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Sales-Pardo, M.
Science 357 (6347) , 128 -129 (2017).

In the 1970s, ecologists began to speculate that modular systems—which are organized into blocks or modules—can better contain perturbations and are therefore more resilient against external damage (1). This simple concept can be applied to any networked system, be it an ecosystem, cellular metabolism, traffic flows, human disease contagion, a

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Esteve-Altava, B, Valles-Catala, T, Guimera, R, Sales-Pardo, M, Rasskin-Gutman, D.
Scientific Reports 7 , art. no. 3376 (2017).

Craniosynostosis, the premature fusion of cranial bones, affects the correct development of the skull producing morphological malformations in newborns. To assess the susceptibility of each craniofacial articulation to close prematurely, we used a network model of the skull to quantify the link reliability (an index based on stochastic block models

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Aguilar-Mogas, A, Sales-Pardo, M, Navarro, M, Guimerà, R, Yanes, O.
Anal. Chem. 89 (6) , 3474 -3482 (2017).

Structural annotation of metabolites relies mainly on tandem mass spectrometry (MS/MS) analysis. However, approximately 90% of the known metabolites reported in metabolomic databases do not have annotated spectral data from standards. This situation has fostered the development of computational tools that predict fragmentation patterns in silico and compare these to

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Cobo, S, Ahn, F, Eremin, I, Akbari, A.
Phys. Rev. B 94 , 224507 (2016).

We analyze the spin anisotropy of the magnetic susceptibility of Sr2RuO4 in the presence of spin-orbit coupling and anisotropic strain using quasi-two-dimensional tight-binding parametrization fitted to the angle-resolved photoemission spectroscopy results. Similar to the previous observations we find the in-plane polarization of the low-q magnetic fluctuations and the out-of-plane polarization

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Godoy-Lorite, A, Guimera, R, Moore, C, Sales-Pardo, M.
Proc. Natl. Acad. Sci. USA 113 (50) , 14207 -14212 (2016).

Recommendation systems are designed to predict users’ preferences and provide them with recommendations for items such as books or movies that suit their needs. Recent developments show that some probabilistic models for user preferences yield better predictions than latent feature models such as matrix factorization. However, it has not been

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Zeng, XHT, Duch, J, Sales-Pardo, M, Moreira, JAG, Radicchi, F, Ribeiro, HV, Woodruff, TK, Amaral, LAN .
PLoS Biol. 14(11) , e1002573 (2016).

Collaboration plays an increasingly important role in promoting research productivity and impact. What remains unclear is whether female and male researchers in science, technology, engineering, and mathematical (STEM) disciplines differ in their collaboration propensity. Here, we report on an empirical analysis of the complete publication records of 3,980 faculty members

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Massucci, FA, Wheeler, J, Beltran-Debon, R, Joven, J, Sales-Pardo, M, Guimera, R.
Sci. Adv. 2 , e1501638 (2016).

In a complex system, perturbations propagate by following paths on the network of interactions among the system’s units. In contrast to what happens with the spreading of epidemics, observations of general perturbations are often very sparse in time (there is a single observation of the perturbed system) and in “space”

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Valles-Catala, T, Massucci, FA, Guimera, R, Sales-Pardo, M.
Phys. Rev. X 6 , 011036 (2016).

In complex systems, the network of interactions we observe between systems components is the aggregate of the interactions that occur through different mechanisms or layers. Recent studies reveal that the existence of multiple interaction layers can have a dramatic impact in the dynamical processes occurring on these systems. However, these

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Godoy-Lorite, A, Guimera, R , Sales-Pardo, M.
PLOS ONE 11(1) , e0146113 (2016).

In social networks, individuals constantly drop ties and replace them by new ones in a highly unpredictable fashion. This highly dynamical nature of social ties has important implications for processes such as the spread of information or of epidemics. Several studies have demonstrated the influence of a number of factors

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Guimera, R, Sales-Pardo, M.
Rev. SEBBM 186 , 14 -16 (2015).

Nuevos enfoques nos permiten avanzar en la definición de un nuevo concepto de ruta metabólica, más general y mejor sustentado en la realidad sistémica del metabolismo. Pero todavía se tienen que desarrollar los métodos específicos que permitan extraer significado biológico a partir de la información disponible hoy.

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Pallares, J, Senan, O, Guimera, R, Vernet, A, Aguilar-Mogas, A, Vilahur, G, Badimon, L, Sales-Pardo, M, Cito, S.
Sci. Rep. 5 , 13606 (2015).

Thrombus formation is a multiscale phenomenon triggered by platelet deposition over a protrombotic surface (eg. a ruptured atherosclerotic plaque). Despite the medical urgency for computational tools that aid in the early diagnosis of thrombotic events, the integration of computational models of thrombus formation at different scales requires a comprehensive understanding

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Güell, O, Massucci, FA, Font-Clos, F, Sagués, F, Serrano MÁ.
J. R. Soc. Interface 12 , 20150543 (2015).

Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to the study of a single optimal state, such as maximum biomass yield that is by far the most

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Meo-Evoli, N, Almacellas E, Massucci FA, Gentilella A, Ambrosio S, Kozma SC, Thomas G, Tauler A.
Oncotarget 5 , - (2015).

In addition to being a master regulator of cell cycle progression, E2F1 regulates other associated biological processes, including growth and malignancy. Here, we uncover a regulatory network linking E2F1 to lysosomal trafficking and mTORC1 signaling that involves v-ATPase regulation. By immunofluorescence and time-lapse microscopy we found that E2F1 induces the

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Beltran-Debon, R, Rodriguez-Gallego, E, Fernandez-Arroyo, S, Senan-Campos, O, Massucci, FA, Hernandez-Aguilera, A, Sales-Pardo, M, Guimera, R, Camps, J, Menendez, JA, Joven, J.
Food Funct. 6 , 2957 -2966 (2015).

We explored the acute multifunctional effects of polyphenols from Hibiscus sabdariffa in humans to assess possible consequences on the host's health. The expected dynamic response was studied using a combination of transcriptomics and metabolomics to integrate specific functional pathways through network-based methods and to generate hypotheses established by acute metabolic

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Massucci, FA, Guimera, R, Amaral, LAN, Sales-Pardo, M.
Phys. Rev. E 91 , 062703 (2015).

High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that nutrients are used so as to maximize growth, these reconstructions enable us to predict microbial growth. Although such predictions are

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Bazellieres, E, Conte, V, Elosegui-Artola, A, Serra-Picamal, X, Bintanel-Morcillo, M, Roca-Cusachs, P, Muñoz, JJ, Sales-Pardo, M, Guimera, R, Trepat, T.
Nat. Cell Biol. 17 , 409 -420 (2015).

Dynamics of epithelial tissues determine key processes in development, tissue healing and cancer invasion. These processes are critically influenced by cell–cell adhesion forces. However, the identity of the proteins that resist and transmit forces at cell–cell junctions remains unclear, and how these proteins control tissue dynamics is largely unknown. Here

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Sirer, MI, Maroulis, S, Guimera, R, Wilensky, U, Amaral, LAN.
J. Policy Anal. Manag 34 (2) , 358 -377 (2015).

Existing research highlights that families face geographic, social, and psychological constraints that may limit the extent to which competition can take hold in school choice programs. In this paper, we address the implications of such findings by creating a network of student flows from 11 cohorts of eighth-grade students in

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Cortes-Borda, D, Ruiz-Hernandez, A, Guillén-Gosalbez, G, Llop, M, Guimera, R, Sales-Pardo, M .
Energ. Policy 77 , 21 -30 (2015).

Global warming mitigation has recently become a priority worldwide. A large body of literature dealing with energy related problems has focused on reducing greenhouse gases emissions at an engineering scale. In contrast, the minimization of climate change at a wider macroeconomic level has so far received much less attention. We

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Gavalda-Miralles, A, Otto, JS, Bustamanate, FE, Amaral, LAN, Duch, J, Guimera, R.
CoNEXT '14 Proceedings of the 10th ACM International Conference on emerging Networking Experiments and Technologies , 319 -324 (2014).

Though the impact of file-sharing of copyrighted content has been discussed for over a decade, only in the past few years have countries begun to adopt legislation to criminalize this behavior. These laws impose penalties ranging from warnings and monetary fines to disconnecting Internet service. While their supporters are quick

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Massucci, FA, Pérez Castillo, I, Pérez Vicente, CJ.
Phys. Rev. E 90 , 052708 (2014).

The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly studied force-elongation relation is typically hard. Here we draw from techniques developed in the context of

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Gavalda-Miralles, A, Choffnes, DR, Otto, JS, Sanchez, MA, Bustamante, FE, Amaral, LAN, Duch, J, Guimera, R.
Proc. Natl. Acad. Sci. U. S. A. 111 (43) , 15322 -15327 (2014).

Tens of millions of individuals around the world use decentralized content distribution systems, a fact of growing social, economic, and technological importance. These sharing systems are poorly understood because, unlike in other technosocial systems, it is difficult to gather large-scale data about user behavior. Here, we investigate user activity patterns

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Li, GP, Li, M, Zhang, YW, Wang, D, Li, R, Guimera, R, Gao, JT, Zhang, MQ.
PLOS ONE 9 (5) , e94608 (2014).

Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. In order to gain insight into the organization and structure of the resultant large complex networks formed by interacting molecules, using simulated annealing, a

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Guimera, R, Sales-Pardo, M.
PLOS Comput. Biol. 9 (12) , e1003374 (2013).

Characterizing interactions between drugs is important to avoid potentially harmful combinations, to reduce off-target effects of treatments and to fight antibiotic resistant pathogens, among others. Here we present a network inference algorithm to predict uncharacterized drug-drug interactions. Our algorithm takes, as its only input, sets of previously reported interactions, and

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Massucci, FA, DiNuzzo, M, Giove, F, Maraviglia, B, Pérez Castillo, I, Marinari, E, De Martino, A. .
BMC Systems Biology 7 , 103 (2013).

