• 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
    2021 DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy.Briefings 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 Obesity diminishes response to PD-1-based immunotherapies in renal cancerJournal for ImmunoTherapy of Cancer.  8. 2020
    2020 DeepBL: a deep learning-based approach for in silico discovery of beta-lactamases.Briefings in Bioinformatics2020
    2020 PROSPECT: A web server for predicting protein histidine phosphorylation sitesJournal of Bioinformatics and Computational Biology.  18. 2020
    2020 Mutation-Directed Therapeutics for Neurofibromatosis Type IMolecular Therapy : Nucleic Acids.  20:739-753. 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
    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
    2019 Impaired Tumor-Necrosis-Factor-α-driven Dendritic Cell Activation Limits Lipopolysaccharide-Induced Protection from Allergic Inflammation in InfantsImmunity.  50:225-240.e4. 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 Dynamic regulation of T follicular regulatory cell responses by interleukin 2 during influenza infectionNature Immunology.  18:1249-1260. 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
    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 Biology.  2334-2361. 2014
    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 reactions 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 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 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


    Year Title Altmetric
    2017 A review of stochastic and delay simulation approaches in both time and space in computational cell biology.  241-261. 2017
    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

    Education And Training

  • ETH Zurich, Postdoctoral Fellowship
  • Doctor of Philosophy in Mathematics, University of New Mexico 2006
  • Full Name

  • Tatiana Marquez-Lago