2017

 

SÁNCHEZ-MIR L, SALAT-CANELA C, PAULO E, CARMONA M, AYTÉ J, OLIVA B, HIDALGO E. Phospho-mimicking Atf1 mutants bypass the transcription activating function of the MAP kinase Sty1 of fission yeast. Curr Genet. (2017)(PMID: 28799013)

MARÍN-LÓPEZ MA, PLANAS-IGLESIAS J, AGUIRRE-PLANS J, BONET J, GARCIA-GARCIA J, FERNANDEZ-FUENTES N, OLIVA B.On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures. Bioinformatics. (2017) (PMID: 29028891)

RUBIO-PEREZ C, GUNEY E, AGUILAR D, PIÑERO J, GARCIA-GARCIA J, IADAROLA B, SANZ F, FERNANDEZ-FUENTES N, FURLONG LI, OLIVA B. Genetic and functional characterization of disease associations explains comorbidity. Sci Rep. 7(1):6207 (2017)(PMID: 28740175 )

AGUILAR D, PINART M, KOPPELMAN GH, SAEYS Y, NAWIJN MC, POSTMA DS, AKDIS M, AUFFRAY C, BALLEREAU S, BENET M, GARCÍA-AYMERICH J, GONZÁLEZ JR, GUERRA S, KEIL T, KOGEVINAS M, LAMBRECHT B, LEMONNIER N, MELEN E, SUNYER J, VALENTA R, VALVERDE S, WICKMAN M, BOUSQUET J, OLIVA B, ANTÓ JM.Computational analysis of multimorbidity between asthma, eczema and rhinitis.PLoS One. 12(6):e0179125 (2017)(PMID: 28598986)

VALLS-COMAMALA V, GUIVERNAU B, BONET J, PUIG M, PERÁLVAREZ-MARÍN A, PALOMER E, FERNÀNDEZ-BUSQUETS X, ALTAFAJ X, TAJES M, PUIG-PIJOAN A, VICENTE R, OLIVA B, MUÑOZ FJ. The antigen-binding fragment of human gamma immunoglobulin prevents amyloid β-peptide folding into β-sheet to form oligomers. Oncotarget 8(25):41154-41165(2017)(PMID: 28467807 )

SALAT-CANELA C, PAULO E, SÁNCHEZ-MIR L, CARMONA M, AYTÉ J, OLIVA B, HIDALGO E.Deciphering the role of the signal- and Sty1 kinase-dependent phosphorylation of the stress-responsive transcription factor Atf1 on gene activation.J Biol Chem. 292(33):13635-13644. (2017)(PMID: 28652406)

GARCIA-GARCIA J, VALLS-COMAMALA V, GUNEY E, ANDREU D, MUÑOZ FJ, FERNANDEZ-FUENTES N, OLIVA B. iFraG: A protein-protein interface prediction server based on sequence fragments. J Mol Biol. 3;429(3):382-389. (2017)(PMID: 27956148)

 

2016

HILL SM, HEISER LM, COKELAER T, UNGER M, NESSER NK, CARLIN DE, ZHANG Y, SOKOLOV A, PAULL EO, WONG CK, GRAIM K, BIVOL A, WANG H, ZHU F, AFSARI B, DANILOVA LV, FAVOROV AV, LEE WS, TAYLOR D, HU CW, LONG BL, NOREN DP, BISBERG AJ; HPN-DREAM CONSORTIUM, MILLS GB, GRAY JW, KELLEN M, NORMAN T, FRIEND S, QUTUB AA, FERTIG EJ, GUAN Y, SONG M, STUART JM, SPELLMAN PT, KOEPPL H, STOLOVITZKY G, SAEZ-RODRIGUEZ J, MUKHERJEE S. ET AL. Inferring causal molecular networks: empirical assessment through a community-based effort. Nat Methods. 13(4):310-8. (2016) (PMID: 26901648)


WRIGHT RH, LIOUTAS A, LE DILY F, SORONELLAS D, POHL A, BONET J, NACHT AS, SAMINO S, FONT-MATEU J, VICENT GP, WIERER M, TRABADO MA, SCHELHORN C, CAROLIS C, MACIAS MJ, YANES O, OLIVA B, BEATO M. ADP-ribose-derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling. Science. 352(6290):1221-5 (2016) (PMID: 27257257)

POGLAYEN D, MARÍN-LÓPEZ MA, BONET J, FORNES O, GARCIA-GARCIA J, PLANAS-IGLESIAS J, SEGURA J, OLIVA B, FERNANDEZ-FUENTES N. InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research. Biochem Soc Trans. Jun 15;44(3):917-24. (2016) (PMID: 27284060)

