Imperial College London

ProfessorMauricioBarahona

Faculty of Natural SciencesDepartment of Mathematics

Chair in Biomathematics
 
 
 
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Contact

 

m.barahona Website

 
 
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Location

 

6M31Huxley BuildingSouth Kensington Campus

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Summary

 

Summary

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.

STudentship available 

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.

Selected Publications

Journal Articles

Liu Z, Barahona M, 2017, Geometric multiscale community detection: Markov stability and vector partitioning, Journal of Complex Networks, ISSN:2051-1329

Kiselev VY, Kirschner K, Schaub MT, et al., 2017, SC3: consensus clustering of single-cell RNA-seq data, Nature Methods, Vol:14, ISSN:1548-7091, Pages:483-+

Schaub MT, O'Clery N, Billeh YN, et al., 2016, Graph partitions and cluster synchronization in networks of oscillators, Chaos, Vol:26, ISSN:1054-1500

Kuntz J, Ottobre M, Stan G-B, 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

Amor BRC, Schaub MT, Yaliraki S, 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

Bacik KA, Schaub MT, Beguerisse-Diaz M, et al., 2016, Flow-Based Network Analysis of the Caenorhabditis elegans Connectome, PLOS Computational Biology, Vol:12, ISSN:1553-734X

Beguerisse-Diaz M, McLennan AK, Garduño-Hernández G, et al., 2017, The 'who' and 'what' of #diabetes on Twitter, Digital Health, Vol:3, ISSN:2055-2076, Pages:1-29

Sim A, Yaliraki SN, Barahona M, et al., 2015, Great cities look small., Journal of the Royal Society Interface, Vol:12, ISSN:1742-5689

Noseda M, Harada M, McSweeney S, 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

Schaub MT, Billeh YN, Anastassiou CA, 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

Branch T, Girvan P, Barahona M, 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

Georgiou PS, Barahona M, Yaliraki SN, et al., 2014, On memristor ideality and reciprocity, Microelectronics Journal, Vol:45, ISSN:0026-2692, Pages:1363-1371

Billeh YN, Schaub MT, Anastassiou CA, 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

Amor B, Yaliraki SN, Woscholski R, 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

Beguerisse-Díaz M, Garduño-Hernández G, Vangelov B, 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

Georgiou PS, Barahona M, Yaliraki SN, 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

Schaub MT, Delvenne J-C, Yaliraki SN, 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

Chang HH, Hemberg M, Barahona M, et al., 2008, Transcriptome-wide noise controls lineage choice in mammalian progenitor cells, Nature, Vol:453, ISSN:0028-0836, Pages:544-U10

Chapters

Amor B, Vuik S, Callahan R, 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

Delvenne J-C, Schaub MT, Yaliraki S, 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

Conference

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

Patents

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

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