Background: The energetics of cerebral activity critically relies on the functional and metabolic interactions between neurons and astrocytes. Important open questions include the relation between neuronal versus astrocytic energy demand, glucose uptake and intercellular lactate transfer, as well as their dependence on the level of activity.

Results: We have developed a...

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Capitan, JA, Arenas, A, Guimera, R.
J. Theor. Biol. 334 , 35 -44 (2013).

In food webs, the degree of intervality of consumers' diets is an indicator of the number of dimensions that are necessary to determine the niche of a species. Previous studies modeling food-web structure have shown that real networks are compatible with a high degree of diet contiguity. However, current models

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Massucci FA, Font-Clos F, De Martino A, Pérez Castillo I..
Metabolites 2013 , 838-852 (2013).

Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production and consumption fluxes for each chemical species in the system. In some cases, the complexity of the solution

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Rovira-Asenjo, N, Gumi, T, Sales-Pardo, M, Guimera, R.
Sci. Rep. 3 , art. no. 1999 (2013).

Despite the well-documented benefits of working in teams, teamwork also results in communication, coordination and management costs, and may lead to personal conflict between team members. In a context where teams play an increasingly important role, it is of major importance to understand conflict and to develop diagnostic tools to

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Sales-Pardo, M, Diermeier, D, Amaral, LAN.
PLOS ONE 8 (5) , e58989 (2013).

Social groups of interacting agents display an ability to coordinate in the absence of a central authority, a phenomenon that has been recently amplified by the widespread availability of social networking technologies. Models of opinion formation in a population of agents have proven a very useful tool to investigate these

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Pah, AR, Guimera, R, Mustoe, AM, Amaral, LAN.
Sci. Rep. 3 , art. no. 1695 (2013).

The difficulty in annotating the vast amounts of biological information poses one of the greatest current challenges in biological research. The number of genomic, proteomic, and metabolomic datasets has increased dramatically over the last two decades, far outstripping the pace of curation efforts. Here, we tackle the challenge of curating

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Duch, J, Zeng, XHT, Sales-Pardo, M, Radicchi, F, Otis, S, Woodruff, TK, Amaral, LAN.
PLOS ONE , 7(12): e51332 (2012).

Many studies demonstrate that there is still a significant gender bias, especially at higher career levels, in many areas including science, technology, engineering, and mathematics (STEM). We investigated field-dependent, gender-specific effects of the selective pressures individuals experience as they pursue a career in academia within seven STEM disciplines. We built

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Seaver, SMD, Sales-Pardo, M, Guimera, R, Amaral, LAN.
PLOS Comput. Bio. , 8(11): e1002762 (2012).

The ability of microbial species to consume compounds found in the environment to generate commercially-valuable products has long been exploited by humanity. The untapped, staggering diversity of microbial organisms offers a wealth of potential resources for tackling medical, environmental, and energy challenges. Understanding microbial metabolism will be crucial to many

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Font-Clos, F, Massucci, FA, Pérez Castillo I.
J. Stat. Mech.-Theory Exp. , P11003 (2012).

In this work we introduce a novel weighted message-passing algorithm based on the cavity method for estimating volume-related properties of random polytopes, properties which are relevant in various research fields ranging from metabolic networks, to neural networks, to compressed sensing. We propose, as opposed to adopting the usual approach consisting

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Guimera, R.
Front. Gene. 3 , 183 (2012).

A book review on "Networks: an introduction"

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Guimera, R, Llorente, A, Moro, E, Sales-Pardo, M.
PLOS ONE 7 (9) , e44620 (2012).

With ever-increasing available data, predicting individuals' preferences and helping them locate the most relevant information has become a pressing need. Understanding and predicting preferences is also important from a fundamental point of view, as part of what has been called a ?new? computational social science. Here, we propose a novel

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Stouffer, DB, Sales-Pardo, M, Sirer, MI, Bascompte, J.
Science 335 , 1489 -1492 (2012).

Studies of ecological networks (the web of interactions between species in a community) demonstrate an intricate link between a community?s structure and its long-term viability. It remains unclear, however, how much a community?s persistence depends on the identities of the species present, or how much the role played by each

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N. Rovira-Asenjo, S. Ozgen, M. Medir, J. Tous, J. R. Alabart.
The Spanish journal of psychology 15 , 216 -226 (2012).

The selection process of team leaders is fundamental if the effectiveness of teams is to be guaranteed. Human values have proven to be an important factor in the behaviour of individuals and leaders. The aim of this study is twofold. The first is to validate Schwartz’s survey of human values.

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Gavalda, A, Duch, J, Gomez-Gardeñes, J.
Phys. Rev. E 85 , 026112 (2012).