ALVAREZ-CIENFUEGOS A, NUÑEZ-PRADO N, COMPTE M, CUESTA AM, BLANCO-TORIBIO A, HARWOOD SL, VILLATE M, MERINO N, BONET J, NAVARRO R, MUÑOZ-BRIONES C, SØRENSEN KM, MØLGAARD K, OLIVA B, SANZ L, BLANCO FJ, ALVAREZ-VALLINA L. Intramolecular trimerization, a novel strategy for making multispecific antibodies with controlled orientation of the antigen binding domains. Sci Rep. 6:28643. ( 2016) (PMID: 27345490)

SIEBERTS SK, ZHU F, GARCÍA-GARCÍA J, STAHL E, PRATAP A, PANDEY G, PAPPAS D, AGUILAR D, ANTON B, BONET J, EKSI R, FORNÉS O, GUNEY E, LI H, MARÍN MA, PANWAR B, PLANAS-IGLESIAS J, POGLAYEN D, CUI J, FALCAO AO, SUVER C, HOFF B, BALAGURUSAMY VS, DILLENBERGER D, NETO EC, NORMAN T, AITTOKALLIO T, AMMAD-UD-DIN M, AZENCOTT CA, BELLÓN V, BOEVA V, BUNTE K, CHHEDA H, CHENG L, CORANDER J, DUMONTIER M, GOLDENBERG A, GOPALACHARYULU P, HAJILOO M, HIDRU D, JAISWAL A, KASKI S, KHALFAOUI B, KHAN SA, KRAMER ER, MARTTINEN P, MEZLINI AM, MOLPARIA B, PIRINEN M, SAARELA J, SAMWALD M, STOVEN V, TANG H, TANG J, TORKAMANI A, VERT JP, WANG B, WANG T, WENNERBERG K, WINEINGER NE, XIAO G, XIE Y, YEUNG R, ZHAN X, ZHAO C; MEMBERS OF THE RHEUMATOID ARTHRITIS CHALLENGE CONSORTIUM, GREENBERG J, KREMER J, MICHAUD K, BARTON A, COENEN M, MARIETTE X, MICELI C, SHADICK N, WEINBLATT M, DE VRIES N, TAK PP, GERLAG D, HUIZINGA TW, KURREEMAN F, ALLAART CF, LOUIS BRIDGES S JR, CRISWELL L, MORELAND L, KLARESKOG L, SAEVARSDOTTIR S, PADYUKOV L, GREGERSEN PK, FRIEND S, PLENGE R, STOLOVITZKY G, OLIVA B, GUAN Y, MANGRAVITE LM, BRIDGES SL, CRISWELL L, MORELAND L, KLARESKOG L, SAEVARSDOTTIR S, PADYUKOV L, GREGERSEN PK, FRIEND S, PLENGE R, STOLOVITZKY G, OLIVA B, GUAN Y, MANGRAVITE LM. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nat Commun. 7:12460 (2016)(PMID: 27549343)

GUBERN A, JOAQUIN M, MARQUÈS M, MASERES P, GARCIA-GARCIA J, AMAT R, GONZÁLEZ-NUÑEZ D, OLIVA B, REAL FX, DE NADAL E, POSAS F. The N-Terminal Phosphorylation of RB by p38 Bypasses Its Inactivation by CDKs and Prevents Proliferation in Cancer Cells. Mol Cell. 64(1):25-36 ( 2016)(PMID: 27642049)

WRIGHT RH, FERNANDEZ-FUENTES N, OLIVA B, BEATO M. Insight into the machinery that oils chromatin dynamics. Nucleus. 7(6):532-539. doi: 10.1080/19491034.2016.1255392. (2016)(PMID: 27893319 )

GUIVERNAU B, BONET J, VALLS-COMAMALA V, BOSCH-MORATÓ M, GODOY JA, INESTROSA NC, PERÁLVAREZ-MARÍN A, FERNÁNDEZ-BUSQUETS X, ANDREU D, OLIVA B, MUÑOZ FJ. Amyloid-β Peptide Nitrotyrosination Stabilizes Oligomers and Enhances NMDAR-Mediated Toxicity. J Neurosci. Nov 16;36(46):11693-11703. (2016)(PMID: 27852777)

2015

 

RESA-INFANTE P, PATERSON D, BONET J, OTTE A, OLIVA B, FODOR E, GABRIEL G. Targeting importin-α7 as a therapeutic approach against pandemic influenza viruses. J. Virol. JVI.00583-15. (2015) PubMed PMID: 26085167

