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Depósito Digital de Documentos de la UAB Encontrados 62 registros  1 - 10siguientefinal  ir al registro: La búsqueda tardó 0.01 segundos. 
1.
11 p, 1.3 MB Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools / García-Prieto, Carlos A (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ; Martínez Jiménez, Francisco (Institute for Research in Biomedicine (IRB Barcelona)) ; Valencia, Alfonso (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ; Porta-Pardo, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)
Motivation: The analysis of cancer genomes provides fundamental information about its etiology, the processes driving cell transformation or potential treatments. While researchers and clinicians are often only interested in the identification of oncogenic mutations, actionable variants or mutational signatures, the first crucial step in the analysis of any tumor genome is the identification of somatic variants in cancer cells (i. [...]
2022 - 10.1093/bioinformatics/btac306
Bioinformatics, Vol. 38 Núm. 12 (15 2022) , p. 3181-3191  
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2.
4 p, 5.0 MB RegioneReloaded : Evaluating the association of multiple genomic region sets / Malinverni, Roberto (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ; Corujo, David (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ; Gel, Bernat (Institut Germans Trias i Pujol. Hospital Universitari Germans Trias i Pujol) ; Buschbeck, Marcus (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)
Motivation: Next-generation sequencing methods continue improving the annotation of genomes in part by determining the distribution of features such as epigenetic marks. Evaluating and interpreting the association between genomic regions and their features has become a common and challenging analysis in genomic and epigenomic studies. [...]
2023 - 10.1093/bioinformatics/btad704
Bioinformatics, Vol. 39 Núm. 11 (november 2023)  
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3.
10 p, 1.4 MB Assessment of transfer methods for comparative genomics of regulatory networks in Bacteria / Kılıç, Sefa (University of Maryland Baltimore County. Department of Biological Sciences) ; Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences)
Background: Comparative genomics can leverage the vast amount of available genomic sequences to reconstruct and analyze transcriptional regulatory networks in Bacteria, but the efficacy of this approach hinges on the ability to transfer regulatory network information from reference species to the genomes under analysis. [...]
2016 - 10.1186/s12859-016-1113-7
BMC bioinformatics, Vol. 17, Suppl. 8 (August 2016) , art. 277  
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4.
5 p, 395.9 KB Characterization of the SOS meta-regulon in the human gut microbiome / Cornish, Joseph P. (University of Maryland Baltimore County. Department of Biological Sciences) ; Sanchez-Alberola, Neus (University of Maryland Baltimore County. Department of Biological Sciences) ; O'Neill, Patrik K. (University of Maryland Baltimore County. Department of Biological Sciences) ; O'Keefe, Ronald (University of Maryland Baltimore County. Department of Biological Sciences) ; Gheba, Jameel (University of Maryland Baltimore County. Department of Biological Sciences) ; Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences)
Motivation: Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks by characterizing the SOS meta-regulon in the human gut microbiome. [...]
2014 - 10.1093/bioinformatics/btt753
Bioinformatics, Vol. 30, Issue 9 (May 2014) , p. 1193-1197  
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5.
7 p, 1.0 MB BioWord: a sequence manipulation suite for Microsoft Word / Anzaldi, Laura J. (University of Maryland Baltimore County. Department of Biological Sciences) ; Muñoz-Fernández, Daniel (Universitat Autònoma de Barcelona. Departament de Ciències de la Computació) ; Erill, Ivan (Universitat Autònoma de Barcelona. Departament de Ciències de la Computació)
Background: The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. [...]
2012 - 10.1186/1471-2105-13-124
BMC bioinformatics, Vol. 13 (June 2012) , art. 124  
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6.
22 p, 713.8 KB A reexamination of information theory-based methods for DNA-binding site identification / Erill, Ivan (University of Maryland Baltimore County. Department of Biological Sciences) ; O'Neill, Michael C (University of Maryland Baltimore County. Department of Biological Sciences)
Background: Searching for transcription factor binding sites in genome sequences is still an open problem in bioinformatics. Despite substantial progress, search methods based on information theory remain a standard in the field, even though the full validity of their underlying assumptions has only been tested in artificial settings. [...]