In this paper we study the jamming transition in complex adaptive networks. We introduce an adaptation mechanism that modifies the weight of the communication channels in order to delay the congestion onset. Adaptivity takes place locally as it is driven by each node of the network. Surprisingly, regardless of the

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Guimera, R, Sales-Pardo, M.
PLOS ONE 6 (11) , e27188 (2011).

Successful attempts to predict judges' votes shed light into how legal decisions are made and, ultimately, into the behavior and evolution of the judiciary. Here, we investigate to what extent it is possible to make predictions of a justice's vote based on the other justices' votes in the same case.

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Bianco, CL, Massucci, FA, Ruffini, R.
Int. J. Mod. Phys. D 20 , 1919 -1929 (2011).

Due to the ultrarelativistic velocity of the expanding "fireshell" (Lorentz gamma factor gamma similar to 10(2) -10(3)), photons emitted at the same time from the fireshell surface do not reach the observer at the same arrival time. In interpreting Gamma-Ray Bursts (GRBs) it is crucial to determine the properties of

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Quapp, W, Bofill, JM, Aguilar-Mogas, A.
Theor. Chem. Acc. 129 , 803 -821 (2011).

Valley-ridge inflection points (VRI) on the potential energy surface for the ring opening of the cyclopropyl radical to allyl radical are determined using the tool of Newton trajectories (Quapp and Schmidt in Theor Chem Acc 128: 47, 2011). VRIs play a role in the understanding of bifurcating reactions. The region

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Gao, JT, Guimera, R, Lia, H, Mendes Pinto, I, Sales-Pardo, M, Wai, SC, Rubinstein, B, Li, R.
Proc. Natl. Acad. Sci. U. S. A. 108 , 7647 -7652 (2011).

In this study, we investigated on a systems level how complex protein interactions underlying cell polarity in yeast determine the dynamic association of proteins with the polar cortical domain (PCD) where they localize and perform morphogenetic functions. We constructed a network of physical interactions among >100 proteins localized to the

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Gonzalez, J, Caballero, M, Aguilar-Mogas, A, Torrent-Sucarrat, M, Crehuet, R, Sole, A, Gimenez, X, Olivella, S, Bofill, JM, Anglada, JM.
Theor. Chem. Acc. 128 , 579 -592 (2011).

The reaction between the HO radical and (H2O)n (n = 1, 3) clusters has been investigated employing high-level quantum mechanical calculations using DFT-BH&HLYP, QCISD, and CCSD(T) theoretical approaches in connection with the 6-311 + G(2df,2p), aug-cc-pVTZ, and aug-cc-pVQZ basis sets. The rate constants have also been calculated and the tunneling

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Guimera, R, Stouffer, DB, Sales-Pardo, M, Leicht, EA, Newman, MEJ, Amaral, LAN.
Ecology 91 , 2941 -2951 (2010).

The response of an ecosystem to perturbations is mediated by both antagonistic and facilitative interactions between species. It is thought that a community's resilience depends crucially on the food web---the network of trophic interactions---and on the food web's degree of compartmentalization. Despite its ecological importance, compartmentalization and the mechanisms that

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Maroulis, S, Guimera, R, Petry, H, Stringer, MJ, Gomez, LM, Amaral, LAN, Wilensky, U.
Science 330 , 38 -39 (2010).

Agent-based modeling and network analysis can help integrate knowledge on "micro-level" mechanisms and "macro-level" effects.

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Aguilar-Mogas, A, Gimenez, X, Bofill, JM.
J. Comput. Chem. 31 , 2510 -2525 (2010).

The intrinsic reaction coordinate (IRC) curve is used widely as a representation of the Reaction Path and can be parameterized taking the potential energy as a reaction coordinate (Aguilar-Mogas et al., J Chem Phys 2008, 128, 104102). Taking this parameterization and its variational nature, an algorithm is proposed that permits

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Stringer, MJ, Sales-Pardo, M, Amaral, LAN.
J. Am. Soc. Inf. Sci. Technol. 61 , 1377 -1385 (2010).

A central issue in evaluative bibliometrics is the characterization of the citation distribution of papers in the scientific literature. Here, we perform a large-scale empirical analysis of journals from every field in Thomson Reuters' Web of Science database. We find that only 30 of the 2,184 journals have citation distributions

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Choffnes, DR, Duch, J, Malmgren, RD, Guimera, R, Bustamante, FE, Amaral, LAN.
Proc. of the 9th International Workshop on Peer-to-Peer Systems (IPTPS) , (2010).

While P2P systems benefit from large numbers of interconnected nodes, each of these connections provides an opportunity for eavesdropping. Using only the connection patterns gathered from 10,000 BitTorrent (BT) users during a one-month period, we determine whether randomized connection patterns give rise to communities of users. Even though connections in

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Arenas, A, Cabrales, A, Danon, L, Diaz-Guilera, A, Guimera, R, Vega-Redondo, F.
Rev. Econ. Des. 14 , 75 -93 (2010).

