All Stories

  1. Hyperspectral unmixing for Raman spectroscopy via physics-constrained autoencoders

    Article • Proceedings of the National Academy of Sciences, October 2024, Proceedings of the National Academy of Sciences

    Mauricio Barahona

  2. Algorithm 1044: PyGenStability, a Multiscale Community Detection with Generalized Markov Stability

    Article • ACM Transactions on Mathematical Software, June 2024, ACM (Association for Computing Machinery)

    Mauricio Barahona

  3. Learning spatiotemporal signals using a recurrent spiking network that discretizes time

    Article • PLoS Computational Biology, January 2020, PLOS

    Mauricio Barahona

  4. Graph-based data clustering via multiscale community detection

    Article • Applied Network Science, January 2020, Springer Science + Business Media

    Mauricio Barahona

  5. Unsupervised Graph-Based Learning Predicts Mutations That Alter Protein Dynamics

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Mauricio Barahona

  6. An edge-based formulation of elastic network models

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Mauricio Barahona

  7. Data-driven unsupervised clustering of online learner behaviour

    Article • npj Science of Learning, September 2019, Springer Science + Business Media

    Mauricio Barahona

  8. Beyond local gradient-sensing: memory effects in bacterial chemotactic navigation

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Mauricio Barahona

  9. Bounding the stationary distributions of the chemical master equation via mathematical programming

    Article • The Journal of Chemical Physics, July 2019, American Institute of Physics

    Mauricio Barahona

  10. Precision identification of high-risk phenotypes and progression pathways in severe malaria without requiring longitudinal data

    Article • npj Digital Medicine, July 2019, Springer Science + Business Media

    Mauricio Barahona

  11. Learning spatiotemporal signals using a recurrent spiking network that discretizes time

    Article • July 2019, Cold Spring Harbor Laboratory Press

    Mauricio Barahona

  12. Stochastic modelling reveals mechanisms of metabolic heterogeneity

    Article • Communications Biology, March 2019, Springer Science + Business Media

    Mauricio Barahona

  13. The Exit Time Finite State Projection Scheme: Bounding Exit Distributions and Occupation Measures of Continuous-Time Markov Chains

    Article • SIAM Journal on Scientific Computing, January 2019, Society for Industrial & Applied Mathematics (SIAM)

    Mauricio Barahona

  14. Guiding interoperable electronic health records through patient-sharing networks

    Article • npj Digital Medicine, December 2018, Springer Science + Business Media

    Mauricio Barahona

  15. Collective search with finite perception: transient dynamics and search efficiency

    Article • September 2018, Cold Spring Harbor Laboratory Press

    Mauricio Barahona

  16. Flux-dependent graphs for metabolic networks

    Article • npj Systems Biology and Applications, August 2018, Springer Science + Business Media

    Mauricio Barahona

  17. Allostery and cooperativity in multimeric proteins: bond-to-bond propensities in ATCase

    Article • Scientific Reports, July 2018, Springer Science + Business Media

    Mauricio Barahona

  18. Computational Re-design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation

    Article • Cell Systems, April 2018, Elsevier

    Mauricio Barahona

  19. Flux-dependent graphs for metabolic networks

    Article • March 2018, Cold Spring Harbor Laboratory Press

    Mauricio Barahona

  20. Modelling the Dynamics of Biological Systems with the Geometric Hidden Markov Model

    Article • November 2017, Cold Spring Harbor Laboratory Press

    Mauricio Barahona

  21. Computational Re-Design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation

    Article • August 2017, Cold Spring Harbor Laboratory Press

    Mauricio Barahona

  22. Geometric multiscale community detection: Markov stability and vector partitioning

    Article • Journal of Complex Networks, July 2017, Oxford University Press (OUP)

    Mauricio Barahona

  23. Kinetic Analysis Reveals the Identity of Aβ-Metal Complex Responsible for the Initial Aggregation of Aβ in the Synapse

    Article • ACS Chemical Neuroscience, June 2017, American Chemical Society (ACS)

