Publications

Journal(*equal contribution)

J Lam*, Y Li*, L Zhu, R Umarov, H Jiang, A Heliou, F Sheong, T Liu, Y Long, Y Li, L Fang, R Altman, W Chen, X Huang, X Gao. A deep learning framework to predict binding preference of RNA constituents on protein surface. Nature Communications, 2019 [KAUST News] [Chinese introduction] [PDF] [Code] [Server]
G Jia, Y Li, H Zhang, I Chattopadhyay, A Jensen, D Blair, L Davis, P Robinson, T Dahlén, S Brunak, M Benson, G Edgren, N Cox, X Gao, A Rzhetsky. Estimating heritability and genetic correlations from large health datasets in the absence of genetic data. Nature Communications, 2019 [PDF]
J Lei, G Sheng, P Cheung, S Wang, Y Li, X Gao, Y Zhang, Y Wang, X Huang, Two symmetric Arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage, Proceedings of the National Academy of Sciences of the United States of America (PNAS), 2019
Y Li*, S Wang*, C Bi, Z Qiu, M Li, X Gao, DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing, Bioinformatics, accepted
Y Li, T Zhang, S Sun, X Gao, Accelerating Flash Calculation through Deep Learning Methods, Journal of Computational Physics, 2019, [PDF]
Y Li, C Huang, L Ding, Z Li, Y Pan, X Gao, Deep learning in bioinformatics: introduction, application, and perspective in big data era, Methods, 2019 [PDF][Code]
Z Zou, S Tian, X Gao, Y Li, mlDEEPre: Multi-functional enzyme function prediction with hierarchical multi-label deep learning, Frontiers in Genetics, 2019 [PDF][Server]
R Umarov, H Kuwahara, Y Li, X Gao, V Solovyev, Promoter analysis and prediction in the human genome using sequence-based deep learning models, Bioinformatics, 2019 [PDF][Server]
U Hameed, C Liao, A Radhakrishnan, F Huser, S Aljedani, X Zhao, A Momin, F Melo, X Guo, C Brooks, Y Li, X Cui, X Gao, J Ladury, L Jaremko, M Jaremko, J Li, S, Arold, H-NS uses an autoinhibitory conformational switch to achieve environment-controlled gene silencing, Nucleic Acids Research (NAR), 2018
Z Xia, Y Li, B Zhang, Z Li, Y Hu, W Chen, X Gao, DeeReCT-PolyA: a robust and generic deep learning method for PAS identification, Bioinformatics, 2018 [PDF][Code]
Y Li, R Han, C Bi, M Li, S Wang, X Gao, DeepSimulator: a deep simulator for nanopore sequencing, Bioinformatics, 2018 [PDF][Code]
Y Li, F Xu, F Zhang, P Xu, M Fan, L Li, X Gao, R Han, DLBI: Deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy, Bioinformatics, 2018 [PDF][Code]
S Wang, S Fei, Z Wang, Y Li, J Xu, F Zhao, X Gao, PredMP: a web server for de novo prediction and visualization of membrane proteins, Bioinformatics, 2018 [PDF][Server]
R Han, Y Li, X Gao, S Wang, An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing, Bioinformatics, 2018 [PDF][Code]
V Kordopati, A Salhi, R Razali, A Radovanovic, F Tifratene, M Uludag, Y Li, A Bokhari, A AlSaieedi, A Raies, C Neste, M Essack, V Bajic, DES-Mutation: System for Exploring Links of Mutations and Diseases, Scientific Reports, 2018 [PDF][Server]
R Han, X Wan, L Li, A Lawrence, P Yang, Y Li, S Wang, F Sun, Z Liu, X Gao, F Zhang, AuTom-dualx: a toolkit for fully automatic ﬁducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction, Bioinformatics, 2018
Y Li, S Wang, R Umarov, B Xie, M Fan, L Li, X Gao, DEEPre: sequence-based enzyme EC number prediction by deep learning, Bioinformatics, 2017 [PDF][Server]
H Dai, R Umarov, H Kuwahara, Y Li, L Song, X Gao, Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape, Bioinformatics, 2017 [PDF][Server]
S Wu, D Wang, J Liu, Y Feng, J Weng, Y Li, X Gao, J Liu, W Wang. The dynamic multisite interactions between two intrinsically disordered proteins, Angewandte Chemie, 2017
X Li, Q Tao, Y Fang, C Cheng, Y Hao, J Qi, Y Li, W Zhang, Y Wang, X Zhang. Reward sensitivity predicts ice cream-related attentional bias assessed by inattentional blindness, Appetite, 2015

Conference(*equal contribution)

X Chen*, Y Li*, R Umarov, X Gao, L Song, RNA Secondary Structure Prediction By Learning Unrolled Algorithms, Eighth International Conference on Learning Representations (ICLR-2020), Oral (Accpetance rate=48/2594=1.85%)
L Ding, M Yu, L Liu, F Zhu, Y Liu, Y Li, L Shao, Two Generator Game: Learning to Sample via Linear Goodness-of-Fit Test, Thirty-third Conference on Neural Information Processing Systems (NeurIPS-19)
L Ding, Z Liu, Y Li, S Liao, Y Liu, P Yang, G Yu, L Shao, X Gao, Linear Kernel Tests via Empirical Likelihood for High Dimensional Data, The Thirty-Third AAAI Conference on Artificial Intelligence (AAAI-19)
L Ding, S Liao, Y Liu, Y Li, P Yang, Y Pan, C Huang, L Shao, X Gao, Approximate Kernel Selection with Strong Approximate Consistency, The Thirty-Third AAAI Conference on Artificial Intelligence (AAAI-19)
Y Li*, F Xu*, F Zhang, P Xu, M Fan, L Li, X Gao, R Han, DLBI: Deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy, The Twenty-Sixth Conference on Intelligent Systems for Molecular Biology (ISMB-18)
R Han, Y Li, X Gao, S Wang, An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing, The Seventeenth European Conference on Computational Biology (ECCB-18)

Preprint or under review(*equal contribution)

H Li*, S Tian*, Y Li*, R Tan, Y Pan, C Huang, Y Xu, and X Gao, Modern Deep Learning in Bioinformatics, under review
Y Li, Z Li, L Ding, Y Hu, W Chen, X Gao, SupportNet: solving catastrophic forgetting in class incremental learning with support data, arxiv.org/abs/1806.02942
Y Li, L Ding, X Gao, On the decision boundary of deep neural networks, arxiv.org/abs/1808.05385
Y Li, H Kuwahara, P Yang, L Song, X Gao, PGCN: Disease gene prioritization by disease and gene embedding through graph convolutional neural networks, bioRxiv 532226

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