We propose a stylized model of a problem-solving organization whose internal communication structure is given by a fixed network. Problems arrive randomly anywhere in this network and must find their way to their respective specialized solvers by relying on local information alone. The organization handles multiple problems simultaneously. For this

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Arias, S. Galera, E. Muñoz, A. García, F. Magarolas, D. Ollé, N. Sáez, J.A. Mera, N. Rovira-Asenjo .
International Journal of Arts and Sciences 3 , 189 -198 (2010).

The educational method known as “Project-Based Learning”, which is applied in the Escola Tècnica Superior d’Enginyeria Química (ETSEQ) of the Universitat Rovira i Virgili (URV), provides an appropriate environment for testing current trends concerning leadership in teams. Recent studies have shown that men exercise an autocratic and transactional leadership style

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Guimera, R, Sales-Pardo, M.
Proc. Natl. Acad. Sci. U. S. A. 106 , 22073 -22078 (2009).

Network analysis is currently used in a myriad of contexts, from identifying potential drug targets to predicting the spread of epidemics and designing vaccination strategies and from finding friends to uncovering criminal activity. Despite the promise of the network approach, the reliability of network data is a source of great

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Sawardecker, EN, Amundsen, CA, Sales-Pardo, M, Amaral, LAN.
Eur. Phys. J. B 72 , 671 -677 (2009).

Most real-world networks considered in the literature have a modular structure. Analysis of these real-world networks often are performed under the assumption that there is only one type of node. However, social and biochemical systems are often bipartite networks, meaning that there are two exclusive sets of nodes, and that

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Agusti Solanas, Arnau Gavalda and Robert Rallo.
International Conference on Artificial Neural Networks LNCS 5768 , 525 -535 (2009).

The protection of personal privacy is paramount, and consequently many e?orts have been devoted to the study of data protection techniques. Governments, statistical agencies and corporations must protect the privacy of the individuals while guaranteeing the right of the society to knowledge. Microaggregation is one of the most promising solutions

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Gonzalez, MF, Aguilar-Mogas, A, Gonzalez, J, Crehuet, R, Anglada, JM, Bofill, JM, Gimenez, X.
Theor. Chem. Acc. 123 , 51 -58 (2009).

Formation, persistence and decay of temporarily trapped states, the time-dependent generalization of resonances, are analysed within the framework of Bohmian Mechanics. More specifically, the so-called Bohm's total potential, the sum of classical plus Bohm's quantum potential, is used. It is found that both formation and decay are triggered by the

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Sawardecker, EN, Sales-Pardo, M, Amaral, LAN.
Eur. Phys. J. B 67 , 277 -284 (2009).

Most networks found in social and biochemical systems have modular structures. An important question prompted by the modularity of these networks is whether nodes can be said to belong to a single group. If they cannot, we would need to consider the role of "overlapping communities." Despite some efforts in

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Seaver, SMD, Moreira, AA, Sales-Pardo, M, Malmgren, RD, Diermeier, D, Amaral, LAN.
Eur. Phys. J. B 67 , 369 -375 (2009).

We use agent-based modeling to investigate the effect of conservatism and partisanship on the efficiency with which large populations solve the density classification task - a paradigmatic problem for information aggregation and consensus building. We find that conservative agents enhance the populations' ability to efficiently solve the density classification task

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De Martino, A, Martelli, C, Massucci, FA.
EPL 85 , art. no. 38007 (2009).

We study a simplified, solvable model of a fully connected metabolic network with constrained quenched disorder to mimic the conservation laws imposed by stoichiometry on chemical reactions. Within a spin-glass type of approach, we show that in the presence of a conserved metabolic pool the flux state corresponding to maximal

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Aguilar-Mogas, A, Gimenez, X, Bofill, JM.
J. Chem. Phys. 128 , art. no. 104102 (2008).

The intrinsic reaction coordinate curve (IRC), normally proposed as a representation of a reaction path, is parametrized as a function of the potential energy rather than the arc-length. This change in the parametrization of the curve implies that the values of the energy of the potential energy surface points, where

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Stringer, MJ, Sales-Pardo, M, Amaral, LAN.
PLoS One 3 , art. no. e1683 (2008).

Background: The rise of electronic publishing [1], preprint archives, blogs, and wikis is raising concerns among publishers, editors, and scientists about the present day relevance of academic journals and traditional peer review [2]. These concerns are especially fuelled by the ability of search engines to automatically identify and sort information

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Kho, A, Sales-Pardo, M, Wilson, J.
IEEE Eng. Med. Biol. Mag. 27 , 26 -28 (2008).

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Sales-Pardo, M, Chan, AOB, Amaral, LAN, Guimera, R.
Gene 402 , 81 -93 (2007).

Understanding evolutionary relationships between species can shed new light into the rooting of the tree of life and the origin of eukaryotes, thus, resulting in a long standing interest in accurately assessing evolutionary parameters at time scales on the order of a billion of years. Prior work suggests large variability

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Sales-Pardo, M, Guimera, R, Moreira, AA, Amaral, LAN.
Proc. Natl. Acad. Sci. U. S. A. 104 , 15224 -15229 (2007).

