UAB Digital Repository of Documents 28 records found  1 - 10nextend  jump to record: Search took 0.01 seconds. 
1.
17 p, 2.2 MB PlasForest : a homology-based random forest classifier for plasmid detection in genomic datasets / Pradier, Léa (Université de Montpellier) ; Tissot, Tazzio (Universitat Autònoma de Barcelona. Departament de Genètica i Microbiologia) ; Fiston-Lavier, Anna-Sophie (Centre national de la recherche scientifique (França)) ; Bedhomme, Stéphanie (Université de Montpellier)
Plasmids are mobile genetic elements that often carry accessory genes, and are vectors for horizontal transfer between bacterial genomes. Plasmid detection in large genomic datasets is crucial to analyze their spread and quantify their role in bacteria adaptation and particularly in antibiotic resistance propagation. [...]
2021 - 10.1186/s12859-021-04270-w
BMC bioinformatics, Vol. 22 (June 2021) , art. 349  
2.
17 p, 1.6 MB MADloy : robust detection of mosaic loss of chromosome Y from genotype-array-intensity data / 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  
3.
10 p, 1.3 MB Predicting the artificial immunity induced by RUTI® vaccine against tuberculosis using universal immune system simulator (UISS) / 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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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  
5.
5 p, 900.2 KB AMYCO : evaluation of mutational impact on prion-like proteins aggregation propensity / Iglesias, Valentin (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Conchillo-Solé, Oscar (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Batlle Carreras, Cristina (Universitat Autònoma de Barcelona. 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  
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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)  
7.
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  
8.
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) ; 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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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 (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ; Aguado, Cristina (Universitat Autònoma de Barcelona. 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  
10.
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  

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