Mauricio Barahona obtained a PhD in Theoretical Physics (Dynamical Systems and Condensed Matter) from the Massachusetts Institute of Technology (MIT) under the supervision of Steve Strogatz (Mathematics) and Mehran Kardar (Physics). His thesis dealt with the spatio-temporal dynamics of networks of Josephson junctions - superconducting electronic devices which can be described as coupled nonlinear oscillators. Concurrently, he developed algorithmic tools which, using concepts of information theory and dynamical systems, allow for the sensitive statistical detection of nonlinear dynamics in data.
He then conducted postdoctoral research at Stanford University and the California Institute of Technology. At Stanford, he worked on generic properties of array synchronization with applications to pattern detection. At Caltech, in the Department of Control and Dynamical Systems, he concentrated on rigorous bounds of model reduction techniques, and on the analysis of network dynamics using graph-theoretical concepts.
He came to Imperial as a Lecturer in 2001 and became a Reader in Biomathematics in 2004. In 2011, he moved to the Department of Mathematics as Chair of Biomathematics. Since 2016, he is Director of the EPSRC Centre for Mathematics of Precision Healthcare.
4-year PhD studentship starting October 2017 in collaboration with AstraZeneca (pdf)
Towards avoiding drug resistance through identification of allosteric sites and pathways in protein families
Supervisors: S.N. Yaliraki (Dept. of Chemistry, Imperial), Maria Flocco (AstraZeneca), M. Barahona (Dept. of Mathematics, Imperial)
Resistance to known drugs is currently one of the most pressing problems world-wide, yet the origins of resistance at the molecular level remain poorly understood. To shed light on the mechanistic understanding at the atomistic level, we propose to identify allosteric sites and the pathways of communications that connect them to activity in a family of proteins that have been well studied in the pharma industry but where the development of drug resistance remains unexplained. A recently proposed suite of methods for the construction and analysis of atomistic molecular graphs using stochastic processes and graph partitioning has been shown to identify allosteric sites and pathways of communications and, conversely, to systematically scan for mutations that disrupt them. We propose to use this approach as a starting point to quantitative map allosteric sites on functionally and structurally related protein families and obtain an “atlas” of their propensity for resistance.
Full studentship for UK and EU students.
To apply and for more information, click here.
Liu Z, Barahona M, 2017, Geometric multiscale community detection: Markov stability and vector partitioning, Journal of Complex Networks, ISSN:2051-1329
et al., 2017, SC3: consensus clustering of single-cell RNA-seq data, Nature Methods, Vol:14, ISSN:1548-7091, Pages:483-+
et al., 2016, Graph partitions and cluster synchronization in networks of oscillators, Chaos, Vol:26, ISSN:1054-1500
et al., 2016, BOUNDING STATIONARY AVERAGES OF POLYNOMIAL DIFFUSIONS VIA SEMIDEFINITE PROGRAMMING, SIAM Journal on Scientific Computing, Vol:38, ISSN:1064-8275, Pages:A3891-A3920
et al., 2016, Prediction of allosteric sites and mediating interactions through bond-to-bond propensities, Nature Communications, Vol:7, ISSN:2041-1723
Dattani J, Barahona M, 2017, Stochastic models of gene transcription with upstream drives: Exact solution and sample path characterisation, Journal of the Royal Society Interface, Vol:14, ISSN:1742-5689
et al., 2016, Flow-Based Network Analysis of the Caenorhabditis elegans Connectome, PLOS Computational Biology, Vol:12, ISSN:1553-734X
et al., 2017, The 'who' and 'what' of #diabetes on Twitter, Digital Health, Vol:3, ISSN:2055-2076, Pages:1-29
et al., 2015, Great cities look small., Journal of the Royal Society Interface, Vol:12, ISSN:1742-5689