Extracting understanding from the growing "sea" of biological and socioeconomic data is one of the most pressing scientific challenges facing us. Here, we introduce and validate an unsupervised method for extracting the hierarchical organization of complex biological, social, and technological networks. We define an ensemble of hierarchically nested random graphs,

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Guimera, R, Sales-Pardo, M, Amaral, LAN.
Phys. Rev. E 76 , art. no. 036102 (2007).

Modularity is one of the most prominent properties of real-world complex networks. Here, we address the issue of module identification in two important classes of networks: bipartite networks and directed unipartite networks. Nodes in bipartite networks are divided into two nonoverlapping sets, and the links must have one end node

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Guimera, R, Sales-Pardo, M, Amaral, LAN.
Bioinformatics 23 , 1616 -1622 (2007).

Motivation: The lack of new antimicrobials, combined with increasing microbial resistance to old ones, poses a serious threat to public health. With hundreds of genomes sequenced, systems biology promises to help in solving this problem by uncovering new drug targets. Results: Here, we propose an approach that is based on

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Guimera, R, Sales-Pardo, M, Amaral, LAN.
Nat. Phys. 3 , 63 -69 (2007).

In physical, biological, technological and social systems, interactions between units give rise to intricate networks. These-typically non-trivial-structures, in turn, critically affect the dynamics and properties of the system. The focus of most current research on complex networks is, still, on global network properties. A caveat of this approach is that

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Aguilar-Mogas, A, Crehuet, R, Gimenez, X, Bofill, JM.
Mol. Phys. 105 , 2475 -2492 (2007).

A mathematical analysis of several algorithms, for the integration of the differential equation associated to the Intrinsic Reaction Coordinate path, is performed. This analysis first shows that the Intrinsic Reaction Coordinate path can be derived from a variational problem, so that it has the properties of an extremal curve. Then,

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Aguilar-Mogas, A, Gimenez, X, Bofill, J.
Chem. Phys. Lett. 432 , 375 -382 (2006).

A new algorithm for the integration of the intrinsic reaction coordinate path on a potential energy surface is proposed, based in solving the set of differential equations associated to the corresponding characteristic curve, rather than the differential equation of the curve itself. The integration of this set of differential equations

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Guimera, R, Danon, L, Diaz-Guilera, A, Giralt, E, Arenas, A.
J. Econ. Behav. Organ. 61 , 653 -667 (2006).

The formal chart of an organization is intended to prescribe how employees interact. However, ties between individuals arise for personal, political, and cultural reasons. The characterization of the structure of such informal networks behind the formal chart is a key element for successful management. We surmise that the exchange of

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Amaral, LAN, Guimera, R.
Nat. Phys. 2 , 75 -76 (2006).

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Guimera, R, Sales-Pardo, M.
Mol. Syst. Biol. 2 , art. no. 42 (2006).

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Guimera, R, Mossa, S, Turtschi, A, Amaral, LAN.
Proc. Natl. Acad. Sci. U. S. A. 102 , 7794 -7799 (2005).

We analyze the global structure of the worldwide air transportation network, a critical infrastructure with an enormous impact on local, national, and international economies. We find that the worldwide air transportation network is a scale-free small-world network. In contrast to the prediction of scale-free network models, however, we find that

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Sales-Pardo, M, Guimera, R, Moreira, AA, Widom, J, Amaral, LAN.
Phys. Rev. E 71 , art. no. 051902 (2005).

To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model

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Stouffer, DB, Camacho, J, Guimera, R, Ng, CA, Amaral, LAN.
Ecology 86 , 1301 -1311 (2005).

Understanding the structure of food webs, and the mechanisms that give rise to this structure, is one of the most challenging problems in ecology. We analyze from a statistical physics perspective the network structure of model food webs and of 15 community food webs from a variety of environments, including

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Guimera, R, Uzzi, B, Spiro, J, Amaral, LAN.
Science 308 , 697 -702 (2005).

Agents in creative enterprises are embedded in networks that inspire, support, and evaluate their work. Here, we investigate how the mechanisms by which creative teams self-assemble determine the structure of these collaboration networks. We propose a model for the self-assembly of creative teams that has its basis in three parameters:

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Guimera, R, Amaral, LAN.
Nature 433 , 895 -900 (2005).

High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major scientific challenge. Here, we propose a methodology that enables us to extract and display information contained

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Guimera, R, Amaral, LAN.
J. Stat. Mech.-Theory Exp. , art. no. P02001 (2005).

Integrative approaches to the study of complex systems demand that one knows the manner in which the parts comprising the system are connected. The structure of the complex network defining the interactions provides insight into the function and evolution of the components of the system. Unfortunately, the large size and

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Guimera, R, Sales-Pardo, M, Amaral, LAN.
Phys. Rev. E 70 , art. no. 025101 (2004).

