UAB Digital Repository of Documents 30 records found  1 - 10nextend  jump to record: Search took 0.01 seconds. 
1.
8 p, 674.6 KB DisProt : intrinsic protein disorder annotation in 2020 / Hatos, Andras (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 (Biological Computation and Process Laboratory. Chemical Process and Energy Resources Institute. Centre for Research and Technology Hellas) ; Chemes, Lucía (Departamento de Fisiología y Biología Molecular y Celular (DFBMC). Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires) ; Davey, NormanE. (Division of Cancer Biology. Institute of Cancer Research) ; 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 (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 de Recherche en Biologie Cellulaire de Montpellier (CRBM). UMR 5237 CNRS. Université 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 (Bioinformatics Unit. Fundación Instituto Leloir) ; Martínez-Pérez, Elisabeth (Bioinformatics Unit. Fundación Instituto Leloir) ; 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. (Biological Computation and Process Laboratory. Chemical Process and Energy Resources Institute. Centre for Research and Technology Hellas) ; 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 J. (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, Jordi (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 C.E. (CNR Institute of Neurosceince) ; Piovesan, Daminao (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  
2.
6 p, 700.6 KB IMKT : the integrative McDonald and Kreitman test / Murga Moreno, Jesús (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Coronado-Zamora, Marta (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Hervas Fernández, Sergi (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasi") ; Casillas Viladerrams, Sònia (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasi") ; 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  
3.
10 p, 3.7 MB PopHumanScan : the online catalog of human genome adaptation / Murga Moreno, Jesús (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Coronado-Zamora, Marta (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Bodelón, Alejandra (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 (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasi")
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  
4.
8 p, 2.9 MB Aggrescan3D (A3D) 2.0 : prediction and engineering of protein solubility / Kuriata, Aleksander (Centrum Nauk Biologiczno-Chemicznych Uniwersytetu Warszawskiego) ; Iglesias, Valentin (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Pujols, Jordi (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  
5.
9 p, 4.9 MB Cucurbit Genomics Database (CuGenDB) : A central portal for comparative and functional genomics of cucurbit crops / Zheng, Yi (Cornell University. Boyce Thompson Institute) ; Wu, Shan (Cornell University. Boyce Thompson Institute) ; Bai, Yang (Cornell University. Boyce Thompson Institute) ; Sun, Honghe (Beijing Academy of Agriculture and Forestry Sciences. National Engineering Research Center for Vegetables) ; Jiao, Chen (Cornell University. Boyce Thompson Institute) ; Guo, Shaogui (Beijing Academy of Agriculture and Forestry Sciences. National Engineering Research Center for Vegetables) ; Zhao, Kun (Cornell University. Boyce Thompson Institute) ; Blanca, Jose (Universitat Politècnica de València. Institut Universitari de Conservació i Millora de l'Agrodiversitat Valenciana) ; Zhang, Zhonghua (Chinese Academy of Agricultural Sciences. Institute of Vegetables and Flowers) ; Huang, Sanwen (Chinese Academy of Agricultural Sciences. Agricultural Genomics Institute at Shenzhen) ; Xu, Yong (Beijing Academy of Agriculture and Forestry Sciences. National Engineering Research Center for Vegetables) ; Weng, Yiqun (University of Wisconsin. Department of Horticulture) ; Mazourek, Michael (Cornell University. Plant Breeding and Genetics Section) ; Reddy, Umesh K. (West Virginia State University. Department of Biology) ; Ando, Kaori (U.S. Crop Improvement and Protection Research Unit. Department of Agriculture-Agricultural Research Service) ; McCreight, James D. (Crop Improvement and Protection Research Unit. Department of Agriculture-Agricultural Research Service) ; Schaffer, Arthur A. (Volcani Center. Plant Science Institute) ; Burger, Joseph (Newe Yaar Research Center. Plant Science Institute) ; Tadmor, Yaakov (Newe Yaar Research Center. Plant Science Institute) ; Katzir, Nurit (Newe Yaar Research Center. Plant Science Institute) ; Tang, Xuemei (Cornell University. Boyce Thompson Institute) ; Liu, Yang (Cornell University. Horticulture Section) ; Giovannoni, James J. (U.S. Robert W. Holley Center for Agriculture and Health. Department of Agriculture-Agricultural Research Service) ; Ling, Kai-Shu (U.S. Vegetable Laboratory. Department of Agriculture-Agricultural Research Service) ; Wechter, W. Patrick (U.S. Vegetable Laboratory. Department of Agriculture-Agricultural Research Service) ; Levi, Amnon (U.S. Vegetable Laboratory. Department of Agriculture-Agricultural Research Service) ; Garcia Mas, Jordi (Centre de Recerca en Agrigenòmica) ; Grumet, Rebecca (Michigan State University. Department of Horticulture) ; Fei, Zhangjun (U.S. Robert W. Holley Center for Agriculture and Health. Department of Agriculture-Agricultural Research Service)
The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. [...]
2019 - 10.1093/nar/gky944
Nucleic acids research, Vol. 47, Issue D1 (January 2019) , p. D1128-D1136  
6.
9 p, 1.4 MB The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE : Consequences for the transposition mechanism of MITEs / Loot, Céline (Laboratori de Genètica Molecular Vegetal (CSIC-IRTA). Departament de Genètica Molecular) ; Santiago, Néstor (Laboratori de Genètica Molecular Vegetal (CSIC-IRTA). Departament de Genètica Molecular) ; Sanz, Alicia (Laboratori de Genètica Molecular Vegetal (CSIC-IRTA). Departament de Genètica Molecular) ; Casacuberta i Suñer, Josep M. 1962- (Laboratori de Genètica Molecular Vegetal (CSIC-IRTA). Departament de Genètica Molecular)
MITEs (miniature inverted-repeated transposable elements) are a particular class of defective DNA transposons usually present within genomes as high copy number populations of highly homogeneous elements. [...]