et al., 2015, PDGFRα demarcates the cardiogenic clonogenic Sca1(+) stem/progenitor cell in adult murine myocardium., Nature Communications, Vol:6, ISSN:2041-1723, Pages:6930-6930
et al., 2015, Emergence of Slow-Switching Assemblies in Structured Neuronal Networks, PLOS Computational Biology, Vol:11, ISSN:1553-734X
Lambiotte R, Delvenne JC, Barahona M, 2014, Random walks, Markov processes and the multiscale modular organization of complex networks, Ieee Transactions on Network Science and Engineering, Vol:1, Pages:76-90
Wang B, Barahona M, Buck M, 2015, Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities, Nucleic Acids Research, Vol:43, ISSN:0305-1048, Pages:1955-1964
et al., 2015, Introduction of a Fluorescent Probe to Amyloid-beta to Reveal Kinetic Insights into Its Interactions with Copper(II), Angewandte Chemie - International Edition, Vol:54, ISSN:1433-7851, Pages:1227-1230
et al., 2014, On memristor ideality and reciprocity, Microelectronics Journal, Vol:45, ISSN:0026-2692, Pages:1363-1371
et al., 2014, Revealing cell assemblies at multiple levels of granularity, Journal of Neuroscience Methods, Vol:236, ISSN:0165-0270, Pages:92-106
Wang B, Barahona M, Buck M, 2014, Engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks, Nucleic Acids Research, Vol:42, ISSN:0305-1048, Pages:9484-9492
et al., 2014, Uncovering allosteric pathways in caspase-1 using Markov transient analysis and multiscale community detection, Molecular Biosystems, Vol:10, ISSN:1742-206X, Pages:2247-2258
et al., 2014, Interest communities and flow roles in directed networks: the Twitter network of the UK riots, J. R. Soc. Interface 6 December 2014, Vol:11
et al., 2012, Device Properties of Bernoulli Memristors, Proceedings of the IEEE, Vol:100, ISSN:0018-9219, Pages:1938-1950
Wang B, Barahona M, Buck M, 2013, A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals, Biosensors & Bioelectronics, Vol:40, ISSN:0956-5663, Pages:368-376
Beguerisse Diaz M, Desikan R, Barahona M, 2016, Linear models of activation cascades: analytical solutions and coarse-graining of delayed signal transduction, Journal of the Royal Society Interface, Vol:13, ISSN:1742-5689
et al., 2012, Markov Dynamics as a Zooming Lens for Multiscale Community Detection: Non Clique-Like Communities and the Field-of-View Limit, PLOS One, Vol:7, ISSN:1932-6203
Delvenne J-C, Yaliraki SN, Barahona M, 2010, Stability of graph communities across time scales, Proceedings of the National Academy of Sciences of the United States of America, Vol:107, ISSN:0027-8424, Pages:12755-12760
Strelkowa N, Barahona M, 2010, Switchable genetic oscillator operating in quasi-stable mode, Journal of the Royal Society Interface, Vol:7, ISSN:1742-5689, Pages:1071-1082
Barahona M, Poon CS, 1996, Detection of nonlinear dynamics in short, noisy time series, Nature, Vol:381, ISSN:0028-0836, Pages:215-217
Barahona M, Pecora LM, 2002, Synchronization in small-world systems, Physical Review Letters, Vol:89, ISSN:0031-9007
et al., 2008, Transcriptome-wide noise controls lineage choice in mammalian progenitor cells, Nature, Vol:453, ISSN:0028-0836, Pages:544-U10
et al., 2016, Community detection and role identification in directed networks: understanding the Twitter network of the care.data debate, Dynamic Networks and Cyber-Security, Editor(s): Adams, Heard, World Scientific, Pages:111-136, ISBN:978-1-60558752-3
et al., 2013, The stability of a graph partition: A dynamics-based framework for community detection, Dynamics On and Of Complex Networks, Volume 2, Editor(s): Mukherjee, Choudhury, Peruani, Ganguly, Mitra, Springer, Pages:221-242, ISBN:978-1-4614-6728-1
Jadbabaie A, Motee N, Barahona M, 2004, On the stability of the Kuramoto model of coupled nonlinear oscillators, American Control Conference, IEEE, Pages:4296-4301, ISSN:0743-1619
Poon, C.S., Barahona, M., Merrill, C.K., 1996, Method and apparatus for detecting nonlinearity in a dynamical system, US, United States Patent 5792062, World WO1997043722