OLIVA B, FERNANDEZ-FUENTES N. Knowledge-based modeling of peptides at protein interfaces: PiPreD. Bioinformatics. 31(9): 1405-10(2015) PubMed PMID:25540186

SEGURA J, MARÍN-LÓPEZ MA, JONES PF, OLIVA B, FERNANDEZ-FUENTES N. VORFFIP-Driven Dock: V-D2OCK, a Fast and Accurate Protein Docking Strategy. PLoS One. Mar 12;10(3):e0118107. (2015) PubMed PMID: 25763838

MARTÍNEZ-ARANDA A, HERNÁNDEZ V, GUNEY E, MUIXÍ L, FOJ R, BAIXERAS N, CUADRAS D, MORENO V, URRUTICOECHEA A, GIL M, OLIVA B, MORENO F, GONZÁLEZ-SUAREZ E, VIDAL N, ANDREU X, SEGUÍ MA, BALLESTER R, CASTELLA E, SIERRA A. FN14 and GRP94 expression are prognostic/predictive biomarkers of brain metastasis outcome that open up new therapeutic strategies. Oncotarget. 6(42):44254-73 ( 2015) PubMed PMID: 26497551

 

2014

 

JAUME BONET, JOAN PLANAS-IGLESIAS, JAVIER GARCIA-GARCIA, MANUEL A. MARÍN-LÓPEZ, NARCIS FERNANDEZ-FUENTES, BALDO OLIVA. ArchDB 2014: structural classification of loops in proteins. Nucleic Acids Research 42(Database issue):D315-9 (2014) PubMed PMID:24265221

GUNEY E, GARCIA-GARCIA J, OLIVA B. GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms. Bioinformatics Jun 15;30(12):1789-90 (2014) PubMed PMID 24532728

VIVES-ADRIAN L, LUJAN C, OLIVA B, VAN DER LINDEN L, SELISKO B, COUTARD B, CANARD B, VAN KUPPEVELD FJ, FERRER-ORTA C, VERDAGUER N. The crystal structure of a Cardiovirus RNA-dependent RNA polymerase reveals an unusual conformation of the polymerase active site. J Virol. May;88(10):5595-607 (2014) PubMed PMID: 24600002

BONET J, SEGURA J, PLANAS-IGLESIAS J, OLIVA B,  FERNANDEZ-FUENTES N Frag'r'Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design. Bioinformatics. Jul 1;30(13):1935-6 (2014) PubMed PMID:2460398

GUNEY E, OLIVA B. Analysis of the robustness of network-based disease-gene prioritization methods reveals redundancy in the human interactome and functional diversity of disease-genes. PLoS One Apr 14;9(4):e9468 (2014) PubmMed PMID:24733074

FORNES O, GARCIA-GARCIA J, BONET J, OLIVA B On the Use of Knowledge-Based Potentials for the Evaluation of Models of Protein-Protein Protein-DNA, and Protein-RNA Interactions. Adv Protein Chem Struct Biol. 2014;94:77-120 (2014)PubMed PMID:24629186

2013

A PUJOL, R VALLS, V RADOVANOVIC, E GUNEY, J GARCIA-GARCIA, VC DOMENECH, LC GONZÁLEZ, JM MAS, B OLIVA. Virtual-organism toy-model as a tool to develop bioinformatics approaches of Systems Biology for medical-target discovery. arXiv:1301.2528 (2013)

BLANCO-TORIBIO A, SAINZ-PASTOR N, ÁLVAREZ-CIENFUEGOS A, MERINO N, CUESTA ÁM, SÁNCHEZ-MARTÍN D, BONET J, SANTOS-VALLE P, SANZ L, OLIVA B, BLANCO FJ, ÁLVAREZ-VALLINA L. Generation and characterization of monospecific and bispecific hexavalent trimerbodies. MAbs. 5(1):70-9 (2013)PubMed PMID: 23221741

PLANAS-IGLESIAS J, BONET J, GARCÍA-GARCÍA J, MARÍN-LÓPEZ MA, FELIU E, OLIVA B. Understanding Protein-Protein Interactions Using Local Structural Features. J Mol Biol. 425(7):1210-24 (2013) PubMed PMID: 23353828

GARRIGA D, FERRER-ORTA C, QUEROL-AUDÍ J, OLIVA B, VERDAGUER N. Role of Motif B Loop in Allosteric Regulation of RNA-Dependent RNA Polymerization Activity. J Mol Biol. 425(13):2279-87 (2013) PMID: 23542342

