Updated link to the publications of the group: link
Bustamante, A.; Rivera, R.; Floor, M.; Babul, J.; Baez, M. Single-molecule optical tweezers reveals folding steps of the domain swapping mechanism of a protein. Biophysical Journal, 2021 https://doi.org/10.1016/j.bpj.2021.09.026
Marruecos, L.; Bertran, J.; Álvarez-Villanueva, D.; Mulero, M.C.; Guillén, Y.; Palma, L.G.; Floor, M.; Vert, A.; Arce-Gallego, S.; Pecharroman, I.; Batlle, L.; Villà-Freixa, J.; Ghosh, G.; Bigas, A.; Espinosa, L. Dynamic chromatin association of IκBα is regulated by acetylation and cleavage of histone H4 EMBO Reports, (e52649), 2021, ISSN: 1469-3178. https://doi.org/10.15252/embr.202152649
Floor, M.; Li, K.; Estevez-Gay, M.; Agulló, L.; Muñoz-Torres, P.M.; Hwang, J. K.; Osuna, S.; Villà-Freixa, J. SBMOpenMM: A Builder of Structure-Based Models for OpenMM. J Chem Inf Model, 61 (7), pp. 3166-3171, 2021, ISSN: 1549-960X. https://pubs.acs.org/doi/10.1021/acs.jcim.1c00122
O. Contreras-Rodriguez, M. Arnoriaga-Rodríguez, R. Miranda-Olivos, G. Blasco, C. Biarnés, J. Puig, J. Rivera-Pinto, M. L. Calle, V. Pérez-Brocal, A. Moya, C. Coll, L. Ramió-Torrentà, C. Soriano-Mas & J. M. Fernandez-Real. Obesity status and obesity-associated gut dysbiosis effects on hypothalamic structural covariance. Int J Obes (2021). https://doi.org/10.1038/s41366-021-00953-9
Aguirre-Plans, J.; Meseguer, A., Molina-Fernandez, R.; Marín-López, M. A.; Jumde, G.; Casanova, K.; …; Fernandez-Fuentes, N.; Oliva, B (2021) SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions. BMC Bioinformatics, 22, (1), https://doi.org/10.1186/s12859-020-03770-5
Redondo, A.; Wood, D.; Amaral, S.; Ferré, J.; Goti, D.; Bertran, J. Production of toxoplasma gondii recombinant antigens in genome-edited escherichia coli. Applied Biochemistry and Microbiology, 57, (2), 2021, pp. 152-160. https://doi.org/10.1134/S0003683821020137
Mirela-Bota, P.; Aguirre-Plans, J.; Meseguer, A.; Galletti, C.; Segura, J.; Planas-Iglesias, J.; Fernandez-Fuentes, N. Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data. Journal of Molecular Biology, 433, (11), 2021. https://doi.org/10.1016/j.jmb.2020.09.015
Perez-Amill, L., Suñe, G., Antoñana-Vildosola, A., Castella, M.; Najjar, A., Bonet, J., Fernandez, N.; …; Martín-Antonio, B. Preclinical developmet of a humanized chimeric antigen receptor against B-cell maturation antigen for multiple myeloma. Haematologica, 106, (1), 2021, pp. 173-184. https://doi.org/10.3324/haematol.2019.228577
Aguirre-Plans, J.; Piñero, J.; Souza, T.; Callegaro, G.; Kunnen, S.J.; Sanz, F.; …; Fernandez-Fuentes, N.; …; Oliva, B. An ensemble learning approach for modeling the systems biology of drug-induced injury. Biology Direct, 16, (1), 2021, https://doi.org/10.1186/s13062-020-00288-x
Badia-Villanueva, M.; Defaus, S.; Foj, R.; Andreu, D.; Oliva, B.; Sierra, A.; Fernandez-Fuentes, N. Evaluation of computationally designed peptides against tweak, a cytokine of the tumour necrosis factor ligand family. International Journal of Molecular Sciences, 22, (3), 2021 https://doi.org/10.3390/ijms22031066
Guerrero-Puigdevall, M., Fernandez-Fuentes, N., & Frigola, J. Stabilisation of half MCM ring by Cdt1 during DNA insertion. Nature Communications, 12, (1), 2021. https://doi.org/10.1038/s41467-021-21932-8
Meseguer, A.; Arman, F.; Fornes, O.; Molina-Fernandez, R.; Bonet, J.; Fernandez-Fuentes, N.; et al. On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: Application on human CTCF. NAR Genomics and Bioinformatics, 2, (3), 2021, https://doi.org/10.1093/nargab/lqaa046
Oriol-Tordera, B., Olvera, A., Duran-Castells, C. Llano, A., Mothe, B., Massanella, M., Dalmau, J., Ganoza, C., Sanchez, J., Calle, M.L., Clotet, B., Martinez-Picado, J., Negredo, E., Blanco, J., Hartigan-O’Connor, D., Brander, C., Ruiz Riol, M. (2020) TL1A-DR3 plasma levels are predictive of HIV-1 disease control, and DR3 costimulation boosts HIV-1-specific T cell responses. Journal of Immunology, 2020, 205(12), pp. 3348–3357 DOI: 10.4049/jimmunol.2000933
Susin A., Wang Y, Lê Cao K-A, Calle M.L. Variable selection in microbiome compositional data analysis. NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020, lqaa029, https://doi.org/10.1093/nargab/lqaa029
Brena, D., Bertran, J., Porta-de-la-Riva, M., Guillén, Y., Cornes, E. et al. (2020). Ancestral function of Inhibitors-of-kappaB regulates Caenorhabditis elegans development . Scientific Reports, 10(1), 16153-0 doi: 10.1038/s41598-020-73146-5.
