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14 p, 1.6 MB |
Efficient randomization of biological networks while preserving functional characterization of individual nodes
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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
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11 p, 3.1 MB |
GPCRtm : An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors
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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
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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
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König, Caroline (Universitat Politècnica de Catalunya. Departament de Ciencies 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
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11 p, 2.4 MB |
From raw data to data-analysis for magnetic resonance spectroscopy - the missing link : jMRUI2XML
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Mocioiu, Victor (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Ortega-Martorell, Sandra (Liverpool John Moores University. Department of Mathematics and Statistics) ;
Olier, Iván (University of Manchester. Institute of Population Health) ;
Jablonski, Michal (Institute of Scientific Instruments of the CAS (Brno, República Txeca)) ;
Starcukova, Jana (Institute of Scientific Instruments of the CAS (Brno, República Txeca)) ;
Lisboa, Paulo J. G. (Liverpool John Moores University. Department of Mathematics and Statistics) ;
Arús i Caraltó, Carles (Universitat Autònoma de Barcelona. Departament de Bioquímica i Biologia Molecular) ;
Julià Sapé, Ma. Margarita (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Background: Magnetic resonance spectroscopy provides metabolic information about living tissues in a non-invasive way. However, there are only few multi-centre clinical studies, mostly performed on a single scanner model or data format, as there is no flexible way of documenting and exchanging processed magnetic resonance spectroscopy data in digital format. [...]
2015 - 10.1186/s12859-015-0796-5
BMC bioinformatics, Vol. 16, N. 378 (November 2015) , p. 1-11
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Non-negative matrix factorisation methods for the spectral decomposition of MRS data from human brain tumours
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Ortega-Martorell, Sandra (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Lisboa, Paulo J. G. (Liverpool John Moores University. Department of Mathematics and Statistics) ;
Vellido, Alfredo (Universitat Politècnica de Catalunya. Departament de Llenguatges i Sistemes Informàtics) ;
Julià Sapé, Ma. Margarita (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Arús i Caraltó, Carles (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Background: In-vivo single voxel proton magnetic resonance spectroscopy (SV 1H-MRS), coupled with supervised pattern recognition (PR) methods, has been widely used in clinical studies of discrimination of brain tumour types and follow-up of patients bearing abnormal brain masses. [...]
2012 - 10.1186/1471-2105-13-38
BMC bioinformatics, Vol. 13, N. 38 (March 2012) , p. 1-20
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