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21.
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15 p, 7.0 MB |
Inactivation of the dimeric Rap anti-repressor of the conjugation operon is mediated by peptide-induced tetramerization
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Crespo, Isidro (ALBA Laboratori de Llum de Sincrotró) ;
Bernardo, Nerea (ALBA Laboratori de Llum de Sincrotró) ;
Miguel-Arribas, Andrés (Centro de Biología Molecular Severo Ochoa) ;
Singh, Praveen K. (Centro de Biología Molecular Severo Ochoa) ;
Luque-Ortega, Juan Román (Centro de Investigaciones Biológicas (Madrid)) ;
Alfonso, Carlos (Centro de Investigaciones Biológicas (Madrid)) ;
Malfois, Marc (ALBA Laboratori de Llum de Sincrotró) ;
Meijer, Wilfried J. J. (Centro de Biología Molecular Severo Ochoa) ;
Boer, Roeland (ALBA Laboratori de Llum de Sincrotró)
Quorum sensing allows bacterial cells to communicate through the release of soluble signaling molecules into the surrounding medium. It plays a pivotal role in controlling bacterial conjugation in Gram-positive cells, a process that has tremendous impact on health. [...]
2020 -  10.1093/nar/gkaa540
Nucleic acids research, Vol. 48, issue 14 (Aug. 2020) , p. 8113-8127
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22.
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6 p, 1.6 MB |
HomolWat : a web server tool to incorporate 'homologous' water molecules into GPCR structures
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Mayol, Eduardo (Universitat Autònoma de Barcelona. Departament de Pediatria, Obstetrícia i Ginecologia i Medicina Preventiva i Salut Pública) ;
García Recio, Ädrian (Universitat Autònoma de Barcelona. Departament de Pediatria, Obstetrícia i Ginecologia i Medicina Preventiva i Salut Pública) ;
Tiemann, Johanna K. S. (Medical University Leipzig. Institute of Medical Physics and Biophysics) ;
Hildebrand, Peter W. (Medical University Leipzig. Institute of Medical Physics and Biophysics) ;
Guixà González, Ramon (Paul Scherrer Institute. Laboratory of Biomolecular Research) ;
Olivella, Mireia (Universitat de Vic - Universitat Central de Catalunya. Departament de Biociències) ;
Cordomí Montoya, Arnau (Universitat Autònoma de Barcelona. Departament de Pediatria, Obstetrícia i Ginecologia i Medicina Preventiva i Salut Pública)
Internal water molecules play an essential role in the structure and function of membrane proteins including G protein-coupled receptors (GPCRs). However, technical limitations severely influence the number and certainty of observed water molecules in 3D structures. [...]
2020 - 10.1093/nar/gkaa440
Nucleic acids research, Vol. 48 (june 2020) , p. W54-W59
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23.
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24.
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25.
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9 p, 3.1 MB |
Assessment of kinship detection using RNA-seq data
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Blay, Natalia (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Casas Masnou, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Galván-Femenía, Iván (Institut Germans Trias i Pujol. Hospital Universitari Germans Trias i Pujol) ;
Graffelman, Jan (Department of Biostatistics, University of Washington) ;
de Cid, Rafael (Institut Germans Trias i Pujol. Hospital Universitari Germans Trias i Pujol) ;
Vavouri, Tanya (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Universitat Autònoma de Barcelona
Analysis of RNA sequencing (RNA-seq) data from related individuals is widely used in clinical and molecular genetics studies. Prediction of kinship from RNA-seq data would be useful for confirming the expected relationships in family based studies and for highlighting samples from related individuals in case-control or population based studies. [...]
2019 - 10.1093/nar/gkz776
Nucleic acids research, Vol. 47 (september 2019) , p. e136
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26.