García-Recio, A., Navarro, G., Franco, R., Olivella, M., Guixà-González, R., Cordomí A. (2020). DIMERBOW: exploring possible GPCR dimer interfaces. Bioinformatics Oxford, 36(10), 3271-3272. doi: 10.1093/bioinformatics/btaa117.
Velasco-Hernandez, T., Zanetti, S.R., Roca-Ho, H., Gutierrez-Aguera, F., Petazzi, P., Sánchez-Martínez, D., Fernández-Fuentes, N., Menendez P. (2020). Efficient elimination of primary B-ALL cells in vitro and in vivo using a novel 4-1BB-based CAR targeting a membrane-distal CD22 epitope. Journal for immunotherapy of cancer, 8(2), 000896-0 doi: 10.1136/jitc-2020-000896.
Mayol, E., García-Recio, A., Tiemann, J.K.S., Hildebrand, P.W., Guixà-González, R., Olivella, M., Cordomí A. (2020). HomolWat: a web server tool to incorporate «homologous» water molecules into GPCR structures. Nucleic Acids Research, 48(1), 54-59. doi: 10.1093/nar/gkaa440.
Marruecos, L., Bertran, J., Guillén, Y., González, J., Batlle, R., López-Arribillaga, E., Garrido, M., Ruiz-Herguido, C., Lisiero, D., González-Farré, M., Arce, S., Iglesias, M., Nebreda, A.R., Miyamoto, S., Bigas, A., Espinosa Ll. (2020). Iκbα Deficiency Imposes a Fetal Phenotype to Intestinal Stem Cells. EMBO Reports, https://doi.org/10.2139/ssrn.3389376.
Jorba, G., Aguirre-Plans, J., Junet, V., Segú-Vergés, C., Ruiz, J. L., Pujol, A., Fuentes, N., Mas, JM., Oliva B. (2020). In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan. PLoS ONE, 15(2), https://doi.org/10.1371/journal.pone.0228926.
Xu, L., Wang, F., Dempere-Marco, L., Wang, Q., Yang, Y., Hu XP. (2020). Path-Based Analysis for Structure-Preserving Image Filtering. Journal of Mathematical Imaging and Vision, 176-195. https://doi.org/10.1007/s10851-019-00941-9.
Oriol-Tordera, B., Berdasco, M., Llano, A., Mothe, B., Galvez, C., Martínez-Picado, J., Carrillo, J., Blanco, J, … Clotet, B., Calle, M.L., Brander, C., Ruiz Riol M. (2020). Methylation regulation of antiviral host factors, Interferon Stimulated Genes (ISGs) and T-cell responses associated with natural HIV control. PLoS Pathogens, 16(8), 1008678-0 doi: 10.1371/journal.ppat.1008678.
Santos-Gomez, A.; Miguez-Cabello, F.; Garcia-Recio, A.; Locubiche-Serra, S.; Garcia-Diaz, R.; Soto-Insuga, V.; Olivella, M., et al. Disease-associated GRIN protein truncating variants trigger NMDA receptor loss-of-function. Human Molecular Genetics, 29, (4), 2020, pp. 3859-3871. https://doi.org/10.1093/hmg/ddaa220
Simonet, N.G., Thackray, J.K., Vazquez, B N., Ianni, A., Espinosa-Alcantud, M., Morales-Sanfrutos, J., Olivella, M. et al. (2020). SirT7 auto-ADP-ribosylation regulates glucose starvation response through mH2A1 . Science advances, 6(30), 0-0. doi: 10.1126/sciadv.aaz2590.
Rodríguez-Espigares, I.; Torrens-Fontanals, M.; Tiemann, JKS.; Aranda-García, D.; Ramírez-Anguita, JM.; …;Olivella, M. ; et al. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature Methods, 17, 2020, pp. 777-787. https://doi.org/10.1038/s41592-020-0884-y
Altarriba-Bartes, A., Calle, M., Susín, A., Gonçalves, B., Vives, M., Sampaio, J., Peña J. (2020). Analysis of the winning probability and the scoring actions in the American professional soccer championship. Revista internacional de ciencias del deporte, 16(59), 67-84. https://doi.org/10.5232/ricyde2020.05906.
Meseguer, A., Dominguez, L., Bota, P.M., Aguirre-Plans, J., Bonet, J., Fernandez-Fuentes, N. et al. (2020). Using collections of structural models to predict changes of binding affinity caused by mutations in protein-protein interactions. Protein Science, 29(10), 2112-2130 doi: 10.1002/pro.3930.
