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Tensorial and bipartite block models for link prediction in layered networks and temporal networks.

Tarrés-Deulofeu M, Godoy-Lorite A, Guimerà R, Sales-Pardo M.

Phys Rev E. 2019 Mar;99(3-1):032307. doi: 10.1103/PhysRevE.99.032307.


CliqueMS: A computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network.

Senan O, Aguilar-Mogas A, Navarro M, Capellades J, Noon L, Burks D, Yanes O, Guimerà R, Sales-Pardo M.

Bioinformatics. 2019 Mar 23. pii: btz207. doi: 10.1093/bioinformatics/btz207. [Epub ahead of print]


Adaptive metabolic pattern biomarker for disease monitoring and staging of lung cancer with liquid biopsy.

Garcia-Algar M, Fernandez-Carrascal A, Olano-Daza A, Guerrini L, Feliu N, Parak WJ, Guimera R, Garcia-Rico E, Alvarez-Puebla RA.

NPJ Precis Oncol. 2018 Aug 8;2:16. doi: 10.1038/s41698-018-0059-9. eCollection 2018.


Consistencies and inconsistencies between model selection and link prediction in networks.

Vallès-Català T, Peixoto TP, Sales-Pardo M, Guimerà R.

Phys Rev E. 2018 Jun;97(6-1):062316. doi: 10.1103/PhysRevE.97.062316.


Regulation of cell cycle progression by cell-cell and cell-matrix forces.

Uroz M, Wistorf S, Serra-Picamal X, Conte V, Sales-Pardo M, Roca-Cusachs P, Guimerà R, Trepat X.

Nat Cell Biol. 2018 Jun;20(6):646-654. doi: 10.1038/s41556-018-0107-2. Epub 2018 May 25.


Leader evaluation and team cohesiveness in the process of team development: A matter of gender?

Rovira-Asenjo N, Pietraszkiewicz A, Sczesny S, Gumí T, Guimerà R, Sales-Pardo M.

PLoS One. 2017 Oct 23;12(10):e0186045. doi: 10.1371/journal.pone.0186045. eCollection 2017.


Bone Fusion in Normal and Pathological Development is Constrained by the Network Architecture of the Human Skull.

Esteve-Altava B, Vallès-Català T, Guimerà R, Sales-Pardo M, Rasskin-Gutman D.

Sci Rep. 2017 Jun 13;7(1):3376. doi: 10.1038/s41598-017-03196-9.


iMet: A Network-Based Computational Tool To Assist in the Annotation of Metabolites from Tandem Mass Spectra.

Aguilar-Mogas A, Sales-Pardo M, Navarro M, Guimerà R, Yanes O.

Anal Chem. 2017 Mar 21;89(6):3474-3482. doi: 10.1021/acs.analchem.6b04512. Epub 2017 Mar 3.


Accurate and scalable social recommendation using mixed-membership stochastic block models.

Godoy-Lorite A, Guimerà R, Moore C, Sales-Pardo M.

Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):14207-14212. Epub 2016 Nov 23.


Inferring propagation paths for sparsely observed perturbations on complex networks.

Massucci FA, Wheeler J, Beltrán-Debón R, Joven J, Sales-Pardo M, Guimerà R.

Sci Adv. 2016 Oct 21;2(10):e1501638. eCollection 2016 Oct.


Long-Term Evolution of Email Networks: Statistical Regularities, Predictability and Stability of Social Behaviors.

Godoy-Lorite A, Guimerà R, Sales-Pardo M.

PLoS One. 2016 Jan 6;11(1):e0146113. doi: 10.1371/journal.pone.0146113. eCollection 2016.


A comprehensive study on different modelling approaches to predict platelet deposition rates in a perfusion chamber.

Pallarès J, Senan O, Guimerà R, Vernet A, Aguilar-Mogas A, Vilahur G, Badimon L, Sales-Pardo M, Cito S.

Sci Rep. 2015 Sep 22;5:13606. doi: 10.1038/srep13606.


Experiences with workflows for automating data-intensive bioinformatics.

Spjuth O, Bongcam-Rudloff E, Hernández GC, Forer L, Giovacchini M, Guimera RV, Kallio A, Korpelainen E, Kańduła MM, Krachunov M, Kreil DP, Kulev O, Łabaj PP, Lampa S, Pireddu L, Schönherr S, Siretskiy A, Vassilev D.

Biol Direct. 2015 Aug 19;10:43. doi: 10.1186/s13062-015-0071-8.


The acute impact of polyphenols from Hibiscus sabdariffa in metabolic homeostasis: an approach combining metabolomics and gene-expression analyses.