    Mauricio Barahona

  24. GlnK Facilitates the Dynamic Regulation of Bacterial Nitrogen Assimilation

    Article • Biophysical Journal, May 2017, Elsevier

    Mauricio Barahona

  25. GlnK facilitates the dynamic regulation of bacterial nitrogen assimilation

    Article • April 2017, Cold Spring Harbor Laboratory Press

    Mauricio Barahona

  26. SC3: consensus clustering of single-cell RNA-seq data

    Article • Nature Chemical Biology, March 2017, Springer Science + Business Media

    Mauricio Barahona

  27. Toward Precision Healthcare: Context and Mathematical Challenges

    Article • Frontiers in Physiology, March 2017, Frontiers

    Mauricio Barahona

  28. The ‘who’ and ‘what’ of #diabetes on Twitter

    Article • Digital Health, January 2017, SAGE Publications

    Mauricio Barahona

  29. Stochastic models of gene transcription with upstream drives: exact solution and sample path characterization

    Article • Journal of The Royal Society Interface, January 2017, Royal Society Publishing

    Mauricio Barahona

  30. Graph partitions and cluster synchronization in networks of oscillators

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, September 2016, American Institute of Physics

    Mauricio Barahona

  31. Prediction of allosteric sites and mediating interactions through bond-to-bond propensities

    Article • Nature Communications, August 2016, Springer Science + Business Media

    Mauricio Barahona

  32. Flow-Based Network Analysis of the Caenorhabditis elegans Connectome

    Article • PLoS Computational Biology, August 2016, PLOS

    Mauricio Barahona

  33. Linear models of activation cascades: analytical solutions and coarse-graining of delayed signal transduction

    Article • Journal of The Royal Society Interface, August 2016, Royal Society Publishing

    Mauricio Barahona

  34. Community detection and role identification in directed networks: Understanding the Twitter network of the care.data debate

    Article • March 2016, World Scientific Pub Co Pte Lt

    Mauricio Barahona

  35. Window functions and sigmoidal behaviour of memristive systems

    Article • International Journal of Circuit Theory and Applications, February 2016, Wiley

    Mauricio Barahona

  36. Bounding Stationary Averages of Polynomial Diffusions via Semidefinite Programming

    Article • SIAM Journal on Scientific Computing, January 2016, Society for Industrial & Applied Mathematics (SIAM)

    Mauricio Barahona

  37. Great cities look small

    Article • Journal of The Royal Society Interface, July 2015, Royal Society Publishing

    Mauricio Barahona

  38. Emergence of Slow-Switching Assemblies in Structured Neuronal Networks

    Article • PLoS Computational Biology, July 2015, PLOS

    Mauricio Barahona

  39. PDGFRα demarcates the cardiogenic clonogenic Sca1+ stem/progenitor cell in adult murine myocardium

    Article • Nature Communications, May 2015, Springer Science + Business Media

    Mauricio Barahona

  40. Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities

    Article • Nucleic Acids Research, January 2015, Oxford University Press (OUP)

    Mauricio Barahona

  41. Dynamics of Cluster Synchronisation in Modular Networks: Implications for Structural and Functional Networks

    Article • January 2015, Springer Science + Business Media

    Mauricio Barahona

  42. Secondary Metal Binding to Amyloid-Beta Monomer is Insignificant under Synaptic Conditions

    Article • Biophysical Journal, January 2015, Elsevier

    Mauricio Barahona

  43. Introduction of a Fluorescent Probe to Amyloid-β to Reveal Kinetic Insights into Its Interactions with Copper(II)

    Article • Angewandte Chemie, December 2014, Wiley

    Mauricio Barahona

  44. On memristor ideality and reciprocity

    Article • Microelectronics Journal, November 2014, Elsevier

    Mauricio Barahona

  45. Interest communities and flow roles in directed networks: the Twitter network of the UK riots

    Article • Journal of The Royal Society Interface, October 2014, Royal Society Publishing

    Mauricio Barahona

  46. Revealing cell assemblies at multiple levels of granularity

    Article • Journal of Neuroscience Methods, October 2014, Elsevier

    Mauricio Barahona

  47. Engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks

    Article • Nucleic Acids Research, July 2014, Oxford University Press (OUP)

    Mauricio Barahona

  48. Random Walks, Markov Processes and the Multiscale Modular Organization of Complex Networks

    Article • IEEE Transactions on Network Science and Engineering, July 2014, Institute of Electrical & Electronics Engineers (IEEE)

