Vidal, Ramon Oliveira

[["dc.bibliographiccitation.artnumber","160090"],["dc.bibliographiccitation.journal","Scientific Data"],["dc.bibliographiccitation.volume","3"],["dc.contributor.author","Centeno, Tonatiuh Pena"],["dc.contributor.author","Shomroni, Orr"],["dc.contributor.author","Hennion, Magali"],["dc.contributor.author","Halder, Rashi"],["dc.contributor.author","Vidal, Ramon"],["dc.contributor.author","Rahman, Raza-Ur"],["dc.contributor.author","Bonn, Stefan"],["dc.date.accessioned","2017-09-07T11:52:23Z"],["dc.date.available","2017-09-07T11:52:23Z"],["dc.date.issued","2016"],["dc.identifier.doi","10.1038/sdata.2016.90"],["dc.identifier.gro","3144912"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/14127"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2588"],["dc.notes.intern","Crossref Import"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","public"],["dc.relation.issn","2052-4463"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","16913"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Scientific Reports"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Mandad, Sunit"],["dc.contributor.author","Rahman, Raza-Ur"],["dc.contributor.author","Centeno, Tonatiuh Pena"],["dc.contributor.author","Vidal, Ramon O."],["dc.contributor.author","Wildhagen, Hanna"],["dc.contributor.author","Rammner, Burkhard"],["dc.contributor.author","Keihani, Sarva"],["dc.contributor.author","Opazo, Felipe"],["dc.contributor.author","Urban, Inga"],["dc.contributor.author","Ischebeck, Till"],["dc.contributor.author","Kirli, Koray"],["dc.contributor.author","Benito, Eva"],["dc.contributor.author","Fischer, André"],["dc.contributor.author","Yousefi, Roya Y."],["dc.contributor.author","Dennerlein, Sven"],["dc.contributor.author","Rehling, Peter"],["dc.contributor.author","Feußner, Ivo"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Bonn, Stefan"],["dc.contributor.author","Rizzoli, Silvio O."],["dc.contributor.author","Fornasiero, Eugenio F."],["dc.date.accessioned","2019-07-09T11:50:21Z"],["dc.date.available","2019-07-09T11:50:21Z"],["dc.date.issued","2018"],["dc.description.abstract","The homeostasis of the proteome depends on the tight regulation of the mRNA and protein abundances, of the translation rates, and of the protein lifetimes. Results from several studies on prokaryotes or eukaryotic cell cultures have suggested that protein homeostasis is connected to, and perhaps regulated by, the protein and the codon sequences. However, this has been little investigated for mammals in vivo. Moreover, the link between the coding sequences and one critical parameter, the protein lifetime, has remained largely unexplored, both in vivo and in vitro. We tested this in the mouse brain, and found that the percentages of amino acids and codons in the sequences could predict all of the homeostasis parameters with a precision approaching experimental measurements. A key predictive element was the wobble nucleotide. G-/C-ending codons correlated with higher protein lifetimes, protein abundances, mRNA abundances and translation rates than A-/U-ending codons. Modifying the proportions of G-/C-ending codons could tune these parameters in cell cultures, in a proof-of-principle experiment. We suggest that the coding sequences are strongly linked to protein homeostasis in vivo, albeit it still remains to be determined whether this relation is causal in nature."],["dc.identifier.doi","10.1038/s41598-018-35277-8"],["dc.identifier.pmid","30443017"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/15918"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59754"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/209"],["dc.identifier.url","https://sfb1190.med.uni-goettingen.de/production/literature/publications/44"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation","info:eu-repo/grantAgreement/EC/FP7/339580/EU//MITRAC"],["dc.relation","info:eu-repo/grantAgreement/EC/FP7/614765/EU//NEUROMOLANATOMY"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation","SFB 1190: Transportmaschinen und Kontaktstellen zellulärer Kompartimente"],["dc.relation","SFB 1190 | P09: Proteinsortierung in der Synapse: Prinzipien und molekulare Organisation"],["dc.relation.issn","2045-2322"],["dc.relation.workinggroup","RG A. Fischer (Epigenetics and Systems Medicine in Neurodegenerative Diseases)"],["dc.relation.workinggroup","RG Rehling (Mitochondrial Protein Biogenesis)"],["dc.relation.workinggroup","RG Rizzoli (Quantitative Synaptology in Space and Time)"],["dc.relation.workinggroup","RG Urlaub (Bioanalytische Massenspektrometrie)"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.subject.ddc","610"],["dc.title","The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","4230"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Fornasiero, Eugenio F."],["dc.contributor.author","Mandad, Sunit"],["dc.contributor.author","Wildhagen, Hanna"],["dc.contributor.author","Alevra, Mihai"],["dc.contributor.author","Rammner, Burkhard"],["dc.contributor.author","Keihani, Sarva"],["dc.contributor.author","Opazo, Felipe"],["dc.contributor.author","Urban, Inga"],["dc.contributor.author","Ischebeck, Till"],["dc.contributor.author","Sakib, M. Sadman"],["dc.contributor.author","Fard, Maryam K."],["dc.contributor.author","Kirli, Koray"],["dc.contributor.author","Centeno, Tonatiuh