Rocafort M., Noguera-Julià M., Rivera J., Pastor L., Guillén Y., Langhorst J., Parera M., Mandomando I., Carrillo J., Urrea V., Rodríguez C., Casadellà M., Calle M.L., Clotet B., Blanco J., Naniche D., Paredes R. Evolution of the gut microbiome following acute HIV-1 infection. Microbiome, Volume 7, Issue 73, 11 May 2019, https://doi.org/10.1186/s40168-019-0687-5
Calle ML. Statistical Analysis of Metagenomics Data. Genomics & Informatics, Volume 17, Issue 1, 31 March 2019, https://doi.org/10.5808/GI.2019.17.1.e6
López de Maturana E, Alonso L, Alarcón P, Adoración Martín-Antoniano I, Pineda S, Piorno L, Calle ML and Malats N. Challenges in the Integration of Omics and Non-Omics Data. Genes, Volume 10, Issue 3, 2 January 2019, Page 238, https://doi.org/10.3390/genes10030238
Navarro-Roldán, Miguel A., Amat, Carles, Bau, Josep, Gemeno César. (2019). Extremely low neonicotinoid doses alter navigation of pest insects along pheromone plumes . Scientific Reports, 9(1), https://doi.org/10.1038/s41598-019-44581-w.
Xu, Lijuan, Ji, Zhihang, Dempere-Marco, Laura, Wang, Fan, Hu Xioapeng. (2019). Gestalt-Grouping based on Path Analysis for Saliency Detection . Signal Processing: Image Communication, 78, 9-20. https://doi.org/10.1016/j.image.2019.05.017.
Bedia, C., Badia, M., Muixí, L., Levade, T., Tauler, R., Sierra A. (2019). GM2-GM3 gangliosides ratio is dependent on GRP94 through down-regulation of GM2-AP cofactor in brain metastasis cells . Scientific Reports, 9(1), https://doi.org/10.1038/s41598-019-50761-5.
Aguirre-Plans, J., Piñero, J., Sanz, F., Furlong, L. I., Fernandez-Fuentes, N., Oliva, B., Guney E. (2019). GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets . Journal of Molecular Biology, 431(13), 2477-2484. https://doi.org/10.1016/j.jmb.2019.02.027.
Colomer, C., Margalef, P., Villanueva, A., Vert, A., Pecharroman, I., Solé, L., González-Farré, M., Alonso, J., Montagut, C., Martinez-Iniesta, M., Bertran, J., Borràs, E., Iglesias, M., Sabidó, E., Bigas, A., Boulton, S.J., Espinosa L. (2019). IKK¿ Kinase Regulates the DNA Damage Response and Drives Chemo-resistance in Cancer . Molecular Cell, 75(4), 669-682. https://doi.org/10.1016/j.molcel.2019.05.036.
Mayol, E., Campillo, M., Cordomi, A., Olivella M. (2019). Inter-residue interactions in alpha-helical transmembrane proteins . Bioinformatics, 35(15), 2578-2584. https://doi.org/10.1093/bioinformatics/bty978.
Soto, D., Olivella, M., Grau, C., Armstrong, J., Alcon, C., Gasull, X., Altafaj X. (2019). l-Serine dietary supplementation is associated with clinical improvement of loss-of-function GRIN2B -related pediatric encephalopathy . Science Signaling, 12(586), https://doi.org/10.1126/scisignal.aaw0936.
Font, A., Domenech, M., Ramirez, J. L., Gago, J., Carrato, C., Cadenas, B. et al. (2019). Potential role of a clinical, taxonomical classification and RNA expression integrated signature to predict response to neoadjuvant platinum-based chemotherapy in muscle-invasive bladder cancer (MIBC) patients. Annals of Oncology, 30.
Xu, L., Dempere-Marco, L., Wang, F., Ji, Z., Hu X.P. (2019). Towards Path-based Semantic Dissimilarity Estimation for Scene Representation using Bottleneck Analysis . IET Computer Vision, 13(8), 691-699. https://doi.org/10.1049/iet-cvi.2018.5560.
Rivera Pinto J, Egozcue JJ, Pawlowsky-Glahn V, Paredes R, Noguera-Julian M, Calle ML (2018) Balances: a new perspective for microbiome analysis. mSystems 3 (4), https://msystems.asm.org/content/3/4/e00053-18
Soto, D., Olivella, M., Grau, C., Armstrong, J., Alcon, C., Gasull, X. et al. (2018). Rett-like severe encephalopathy caused by a de novo GRIN2B mutation is attenuated by D-serine dietary supplement . Biological Psychiatry, 83(2), 160-172. https://doi.org/10.1016/j.biopsych.2017.05.028.