2006 - 10.1093/nar/gkl688
Nucleic acids research, Vol. 34, Issue 18 (October 2006) , p. 5238-5246  
7.
13 p, 1.7 MB RinA controls phage-mediated packaging and transfer of virulence genes in Gram-positive bacteria / Ferrer, Maria Desamparados (Instituto Valenciano de Investigaciones Agrarias) ; Quiles Puchalt, Nuria (Instituto Valenciano de Investigaciones Agrarias) ; Harwich, Michael D. (Virginia Commonwealth University School of Medicine. Department of Microbiology and Immunology) ; Tormo Mas, María Ángeles (Instituto Valenciano de Investigaciones Agrarias) ; Campoy Sánchez, Susana (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ; Barbé García, Jordi (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ; Lasa, Íñigo (Universidad Pública de Navarra) ; Novick, Richard P. (New York University Medical Center) ; Christie, Gail E. (Virginia Commonwealth University School of Medicine. Department of Microbiology and Immunology) ; Penadés, José R. (Instituto de Investigación en Ganadería de Montaña)
Phage-mediated transfer of microbial genetic elements plays a crucial role in bacterial life style and evolution. In this study, we identify the RinA family of phage-encoded proteins as activators required for transcription of the late operon in a large group of temperate staphylococcal phages. [...]
2011 - 10.1093/nar/gkr158
Nucleic acids research, Vol. 39, Núm. 14 (August 2011) , p. 5866-5878  
8.
17 p, 5.8 MB Novel regulatory mechanism of establishment genes of conjugative plasmids / Val-Calvo, Jorge (Centro de Biología Molecular Severo Ochoa (CSIC-UAM)) ; Luque-Ortega, Juan Roman (Centro de Investigaciones Biológicas) ; Crespo, Isidro (ALBA Laboratori de Llum de Sincrotró) ; Miguel Arribas, Andrés (Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)) ; Abia, David (Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)) ; Sánchez-Hevia, Dione L. (Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)) ; Serrano, Ester (Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)) ; Gago-Córdoba, César (Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)) ; Ares, Saúl (Universidad Carlos III de Madrid) ; Alfonso, Carlos (Centro de Investigaciones Biológicas (Madrid)) ; Rojo, Fernando (Centro Nacional de Biotecnología (CSIC)) ; Wu, Ling J. (Newcastle University) ; Boer, Dirk Roeland (ALBA Laboratori de Llum de Sincrotró) ; Meijer, Wilfried J. J. (Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM))
The principal route for dissemination of antibiotic resistance genes is conjugation by which a conjugative DNA element is transferred from a donor to a recipient cell. Conjugative elements contain genes that are important for their establishment in the new host, for instance by counteracting the host defense mechanisms acting against incoming foreign DNA. [...]
2018 - 10.1093/nar/gky996
Nucleic acids research, Vol. 46, Issue 22 (December 2018) , p. 11910-11926  
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7 p, 1.1 MB PMut : a web-based tool for the annotation of pathological variants on proteins, 2017 update / López-Ferrando, Víctor (Joint Program BSC-CRG-IRB Research Program for Computational Biology) ; Gazzo, Andrea (Joint Program BSC-CRG-IRB Research Program for Computational Biology) ; de la Cruz, Xavier (Vall d'Hebron Institut de Recerca) ; Orozco, Modesto (Universitat de Barcelona. Departament de Bioquímica i de Biologia Molecular) ; Gelpí, Josep Ll (Universitat de Barcelona. Departament de Bioquímica i de Biologia Molecular)
We present here a full update of the PMut predictor, active since 2005 and with a large acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine has been renewed, and converted into a fully featured standalone training and prediction engine that not only powers PMut web portal, but that can generate custom predictors with alternative training sets or validation schemas. [...]
2017 - 10.1093/nar/gkx313
Nucleic acids research, Vol. 45 (april 2017) , p. W222-W228  
10.
4 p, 947.1 KB MultitaskProtDB-II : an update of a database of multitasking/moonlighting proteins / Franco-Serrano, Luís (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Hernández, Sergio (Universitat Autònoma de Barcelona. Departamento de Bioquímia i Biologia Molecular) ; Calvo, Alejandra (Universidad de la República Regional Norte-Salto. Laboratorio de Inmunología) ; Severi, María A. (Universidad de la República Regional Norte-Salto. Laboratorio de Inmunología) ; Ferragut, Gabriela (Universidad de la República Regional Norte-Salto. Laboratorio de Inmunología) ; Pérez-Pons, Josep A. (Josep Antoni) (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Piñol Ribas, Jaume (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Pich, Òscar M. (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Mozo Villarias, Ángel (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Amela Abellan, Isaac (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Querol Murillo, Enrique (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Cedano Rodríguez, Juan Antonio (Universidad de la República Regional Norte-Salto. Laboratorio de Inmunología)
Multitasking, or moonlighting, is the capability of some proteins to execute two or more biological functions. MultitaskProtDB-II is a database of multifunctional proteins that has been updated. In the previous version, the information contained was: NCBI and UniProt accession numbers, canonical and additional biological functions, organism, monomeric/oligomeric states, PDB codes and bibliographic references. [...]
2017 - 10.1093/nar/gkx1066
Nucleic acids research, Vol. 46, Database issue D645-D648 (2018) , p. D645-D648  

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