Genomes and Genes
Affiliation: Hospital del Mar
- Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationshipsJordi Espadaler
Grup de Bioinformàtica Estructural GRIB IMIM, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain
Bioinformatics 21:3360-8. 2005....
- Topological comparison of methods for predicting transcriptional cooperativity in yeastDaniel Aguilar
Structural Bioinformatics Group GRIB, IMIM Universitat Pompeu Fabra, C Doctor Aiguader, 88, Barcelona 08003, Spain
BMC Genomics 9:137. 2008....
- Prediction of enzyme function by combining sequence similarity and protein interactionsJordi Espadaler
Laboratori de Bioinformàtica Estructural GRIB, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra IMIM, 08003 Barcelona, Catalonia, Spain
BMC Bioinformatics 9:249. 2008..Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar interacting partners...
- ModLink+: improving fold recognition by using protein-protein interactionsOriol Fornes
Structural Bioinformatics Lab GRIB IMIM, Universitat Pompeu Fabra, Parc de Recerca Biomédica de Barcelona PRBB, Barcelona, Catalonia, Spain
Bioinformatics 25:1506-12. 2009..Here, we present an improved version of the method that addresses this limitation. We also compare our method to other state-of-the-art fold assignment methodologies...
- Functional clustering of metastasis proteins describes plastic adaptation resources of breast-cancer cells to new microenvironmentsBerta Martín
Centre d Oncologia Molecular, IDIBELL, Hospital Duran i Reynals, CSUB, L Hospitalet Llobregat, Barcelona, Spain
J Proteome Res 7:3242-53. 2008..71 x 10(-2)) and protein amino acid phosphorylation (p-value FDR = 3.28 x 10(-2)) might be the most significant biological process differentially increased in liver metastasis...
- Characterization of protein hubs by inferring interacting motifs from protein interactionsRamon Aragues
Structural Bioinformatics Lab GRIB, Universitat Pompeu Fabra IMIM, Barcelona Research Park of Biomedicine PRBB, Barcelona, Catalonia, Spain
PLoS Comput Biol 3:1761-71. 2007..The proposed method will help us discover unknown interacting motifs and provide biological insights about protein hubs and their roles in interaction networks...
- Expression of endoplasmic reticulum stress proteins is a candidate marker of brain metastasis in both ErbB-2+ and ErbB-2- primary breast tumorsRebeca Sanz-Pamplona
Biological Clues of the Invasive and Metastatic Phenotype Group, Bellvitge Biomedical Research Institute IDIBELL, Barcelona, Spain
Am J Pathol 179:564-79. 2011..16) than ErbB-2 (LR = 0.42). We conclude that, in breast carcinomas, certain proteins associated with the endoplasmic reticulum stress phenotype are candidate markers of brain metastasis...
- Biana: a software framework for compiling biological interactions and analyzing networksJavier Garcia-Garcia
Structural Bioinformatics Lab, Universitat Pompeu Fabra IMIM, Barcelona Research Park of Biomedicine, Barcelona, Catalonia, Spain
BMC Bioinformatics 11:56. 2010..In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties...
- Underexpression of transcriptional regulators is common in metastatic breast cancer cells overexpressing Bcl-xLOlga Mendez
Centre d Oncologia Molecular, Institut de Recerca Oncologica, IDIBELL, Hospital Duran i Reynals, Gran Via s n, Km 2, 7, E 08907 L Hospitalet Ll, Barcelona, Spain
Carcinogenesis 27:1169-79. 2006....
- iLoops: a protein-protein interaction prediction server based on structural featuresJoan Planas-Iglesias
Structural Bioinformatics Laboratory, Universitat Pompeu Fabra, 08003 Barcelona, Spain
Bioinformatics 29:2360-2. 2013..The server evaluates the putative interaction using a random forest classifier...
- Understanding protein-protein interactions using local structural featuresJoan Planas-Iglesias
Structural Bioinformatics Group GRIB IMIM, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, C Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
J Mol Biol 425:1210-24. 2013..We have tested our method on several sets with unbalanced ratios of interactions and non-interactions to simulate real conditions, obtaining accuracies higher than 25% in the most unfavorable circumstances...
- Functional pathways shared by liver and lung metastases: a mitochondrial chaperone machine is up-regulated in soft-tissue breast cancer metastasisRebeca Sanz
Centre d Oncologia Molecular, Institut de Recerca Oncològica IDIBELL, Hospital Duran i Reynals, Gran Via, S N, Km 2 7, L Hospitalet Ll, 08907, Barcelona, Spain
Clin Exp Metastasis 24:673-83. 2007....