SANTANA-CODINA N, CARRETERO R, SANZ-PAMPLONA R, CABRERA T, GUNEY E, OLIVA B, CLEZARDIN P, OLARTE OE, LOZA-ALVAREZ P, MÉNDEZ-LUCAS A, PERALES JC, SIERRA A. A transcriptome-proteome integrated network identifies ERp57 as a hub that mediates bone metastasis. Mol. Cell Proteomics 12(8):2111-25 (2013)PubMed PMID:23625662

MARTÍNEZ HOYER, S., ARANGUREN IBAÑEZ, A, GARCIA-GARCIA, J., SERRANO-CANDELAS, E., VILARDELL, J., NUNES, V., AGUADO, F. OLIVA, B., ITARTE, E., PÉREZ-RIBA,M. Protein kinase CK2-dependent phosphorylation of the human Regulators of Calcineurin reveals a novel mechanism regulating the calcineurin-NFATc signaling pathway. Biochim Biophys Acta. 1833(10):2311-2321 (2013)PubMed 23732701

ENGIN HB, GUNEY E, KESKIN O, OLIVA B, GURSOY A. Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PLoS One. 8(11):e81035 (2013) PubMed PMID:23842807

PLANAS-IGLESIAS J, MARIN-LOPEZ MA, BONET J, GARCIA-GARCIA J, OLIVA B. iLoops: a protein-protein interaction prediction server based on structural features. Bioinformatics. 29(18):2360-2362 (2013)PubMed PMID:23842807

RIVERA-HERNÁNDEZ G, MARIN-ARGANY M, BLASCO-MORENO B, BONET J, OLIVA B, VILLEGAS S. Elongation of the C-terminal domain of an anti-amyloid β single-chain variable fragment increases its thermodynamic stability and decreases its aggregation tendency. MAbs. 5(5):678-89 (2013)PubMed PMID:23924802

2012

Blanco-Toribio A, Sainz-Pastor N, Alvarez-Cienfuegos A, Merino N, Cuesta AM, Sánchez-Martín D, Bonet J, Santos-Valle P, Sanz L, Oliva B, Blanco FJ, Alvarez-Vallina L. Generation and characterization of monospecific and bispecific hexavalent trimerbodies. MAbs. 2012 Dec 5;5(1). PubMed PMID: 23221741.

Wright RH, Castellano G, Bonet J, Le Dily F, Font-Mateu J, Ballaré C, Nacht AS, Soronellas D, Oliva B, Beato M. CDK2-dependent activation of PARP-1 is required for hormonal gene regulation in breast cancer cells. Genes Dev. 2012 Sep 1;26(17):1972-83. PubMed PMID: 22948662.

Guney E, Oliva B. Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization. PLoS One. 2012;7(9):e43557. PubMed PMID: 23028459.

Aguilar D, Oliva B, Marino Buslje C. Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features. PLoS One. 2012;7(7):e41430. PubMed PMID: 22848494.

Sanz-Pamplona R, García-García J, Franco S, Messeguer X, Driouch K, Oliva B, Sierra A. A taxonomy of organ-specific breast cancer metastases based on a protein-protein interaction network. Chem Biodivers. Mol Biosyst. 2012 Aug;8(8):2085-96. PubMed PMID: 22710377.

Garcia-Garcia J, Schleker S, Klein-Seetharaman J, Oliva B. BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. Chem Biodivers. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W147-51. PubMed PMID: 22689642.

Schleker S, Garcia-Garcia J, Klein-Seetharaman J, Oliva B. Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. Chem Biodivers. 2012 May;9(5):991-1018. PubMed PMID: 22589098.

Aguilar D, Oliva B. Functional and topological characterization of transcriptional cooperativity in yeast. BMC Res Notes. 2012 May 10;5:227. PubMed PMID: 22574744.

Planas-Iglesias J, Guney E, García-García J, Robertson KA, Raza S, Freeman TC, Ghazal P, Oliva B. Extending signaling pathways with protein-interaction networks. Application to apoptosis. OMICS. 2012 May;16(5):245-56. PubMed PMID: 22385281.

Guney E, Sanza R, Sierra A, Oliva B. Understanding Cancer Progression Using Protein Interaction Networks. Systems Biology in Cancer Research and Drug Discovery. Part 2, 167-195. Springer 2012. Ed. Asfar S. Azmi. DOI: 10.1007/978-94-007-4819-4_7 [BOOK CHAPTER].