The mechanisms by which modularity emerges in complex networks are not well understood but recent reports have suggested that modularity may arise from evolutionary selection. We show that finding the modularity of a network is analogous to finding the ground-state energy of a spin system. Moreover, we demonstrate that, due

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Arenas, A, Danon, L, Diaz-Guilera, A, Gleiser, PM, Guimera, R.
Eur. Phys. J. B 38 , 373 -380 (2004).

We present an empirical study of different social networks obtained from digital repositories. Our analysis reveals the community structure and provides a useful visualising technique. We investigate the scaling properties of the community size distribution, and find that all the networks exhibit power law scaling in the community size distributions

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Guimera, R, Amaral, LAN.
Eur. Phys. J. B 38 , 381 -385 (2004).

Recently, we have presented the first exhaustive analysis of the world-wide airport network. Two important results of that study are that: (i) the world-wide airport network is a small-world network with power-law decaying degree and betweenness centrality distributions; (ii) the most connected cities (largest degree) are typically not the most

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Arenas, A, Danon, L, Diaz-Guilera, A, Guimera, R.
LECT NOTE COMPUT SCI 3038 , 1078 -1085 (2004).

We present a formalism that is able to cope with search and congestion simultaneously. This formalism avoids the problem of simulating the dynamics of the search-communication process which turns out to be impracticable, specially close to the congestion point where search costs (time) diverge.

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Palassini, M, Sales, M, Ritort, F.
Phys. Rev. B 68 , art. no. 224430 (2003).

We present a numerical study of the order-parameter fluctuations for Ising spin glasses in three and four dimensions at very low temperatures and without an external field. Accurate measurements of two previously introduced parameters A and G show that the order parameter is not self-averaging, consistent with a zero-temperature thermal

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Bofill, P, Guimera, R, Torras, C.
Neural Netw. 16 , 1421 -1428 (2003).

This paper describes an experimental comparison between a discrete stochastic optimization procedure (Simulated Annealing, SA) and a continuous deterministic one (Mean Field Annealing), as applied to the generation of Balanced Incomplete Block Designs (BIBDs). A neural cost function for BIBD generation is proposed with connections of arity four, and its

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Guimera, R, Danon, L, Diaz-Guilera, A, Giralt, F, Arenas, A.
Phys. Rev. E 68 , art. no. 065103 (2003).

We propose a procedure for analyzing and characterizing complex networks. We apply this to the social network as constructed from email communications within a medium sized university with about 1700 employees. Email networks provide an accurate and nonintrusive description of the flow of information within human organizations. Our results reveal

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Picco, M, Ritort, F, Sales, M.
Phys. Rev. B 67 , art. no. 184421 (2003).

An approach to determine the value of the zero-temperature thermal exponent theta in spin glasses is presented. It consists in describing the energy level spectrum in spin glasses only in terms of the properties of the lowest energy droplets and the lowest droplet exponents (LDE's) lambda(l),theta(l) that describe the statistics

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Sales, M, Bouchaud, JP, Ritort, F.
J. Phys. A-Math. Gen. 36 , 665 -684 (2003).

We study analytically and numerically the role of temperature shifts in the simplest model where the energy landscape is explicitly hierarchical, namely the Sinai model. This model has both attractive features (there are valleys within valleys in a strict self-similar sense), but also one important drawback: there is no phase

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Arenas, A, Cabrales, A, Diaz-Guilera, A, Guimera, R, Vega-Redondo, F.
LECT NOTES PHYS 625 , 175 -194 (2003).

A model of communication that is able to cope simultaneously with the problems of search and congestion is presented. We investigate the communication dynamics in model networks. Those networks consist in a regular lattice ordering plus some long-range short-cuts with a given probability. The destination nodes of the short-cuts are

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Guimera, R, Diaz-Guilera, A, Vega-Redondo, F, Cabrales, A, Arenas, A.
Phys. Rev. Lett. 89 , art. no. 248701 (2002).

The problem of searchability in decentralized complex networks is of great importance in computer science, economy, and sociology. We present a formalism that is able to cope simultaneously with the problem of search and the congestion effects that arise when parallel searches are performed, and we obtain expressions for the

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Guimera, R, Arenas, A, Diaz-Guilera, A, Giralt, F.
Phys. Rev. E 66 , art. no. 026704 (2002).

We study the dynamical properties of a collection of models for communication processes, characterized by a single parameter xi representing the relation between information load of the nodes and its ability to deliver this information. The critical transition to congestion reported so far occurs only for xi=1. This case is

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Camacho, J, Guimera, R, Amaral, LAN.
Phys. Rev. Lett. 88 , art. no. 228102 (2002).

We analyze the properties of seven community food webs from a variety of environments, including freshwater, marine-freshwater interfaces, and terrestrial environments. We uncover quantitative unifying patterns that describe the properties of the diverse trophic webs considered and suggest that statistical physics concepts such as scaling and universality may be useful

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Sales, M, Yoshino, H.
Phys. Rev. E 65 , art. no. 066131 (2002).

