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UAB Digital Repository of Documents 34 records found  1 - 10nextend  jump to record: Search took 0.01 seconds. 
1.
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  
Detailed record - Creative Commons
2.
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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3.
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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4.
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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5.
6 p, 1.4 MB TMalphaDB and TMbetaDB : web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins / Perea, Marc (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ; Lugtenburg, Ivar (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ; Mayol, Eduardo (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ; Cordomí Montoya, Arnau (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ; Deupi, Xavier (Condensed Matter Theory Group and Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen PSI, Switzeland) ; Pardo Carrasco, Leonardo (Universitat Autònoma de Barcelona. Laboratori de Medicina Computacional) ; Olivella, Mireia (Universitat de Vic. Departament de Biologia de Sistemes)
Membrane proteins represent over 25 % of human protein genes and account for more than 60 % of drug targets due to their accessibility from the extracellular environment. The increasing number of available crystal structures of these proteins in the Protein Data Bank permits an initial estimation of their structural properties. [...]
2015 - 10.1186/s12859-015-0699-5
BMC bioinformatics, Vol. 16, Num. 1 (august 2015)  
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6.
13 p, 1.3 MB Moving forward through the in silico modeling of tuberculosis : a further step with UISS-TB / Russo, Giulia (University of Catania) ; Sgroi, Giuseppe (University of Catania) ; Parasiliti Palumbo, Giuseppe Alessandro (University of Catania) ; Pennisi, Marzio (University of Eastern Piedmont) ; Juarez, Miguel A. (University of Sheffield) ; Cardona, Pere-Joan (Institut Germans Trias i Pujol. Hospital Universitari Germans Trias i Pujol) ; Motta, Santo (National Research Council of Italy) ; Walker, Kenneth B. (TuBerculosis Vaccine Initiative (TBVI)) ; Fichera, Epifanio (Etna Biotech S.r.l) ; Viceconti, Marco (University of Bologna) ; Pappalardo, Francesco (University of Catania) ; Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia
In 2018, about 10 million people were found infected by tuberculosis, with approximately 1. 2 million deaths worldwide. Despite these numbers have been relatively stable in recent years, tuberculosis is still considered one of the top 10 deadliest diseases worldwide. [...]
2020 - 10.1186/s12859-020-03762-5
BMC bioinformatics, Vol. 21 (december 2020)  
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7.
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 de 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  
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8.
17 p, 1.6 MB MADloy : robust detection of mosaic loss of chromosome Y from genotype-array-intensity data / González, Juan Ramón (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, Tõnu (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  
Detailed record - Creative Commons
9.
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, Mercè (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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10.
13 p, 1.6 MB HIV drug resistance prediction with weighted categorical kernel functions / Ramon, Elies (Centre de Recerca en Agrigenòmica) ; Belanche Muñoz, Lluís A. (Lluís Antoni) (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  
Detailed record - Creative Commons

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