Ring T Cardé Josep Bau Joseph S Elkinton. Comparison of Attraction and Trapping Capabilities of Bucket- and Delta-Style Traps With Different Pheromone Emission Rates for Gypsy Moths (Lepidoptera: Erebidae): Implications for Understanding Range of Attraction and Utility in Surveillance. Environmental Entomology, Volume 47, Issue 1, 8 February 2018, Pages 107–113, https://doi.org/10.1093/ee/nvx185
Vesterbacka J, Rivera J, Noyan K, Parera M, Neogi U, Calle M, Paredes R, Sönnerborg A, Noguera-Julian M & Nowak P. Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers, Scientific Reports 7, Article number: 6269 (2017) doi:10.1038/s41598-017-06675-1 https://www.nature.com/articles/s41598-017-06675-1
Soto D, Olivella M, Grau C, Armstrong J, Alcon C, Gasull X, Gómez de Salazar M, Gratacòs-Batlle E, Ramos-Vicente D, Fernández-Dueñas V, Ciruela F, Bayés À, Sindreu C, López-Sala A, García-Cazorla À, Altafaj X. Rett-like Severe Encephalopathy Caused by a De Novo GRIN2B Mutation Is Attenuated by D-serine Dietary Supplement. Biol Psychiatry. 2017 Jun 16. pii: S0006-3223(17)31671-2. doi: 10.1016/j.biopsych.2017.05.028. [Epub ahead of print] https://www.ncbi.nlm.nih.gov/pubmed/28734458
Molinos-Albert LM, Bilbao E, Agulló L, Marfil S, García E, Rodríguez de la Concepción ML, Izquierdo-Useros N, Vilaplana C, Nieto-Garai JA, Contreras FX, Floor M, Cardona PJ, Martinez-Picado J, Clotet B, Villà-Freixa J, Lorizate M, Carrillo J & Blanco J. Proteoliposomal formulations of an HIV-1 gp41-based miniprotein elicit a lipid-dependent immunodominant response overlapping the 2F5 binding motif. Scientific Reports 7, Article number: 40800 (2017) doi:10.1038/srep40800 https://www.nature.com/articles/srep40800
V Pallarés, M Hernández, L Dempere-Marco. Eye-Tracking Data in Visual Search Tasks: A Hallmark of Cognitive Function. Converging Clinical and Engineering Research on Neurorehabilitation II, (2017) 873-877 https://link.springer.com/chapter/10.1007/978-3-319-46669-9_142
Rubio-Perez C, Guney E, Aguilar D, Piñero J, Garcia-Garcia J, Iadarola B, Sanz F, Fernandez-Fuentes N, Furlong L.I., Oliva B. Genetic and functional characterization of disease associations explains comorbidity. Scientific Reports 7, Article number: 6207 (2017) doi:10.1038/s41598-017-04939-4 https://www.nature.com/articles/s41598-017-04939-4
Oriol-Tordera B, Llano A, Ganoza C, Cate S, Hildebrand W, Sanchez J, Calle ML, Brander C, Olvera A. Impact of HLA-DRB1 allele polymorphisms on control of HIV infection in a Peruvian MSM cohort. HLA 90(4):234-237. (2017) doi: 10.1111/tan.13085 http://onlinelibrary.wiley.com/doi/10.1111/tan.13085/abstract
Rivera-Pinto J, Estany C, Paredes R, Calle M, Noguera-Julián M, the MetaHIV-Pheno Study Group (2017) Statistical Challenges for Human Microbiome Analysis. In: Ainsbury E., Calle M., Cardis E., Einbeck J., Gómez G., Puig P. (eds) Extended Abstracts Fall 2015. Trends in Mathematics, vol 7. Birkhäuser, Cham https://link.springer.com/chapter/10.1007/978-3-319-55639-0_8
Gallego V, Calle ML, Oller R. Kernel-Based Measure of Variable Importance for Genetic Association Studies. The International Journal of Biostatistics (2017) doi:10.1515/ijb-2016-0087 https://www.ncbi.nlm.nih.gov/pubmed/28628480
Oyama LB, Crochet JA, Edwards JE, Girdwood SE, Cookson AR, Fernandez-Fuentes N, Hilpert K, Golyshin PN, Golyshina OV, Privé F, Hess M, Mantovani HC, Creevey CJ, Huws SA. Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis. Front Chem. 2017 Jul 12;5:51. doi: 10.3389/fchem.2017.00051. eCollection 2017. https://www.ncbi.nlm.nih.gov/pubmed/28748180
Mateo, F., Arenas, E., Aguilar, H., Sierra, A., Pujana, M. (2016). Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition. Oncogene (2017) 36, 2737–2749; doi:10.1038/onc.2016.427 http://www.nature.com/onc/journal/v36/n19/full/onc2016427a.html
Hedegaard J, Lamy P, Nordentoft I, Algaba F, Høyer S, Ulhøi BP, Vang S, Reinert T, Hermann GG, Mogensen K, Houlberg Thomsen MB, Nielsen MM, Marquez M, Segersten U, Aine M, Hoglund M, Birkenkamp-Demtroder K, Fristrup N, Borre M, Hartmann A, Stohr R, Wach S, Keck B, Seitz AK, Nawroth R, Maurer T, Tulic C, Simic T, Junker K, Horstmann M, Harving N, Petersen AC, Calle ML, Steyerberg EW, Beukers W, van Kessel KEM, Bjerggaard Jensen B, Skou Pedersen J, Malmstrom PU, Malats N, Real FX, Zwarthoff EC, Ørntoft TF, and Dyrskjøt L. Comprehensive Transcriptional Analysis of Early-Stage Urothelial Carcinoma, Cancer Cell (2016) http://dx.doi.org/10.1016/j.ccell.2016.05.004
Sanchez Calle, A., Nair, N., KoKo Oo, A., Prieto-Vila, M., Koga, M., Cahya Khayrani, A., Hussein, M., Hurley, L., Vaidyanath, A., Seno, A., Iwasaki, Y., Calle, M., Kasai, T., Seno M. . (2016). A new PDAC mouse model originated from iPSCs-converted pancreatic cancer stem cells (CSCcm). American Journal of Cancer Research., 6(12), 2799-2815. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199755/