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8 p, 674.6 KB |
DisProt : intrinsic protein disorder annotation in 2020
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Hatos, András (University of Padova. Department of Biomedical Sciences) ;
Hajdu-Soltész, Borbála (MTA-ELTE Lendület Bioinformatics Research Group. Department of Biochemistry. Eötvös Loránd University) ;
Monzon, Alexander M. (Department of Biomedical Sciences. University of Padova) ;
Palopoli, Nicolas (Departamento de Ciencia y Tecnología. Universidad Nacional de Quilmes-CONICET) ;
Álvarez, Lucía (Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO. Universidad Nacional de San Martín) ;
Aykac-Fas, Burcu (Computational Biology Laboratory. Danish Cancer Society Research Center) ;
Bassot, Claudio (Department of Biochemistry and Biophysics and Science for Life Laboratory. Stockholm University. Box 1031) ;
Benítez, Guillermo I. (Departamento de Ciencia y Tecnología. Universidad Nacional de Quilmes-CONICET) ;
Bevilacqua, Martina (Department of Biomedical Sciences. University of Padova) ;
Chasapi, Anastasia (Centre for Research and Technology Hellas (Tessalònica, Grècia)) ;
Chemes, Lucía Beatriz (Universidad de Buenos Aires. Departamento de Fisiología y Biología Molecular y Celular) ;
Davey, Norman E. (Institute of Cancer Research (Londres, Regne Unit)) ;
Davidović, Radoslav (Laboratory for Bioinformatics and Computational Chemistry. Institute of Nuclear Sciences Vinca. University of Belgrade) ;
Dunker, A. Keith (Center for Computational Biology and Bioinformatics. Indiana University School of Medicine) ;
Elofsson, Arne (Department of Biochemistry and Biophysics and Science for Life Laboratory. Stockholm University. Box 1031) ;
Gobeill, Julien (Swiss Institute of Bioinformatics and HES-SO\HEG) ;
Foutel, Nicolás S. G. (Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO. Universidad Nacional de San Martín) ;
Sudha, Govindarajan (Department of Biochemistry and Biophysics and Science for Life Laboratory. Stockholm University. Box 1031) ;
Guharoy, Mainak (VIB-VUB Center for Structural Biology. Flanders Institute for Biotechnology (VIB)) ;
Horvath, Tamas (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Iglesias, Valentin (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Kajava, Andrey V. (Institut de Biologie Computationnelle(IBC)) ;
Kovacs, Orsolya P. (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Lamb, John (Department of Biochemistry and Biophysics and Science for Life Laboratory. Stockholm University. Box 1031) ;
Lambrughi, Matteo (Computational Biology Laboratory. Danish Cancer Society Research Center) ;
Lazar, Tamas (VIB-VUB Center for Structural Biology. Flanders Institute for Biotechnology (VIB)) ;
Leclercq, Jeremy Y. (Centre National de la Recherche Scientifique (França). Centre de Recherche en Biologie Cellulaire de Montpellier) ;
Leonardi, Emanuela (Fondazione Istituto di Ricerca Pediatrica (IRP). Città della Speranza) ;
Macedo-Ribeiro, Sandra (Instituto de Biologia Molecular e Celular (IBMC). Instituto de Investigação e Inovação em Saúde (i3S). Universidade Do Porto) ;
Macossay-Castillo, Mauricio (VIB-VUB Center for Structural Biology. Flanders Institute for Biotechnology (VIB)) ;
Maiani, Emiliano (Computational Biology Laboratory. Danish Cancer Society Research Center) ;
Manso, José A. (Instituto de Biologia Molecular e Celular (IBMC). Instituto de Investigação e Inovação em Saúde (i3S). Universidade Do Porto) ;
Marino-Buslje, Cristina (Fundación Instituto Leloir (Buenos Aires, Argentina)) ;
Martínez-Pérez, Elisabeth (Fundación Instituto Leloir (Buenos Aires, Argentina)) ;
Mészáros, Bálint (MTA-ELTE Lendület Bioinformatics Research Group. Department of Biochemistry. Eötvös Loránd University) ;
Mičetić, Ivan (Department of Biomedical Sciences. University of Padova) ;
Minervini, Giovanni (Department of Biomedical Sciences. University of Padova) ;
Murvai, Nikoletta (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Necci, Marco (Department of Biomedical Sciences. University of Padova) ;
Ouzounis, Christos A. (Centre for Research and Technology Hellas (Tessalònica, Grècia)) ;
Pajkos, Mátyás (MTA-ELTE Lendület Bioinformatics Research Group. Department of Biochemistry. Eötvös Loránd University) ;
Paladin, Lisanna (Department of Biomedical Sciences. University of Padova) ;
Pancsa, Rita (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Papaleo, Elena (Translational Disease Systems Biology. Faculty of Health and Medical Sciences. Novo Nordisk Foundation Center. Protein Research University of Copenhagen) ;
Parisi, Gustavo (Departamento de Ciencia y Tecnología. Universidad Nacional de Quilmes-CONICET) ;
Pasche, Emilie (Swiss Institute of Bioinformatics and HES-SO\HEG) ;
