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11.
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12.
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3 p, 1.6 MB |
The PRALINE database : protein and Rna humAn singLe nucleotIde variaNts in condEnsates
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Vandelli, Andrea (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Arnal, Magdalena (University Sapienza Rome) ;
Monti, Michele (Istituto Italiano di Tecnologia) ;
Fiorentino, Jonathan (Istituto Italiano di Tecnologia) ;
Broglia, Laura (Istituto Italiano di Tecnologia) ;
Colantoni, Alessio (University Sapienza Rome) ;
Sánchez de Groot, Natalia (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Torrent Burgas, Marc (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Armaos, Alexandros (Istituto Italiano di Tecnologia) ;
Tartaglia, Gian Gaetano (Istituto Italiano di Tecnologia)
Biological condensates are membraneless organelles with different material properties. Proteins and RNAs are the main components, but most of their interactions are still unknown. Here, we introduce PRALINE, a database for the interrogation of proteins and RNAs contained in stress granules, processing bodies and other assemblies including droplets and amyloids. [...]
2023 -  10.1093/bioinformatics/btac847
Bioinformatics, Vol. 39, Num.1 (January 2023) , art. btac847
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13.
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7 p, 1.3 MB |
Optimal gap-affine alignment in O (s) space
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Marco-Sola, Santiago (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius) ;
Eizenga, Jordan (University of California. Genomics Institute) ;
Guarracino, Andrea (University of Tennessee Health Science Center. Department of Genetics, Genomics and Informatics) ;
Paten, Benedict (University of California. Santa Cruz Genomics Institute) ;
Garrison, Erik (University of Tennessee Health Science Center. Department of Genetics, Genomics and Informatics) ;
Moreto, Miquel (Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius)
Pairwise sequence alignment remains a fundamental problem in computational biology and bioinformatics. Recent advances in genomics and sequencing technologies demand faster and scalable algorithms that can cope with the ever-increasing sequence lengths. [...]
2023 - 10.1093/bioinformatics/btad074
Bioinformatics, Vol. 39, Issue 2 (February 2023) , art. btad074
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14.
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9 p, 1.1 MB |
Refinement of computational identification of somatic copy number alterations using DNA methylation microarrays illustrated in cancers of unknown primary
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Blecua, Pedro (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Davalos, Veronica (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
De Villasante, Izar (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Merkel, Angelika (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Musulén, Eva (Hospital Universitari General de Catalunya) ;
Coll-Sanmartin, Laia (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Esteller, M (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)
High-throughput genomic technologies are increasingly used in personalized cancer medicine. However, computational tools to maximize the use of scarce tissues combining distinct molecular layers are needed. [...]
2022 - 10.1093/bib/bbac161
Briefings in Bioinformatics, Vol. 23 Núm. 5 (september 2022) , p. bbac161
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15.
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11 p, 1.0 MB |
IgIDivA : immunoglobulin intraclonal diversification analysis
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Zaragoza-Infante, Laura (Aristotle University of Thessalonik) ;
Junet, Valentin (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pechlivanis, Nikos (Centre for Research and Technology Hellas (Tessalònica, Grècia)) ;
Fragkouli, Styliani-Christina (Centre for Research and Technology Hellas (Tessalònica, Grècia)) ;
Amprachamian, Serovpe (Centre for Research and Technology Hellas (Tessalònica, Grècia)) ;
Koletsa, Triantafyllia (Aristotle University of Thessaloniki) ;
Chatzidimitriou, Anastasia (Centre for Research and Technology Hellas (Tessalònica, Grècia)) ;
Papaioannou, Maria (Aristotle University of Thessaloniki) ;
Stamatopoulos, Kostas (Centre for Research and Technology Hellas (Tessalònica, Grècia)) ;
Agathangelidis, Andreas (University of Athens) ;
Psomopoulos, Fotis (Centre for Research and Technology Hellas (Tessalònica, Grècia))
Intraclonal diversification (ID) within the immunoglobulin (IG) genes expressed by B cell clones arises due to ongoing somatic hypermutation (SHM) in a context of continuous interactions with antigen(s). [...]
2022 - 10.1093/bib/bbac349
Briefings in Bioinformatics, Vol. 23, Issue 5 (September 2022) , art. bbac349
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16.
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12 p, 1.5 MB |
Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data
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Sidorczuk, Katarzyna (University of Wrocław) ;
Gagat, Przemysław (University of Wrocław) ;
Pietluch, Filip (University of Wrocław) ;
Kała, Jakub (Warsaw University of Technology) ;
Rafacz, Dominik (Warsaw University of Technology) ;
Bąkała, Laura (Warsaw University of Technology) ;
Słowik, Jadwiga (Warsaw University of Technology) ;
Kolenda, Rafał (Wrocław University of Environmental and Life Sciences) ;
Rödiger, Stefan (Brandenburg University of Technology Cottbus-Senftenberg) ;
Fingerhut, Legana C H W (James Cook University. Department of Molecular and Cell Biology) ;
Cooke, Ira R (James Cook University. Department of Molecular and Cell Biology) ;
Mackiewicz, Paweł (University of Wrocław) ;
Burdukiewicz, Michał (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Antimicrobial peptides (AMPs) are a heterogeneous group of short polypeptides that target not only microorganisms but also viruses and cancer cells. Due to their lower selection for resistance compared with traditional antibiotics, AMPs have been attracting the ever-growing attention from researchers, including bioinformaticians. [...]
2022 - 10.1093/bib/bbac343
Briefings in Bioinformatics, Vol. 23, Issue 5 (September 2022) , art. bbac343
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17.
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3 p, 240.8 KB |
PCIG : a web-based application to explore immune-genomics interactions across cancer types
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Pedrola, Anna (Vall d'Hebron Institut d'Oncologia) ;
Franch-Expósito, Sebastià (Memorial Sloan Kettering Cancer Center) ;
Lahoz, Sara (Institut d'Investigacions Biomèdiques August Pi i Sunyer) ;
Esteban-Fabró, Roger (Institut d'Investigacions Biomèdiques August Pi i Sunyer) ;
Dienstmann, Rodrigo (Vall d'Hebron Institut d'Oncologia) ;
Bassaganyas, Laia (University of Cambridge. Department of Medical Genetics) ;
Camps, Jordi (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia)
Genomic alterations can modulate the tumor immunophenotype depending on their nature and tissue of origin. Although this immune-genomic interaction may shape disease progression and response to immunotherapy, the factors governing such dynamics and the influence of each tissue-specific context remain poorly understood. [...]
2022 - 10.1093/bioinformatics/btac111
Bioinformatics, Vol. 38, Issue 8 (March 2022) , p. 2374-2376
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18.
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19.
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9 p, 748.7 KB |
CuBlock : a cross-platform normalization method for gene-expression microarrays
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Junet, Valentin (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Farrés, Judith (Anaxomics Biotech SL) ;
Mas, José M. (Anaxomics Biotech SL) ;
Daura i Ribera, Xavier (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Cross-(multi)platform normalization of gene-expression microarray data remains an unresolved issue. Despite the existence of several algorithms, they are either constrained by the need to normalize all samples of all platforms together, compromising scalability and reuse, by adherence to the platforms of a specific provider, or simply by poor performance. [...]
2021 - 10.1093/bioinformatics/btab105
Bioinformatics, Vol. 37, Issue 16 (August 2021) , p. 2365-2373
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20.
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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
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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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