Pérez-Santiago, Josué, Ouchi, Dan, Urrea, Victor, Carrillo, Jorge, Cabrera, Cecilia, Villà-Freixa, Jordi, Puig, Jordi, Paredes, Roger, Negredo, Eugènia, Clotet, Bonaventura, Massanella, Marta, Blanco Julià. (2016). ART-suppressed subjects with low CD4 T-cell counts segregate according to opposite immunological phenotypes. AIDS., 30(15), 2275-2287. doi: 10.1097/QAD.0000000000001205. https://www.ncbi.nlm.nih.gov/pubmed/27427875
Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, Estany C, Herrero C, Saz J, Sirera G, Torrela A, Navarro J, Crespo M, Brander C, Negredo E, Blanco J,Guarner F, Calle ML,Bork P,Sönnerborg A,Clotet B,Paredes R, Gut Microbiota Linked to Sexual Preference and HIV Infection, EBioMedicine (2016), http://dx.doi.org/10.1016/j.ebiom.2016.01.032
M Balagué, L Dempere-Marco. (2016) Multi-item Working Memory Capacity: What Is the Role of the Stimulation Protocol? International Conference on Artificial Neural Networks, 264-271 https://link.springer.com/chapter/10.1007/978-3-319-44778-0_31
V Pallarés, L Rami, L Dempere-Marco (2016) A Novel Method for Disentangling Strategies from Visual Search. BIOSIGNALS, 271-276
Gómez-Tamayo, J.C., Cordomí, A., Olivella, M., Mayol, E., Fourmy, D., Pardo L. (2016). Analysis of the interactions of sulfur-containing amino acids in membrane proteins. Protein Science., 25(8), 1517-1524. https://www.ncbi.nlm.nih.gov/pubmed/27240306
Agulló, L., Buch, I., Gutiérrez-de-Terán, H., Garcia-Dorado, D., Villà-Freixa J. (2016). Computational exploration of the binding mode of heme-dependent stimulators into the active catalytic domain of soluble guanylate cyclase. Proteins., 84(10), 1534-1548. doi: 10.1002/prot.25096. http://onlinelibrary.wiley.com/doi/10.1002/prot.25096/abstract
Porta, A., Barrabés,J.A., Candell-Riera, J., Agulló, L., Aguadé-Bruix, S., de León, G., Figueras, J., Garcia-Dorado D. (2016). Plasma B-type natriuretic peptide levels are poorly related to the occurrence of ischemia or ventricular arrhythmias during symptom-limited exercise in low-risk patients. Archives of Medical Science., 12(2), 341-348. doi: 10.5114/aoms.2016.59258.
Bau, J., Cardé R.T. (2016). Simulation Modeling to Interpret the Captures of Moths in Pheromone-Baited Traps Used for Surveillance of Invasive Species: the Gypsy Moth as a Model Case. Journal of Chemical Ecology., , 0-0. doi: 10.1007/s10886-016-0765-0.
Vilor-Tejedor, N. ; Gonzalez, J.R ; Calle, M.L, Efficient and powerful method for combining p-values in Genome-wide Association Studies, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Issue: 99 (2016) DOI:10.1109/TCBB.2015.2509977
Luis Agulló, Sunny Malhotra, Nicolás Fissolo, Xavier Montalban, Manuel Comabella, Molecular dynamics and intracellular signaling of the TNF-R1 with the R92Q mutation, Journal of Neuroimmunology, Volume 289, 15 December 2015, Pages 12–20, doi:10.1016/j.jneuroim.2015.10.003
Perea M, Lugtenburg I, Mayol E, Cordomí A, Deupí X, Pardo L, Olivella M. TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins. BMC Bioinformatics. 2015 Aug 20;16:266. doi: 10.1186/s12859-015-0699-5.
Josep Bau; Ring T. Carde. Modeling Optimal Strategies for Finding a Resource-Linked, Windborne Odor Plume: Theories, Robotics, and Biomimetic Lessons from Flying Insects. Integrative and Comparative Biology 2015; doi: 10.1093/icb/icv036
Gallardo F, Padrón A, Garcia-Carbonell R, Rius C, González-Perez A, Arumí-Uria M, Iglesias M, Nonell L, Bellosillo B, Segura S, Pujol RM, Lopez-Bigas N, Bertran J, Bigas A, Espinosa L. Cytoplasmic accumulation of NCoR in malignant melanoma: consequences of altered gene repression and prognostic significance. Oncotarget. 2015 Apr 20;6(11):9284-94. http://www.ncbi.nlm.nih.gov/pubmed/25823659
Lisa De Lorenzi, Jordi Planas, Elena Rossi, Luca Malagutti, Pietro Parma. New cryptic karyotypic differences between cattle (Bos taurus) and goat (Capra hircus). Chromosome Research, January 2015, 1-11
N.Vilor, M.L. Calle. Global Adaptive Rank Truncated Product method for gene-set analysis in Association Studies. Biometrical Journal, (2014) DOI: 10.1002/bimj.201300192
N. Drechsel, C. Fenell, K. A. Dill, and J. Villà-Freixa, “TRIFORCE: Tessellated Semi-analytical Solvent Exposed Surface Areas and Derivatives,” J. chem. theor. comp., 10 (9), pp 4121–4132, 2014 http://pubs.acs.org/doi/abs/10.1021/ct5002818
Marta Tajesa, Abel Eraso-Pichot, Fanny Rubio-Moscardó, Biuse Guivernau, Eva Ramos-Fernández, Mònica Bosch-Morató, Francesc Xavier Guix, Jordi Clarimón, Gian Pietro Miscione, Mercè Boada, Gabriel Gil-Gómez, Toshiharu Suzuki, Henrik Molina, Jordi Villà-Freixa, Rubén Vicente and Francisco J. Muñoz. Methylglyoxal Produced by Amyloid-Peptide-Induced Nitrotyrosination of Triosephosphate Isomerase Triggers Neuronal Death in Alzheimer’s Disease. Journal of Alzheimer’s Disease 41 (2014) 273–288. DOI 10.3233/JAD-131685
