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41 p, 5.1 MB |
TOR complex 1 negatively regulates NDR kinase Cbk1 to control cell separation in budding yeast
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Foltman, Magdalena (Universidad de Cantabria) ;
Mendez, Iván (Universidad de Cantabria) ;
Bech-Serra, Joan J. (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
De La Torre, Carolina (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Brace, Jennifer L. (Northwestern University, Evanston, Illinois, United States of America) ;
Weiss, Eric L. (Northwestern University, Evanston, Illinois, United States of America) ;
Lucas, María (Universidad de Cantabria) ;
Queralt, Ethel (Instituto de Biomedicina de Valencia (IBV-CSIC)) ;
Sanchez-Diaz, Alberto (Universidad de Cantabria)
The target of rapamycin (TOR) signalling pathway plays a key role in the coordination between cellular growth and the cell cycle machinery in eukaryotes. The underlying molecular mechanisms by which TOR might regulate events after anaphase remain unknown. [...]
2023 -  10.1371/journal.pbio.3002263
PLoS biology, Vol. 21 Núm. 8 (august 2023)
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11 p, 711.9 KB |
Transcription-based prediction of response to IFNbeta using supervised computational methods
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Baranzini, Sergio E. (University of California, San Francisco) ;
Mousavi, Parvin (Queen's University, Kingston, Ontario) ;
Rio, Jordi (Hospital Universitari Vall d'Hebron) ;
Caillier, Stacy J. (University of California, San Francisco) ;
Stillman, Althea (University of California, San Francisco) ;
Villoslada, Pablo (Clínica Universidad de Navarra) ;
Wyatt, Mathew M. (University of California, San Francisco) ;
Comabella, Manuel (Hospital Universitari Vall d'Hebron) ;
Greller, Larry D. (Biosystemix, Sydenham, Ontario) ;
Somogyi, Roland (Biosystemix, Sydenham, Ontario) ;
Montalban, Xavier (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Oksenberg, Jorge (University of California, San Francisco)
Changes in cellular functions in response to drug therapy are mediated by specific transcriptional profiles resulting from the induction or repression in the activity of a number of genes, thereby modifying the preexisting gene activity pattern of the drug-targeted cell(s). [...]
2005 - 10.1371/journal.pbio.0030002
PLoS biology, Vol. 3 Núm. 1 (2005) , art. e2
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17 p, 1.6 MB |
The structural coverage of the human proteome before and after AlphaFold
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Porta-Pardo, Eduard (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ruiz-Serra, Victoria (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Valentini, Samuel (University of Trento) ;
Valencia, Alfons (Institució Catalana de Recerca i Estudis Avançats) ;
Universitat Autònoma de Barcelona
The protein structure field is experiencing a revolution. From the increased throughput of techniques to determine experimental structures, to developments such as cryo-EM that allow us to find the structures of large protein complexes or, more recently, the development of artificial intelligence tools, such as AlphaFold, that can predict with high accuracy the folding of proteins for which the availability of homology templates is limited. [...]
2022 - 10.1371/journal.pcbi.1009818
PLoS computational biology, Vol. 18 Núm. 1 (january 2022) , p. e1009818
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22 p, 2.3 MB |
ISOTOPE : ISOform-guided prediction of epiTOPEs in cancer
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Trincado Alonso, Juan Luis, 1987- (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Reixachs Solé, Marina (EMBL Australia Partner Laboratory Network at the Australian National University) ;
Pérez Granado, Judith (Hospital del Mar (Barcelona, Catalunya)) ;
Fugmann, Tim (Philochem AG) ;
Sanz, Ferran (Hospital del Mar (Barcelona, Catalunya)) ;
Yokota, Jun (National Cancer Center Research Institute (NCCRI)) ;
Eyras, Eduardo (Institut Hospital del Mar d'Investigacions Mèdiques)
Immunotherapies provide effective treatments for previously untreatable tumors and identifying tumor-specific epitopes can help elucidate the molecular determinants of therapy response. Here, we describe a pipeline, ISOTOPE (ISOform-guided prediction of epiTOPEs In Cancer), for the comprehensive identification of tumor-specific splicing-derived epitopes. [...]