Planas-Iglesias J, Bonet J, Marín-López MA, Feliu E, Gursoy A, Oliva B. Structural Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from Sequence. Protein-Protein Interactions-Computational and Experimental Tools. Weibo Cai (Ed). 2012 InTech ISBN 978-953-51-0397-4 [BOOK CHAPTER].

Garcia-Garcia J, Bonet J, Guney E, Fornes O, Planas J, Oliva B. Networks of Protein-Protein Interactions: From Uncertainty to Molecular Details. Molecular Informatics. 01/2012; 31(5):342-362.

Segura J, Oliva B, Fernandez-Fuentes N. CAPS-DB: a structural classification of helix-capping motifs. Nucleic Acids Res. 2012 Jan;40(Database issue):D479-85. PubMed PMID: 22021380.

2011

Sanz-Pamplona R, Aragüés R, Driouch K, Martín B, Oliva B, Gil M, Boluda S, Fernández PL, Martínez A, Moreno V, Acebes JJ, Lidereau R, Reyal F, Van de Vijver MJ, Sierra A. Expression of Endoplasmic Reticulum Stress Proteins Is a Candidate Marker of Brain Metastasis in both ErbB-2(+) and ErbB-2(-) Primary Breast Tumors. Am J Pathol. 2011 Jun 24. PubMed PMID: 21708117.

Feliu E, Aloy P, Oliva B. On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking. Protein Sci. 2011 Jan 6. PubMed PMID: 21213252.

Cerdà-Costa N, Bonet J, Fernández MR, Avilés FX, Oliva B, Villegas S. Prediction of a new class of RNA recognition motif. J Mol Model. 2010 Nov 17. PubMed PMID: 21082207.

2010

Feliu E, Oliva B. How different from random are docking predictions when ranked by scoring functions? Proteins. 2010 Aug 17. PubMed PMID: 20848549.

Cuesta AM, Sainz-Pastor N, Bonet J, Oliva B, Alvarez-Vallina L. Multivalent antibodies: when design surpasses evolution. Trends Biotechnol. 2010 Jul;28(7):355-62. PubMed PMID: 20447706.

Romero-Isart N, Oliva B, Vasák M. Influence of NH-Sgamma bonding interactions on the structure and dynamics of metallothioneins. J Mol Model. 2010 Mar;16(3):387-94. PubMed PMID: 19609577.

Garcia-Garcia J, Guney E, Aragues R, Planas-Iglesias J, Oliva B. Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics. 2010 Jan 27;11:56. PubMed PMID: 20105306.

2009

Hermoso A, Espadaler J, Enrique Querol E, Aviles FX, Sternberg MJ, Oliva B, Fernandez-Fuentes N. Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB). Bioinform Biol Insights. 2009 Nov 24;1:77-90. PubMed PMID: 20066127; PubMed Central PMCID: PMC2789696.

Aloy P, Oliva B. Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations. BMC Struct Biol. 2009 Nov 16;9:71. PubMed PMID: 19917096; PubMed Central PMCID: PMC2783033.

Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, Oliva B. ModLink+: improving fold recognition by using protein-protein interactions. Bioinformatics. 2009 Jun 15;25(12):1506-12. PubMed PMID: 19357100; PubMed Central PMCID: PMC2687990.

Gitter A, Siegfried Z, Klutstein M, Fornes O, Oliva B, Simon I, Bar-Joseph Z. Backup in gene regulatory networks explains differences between binding and knockout results. Mol Syst Biol. 2009;5:276. PubMed PMID: 19536199; PubMed Central PMCID: PMC2710864.

Cuesta AM, Sánchez-Martín D, Sanz L, Bonet J, Compte M, Kremer L, Blanco FJ, Oliva B, Alvarez-Vallina L. In vivo tumor targeting and imaging with engineered trivalent antibody fragments containing collagen-derived sequences. PLoS One. 2009;4(4):e5381. PubMed PMID: 19401768; PubMed Central PMCID: PMC2670539.

Scheper J, Oliva B, Villà-Freixa J, Thomson TM. Analysis of electrostatic contributions to the selectivity of interactions between RING-finger domains and ubiquitin-conjugating enzymes. Proteins. 2009 Jan;74(1):92-103. PubMed PMID: 18615712.

2008

Hofmann-Apitius M, Fluck J, Furlong L, Fornes O, Kolárik C, Hanser S, Boeker M, Schulz S, Sanz F, Klinger R, Mevissen T, Gattermayer T, Oliva B, Friedrich CM. Knowledge environments representing molecular entities for the virtual physiological human. Philos Transact A Math Phys Eng Sci. 2008 Sep 13;366(1878):3091-110. PubMed PMID: 18559317.