Beltrán-Debón R, Rodríguez-Gallego E, Fernández-Arroyo S, Senan-Campos O, Massucci FA, Hernández-Aguilera A, Sales-Pardo M, Guimerà R, Camps J, Menendez JA, Joven J.

Food Funct. 2015 Sep;6(9):2957-66. doi: 10.1039/c5fo00696a.


Scaling and optimal synergy: Two principles determining microbial growth in complex media.

Massucci FA, Guimerà R, Amaral LA, Sales-Pardo M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Jun;91(6):062703. Epub 2015 Jun 8.


Control of cell-cell forces and collective cell dynamics by the intercellular adhesome.

Bazellières E, Conte V, Elosegui-Artola A, Serra-Picamal X, Bintanel-Morcillo M, Roca-Cusachs P, Muñoz JJ, Sales-Pardo M, Guimerà R, Trepat X.

Nat Cell Biol. 2015 Apr;17(4):409-20. doi: 10.1038/ncb3135.


Community-driven development for computational biology at Sprints, Hackathons and Codefests.

Möller S, Afgan E, Banck M, Bonnal RJ, Booth T, Chilton J, Cock PJ, Gumbel M, Harris N, Holland R, Kalaš M, Kaján L, Kibukawa E, Powel DR, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Sloggett C, Soiland-Reyes S, Spooner W, Steinbiss S, Tille A, Travis AJ, Guimera R, Katayama T, Chapman BA.

BMC Bioinformatics. 2014;15 Suppl 14:S7. doi: 10.1186/1471-2105-15-S14-S7. Epub 2014 Nov 27.


Impact of heterogeneity and socioeconomic factors on individual behavior in decentralized sharing ecosystems.

Gavaldà-Miralles A, Choffnes DR, Otto JS, Sánchez MA, Bustamante FE, Amaral LA, Duch J, Guimerà R.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15322-7. doi: 10.1073/pnas.1309389111. Epub 2014 Oct 6.


ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks.

Li G, Li M, Zhang Y, Wang D, Li R, Guimerà R, Gao JT, Zhang MQ.

PLoS One. 2014 May 1;9(5):e94608. doi: 10.1371/journal.pone.0094608. eCollection 2014.


A network inference method for large-scale unsupervised identification of novel drug-drug interactions.

Guimerà R, Sales-Pardo M.

PLoS Comput Biol. 2013;9(12):e1003374. doi: 10.1371/journal.pcbi.1003374. Epub 2013 Dec 5.


Fastphylo: fast tools for phylogenetics.

Khan MA, Elias I, Sjölund E, Nylander K, Guimera RV, Schobesberger R, Schmitzberger P, Lagergren J, Arvestad L.

BMC Bioinformatics. 2013 Nov 20;14:334. doi: 10.1186/1471-2105-14-334.


Predicting future conflict between team-members with parameter-free models of social networks.

Rovira-Asenjo N, Gumí T, Sales-Pardo M, Guimerà R.

Sci Rep. 2013;3:1999. doi: 10.1038/srep01999.


Degree of intervality of food webs: from body-size data to models.

Capitán JA, Arenas A, Guimerà R.

J Theor Biol. 2013 Oct 7;334:35-44. doi: 10.1016/j.jtbi.2013.06.004. Epub 2013 Jun 13.


Use of a global metabolic network to curate organismal metabolic networks.

Pah AR, Guimerà R, Mustoe AM, Amaral LA.

Sci Rep. 2013;3:1695. doi: 10.1038/srep01695.


Phenomenological model for predicting the catabolic potential of an arbitrary nutrient.

Seaver SM, Sales-Pardo M, Guimerà R, Amaral LA.

PLoS Comput Biol. 2012;8(11):e1002762. doi: 10.1371/journal.pcbi.1002762. Epub 2012 Nov 1.


Predicting human preferences using the block structure of complex social networks.

Guimerà R, Llorente A, Moro E, Sales-Pardo M.

PLoS One. 2012;7(9):e44620. doi: 10.1371/journal.pone.0044620. Epub 2012 Sep 11.


Justice blocks and predictability of U.S. Supreme Court votes.

Guimerà R, Sales-Pardo M.

PLoS One. 2011;6(11):e27188. doi: 10.1371/journal.pone.0027188. Epub 2011 Nov 9.


Modular coherence of protein dynamics in yeast cell polarity system.

Gao JT, Guimerà R, Li H, Pinto IM, Sales-Pardo M, Wai SC, Rubinstein B, Li R.

