Roger Guimerà

Roger Guimerà
Catalan Institution for Research and Advanced Studies | ICREA

Doctor of Philosophy

About

122
Publications
25,987
Reads
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15,547
Citations
Additional affiliations
January 2010 - October 2015
Catalan Institution for Research and Advanced Studies
Position
  • ICREA Research Professor at Universitat Rovira i Virgili
January 2003 - December 2009
Northwestern University
Position
  • Professor
September 2000 - December 2000
Boston University
Position
  • Visitor

Publications

Publications (122)
Article
Full-text available
Metabolic plasticity is the ability of a biological system to adapt its metabolic phenotype to different environmental stressors. We used a whole-body and tissue-specific phenotypic, functional, proteomic, metabolomic and transcriptomic approach to systematically assess metabolic plasticity in diet-induced obese mice after a combined nutritional an...
Article
A key question in human gut microbiome research is what are the robust structural patterns underlying its taxonomic composition. Herein, we use whole metagenomic datasets from healthy human guts to show that such robust patterns do exist, albeit not in the conventional enterotype sense. We first introduce the concept of mixed-membership enterotypes...
Preprint
Full-text available
Given a finite and noisy dataset generated with a closed-form mathematical model, when is it possible to learn the true generating model from the data alone? This is the question we investigate here. We show that this model-learning problem displays a transition from a low-noise phase in which the true model can be learned, to a phase in which the...
Article
Full-text available
Network inference is the process of learning the properties of complex networks from data. Besides using information about known links in the network, node attributes and other forms of network metadata can help solve network inference problems. Indeed, several approaches have been proposed to introduce metadata into probabilistic network models an...
Article
Full-text available
Many studies have shown that there are regularities in the way human beings make decisions. However, our ability to obtain models that capture such regularities and can accurately predict unobserved decisions is still limited. We tackle this problem in the context of individuals who are given information relative to the evolution of market prices a...
Article
Full-text available
We design a “wisdom-of-the-crowds” GRN inference pipeline, and couple it to complex network analysis, to understand the organisational principles governing gene regulation in long-lived glp-1/Notch C. elegans. The GRN has three layers (input, core, output) and is topologically equivalent to bow-tie/hourglass structures prevalent among metabolic net...
Preprint
Full-text available
Network inference is the process of learning the properties of complex networks from data. Besides using information about known links in the network, node attributes and other forms of network metadata can help to solve network inference problems. Indeed, several approaches have been proposed to introduce metadata into probabilistic network models...
Preprint
Full-text available
Many studies have shown that there are regularities in the way human beings make decisions. However, our ability to obtain models that capture such regularities and can accurately predict unobserved decisions is still limited. We tackle this problem in the context of individuals who are given information relative to the evolution of market prices a...
Preprint
Full-text available
Metabolic plasticity is the ability of a biological system to adapt its metabolic phenotype to different environmental stressors. We used a whole-body and tissue-specific phenotypic, functional, metabolomic and transcriptomic approach to systematically assess metabolic plasticity in diet-induced obese mice after a combined nutritional and exercise...
Preprint
Full-text available
Closed-form, interpretable mathematical models have been instrumental for advancing our understanding of the world; with the data revolution, we may now be in a position to uncover new such models for many systems from physics to the social sciences. However, to deal with increasing amounts of data, we need "machine scientists" that are able to ext...
Preprint
Ever since Nikuradse's experiments on turbulent friction in 1933, there have been theoretical attempts to describe his measurements by collapsing the data into single-variable functions. However, this approach, which is common in other areas of physics and in other fields, is limited by the lack of rigorous quantitative methods to compare alternati...
Preprint
Full-text available
Advancing our understanding of human behavior hinges on the ability of theories to unveil the mechanisms underlying such behaviors. Measuring the ability of theories and models to predict unobserved behaviors provides a principled method to evaluate their merit and, thus, to help establish which mechanisms are most plausible. Here, we propose model...
Article
Reducing inequality is essential for sustainable development, yet our understanding of its many dimensions and driving forces is still limited. Here we study the global distribution of 25 environmental burdens encompassing natural resources (water, materials and land use) and air emissions, all related to activities underpinning human welfare. We f...
Article
Ever since Nikuradse’s experiments on turbulent friction in 1933, there have been theoretical attempts to describe his measurements by collapsing the data into single-variable functions. However, this approach, which is common in other areas of physics and in other fields, is limited by the lack of rigorous quantitative methods to compare alternati...
Preprint
Full-text available
With the overwhelming online products available in recent years, there is an increasing need to filter and deliver relevant personalized advice for users. Recommender systems solve this problem by modeling and predicting individual preferences for a great variety of items such as movies, books or research articles. In this chapter, we explore rigor...
Article
Full-text available
Closed-form, interpretable mathematical models have been instrumental for advancing our understanding of the world; with the data revolution, we may now be in a position to uncover new such models for many systems from physics to the social sciences. However, to deal with increasing amounts of data, we need “machine scientists” that are able to ext...