    Mauricio Barahona

  49. P595PDGFRalpha demarcates the cardiogenic and clonogenic Sca-1+ stem cell

    Article • Cardiovascular Research, June 2014, European Society of Cardiology

    Mauricio Barahona

  50. HhexandCer1Mediate the Sox17 Pathway for Cardiac Mesoderm Formation in Embryonic Stem Cells

    Article • Stem Cells, May 2014, Wiley

    Mauricio Barahona

  51. Structure of complex networks: Quantifying edge-to-edge relations by failure-induced flow redistribution

    Article • Network Science, April 2014, Cambridge University Press

    Mauricio Barahona

  52. Uncovering allosteric pathways in caspase-1 using Markov transient analysis and multiscale community detection

    Article • Molecular BioSystems, January 2014, Royal Society of Chemistry

    Mauricio Barahona

  53. Finding role communities in directed networks using Role-Based Similarity, Markov Stability and the Relaxed Minimum Spanning Tree

    Article • December 2013, Institute of Electrical & Electronics Engineers (IEEE)

    Mauricio Barahona

  54. Ideal memristors as reciprocal elements

    Article • December 2013, Institute of Electrical & Electronics Engineers (IEEE)

    Mauricio Barahona

  55. On periodic reference tracking using batch-mode reinforcement learning with application to gene regulatory network control

    Article • December 2013, Institute of Electrical & Electronics Engineers (IEEE)

    Mauricio Barahona

  56. Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC In Vivo

    Article • mBio, November 2013, ASM Journals

    Mauricio Barahona

  57. Observability and coarse graining of consensus dynamics through the external equitable partition

    Article • Physical Review E, October 2013, American Physical Society (APS)

    Mauricio Barahona

  58. Rewiring cell signalling through chimaeric regulatory protein engineering

    Article • Biochemical Society Transactions, September 2013, Portland Press Ltd.

    Mauricio Barahona

  59. Tuning the dials of Synthetic Biology

    Article • Microbiology, May 2013, Society for General Microbiology

    Mauricio Barahona

  60. Decentralised minimum-time consensus

    Article • Automatica, May 2013, Elsevier

    Mauricio Barahona

  61. Risk factor-dependent dynamics of atopic dermatitis: modelling multi-scale regulation of epithelium homeostasis

    Article • Interface Focus, February 2013, Royal Society Publishing

    Dr Masahiro Ono, Mauricio Barahona

  62. A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals

    Article • Biosensors and Bioelectronics, February 2013, Elsevier

    Mauricio Barahona

  63. Communities in Evolving Networks: Definitions, Detection, and Analysis Techniques

    Article • January 2013, Springer Science + Business Media

    Mauricio Barahona

  64. Robustness of random graphs based on graph spectra

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, October 2012, American Institute of Physics

    Mauricio Barahona

  65. Combinatorial stresses kill pathogenic Candida species

    Article • Medical Mycology, October 2012, Oxford University Press (OUP)

    Dr Tom Thorne, Mauricio Barahona

  66. Encoding dynamics for multiscale community detection: Markov time sweeping for the map equation

    Article • Physical Review E, August 2012, American Physical Society (APS)

    Mauricio Barahona

  67. Engineering and ethical perspectives in synthetic biology

    Article • EMBO Reports, June 2012, EMBO

    Mauricio Barahona

  68. Device Properties of Bernoulli Memristors

    Article • Proceedings of the IEEE, June 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Panayiotis Georgiou, Mauricio Barahona

  69. Sensory experience modifies spontaneous state dynamics in a large-scale barrel cortical model

    Article • Journal of Computational Neuroscience, March 2012, Springer Science + Business Media

    Mauricio Barahona

  70. Quantitative measure of hysteresis for memristors through explicit dynamics

    Article • Proceedings of the Royal Society A Mathematical Physical and Engineering Sciences, March 2012, Royal Society Publishing

    Panayiotis Georgiou, Mauricio Barahona

  71. Markov Dynamics as a Zooming Lens for Multiscale Community Detection: Non Clique-Like Communities and the Field-of-View Limit

    Article • PLoS ONE, February 2012, PLOS

    Mauricio Barahona

  72. Squeeze-and-breathe evolutionary Monte Carlo optimization with local search acceleration and its application to parameter fitting

    Article • Journal of The Royal Society Interface, January 2012, Royal Society Publishing

