In the following list, I suggest reading first those articles:
[1] 
S. Grauwin, G. Beslon, E. Fleury, S. Franceschelli, C. Robardet, J.B.
Rouquier, and P. Jensen.
Complex systems science: dreams of universality, reality of
interdisciplinarity.
PlosOne, 2011.
Accepted.
[ bib ]
Thanks to a large database (215 000 records) of relevant articles, we empirically study the “complex systems” field and its claims to find universal principles applying to systems in general. Study of the references shared by the papers allows us to obtain a global point of view on the structure of this highly interdisciplinary field. We show that its overall coherence does not arise from a universal theory but instead from computational techniques and fruitful adaptations of the idea of selforganization to specific systems. At a more local level, specifically interdisciplinary, we find that understanding between vastly different scientific cultures is possible thanks to “trading zones”, i.e. subcommunities that manage to work at the interface around specific tools (a DNA microchip) or concepts (a network).

[2] 
D. Regnault, J.B. Rouquier, and E. Thierry.
Stochastic minority on graphs.
Theoretical Computer Science, Special issue on Cellular
automata and Discrete dynamical systems, 2011.
In
press, arXiv: 1011.5119.
[ bib 
DOI ]
Cellular automata have been mainly studied on very regular graphs carrying the vertices (like lines or grids) and under synchronous dynamics (all vertices update simultaneously). In this paper, we study how the asynchronism and the graph act upon the dynamics of the classical Minority rule. Minority has been wellstudied for synchronous updates and is thus a reasonable choice to begin with. Yet, beyond its apparent simplicity, this rule yields complex behaviors when asynchronism is introduced. We investigate the transitory part as well as the asymptotic behavior of the dynamics under full asynchronism (also called sequential: only one random vertex updates at each time step) for several types of graphs. Such a comparative study is a first step in understanding how the asynchronous dynamics is linked to the topology (the graph). Keywords: cellular automata; minority; asynchronism; graph; perturbation 
[3] 
P. Jensen, J.B. Rouquier, N. Ovtracht, and C. Robardet.
Characterizing the speed and paths of shared bicycles in Lyon.
Transportation Research Part D: Transport and Environment,
15(8):522  524, 2010.
arXiv: 1011.6266.
[ bib 
DOI 
.pdf ]
Thanks to numerical data gathered by Lyon's shared bicycling system Vélo'v, we are able to analyze 11.6 millions bicycle trips, leading to the first robust characterization of urban bikers' behaviors. We show that bicycles outstrip cars in downtown Lyon, by combining high speed and short paths.These data also allows us to calculate Vélo'v fluxes on all streets, pointing to interesting locations for bike paths. Keywords: Vélov; transport; average speed; bike; cycling; bike lane; cycleway; bike path; path; car 
[4] 
P. Borgnat, C. Robardet, J.B. Rouquier, E. Fleury, P. Abry, and P. Flandrin.
Shared bicycles in a city: A signal processing and data analysis
perspective.
Advances in Complex Systems, 2010.
Accepted.
[ bib 
http ]
Community shared bicycle systems, like the Vélo'v program launched in Lyon in May 2005, are public transportation programs that can be studied as a complex system composed of interconnected stations that exchange bicycles. They generate digital footprints that reveal the activity in the city over time and space, making possible a quantitative analysis of people’s movements. A careful study relying on nonstationary statistical modeling and data mining is done to first model the time evolution of the dynamics of movements with Vélo'v, that is mostly cyclostationary over the week with nonstationary evolutions over larger timescales, and second to disentangle the spatial patterns to understand and visualize the flows of Vélo'v bicycles in the city. This study gives insights about social behaviors of the users of this intermodal transportation system, the objective being to help in designing and planning policy in urban transportation. Repris dans les media :

