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Samuel Johnson


  Sam Johnson

Dr Samuel Johnson

Warwick Zeeman Lecturer
Assistant Professor
 
Office: D2.11
Phone: +44 (0)24 761 50209
Email: S dot Johnson dot 2 at warwick dot ac dot uk

Teaching Responsibilities 2016/17:
Term 2: CO923 Computational Methods for Complex Systems

Research Interests:
Complex networks, dynamical systems, nonequilibrium physics, ecology, computational neuroscience, cooperation


Some links: arXiv, Blog, Google Scholar, ORCID, LinkedIn


Most relevant publications:

S. Johnson and N.S. Jones, Looplessness in networks is linked to trophic coherence, PNAS 114, 5618 (2017) (arXiv)

A.P. Millán, J.J. Torres, S. Johnson, and J. Marro, The concurrence of form and function in developing networks: An explanation for synaptic pruning, submitted (2017) (arXiv)

J. Klaise and S. Johnson, The origin of motif families in food webs, Scientific Reports 7, 16197 (2017) (arXiv)

W. Guo, X. Lu, and S. Johnson, The Spatial Ecology of War and Peace, submitted (2016) (arXiv)

J. Klaise and S. Johnson, From neurons to epidemics: How trophic coherence affects spreading processes, Chaos 26, 065310 (2016) (arXiv)

V. Domínguez-García, S. Johnson, and M.A. Muñoz, Intervality and coherence in complex networks, Chaos 26, 065308 (2016) (arXiv)

S. Johnson, Escaping the Tragedy of the Commons through Targeted Punishment, Royal Society Open Science 2, 150223 (2015) (open access)

A.P. Millán, J.J. Torres, S. Johnson, and J. Marro, Evolution of brain network structure under a critical condition as induced by local currents, Int. J. Complex Systems in Science 5, 43-47 (2015) (open access)

S. Johnson, V. Domínguez-García, L. Donetti, and M.A. Muñoz, Trophic coherence determines food-web stability, PNAS 111, 17923 (2014) (arXiv)

H.L. Mills, S. Johnson, M. Hickman, N.S. Jones, and C. Colijn, Errors in reported degrees and Respondent Driven Sampling: Implications for bias, Drug and Alcohol Dependence 142, 120 (2014)

S. Johnson, V. Domínguez-García, and M.A. Muñoz, Factors determining nestedness in complex networks, PLOS ONE 8(9), e74025 (2013) (open access)

S. Johnson, J.J. Torres, and J. Marro, Robust short-term memory without synaptic learning, PLOS ONE 8(1), e50276 (2013) (open access)

S. de Franciscis, S. Johnson, and J.J. Torres, Enhancing neural network performance via assortativity, Physical Review E 83, 036114 (2011) (arXiv)

S. Johnson, Interplay between Network Topology and Dynamics in Neural Systems, PhD thesis (2011) (arXiv)

S. Johnson, J.J. Torres, J. Marro, and M.A. Muñoz, Entropic origin of disassortativity in complex networks, Physical Review Letters 104, 108702 (2010) (arXiv)

S. Johnson, J. Marro, and J.J. Torres, Evolving networks and the development of neural systems, Journal of Statistical Mechanics (2010) P03003 (arXiv)

J.J. Torres, S. de Franciscis, S. Johnson, and J. Marro, Excitable networks: Nonequilibrium criticality and optimum topology, International Journal of Bifurcation and Chaos 20, 869-75 (2010)

S. Johnson, J.J. Torres, and J. Marro, Nonlinear preferential rewiring in fixed-size networks as a diffusion process, Physical Review E 79, 050104(R) (2009) (arXiv)

S. Johnson, J. Marro, J.F. Mejias, and J.J. Torres, Development of neural network structure with biological mechanisms, Lecture Notes in Computer Science 5517, 228 (2009)

J.F. Mejias, J.J. Torres, S. Johnson, and H.J. Kappen, Switching dynamics of neural systems in the presence of multiplicative colored noise, Lecture Notes in Computer Science 5517, 17 (2009)

S. Johnson, J. Marro, and J.J. Torres, Functional optimization in complex excitable networks, EPL (Europhysics Letters) 83, 46006 (2008) (arXiv)


Network Data:

Below are all the network data used for Looplessness in networks is linked to trophic coherence, S Johnson & NS Jones (arXiv) (2017) (the paper formerly known as "Spectra and cycle structure of trophically coherent graphs"). The data set is a compilation of directed networks obtained from various sources. For each network we provide the adjacency matrix as a list of edges in a text file: the numbers in the first column are labels for the in-node and those in the second are the out-node (i.e. the entry "42 3" means there is a directed edge from node 3 to node 42). Directed edges have different meanings depending on the nature of the network. For example, in food webs the edges go from prey (resource species) to predator (consumer species). In many of the original data there was more information than we give here, such as node descriptions or edge weights. The 63 networks are provided in four zipped folders, containing 42 food webs, eight gene regulatory networks (GRNs), seven metabolic networks, and six miscellaneous networks (the neural network of C. elegans, the Gnutella P2P network, two networks of trading nations, and the word adjacency network of Green Eggs and Ham). For the sources of these data and whom to cite when using them, please see the tables in the Supplementary Info of Looplessnes in networks is linked to trophic coherence (freely available on the arXiv). See also Wikipedia: Trophic Coherence.

Download:

Food Webs

Gene Regulatory Networks

Metabolic Networks

Miscellaneous Networks

Some sites with network data:

R.M. Thompson and C.R. Townsend's Interaction Web Data Base

Uri Alon's website

RegulonDB

Young Lab

The ENCODE Project: ENCyclopedia Of DNA Elements

CCNR - László Barabási

Mark Newman's website

Stanford Large Network Dataset Collection

Pajek datasets

Alex Arenas' website


Teaching Responsibilities 2014/15:

Workshops/conferences/seminars:

Recent research grants:

Recent awards & prizes:

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