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UAB Digital Repository of Documents 25 records found  1 - 10nextend  jump to record: Search took 0.00 seconds. 
1.
13 p, 1.6 MB HIV drug resistance prediction with weighted categorical kernel functions / Ramon, Elies (Centre de Recerca en Agrigenòmica) ; Belanche-Muñoz, Lluís (Universitat Politècnica de Catalunya. Departament de Ciències de la Computació) ; Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica)
Background: Antiretroviral drugs are a very effective therapy against HIV infection. However, the high mutation rate of HIV permits the emergence of variants that can be resistant to the drug treatment. [...]
2019 - 10.1186/s12859-019-2991-2
BMC bioinformatics, Vol. 20 (July 2019) , art. 410  
Detailed record - Creative Commons
2.
5 p, 900.2 KB AMYCO : evaluation of mutational impact on prion-like proteins aggregation propensity / Iglesias, Valentin (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Conchillo-Solé, Oscar (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Batlle Carreras, Cristina (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Ventura, Salvador (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Background: around 1% of human proteins are predicted to contain a disordered and low complexity prion-like domain (PrLD). Mutations in PrLDs have been shown promote a transition towards an aggregation-prone state in several diseases. [...]
2019 - 10.1186/s12859-019-2601-3
BMC bioinformatics, Vol. 20 (2019) , art. 24  
Detailed record - Creative Commons
3.
8 p, 426.0 KB SNP calling by sequencing pooled samples / Perez-Enciso, Miguel (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments) ; Esteve Codina, Anna (Centre de Recerca en Agrigenòmica) ; Ferretti, Luca (Centre de Recerca en Agrigenòmica) ; Raineri, Emanuele (Centre Nacional d'Anàlisi Genòmica) ; Nevado, Bruno (University of Oxford. Department of Plant Sciences) ; Heath, Simon (Centre Nacional d'Anàlisi Genòmica)
Performing high throughput sequencing on samples pooled from different individuals is a strategy to characterize genetic variability at a small fraction of the cost required for individual sequencing. [...]
2012 - 10.1186/1471-2105-13-239
BMC bioinformatics, Vol. 13 (2012)  
Detailed record - Creative Commons
4.
14 p, 1.6 MB Efficient randomization of biological networks while preserving functional characterization of individual nodes / Iorio, Francesco (European Bioinformatics Institute. European Molecular Biology Laboratory) ; Bernardo-Faura, Martí (Centre de Recerca en Agrigenòmica) ; Gobbi, Andrea (Fondazione Bruno Kessler) ; Cokelaer, Thomas (Institut Pasteur. The Center of Bioinformatics, Biostatistics and Integrative Biology) ; Jurman, Giuseppe. (Fondazione Bruno Kessler) ; Saez-Rodriguez, Julio (RWTH Aachen University. Joint Research Centre for Computational Biomedicine)
Background: Networks are popular and powerful tools to describe and model biological processes. Many computational methods have been developed to infer biological networks from literature, high-throughput experiments, and combinations of both. [...]
2016 - 10.1186/s12859-016-1402-1
BMC bioinformatics, Vol. 17 (2016) , art. 542  
Detailed record - Creative Commons
5.
11 p, 3.1 MB GPCRtm : An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors / Rios Azuara, Santiago (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ; Fernandez, Marta F. (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ; Caltabiano, Gianluigi 1978- (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ; Campillo Grau, María Mercedes (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ; Pardo Carrasco, Leonardo (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ; González Wong, Angel (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional)
Protein sequence alignments and database search methods use standard scoring matrices calculated from amino acid substitution frequencies in general sets of proteins. These general-purpose matrices are not optimal to align accurately sequences with marked compositional biases, such as hydrophobic transmembrane regions found in membrane proteins. [...]
2015 - 10.1186/s12859-015-0639-4
BMC bioinformatics, Vol. 16 (July 2015) , art. 2016  
Detailed record - Creative Commons
6.
13 p, 2.1 MB Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm / Lucas-Lledó, José Ignacio (Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB)) ; Vicente Salvador, David (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Aguado, Cristina (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Cáceres Aguilar, Mario (Institució Catalana de Recerca i Estudis Avançats)
Population genetics and association studies usually rely on a set of known variable sites that are then genotyped in subsequent samples, because it is easier to genotype than to discover the variation. [...]
2014 - 10.1186/1471-2105-15-163
BMC bioinformatics, Vol. 15 (May 2014) , art. 163  
Detailed record - Creative Commons
7.
7 p, 968.3 KB Qxpak.5 : old mixed model solutions for new genomics problems / Perez-Enciso, Miguel (Centre de Recerca en Agrigenòmica) ; Misztal, Ignacy (University of Georgia. Department of Animal and Dairy Science)
Mixed models have a long and fruitful history in statistics. They are pertinent to genomics problems because they are highly versatile, accommodating a wide variety of situations within the same theoretical and algorithmic framework. [...]
2011 - 10.1186/1471-2105-12-202
BMC bioinformatics, Vol. 12 (May 2011) , art. 202  
Detailed record - Creative Commons
8.
8 p, 741.7 KB PCOPGene-Net : holistic characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships / Huerta Casado, Mario (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Cedano Rodríguez, Juan Antonio (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ; Peña, Dario (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Rodriguez, Antonio (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Querol Murillo, Enrique (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Microarray technology is so expensive and powerful that it is essential to extract maximum value from microarray data, specially from large-sample-series microarrays. Our web tools attempt to respond to these researchers' needs by facilitating the possibility to test and formulate from a hypothesis to entire models under a holistic point of view. [...]
2009 - 10.1186/1471-2105-10-138
BMC bioinformatics, Vol. 10 (2009) , art. 138  
Detailed record - Creative Commons
9.
14 p, 1.9 MB Label noise in subtype discrimination of class C G protein-coupled receptors : a systematic approach to the analysis of classification errors / König, Caroline (Universitat Politècnica de Catalunya. Departament de Ciències de la Computació) ; Cárdenas, Martha I. (Universitat Politècnica de Catalunya. Departament de Ciencies de la Computació) ; Giraldo, Jesús (Universitat Autònoma de Barcelona. Institut de Neurociències) ; Alquézar, René (Universitat Politècnica de Catalunya. Departament de Ciencies de la Computació) ; Vellido, Alfredo (Universitat Politècnica de Catalunya. Departament de Llenguatges i Sistemes Informàtics)
Background: The characterization of proteins in families and subfamilies, at different levels, entails the definition and use of class labels. When the adscription of a protein to a family is uncertain, or even wrong, this becomes an instance of what has come to be known as a label noise problem. [...]
2015 - 10.1186/s12859-015-0731-9
BMC bioinformatics, Vol. 16, N. 314 (September 2015) , p. 1-14  
Detailed record - Creative Commons
10.
15 p, 1.6 MB Quantifying conformational changes in GPCRs : glimpse of a common functional mechanism / Dalton, James A. R (Universitat Autònoma de Barcelona. Institut de Neurociències) ; Lans, Isaias (Universitat Autònoma de Barcelona. Institut de Neurociències) ; Giraldo, Jesús (Universitat Autònoma de Barcelona. Institut de Neurociències)
Background: G-protein-coupled receptors (GPCRs) are important drug targets and a better understanding of their molecular mechanisms would be desirable. The crystallization rate of GPCRs has accelerated in recent years as techniques have become more sophisticated, particularly with respect to Class A GPCRs interacting with G-proteins. [...]
2015 - 10.1186/s12859-015-0567-3
BMC bioinformatics, Vol. 16 N. 124 (April 2015) , p. 1-15  
Detailed record - Creative Commons

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