André Leier

43 papers A 2B 2Misc 2Journal 34Unranked 2
YearRankTypeTitle / Venue / Authors
2023 J jnl
The hitchhikers' guide to RNA sequencing and functional analysis.
Briefings Bioinform.
Jiung-Wen Chen, Lisa Shrestha, George Green, André Leier, Tatiana T. Marquez-Lago
2022 J jnl
Positive-unlabeled learning in bioinformatics and computational biology: a brief review.
Briefings Bioinform.
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
2021 J jnl
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria.
Nucleic Acids Res.
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
2021 J jnl
BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data.
Frontiers Big Data
Jinxiang Chen, Fuyi Li, Miao Wang, Junlong Li, Tatiana T. Marquez-Lago, André Leier, Jerico Revote, Shuqin Li, Quanzhong Liu, Jiangning Song
2021 J jnl
Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides.
Briefings Bioinform.
Jing Xu, Fuyi Li, André Leier, Dongxu Xiang, Hsin-Hui Shen, Tatiana T. Marquez-Lago, Jian Li, Dong-Jun Yu, Jiangning Song
2021 J jnl
DeepBL: a deep learning-based approach for
Briefings Bioinform.
Yanan Wang, Fuyi Li, Manasa Bharathwaj, Natalia C. Rosas, André Leier, Tatsuya Akutsu, Geoffrey I. Webb, Tatiana T. Marquez-Lago, Jian Li, Trevor Lithgow, Jiangning Song
2021 J jnl
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy.
Briefings Bioinform.
Ruopeng Xie, Jiahui Li, Jiawei Wang, Wei Dai, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Trevor Lithgow, Jiangning Song, Yanju Zhang
2020 J jnl
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction.
Briefings Bioinform.
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
2020 J jnl
DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites.
Bioinform.
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
2020 J jnl
Improved cytokine-receptor interaction prediction by exploiting the negative sample space.
BMC Bioinform.
Abhigyan Nath, André Leier
2020 J jnl
PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs.
Bioinform.
Cangzhi Jia, Yue Bi, Jinxiang Chen, André Leier, Fuyi Li, Jiangning Song
2020 J jnl
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact.
Briefings Bioinform.
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
2020 J jnl
PROSPECT: A web server for predicting protein histidine phosphorylation sites.
J. Bioinform. Comput. Biol.
Zhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Geoffrey I. Webb, Abdelkader Baggag, Halima Bensmail, Jiangning Song
2020 J jnl
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins.
Bioinform.
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
2020 — conf
PhosTransfer: A Deep Transfer Learning Framework for Kinase-Specific Phosphorylation Site Prediction in Hierarchy.
PAKDD (2)
Ying Xu, Campbell Wilson, André Leier, Tatiana T. Marquez-Lago, James C. Whisstock, Jiangning Song
2020 Misc conf
Prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learning.
AMIA
Ying Xu, André Leier, Tatiana T. Marquez-Lago, Jue Xie, Antonio Jimeno-Yepes, James C. Whisstock, Campbell Wilson, Jiangning Song
2020 J jnl
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information.
Genom. Proteom. Bioinform.
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
2020 J jnl
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data.
Briefings Bioinform.
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
2019 J jnl
Bastion3: a two-layer ensemble predictor of type III secreted effectors.
Bioinform.
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
2019 J jnl
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework.
Briefings Bioinform.
Yanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Jiangning Song
2019 J jnl
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.
Briefings Bioinform.
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
2019 J jnl
MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters.
Bioinform.
Meng Zhang, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Cunshuo Fan, Chee Keong Kwoh, Kuo-Chen Chou, Jiangning Song, Cangzhi Jia
2019 J jnl
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.
Briefings Bioinform.
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
2019 J jnl
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.
Briefings Bioinform.
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
2018 J jnl
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.
Bioinform.
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
2018 J jnl
Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.
Briefings Bioinform.
Yi An, Jiawei Wang, Chen Li, André Leier, Tatiana T. Marquez-Lago, Jonathan Wilksch, Yang Zhang, Geoffrey I. Webb, Jiangning Song, Trevor Lithgow
2018 J jnl
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.
Bioinform.
Jiangning Song, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I. Webb, Robert N. Pike
2018 J jnl
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.
Bioinform.
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
2018 J jnl
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences.
Bioinform.
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
2017 J jnl
POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.
Bioinform.
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
2014 J jnl
Emergence in simulated evolution.
Genet. Program. Evolvable Mach.
André Leier
2011 J jnl
Stochastic adaptation and fold-change detection: from single-cell to population behavior.
BMC Syst. Biol.
Tatiana T. Marquez-Lago, André Leier
2010 J jnl
Probability distributed time delays: integrating spatial effects into temporal models.
BMC Syst. Biol.
Tatiana T. Marquez-Lago, André Leier, Kevin Burrage
2007 J jnl
Analysis of Preferential Network Motif Generation in an Artificial Regulatory Network Model Created by Duplication and Divergence.
Adv. Complex Syst.
André Leier, P. Dwight Kuo, Wolfgang Banzhaf
2007 J jnl
Modelling and simulation techniques for membrane biology.
Briefings Bioinform.
Kevin Burrage, John Hancock, André Leier, Dan V. Nicolau Jr.
2007 Misc conf
Stochastic Modelling and Simulation of Coupled Autoregulated Oscillators in a Multicellular Environment: The her1/her7 Genes.
International Conference on Computational Science (1)
André Leier, Kevin Burrage, Pamela M. Burrage
2006 B conf
Evolving Noisy Oscillatory Dynamics in Genetic Regulatory Networks.
EuroGP
André Leier, P. Dwight Kuo, Wolfgang Banzhaf, Kevin Burrage
2006 J jnl
Oscillatory Regulation of Hes1: Discrete Stochastic Delay Modelling and Simulation.
PLoS Comput. Biol.
Manuel Barrio, Kevin Burrage, André Leier, Tianhai Tian
2004 — conf
Comparison of Selection Strategies for Evolutionary Quantum Circuit Design.
GECCO (2)
André Leier, Wolfgang Banzhaf
2004 — —
Evolution of quantum algorithms using genetic programming.
André Leier
2004 A conf
Evolving Dynamics in an Artificial Regulatory Network Model.
PPSN
P. Dwight Kuo, André Leier, Wolfgang Banzhaf
2003 A conf
Evolving Hogg's Quantum Algorithm Using Linear-Tree GP.
GECCO
André Leier, Wolfgang Banzhaf
2003 B conf
Exploring the search space of quantum programs.
IEEE Congress on Evolutionary Computation
André Leier, Wolfgang Banzhaf