We examine the sensitiveness of the free-energy landscape of a directed polymer in random media with respect to various kinds of infinitesimally weak perturbation including the intriguing case of temperature chaos. To this end, we combine the replica Bethe Ansatz approach outlined by Sales and Yoshino (e-print cond-mat/0112384), the mapping

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Camacho, J, Guimera, R, Amaral, LAN.
Phys. Rev. E 65 , art. no. 030901 (2002).

We investigate numerically and analytically a recently proposed model for food webs [Nature 404, 180 (2000)] in the limit of large web sizes and sparse interaction matrices. We obtain analytical expressions for several quantities with ecological interest, in particular, the probability distributions for the number of prey and the number

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Guimera, R, Arenas, A, Diaz-Guilera, A.
Physica A 299 , 247 -252 (2001).

We study a general and simple model for communication processes. In the model, agents in a network (in particular, an organization) interchange information packets following simple rules that take into account the limited capability of the agents to deal with packets and the cost associated with the existence of open

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Sales, M, Bouchaud, JP.
Europhys. Lett. 56 , 181 -186 (2001).

We show that the Random Energy Model has interesting rejuvenation properties in its frozen phase. Different susceptibilities to temperature changes, for the free energy and for other ( magnetic) observables, can be computed exactly. These susceptibilities diverge at the transition temperature, as (1T/T-c)(-3) for the free energy.

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Ritort, F, Sales, M.
J. Phys. A-Math. Gen. 34 , L333 -L339 (2001).

We present a constructive approach to obtain information about the compactness and shape of large-scale lowest excitations in disordered systems by studying order parameter fluctuations (OPF) at low temperatures. We show that the parameter G that measures OFF is 1/3 at T = 0 provided the ground state is unique

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Arenas, A, Diaz-Guilera, A, Guimera, R.
Phys. Rev. Lett. 86 , 3196 -3199 (2001).

We present a simple model of communication in networks with hierarchical branching. We analyze the behavior of the model from the viewpoint of critical systems under different situations. For certain values of the parameters, a continuous phase transition between a sparse and a congested regime is observed and accurately described

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Picco, M, Ritort, F, Sales, M.
Eur. Phys. J. B 19 , 565 -582 (2001).

The rise of parameters measuring order-parameter fluctuations: (OPF) has been encouraged by the recent results reported in reference [2,3] which show that two of these parameters, G and G,, take universal values in the lim(T -->0). In this paper we present a detailed study of parameters measuring OPF for two

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Ritort, F, Sales, M.
J. Phys. A-Math. Gen. 33 , 6505 -6526 (2000).

We study order-parameter fluctuations (OPF) in disordered systems by considering the behaviour of some recently introduced parameters G, G(c) which have proven very useful in locating phase transitions. We prove that both parameters G (for disconnected overlap disorder averages) and G(c) (for connected disorder averages) take the respective universal values

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Sales, M, Hernandez, JM, Tejada, J, Martinez, JL.
Phys. Rev. B 60 , 14557 -14560 (1999).

In this paper we discuss both theoretical and experimental results on the time dependence of the heat capacity of oriented Mn(12) magnetic clusters when a magnetic field is applied along their easy axis. Our calculations are based on the existence of two contributions. The first one is associated with the

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del Barco, E, Hernandez, JM, Sales, M, Tejada, J, Rakoto, H, Broto, JM, Chudnovsky, EM.
Phys. Rev. B 60 , 11898 -11901 (1999).

We report experimental studies and suggest a quantitative model of spin relaxation in Mn-12 acetate in a pulsed magnetic field in the temperature range 1.9-5.0 K. When the field applied along the anisotropy axis is swept at 140 T/s through a nonmagnetized Mn-12 acetate sample, the sample's magnetization switches, within

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Bohigas, X, del Barco, E, Sales, M, Tejada, J.
J. Magn. Magn. Mater. 196 , 455 -457 (1999).

In this paper, we comment on experiments we have carried out on ceramic perovskites of composition La0.65Ca0.35Ti1-xMnxO3. From low- and high-field magnetic measurements recorded at different temperatures, we have discovered the existence of a large entropic change associated to the ferrimagnetic-paramagnetic transition. Our conclusion is that these materials are excellent

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Bohigas, X, Tejada, J, del Barco, E, Zhang, XX, Sales, M.
Appl. Phys. Lett. 73 , 390 -392 (1998).

A large entropy variation (magnetocaloric effect) has been discovered in ceramic perovskites with the formulas La0.65Ca0.35Ti1-xMnxO3-z and La0.5+x+yLi0.5-3yTi1-3xMn3xO3-z. Both Curie temperature and entropy change were studied from 4.2 to 400 K for different stoichiometric compositions and applied magnetic fields. Our conclusion is that these materials are excellent candidates for working

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