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1. Full Text LRH-1 agonism favours an immune-islet dialogue which protects against diabetes mellitus
by Cobo-Vuilleumier, Nadia and Lorenzo, Petra I and Rodríguez, Noelia García and Herrera Gómez, Irene De Gracia and Fuente-Martin, Esther and López-Noriega, Livia and Mellado-Gil, José Manuel and Romero-Zerbo, Silvana-Yanina and Baquié, Mathurin and Lachaud, Christian Claude and Stifter, Katja and Perdomo, German and Bugliani, Marco and De Tata, Vincenzo and Bosco, Domenico and Parnaud, Geraldine and Pozo, David and Hmadcha, Abdelkrim and Florido, Javier P and Toscano, Miguel G and De Haan, Peter and Schoonjans, Kristina and Sánchez Palazón, Luis and Marchetti, Piero and Schirmbeck, Reinhold and Martín-Montalvo, Alejandro and Meda, Paolo and Soria, Bernat and Bermúdez-Silva, Francisco-Javier and St-Onge, Luc and Gauthier, Benoit R
Nature Communications, ISSN 2041-1723, 12/2018, Volume 9, Issue 1, pp. 1488 - 15
Type 1 diabetes mellitus (T1DM) is due to the selective destruction of islet beta cells by immune cells. Current therapies focused on repressing the immune... 
LIVER RECEPTOR HOMOLOG-1 | RISK-FACTORS | DENDRITIC CELLS | ALPHA-CELLS | MACROPHAGES | REGENERATION | MULTIDISCIPLINARY SCIENCES | BETA-CELLS | REGULATORY T-CELLS | MONOCYTE CHEMOATTRACTANT PROTEIN-1 | MICE | Islets of Langerhans - drug effects | Apoptosis - drug effects | Streptozocin | Diabetes Mellitus, Type 2 - genetics | Humans | Diabetes Mellitus, Experimental - genetics | Male | Transplantation, Heterologous | Diabetes Mellitus, Experimental - therapy | T-Lymphocytes, Regulatory - pathology | T-Lymphocytes, Regulatory - immunology | Receptors, Cytoplasmic and Nuclear - immunology | Diabetes Mellitus, Type 2 - immunology | Islets of Langerhans Transplantation | Female | Diabetes Mellitus, Experimental - chemically induced | Macrophages - immunology | Cell Survival - drug effects | Islets of Langerhans - pathology | Macrophages - pathology | Mice, Inbred C57BL | Gene Expression Regulation | Islets of Langerhans - immunology | Phenalenes - pharmacology | Receptors, Cytoplasmic and Nuclear - agonists | Receptors, Cytoplasmic and Nuclear - genetics | Immunity, Innate | Insulin-Secreting Cells - immunology | Hypoglycemic Agents - pharmacology | Diabetes Mellitus, Experimental - immunology | Insulin - metabolism | T-Lymphocytes, Regulatory - drug effects | Animals | Insulin-Secreting Cells - drug effects | Cell Communication - drug effects | Macrophages - drug effects | Mice | Diabetes Mellitus, Type 2 - pathology | Insulin-Secreting Cells - pathology | Repressing | Animal models | Cell survival | Target recognition | Secretion | Liver | Diabetes mellitus | Organs | Homology | Diabetes mellitus (insulin dependent) | Glucose | Insulin | Beta cells | Regeneration | Hyperglycemia | Hepatocytes | Islet cells | Diabetes | Islets of Langerhans | Pancreas | Apoptosis | Immune system
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2. Full Text Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade
by López Díaz, María and Rueda, Antonio and Florido, Javier P and Blasco, Lucia and Fernández García, Laura and Trastoy Pena, Rocío and Fernández Cuenca, Felipe and Martínez Martínez, Luis and Vila Estapé, Jordi and Pascual, Alvaro and Bou, Germán and Tomás, María
ISSN 2045-2322, 02/2018
In this study, we compared eighteen clinical strains of A. baumannii belonging to the ST-2 clone and isolated from patients in the same intensive care unit... 
