Selected Publications

Academic Article

Year Title Altmetric
2023 The hitchhikers' guide to RNA sequencing and functional analysis.Briefings in Bioinformatics2023
2022 Targeted exon skipping of NF1 exon 17 as a therapeutic for neurofibromatosis type I 2022
2022 BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing DataFrontiers in Big Data.  4. 2022
2022 Positive-unlabeled learning in bioinformatics and computational biology: A brief reviewBriefings in Bioinformatics.  23. 2022
2022 Systematic Characterization of Lysine Post-translational Modification Sites Using MUscADELMethods in Molecular Biology.  2499:205-219. 2022
2021 Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptidesBriefings in Bioinformatics.  22. 2021
2021 DeepBL: A deep learning-based approach for in silico discovery of beta-lactamasesBriefings in Bioinformatics.  22. 2021
2021 DeepVF: A deep learning-based hybrid framework for identifying virulence factors using the stacking strategyBriefings in Bioinformatics.  22. 2021
2021 BastionHub: A universal platform for integrating and analyzing substrates secreted by Gram-negative bacteriaNucleic Acids Research.  49:D651-D659. 2021
2020 Improved cytokine–receptor interaction prediction by exploiting the negative sample spaceBMC Bioinformatics.  21. 2020
2020 PASSION: An ensemble neural network approach for identifying the binding sites of RBPs on circRNAsBioinformatics.  36:4276-4282. 2020
2020 PROSPECT: A web server for predicting protein histidine phosphorylation sitesJournal of Bioinformatics and Computational Biology.  18. 2020
2020 Regulating the regulators: role of phosphorylation in modulating the function of the GBF1/BIG family of Sec7 ARF-GEFsFEBS Letters.  594:2213-2226. 2020
2020 Mutation-Directed Therapeutics for Neurofibromatosis Type I 2020
2020 ILearn: An integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence dataBriefings in Bioinformatics.  21:1047-1057. 2020
2020 PRISMOID: A comprehensive 3D structure database for post-translational modifications and mutations with functional impactBriefings in Bioinformatics.  21:1069-1079. 2020
2020 DeepCleave: A deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sitesBioinformatics.  36:1057-1065. 2020
2020 PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteinsBioinformatics.  36:704-712. 2020
2020 Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information 2020
2020 Prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learningProceedings / AMIA ... Annual Symposium. AMIA Symposium.  2020:1325-1334. 2020
2019 Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning frameworkBriefings in Bioinformatics.  20:2185-2199. 2019
2019 Large-scale comparative assessment of computational predictors for lysine post-translational modification sitesBriefings in Bioinformatics.  20:2267-2290. 2019
2019 Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: A comprehensive revisit and benchmarking of existing methodsBriefings in Bioinformatics.  20:2150-2166. 2019
2019 MULTiPly: A novel multi-layer predictor for discovering general and specific types of promotersBioinformatics.  35:2957-2965. 2019
2019 A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding predictionBriefings in Bioinformatics.  21:1119-1135. 2019
2019 Bastion3: A two-layer ensemble predictor of type III secreted effectorsBioinformatics.  35:2017-2028. 2019
2018 Quokka: A comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteomeBioinformatics.  34:4223-4231. 2018
2018 Bastion6: A bioinformatics approach for accurate prediction of type VI secreted effectorsBioinformatics.  34:2546-2555. 2018
2018 IFeature: A Python package and web server for features extraction and selection from protein and peptide sequencesBioinformatics.  34:2499-2502. 2018
2018 PROSPERous: High-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracyBioinformatics.  34:684-687. 2018
2018 Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VIBriefings in Bioinformatics.  19:148-161. 2018
2017 Knowledge-Transfer learning for prediction of matrix metalloprotease substrate-cleavage sitesScientific Reports.  7. 2017
2017 PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selectionScientific Reports.  7. 2017
2017 Systematic analysis and prediction of type IV secreted effector proteins by machine learning approachesBriefings in Bioinformatics.  20:931-951. 2017
2017 POSSUM: A bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profilesBioinformatics.  33:2756-2758. 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 degummingApplied Microbiology and Biotechnology.  101:2919-2929. 2017
2017 Exact product formation rates for stochastic enzyme kinetics 2017
2016 Receptor dimer stabilization By hierarchical plasma membrane microcompartments regulates cytokine signalingScience Advances.  2. 2016
2015 Delay chemical master equation: Direct and closed-form solutionsProceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences.  471. 2015
2015 The Spatial Chemical Langevin Equation and Reaction Diffusion Master Equations: Moments and qualitative solutionsTheoretical Biology and Medical Modelling.  12. 2015
2014 Exact model reduction with delays: Closed-form distributions and extensions to fully bi-directional monomolecular reactions 2014
2014 Emergence in simulated evolutionGenetic Programming and Evolvable Machines.  15:79-81. 2014
2013 Reduction of chemical reaction networks through delay distributionsJournal of Chemical Physics.  138. 2013
2012 Anomalous diffusion and multifractional Brownian motion: Simulating molecular crowding and physical obstacles in systems biologyIET Systems Biology.  6:134-142. 2012
2012 Integrative physical oncologyWiley Interdisciplinary Reviews: Systems Biology and Medicine.  4:1-14. 2012
2011 Correction factors for boundary diffusion in reaction-diffusion master equationsJournal of Chemical Physics.  135. 2011
2011 Stochastic adaptation and fold-change detection: From single-cell to population behaviorBMC Systems Biology.  5. 2011
2010 Probability distributed time delays: Integrating spatial effects into temporal modelsBMC Systems Biology.  4. 2010
2008 Generalized binomial τ-leap method for biochemical kinetics incorporating both delay and intrinsic noiseJournal of Chemical Physics.  128. 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 biologyBriefings in Bioinformatics.  8:234-244. 2007
2007 Analysis of preferential network motif generation in an artificial regulatory network model created by duplication and divergence 2007
2006 Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergenceBiosystems.  85:177-200. 2006
2006 Oscillatory regulation of hes1: Discrete stochastic delay modelling and simulationPLoS Computational Biology.  2:1017-1030. 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 strandsBiosystems.  57:13-22. 2000


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

Education And Training

  • Doctor of Philosophy in Mathematics and Computer Science, TU Dortmund University 2004
  • Full Name

  • Andre Leier