2021 - 10.1371/journal.pcbi.1009411
PLoS computational biology, Vol. 17 Núm. 9 (september 2021) , p. e1009411
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17 p, 749.7 KB |
Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD
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Marcon, Yannick (Epigeny. St Ouen) ;
Bishop, Tom (University of Cambridge. MRC Epidemiology Unit) ;
Avraam, Demetris (Newcastle University. Population Health Sciences Institute) ;
Escriba-Montagut, Xavier (Universitat Pompeu Fabra) ;
Ryser-Welch, Patricia (Newcastle University. Population Health Sciences Institute) ;
Wheater, Stuart (Arjuna Technologies) ;
Burton, Paul (Population Health Sciences Institute, Newcastle University, Newcastle, United Kingdom) ;
González, Juan Ramón (Universitat Autònoma de Barcelona. Departament de Matemàtiques)
Combined analysis of multiple, large datasets is a common objective in the health- and biosciences. Existing methods tend to require researchers to physically bring data together in one place or follow an analysis plan and share results. [...]
2021 - 10.1371/journal.pcbi.1008880
PLoS computational biology, Vol. 17, Issue 3 (March 2021) , art e1008880
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33 p, 3.8 MB |
On the evolution and development of morphological complexity : A view from gene regulatory networks
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Hagolani, Pascal F. (Evo-devo Helsinki community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland) ;
Zimm, Roland (Institute of Functional Genomics, École Normale Superieure, Lyon, France) ;
Vroomans, Renske (Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands) ;
Salazar Ciudad, Isaac (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia)
How does morphological complexity evolve? This study suggests that the likelihood of mutations increasing phenotypic complexity becomes smaller when the phenotype itself is complex. In addition, the complexity of the genotype-phenotype map (GPM) also increases with the phenotypic complexity. [...]
2021 - 10.1371/journal.pcbi.1008570
PLoS computational biology, Vol. 17 (february 2021)
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9 p, 2.0 MB |
Evolution of the Division of Labor between Genes and Enzymes in the RNA World
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Boza, Gergely (Eötvös Loránd University. Department of Plant Systematics, Ecology and Theoretical Biology) ;
Szilágyi, András (Eötvös Loránd University. Department of Plant Systematics, Ecology and Theoretical Biology) ;
Kun, Ádám (Eötvös Loránd University. Department of Plant Systematics, Ecology and Theoretical Biology) ;
Santos, Mauro (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Szathmáry, Eörs (Eötvös Loránd University. Department of Plant Systematics, Ecology and Theoretical Biology)
The RNA world is a very likely interim stage of the evolution after the first replicators and before the advent of the genetic code and translated proteins. Ribozymes are known to be able to catalyze many reaction types, including cofactor-aided metabolic transformations. [...]
2014 - 10.1371/journal.pcbi.1003936
PLoS computational biology, Vol. 10, Issue 12 (December 2014) , art. e1003936
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14 p, 2.2 MB |
A Computational Model of the Fetal Circulation to Quantify Blood Redistribution in Intrauterine Growth Restriction
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Garcia-Canadilla, Patricia (Universitat Pompeu Fabra) ;
Rudenick, Paula A. (Hospital Universitari Vall d'Hebron. Institut de Recerca) ;
Crispi, Fatima (Institut d'Investigacions Biomèdiques August Pi i Sunyer) ;
Cruz-Lemini, Monica (Institut d'Investigacions Biomèdiques August Pi i Sunyer) ;
Palau, Georgina (Universitat Pompeu Fabra) ;
Camara, Oscar (Universitat Pompeu Fabra) ;
Gratacos, Eduard (Institut d'Investigacions Biomèdiques August Pi i Sunyer) ;
Bijens, Bart H. (Institució Catalana de Recerca i Estudis Avançats) ;
Universitat Autònoma de Barcelona
Intrauterine growth restriction (IUGR) due to placental insufficiency is associated with blood flow redistribution in order to maintain delivery of oxygenated blood to the brain. Given that, in the fetus the aortic isthmus (AoI) is a key arterial connection between the cerebral and placental circulations, quantifying AoI blood flow has been proposed to assess this brain sparing effect in clinical practice. [...]
2014 - 10.1371/journal.pcbi.1003667
PLoS computational biology, Vol. 10 (june 2014)
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