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17 p, 1.6 MB |
MADloy : robust detection of mosaic loss of chromosome Y from genotype-array-intensity data
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González Ruiz, Juan R. (Universitat Autònoma de Barcelona. Departament de Matemàtiques) ;
López-Sánchez, Marcos (Centro de Investigación Biomédica en Red de Enfermedades Raras) ;
Cáceres, Alejandro (Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública) ;
Puig, Pedro (Universitat Autònoma de Barcelona. Departament de Matemàtiques) ;
Esko, Tonu (University of Tartu. Estonian Genome Centre Science Centre) ;
Pérez-Jurado, Luis Alberto (University of Adelaide. South Australian Health and Medical Research Institute)
Accurate protocols and methods to robustly detect the mosaic loss of chromosome Y (mLOY) are needed given its reported role in cancer, several age-related disorders and overall male mortality. Intensity SNP-array data have been used to infer mLOY status and to determine its prominent role in male disease. [...]
2020 -  10.1186/s12859-020-03768-z
BMC bioinformatics, Vol. 21 (November 2020) , art. 533
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10 p, 1.3 MB |
Predicting the artificial immunity induced by RUTI® vaccine against tuberculosis using universal immune system simulator (UISS)
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Pennisi, Marzio (University of Catania. Department of Mathematics and Computer Science) ;
Russo, Giulia (Department of Drug Sciences. University of Catania) ;
Sgroi, Giuseppe (Department of Mathematics and Computer Science. University of Catania) ;
Bonaccorso, Angela (Department of Drug Sciences. University of Catania) ;
Parasiliti Palumbo, Giuseppe Alessandro (Department of Mathematics and Computer Science. University of Catania) ;
Fichera, Epifanio (Etna Biotech S.r.l.) ;
Kumar Mitra, Dipendra (All India Institute of Medical Sciences (Nova Delhi, Índia)) ;
Walker, Kenneth B. (TuBerculosis Vaccine Initiative (TBVI)) ;
Cardona, Pere-Joan (Institut Germans Trias i Pujol. Hospital Universitari Germans Trias i Pujol) ;
Amat, Merce (Archivel Farma S.L) ;
Viceconti, Marco (Department of Industrial Engineering. Alma Mater Studiorum. University of Bologna) ;
Pappalardo, Francesco (Department of Drug Sciences. University of Catania)
Background: Tuberculosis (TB) represents a worldwide cause of mortality (it infects one third of the world's population) affecting mostly developing countries, including India, and recently also developed ones due to the increased mobility of the world population and the evolution of different new bacterial strains capable to provoke multi-drug resistance phenomena. [...]
2019 - 10.1186/s12859-019-3045-5
BMC bioinformatics, Vol. 20 (December 2019) , p. 504
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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) ;
Gonzalez, 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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