, C Chen, Z Meng, X Cui 2021 IEEE international conference on bioinformatics and biomedicine (BIBM …, 2021 | 9 | 2021 |
rzMLP-DTA: gMLP network with ReZero for sequence-based drug-target affinity prediction Z Qiu, Q Jiao, Y Wang, C Chen, D Zhu, X Cui 2021 IEEE international conference on bioinformatics and biomedicine (BIBM …, 2021 | 8 | 2021 |
Edge-gated graph neural network for predicting protein-ligand binding affinities Q Jiao, Z Qiu, Y Wang, C Chen, Z Yang, X Cui 2021 IEEE international conference on bioinformatics and biomedicine (BIBM …, 2021 | 8 | 2021 |
SBOLme: a repository of SBOL parts for metabolic engineering H Kuwahara, X Cui, R Umarov, R Grunberg, CJ Myers, X Gao ACS Synthetic Biology 6 (4), 732-736, 2017 | 8 | 2017 |
Towards reliable automatic protein structure alignment X Cui, SC Li, D Bu, M Li Proceedings of the 13th International Workshop on Algorithms in …, 2013 | 7 | 2013 |
SVLR: genome structural variant detection using Long-read sequencing data W Gu, A Zhou, L Wang, S Sun, X Cui, D Zhu Journal of Computational Biology 28 (8), 774-788, 2021 | 6 | 2021 |
Learning protein structural fingerprints under the label-free supervision of domain knowledge Y Min, S Liu, C Lou, X Cui 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …, 2018 | 6 | 2018 |
Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles? X Cui, SC Li, D Bu, B Alipanahi, M Li Algorithms for Molecular Biology 8, 1-13, 2013 | 6 | 2013 |