Positions

Selected Publications

Academic Article

Year Title Altmetric
2020 Improved cytokine–receptor interaction prediction by exploiting the negative sample space.  BMC Bioinformatics.  21. 2020
2020 PASSION: An ensemble neural network approach for identifying the binding sites of RBPs on circRNAs.  Bioinformatics.  36:4276-4282. 2020
2020 DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy..  Briefings in Bioinformatics.  2020
2020 ILearn: An integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data.  Briefings in Bioinformatics.  21:1047-1057. 2020
2020 PRISMOID: A comprehensive 3D structure database for post-translational modifications and mutations with functional impact.  Briefings in Bioinformatics.  21:1069-1079. 2020
2020 DeepCleave: A deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites.  Bioinformatics.  36:1057-1065. 2020
2020 PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins.  Bioinformatics.  36:704-712. 2020
2019 Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework.  Briefings in Bioinformatics.  20:2185-2199. 2019
2019 Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.  Briefings 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 methods.  Briefings in Bioinformatics.  20:2150-2166. 2019
2019 MULTiPly: A novel multi-layer predictor for discovering general and specific types of promoters.  Bioinformatics.  35:2957-2965. 2019
2019 A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction.  Briefings in Bioinformatics.  21:1119-1135. 2019
2019 Bastion3: A two-layer ensemble predictor of type III secreted effectors.  Bioinformatics.  35:2017-2028. 2019
2018 Quokka: A comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.  Bioinformatics.  34:4223-4231. 2018
2018 Bastion6: A bioinformatics approach for accurate prediction of type VI secreted effectors.  Bioinformatics.  34:2546-2555. 2018
2018 IFeature: A Python package and web server for features extraction and selection from protein and peptide sequences.  Bioinformatics.  34:2499-2502. 2018
2018 PROSPERous: High-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.  Bioinformatics.  34:684-687. 2018
2018 Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.  Briefings in Bioinformatics.  19:148-161. 2018
2017 Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.  Briefings in Bioinformatics.  20:931-951. 2017
2017 POSSUM: A bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.  Bioinformatics.  33:2756-2758. 2017
2017 Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming.  Applied Microbiology and Biotechnology.  101:2919-2929. 2017
2011 Stochastic adaptation and fold-change detection: From single-cell to population behavior.  BMC Systems Biology.  5. 2011
2010 Probability distributed time delays: Integrating spatial effects into temporal models.  BMC Systems Biology.  4. 2010
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 DIVERGENCE.  Advances in Complex Systems.  10:155-172. 2007
2007 ANALYSIS OF PREFERENTIAL NETWORK MOTIF GENERATION IN AN ARTIFICIAL REGULATORY NETWORK MODEL CREATED BY DUPLICATION AND DIVERGENCE.  Advances in Complex Systems.  10:155-172. 2007
2007 Analysis of preferential network motif generation in an artificial regulatory network model created by duplication and divergence.  Advances in Complex Systems.  10:155-172. 2007
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
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

Education And Training

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

    • Full Name

  • Andre Leier