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2020 – today
- 2024
[j16]Ke Chen
, Thomas Litfin, Jaswinder Singh, Jian Zhan, Yaoqi Zhou:
MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search. Genom. Proteom. Bioinform. 22(1) (2024)- 2023
- [j15]Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, Alex S. Holehouse, Daniel A. Griffith, Ryan J. Emenecker, Ashwini Patil, Ronesh Sharma, Tatsuhiko Tsunoda, Alok Sharma, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan:
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 51(W1): 62-69 (2023) - 2022
- [j14]Md. Solayman, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou, Jian Zhan:
Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives. Briefings Bioinform. 23(3) (2022) - [j13]Jaspreet Singh, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou:
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model. Bioinform. 38(7): 1888-1894 (2022) - [j12]Jaswinder Singh, Kuldip K. Paliwal, Thomas Litfin, Jaspreet Singh, Yaoqi Zhou:
Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling. Bioinform. 38(16): 3900-3910 (2022) - 2021
- [j11]Jaswinder Singh, Kuldip K. Paliwal, Tongchuan Zhang, Jaspreet Singh, Thomas Litfin, Yaoqi Zhou:
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning. Bioinform. 37(17): 2589-2600 (2021) - [j10]Jaspreet Singh, Thomas Litfin, Kuldip K. Paliwal, Jaswinder Singh, Anil Kumar Hanumanthappa, Yaoqi Zhou:
SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning. Bioinform. 37(20): 3464-3472 (2021) - [j9]Tongchuan Zhang, Jaswinder Singh, Thomas Litfin, Jian Zhan, Kuldip K. Paliwal, Yaoqi Zhou:
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis. Bioinform. 37(20): 3494-3500 (2021) - 2020
- [j8]Jack Hanson, Thomas Litfin, Kuldip K. Paliwal, Yaoqi Zhou:
Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning. Bioinform. 36(4): 1107-1113 (2020) - [j7]Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning. J. Comput. Biol. 27(5): 796-814 (2020) - [j6]Yufeng Cai, Xiongjun Li, Zhe Sun, Yutong Lu, Huiying Zhao, Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou, Yuedong Yang:
SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. J. Comput. Chem. 41(8): 745-750 (2020)
2010 – 2019
- 2019
- [j5]Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks. Bioinform. 35(14): 2403-2410 (2019) - [j4]Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou:
SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning. Genom. Proteom. Bioinform. 17(6): 645-656 (2019) - [j3]Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. J. Chem. Inf. Model. 59(2): 924-930 (2019) - 2018
- [j2]Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks. Bioinform. 34(23): 4039-4045 (2018) - 2017
- [j1]Thomas Litfin, Yaoqi Zhou, Yuedong Yang:
SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library. Bioinform. 33(8): 1238-1240 (2017)
Coauthor Index
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