    Mauricio Barahona

  73. Compound stress response in stomatal closure: a mathematical model of ABA and ethylene interaction in guard cells

    Article • BMC Systems Biology, January 2012, Springer Science + Business Media

    Mauricio Barahona

  74. Stochastic oscillatory dynamics of generalized repressilators

    Article • January 2012, American Institute of Physics

    Mauricio Barahona

  75. Decentralised minimal-time consensus

    Article • December 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Mauricio Barahona

  76. Spectral Measure of Structural Robustness in Complex Networks

    Article • IEEE Transactions on Systems Man and Cybernetics - Part A Systems and Humans, November 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Mauricio Barahona

  77. Protein multi-scale organization through graph partitioning and robustness analysis: application to the myosin–myosin light chain interaction

    Article • Physical Biology, August 2011, Institute of Physics Publishing

    Mauricio Barahona

  78. Flow graphs: Interweaving dynamics and structure

    Article • Physical Review E, July 2011, American Physical Society (APS)

    Mauricio Barahona

  79. Robustness of regular ring lattices based on natural connectivity

    Article • International Journal of Systems Science, July 2011, Taylor & Francis

    Mauricio Barahona

  80. Transient dynamics around unstable periodic orbits in the generalized repressilator model

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, April 2011, American Institute of Physics

    Mauricio Barahona

  81. Obtaining certificates for complete synchronisation of coupled oscillators

    Article • Physica D Nonlinear Phenomena, April 2011, Elsevier

    Mauricio Barahona

  82. Natural Connectivity of Complex Networks

    Article • Chinese Physics Letters, July 2010, Institute of Physics Publishing

    Mauricio Barahona

  83. Stability of graph communities across time scales

    Article • Proceedings of the National Academy of Sciences, June 2010, Proceedings of the National Academy of Sciences

    Mauricio Barahona

  84. Crowding-Induced Anisotropic Transport Modulates Reaction Kinetics in Nanoscale Porous Media

    Article • The Journal of Physical Chemistry B, April 2010, American Chemical Society (ACS)

    Mauricio Barahona

  85. The Effect of Spatially Inhomogeneous Extracellular Electric Fields on Neurons

    Article • Journal of Neuroscience, February 2010, Society for Neuroscience

    Mauricio Barahona

  86. Switchable genetic oscillator operating in quasi-stable mode

    Article • Journal of The Royal Society Interface, January 2010, Royal Society Publishing

    Mauricio Barahona

  87. Solutions of weakly reversible chemical reaction networks are bounded and persistent*

    Article • IFAC Proceedings Volumes, January 2010, Elsevier

    Mauricio Barahona

  88. Interplay between spontaneous and sensory activities in barrel cortex: a computational study

    Article • BMC Neuroscience, July 2009, Springer Science + Business Media

    Mauricio Barahona

  89. An analysis of the Map Seeking Circuit and Monte Carlo extensions

    Article • April 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Mauricio Barahona

  90. X-ray diffraction measurement of the monolayer spontaneous curvature of dioleoylphosphatidylglycerol

    Article • Chemistry and Physics of Lipids, July 2008, Elsevier

    Mauricio Barahona

  91. A Dominated Coupling From The Past algorithm for the stochastic simulation of networks of biochemical reactions

    Article • BMC Systems Biology, May 2008, Springer Science + Business Media

    Mauricio Barahona

  92. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

    Article • Nature, May 2008, Springer Science + Business Media

    Mauricio Barahona

  93. Biophysical Regulation of Lipid Biosynthesis in the Plasma Membrane

    Article • Biophysical Journal, April 2008, Elsevier

    Mauricio Barahona

  94. Chemistry across scales: from molecules to cells

    Article • Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, September 2007, Royal Society Publishing

    Mauricio Barahona

  95. Full analogue electronic realisation of the Hodgkin-Huxley neuronal dynamics in weak-inversion CMOS

    Article • August 2007, Institute of Electrical & Electronics Engineers (IEEE)

    Mauricio Barahona

  96. Perfect Sampling of the Master Equation for Gene Regulatory Networks

    Article • Biophysical Journal, July 2007, Elsevier

    Mauricio Barahona

  97. Noise characteristics of interlocked repressilators

    Article • BMC Systems Biology, May 2007, Springer Science + Business Media

    Mauricio Barahona

  98. A Dynamical Model of Lipoprotein Metabolism

    Article • The Bulletin of Mathematical Biophysics, March 2007, Springer Science + Business Media

    Mauricio Barahona

  99. Stochastic Kinetics of Viral Capsid Assembly Based on Detailed Protein Structures

    Article • Biophysical Journal, May 2006, Elsevier

    Mauricio Barahona

  100. Synchronization in Small-World Systems

    Article • Physical Review Letters, July 2002, American Physical Society (APS)

    Mauricio Barahona

  101. Self-Assembled, Deterministic Carbon Nanotube Wiring Networks This work was funded by the Office of Naval Research, DARPA, and an NSF-FRG grant.

