2023

MIE KOBAYASHI-ISHIHARA, KATARÍNA FRAZÃO SMUTNÁ, FLORENCIA E ALONSO, JORDI ARGILAGUET, ANNA ESTEVE-CODINA, KERSTIN GEIGER, MERITXELL GENESCÁ, JUDITH GRAU-EXPÓSITO, CLARA DURAN-CASTELLS, SELINA ROGENMOSER, RENÉ BÖTTCHER, JENNIFER JUNGFLEISCH, BALDOMERO OLIVA, JAVIER P MARTINEZ, MANQING LI, MICHAEL DAVID, MAKOTO YAMAGISHI, MARTA RUIZ-RIOL, CHRISTIAN BRANDER, YASUKO TSUNETSUGU-YOKOTA, MARIA J BUZON, JUANA DÍEZ, ANDREAS MEYERHANS “Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells”. bioRxiv 2022.11. 09.512793 (2022) Communications biology 6(1): 487 (2023)

POL PICÓN-PAGÈS, HUGO FANLO-UCAR, VÍCTOR HERRERA-FERNÁNDEZ, SIRA AUSELLÉ-BOSCH, LORENA GALERA-LÓPEZ, DANIELA A GUTIÉRREZ, ANDRÉS OZAITA, ALEJANDRA R ÁLVAREZ, BALDOMERO OLIVA, FRANCISCO J MUÑOZ. “Amyloid β-Peptide Causes the Permanent Activation of CaMKIIα through Its Oxidation”. International Journal of Molecular Sciences 23 (23), 15169 (2022).

RUBÉN MOLINA-FERNÁNDEZ, POL PICÓN-PAGÈS, ALEJANDRO BARRANCO-ALMOHALLA, GIULIA CREPIN, VÍCTOR HERRERA-FERNÁNDEZ, ANNA GARCÍA-ELÍAS, HUGO FANLO-UCAR, XAVIER FERNÀNDEZ-BUSQUETS, JORDI GARCÍA-OJALVO, BALDOMERO OLIVA, FRANCISCO J MUÑOZ. Differential regulation of insulin signalling by monomeric and oligomeric amyloid beta-peptide. Brain Communications 4(5), fcac243 (2022)

VALENTIN JUNET, PEDRO MATOS‐FILIPE, JUAN MANUEL GARCÍA‐ILLARRAMENDI, ESTHER RAMÍREZ, BALDO OLIVA, JUDITH FARRÉS, XAVIER DAURA, JOSÉ MANUEL MAS, RAFAEL MORALES. A decision support system based on artificial intelligence and systems biology for the simulation of pancreatic cancer patient status. CPT: Pharmacometrics & Systems Pharmacology (2023).

PATRICIA MIRELA BOTA, ALTAIR C HERNANDEZ, JOAN SEGURA, ORIOL GALLEGO, BALDO OLIVA, NARCIS FERNANDEZ-FUENTES. CM2D3: Furnishing the human interactome with structural models of protein complexes derived by comparative modeling and docking. Journal of Molecular Biology. 21 March 2023, 168055 (2023)

POL PICÓN-PAGÈS, MÒNICA BOSCH-MORATÓ, LAIA SUBIRANA, FRANCISCA RUBIO-MOSCARDÓ, BIUSE GUIVERNAU, HUGO FANLO-UCAR, MELISA ECE ZEYLAN, SIMGE SENYUZ, VÍCTOR HERRERA-FERNÁNDEZ, RUBÉN VICENTE, JOSÉ M FERNÁNDEZ-FERNÁNDEZ, JORDI GARCÍA-OJALVO, ATTILA GURSOY, OZLEM KESKIN, BALDOMERO OLIVA, FRANCESC POSAS, EULÀLIA DE NADAL, FRANCISCO J MUÑOZ. A Genome-Wide Functional Screen Identifies Enhancer and Protective Genes for Amyloid Beta-Peptide Toxicity. International Journal of Molecular Sciences. 24(2):1278 (2023)