Bacteriophages | Gram-negative bacteria | Bacteriòfags | Bacteris gramnegatius
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3. Full Text NgsCAT: A tool to assess the efficiency of targeted enrichment sequencing
by López-Domingo, Francisco J and Florido, Javier P and Rueda, Antonio and Dopazo, Joaquín and Santoyo-Lopez, Javier
Bioinformatics, ISSN 1367-4803, 06/2014, Volume 30, Issue 12, pp. 1767 - 1768
Motivation: Targeted enrichment sequencing by next-generation sequencing is a common approach to interrogate specific loci or the whole exome in the human... 
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | PERFORMANCE | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Exome | Software | Genome, Human | High-Throughput Nucleotide Sequencing - methods | Sequence Analysis, DNA - methods | Humans
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4. Full Text 267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation
by Dopazo, Joaquín and Amadoz, Alicia and Bleda, Marta and Garcia-Alonso, Luz and Alemán, Alejandro and García-García, Francisco and Rodriguez, Juan A and Daub, Josephine T and Muntané, Gerard and Rueda, Antonio and Vela-Boza, Alicia and López-Domingo, Francisco J and Florido, Javier P and Arce, Pablo and Ruiz-Ferrer, Macarena and Méndez-Vidal, Cristina and Arnold, Todd E and Spleiss, Olivia and Alvarez-Tejado, Miguel and Navarro, Arcadi and Bhattacharya, Shomi S and Borrego, Salud and Santoyo-López, Javier and Antiñolo, Guillermo
Molecular Biology and Evolution, ISSN 0737-4038, 05/2016, Volume 33, Issue 5, pp. 1205 - 1218
Recent results from large-scale genomic projects suggest that allele frequencies, which are highly relevant for medical purposes, differ considerably across... 
pharmacogenomic variants | exome sequencing | population variability | disease variants | Genetic Predisposition to Disease | Disease - genetics | Gene Frequency | Humans | Pharmacogenomic Testing | Polymorphism, Genetic | Exome | Genetic Variation | Drug Resistance - genetics | Genetics, Population - methods | Spain - epidemiology | Internet | Databases, Nucleic Acid | Pharmacogenomic variants | Farmacogenòmica | Disease variants | Population variability | Exome sequencing | Discoveries
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5. Full Text Genomic Evolution of Two Acinetobacter baumannii Clinical Strains from ST-2 Clones Isolated in 2000 and 2010 (ST-2_clon_2000 and ST-2_clon_2010)
by López Díaz, María and Rueda, Antonio and Florido, Javier P and Blasco, Lucia and Gato, Eva and Fernández García, Laura and Martínez Martínez, Luis and Fernández Cuenca, Felipe and Pachón, Jerónimo and Cisneros, José Miguel and Garnacho Montero, José and Vila Estapé, Jordi and Rodríguez-Baño, Jesús and Pascual, Alvaro and Bou, Germán and Tomás, María
ISSN 2169-8287, 10/2016
Acinetobacter baumannii is a successful nosocomial pathogen due to its ability to persist in hospital environments by acquiring mobile elements such as... 
Genomics | Gram-negative bacteria | Bacteris gramnegatius | Genòmica
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6. Full Text Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: Structural information, non-gaps percentage and totally conserved columns
by Ortuño, Francisco M and Valenzuela, Olga and Rojas, Fernando and Pomares, Hector and Florido, Javier P and Urquiza, Jose M and Rojas, Ignacio
Bioinformatics, ISSN 1367-4803, 09/2013, Volume 29, Issue 17, pp. 2112 - 2121
Motivation: Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological... 
PROTEIN SEQUENCES | HIGH-THROUGHPUT | BIOCHEMICAL RESEARCH METHODS | PHYLOGENETIC TREES | ACCURACY | CONSISTENCY | PROGRAMS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | SECONDARY STRUCTURE | GENERATION | PENALTIES | HOMOLOGY | Sequence Alignment - methods | Sequence Analysis, Protein | Algorithms | Databases, Protein | Protein Conformation | Proteins - classification | Phylogeny
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7. Full Text Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade
by López, M and Rueda, A and Florido, J.P and Blasco, L and Fernández-García, L and Trastoy, R and Fernández-Cuenca, F and Martínez-Martínez, L and Vila, J and Pascual, A and Bou, G and Tomas, M
Scientific Reports, ISSN 2045-2322, 12/2018, Volume 8, Issue 1, pp. 2523 - 15
In this study, we compared eighteen clinical strains of A. baumannii belonging to the ST-2 clone and isolated from patients in the same intensive care unit... 
