Probability distributed time delays: integrating spatial effects into temporal models. - Tatiana T. Marquez-Lago; André Leier; Kevin Burrage (BMC Syst. Biol., 2010)

Stochastic adaptation and fold-change detection: from single-cell to population behavior. - Tatiana T. Marquez-Lago; André Leier (BMC Syst. Biol., 2011)

The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed Mitosis. - Eder Zavala; Tatiana T. Marquez-Lago (PLoS Comput. Biol., 2014)

POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles. - Jiawei Wang 002; Bingjiao Yang; Jerico Nico De Leon Revote; André Leier; Tatiana T. Marquez-Lago; Geoffrey I. Webb; Jiangning Song; Kuo-Chen Chou; Trevor Lithgow (Bioinform., 2017)

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI. - Yi An; Jiawei Wang 002; Chen Li 021; André Leier; Tatiana T. Marquez-Lago; Jonathan Wilksch; Yang Zhang 010; Geoffrey I. Webb; Jiangning Song; Trevor Lithgow (Briefings Bioinform., 2018)

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences. - Zhen Chen 009; Pei Zhao; Fuyi Li; André Leier; Tatiana T. Marquez-Lago; Yanan Wang 003; Geoffrey I. Webb; Alexander Ian Smith; Roger J. Daly; Kuo-Chen Chou; Jiangning Song (Bioinform., 2018)

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. - Fuyi Li; Chen Li 021; Tatiana T. Marquez-Lago; André Leier; Tatsuya Akutsu; Anthony W. Purcell; Alexander Ian Smith; Trevor Lithgow; Roger J. Daly; Jiangning Song; Kuo-Chen Chou (Bioinform., 2018)

PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. - Jiangning Song; Fuyi Li; André Leier; Tatiana T. Marquez-Lago; Tatsuya Akutsu; Gholamreza Haffari; Kuo-Chen Chou; Geoffrey I. Webb; Robert N. Pike (Bioinform., 2018)

Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. - Jiawei Wang 002; 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 (Bioinform., 2018)

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. - Zhen Chen 009; Xuhan Liu; Fuyi Li; Chen Li 021; Tatiana T. Marquez-Lago; André Leier; Tatsuya Akutsu; Geoffrey I. Webb; Dakang Xu; Alexander Ian Smith; Lei Li 013; Kuo-Chen Chou; et al. (Briefings Bioinform., 2019)

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. - Fuyi Li; Yanan Wang 003; Chen Li 021; 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; et al. (Briefings Bioinform., 2019)

Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. - Jiawei Wang 002; Bingjiao Yang; Yi An; Tatiana T. Marquez-Lago; André Leier; Jonathan Wilksch; Qingyang Hong; Yang Zhang 010; Morihiro Hayashida; Tatsuya Akutsu; Geoffrey I. Webb; Richard A. Strugnell; et al. (Briefings Bioinform., 2019)

Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework. - Yanju Zhang; Ruopeng Xie; Jiawei Wang 002; André Leier; Tatiana T. Marquez-Lago; Tatsuya Akutsu; Geoffrey I. Webb; Kuo-Chen Chou; Jiangning Song (Briefings Bioinform., 2019)

Bastion3: a two-layer ensemble predictor of type III secreted effectors. - Jiawei Wang 002; Jiahui Li 007; Bingjiao Yang; Ruopeng Xie; Tatiana T. Marquez-Lago; André Leier; Morihiro Hayashida; Tatsuya Akutsu; Yanju Zhang; Kuo-Chen Chou; Joel Selkrig; Tieli Zhou; et al. (Bioinform., 2019)

MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters. - Meng Zhang 046; Fuyi Li; Tatiana T. Marquez-Lago; André Leier; Cunshuo Fan; Chee Keong Kwoh 001; Kuo-Chen Chou; Jiangning Song; Cangzhi Jia (Bioinform., 2019)

Prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learning. - Ying Xu; André Leier; Tatiana T. Marquez-Lago; Jue Xie; Antonio Jimeno-Yepes; James C. Whisstock; Campbell Wilson; Jiangning Song (AMIA, 2020)

PhosTransfer: A Deep Transfer Learning Framework for Kinase-Specific Phosphorylation Site Prediction in Hierarchy. - Ying Xu; Campbell Wilson; André Leier; Tatiana T. Marquez-Lago; James C. Whisstock; Jiangning Song (PAKDD (2), 2020)

iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. - Zhen Chen 009; Pei Zhao; Fuyi Li; Tatiana T. Marquez-Lago; André Leier; Jerico Nico De Leon Revote; Yan Zhu 006; David R. Powell; Tatsuya Akutsu; Geoffrey I. Webb; Kuo-Chen Chou; Alexander Ian Smith; et al. (Briefings Bioinform., 2020)

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. - Fuyi Li; Cunshuo Fan; Tatiana T. Marquez-Lago; André Leier; Jerico Nico De Leon Revote; Cangzhi Jia; Yan Zhu 006; Alexander Ian Smith; Geoffrey I. Webb; Quanzhong Liu; Leyi Wei; Jian Li 052; et al. (Briefings Bioinform., 2020)

A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. - Shutao Mei; Fuyi Li; André Leier; Tatiana T. Marquez-Lago; Kailin Giam; Nathan P. Croft; Tatsuya Akutsu; Alexander Ian Smith; Jian Li 052; Jamie Rossjohn; Anthony W. Purcell; Jiangning Song (Briefings Bioinform., 2020)

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites. - 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 (Bioinform., 2020)

PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. - Yanju Zhang; Sha Yu; Ruopeng Xie; Jiahui Li 007; André Leier; Tatiana T. Marquez-Lago; Tatsuya Akutsu; Alexander Ian Smith; Zongyuan Ge; Jiawei Wang 002; Trevor Lithgow; Jiangning Song (Bioinform., 2020)

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information. - Fuyi Li; André Leier; Quanzhong Liu; Yanan Wang 003; Dongxu Xiang; Tatsuya Akutsu; Geoffrey I. Webb; Alexander Ian Smith; Tatiana T. Marquez-Lago; Jian Li 052; Jiangning Song (Genom. Proteom. Bioinform., 2020)

PROSPECT: A web server for predicting protein histidine phosphorylation sites. - Zhen Chen 009; Pei Zhao; Fuyi Li; André Leier; Tatiana T. Marquez-Lago; Geoffrey I. Webb; Abdelkader Baggag; Halima Bensmail; Jiangning Song (J. Bioinform. Comput. Biol., 2020)

DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy. - Ruopeng Xie; Jiahui Li 007; Jiawei Wang 002; Wei Dai; André Leier; Tatiana T. Marquez-Lago; Tatsuya Akutsu; Trevor Lithgow; Jiangning Song; Yanju Zhang (Briefings Bioinform., 2021)

Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides. - Jing Xu 008; Fuyi Li; André Leier; Dongxu Xiang; Hsin-Hui Shen; Tatiana T. Marquez-Lago; Jian Li 052; Dong-Jun Yu; Jiangning Song (Briefings Bioinform., 2021)

BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data. - Jinxiang Chen; Fuyi Li; Miao Wang; Junlong Li; Tatiana T. Marquez-Lago; André Leier; Jerico Revote; Shuqin Li; Quanzhong Liu; Jiangning Song (Frontiers Big Data, 2021)

BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. - Jiawei Wang 002; Jiahui Li 007; Yi Hou; Wei Dai; Ruopeng Xie; Tatiana T. Marquez-Lago; André Leier; Tieli Zhou; Von Torres; Iain Hay; Christopher Stubenrauch; Yanju Zhang; et al. (Nucleic Acids Res., 2021)

The hitchhikers' guide to RNA sequencing and functional analysis. - Jiung-Wen Chen; Lisa Shrestha; George Green; André Leier; Tatiana T. Marquez-Lago (Briefings Bioinform., 2023)