[5] 
P. Jensen, J.B. Rouquier, P. Kreimer, and Y. Croissant.
Scientists who engage with society perform better academically.
Science and Public Policy, 35(7):527541, Aug 2008.
arXiv:
0810.4672.
[ bib 
DOI 
http ]
Most scientific institutions acknowledge the importance of opening the socalled 'ivory tower' of academic research through popularization, industrial collaboration or teaching. However, little is known about the actual openness of scientific institutions and how their proclaimed priorities translate into concrete measures. This paper gives an idea of some actual practices by studying three key points: the proportion of researchers who are active in wider dissemination, the academic productivity of these scientists, and the institutional recognition of their wider dissemination activities in terms of their careers. We analyze extensive data about the academic production, career recognition and teaching or public/industrial outreach of several thousand of scientists, from many disciplines, from France's Centre National de la Recherche Scientifique. We find that, contrary to what is often suggested, scientists active in wider dissemination are also more active academically. However, their dissemination activities have almost no impact (positive or negative) on their careers. Keywords: popularization; vulgarization:dissemination; hindex; bibliometry; bibliometric indicator; promotion; scientific career; academic career; teaching; industrial collaboration 
[6] 
P. Jensen, J.B. Rouquier, and Y. Croissant.
Testing bibliometric indicators by their prediction of scientists
promotions.
Scientometrics, 78(3), March 2009.
arXiv: 0811.0237.
[ bib 
DOI ]
We have developed a method to obtain robust quantitative bibliometric indicators for several thousand scientists. This allows us to study the dependence of bibliometric indicators (such as number of publications, number of citations, Hirsch index...) on the age, position, etc. of CNRS scientists. Our data suggests that the normalized h index (h divided by the career length) is not constant for scientists with the same productivity but differents ages. Keywords: bibliometric indicators; hindex; Hirsch index; career; scientific career; academic career; promotion; citations 
[7] 
J.B. Rouquier and M. Morvan.
Coalescing cellular automata: Synchronization by common random source
for asynchronous updating.
Journal of Cellular Automata, 4:5578, 2009.
arXiv: 0712.1992.
[ bib 
.html ]
We say that a Cellular Automata (CA) is coalescing when its execution on two distinct (random) initial configurations in the same asynchronous mode (the same cells are updated in each configuration at each time step) makes both configurations become identical after a reasonable time. We prove coalescence for two elementary rules, non coalescence for two other, and show that there exists infinitely many coalescing CA. We then conduct an experimental study on all elementary CA and show that some rules exhibit a phase transition, which belongs to the universality class of directed percolation.

[8] 
C. R. Shalizi, R. Haslinger, J.B. Rouquier, K. L. Klinkner, and C. Moore.
Automatic filters for the detection of coherent structure in
spatiotemporal systems.
Physical Review E, 73(3):036104, March 2005.
arXiv:
nlin.CG/0508001.
[ bib 
DOI 
http ]
Most current methods for identifying coherent structures in spatiallyextended systems rely on prior information about the form which those structures take. Here we present two new approaches to automatically filter the changing configurations of spatial dynamical systems and extract coherent structures. One, local sensitivity filtering, is a modification of the local Lyapunov exponent approach suitable to cellular automata and other discrete spatial systems. The other, local statistical complexity filtering, calculates the amount of information needed for optimal prediction of the system's behavior in the vicinity of a given point. By examining the changing spatiotemporal distributions of these quantities, we can find the coherent structures in a variety of patternforming cellular automata, without needing to guess or postulate the form of that structure. We apply both filters to elementary and cyclical cellular automata (ECA and CCA) and find that they readily identify particles, domains and other more complicated structures. We compare the results from ECA with earlier ones based upon the theory of formal languages, and the results from CCA with a more traditional approach based on an order parameter and free energy. While sensitivity and statistical complexity are equally adept at uncovering structure, they are based on different system properties (dynamical and probabilistic, respectively), and provide complementary information. Keywords: filtering; local sensitivity; local statistical complexity; elementary cellular automata; cyclic cellular automata; coherent structures 
[9] 
C. Moore, X. Yan, Y. Zhu, J.B. Rouquier, and T. Lane.
Active learning for hidden attributes in networks.
In KDD (International Conference on Knowledge Discovery and Data
Mining), 2011.
Accepted. Acceptance rate: 17.5%.
[ bib ]
Preferential attachment is a popular model of growing networks. We consider a generalized model with random node removal, and a combination of preferential and random attachment. Using a highdegree expansion of the master equation, we identify a topological phase transition depending on the rate of node removal and the relative strength of preferential vs. random attachment, where the degree distribution goes from a power law to one with an exponential tail.

