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André Leier
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2020 – today
- 2023
- [j33]Jiung-Wen Chen
, Lisa Shrestha
The hitchhikers' guide to RNA sequencing and functional analysis. Briefings Bioinform. 24(1) (2023) - 2022
- [j32]Fuyi Li, Shuangyu Dong, André Leier, Meiya Han, Xudong Guo, Jing Xu, Xiaoyu Wang, Shirui Pan, Cangzhi Jia, Yang Zhang, Geoffrey I. Webb
Positive-unlabeled learning in bioinformatics and computational biology: a brief review. Briefings Bioinform. 23(1) (2022) - 2021
- [j31]Ruopeng Xie
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy. Briefings Bioinform. 22(3) (2021) - [j30]Jing Xu, Fuyi Li
Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides. Briefings Bioinform. 22(5) (2021) - [j29]Jinxiang Chen, Fuyi Li
BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data. Frontiers Big Data 4 (2021) - [j28]Jiawei Wang
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. Nucleic Acids Res. 49(Database-Issue): D651-D659 (2021) - 2020
- [j27]Zhen Chen
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. Briefings Bioinform. 21(3): 1047-1057 (2020) - [j26]Fuyi Li
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. Briefings Bioinform. 21(3): 1069-1079 (2020) - [j25]Shutao Mei, Fuyi Li
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. Briefings Bioinform. 21(4): 1119-1135 (2020) - [j24]Yanju Zhang, Sha Yu, Ruopeng Xie
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. Bioinform. 36(3): 704-712 (2020) - [j23]Fuyi Li
DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites. Bioinform. 36(4): 1057-1065 (2020) - [j22]Cangzhi Jia, Yue Bi, Jinxiang Chen, André Leier, Fuyi Li
PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs. Bioinform. 36(15): 4276-4282 (2020) - [j21]Abhigyan Nath
Improved cytokine-receptor interaction prediction by exploiting the negative sample space. BMC Bioinform. 21(1): 493 (2020) - [j20]Fuyi Li
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information. Genom. Proteom. Bioinform. 18(1): 52-64 (2020) - [j19]Zhen Chen
PROSPECT: A web server for predicting protein histidine phosphorylation sites. J. Bioinform. Comput. Biol. 18(4): 2050018:1-2050018:17 (2020) - [c8]Ying Xu, André Leier, Tatiana T. Marquez-Lago, Jue Xie, Antonio Jimeno-Yepes, James C. Whisstock, Campbell Wilson, Jiangning Song:
Prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learning. AMIA 2020 - [c7]Ying Xu, Campbell Wilson, André Leier, Tatiana T. Marquez-Lago, James C. Whisstock, Jiangning Song
PhosTransfer: A Deep Transfer Learning Framework for Kinase-Specific Phosphorylation Site Prediction in Hierarchy. PAKDD (2) 2020: 384-395
2010 – 2019
- 2019
- [j18]Jiawei Wang
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. Briefings Bioinform. 20(3): 931-951 (2019) - [j17]Fuyi Li
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. Briefings Bioinform. 20(6): 2150-2166 (2019) - [j16]Yanju Zhang, Ruopeng Xie
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework. Briefings Bioinform. 20(6): 2185-2199 (2019) - [j15]Zhen Chen
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. Briefings Bioinform. 20(6): 2267-2290 (2019) - [j14]Jiawei Wang
Bastion3: a two-layer ensemble predictor of type III secreted effectors. Bioinform. 35(12): 2017-2028 (2019) - [j13]Meng Zhang
MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters. Bioinform. 35(17): 2957-2965 (2019) - 2018
- [j12]Yi An, Jiawei Wang
Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI. Briefings Bioinform. 19(1): 148-161 (2018) - [j11]Jiangning Song
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. Bioinform. 34(4): 684-687 (2018) - [j10]Zhen Chen
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences. Bioinform. 34(14): 2499-2502 (2018) - [j9]Jiawei Wang
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. Bioinform. 34(15): 2546-2555 (2018) - [j8]Fuyi Li
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. Bioinform. 34(24): 4223-4231 (2018) - 2017
- [j7]Jiawei Wang
POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles. Bioinform. 33(17): 2756-2758 (2017) - 2014
- [j6]André Leier
Emergence in simulated evolution. Genet. Program. Evolvable Mach. 15(1): 79-81 (2014) - 2011
- [j5]Tatiana T. Marquez-Lago, André Leier
Stochastic adaptation and fold-change detection: from single-cell to population behavior. BMC Syst. Biol. 5: 22 (2011) - 2010
- [j4]Tatiana T. Marquez-Lago, André Leier
Probability distributed time delays: integrating spatial effects into temporal models. BMC Syst. Biol. 4: 19 (2010)
2000 – 2009
- 2007
- [j3]André Leier, P. Dwight Kuo, Wolfgang Banzhaf
Analysis of Preferential Network Motif Generation in an Artificial Regulatory Network Model Created by Duplication and Divergence. Adv. Complex Syst. 10(2): 155-172 (2007) - [j2]Kevin Burrage
Modelling and simulation techniques for membrane biology. Briefings Bioinform. 8(4): 234-244 (2007) - [c6]André Leier, Kevin Burrage, Pamela M. Burrage:
Stochastic Modelling and Simulation of Coupled Autoregulated Oscillators in a Multicellular Environment: The her1/her7 Genes. International Conference on Computational Science (1) 2007: 778-785 - 2006
- [j1]Manuel Barrio
Oscillatory Regulation of Hes1: Discrete Stochastic Delay Modelling and Simulation. PLoS Comput. Biol. 2(9) (2006) - [c5]André Leier
Evolving Noisy Oscillatory Dynamics in Genetic Regulatory Networks. EuroGP 2006: 290-299 - 2004
- [b1]André Leier:
Evolution of quantum algorithms using genetic programming. Dortmund University of Technology, 2004, pp. 1-190 - [c4]André Leier, Wolfgang Banzhaf:
Comparison of Selection Strategies for Evolutionary Quantum Circuit Design. GECCO (2) 2004: 557-568 - [c3]P. Dwight Kuo, André Leier, Wolfgang Banzhaf:
Evolving Dynamics in an Artificial Regulatory Network Model. PPSN 2004: 571-580 - 2003
- [c2]André Leier
Exploring the search space of quantum programs. IEEE Congress on Evolutionary Computation 2003: 170-177 - [c1]André Leier, Wolfgang Banzhaf:
Evolving Hogg's Quantum Algorithm Using Linear-Tree GP. GECCO 2003: 390-400
Coauthor Index
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