UAB Digital Repository of Documents 35 records found  1 - 10nextend  jump to record: Search took 0.02 seconds. 
1.
2 p, 462.8 KB Link-HD : a versatile framework to explore and integrate heterogeneous microbial communities / Zingaretti, Laura M. (Centre de Recerca en Agrigenòmica) ; Renand, Gilles (Université Paris-Saclay. Institut National de la Recherche Agronomique. Génétique Animale et Biologie Intégrative (France)) ; Morgavi, Diego P. (Clermont Auvergne University. Institut National de la Recherche Agronomique. Physiologie Animale et des Systèmes d'Élevage (France)) ; Ramayo-Caldas, Yuliaxis (Université Paris-Saclay. Institut National de la Recherche Agronomique. Génétique Animale et Biologie Intégrative (France))
Motivation: We present Link-HD, an approach to integrate multiple datasets. Link-HD is a generalization of 'Structuration des Tableaux A Trois Indices de la Statistique-Analyse Conjointe de Tableaux', a family of methods designed to integrate information from heterogeneous data. [...]
2020 - 10.1093/bioinformatics/btz862
Bioinformatics, Vol. 36, Issue 7 (April 2020) , p. 2298-2299  
2.
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) ; Pérez-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  
3.
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 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  
4.
8 p, 426.0 KB SNP calling by sequencing pooled samples / Pérez-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)  
5.
7 p, 1.9 MB T-lex3 : An accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data / Bogaerts-Márquez, María (Universitat Pompeu Fabra. Institut de Biologia Evolutiva) ; Barron, Maite G. (Universitat Pompeu Fabra. Institut de Biologia Evolutiva) ; Fiston-Lavier, Anna-Sophie (Institut des Sciences de l'Evolution de Montpellier) ; Vendrell Mir, Pol (Centre de Recerca en Agrigenòmica) ; Castanera, Raúl (Centre de Recerca en Agrigenòmica) ; Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ; González, Josefa (Universitat Pompeu Fabra. Institut de Biologia Evolutiva)
Motivation: Transposable elements (TEs) constitute a significant proportion of the majority of genomes sequenced to date. TEs are responsible for a considerable fraction of the genetic variation within and among species. [...]
2020 - 10.1093/bioinformatics/btz727
Bioinformatics, Vol. 36, Issue 4 (February 2020) , p. 1191-1197  
6.
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  
7.
3 p, 164.2 KB karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data / Gel, Bernat (Institut Germans Trias i Pujol. Institut de Medicina Predictiva i Personalitzada del Càncer) ; Serra, Eduard (Institut Germans Trias i Pujol. Institut de Medicina Predictiva i Personalitzada del Càncer) ; Universitat Autònoma de Barcelona
Abstract. Motivation: Data visualization is a crucial tool for data Exploration, analysis and interpretation. For the visualization of genomic data there lacks a tool to create customizable non-circular plots of whole genomes from any species. [...]
2017
Bioinformatics, Vol. 33 Núm. 19 (2017) , p. 3088-3090  
8.
11 p, 1.1 MB Optimized next-generation sequencing genotype-haplotype calling for genome variability analysis / Navarro Fernández, Javier (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius) ; Nevado, Bruno (University of Oxford. Department of Plant Sciences) ; Hernández Budé, Porfidio (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius) ; Vera Rodríguez, Gonzalo (Centre de Recerca en Agrigenòmica) ; Ramos-Onsins, Sebastián E. (Centre de Recerca en Agrigenòmica)
The accurate estimation of nucleotide variability using next-generation sequencing data is challenged by the high number of sequencing errors produced by new sequencing technologies, especially for nonmodel species, where reference sequences may not be available and the read depth may be low due to limited budgets. [...]
2017 - 10.1177/1176934317723884
Evolutionary bioinformatics online, Vol. 13, (August 2017) , p. 1-11  
9.
6 p, 1.2 MB Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS / Montemuiño, Carlos (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius) ; Espinosa Morales, Antonio Miguel (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius) ; Moure López, Juan Carlos (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius) ; Vera Rodríguez, Gonzalo (Centre de Recerca en Agrigenòmica) ; Hernández Budé, Porfidio (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius) ; Ramos-Onsins, Sebastián E. (Centre de Recerca en Agrigenòmica)
The msParSm application is an evolution of msPar, the parallel version of the coalescent simulation program ms, which removes the limitation for simulating long stretches of DNA sequences with large recombination rates, without compromising the accuracy of the standard coalescence. [...]
2016 - 10.4137/EBO.S40268
Evolutionary bioinformatics online, Vol. 12 (Oct. 2016) , p. 223-228  
10.
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  

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