- ArchDB 2014: structural classification of loops in proteinsJaume Bonet
Structural Bioinformatics Lab GRIB IMIM, Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine PRBB, Barcelona, Catalonia, 08950, Spain and Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA Aberystwyth, Ceredigion, UK
Nucleic Acids Res 42:D315-9. 2014..The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses...
- InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical researchDaniel Poglayen
Structural Bioinformatics Lab GRIB IMIM, Department of Experimental and Health Science, University Pompeu Fabra, Barcelona 08005, Catalonia, Spain
Biochem Soc Trans 44:917-24. 2016..We provided details on each specific resource, aims and purpose and compare with equivalent tools in the literature. All the tools are presented in a centralized, one-stop, web site: InteractoMIX (http://interactomix.com). ..
- Identification of function-associated loop motifs and application to protein function predictionJordi Espadaler
Group de Bioinformàtica Estructural GRIB IMIM, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra 08003 Barcelona, Catalonia, Spain
Bioinformatics 22:2237-43. 2006..This identification can be used on sequence annotations...
- Exploiting protein-protein interaction networks for genome-wide disease-gene prioritizationEmre Guney
Structural Bioinformatics Group, GRIB, Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine, Barcelona, Catalonia, Spain
PLoS ONE 7:e43557. 2012..Our findings suggest that GUILD helps to identify genes implicated in the pathology of human disorders independent of the loci associated with the disorders...
- BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inferenceJavier Garcia-Garcia
Structural Bioinformatics Laboratory GRIB IMIM, Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine PRBB, 08003 Barcelona, Catalonia, Spain
Nucleic Acids Res 40:W147-51. 2012..The specificity is between 72 and 98%, whereas sensitivity varies between 1 and 59%, depending on the sequence identity cut-off used to calculate similarities between sequences. BIPS is freely accessible at http://sbi.imim.es/BIPS.php...
- Extending signaling pathways with protein-interaction networks. Application to apoptosisJoan Planas-Iglesias
Structural Bioinformatics Group, GRIB, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
OMICS 16:245-56. 2012..We provide our predictions at http://sbi.imim.es/web/Apoptosis.php...
- Predicting cancer involvement of genes from heterogeneous dataRamon Aragues
Structural Bioinformatics Lab, GRIB, Universitat Pompeu Fabra IMIM, Barcelona Research Park of Biomedicine PRBB, 08003 Barcelona, Catalonia, Spain
BMC Bioinformatics 9:172. 2008..Computational approaches are used to prioritize between genes putatively involved in cancer, usually based on further analyzing experimental data...
- FN14 and GRP94 expression are prognostic/predictive biomarkers of brain metastasis outcome that open up new therapeutic strategiesAntonio Martínez-Aranda
Biological Clues of the Invasive and Metastatic Phenotype Group, Molecular Oncology Department, Bellvitge Biomedical Research Institute IDIBELL, 08907 L Hospitalet de Llobregat, Barcelona, Spain
Oncotarget 6:44254-73. 2015..In conclusion our results indicate that FN14 and GRP94 are prediction/prognosis markers which open up new possibilities for preventing/treating brain metastasis. ..
- iFraG: A protein-protein interface prediction server based on sequence fragmentsJavier Garcia-Garcia
Structural Bioinformatics Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C Dr Aiguader 88, 08003, Barcelona, Spain
J Mol Biol . 2016..Moreover, as a proof of concept we include the experimental validation on the successful prediction of a peptide competing with the aggregation of β-amyloid in Alzheimer's disease. iFrag is freely accessible at http://sbi.imim.es/iFrag...
- Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformationsPatrick Aloy
Institut de Recerca Biomèdica and Barcelona Supercomputing Center, 10 12 08028 Barcelona, Catalonia, Spain
BMC Struct Biol 9:71. 2009..The selection of the closest model to the native conformation has thus become crucial for structure prediction. Several methods have been developed to score protein models by energies, knowledge-based potentials and combination of both...
- Analysis of electrostatic contributions to the selectivity of interactions between RING-finger domains and ubiquitin-conjugating enzymesJohanna Scheper
Department of Molecular and Cell Biology, Instituto de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Cientificas, Barcelona, Spain
Proteins 74:92-103. 2009..The application of some of these rules of interaction selectivity has permitted us to experimentally manipulate the selectivity of interaction of the RING-finger domain-E2 pairs under study...