JASMIN REES, GAURAB SARANGI, QING CHENG, MARTIN FLOOR, AIDA ANDRES, BALDO OLIVA, JORDI VILLA-FREIXA, ELIAS ARNER, SERGI CASTELLANO. Ancient loss of catalytic selenocysteine spurred convergent adaptation in a mammalian oxidoreductase. bioRxiv 2023.01. 03.522577

PABLO COTO-SEGURA, CRISTINA SEGÚ-VERGÉS, ANTONIO MARTORELL, DAVID MORENO-RAMÍREZ, GUILLEM JORBA, VALENTIN JUNET, FILIPPO GUERRI, XAVIER DAURA, BALDOMERO OLIVA, CARLOS CARA, OLAYA SUÁREZ-MAGDALENA, SONYA ABRAHAM, JOSÉ MANUEL MAS.A quantitative systems pharmacology model for certolizumab pegol treatment in moderate-to-severe psoriasis. Front Immunol.  14: 1212981. (2023)

IRENE PAZOS, MARTA PUIG‐TINTÓ, LAURA BETANCUR, JORGE CORDERO, NEREIDA JIMÉNEZ‐MENÉNDEZ, MARC ABELLA, ALTAIR C HERNÁNDEZ, ANA G DURAN, EMI ADACHI‐FERNÁNDEZ, CARLA BELMONTE‐MATEOS, SUSANA SABIDO‐BOZO, SÉBASTIEN TOSI, AKIKO NEZU, BALDOMERO OLIVA, JULIEN COLOMBELLI, TODD R GRAHAM, TAMOTSU YOSHIMORI, MANUEL MUÑIZ, MAHO HAMASAKI, ORIOL GALLEGO. The P4-ATPase Drs2 interacts with and stabilizes the multisubunit tethering complex TRAPPIII in yeast. EMBO Reports 24:e56134. (2023)

PATRICIA MIRELA BOTA, BALDO OLIVA, NARCIS FERNANDEZ-FUENTES. Theoretical 3D Modeling of NLRP3 Inflammasome Complex. Methods in Molecular Biology book series (MIMB,volume 2696) (2023)

PATRICK GOHL, JAUME BONET, ORIOL FORNES, JOAN PLANAS-IGLESIAS, NARCÍS FERNANDEZ-FUENTES & BALDOMERO OLIVA SBILib: a handle for protein modeling and engineering. Bioinformatics 10.1093/bioinformatics/btad613 (2023)

MELISA ECE ZEYLAN, SIMGE SENYUZ, POL PICON-PAGES, ANNA GARCIA-ELIAS, MARTA TAJES, FRANCISCO MUÑOZ, BALDO OLIVA, JORDI GARCIA-OJALVO, EDUARD BARBU, RAUL VICENTE, STANLEY NATTEL, ANGEL OIS-SANTIAGO, ALBERT PUIG-PIJOAN, OZLEM KESKIN, ATTILA GURSOY. Revealing Shared Proteins and Pathways in Cardiovascular and Cognitive Diseases Using Protein Interaction Network Analysis. bioRxiv doi: https://doi.org/10.1101/2023.08.03.551914 (2023)

2022

Oriol Fornes, Alberto Meseguer, Joaquim Aguirre-Plans, Patrick Gohl, Patricia Mireia-Bota, Ruben Molina-Fernandez, Jaume Bonet, Altair Chinchilla, Ferran Pegenaute, Oriol Gallego, Narcis Fernandez-Fuentes, Baldo Oliva. ModCRE: a structure homology-modeling approach to predict TF binding in cis-regulatory elements. bioRxiv, 2022

Alberto Meseguer, Patricia Bota, Narcis Fernández-Fuentes, Baldo Oliva. Prediction of Protein–Protein Binding Affinities from Unbound Protein Structures. Computational Methods for Estimating the Kinetic Parameters of Biological Systems, 335-351, 2022

Cristiano Galletti, Joaquim Aguirre-Plans, Baldo Oliva, Narcis Fernandez-Fuentes. Prediction of Adverse Drug Reaction Linked to Protein Targets Using Network-Based Information and Machine Learning.  Frontiers in bioinformatics, 2, 2022

Jose Luis Villanueva-Canas, Narcis Fernandez-Fuentes, Catherine Teyssier, Malgorzata Ewa Rogalska, Ferran Pegenaute Perez, Baldomero Oliva, Cedric Notredame, Miguel Beato, Priyanka Sharma. Evolutionary insights reveal a new role of PADI2 in transcriptional elongation. bioRxiv, 2022

Pedro Matos-Filipe, Juan Manuel García-Illarramendi, Guillem Jorba, Baldo Oliva, Judith Farrés, José Manuel Mas. The usage of transcriptomics datasets as sources of Real-World Data for clinical trialling. bioRxiv, 2022

Neus Mestre-Farràs, Santiago Guerrero, Nadine Bley, Ezequiel Rivero, Olga Coll, Eva Borràs, Eduard Sabido, Alberto Indacochea, Carlos Casillas-Serra, Aino I Järvelin, Baldomero Oliva, Alfredo Castello, Stefan Hüttelmaier, Fátima Gebauer Melanoma RBPome identification reveals PDIA6 as an unconventional RNA-binding protein involved in metastasis. Nucleic acids research 50,14, 8207-8225 2022

Daniela Ionescu, Alejandro Peñín‐Franch, Anna Mensa‐Vilaró, Paola Castillo, Laura Hurtado‐Navarro, Cristina Molina‐López, Silvia Romero‐Chala, Susana Plaza, Virginia Fabregat, Segundo Buján, Joana Marques, Ferran Casals, Jordi Yagüe, Baldomero Oliva, Luis Miguel Fernández‐Pereira, Pablo Pelegrín, Juan I Aróstegui. First Description of Late‐Onset Autoinflammatory Disease Due to Somatic NLRC4 Mosaicism. Arthritis and Reumatology 74, 4, 692-699. 2022

Raquel Fernández-Ginés, José Antonio Encinar, John D Hayes, Baldo Oliva, Maria Isabel Rodríguez-Franco, Ana I Rojo, Antonio Cuadrado.  An inhibitor of interaction between the transcription factor NRF2 and the E3 ubiquitin ligase adapter β-TrCP delivers anti-inflammatory responses in mouse liver. Redox Biology 55, 102396, 2022

Alfonso José Tapiz i Reula, Alexis-Virgil Cochino, Andreia L Martins, Diego Angosto-Bazarra, Iñaki Ortiz de Landazuri, Anna Mensa-Vilaró, Marta Cabral, Alberto Baroja-Mazo, María C Baños, Zulema Lobato-Salinas, Virginia Fabregat, Susana Plaza, Jordi Yagüe, Ferran Casals, Baldomero Oliva, Antonio E Figueiredo, Pablo Pelegrín, Juan I Aróstegui. Characterization of novel pathogenic variants leading to caspase-8 cleavage-resistant RIPK1-induced autoinflammatory syndrome. Journal of Clinical Immunology, 42,7 1421-1432, 2022

Altair C Hernandez, Baldo Oliva, Damien P Devos, Oriol Gallego. Live-Cell Structural Biology to Solve Molecular Mechanisms: Structural Dynamics in the Exocyst Function. Protein Interactions: The Molecular Basis of Interactomics (Ed. John Wiley & Sons), 2022

2021

M Badia-Villanueva, S Defaus, R Foj, D Andreu, B Oliva, A Sierra, Narcis Fernandez-Fuentes Evaluation of computationally designed peptides against TWEAK, a cytokine of the tumour necrosis factor ligand family. International journal of molecular sciences 22 (3), 1066 (2021)

Enric Carcereny, Alonso Fernández-Nistal, Araceli López, Carmen Montoto, Andrea Naves, Cristina Segú-Vergés, Mireia Coma, Guillem Jorba, Baldomero Oliva And Jose Manuel Mas. Head to head evaluation of second generation ALK inhibitors brigatinib and alectinib as first-line treatment for ALK+ NSCLC using an in silico systems biology-based approach. Oncotarget. 12:316-332. (2021)

J Aguirre-Plans, A Meseguer, R Molina-Fernandez, Ma Marín-López, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornes, Narcis Fernandez-Fuentes, Baldo Oliva SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions. BMC bioinformatics 22 (1), 1-13 (2021)

J Aguirre-Plans, J Piñero, T Souza, G Callegaro, Sj Kunnen, F Sanz, Narcis Fernandez-Fuentes, Laura I Furlong, Emre Guney, Baldo Oliva. An ensemble learning approach for modeling the systems biology of drug-induced injury. Biology Direct 16 (1), 1-14 (2021) (commented in the Conversation reviews of Spanish edition: https://theconversation.com/inteligencia-artificial-para-predecir-si-un-farmaco-producira-dano-hepatico-157439)

Mirela-Bota P, Aguirre-Plans J, Meseguer A, Galletti C, Segura J, Planas-Iglesias J, Garcia-Garcia J, Guney E, Oliva B, Fernandez-Fuentes N. Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data. J Mol Biol. 433(11):166656. doi: 10.1016/j.jmb.2020.09.015. (2021)

Bernat Anton, Mireia Besalú, Oriol Fornes, Jaume Bonet, Alexis Molina, Ruben Molina-Fernandez, Gemma De Las Cuevas, Narcis Fernandez-Fuentes, Baldo Oliva. On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction. NAR genomics and bioinformatics 3(2): lqab027 (2021)

Andriy Kryshtafovych,  John Moult, Wendy M. Billings, Dennis Della Corte,  Krzysztof Fidelis,  Sohee Kwon, Kliment Olechnovič,  Chaok Seok,  Česlovas Venclovas, Jonghun Won, Casp-Covid Participants. Modeling SARS-CoV-2 proteins in the CASP-commons experiment. online:05 October 2021. DOI: 10.1002/prot.26231 (2021)

A. Tapia-Abellán , D. Angosto-Bazarra , C. Alarcón-Vilamaría C. Baños,Iva Hafner-Bratkovič , B. Oliva ,  P. Pelegrín.  Sensing low intracellular potassium by NLRP3 results in a stable open structure that promotes inflammasome activation. Science Advances, Vol 7, Issue 38, DOI: 10.1126/sciadv.abf4468 (2021)

Xavier Farré,  Ruben Molina-Fernandez,  Fabio Barteri,  Paul R H J Timmers, Peter K Joshi,  Baldomero Oliva,  Sandra Acosta,  Borja Esteve-Altava,  Arcadi Navarro,  Gerard Muntané . Comparative Analysis of Mammal Genomes Unveils Key Genomic Variability for Human Life Span. Molecular Biology and Evolution, msab219, https://doi.org/10.1093/molbev/msab219. (2021)

Ionescu D, Peñín-Franch A, Mensa-Vilaró A, Castillo P, Hurtado-Navarro L, Molina-López C, Romero-Chala S, Plaza S, Fabregat V, Buján S, Marques J, Casals F, Yagüe J, Oliva B, Fernández-Pereira Lm, Pelegrín P, Aróstegui Ji. First Description of Late-Onset Autoinflammatory Disease Due to Somatic NLRC4 Mosaicism. Arthritis Rheumatol.  Oct 20. doi: 10.1002/art.41999. (2021)

Martínez-Monseny Af, Edo A, Casas-Alba D, Izquierdo-Serra M, Bolasell M, Conejo D, Martorell L, Muchart J, Carrera L, Ortez Ci, Nascimento A, Oliva B, Fernández-Fernández Jm, Serrano M. CACNA1A Mutations Causing Early Onset Ataxia: Profiling Clinical, Dysmorphic and Structural-Functional Findings. Int J Mol Sci. 22(10):5180. doi: 10.3390/ijms22105180. (2021)

Galletti C, Bota Pm, Oliva B, Fernandez-Fuentes N. Mining drug-target and drug-adverse drug reaction databases to identify target-adverse drug reaction relationships. Database (Oxford). 2021:baab068. doi: 10.1093/database/baab068. (2021)

N Fernandez-Fuentes, R Molina, B Oliva A Collection of Designed Peptides to Target SARS-CoV-2 Spike RBD—ACE2 Interaction. International Journal of Molecular Sciences 22 (21), 11627 (2021)

Gutierrez-Casares Jr, Quintero J, Jorba G, Junet V, Martinez V, Pozo-Rubio T, Oliva B, Daura X, Mas Jm, Montoto C. Methods To Develop an in silico Clinical Trial: Computational Head-To-Head Comparison Of Lisdexamfetamine And Methylpenidate. Frontiers in psychiatry 12: 741170 (2021)

2020

Guillem Jorba, Joaquim Aguirre-Plans, Valentin Junet, Cristina Segú-Vergés, José Luis Ruiz, Albert Pujol, Narcís Fernández-Fuentes, José Manuel Mas, Baldo Oliva. In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan. PLoS One. 2020 Feb 13;15(2):e0228926. doi: 10.1371/journal.pone.0228926.

Patricia Mirela-Bota, Joaquim Aguirre-Plans, Alberto Meseguer, Cristiano Galletti, Joan Segura, Joan Planas-Iglesias, Javi Garcia-Garcia, Emre Guney, Baldo Oliva, Narcis Fernandez-Fuentes. Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein–Protein Interaction Data. J Mol Biol. 2020 Sep 23;S0022-2836(20)30557-X. doi: 10.1016/j.jmb.2020.09.015.

Alberto Meseguer, Lluis Dominguez, Patricia M Bota, Joaquim Aguirre‐Plans, Jaume Bonet, Narcis Fernandez‐Fuentes, Baldo Oliva. Using collections of structural models to predict changes of binding affinity caused by mutations in protein–protein interactions. Protein Sci. 2020 Oct;29(10):2112-2130. doi: 10.1002/pro.3930.

Alberto Meseguer, Filip Årman, Oriol Fornes, Ruben Molina-Fernández, Jaume Bonet, Narcis Fernandez-Fuentes, Baldo Oliva. On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF. NAR Genomics and Bioinformatics. 2020. 2(3): lqaa046. doi: 10.1093/nargab/lqaa046

Laura Artigas, Mireia Coma, Pedro Matos-Filipe, Joaquim Aguirre-Plans, Judith Farrés, Raquel Valls, Narcis Fernandez-Fuentes, Juan de la Haba-Rodriguez, Alex Olvera, Jose Barbera, Rafael Morales, Baldo Oliva, Jose Manuel Mas. In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm. PLoS One. 2020 Oct 2;15(10):e0240149. doi: 10.1371/journal.pone.0240149.

Ruben Molina, Baldo Oliva, Narcis Fernandez-Fuentes.A collection of designed peptides to target SARS-Cov-2–ACE2 interaction: PepI-Covid19 database. bioRxiv, 2020; doi: https://doi.org/10.1101/2020.04.28.051789

Joaquim Aguirre-Plans, Janet Piñero, Daniel Aguilar, Emre Guney, Ferran Sanz, Laura I. Furlong, Narcis Fernandez-Fuentes, and Baldo Oliva A review of Network Medicine Approaches to Understand Comorbidity. Nova Science Publishers Inc. Volume 158 pp 1-42. 2020.

Sandra Walsh, Mercé Izquierdo-Serra, Sandra Acosta, Albert Edo, Maria Lloret, Roser Moret, Elena Bosch, Baldo Oliva, Jaume Bertranpetit, José Manuel Fernández-Fernández. Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population. Scientific reports 10:1 1-16 2020

2019

Sharma P, Lioutas A, Fernandez-Fuentes N, Quilez J, Carbonell-Caballero J, Wright RHG, Di Vona Ch, Le Dily F, Schüller R, Eick D, Oliva B, Beato M. Arginine Citrullination at the C-Terminal Domain Controls RNA Polymerase II Transcription . Mol Cell, 2019; 73 (1): 84-96.e7. PMID: 30472187 . DOI: 10.1016/ j.molcel.2018.10.016.

Daniel Aguilar, Nathanael Lemonnier, Gerard H Koppelman, Erik Melén, Baldo Oliva, Mariona Pinart, Stefano Guerra, Jean Bousquet, Josep M Anto. Understanding allergic multimorbidity within the non-eosinophilic interactome. PloS one, 2019 14 (11), e0224448

Aguirre-Plans J, Piñero J, Sanz F, Furlong LI, Fernandez-Fuentes N, Oliva B, Guney E. GUILDify v2.0: A tool to identify molecular networks underlying human diseases, their comorbidities and their druggable targets. J Mol Biol, 2019. pii: S0022-2836 (19) 30117-2.. PMID: 30851278 . DOI: 10.1016/ j.jmb.2019.02.027.

Picón-Pagès P, Bonet J, García-García J, Garcia-Buendia J, Gutierrez D, Valle J, Gómez-Casuso CES, Sidelkivska V, Alvarez A, Perálvarez-Marín A, Suades A, Fernàndez-Busquets X, Andreu D, Vicente R, Oliva B, Muñoz FJ. Human Albumin Impairs Amyloid beta-peptide Fibrillation Through its C-terminus: From docking Modeling to Protection Against Neurotoxicity in Alzheimer's disease. Comput Struct Biotechnol J, 2019; 17: 963-971  . PMID: 31360335 . DOI: 10.1016/j.csbj.2019.06.017.

Patricia Resa‐Infante, Jaume Bonet, Swantje Thiele, Malik Alawi, Stephanie Stanelle‐Bertram, Berfin Tuku, Sebastian Beck, Baldo Oliva, Gülsah Gabriel. Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin‐α7 mediated nuclear import pathway. The FEBS journal, 2019; 286 (17), 3374-3388

Bernat Blasco-Moreno, Leire de Campos-Mata, René Böttcher, José García-Martínez, Jennifer Jungfleisch, Danny D Nedialkova, Shiladitya Chattopadhyay, María-Eugenia Gas, Baldomero Oliva, José E Pérez-Ortín, Sebastian A Leidel, Mordechai Choder, Juana Díez. The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins. Nature communications, 2019; 10 (1), 1-15

2018

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. 34(4): 592-598 (2018)

ANTONIO CUADRADO, GINA MANDA, AHMED HASSAN, MARÍA JOSÉ ALCARAZ, CORAL BARBAS, ANDREAS DAIBER, PIETRO GHEZZI, RAFAEL LEÓN, MANUELA G LÓPEZ, BALDO OLIVA, MARTA PAJARES, ANA I ROJO, NATALIA ROBLEDINOS-ANTÓN, ANGELA M VALVERDE, EMRE GUNEY, HARALD HHW SCHMIDT. Transcription factor NRF2 as a therapeutic target for chronic diseases: a systems medicine approach. Pharmacological reviews 70 (2), 348-383 (2018

JOAQUIM AGUIRRE-PLANS, JANET PIÑERO, JÖRG MENCHE, FERRAN SANZ, LAURA I FURLONG, HHHW SCHMIDT, BALDO OLIVA, EMRE GUNEY. Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology. Pharmaceuticals 11:61 (2018)

V SALGADO-MENDIALDÚA, J AGUIRRE-PLANS, E GUNEY, R REIG-VIADER, R MALDONADO, À BAYÉS, B OLIVA, A OZAITA. Delta9-tetrahydrocannabinol modulates the proteasome system in the brain. Biochemical Pharmacology 157: 159-168 (2018)

JANET PIÑERO, ABEL GONZALEZ-PEREZ, EMRE GUNEY, JOAQUIM AGUIRRE-PLANS, FERRAN SANZ, BALDO OLIVA AND LAURA I. FURLONG. Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response. Frontiers in Genetics 9:412 (2018)

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.