IMPACT | PHAST | GENE | ACYL-HOMOSERINE LACTONE | MULTIDISCIPLINARY SCIENCES | RESISTANCE | ECOLOGY | MECHANISMS | IDENTIFICATION | EPIDEMIOLOGY | VIBRIOPHAGES | Proteins | β-Lactamase | Plasmids | Strains (organisms) | Infectivity | Phages | Bacteriophages | Gram-negative bacteria | Bacteriòfags | Bacteris gramnegatius
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8. Full Text Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques
by Ortuño, Francisco M and Valenzuela, Olga and Pomares, Hector and Rojas, Fernando and Florido, Javier P and Urquiza, Jose M and Rojas, Ignacio
Nucleic Acids Research, ISSN 0305-1048, 01/2013, Volume 41, Issue 1, pp. e26 - e26
Multiple sequence alignments (MSAs) have become one of the most studied approaches in bioinformatics to perform other outstanding tasks such as structure... 
UNIPROT | MUTUAL INFORMATION | SELECTION | GENE ONTOLOGY | BIOCHEMISTRY & MOLECULAR BIOLOGY | KNOWLEDGE | Databases, Genetic | Least-Squares Analysis | Sequence Alignment - methods | Sequence Analysis, Protein | Reproducibility of Results | Support Vector Machine | Methods Online
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9. Full Text Genomic evolution of two Acinetobacter baumannii clinical strains from ST-2 clones isolated in 2000 and 2010 (ST-2_clon_2000 and ST-2_clon_2010)
by López, M and Rueda, A and Florido, J.P and Blasco, L and Gato, E and Fernández-García, L and Martínez-Martínez, L and Fernández-Cuenca, F and Pachón, J and Cisneros, J.M and Garnacho-Montero, J and Vila, J and Rodríguez-Baño, J and Pascual, A and Bou, G and Tomása, M
Genome Announcements, ISSN 2169-8287, 2016, Volume 4, Issue 5
Acinetobacter baumannii is a successful nosocomial pathogen due to its ability to persist in hospital environments by acquiring mobile elements such as... 
Gram-negative bacteria | Bacteris gramnegatius | Genomics | Genòmica
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10. Full Text Optimization of multiple sequence alignment methodologies using a multiobjective evolutionary algorithm based on NSGA-II
by Ortuno, F and Florido, J. P and Urquiza, J. M and Pomares, H and Prieto, A and Rojas, I
2012 IEEE Congress on Evolutionary Computation, ISSN 1089-778X, 06/2012, pp. 1 - 8
Multiple sequence alignment (MSA) is one of the most studied approach in Bioinformatics to carry out other outstanding tasks like structural predictions,... 
Algorithm design and analysis | NSGA-II | Clustering algorithms | Evolutionary computation | evolutionary algorithms | Muscles | multiobjective | multiple sequence alignment (MSA) | Optimization | Biological cells | optimization
Conference Proceeding
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11. Full Text A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
by Su, Zhenqiang and Labaj, Pawel P and Li, Sheng and Thierry-Mieg, Jean and Thierry-Mieg, Danielle and Shi, Wei and Wang, Charles and Schroth, Gary P and Setterquist, Robert A and Thompson, John F and Jones, Wendell D and Xiao, Wenzhong and Xu, Weihong and Jensen, Roderick V and Kelly, Reagan and Xu, Joshua and Conesa, Ana and Furlanello, Cesare and Gao, Hanlin and Hong, Huixiao and Jafari, Nadereh and Letovsky, Stan and Liao, Yang and Lu, Fei and Oakeley, Edward J and Peng, Zhiyu and Praul, Craig A and Santoyo-Lopez, Javier and Scherer, Aneas and Shi, Tieliu and Smyth, Gordon K and Staedtler, Frank and Sykacek, Peter and Tan, Xin-Xing and Thompson, E. Aubrey and Vandesompele, Jo and Wang, May D and Wang, Jian and Wolfinger, Russell D and Zavadil, Jiri and Auerbach, Scott S and Bao, Wenjun and Binder, Hans and Blomquist, Thomas and Brilliant, Murray H and Bushel, Pierre R and Cain, Weimin and Catalano, Jennifer G and Chang, Ching-Wei and Chen, Tao and Chen, Geng and Chen, Rong and Chierici, Marco and Chu, Tzu-Ming and Clevert, Djork-Arne and Deng, Youping and Derti, Adnan and Devanarayan, Viswanath and Dong, Zirui and