    Article • Angewandte Chemie, January 2002, Wiley

    Mauricio Barahona

  102. A new bound of the /spl Lscr//sub 2/[0, T]-induced norm and applications to model reduction

    Article • January 2002, Institute of Electrical & Electronics Engineers (IEEE)

    Mauricio Barahona

  103. Titration of chaos with added noise

    Article • Proceedings of the National Academy of Sciences, June 2001, Proceedings of the National Academy of Sciences

    Mauricio Barahona

  104. Pinned states in Josephson arrays: A general stability theorem

    Article • September 1998, American Physical Society (APS)

    Mauricio Barahona

  105. Erratum: Superconducting states and depinning transitions of Josephson ladders [Phys. Rev. B57, 1181 (1998)]

    Article • September 1998, American Physical Society (APS)

    Mauricio Barahona

  106. Dynamics of one-dimensional Josephson-junction arrays

    Article • Physica D Nonlinear Phenomena, August 1998, Elsevier

    Mauricio Barahona

  107. Row-switched states in two-dimensional underdamped Josephson-junction arrays

    Article • May 1998, American Physical Society (APS)

    Mauricio Barahona

  108. Superconducting states and depinning transitions of Josephson ladders

    Article • January 1998, American Physical Society (APS)

    Mauricio Barahona

  109. Intrinsic phase-locked state in two-dimensional Nb Josephson arrays

    Article • IEEE Transactions on Applied Superconductivity, June 1997, Institute of Electrical & Electronics Engineers (IEEE)

    Mauricio Barahona

  110. Resonances of dynamical checkerboard states in Josephson arrays with self-inductance

    Article • May 1997, American Physical Society (APS)

    Mauricio Barahona

  111. Detection of nonlinear dynamics in short, noisy time series

    Article • Nature, May 1996, Springer Science + Business Media

    Mauricio Barahona

  112. Ba2(RE)Cu3O7−δ(RE=La, Pr, Nd, Sm, Gd): Crystal growth, structure and magnetic properties

    Article • Solid State Ionics, February 1989, Elsevier

    Mauricio Barahona

  113. Ba2PrCu3O7: Crystal growth, structure and magnetic properties

    Article • Solid State Communications, July 1988, Elsevier

    Professor Juan Rodriguez-Carvajal, Mauricio Barahona

  114. Ba2Pr.34+Pr.73+Cu.73+Cu2.32+O7 : Crystal growth, structure and magnetic properties

    Article • Physica C Superconductivity, June 1988, Elsevier

    Professor Juan Rodriguez-Carvajal, Mauricio Barahona

  115. The rare-earth H.T.S.C. family Ba2(RE)Cu3O7; structural, electrical and magnetic studies (RE=Y,Nd,Sm,Eu,Gd,Dy,Ho,Er,Tm)

    Article • Materials Research Bulletin, March 1988, Elsevier

    Professor Flaviano Garcia-Alvarado, Mauricio Barahona

  116. REBa2Cu3O7−δ (RE = Pr, Nd, Sm, Gd): Crystal growth, structure and magnetism

    Article • Solid State Ionics, March 1988, Elsevier

    Mauricio Barahona

  117. Superconducting energy gap and phonon spectra in MBa2Cu3O7−x type materials

    Article • Physica C Superconductivity, January 1988, Elsevier

    Professor Flaviano Garcia-Alvarado, Mauricio Barahona

  118. Infrared and Raman spectra of the new superconducting cuprate perovskites MBa2Cu3O7, M =Nd, Dy, Er, Tm

    Article • Solid State Communications, January 1988, Elsevier

    Mauricio Barahona

  119. Superconducting energy gap inMBa2Cu3O7−δ-type materials

    Article • January 1988, American Physical Society (APS)

    Mauricio Barahona