2009 - doi:10.1186/1471-2105-10-57
BMC bioinformatics, Vol. 10 (2009) , art. 57  
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7.
2 p, 99.7 KB Cloud-Coffee : implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud / Di Tommaso, Paolo (Centre de Regulació Genòmica) ; Orobitg, Miquel (Universitat de Lleida. Departament d'Informàtica i Enginyeria Industrial) ; Guirado, Fernando (Universitat de Lleida. Departament d'Informàtica i Enginyeria Industrial) ; Cores, Fernando (Universitat de Lleida. Departament d'Informàtica i Enginyeria Industrial) ; Espinosa, Antonio (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius) ; Notredame, Cedric (Centre de Regulació Genòmica)
We present the first parallel implementation of the T-Coffee consistency-based multiple aligner. We benchmark it on the Amazon Elastic Cloud (EC2) and show that the parallelization procedure is reasonably effective. [...]
2010 - 10.1093/bioinformatics/btq304
Bioinformatics, Vol. 26, Issue 15 (August 2010) , p. 1903-1904  
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8.
16 p, 399.2 KB In silico analysis reveals substantial variability in the gene contents of the Gammaproteobacteria LexA-regulon / Erill, Ivan (Centro Nacional de Microelectrónica (Espanya)) ; Escribano, Marcos (Centro Nacional de Microelectrónica (Espanya)) ; Campoy Sánchez, Susana (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ; Barbé García, Jordi (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
Motivation: Motif-prediction algorithm capabilities for the analysis of bacterial regulatory networks and the prediction of new regulatory sites can be greatly enhanced by the use of comparative genomics approaches. [...]
2003 - 10.1093/bioinformatics/btg303
Bioinformatics, Vol. 19, issue. 17 (Nov. 2003) , p. 2225-2236  
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9.
5 p, 359.4 KB lme4qtl : Linear mixed models with flexible covariance structure for genetic studies of related individuals / Ziyatdinov, Andrey (Chan School of Public Health) ; Vázquez-Santiago, Miquel (Hospital de la Santa Creu i Sant Pau (Barcelona, Catalunya)) ; Brunel, Helena (Hospital de la Santa Creu i Sant Pau (Barcelona, Catalunya)) ; Martinez-Perez, Angel (Institut d'Investigació Biomèdica Sant Pau) ; Aschard, Hugues (Biostatistique et Biologie Intégrative (C3BI)) ; Soria Fernández, José Manuel (Institut d'Investigació Biomèdica Sant Pau) ; Universitat Autònoma de Barcelona
Quantitative trait locus (QTL) mapping in genetic data often involves analysis of correlated observations, which need to be accounted for to avoid false association signals. This is commonly performed by modeling such correlations as random effects in linear mixed models (LMMs). [...]
2018 - 10.1186/s12859-018-2057-x
BMC bioinformatics, Vol. 19 Núm. 1 (27 2018) , p. 68  
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10.
9 p, 3.9 MB AutoScanJ : A Suite of ImageJ Scripts for Intelligent Microscopy / Tosi, Sébastien (Institute for Research in Biomedicine) ; Lladó, Anna (Institute for Research in Biomedicine) ; Bardia, Lídia (Institute for Research in Biomedicine) ; Rebollo, Elena (Institut de Biologia Molecular de Barcelona) ; Godo Pla, Anna (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ; Stockinger, Petra (Centre de Regulació Genòmica) ; Colombelli, Julien (Institute for Research in Biomedicine)
We developed AutoscanJ, a suite of ImageJ scripts enabling to image targets of interest by automatically driving a motorized microscope at the corresponding locations. For live samples, our software can sequentially detect biological events from their onset and further image them at high resolution, an action that would be impractical by user operation. [...]
2021 - 10.3389/fbinf.2021.627626
Frontiers in Bioinformatics, Vol. 1 (March 2021) , art. 627626  
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Depósito Digital de Documentos de la UAB : Encontrados 62 registros   1 - 10siguientefinal  ir al registro:
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