Barbosa Pereira, Pedro José (Instituto de Biologia Molecular e Celular (IBMC). Instituto de Investigação e Inovação em Saúde (i3S). Universidade Do Porto) ;
Promponas, Vasilis J. (Bioinformatics Research Laboratory. Department of Biological Sciences. University of Cyprus) ;
Pujols Pujol, Jordi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Quaglia, Federica (Department of Biomedical Sciences. University of Padova) ;
Ruch, Patrick (Swiss Institute of Bioinformatics and HES-SO\HEG) ;
Salvatore, Marco (Department of Biochemistry and Biophysics and Science for Life Laboratory. Stockholm University. Box 1031) ;
Schad, Eva (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Szabo, Beata (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Szaniszló, Tamás (MTA-ELTE Lendület Bioinformatics Research Group. Department of Biochemistry. Eötvös Loránd University) ;
Tamana, Stella (Bioinformatics Research Laboratory. Department of Biological Sciences. University of Cyprus) ;
Tantos, Agnes (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Veljkovic, Nevena (Laboratory for Bioinformatics and Computational Chemistry. Institute of Nuclear Sciences Vinca. University of Belgrade) ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Vranken, Wim (Interuniversity Institute of Bioinformatics in Brussels (IB2). ULB-VUB) ;
Dosztányi, Zsuzsanna (MTA-ELTE Lendület Bioinformatics Research Group. Department of Biochemistry. Eötvös Loránd University) ;
Tompa, Peter (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Tosatto, Silvio (CNR Institute of Neurosceince) ;
Piovesan, Damiano (Department of Biomedical Sciences. University of Padova)
The Database of Protein Disorder (DisProt, URL: https://disprot. org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. [...]
2020 - 10.1093/nar/gkz975
Nucleic acids research, Vol. 48, issue D1 (Jan. 2020) , p. D269-D276
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27.
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6 p, 700.6 KB |
IMKT : the integrative McDonald and Kreitman test
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Murga-Moreno, Jesus (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Coronado-Zamora, Marta (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Hervás Fernández, Sergi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Casillas Viladerrams, Sònia (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Barbadilla Prados, Antonio (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
The McDonald and Kreitman test (MKT) is one of the most powerful and widely used methods to detect and quantify recurrent natural selection using DNA sequence data. Here we present iMKT (acronym for integrative McDonald and Kreitman test), a novel web-based service performing four distinct MKT types. [...]
2019 - 10.1093/nar/gkz372
Nucleic acids research, Vol. 47, issue W1 (Jan. 2019) , p. W283-W288
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28.
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10 p, 3.7 MB |
PopHumanScan : the online catalog of human genome adaptation
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Murga-Moreno, Jesus (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Coronado-Zamora, Marta (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Bodelon de Frutos, Alejandra (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Barbadilla Prados, Antonio (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Casillas Viladerrams, Sònia (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Since the migrations that led humans to colonize Earth, our species has faced frequent adaptive challenges that have left signatures in the landscape of genetic variation and that we can identify in our today-s genomes. [...]
2019 - 10.1093/nar/gky959
Nucleic acids research, Vol. 47, issue D1 (Jan 2019) , p. D1080-D1089
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29.
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10 p, 1.2 MB |
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
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Köhler, Sebastian (Monarch Initiative) ;
Carmody, Leigh (Jackson Laboratory for Genomic Medicine) ;
Vasilevsky, Nicole (Oregon Health and Science University) ;
Jacobsen, Julius O. B. (Queen Mary University of London) ;
Danis, Daniel (Jackson Laboratory for Genomic Medicine) ;
Gourdine, Jean-Philippe (Oregon Health and Science University) ;
Gargano, Michael A. (Jackson Laboratory for Genomic Medicine) ;
Harris, Nomi (Lawrence Berkeley National Laboratory) ;
Matentzoglu, Nicolas (European Bioinformatics Institute) ;
McMurry, Julie A. (Oregon State University) ;
Osumi-Sutherland, David (European Bioinformatics Institute) ;