Martín B, Sanz R, Aragüés R, Oliva B, Sierra A. Functional clustering of metastasis proteins describes plastic adaptation resources of breast-cancer cells to new microenvironments. J Proteome Res. 2008 Aug;7(8):3242-53. PubMed PMID: 18582095.

Aragüés R, Garcia-Garcia J, Oliva B. Integration and prediction of PPI using multiple resources from public databases. J Proteomics and Bioinformatics. 2008. 166-187.

Aguilar D, Skrabanek L, Gross SS, Oliva B, Campagne F. Beyond tissueInfo: functional prediction using tissue expression profile similarity searches. Nucleic Acids Res. 2008 Jun;36(11):3728-37. PubMed PMID: 18483083; PubMed Central PMCID: PMC2441795.

Espadaler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, Oliva B. Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics. 2008 May 27;9:249. PubMed PMID: 18505562; PubMed Central PMCID: PMC2430716.

Aragues R, Sander C, Oliva B. Predicting cancer involvement of genes from heterogeneous data. BMC Bioinformatics. 2008 Mar 27;9:172. PubMed PMID: 18371197; PubMed Central PMCID: PMC2330045.

Aguilar D, Oliva B. Topological comparison of methods for predicting transcriptional cooperativity in yeast. BMC Genomics. 2008 Mar 25;9:137. PubMed PMID: 18366726; PubMed Central PMCID: PMC2315657.

van Mulligen EM, Cases M, Hettne K, Molero E, Weeber M, Robertson KA, Oliva B, de la Calle G, Maojo V. Training multidisciplinary biomedical informatics students: three years of experience. J Am Med Inform Assoc. 2008 Mar-Apr;15(2):246-54. PubMed PMID: 18096914; PubMed Central PMCID: PMC2274784.

Martín B, Aragüés R, Sanz R, Oliva B, Boluda S, Martínez A, Sierra A. Biological pathways contributing to organ-specific phenotype of brain metastatic cells. J Proteome Res. 2008 Mar;7(3):908-20. PubMed PMID: 18257520.

Moreno-Estrada A, Casals F, Ramírez-Soriano A, Oliva B, Calafell F, Bertranpetit J, Bosch E. Signatures of selection in the human olfactory receptor OR5I1 gene. Mol Biol Evol. 2008 Jan;25(1):144-54. PubMed PMID: 17981927.

2007

Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B. Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comput Biol. 2007 Sep;3(9):1761-71. PubMed PMID: 17941705; PubMed Central PMCID: PMC1976338.

Cockell SJ, Oliva B, Jackson RM. Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking. Bioinformatics. 2007 Mar 1;23(5):573-81. PubMed PMID: 17237047.

Sanz R, Aragüés R, Stresing V, Martín B, Landemaine T, Oliva B, Driouch K, Lidereau R, Sierra A. Functional pathways shared by liver and lung metastases: a mitochondrial chaperone machine is up-regulated in soft-tissue breast cancer metastasis. Clin Exp Metastasis. 2007;24(8):673-83. PubMed PMID: 18008173.

2006

Espadaler J, Querol E, Aviles FX, Oliva B. Identification of function-associated loop motifs and application to protein function prediction. Bioinformatics. 2006 Sep 15;22(18):2237-43. PubMed PMID: 16870939.

Gargallo R, Cedano J, Mozo-Villarias A, Querol E, Oliva B. Study of the influence of temperature on the dynamics of the catalytic cleft in 1,3-1,4-beta-glucanase by molecular dynamics simulations. J Mol Model. 2006 Sep;12(6):835-45. Epub 2006 Mar 9. PubMed PMID: 16525847.

Méndez O, Martín B, Sanz R, Aragüés R, Moreno V, Oliva B, Stresing V, Sierra A. Underexpression of transcriptional regulators is common in metastatic breast cancer cells overexpressing Bcl-xL. Carcinogenesis. 2006 Jun;27(6):1169-79. PubMed PMID: 16492678.

Aragues R, Jaeggi D, Oliva B. PIANA: protein interactions and network analysis. Bioinformatics. 2006 Apr 15;22(8):1015-7. PubMed PMID: 16510498.

Fernandez-Fuentes N, Oliva B, Fiser A. A supersecondary structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Res. 2006 Apr 14;34(7):2085-97. PubMed PMID: 16617149; PubMed Central PMCID: PMC1440879.

2005

España L, Martín B, Aragüés R, Chiva C, Oliva B, Andreu D, Sierra A. Bcl-x(L)-mediated changes in metabolic pathways of breast cancer cells: from survival in the blood stream to organ-specific metastasis. Am J Pathol. 2005 Oct;167(4):1125-37. PubMed PMID: 16192647; PubMed Central PMCID: PMC1603674.

Fernandez-Fuentes N, Querol E, Aviles FX, Sternberg MJ, Oliva B. Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops. Proteins. 2005 Sep 1;60(4):746-57. PubMed PMID: 16021623.

Espadaler J, Romero-Isart O, Jackson RM, Oliva B. Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships. Bioinformatics. 2005 Aug 15;21(16):3360-8. PubMed PMID: 15961445.

Centeno NB, Planas-Iglesias J, Oliva B. Comparative modelling of protein structure and its impact on microbial cell factories. Microb Cell Fact. 2005 Jun 30;4:20. PubMed PMID: 15989691; PubMed Central PMCID: PMC1183243.

Espadaler J, Aragüés R, Eswar N, Marti-Renom MA, Querol E, Avilés FX, Sali A, Oliva B. Detecting remotely related proteins by their interactions and sequence similarity. Proc Natl Acad Sci U S A. 2005 May 17;102(20):7151-6. Erratum in: Proc Natl Acad Sci U S A. 2005 Jun 28;102(26):9429. PubMed PMID: 15883372; PubMed Central PMCID: PMC1129109.

2004

Garriga D, Díez J, Oliva B. Modeling the helicase domain of Brome mosaic virus 1a replicase. J Mol Model. 2004 Dec;10(5-6):382-92. PubMed PMID: 15597207.

Andrés AM, Soldevila M, Navarro A, Kidd KK, Oliva B, Bertranpetit J. Positive selection in MAOA gene is human exclusive: determination of the putative amino acid change selected in the human lineage. Hum Genet. 2004 Oct;115(5):377-86. PubMed PMID: 15349769.

Fernandez-Fuentes N, Hermoso A, Espadaler J, Querol E, Aviles FX, Oliva B. Classification of common functional loops of kinase super-families. Proteins. 2004 Aug 15;56(3):539-55. PubMed PMID: 15229886.

Soldevila M, Andrés AM, Blancher A, Calafell F, Ordoñez M, Pumarola M, Oliva B, Aramburu J, Bertranpetit J. Variation of the prion gene in chimpanzees and its implication for prion diseases. Neurosci Lett. 2004 Jan 30;355(3):157-60. PubMed PMID: 14732455.

Espadaler J, Fernandez-Fuentes N, Hermoso A, Querol E, Aviles FX, Sternberg MJ, Oliva B. ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D185-8. PubMed PMID: 14681390; PubMed Central PMCID: PMC308737.

2003

Aguilar D, Oliva B, Aviles FX, Querol E. SNOW: standard nomenclature wizard to help searching for (bio) chemical standardized names. Bioinformatics. 2003 Dec 12;19(18):2492-3. PubMed PMID: 14668242.

Gargallo R, Hünenberger PH, Avilés FX, Oliva B. Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions. Protein Sci. 2003 Oct;12(10):2161-72. PubMed PMID: 14500874; PubMed Central PMCID: PMC2366931.

Repiso A, Pérez de la Ossa P, Avilés X, Oliva B, Juncá J, Oliva R, Garcia E, Vives-Corrons JL, Carreras J, Climent F. Red blood cell phosphosphoglycerate mutase. Description of the first human BB isoenzyme mutation. Haematologica. 2003 Mar;88(3):ECR07. PubMed PMID: 12651285.

2002

Barbosa Pereira PJ, Segura-Martín S, Oliva B, Ferrer-Orta C, Avilés FX, Coll M, Gomis-Rüth FX, Vendrell J. Human procarboxypeptidase B: three-dimensional structure and implications for thrombin-activatable fibrinolysis inhibitor (TAFI). J Mol Biol. 2002 Aug 16;321(3):537-47. PubMed PMID: 12162965.

Aloy P, Oliva B, Querol E, Aviles FX, Russell RB. Structural similarity to link sequence space: new potential superfamilies and implications for structural genomics. Protein Sci. 2002 May;11(5):1101-16. PubMed PMID: 11967367; PubMed Central PMCID: PMC2373547.

Aguilar D, Oliva B, Aviles FX, Querol E. TranScout: prediction of gene expression regulatory proteins from their sequences. Bioinformatics. 2002 Apr;18(4):597-607. PubMed PMID: 12016057.