[10] 
X. R. Yan, Y. J. Zhu, J.B. Rouquier, and C. Moore.
Active learning for hidden attributes in networks.
In E. Airoldi, J. Kleinberg, J. Leskovec, and J. Tenenbaum, editors,
22nd Annual Conference on Neural Information Processing Systems,
Workshop on Analyzing Networks and Learning with Graphs, December 2009.
arXiv: 1005.0794.
.
[ bib 
.pdf ]
In many networks, vertices have hidden attributes that are correlated with the network’s topology. For instance, in social networks, people are more likely to be friends if they are demographically similar. In food webs, predators typically eat prey of lower body mass. Keywords: active learning; collective classification; machine learning; foodweb; complex networks; node label; mutual information 
[11] 
P. Borgnat, P. Abry, P. Flandrin, and J.B. Rouquier.
Studying Lyon's Vélo'v: A statistical cyclic model.
In Proceedings of the European Conference on Complex Systems
(ECCS). Complex System Society, September 2009.
.
[ bib 
http ]
Lyon's community bicycle program called Vélo'v is a major initiative in shared public transportation, in activity since May 2005. It is studied here at a global level, to assess the evolution with time of the number of hired bikes. Based on the entire Vélo'v data set, up to December 2007, a statistical model is proposed to describe the daily and weekly patterns in a cyclostationary manner, jointly with the nonstationary evolutions over larger timescales larger. Combining this model with linear statistical regression, a procedure is developed for the prediction of the number of bikes hired per hour. This prediction method involves several explanation factors such as the number of subscribed users, the time in the week, the occurrence of holidays or strikes, and weather parameters (temperature, volume of rain). The conclusion is that, for most days, the observation of the number of actually hired bicyles is satisfyingly explained and predicted by the model proposed here. Keywords: Complex System; Community bicycle program ; Vélo'v; Cyclostationarity; AutoRegressive Process 
[12] 
J.B. Rouquier and M. Morvan.
Combined effect of topology and synchronism perturbation on cellular
automata: Preliminary results.
In H. Umeo, S. Morishita, and K. Nishinari, editors, ACRI,
volume 5191 of LNCS. Springer Berlin, 2008.
.
.
[ bib 
DOI 
.pdf ]
The aim of this paper is to experimentally study the combined effect of the introduction of two kinds of structural perturbations to the behavior of cellular automata. We present the results obtained by simultaneously perturbing synchronism and topology of elementary cellular automata. We show that very interesting and different behaviors appear, including phase transitions and non monotonicity (i.e. introduction of both perturbations is less effective than the introduction of only one of them). These results lead us to think that this study is worth to be now developed more accurately. Keywords: cellular automata; perturbation; topology perturbation; synchronism; synchronism perturbation; complex system 
[13] 
J.B. Rouquier.
An exhaustive experimental study of synchronization by forcing on
elementary cellular automata.
In B. Durand, editor, Proceedings of the First Symposium on
Cellular Automata, pages 250261. MCCME Publishing House, Moscow, April
2008.
.
[ bib 
http ]
We study a way of coupling two configurations of the same cellular automaton rule for all elementary cellular automata (ECA). We experimentally show that there are only two possible behaviors: either synchronization for all coupling strength, or a phase transition. This transition is shown to belong to the directed percolation universality class, even for a non chaotic rule and for rules with particles.

[14] 
J.B. Rouquier and M. Morvan.
Coalescing cellular automata.
In V. N. Alexandrov, G. D. van Albada, P. M. A. Sloot, and
J. Dongarra, editors, Proceedings of the 6th International Conference on
Computational Science (ICCS), volume 3993 of Lectures Notes in Computer
Science, pages 321328. Springer Berlin, May 2006.
, arXiv:
nlin.CG/0610009.
.
[ bib 
DOI 
http ]
We say that a Cellular Automata (CA) is coalescing when its execution on two distinct (random) initial configurations in the same asynchronous mode (the same cells are updated in each configuration at each time step) makes both configurations become identical after a reasonable time. We prove coalescence for two elementary rules and show that there exists infinitely many coalescing CA. We then conduct an experimental study on all elementary CA and show that some rules exhibit a phase transition, which belongs to the universality class of directed percolation. There is an extended journal version in [7]. Keywords: cellular automata; directed percolation; asynchronous cellular automata; phase transition 
[15] 
D. Regnault, J.B. Rouquier, and E. Thierry.
Stochastic minority on graphs.
Technical report, LIP, ENS Lyon, Université de Lyon, April 2008.
.
[ bib 
http ]
Cellular automata have been mainly studied on very regular graphs carrying the cells (like lines or grids) and under synchronous dynamics (all cells update simultaneously). In this paper we study how the asynchronism and the topology of cells act upon the dynamics of the classical Minority rule. Beyond its apparent simplicity, this rule yields complex behaviors which are clearly linked to the structure of the graph carrying the cells. There is an extended journal version in [2]. 
[16] 
J.B. Rouquier.
Robustesse et émergence dans les systèmes complexes: le
modèle des automates cellulaires.
PhD thesis, École Normale Supérieure de Lyon, December 2008.
.
[ bib 
http ]
See the page dedicated to my thesis. 
[17]  J.B. R. Pablo Jensen, Andrea Apolloni. Quelques éléments sur la géographie de la recherche en europe. Données Urbaines, 2011. Submitted. [ bib ] 
[18]  J.B. Rouquier, I. Alvarez, P.H. Wuillemin, and R. Reuillon. A kdtree algorithm to find and store hypervolumes. 2011. [ bib ] 
[19]  L. Merchez and J.B. Rouquier. L'usage des vélos en libre service (VLS) comme révélateur des rythmes urbains : le cas des stations de Vélo'v à Lyon. Données Urbaines, 2010. Submitted. [ bib ] 
[20]  C. Moore, J.B. Rouquier, and D. Sherrington. Topological phase transition in complex networks. European Physics Journal B, 2010. In preparation. [ bib ] 
[21]  P.Y. Louis and J.B. Rouquier. Timetocoalescence for interacting particle systems: Parallel versus sequential updating. Statistics and Computing, 2010. In preparation. [ bib ] 
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