- On the use of knowledge-based potentials for the evaluation of models of protein-protein, protein-DNA, and protein-RNA interactionsOriol Fornes
Structural Bioinformatics Lab GRIB, Departament de Ciѐncies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
Adv Protein Chem Struct Biol 94:77-120. 2014..Moreover, we provide ready-to-use resources for docking and benchmarking protein interactions. ..
- Protein kinase CK2-dependent phosphorylation of the human Regulators of Calcineurin reveals a novel mechanism regulating the calcineurin-NFATc signaling pathwaySergio Martínez-Høyer
Bellvitge Biomedical Research Institute IDIBELL, L Hospitalet de Llobregat, Barcelona, Catalonia, Spain
Biochim Biophys Acta 1833:2311-21. 2013..The knowledge of how RCAN proteins modulate the calcineurin-NFATc pathway paves the way for the development of potent novel selective immunosuppressant drugs. ..
- PIANA: protein interactions and network analysisRamon Aragues
Structural Bioinformatics Group GRIB IMIM, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, C Doctor Aiguader, 83, Barcelona 08003, Catalonia, Spain
Bioinformatics 22:1015-7. 2006..PIANA can also be used as a stand-alone application to create protein interaction networks and perform tasks such as predicting protein interactions and helping to identify spots in a 2D electrophoresis gel...
- GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithmsEmre Guney
Departament de Ciencies Experimentals i de la Salut, Structural Bioinformatics Group GRIB IMIM, Universitat Pompeu Fabra, Barcelona, 08003 Catalonia, Spain
Bioinformatics 30:1789-90. 2014..It also prioritizes drugs based on the ranking of their targets, unleashing opportunities for repurposing drugs for novel therapies...
- The crystal structure of a cardiovirus RNA-dependent RNA polymerase reveals an unusual conformation of the polymerase active siteLaia Vives-Adrián
Institut de Biologia Molecular de Barcelona CSIC, Parc Cientific de Barcelona, Barcelona, Spain
J Virol 88:5595-607. 2014....
- Bcl-x(L)-mediated changes in metabolic pathways of breast cancer cells: from survival in the blood stream to organ-specific metastasisLaura España
Centre d Oncologia Molecular, Institut de Recerca Oncològica IDIBELL, Hosp Duran i Reynals, C S U B, 08907 L Hospitalet de Llobregat, Barcelona, Spain
Am J Pathol 167:1125-37. 2005..In conclusion, Bcl-x(L) mediates a phenotype in which redox pathways and glycolysis are coupled to protect breast cancer metastatic cells during transit from the primary tumor to the metastatic state...
- Knowledge-based modeling of peptides at protein interfaces: PiPreDBaldo Oliva
Structural Bioinformatics Lab GRIB, Departament de Ciencies Experimental i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
Bioinformatics 31:1405-10. 2015..In this context, peptides are gaining momentum as emerging agents for the modulation of PPIs...
- Functional and topological characterization of transcriptional cooperativity in yeastDaniel Aguilar
Structural Bioinformatics Group, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, C Dr, Aiguader 88, 08003 Barcelona, Spain
BMC Res Notes 5:227. 2012....
- Mapping the mutual information network of enzymatic families in the protein structure to unveil functional featuresDaniel Aguilar
Structural Bioinformatics Group, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Spain
PLoS ONE 7:e41430. 2012..Finally, we discovered a significant enrichment of functional residues (e.g. metal binding, susceptibility to detrimental mutations) in the clusters, which could be the foundation of new prediction tools...
- Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative DockingSimon J Cockell
Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
Bioinformatics 23:573-81. 2007..Here we describe a novel method that uses structural models to reduce a large number of in silico predictions to a high confidence subset that is amenable to experimental validation...
- Beyond tissueInfo: functional prediction using tissue expression profile similarity searchesDaniel Aguilar
HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1305 York Ave, New York, NY 10021, USA
Nucleic Acids Res 36:3728-37. 2008..Since the approach does not use sequence similarity, we expect that TEPSS will be useful for various gene discovery applications. TEPSS programs and data are distributed at http://icb.med.cornell.edu/crt/tepss/index.xml...
- Knowledge environments representing molecular entities for the virtual physiological humanMartin Hofmann-Apitius
Bonn Aachen International Center for Information Technology, University of Bonn, Dahlmannstrasse 2, 53113 Bonn, Germany
Philos Trans A Math Phys Eng Sci 366:3091-110. 2008..Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH...