140.- Huerta M., Cedano J., Peña D., Rodríguez A. & Querol E. PCOPGene-Net : Holistic characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships. BMC Bioinformatics, 10, 138 (2009).
139.- Thavasi V., Lazarova T., Filipek S., Kolinski M., Querol E., Kumar A., Ramakrishna S., Padrós E. & Renugopalakrishnan V. Study on the feasibility of bacteriorhodopsin as bio-photosensitizer in excitonic solar cell: A first report. J. Nanosci. Nanotechnol., 9, 1679-1687 (2009).
138.- Hernández S., Gómez A., Cedano J. & Querol E. Omics techniques and identification of pathogen virulence genes. Application to the analysis of respiratory pathogens. J. Comput. Sci & Sys. Biol., 2, 124-132 (2009).
137.- Lazarova T., Querol E. & Padrós E. Coupling Between the Retinal Thermal Isomerization and the Glu194 Residue of Bacteriorhodopsin. Photochem. & Photobiol., 85, 617-623 (2009).
136.- Perálvarez-Marín A., Lorenz-Fonfria V., Simón-Vazquez R., Gomariz M., Meseguer I., Querol E. & Padrós E. Influence of proline on the thermostability of the active site and membrane arrangement of transmembrane proteins. Biophys. J. 95, 4384-4395 (2008).
135.- Cedano J., Huerta M. & Querol E. NCR-PCOPGene: An exploratory tool for analysis of sample classes effect on gene-expression relationships. Advances in Bioinformatics. ID789026, 1-7 (2008).
134.- Pich OC., Burgos R., Ferrer-Navarro M., Querol E. & Piñol J. Role of Mycoplasma genitalium MG218 and MG317 cytoskeletal proteins in terminal organelle organization, gliding motility and cytadherence. Microbiology, 154, 3188-3198 (2008).
133.- Burgos R., Pich OC., Querol E. & Piñol J. Deletion of the Mycoplasma genitalium MG_217 gene modifies the cell gliding behaviour by altering the terminal organelle curvature. Mol. Microbiol., 69,1029-1040 (2008).
132.- Espadaler J., Eswar N., Querol E., Avilés F. X., Sali A., Martí-Renom M. & Oliva B. Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics, 9, 249 (2008).
131.- Huerta M., Cedano J. & Querol E. Analysis of non-linear relations between expression profiles by the principal curves of oriented-points. J. Bioinf. Comput. Biol., 6, 367-386 (2008).
130.- Gómez A., Cedano J., Espadaler J., Hermoso A., Piñol J. & Querol E. Prediction of protein function improving sequence remote alignment search by a fuzzy logic algorithm. Protein J. 27, 130-139 (2008).
129.- Amela I., Cedano J. & Querol E. Pathogen Proteins Eliciting Antibodies do not Share Epitopes with Host Proteins: A Bioinformatics Approach. PLOS One, 2, e512 (2007).
128.- Lluch-Senar M., Vallmitjana M., Querol E. & Piñol J. A new promoterless vector reveals antisense transcription in Mycoplasma genitalium. Microbiology, 153, 2743-2752 (2007).
127.- Cedano J., Huerta M., Estrada I. Ballllosera F., Conchillo O., Delicado P. & Querol E. A web server for automatic analysis and extraction of relevant biological knowledge. Computers in Biology and Medicine, 37, 1672-1675 (2007).
126.- Perálvarez-Marín A., Lórenz-Fonfría V.A., Bourdelande J.L., Querol E., Kandori H. & Padrós E. Inter-helical hydrogen bonds are key elements for intra-protein signal transduction: the role of Asp115 in bacteriorhodopsin transport function. J. Mol.Biol., 368, 666-676 (2007).
125.- Sepulcre F., Cordomí A., Grazia Proietti M., Perez J. J., García J., Querol E. and Padrós E.X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane. Proteins:Structure Function & Bioinformatics, 67, 360-374 (2007).
124.- Burgos R., Pich OC., Querol E. & Piñol J. Functional análisis of the Mycoplasma genitalium MG312 protein reveals a specific requeriment of the MG312 N-terminal domain for gliding motility. J. Bacteriol., 189, 7014-7023 (2007).
123.- Yanes O., Villanueva J., Querol E. and Avilés F. X. Detection of non-covalent protein interactions by ‘intensity fading’ MALDI-TOF mass spectrometry: applications to proteases and protease inhibitors. Nature Protocols, 2, 119-130 (2007).
122.- Burgos R., Pich Q. O., Ferrer-Navarro M., Baseman J., Querol E. & Piñol J. Mycoplasma genitalium P140 and P110 cytadhesins are reciprocally stabilized and required for cell adhesion and terminal organelle development. J. Bacteriol.,188,8627-8637 (2006).
122.- Huerta M., Cedano J. & Querol E. Analysis of non-linear relation between expression profiles by the Principal Curves of Oriented-Points approach. Applied Bioinformatics. En prensa.
121.- Mozo-Villarias A., Cedano J. & Querol E. Hydrophobic density profiles to predict protein thermostability. The Protein J. 7-8, 529-535 (2006).
120.- Espadaler J., Querol E., Avilés F. X. & Oliva B. Identification of function-associated loop motifs and application to protein function prediction. Bioinformatics , 22, 2237-2243 (2006).
119.- Ferrer-Navarro M., Gómez A., Yanes O., Planell R., Avilés F.X., Pérez-Pons J.A., Piñol J. & Querol E. Proteome of the bacterium Mycoplasma penetrans. J. Proteome Research, 5, 688-694 (2006).
118.- Pich Q. O., Burgos R., Ferrer-Navarro M., Querol E. & Piñol J. Mycoplasma genitalium mg200 and mg386 are related with gliding motiliity and not with cytoadherence. Mol. Microbiol. 60, 1509-1519 (2006).
117.- 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-b-glucanase by Molecular Dynamics simulations. J. Mol. Model.,12, 835-845 (2006).
116.- Perálvarez-Marín A., Bourdelande J.L., Querol E. & Padrós E. The role of proline residues in the dynamics transmembrane helices: the case of bacteriorhodopsin. Mol. Mem. Biol., 23, 127-135 (2006).
115.- Pich Q. O., Burgos R., Planell R., Querol E. & Piñol J.Comparative analysis of antibiotic resistance gene markers in Mycoplasma genitalium and its application in the minimal gene complement analyses. Microbiology, 152, 519-527 (2006).
114.- Mozo-Villarias A. & Querol E. Theoretical Analysis and Computational Predictions of Protein Thermostability. Current Bioinformatics, 1, 25-32 (2006). Review.
113.- Espadaler J., Aragües R., Eswar N., Martí-Renom M., Querol E., Avilés F. X., Sali A. & Oliva B. Detecting remotely related proteins by their Interactions and sequence similarity. Proc. Natl. Acad. Sci. USA, 102, 7151-7156 (2005).
112.- Yanes O., Villanueva J., Querol E. and Avilés F. X. Functional screening of serine protease inhibitors in the medical leech Hirudo medicinalis monitored by Intensity Fading MALDI-TOF MS. Mol. Cell. Proteomics, 4, 1602-1613 (2005).
111.- Calisto B. M., Pich Q. O., Piñol J., Fita I., Querol E. & Carpena X. Crystal structure of a type I restriction-modification S subunit from Mycoplasma genitalium. J. Mol. Biol., 351, 749-762 (2005). Portada de la revista.
110.- Fernandez-Fuentes N., Oliva B., Querol E., Avilés F.X. & Sternberg M.J.E. Prediction of the conformation and geometry of loops in globular proteins. Testing ArchDB, a structural classification of loops. Proteins, 60, 746-757(2005).
109.- Sitja-Arnau M., Molina M. A., Blanco-Aparicio C., Ferrer-Soler L., Avilés F. X., Querol E. & de Llorens R. Potato carboxypeptidase inhibitor blocks EGFR and ErbB-2 dimerization and phosphorylation induced by EGF and TGF-a and modifies EGFR expression. Cancer Letters, 226, 169-184 (2005).
108.- Perálvarez-Marín A., Márquez M., Bourdelande J.L., Querol E. & Padrós E. Thr90 plays a vital role in the structure and function of bacteriorhodopsin. J. Biol. Chem. 279, 16403-16409 (2004).
107.- Hermoso A., Aguilar D., Avilés F. X. and Querol E. TrSDB. A Proteome Database of Transcription Factors. Nucleic Acid Res., 32, D171-173 (2004).
106.- Fernández-Fuentes N., Espadaler J., Querol E., Avilés F. X. & Oliva B. Classification of common functional loops of kinase superfamilies. Proteins , 56, 539-555 (2004).
105.- Yanes O., Villanueva J., Querol E. & Avilés F. X. Intensity Fading Maldi-Tof MS: A novel screening for ligand binding and drug discovery. Drug Discovery Today:Targets, 3 (Suppl.), S23-S30 (2004).
104.- Aguilar D., Oliva B., Avilés F. X., Querol E. & Sternberg M. Analysis of phenetic
threes based on metabolic capabilities. J. Mol. Biol. 340, 491-512 (2004).
103.- Espadaler J., Fernandez-Fuentes N., Hermoso A., Querol E., Avilés F.X., Sternberg M. and Oliva B. ArchDB: Automated protein loop classification as a tool for Structural Genomics. Nucleic Acid Res, 32, D185-188 (2004).
102.- Aguilar D., Oliva B., Avilés F. X. & Querol E. SNOW: helping to fix the biochemical nomenclature problem. Bioinformatics 19, 2492-2493 (2003).
101.- Bronsoms S., Villanueva J., Canals J., Querol E. & Avilés F. X. Análisis of the effect of potato carboxypeptidase inhibitor pro-sequence on the folding of the mature protein. Eur. J.. Biochem., 270, 3641-3650 (2003).
100.- Villanueva J., Villegas V., Serrano L., Querol E. & Avilés F. X. Monitoring disappearance of monomers and generation of resistance to proteolysis during the formation of ADA2h amyloid fibrils by MALDI-TOF MS. Biochem. J., 374, 489-493 (2003).
99.- Villanueva J., Yanes O., Querol E., Serrano L. & Avilés F. X. A general method to identify protein ligands in complex mixtures using MALDI-TOF MS. Analytical Chemistry, 75, 3385-3395 (2003).
98.- Villanueva J., Fernández-Ballester G., Querol E., Avilés F. X. & Serrano L. Ligand screening by exoproteolysis and mass spectrometry in combination with computer modelling. J. Mol. Biol., 330, 1039-1048 (2003).
97.- Mozo A., Cedano J. & Querol E. Minimization of the electic dipole moment increases the thermal stability of proteins. Prot. Engineer. 16, 279-286 (2003).
96.- Gómez A., Domedel N., Cedano J., Piñol J. & Querol E. Do current sequence analysis algorithms disclose multifunctional (moonlighting) proteins?. Bioinformatics, 19, 895-896 (2003).
95.- Ferrer Soler, L., Cedano, J., Querol, E & De Llorens, R. Cloning, expression and purification of human epidermal growth factor using different expression systems. J. Chromatography (B), 788, 113-123 (2003).
94.- Villanueva J., Villegas V., Querol E., Avilés F. X. & Serrano L. Protein secondary structure and stability determined by combining exoproteolysis and MALDI-TOF MS. J. Mass Spectroscopy, 37, 974-984 (2002).
93.- Lazarova T., Sanz C., Sepulcre F., Querol E., & Padros E. Specific effect of chloride on the photocycle of E194Q and E240Q mutants of bacteriorhodopsin As measured by FTIR spectroscopy. Biochemistry, 41, 8176-8183 (2002).
92.- Aloy P., Oliva B., Querol E. & Avilés F. X. & Rusell R. Structural similarity to link sequence space: New potential superfamilies and implications for structural genomics. Protein Science, 11, 1101-1116 (2002).
91.- López I., Querol E., Avilés F. X., Seno M., de Llorens R. & Oliva B. Betacellulin structure modelled from members of the EGF family. J. Mol. Model. 8, 131-144 (2002).
90.- Aguilar D., Oliva B., Avilés F. X. & Querol E. TRANSCOUT: prediction of gene expression regulatory proteins from their sequences. Bioinformatics, 18, 597-607 (2002).
89.- Perálvarez A., Barnadas R., Sabés M., Querol E. & Padrós E. Thr90 is a key residue of the bacteriorhodopsin proton pumping mechanism. FEBS Letters, 508, 399-402 (2001).
88.- Piñol J. & Querol E. Monoclonal Antibodies 1A2 and 3A11 Anti-PRRS Virus. Hybridoma and Hybridomics, 20, 412 (2001).
87.- Gómez A., Cedano J., Oliva B., Piñol J. & Querol E. The gene causing the Best's macular dystrophy (BMD) encodes a putative Na/K-Ca exchanger. DNA Sequence, 12, 431-435 (2001).
86.- Sanz C., Marquez M., Peralvarez A., Elouatik S., Sepulcre F., Querol E., Lazarova T. & Padros E. Contribution of extracellular Glu residues to the structure and function of bacteriorhodopsin: Presence of specific cation binding sites. J. Biol. Chem. 276, 40788-40794 (2001).
85.- Aloy P., Querol E., Avilés F. X. & Sternberg M. Automated structure-based prediction of functional sites in proteins. Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol. 311, 395-408 (2001).
84.- Vallmitjana M., Ferrer-Navarro M., Planell R., Abel M., Ausin C., Querol E., Planas A., & Pérez-Pons J.A. Mechanism of the family 1 ß-glucosidase from Streptomyces sp: catalytic residues and kinetic studies. Biochemistry 40, 5975-5982 (2001).
83.- Mas, J.M., Aloy, P., Martí-Renom M., Oliva, B., Llorens R., Avilés, F.X. & Querol, E. Classification on protein disulphide-bridge topologies. J. Comput. Aided . Mol. Design 15, 477-487 (2001).
82.- Venhudová G., Canals F., Marino C., Querol E. & Avilés F. X. Mutations in the N- and C-terminal tails of Potato Carboxypeptidase Inhibitor influence its oxidative refolding process at the reshuffling stage. J. Biol. Chem. 276, 11683-1690 (2001).
81.- Villanueva J., Canals F., Querol E. & Avilés F. X. Monitoring the expression and purification of recombinant proteins by MALDI-TOF Mass Spectrometry. Enzyme & Microbial Technol. 29, 99-103 (2001).
80.- Oliva B., Daura X., Querol E. & Avilés F. X. & Tapia O. A generalized Langevin dynamics algorithm for simulating biomolecular systems without discrete solvent. Theor. Chem. Acc. 105, 101-109 (2000).
79.- Serra-Hartmann X., Rebordosa X., Piñol J., Querol E. & Martí-Renom M. A. ASAP: analysis of peptide composition. Bioinformatics, 16, 1153-1154 (2000).
78.- Mozo-Villarias A.& Querol E. Engineering Protein Thermostability.
Curr.Topics Biochem. Res. 2, 19-31 (2000). Review.
77.- Naval J., Aguilar D., Pérez-Pons J. A., Piñol J., Lloberas J. & Querol E. An ORF from Bacillus licheniformis encodes a putative DNA repressor.DNA Sequence. 11, 1-7 (2000).
76.- Martí M. A., Stoke R. H., Querol E., Avilés F. X. & Karplus M. The Structures of Scrambled Disulfide Forms of the Potato Carboxypeptidase Inhibitor Predicted by Molecular Dynamics Simulations with Constraints. Proteins:Struct.Funct. Genet. 40, 482-493 (2000).
75.- Villanueva J., Canals F., Villegas V., Querol E. & Avilés F. X. Hydrogen exchange monitored by MALDI-TOF mass spectrometry for rapid characterization of the stability and conformation of proteins. FEBS Letters, 472, 27-33 (2000).
74.- Lazarova T., Sanz C., Querol E. & Padrós E. FTIR evidence for early deprotonation of Asp85 at alkaline pH in the photocycle of bacteriorhodopsin mutants containing E194Q. Biophys. J., 78, 2022-2030 (2000).
73.- Aloy P., Mas J. M., Marti -Renom M., Querol E., Avilés F. X. & 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. Design, 14, 83-92 (2000).
72.- Vendrell J., Querol E., Avilés F. X. Metallocarboxypeptidases and their protein inhibitors. Biochim. Biophys. Acta, 1477, 284-298 (2000). Review.
71.- Marino C., Venhudová G., Molina M. A., Oliva B., Jorba X., Canals F., Avilés F. X. & Querol E. Contribution of the C-tail residues of potato carboxypeptidase inhibitor in binding to carboxypeptidase A. A mutagenesis analysis.
Eur. J. Biochem., 267, 1502-1509 (2000).
70.- Gargallo R., Oliva B., Querol E. & Avilés F. X. Effect of the reaction field electrostatic term on the molecular dynamics simulation of the activation domain of procarboxypeptidase. Prot. Engineer., 13, 21-26 (2000).
69.- Sanz C., Lazarova T., Sepulcre F., Gonzalez R., Bourdelande J.L., Querol E., Pardo L. & Padrós E. Location of cation binding sites within the extracellular domain of bacteriorhodopsin. FEBS Letters, 456, 191-1895 (1999).
68.- Guasch A ., Vallmitjana M., Pérez R., Querol E. Pérez-Pons J.A. & Coll M. Cloning, overexpression, crystallization and preliminary X-ray analysis of a family 1 ß-glucosidase fromStreptomyces sp. Acta Crystal., D55, 679-682 (1999).
67.- Más, J. M., Aloy, P., Oliva, B., Marti M., Llorens R., Molina M. A., Querol, E. & Avilés, F.X. Protein similarities beyond disulphide bridge topology.J. Mol. Biol. 284, 541-548 (1998).
66.- Blanco C., Molina M. A., Más J., Fernández E., Frazier M. L., Querol E., Avilés F. X. & Llorens R. Potato carboxypeptidase inhibitor, a T-knot protein, is an EGF antagonist that inhibits tumor cell growth. J. Biol. Chem., 273, 12370-12377 (1998).
65.- Oliva B., Bates P., Querol E., Avilés F. X. & Sternberg M. J. E. Automated classification of antibody CDR-H3 loops into canonical forms. J. Mol. Biol., 279, 1193-1210 (1998).
64.- Montero E., Cañada F. J., Vallmitjana M., Pérez-Pons J. A., Querol E. & Jimenez-Barbero J. NMR studies of the conformation of thiocellobiose bound to Streptomyces sp ß-glucosidase. FEBS Letters., 421, 243-248 (1998). Portada de revista.
63.- Martí M. A., Stoke R. H., Querol E., Avilés F. X. & Karplus M. Unfolding and refolding of potato carboxypeptidase inhibitor investigated by molecular dynamics studies. J. Mol. Biol., 284, 145-172 (1998).
62.- Aloy P., Moont G., Gabb H., Querol E. Avilés F. X. & Sternberg M. J. E. Modeling repressor proteins binding to DNA. Proteins:Struct. Funct. Genet., 33, 535-549 (1998).
61.- Martí M. A., Oliva B., Q