Article
Full-text available
Motivation: The analysis of biological samples in untargeted metabolomic studies using LC-MS yields tens of thousands of ion signals. Annotating these features is of the utmost importance for answering questions as fundamental as, e.g. how many metabolites are there in a given sample. Results: Here, we introduce CliqueMS, a new algorithm for ann...
Chapter
With the overwhelming online products available in recent years, there is an increasing need to filter and deliver relevant personalized advice for users. Recommender systems solve this problem by modelling and predicting individual preferences for a great variety of items such as movies, books or research articles. In this chapter, we explore rigo...
Article
Full-text available
Advancing our understanding of human behavior hinges on the ability of theories to unveil the mechanisms underlying such behaviors. Measuring the ability of theories and models to predict unobserved behaviors provides a principled method to evaluate their merit and, thus, to help establish which mechanisms are most plausible. Here, we propose model...
Article
Full-text available
It has long been proposed that the cell cycle is regulated by physical forces at the cell-cell and cell-extracellular matrix (ECM) interfaces ¹⁻¹² . However, the evolution of these forces during the cycle has never been measured in a tissue, and whether this evolution affects cell cycle progression is unknown. Here, we quantified cell-cell tension...
Article
Full-text available
Many real-world complex systems are well represented as multilayer networks; predicting interactions in those systems is one of the most pressing problems in predictive network science. To address this challenge, we introduce two stochastic block models for multilayer and temporal networks; one of them uses nodes as its fundamental unit, whereas th...
Article
Full-text available
Leadership positions are still stereotyped as masculine, especially in male-dominated fields (e.g., engineering). So how do gender stereotypes affect the evaluation of leaders and team cohesiveness in the process of team development? In our study participants worked in 45 small teams (4–5 members). Each team was headed by either a female or male le...
Data
Raw data obtained from the responses of leader evaluations by other team members (spreadsheet 1) and from the self-evaluation survey of the leaders (spreadsheet 2). Spreadsheet 3 contains the dictionary of the data. (XLS)
Article
A principled approach to understand network structures is to formulate generative models. Given a collection of models, however, an outstanding key task is to determine which one provides a more accurate description of the network at hand, discounting statistical fluctuations. This problem can be approached using two principled criteria that at fir...
Article
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 an...
Article
Full-text available
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” (only a few perturbed and unp...
Article
Full-text available
The premature fusion of cranial bones, craniosynostosis, 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 modeli...
Article
Full-text available
Untargeted metabolomic studies are revealing large numbers of naturally occurring metabolites that cannot be characterized because their chemical structures and MS/MS spectra are not available in databases. Here we present iMet, a computational tool based on experimental tandem mass spectrometry that could potentially allow the annotation of metabo...
Article
Full-text available
With ever-increasing amounts of online information available, modeling and predicting individual preferences-for books or articles, for example-is becoming more and more important. Good predictions enable us to improve advice to users, and obtain a better understanding of the socio-psychological processes that determine those preferences. We have d...
Article
Full-text available
In complex systems, the network of interactions we observe between system's 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 studie...
Data
Modeling the distribution of logarithmic growth rates. (PDF)
Data
Equivalence between the directed and the undirected network of emails. (PDF)
Data
Predictability of logarithmic growth rates. (PDF)
Data
Social signature and communication strategies. (PDF)
Article
Full-text available
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 com...
Article
Full-text available
We have explored the multifunctional effects of polyphenols in humans adopting the notion that nutrients represent stimuli with consequences in the host’s health status. To assess the expected dynamic response from these stimuli we used transcriptomics and metabolomics to integrate specific functional pathways through network-based methods to gener...
Article
Full-text available
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 on the intricate microscop...
Article
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...
Article
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 unk...
Article
Full-text available
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 the Chicago Public Sc...
Conference Paper
We investigate the issue of how to mitigate global warming by performing changes in an economy. We use of a systematic tool that combines linear programming, environmentally extended input-output models and life cycle assessment. The problem of identifying economic sectors that mainly contribute to global warming is posed in mathematical terms as a...
Conference Paper
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 to point out trends...
Article
Full-text available
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 activi...
Article
Full-text available
Unlabelled: 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,...
Article
Full-text available
Author Summary Over one in four adults older than 57 in the US take five or more prescriptions at the same time; as many as 4% are at risk of a major adverse drug-drug interaction. Potentially beneficial effects of drug combinations, on the other hand, are also important. For example, combinations of drugs with synergistic effects increase the effi...
Article
Full-text available
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 avert it. Here,...