M.M. Vedder, M. Márquez, E.W. de Bekker-Grob, M.L. Calle, L. Dyrskjøt, M. Kogevinas, U. Segersten, P-U Malmström, F. Algaba, W.Beukers, T.F. Ørntoft, E. Zwarthoff, F.X. Real, N. Malats, E.W. Steyerberg. Risk prediction scores for recurrence and progression of non-muscle invasive bladder cancer: An international validation in primary tumours. PlosOne, June 2014. DOI: 10.1371/journal.pone.0096849
Nils J. D. Drechsel, Christopher J. Fennell, Ken A. Dill, and Jordi Villà-Freixa TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and DerivativesJ. Chem. Theory Comput., 2014, 10 (9), pp 4121–4132 DOI: 10.1021/ct5002818
E López de Maturana, SJChanok, AC Picornell, N Rothman, J Herranz, ML Calle, M García-Closas, G Marenne, A Brand, A Tardón, A Carrato, DT Silverman, M Kogevinas, D Gianola, FX Real, N Malats. Whole genome prediction of bladder cancer risk with the bayesian lasso. Genetic Epidemiology, Vol 38, March 2014, DOI: 10.1002/gepi.21809
S.Pineda, R.L.Milne, M.L.Calle, N.Rothman, E.López de Maturana, J.Herranz, M.Kogevinas, S.J.Chanock, A.Tardón, M.Márquez, L.T.Guey, M.García-Closas, J.Lloreta, E.Braum, A.González-Neira, A.Carrato, A.Navarro, D.T.Silverman, F.X.Real, N.Malats (2014) Genetic variation in the TP53 pathway and bladder cancer risk. A comprehensive analysis. PLOSONE. DOI: 10.1371/journal.pone.0089952
E.López de Maturana, Y.Ye, M.L.Calle, N.Rothman, V.Urrea, M.Kogevinas, S.Petrus, S.J.Chanock, A.Tardón, M.García-Closas, A.González-Neira, G.Vellalta, A.Carrato, A.Navarro, B.Lorente-Galdós, DT.Silverman, F.X.Real, X.Wu, N.Malats (2013) Application of Multi-SNP Approaches Bayesian LASSO and AUC-RF to Detect Main Effects of Inflammatory-Gene Variants Associated with Bladder Cancer Risk. PLoS ONE. 8(12):e83745. DOI:10.1371/journal.pone.0083745
Mulero MC., Ferres-Marco D., Islam A, Margalef P., Pecoraro M., Toll A., Drechsel N., Charneco C., Davis S., Bellora N., Gallardo F., López-Arribillaga E., Asensio E., Rodilla V., González J., Iglesias M., Shih V., Albà M., Di Croce L., Hoffmann A., Miyamoto S., Villà-Freixa J., López-Bigas N., M. Keyes W., Domínguez M., Bigas A., Espinosa L. (2013) “Chromatin-bound IκBα regulates a subset of Polycomb- target genes in differentiation and cancer”. Cancer Cell, Volume 24, Issue 2, 151-166 http://www.cell.com/cancer-cell/abstract/S1535-6108%2813%2900279-1. DOI: 10.1016/j.ccr.2013.06.003
Van Lishout F., M Mahachie J., S Gusareva E., Urrea V., Cleynen I., Théâtre E., Charloteaux B., Calle M.L., Wehenkel L., Van Steen K. (2013) “An efficient algorithm to perform multiple testing in epistasis screening”. BMC Bioinformatics. 14:138. http://www.biomedcentral.com/1471-2105/14/138. DOI:10.1186/1471-2105-14-138
Olivella M, Gonzalez A, Deupi X, Pardo L. (2013) “Relation between sequence and structure in membrane proteins”. Bioinformatics. 29 (13): 1589-1592. http://bioinformatics.oxfordjournals.org/content/29/13/1589.long. DOI: 10.1093/bioinformatics/btt249
Olivella M., Caltabiano G., Cordomí A.(2013) “The role of Cysteine 6.47 in class A GPCRs” . BMC Struct Biol. 2013 Mar 15;13:3. DOI:10.1186/1472-6807-13-3
Margalef P., Fernández-Majada V., Villanueva A., Garcia-Carbonell R., Iglesias M., López L., Martínez-Iniesta M., Villà-Freixa J., Mulero MC., Andreu M., Torres F., Mayo M.W., Bigas A., Espinosa L. (2012) A Truncated Form of IKKα Is Responsible for Specific Nuclear IKK Activity in Colorectal Cancer. Cell Reports. http://www.cell.com/cell-reports/fulltext/S2211-1247%2812%2900268-9. DOI: 10.1016/j.celrep.2012.08.028
Dalton J, Kalid O, Schushan M, Ben-Tal N, Villà-Freixa J. (2012) New model of CFTR proposes active channel-like conformation. J Chem Inf Model. http://www.ncbi.nlm.nih.gov/pubmed/22747419. DOI: 10.1021/ci2005884
Porta N, Calle ML, Malat N, Gómez G (2012) A dynamic model for the risk of bladder cancer progression. Statistics in Medicine. Vol. 31, pp 287-300. DOI: 10.1002/sim.4433
De Lorenzi, L., Morando, P., Planas, J., Zannotti, M., Molteni, L. and Parma, P. (2012), Reciprocal translocations in cattle: frequency estimation. Journal of Animal Breeding and Genetics. doi: 10.1111/j.1439-0388.2011.00983.x
Calle ML, Urrea V, Boulesteix AL, Malats N. (2011) AUC-RF: A new strategy for genomic profiling with Random Forest. Hum Hered; 72:121-132. DOI: 10.1159/000330778
T. Cattaert, ML. Calle, S. Dudek, J.M. Mahachie John, F. Van Lishout, V. Urrea, M.D. Ritchie and K. Van Steen. (2011). A detailed view on Model-Based Multifactor Dimensionality Reduction for detecting gene-gene interactions in case-control data in the absence and presence of noise. Annals of Human Genetics, Vol. 75: pp 78-89. DOI: 10.1111/j.1469-1809.2010.00604.x
Calle,ML, Urrea, V, Malats, N, Van Steen, K (2010) mbmdr: an R package for exploring gene-gene interactions associated with binary or quantitative traits. Bioinformatics. Vol. 26 (17), pp 2198–2199. doi: 10.1093/bioinformatics/btq352
Planas, J. and Serrat, J.M. (2010). Gene Promoter Evolution Targets the Center of the Human Protein Interaction Network. Public Library of Science ONE 5(7): e11476.