Dopazo, Joaquin and Du, Tingting and Fang, Hong and Fang, Yongxiang and Fasold, Mario and Fernandez, Anita and Fischer, Matthias and Furio-Tari, Peo and Fuscoe, James C and Caiment, Florian and Gaj, Stan and Gandara, Jorge and Gao, Huan and Ge, Weigong and Gondo, Yoichi and Gong, Binsheng and Gong, Meihua and Gong, Zhuolin and Green, Bridgett and Guo, Chao and Guo, Lei and Guo, Li-Wu and Hadfield, James and Hellemans, Jan and Hochreiter, Sepp and Jia, Meiwen and Jian, Min and Johnson, Charles D and Kay, Suzanne and Kleinjans, Jos and Lababidi, Samir and Levy, Shawn and Li, Quan-Zhen and Li, Li and Li, Peng and Li, Yan and Li, Haiqing and Li, Jianying and Li, Shiyong and Lin, Simon M and Lopez, Francisco J and ... and SEQC/MAQC-III Consortium
Nature Biotechnology, ISSN 1087-0156, 09/2014, Volume 32, Issue 9, pp. 903 - 914
We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the US Food and Drug Administration. Examining Illumina HiSeq,... 
TRANSCRIPTOME | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIAS | GENOME ANNOTATION | DIFFERENTIAL GENE-EXPRESSION | ARRAYS | PCR | Reproducibility of Results | Polymerase Chain Reaction | Sequence Analysis, RNA - standards | RNA sequencing | Genetic research | Methods | Quality control | Quality management | Consortia | Ribonucleic acid--RNA
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12. Full Text PAX4 preserves endoplasmic reticulum integrity preventing beta cell degeneration in a mouse model of type 1 diabetes mellitus
by Mellado-Gil, José Manuel and Jiménez-Moreno, Carmen María and Martin-Montalvo, Alejandro and Alvarez-Mercado, Ana Isabel and Fuente-Martin, Esther and Cobo-Vuilleumier, Nadia and Lorenzo, Petra Isabel and Bru-Tari, Eva and de Gracia Herrera-Gómez, Irene and López-Noriega, Livia and Pérez-Florido, Javier and Santoyo-López, Javier and Spyrantis, Andreas and Meda, Paolo and Boehm, Bernhard O and Quesada, Ivan and Gauthier, Benoit R
Diabetologia, ISSN 0012-186X, 4/2016, Volume 59, Issue 4, pp. 755 - 765
A strategy to enhance pancreatic islet functional beta cell mass (BCM) while restraining inflammation, through the manipulation of molecular and cellular... 
Medicine & Public Health | Human Physiology | Type 1 diabetes | Metabolic Diseases | PAX4 | Internal Medicine | ER homeostasis | Beta cell degeneration | RIP-B7.1 | NOD MICE | ISLETS | INDUCED APOPTOSIS | INSULIN-SECRETION | GALECTIN-9 | MECHANISMS | OVEREXPRESSION | GENE | IN-VIVO | ENDOCRINOLOGY & METABOLISM | STRESS | Homeodomain Proteins - metabolism | Cell Proliferation - physiology | Diabetes Mellitus, Type 1 - pathology | Diabetes Mellitus, Type 1 - metabolism | Endoplasmic Reticulum - metabolism | Male | Insulin-Secreting Cells - metabolism | Animals | Mice, Mutant Strains | Female | Mice | Apoptosis - physiology | Insulin-Secreting Cells - pathology | Paired Box Transcription Factors - metabolism | Prevention | Physiological aspects | Pancreatic beta cells | Analysis
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13. Full Text Differences among Pollen-Allergic Patients with and without Plant Food Allergy
by Cuesta-Herranz, Javier and Barber, Domingo and Blanco, Carlos and Cistero-Bahíma, Ana and Crespo, Jesús F and Fernández-Rivas, Montserrat and Fernández-Sánchez, Javier and Florido, J. Fernando and Ibáñez, M. Dolores and Rodríguez, Rosalía and Salcedo, Gabriel and Garcia, Blanca E and Lombardero, Manuel and Quiralte, Joaquin and Rodriguez, Julia and Sánchez-Monge, Rosa and Vereda, Andrea and Villalba, Mayte and Alonso Díaz de Durana, M. Dolores and Basagaña, Maria and Carrillo, Teresa and Fernández-Nieto, Mar and Tabar, Ana I and Network, V
International Archives of Allergy and Immunology, ISSN 1018-2438, 09/2010, Volume 153, Issue 2, pp. 182 - 192
Background: A considerable number of pollen-allergic patients develops allergy to plant foods, which has been attributed to cross-reactivity between food and... 