López-Torrejón I, Querol E, Avilés FX, Seno M, de Llorens R, Oliva B. Human betacellulin structure modeled from other members of EGF family. J Mol Model. 2002 Apr;8(4):131-44. PubMed PMID: 12111392.

Previous relevant publications

Gómez A, Cedano J, Oliva B, Piñol J, Querol E. The gene causing the Best's macular dystrophy (BMD) encodes a putative ion exchanger. DNA Seq. 2001 Dec;12(5-6):431-5. PubMed PMID: 11913792.

Mas JM, Aloy P, Martí-Renom MA, Oliva B, de Llorens R, Avilés FX, Querol E. Classification of protein disulphide-bridge topologies. J Comput Aided Mol Des. 2001 May;15(5):477-87. PubMed PMID: 11394740.

Marino-Buslje C, Venhudová G, Molina MA, Oliva B, Jorba X, Canals F, Avilés FX, Querol E. Contribution of C-tail residues of potato carboxypeptidase inhibitor to the binding to carboxypeptidase A A mutagenesis analysis. Eur J Biochem. 2000 Mar;267(5):1502-9. PubMed PMID: 10691989.

Aloy P, Mas JM, Martí-Renom MA, Querol E, Avilés FX, Oliva B. Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2. J Comput Aided Mol Des. 2000 Jan;14(1):83-92. PubMed PMID: 10702927.

Gargallo R, Oliva B, Querol E, Avilés FX. Effect of the reaction field electrostatic term on the molecular dynamics simulation of the activation domain of procarboxypeptidase B. Protein Eng. 2000 Jan;13(1):21-6. PubMed PMID: 10679526.

Mas JM, Aloy P, Martí-Renom MA, Oliva B, Blanco-Aparicio C, Molina MA, de Llorens R, Querol E, Avilés FX. Protein similarities beyond disulphide bridge topology. J Mol Biol. 1998 Dec 4;284(3):541-8. PubMed PMID: 9826496.

Feliu JX, Benito A, Oliva B, Avilés FX, Villaverde A. Conformational flexibility in a highly mobile protein loop of foot-and-mouth disease virus: distinct structural requirements for integrin and antibody binding. J Mol Biol. 1998 Oct 23;283(2):331-8. PubMed PMID: 9769208.

Martí-Renom MA, Mas JM, Oliva B, Querol E, Avilés FX. Effects of counter-ions and volume on the simulated dynamics of solvated proteins. Application to the activation domain of procarboxypeptidase B. Protein Eng. 1998 Oct;11(10):881-90. PubMed PMID: 9862207.

Oliva B, Bates PA, Querol E, Avilés FX, Sternberg MJ. Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction. J Mol Biol. 1998 Jun 26;279(5):1193-210. PubMed PMID: 9642095.

Cols N, Romero-Isart N, Capdevila M, Oliva B, González-Duarte P, González-Duarte R, Atrian S. Binding of excess cadmium(II) to Cd7-metallothionein from recombinant mouse Zn7-metallothionein 1. UV-VIS absorption and circular dichroism studies and theoretical location approach by surface accessibility analysis. J Inorg Biochem. 1997 Nov 15;68(3):157-66. PubMed PMID: 9352652.

Aloy P, Cedano J, Oliva B, Avilés FX, Querol E. 'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins. Comput Appl Biosci. 1997 Jun;13(3):231-4. PubMed PMID: 9183525.

Oliva B, Bates PA, Querol E, Avilés FX, Sternberg MJ. An automated classification of the structure of protein loops. J Mol Biol. 1997 Mar 7;266(4):814-30. PubMed PMID: 9102471.

Daura X, Oliva B, Querol E, Avilés FX, Tapia O. On the sensitivity of MD trajectories to changes in water-protein interaction parameters: the potato carboxypeptidase inhibitor in water as a test case for the GROMOS force field. Proteins. 1996 May;25(1):89-103. PubMed PMID: 8727321.

Oliva B, Nilsson O, Wästlund M, Cardenas R, Querol E, Avilés FX, Tapia O. A molecular dynamics study of a model built Pro-36-Gly mutant derived from the potato carboxypeptidase A inhibitor protein. Biochem Biophys Res Commun. 1991 Apr 30;176(2):627-32. PubMed PMID: 2025277.

Oliva B, Wästlund M, Nilsson O, Cardenas R, Querol E, Avilés FX, Tapia O. Stability and fluctuations of the potato carboxypeptidase A protein inhibitor fold: a molecular dynamics study. Biochem Biophys Res Commun. 1991 Apr 30;176(2):616-21. PubMed PMID: 2025275.

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