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Deupi, X., Olivella, M., Sanz, A., Dölker, N., Campillo, M. Pardo, L. (2010). Influence of the g-conformation of Ser and Thr on the structure of transmembrane helices. J Struct Biol, 169(1):116-23. DOI: 10.1016/j.jsb.2009.09.009
Cattaert, T., Urrea, V., Naj, A.C., De Lobel, L., De Wit, V., Fu, M., Mahachie John, J.M., Shen, H., Calle, M.L., Ritchie, M.D., Edwards, T.L. & Van Steen, K. (2010). FAM-MDR: a flexible family-base multifactor dimensionality reduction technique to detect epistasis using related individuals. Public Library of Science ONE, vol 5 (4): e10304. doi:10.1371/journal.pone.0010304
Calle,ML. and Urrea, V. (2010). Stability of Random Forest Importance Measures. Briefings in Bioinformatics, doi: 10.1093/bib/bbq011.
L.T. Guey, M. García-Closas, C. Murta-Nascimento, J. Lloreta, L. Palencia, M. Kogevinas, N. Rothman, G.Vellalta, M.L. Calle, G. Marenne, A. Tardón, A. Carrato, R. García-Closas, C. Serram, D.T. Silverman, S. Chanock, F.X. Real, N. Malats. (2010). Genetic Susceptibility to Distinct Bladder Cancer Subphenotypes. European Urology, vol 57(2) pp 283-92. DOI: 10.1016/j.eururo.2009.08.001
Gómez, G., Calle, ML., Oller, R., Langhor, K. (2009). Tutorial on methods for interval-censored data and their implementation in R. Statistical Modelling, vol 9(4), pp 259–297. DOI: 10.1177/1471082X0900900402
G Calle, ML; Gómez (2008) A Sampling Based Chi-squared Test for Interval-Censored Data, 295-306. In Statistical Models and Methods for Biomedical and Technical Systems. DOI 10.1007/978-0-8176-4619-6_21
Calle,ML., Urrea, V., Vellalta, G. Malats, N., Van Steen, K. (2008). Improving strategies for detecting genetic patterns of disease susceptibility in association studies. Statistics in Medicine, vol 27, pp 6532-654. DOI: 10.1002/sim.3431
Calle,ML., Gómez, G. (2008). A Sampling Based Chi-squared Test for Interval-Censored Data. Statistical Models and Methods for Biomedical and Technical Systems. Edit. Vonta, F., Nikulin, M.S., Limnios, N., Huber-Carol, C. Springer, Statistics for Industry and Technology, ISBN 978-0-8176-4464-2. DOI 10.1007/978-0-8176-4619-6_21
A. Calle, ML., Roura, P., Arnau, A., Yáñez, A., Leiva (2007) Prognostic Factors and Prediction of Residual Survival for Hospitalized Elderly Patients. In Advances in Statistical Methods for the Health Sciences. DOI 10.1007/978-0-8176-4542-7_11
C. Murta-Nascimento, F.X. Real, G. Vellalta, M. Garcia-Closas, N., Rothman, M. Calle, J.Lloreta, A. Tardon, A. Carrato, R. García-Closas, C. Serra, D.T. Silverman, M. Dosemeci, J.A. Sanchez, V. Urrea, S. Chanock, M. Kogevinas, N. Malats. (2007). Bladder cancer prognosis in relationship to variation in 108 genes coding for proteins involved in inflammatory pathways. BJU International, vol 100 (s3), 1–5.
G. Vellalta, N. Rothman, C. Murtanascimento, M. Calle, J. A Sánchez, M. García-Closas, M. Gumá, J. Lloreta, J. Fortuny, A. Tardón, A. Carrato, R. García-Closas, C. Serra, D. T., Silverman, M. Dosemeci, V. Urrea, S. Chanock, M. Kogevinas, F. X Real And N. Malats. (2007). Study of bladder cancer susceptibility conferred by 309 SNPs in 109 genes participating in inflammatory pathways. BJU International, vol 100 (s3), 1–5.