Original Paper | Plant food allergy | Pollen allergy | Immunotherapy | Profilin | Pru p 3 | Component-resolved diagnostics | Asthma | PEACH ALLERGY | RECOMBINANT EXPRESSION | IMMUNOLOGY | MAJOR ALLERGEN | ALLERGY | PURIFICATION | LIPID-TRANSFER PROTEIN | CROSS-REACTIVITY | DOUBLE-BLIND | ANTIBODY-BASED ELISA | SENSITIZATION PROFILES | Food Hypersensitivity - immunology | Skin Tests | Plants, Edible - immunology | Humans | Middle Aged | Adult | Female | Male | Immunoglobulin E - blood | Rhinitis, Allergic, Seasonal - immunology | Food allergies | Pollen | Immunology | Allergies
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14. Full Text The timing of cord clamping and oxidative stress in term newborns
by Diáz-Castro, Javier and Florido, Jesus and Kajarabille, Naroa and Garrido-Sánchez, Maria and Padilla, Carmen and De Paco, Catalina and Navarrete, Luis and Ochoa, Julio J
Pediatrics, ISSN 0031-4005, 08/2014, Volume 134, Issue 2, pp. 257 - 264
BACKGROUND: Clamping and cutting of the umbilical cord is the most prevalent of all operations, but the optimal timing of cord clamping is controversial, with... 
Cord clamping timing (early or late) | Term neonate | Inflammation | Oxidative damage | Antioxidant defense | LIPID-PEROXIDATION | term neonate | oxidative damage | PRETERM INFANTS | PREECLAMPSIA | INTERLEUKIN-6 | cord clamping timing (early or late) | PREGNANCY | TUMOR-NECROSIS-FACTOR | ERYTHROCYTES | inflammation | PEDIATRICS | antioxidant defense | PARTURITION | BLOOD | Postpartum Hemorrhage - prevention & control | Reactive Oxygen Species - metabolism | Catalase - blood | Umbilical Cord - surgery | Constriction, Pathologic | Humans | Ligation - standards | Oxidative Stress - physiology | Tumor Necrosis Factor-alpha - blood | Inflammation Mediators - blood | Labor Stage, Third - physiology | Superoxide Dismutase - blood | Umbilical Cord - blood supply | Pregnancy | Time Factors | Interleukin-6 - blood | Female | Erythrocytes - enzymology | Infant, Newborn - physiology | Placental Circulation - physiology | Pregnancy Outcome | Term Birth | Infants (Newborn) | Oxidative stress | Umbilical cord | Health aspects | Analysis | Risk factors | Pediatrics | Placenta | Newborn babies
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15. Full Text Concordance of opinions between patients and physicians and their relationship with symptomatic control and future risk in patients with moderate–severe asthma
by Crespo-Lessmann, Astrid and Plaza, Vicente and González-Barcala, Francisco-Javier and Fernández-Sánchez, Toni and Sastre, Joaquín
BMJ Open Respiratory Research, ISSN 2052-4439, 09/2017, Volume 4, Issue 1, p. e000189
IntroductionDifferences between the opinions of patients and physicians on the impact of asthma are common. We hypothesised that patient–physician discordance... 
perception of Asthma/breathlessness | Asthma | Health care | Perceptions | Mental depression | Studies | Hospitals | Tuberculosis | Antidepressants | Anxieties | Chronic obstructive pulmonary disease | Clinical medicine | Patient satisfaction | Communication
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