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ORCIDAndré Leier
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Books and Theses
- 2004
[b1]André Leier:
Evolution of quantum algorithms using genetic programming. Dortmund University of Technology, 2004, pp. 1-190
Journal Articles
- 2023
- [j33]Jiung-Wen Chen
, Lisa Shrestha, George Green, André Leier, Tatiana T. Marquez-Lago:
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, Lachlan J. M. Coin, Chen Li, Jiangning Song:
Positive-unlabeled learning in bioinformatics and computational biology: a brief review. Briefings Bioinform. 23(1) (2022) - 2021
- [j31]Ruopeng Xie, Jiahui Li, Jiawei Wang, Wei Dai, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Trevor Lithgow, Jiangning Song, Yanju Zhang:
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, André Leier, Dongxu Xiang, Hsin-Hui Shen, Tatiana T. Marquez-Lago, Jian Li, Dong-Jun Yu, Jiangning Song:
Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides. Briefings Bioinform. 22(5) (2021) - [j29]Jinxiang Chen, Fuyi Li, Miao Wang, Junlong Li, Tatiana T. Marquez-Lago, André Leier, Jerico Revote, Shuqin Li, Quanzhong Liu, Jiangning Song:
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, Jiahui Li, Yi Hou, Wei Dai, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Tieli Zhou, Von Torres, Iain Hay, Christopher Stubenrauch, Yanju Zhang, Jiangning Song, Trevor Lithgow:
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, Pei Zhao, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Yan Zhu, David R. Powell, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Alexander Ian Smith, Roger J. Daly, Jian Li, Jiangning Song:
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, Cunshuo Fan, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Cangzhi Jia, Yan Zhu, Alexander Ian Smith, Geoffrey I. Webb, Quanzhong Liu, Leyi Wei, Jian Li, Jiangning Song:
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, André Leier, Tatiana T. Marquez-Lago, Kailin Giam, Nathan P. Croft, Tatsuya Akutsu, Alexander Ian Smith, Jian Li, Jamie Rossjohn, Anthony W. Purcell, Jiangning Song:
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, Jiahui Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Alexander Ian Smith, Zongyuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song:
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. Bioinform. 36(3): 704-712 (2020) - [j23]Fuyi Li, Jinxiang Chen, André Leier, Tatiana T. Marquez-Lago, Quanzhong Liu, Yanze Wang, Jerico Nico De Leon Revote, Alexander Ian Smith, Tatsuya Akutsu, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song:
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, Jiangning Song:
PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs. Bioinform. 36(15): 4276-4282 (2020) - [j21]Abhigyan Nath, André Leier:
Improved cytokine-receptor interaction prediction by exploiting the negative sample space. BMC Bioinform. 21(1): 493 (2020) - [j20]Fuyi Li, André Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, Alexander Ian Smith, Tatiana T. Marquez-Lago, Jian Li, Jiangning Song:
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information. Genom. Proteom. Bioinform. 18(1): 52-64 (2020) - [j19]Zhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Geoffrey I. Webb, Abdelkader Baggag, Halima Bensmail, Jiangning Song:
PROSPECT: A web server for predicting protein histidine phosphorylation sites. J. Bioinform. Comput. Biol. 18(4): 2050018:1-2050018:17 (2020) - 2019
- [j18]Jiawei Wang, Bingjiao Yang, Yi An, Tatiana T. Marquez-Lago, André Leier, Jonathan Wilksch, Qingyang Hong, Yang Zhang, Morihiro Hayashida, Tatsuya Akutsu, Geoffrey I. Webb, Richard A. Strugnell, Jiangning Song, Trevor Lithgow:
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. Briefings Bioinform. 20(3): 931-951 (2019) - [j17]Fuyi Li, Yanan Wang, Chen Li, Tatiana T. Marquez-Lago, André Leier, Neil D. Rawlings, Gholamreza Haffari, Jerico Nico De Leon Revote, Tatsuya Akutsu, Kuo-Chen Chou, Anthony W. Purcell, Robert N. Pike, Geoffrey I. Webb, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, James C. Whisstock, Jiangning Song:
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, Jiawei Wang, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Jiangning Song:
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, Xuhan Liu, Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Geoffrey I. Webb, Dakang Xu, Alexander Ian Smith, Lei Li, Kuo-Chen Chou, Jiangning Song:
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. Briefings Bioinform. 20(6): 2267-2290 (2019) - [j14]Jiawei Wang, Jiahui Li, Bingjiao Yang, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Morihiro Hayashida, Tatsuya Akutsu, Yanju Zhang, Kuo-Chen Chou, Joel Selkrig, Tieli Zhou, Jiangning Song, Trevor Lithgow:
Bastion3: a two-layer ensemble predictor of type III secreted effectors. Bioinform. 35(12): 2017-2028 (2019) - [j13]Meng Zhang, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Cunshuo Fan, Chee Keong Kwoh, Kuo-Chen Chou, Jiangning Song, Cangzhi Jia:
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, Chen Li, André Leier, Tatiana T. Marquez-Lago, Jonathan Wilksch, Yang Zhang, Geoffrey I. Webb, Jiangning Song, Trevor Lithgow:
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, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I. Webb, Robert N. Pike:
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. Bioinform. 34(4): 684-687 (2018) - [j10]Zhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Yanan Wang, Geoffrey I. Webb, Alexander Ian Smith, Roger J. Daly, Kuo-Chen Chou, Jiangning Song:
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, Bingjiao Yang, André Leier, Tatiana T. Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Yanju Zhang, Tatsuya Akutsu, Kuo-Chen Chou, Richard A. Strugnell, Jiangning Song, Trevor Lithgow:
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. Bioinform. 34(15): 2546-2555 (2018) - [j8]Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Anthony W. Purcell, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, Jiangning Song, Kuo-Chen Chou:
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, Bingjiao Yang, Jerico Nico De Leon Revote, André Leier, Tatiana T. Marquez-Lago, Geoffrey I. Webb, Jiangning Song, Kuo-Chen Chou, Trevor Lithgow:
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, Kevin Burrage:
Probability distributed time delays: integrating spatial effects into temporal models. BMC Syst. Biol. 4: 19 (2010) - 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, John Hancock, André Leier, Dan V. Nicolau Jr.:
Modelling and simulation techniques for membrane biology. Briefings Bioinform. 8(4): 234-244 (2007) - 2006
- [j1]Manuel Barrio, Kevin Burrage, André Leier, Tianhai Tian:
Oscillatory Regulation of Hes1: Discrete Stochastic Delay Modelling and Simulation. PLoS Comput. Biol. 2(9) (2006)
Conference and Workshop Papers
- 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 - 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
- [c5]André Leier, P. Dwight Kuo, Wolfgang Banzhaf, Kevin Burrage:
Evolving Noisy Oscillatory Dynamics in Genetic Regulatory Networks. EuroGP 2006: 290-299 - 2004
- [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, Wolfgang Banzhaf:
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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