Cipriani, Valentina (University College of London) ;
Balhoff, James P. (University of North Carolina at Chapel Hill) ;
Conlin, Tom (Oregon State University) ;
Blau, Hannah (Jackson Laboratory for Genomic Medicine) ;
Baynam, Gareth (Government of Western Australia) ;
Palmer, Richard (Curtin University (Perth, Australia)) ;
Gratian, Dylan (Government of Western Australia) ;
Dawkins, Hugh (Government of Western Australia) ;
Segal, Michael (SimulConsult) ;
Jansen, Anna (UZ Brussel) ;
Muaz, Ahmed (Darlinghurst) ;
Chang, Willie H. (Centre for Computational Medicine. Hospital for Sick Children. Department of Computer Science. University of Toronto) ;
Bergerson, Jenna (National Institutes of Health (Bethesda, Estats Units d'Amèrica)) ;
Laulederkind, Stanley (Marquette University) ;
Yüksel, Z. (Bioscientia GmbH) ;
Beltran i Agulló, Sergi (Universitat Pompeu Fabra) ;
Freeman, Alexandra F. (National Institutes of Health (Bethesda, Estats Units d'Amèrica)) ;
Sergouniotis, Panos (University of Manchester. Manchester Royal Eye Hospital) ;
Durkin, Daniel (Jackson Laboratory for Genomic Medicine) ;
Storm, Andrea L. (National Institutes of Health (Bethesda, Estats Units d'Amèrica)) ;
Hanauer, Marc (INSERM) ;
Brudno, Michael (University of Toronto) ;
Bello, Susan (Jackson Laboratory) ;
Sincan, Murat (Sanford Health) ;
Rageth, Kayli (Sanford Health) ;
Wheeler, Matthew T. (Stanford University School of Medicine) ;
Oegema, Renske (University Medical Center) ;
Lourghi, Halima (INSERM) ;
Della Rocca, Maria G. (National Institutes of Health (Bethesda, Estats Units d'Amèrica)) ;
Thompson, R. (Newcastle University) ;
Castellanos, Francisco (Jackson Laboratory for Genomic Medicine) ;
Priest, James (Stanford University School of Medicine) ;
Cunningham-Rundles, Charlotte (Mount Sinai School of Medicine) ;
Hegde, Ayushi (Jackson Laboratory for Genomic Medicine) ;
Lovering, Ruth Caroline (University College London) ;
Hajek, Catherine (Sanford Imagenetics. Sanford Health) ;
Olry, Annie (INSERM) ;
Notarangelo, Luigi (National Institutes of Health (Bethesda, Estats Units d'Amèrica)) ;
Similuk, Morgan (National Institutes of Health (Bethesda, Estats Units d'Amèrica)) ;
Zhang, Xingmin (Jackson Laboratory for Genomic Medicine) ;
Gómez-Andrés, David (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Lochmüller, Hanns (Ottawa Hospital Research Institute) ;
Dollfus, Hélène (Strasbourg University Hospital) ;
Rosenzweig, Sergio (NIH Clinical Center) ;
Marwaha, Shruti (Stanford University School of Medicine) ;
Rath, Ana (INSERM) ;
Sullivan, Kathleen (University of Pennsylvania Perelman School of Medicine) ;
Smith, Cynthia (Jackson Laboratory) ;
Milner, Joshua D. (National Institute of Allergy and Infectious Diseases (Bethesda, Estats Units d'Amèrica)) ;
Leroux, Dorothée (Strasbourg University Hospital) ;
Boerkoel, Cornelius (Sanford Health) ;
Klion, Amy (National Institutes of Health (Bethesda, Estats Units d'Amèrica)) ;
Carter, Melody C. (National Institutes of Health (Bethesda, Estats Units d'Amèrica)) ;
Groza, Tudor (Darlinghurst) ;
Smedley, Damian (Queen Mary University of London) ;
Haendel, Melissa Anne (Oregon State University) ;
Mungall, Christopher (Lawrence Berkeley National Laboratory) ;
Robinson, Peter N. (University of Connecticut) ;
Universitat Autònoma de Barcelona
The Human Phenotype Ontology (HPO) - a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases - is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. [...]
2019 - 10.1093/nar/gky1105
Nucleic acids research, Vol. 47 Núm. D1 (august 2019) , p. D1018-D1027
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30.
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8 p, 2.9 MB |
Aggrescan3D (A3D) 2.0 : prediction and engineering of protein solubility
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Kuriata, Aleksander (Centrum Nauk Biologiczno-Chemicznych Uniwersytetu Warszawskiego) ;
Iglesias, Valentin (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pujols Pujol, Jordi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Kurcinski, Mateusz (Centrum Nauk Biologiczno-Chemicznych Uniwersytetu Warszawskiego) ;
Kmiecik, Sebastian (Centrum Nauk Biologiczno-Chemicznych Uniwersytetu Warszawskiego) ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Protein aggregation is a hallmark of a growing number of human disorders and constitutes a major bottleneck in the manufacturing of therapeutic proteins. Therefore, there is a strong need of in-silico methods that can anticipate the aggregative properties of protein variants linked to disease and assist the engineering of soluble protein-based drugs. [...]
2019 - 10.1093/nar/gkz321
Nucleic acids research, Vol. 47, issue W1 (July 2019) , p. W300-W307
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