Calle, M.L i Sánchez-Espigares, J.A. (2007). Árboles de Clasificación y Regresión en la Investigación Biomédica. Medicina Clínica, vol 129, pp 702-706. DOI: 10.1157/13112516
Robert G., Peña R. Cabrera C., Coma G., Ruiz-Hernandez R., Guerola R., Clotet B., Ruiz L., Esté J.A., Calle M.L., Bofill M. (2007). Skewed expression and up-regulation of the IL-12 and IL-18 receptors in resting and activated CD4 T cells from HIV-1-infected patients. Journal of Leukocyte Biology, vol 82, pp 72-78. DOI: 10.1189/jlb.1106698
Hough, H, Calle, ML, Curia, A y Serrat, C. (2007). Number of consumers necessary for shelf-life estimations based on survival analysis statistics. Food Quality and Preference, vol 18, pp 771-775. DOI: 10.1016/j.foodqual.2007.01.003
Calle,ML., Roura, P., Arnau, A., Yáñez, A., Leiva, A. (2007). Prognostic Factors and Prediction of Residual Survival for Hospitalized Elderly Patients. Advances in Statistical Methods for the Health Sciences. Edit. Balakrishnan, N., Auget, J.L., Mesbah, M., Molenberghs, G. Springer, Statistics for Industry and Technology, ISBN 0817643680. DOI 10.1007/978-0-8176-4542-7_11
Oller, R., Gómez, G., Calle, M.L. (2007). Interval censoring: identifiability and the constant-sum property. Biometrika, vol 94, pp 61-70. doi: 10.1093/biomet/asm002
de Arquer, GR, Cabrera, C, Coma, G, Ruiz-Hernandez, R, Este, JA, Calle, ML, Bofill, M. (2007). Increased percentage of CD4 T-cells expressing IL-12R beta 1 and IL-18R alpha in HIV-1 infection: a potential compensatory mechanism for the loss of Th1 response. Immunology 120:15-15, Suppl. 1.
Porta-Bleda, N., Calle,ML., Gómez, G., Malats, N. (2007). Regression modelling of competing risks in a bladder cancer study. Proceedings of the 22nd International Workshop on Statistical, J. del Castillo, A. Espinal, and P. Puig editors, pp 512-517. ISBN 978-84-690-5943-2.
Ristic Z, Camargo SM, Romeo E, Bodoy S, Bertran J, Palacin M, Makrides V, Furrer EM, Verrey F. (2006) Neutral amino acid transport mediated by ortholog of imino acid transporter SIT1/SLC6A20 in opossum kidney cells. Am J Physiol Renal Physiol. Vol. 290, pp F880-F887. DOI: 10.1152/ajprenal.00319.2005
Martin L, Comalada M, Marti L, Closs EI, MacLeod CL, Martin del Rio R, Zorzano A, Modolell M, Celada A, Palacin M, Bertran J. (2006). Granulocyte-macrophage colony-stimulating factor increases L-arginine transport through the induction of CAT2 in bone marrow-derived macrophages. Am J Physiol Cell Physiol. Vol. 290, ppC1364-C1372. DOI: 10.1152/ajpcell.00520.2005
Calle, ML, Hough, H, Curia, A, Gómez, G. (2006). Bayesian survival analysis modelling applied to sensory shelf life of foods. Food Quality and Preference vol 17, pp 307-312. DOI: 10.1016/j.foodqual.2005.03.012
Yeramian A, Martin L, Serrat N, Arpa L, Soler C, Bertran J, McLeod C, Palacin M, Modolell M, Lloberas J, Celada A. (2006). Arginine transport via cationic amino acid transporter 2 plays a critical regulatory role in classical or alternative activation of macrophages. J Immunol. Vol. 176; pp 5918-5924. doi: 10.4049/jimmunol.176.10.5918
Yeramian A, Martin L, Arpa L, Bertran J, Soler C, McLeod C, Modolell M, Palacin M, Lloberas J, Celada A (2006). Macrophages require distinct arginine catabolism and transport systems for proliferation and for activation. Eur J Immunol. Vol. 36; pp 1516-1526. DOI: 10.1002/eji.200535694
Baydoun AR, Bertran J, Thakur S, Dawson J, Palacin M, Knowles RG. (2006). y(+) LAT-1 mediates transport of the potent and selective iNOS inhibitor, GW274150, in control J774 macrophages. Amino Acids. Vol. 31, pp 101-109. DOI 10.1007/s00726-005-0311-9
Calle, ML, Espinal, A Gómez, G. (2006). Analyzing sequential spells via conditional survival models. Proceedings 21st International Workshop on Statistical, Hinde, J. Einbeck, J & Newell, J. Editors. ISBN 1-86220-180-3
Calle, M.L. y Gómez, G. (2005). Semiparametric hierarchical model for a regression problem with an interval-censored covariate. Australian and New Zealand Journal of Statistics, vol 47, pp 351-364. DOI: 10.1111/j.1467-842X.2005.00400.x
Bodoy, L. Martín, A. Zorzano, M. Palacín, R. Estévez and J. Bertran (2005). Identification of LAT4, a novel amino acid transporter with system L activity. J Biol Chem. Vol. 280, pp 12002-12011. doi: 10.1074/jbc.M408638200
Bau J, Justus KA, Loudon C, Carde RT (2005) Electroantennographic resolution of pulsed pheromone plumes in two species of moths with bipectinate antennae. Chem Senses 30: 771-780. DOI 10.1093/chemse/bji069