Positions

Overview

  • Research in the Marquez-Lago lab combines (wet lab) experiments involving bioengineering, micro- and molecular biology techniques, with (drylab) data analysis, AI, modeling and simulation techniques. In a nutshell, we investigate (1) host-microbiota interactions in complex human diseases, (2) microbial multi-drug resistance, and (3) gene expression and chromatin organization. In addition, we study (4) the role and effect of mechanical forces ('mechanobiology') and cell compartmentalization in pathogenesis.

    In our work, we integrate experiments and data (DNA/RNA/ATAC/ChIP-seq, metabolomics, proteomics, super-resolution microscopy, etc.) into calibrated models that have predictive power, revealing testable experiments in fundamental biology and translational research. Our research and methods are primarily aimed at identifying effective biomarkers and viable precision therapeutics.
  • 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
    2019 Impaired Tumor-Necrosis-Factor-α-driven Dendritic Cell Activation Limits Lipopolysaccharide-Induced Protection from Allergic Inflammation in Infants 2019
    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 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 Dynamic regulation of T follicular regulatory cell responses by interleukin 2 during influenza infection 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 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 Asymmetrical inheritance of plasmids depends on dynamic cellular geometry and volume exclusion effects 2015
    2015 Simulating stochastic reaction-diffusion systems on and within moving boundaries 2015
    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 Role reversal in a predator-prey interaction 2014
    2014 Exact Probability Distributions of Selected Species in Stochastic Chemical Reaction Networks 2014
    2014 Order reduction of the chemical master equation via balanced realisation 2014
    2014 Exact model reduction with delays: Closed-form distributions and extensions to fully bi-directional monomolecular reactions 2014
    2014 A selection criterion for patterns in reaction-diffusion systems 2014
    2014 Delays induce novel stochastic effects in negative feedback gene circuits 2014
    2014 The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed Mitosis 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 Nuclear envelope morphology constrains diffusion and promotes asymmetric protein segregation in closed mitosis 2012
    2012 Nuclear envelope morphology constrains diffusion and promotes asymmetric protein segregation in closed mitosis 2012
    2012 Integrative physical oncology 2012
    2011 Autonomous Synchronization of Chemically Coupled Synthetic Oscillators 2011
    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 A novel approach to modelling water transport and drug diffusion through the stratum corneum 2010
    2010 Counter-intuitive stochastic behavior of simple gene circuits with negative feedback 2010
    2010 Probability distributed time delays: Integrating spatial effects into temporal models 2010
    2009 A tunable synthetic mammalian oscillator 2009
    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 Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics 2007

    Chapter

    Year Title Altmetric
    2014 Synthetic Biology: Dynamic Modeling and Construction of Cell Systems.  493-544. 2014
    2011 Synthetic Biology: Dynamic Modeling and Construction of Cell Systems.  493-544. 2011

    Research Overview

  • Host-microbiota interactions, antimicrobial resistance, chromatin conformation and gene expression
  • Education And Training

  • ETH Zurich, Postdoctoral Fellowship
  • Full Name

  • Tatiana Marquez-Lago