Positions

Selected Publications

Academic Article

Year Title Altmetric
2018 Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.Computer applications in the biosciences : CABIOS.  34:4223-4231. 2018
2018 Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.Computer applications in the biosciences : CABIOS.  34:2546-2555. 2018
2018 iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences.Computer applications in the biosciences : CABIOS.  34:2499-2502. 2018
2017 PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.Computer applications in the biosciences : CABIOS.  34:684-687. 2017
2017 POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.Computer applications in the biosciences : CABIOS.  33:2756-2758. 2017
2017 PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection.Scientific Reports.  7:6862. 2017
2017 Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites.Scientific Reports.  7:5755. 2017
2017 ESCRT-mediated vesicle concatenation in plant endosomes.Journal of Cell Biology.  216:2167-2177. 2017
2017 Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming.Applied Microbiology and Biotechnology.  101:2919-2929. 2017
2017 Exact Product Formation Rates for Stochastic Enzyme Kinetics.Journal of Physical Chemistry B.  121:13-23. 2017
2016 Receptor dimer stabilization by hierarchical plasma membrane microcompartments regulates cytokine signaling.Science Advances.  2:e1600452. 2016
2016 Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.Briefings in Bioinformatics.  19:148-161. 2016
2015 Delay chemical master equation: direct and closed-form solutions.Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences.  471:20150049. 2015
2015 The Spatial Chemical Langevin Equation and Reaction Diffusion Master Equations: moments and qualitative solutions.Theoretical Biology and Medical Modelling.  12:5. 2015
2014 Exact model reduction with delays: closed-form distributions and extensions to fully bi-directional monomolecular reactions.Interface.  11:20140108. 2014
2014 Emergence in simulated evolutionGenetic Programming and Evolvable Machines.  15:79-81. 2014
2013 Reduction of chemical reaction networks through delay distributions.Journal of Chemical Physics.  138:104114. 2013
2012 Anomalous diffusion and multifractional Brownian motion: simulating molecular crowding and physical obstacles in systems biology.Systems Biology.  6:134-142. 2012
2012 Integrative physical oncology.Wiley Interdisciplinary Reviews: Systems Biology and Medicine.  4:1-14. 2012
2011 Correction factors for boundary diffusion in reaction-diffusion master equations.Journal of Chemical Physics.  135:134109. 2011
2011 Stochastic adaptation and fold-change detection: from single-cell to population behavior.BMC Systems Biology.  5:22. 2011
2010 Probability distributed time delays: integrating spatial effects into temporal models.BMC Systems Biology.  4:19. 2010
2008 Generalized binomial tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise.Journal of Chemical Physics.  128:205107. 2008
2008 Modeling intrinsic noise and delays in chemical kinetics of coupled autoregulated oscillating cellsInternational Journal for Multiscale Computational Engineering.  6:77-86. 2008
2007 Modelling and simulation techniques for membrane biology.Briefings in Bioinformatics.  8:234-244. 2007
2007 ANALYSIS OF PREFERENTIAL NETWORK MOTIF GENERATION IN AN ARTIFICIAL REGULATORY NETWORK MODEL CREATED BY DUPLICATION AND DIVERGENCEAdvances in Complex Systems.  10:155-172. 2007
2007 ANALYSIS OF PREFERENTIAL NETWORK MOTIF GENERATION IN AN ARTIFICIAL REGULATORY NETWORK MODEL CREATED BY DUPLICATION AND DIVERGENCEAdvances in Complex Systems.  10:155-172. 2007
2007 Analysis of preferential network motif generation in an artificial regulatory network model created by duplication and divergenceAdvances in Complex Systems.  10:155-172. 2007
2006 Oscillatory regulation of Hes1: Discrete stochastic delay modelling and simulation.PLoS Computational Biology.  2:e117. 2006
2006 Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence.BioSystems.  85:177-200. 2006
2004 Evolving dynamics in an artificial regulatory network modelLecture Notes in Artificial Intelligence.  3242:571-580. 2004
2003 Evolving Hogg's quantum algorithm using linear-tree GPLecture Notes in Artificial Intelligence.  2723:390-400. 2003
2000 Cryptography with DNA binary strands.BioSystems.  57:13-22. 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

Principal Investigator On

Investigator On

Education And Training

  • Doctor of Philosophy in Mathematics and Computer Science, TU Dortmund University
  • Full Name

  • Andre Leier