Positions

Selected Publications

Academic Article

Year Title Altmetric
2019 MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters 2019
2019 PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. 2019
2019 A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. 2019
2019 PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. 2019
2019 Bastion3: A two-layer ensemble predictor of type III secreted effectors 2019
2019 iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. 2019
2018 Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. 2018
2018 Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. 2018
2018 Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework. 2018
2018 PROSPERous: High-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy 2018
2018 Bastion6: A bioinformatics approach for accurate prediction of type VI secreted effectors 2018
2018 Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI 2018
2018 IFeature: A Python package and web server for features extraction and selection from protein and peptide sequences 2018
2018 Quokka: A comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome 2018
2017 Knowledge-Transfer learning for prediction of matrix metalloprotease substrate-cleavage sites 2017
2017 PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection 2017
2017 Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches 2017
2017 ESC RT-mediated vesicle concatenation in plant endosomes 2017
2017 Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming 2017
2017 Exact product formation rates for stochastic enzyme kinetics 2017
2017 POSSUM: A bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles 2017
2016 Receptor dimer stabilization By hierarchical plasma membrane microcompartments regulates cytokine signaling 2016
2015 Delay chemical master equation: Direct and closed-form solutions 2015
2015 The Spatial Chemical Langevin Equation and Reaction Diffusion Master Equations: Moments and qualitative solutions 2015
2014 Exact model reduction with delays: Closed-form distributions and extensions to fully bi-directional monomolecular reactions 2014
2014 Emergence in simulated evolution 2014
2013 Reduction of chemical reaction networks through delay distributions 2013
2012 Anomalous diffusion and multifractional Brownian motion: Simulating molecular crowding and physical obstacles in systems biology 2012
2012 Integrative physical oncology 2012
2011 Correction factors for boundary diffusion in reaction-diffusion master equations 2011
2011 Stochastic adaptation and fold-change detection: From single-cell to population behavior 2011
2010 Probability distributed time delays: Integrating spatial effects into temporal models 2010
2008 Generalized binomial τ-leap method for biochemical kinetics incorporating both delay and intrinsic noise 2008
2008 Modeling intrinsic noise and delays in chemical kinetics of coupled autoregulated oscillating cells 2008
2007 Modelling and simulation techniques for membrane biology 2007
2007 ANALYSIS OF PREFERENTIAL NETWORK MOTIF GENERATION IN AN ARTIFICIAL REGULATORY NETWORK MODEL CREATED BY DUPLICATION AND DIVERGENCE 2007
2007 ANALYSIS OF PREFERENTIAL NETWORK MOTIF GENERATION IN AN ARTIFICIAL REGULATORY NETWORK MODEL CREATED BY DUPLICATION AND DIVERGENCE 2007
2007 Analysis of preferential network motif generation in an artificial regulatory network model created by duplication and divergence 2007
2006 Oscillatory regulation of hes1: Discrete stochastic delay modelling and simulation 2006
2006 Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence 2006
2004 Evolving dynamics in an artificial regulatory network model 2004
2003 Evolving Hogg's quantum algorithm using linear-tree GP 2003
2000 Cryptography with DNA binary strands 2000

Chapter

Year Title Altmetric
2017 A review of stochastic and delay simulation approaches in both time and space in computational cell biology.  241-261. 2017
2009 Computational approaches for modeling intrinsic noise and delays in genetic regulatory networks.  169-197. 2009
2004 Comparison of selection strategies for evolutionary quantum circuit design.  557-568. 2004

Full Name

  • Andre Leier