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
    2018 Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.Briefings in Bioinformatics2018
    2018 PROSPERous: High-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracyComputer applications in the biosciences : CABIOS.  34:684-687. 2018
    2018 Bastion6: A bioinformatics approach for accurate prediction of type VI secreted effectorsComputer 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 sequencesComputer applications in the biosciences : CABIOS.  34:2499-2502. 2018
    2018 Quokka: A comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteomeComputer applications in the biosciences : CABIOS.  34:4223-4231. 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 Dynamic regulation of T follicular regulatory cell responses by interleukin 2 during influenza infectionNature Immunology.  18:1249-1260. 2017
    2017 ESC RT-mediated vesicle concatenation in plant endosomesJournal of Cell Biology.  216:2167-2177. 2017
    2017 Structure-based engineering of a pectate lyase with improved specific activity for ramie degummingApplied Microbiology and Biotechnology.  101:2919-2929. 2017
    2017 POSSUM: A bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profilesComputer applications in the biosciences : CABIOS.  33:2756-2758. 2017
    2016 Receptor dimer stabilization By hierarchical plasma membrane microcompartments regulates cytokine signalingScience Advances.  2. 2016
    2015 Asymmetrical inheritance of plasmids depends on dynamic cellular geometry and volume exclusion effectsPLoS ONE.  10. 2015
    2015 Simulating stochastic reaction-diffusion systems on and within moving boundariesPLoS ONE.  10. 2015
    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 Role reversal in a predator-prey interactionRoyal Society Open Science.  1. 2014
    2014 Exact Probability Distributions of Selected Species in Stochastic Chemical Reaction NetworksBulletin of Mathematical Biology2014
    2014 Order reduction of the chemical master equation via balanced realisationPLoS ONE.  9. 2014
    2014 Exact model reduction with delays: Closed-form distributions and extensions to fully bi-directional monomolecular reactionsInterface.  11. 2014
    2014 A selection criterion for patterns in reaction-diffusion systemsTheoretical Biology and Medical Modelling.  11. 2014
    2014 Delays induce novel stochastic effects in negative feedback gene circuitsBiophysical Journal.  106:467-478. 2014
    2014 The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed MitosisPLoS Computational Biology.  10. 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 biologySystems Biology.  6:134-142. 2012
    2012 Nuclear envelope morphology constrains diffusion and promotes asymmetric protein segregation in closed mitosisJournal of Cell Biology.  198:143. 2012
    2012 Nuclear envelope morphology constrains diffusion and promotes asymmetric protein segregation in closed mitosisJournal of Cell Biology.  197:921-937. 2012
    2012 Integrative physical oncologyWiley Interdisciplinary Reviews: Systems Biology and Medicine.  4:1-14. 2012
    2011 Autonomous Synchronization of Chemically Coupled Synthetic OscillatorsBulletin of Mathematical Biology.  73:2678-2706. 2011
    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 A novel approach to modelling water transport and drug diffusion through the stratum corneumTheoretical Biology and Medical Modelling.  7. 2010
    2010 Counter-intuitive stochastic behavior of simple gene circuits with negative feedbackBiophysical Journal.  98:1742-1750. 2010
    2010 Probability distributed time delays: Integrating spatial effects into temporal modelsBMC Systems Biology.  4. 2010
    2009 A tunable synthetic mammalian oscillatorNature.  457:309-312. 2009
    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 Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kineticsJournal of Chemical Physics.  127. 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
  • Doctor of Philosophy in Mathematics, University of New Mexico 2006
  • Full Name

  • Tatiana Marquez-Lago