Proc Natl Acad Sci U S A. 2011 May 3;108(18):7647-52. doi: 10.1073/pnas.1017567108. Epub 2011 Apr 18.


Origin of compartmentalization in food webs.

Guimerà R, Stouffer DB, Sales-Pardo M, Leicht EA, Newman ME, Amaral LA.

Ecology. 2010 Oct;91(10):2941-51.


Education. Complex systems view of educational policy research.

Maroulis S, Guimerà R, Petry H, Stringer MJ, Gomez LM, Amaral LA, Wilensky U.

Science. 2010 Oct 1;330(6000):38-9. doi: 10.1126/science.1195153. No abstract available.


Missing and spurious interactions and the reconstruction of complex networks.

Guimerà R, Sales-Pardo M.

Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22073-8. doi: 10.1073/pnas.0908366106. Epub 2009 Dec 14.


Classes of complex networks defined by role-to-role connectivity profiles.

Guimerà R, Sales-Pardo M, Amaral LA.

Nat Phys. 2007;3(1):63-69.


Cartography of complex networks: modules and universal roles.

Guimerà R, Amaral LA.

J Stat Mech. 2005 Feb 1;2005(P02001):nihpa35573.


Module identification in bipartite and directed networks.

Guimerà R, Sales-Pardo M, Amaral LA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Sep;76(3 Pt 2):036102. Epub 2007 Sep 6.


Extracting the hierarchical organization of complex systems.

Sales-Pardo M, Guimerà R, Moreira AA, Amaral LA.

Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15224-9. Epub 2007 Sep 19. Erratum in: Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18874.


Evolution of protein families: is it possible to distinguish between domains of life?

Sales-Pardo M, Chan AO, Amaral LA, Guimerà R.

Gene. 2007 Nov 1;402(1-2):81-93. Epub 2007 Aug 14.


A network-based method for target selection in metabolic networks.

Guimerà R, Sales-Pardo M, Amaral LA.

Bioinformatics. 2007 Jul 1;23(13):1616-22. Epub 2007 Apr 26.


Form follows function: the architecture of complex networks.

Guimerà R, Sales-Pardo M.

Mol Syst Biol. 2006;2:42. Epub 2006 Aug 1. No abstract available.


Mesoscopic modeling for nucleic acid chain dynamics.

Sales-Pardo M, Guimerà R, Moreira AA, Widom J, Amaral LA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 May;71(5 Pt 1):051902. Epub 2005 May 5.


The worldwide air transportation network: Anomalous centrality, community structure, and cities' global roles.

Guimerà R, Mossa S, Turtschi A, Amaral LA.

Proc Natl Acad Sci U S A. 2005 May 31;102(22):7794-9. Epub 2005 May 23.


Team assembly mechanisms determine collaboration network structure and team performance.

Guimerà R, Uzzi B, Spiro J, Amaral LA.

Science. 2005 Apr 29;308(5722):697-702.


Functional cartography of complex metabolic networks.

Guimerà R, Nunes Amaral LA.

Nature. 2005 Feb 24;433(7028):895-900.


Modularity from fluctuations in random graphs and complex networks.

Guimerà R, Sales-Pardo M, Amaral LA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Aug;70(2 Pt 2):025101. Epub 2004 Aug 19.


Self-similar community structure in a network of human interactions.

Guimerà R, Danon L, Díaz-Guilera A, Giralt F, Arenas A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Dec;68(6 Pt 2):065103. Epub 2003 Dec 17.


Comparison of simulated annealing and mean field annealing as applied to the generation of block designs.

Bofill P, Guimerà R, Torras C.

Neural Netw. 2003 Dec;16(10):1421-8.


Optimal network topologies for local search with congestion.

Guimerà R, Díaz-Guilera A, Vega-Redondo F, Cabrales A, Arenas A.

Phys Rev Lett. 2002 Dec 9;89(24):248701. Epub 2002 Nov 21.


Dynamical properties of model communication networks.

Guimerà R, Arenas A, Díaz-Guilera A, Giralt F.

Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Aug;66(2 Pt 2):026704. Epub 2002 Aug 19.


Robust patterns in food web structure.

Camacho J, Guimerà R, Nunes Amaral LA.

Phys Rev Lett. 2002 Jun 3;88(22):228102. Epub 2002 May 16.


Analytical solution of a model for complex food webs.

Camacho J, Guimerà R, Amaral LA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Mar;65(3 Pt 1):030901. Epub 2002 Feb 8.


Communication in networks with hierarchical branching.

Arenas A, Díaz-Guilera A, Guimerà R.

Phys Rev Lett. 2001 Apr 2;86(14):3196-9.


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