Pena"],["dc.contributor.author","Vidal, Ramon O."],["dc.contributor.author","Rahman, Raza-Ur"],["dc.contributor.author","Benito, Eva"],["dc.contributor.author","Fischer, André"],["dc.contributor.author","Dennerlein, Sven"],["dc.contributor.author","Rehling, Peter"],["dc.contributor.author","Feussner, Ivo"],["dc.contributor.author","Bonn, Stefan"],["dc.contributor.author","Simons, Mikael"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Rizzoli, Silvio O."],["dc.date.accessioned","2019-07-09T11:46:03Z"],["dc.date.available","2019-07-09T11:46:03Z"],["dc.date.issued","2018"],["dc.description.abstract","The turnover of brain proteins is critical for organism survival, and its perturbations are linked to pathology. Nevertheless, protein lifetimes have been difficult to obtain in vivo. They are readily measured in vitro by feeding cells with isotopically labeled amino acids, followed by mass spectrometry analyses. In vivo proteins are generated from at least two sources: labeled amino acids from the diet, and non-labeled amino acids from the degradation of pre-existing proteins. This renders measurements difficult. Here we solved this problem rigorously with a workflow that combines mouse in vivo isotopic labeling, mass spectrometry, and mathematical modeling. We also established several independent approaches to test and validate the results. This enabled us to measure the accurate lifetimes of ~3500 brain proteins. The high precision of our data provided a large set of biologically significant observations, including pathway-, organelle-, organ-, or cell-specific effects, along with a comprehensive catalog of extremely long-lived proteins (ELLPs)."],["dc.identifier.doi","10.1038/s41467-018-06519-0"],["dc.identifier.pmid","30315172"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/15388"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59372"],["dc.identifier.url","https://sfb1190.med.uni-goettingen.de/production/literature/publications/42"],["dc.identifier.url","https://sfb1286.uni-goettingen.de/literature/publications/41"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.notes.intern","In goescholar not merged with http://resolver.sub.uni-goettingen.de/purl?gs-1/15611 but duplicate"],["dc.relation","info:eu-repo/grantAgreement/EC/FP7/339580/EU//MITRAC"],["dc.relation","info:eu-repo/grantAgreement/EC/FP7/614765/EU//NEUROMOLANATOMY"],["dc.relation","SFB 1190: Transportmaschinen und Kontaktstellen zellulärer Kompartimente"],["dc.relation","SFB 1190 | P09: Proteinsortierung in der Synapse: Prinzipien und molekulare Organisation"],["dc.relation","SFB 1286: Quantitative Synaptologie"],["dc.relation","SFB 1286 | A03: Dynamische Analyse der Remodellierung der extrazellulären Matrix (ECM) als Mechanismus der Synapsenorganisation und Plastizität"],["dc.relation.issn","2041-1723"],["dc.relation.workinggroup","RG Rehling (Mitochondrial Protein Biogenesis)"],["dc.relation.workinggroup","RG Rizzoli (Quantitative Synaptology in Space and Time)"],["dc.relation.workinggroup","RG Urlaub (Bioanalytische Massenspektrometrie)"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject.ddc","573"],["dc.subject.ddc","612"],["dc.title","Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","S6"],["dc.bibliographiccitation.journal","European Neuropsychopharmacology"],["dc.bibliographiccitation.lastpage","S7"],["dc.bibliographiccitation.volume","40"],["dc.contributor.author","Komorowski, A."],["dc.contributor.author","Singh, A."],["dc.contributor.author","Vidal, R."],["dc.contributor.author","Murgaš, M."],["dc.contributor.author","Pena-Centeno, T."],["dc.contributor.author","Gryglewski, G."],["dc.contributor.author","Kasper, S."],["dc.contributor.author","Wiltfang, J."],["dc.contributor.author","Lanzenberger, R."],["dc.contributor.author","Goya-Maldonado, R."],["dc.date.accessioned","2021-04-14T08:32:03Z"],["dc.date.available","2021-04-14T08:32:03Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1016/j.euroneuro.2020.09.015"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/83791"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation.issn","0924-977X"],["dc.title","P.009 MDK gene expression is correlated with human brain activity during acceptance of monetary rewards"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2205"],["dc.bibliographiccitation.issue","13"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","2207"],["dc.bibliographiccitation.volume","31"],["dc.contributor.author","Capece, Vincenzo"],["dc.contributor.author","Vizcaino, Julio C. Garcia"],["dc.contributor.author","Vidal, Ramon"],["dc.contributor.author","Rahman, Raza-Ur"],["dc.contributor.author","Centeno, Tonatiuh Pena"],["dc.contributor.author","Shomroni, Orr"],["dc.contributor.author","Suberviola, Irantzu"],["dc.contributor.author","Fischer, Andre"],["dc.contributor.author","Bonn, Stefan"],["dc.date.accessioned","2017-09-07T11:43:44Z"],["dc.date.available","2017-09-07T11:43:44Z"],["dc.date.issued","2015"],["dc.description.abstract","Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis' exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. Oasis generates downloadable interactive web reports for easy visualization, exploration and analysis of data on a local system. Finally, Oasis' modular workflow enables for the rapid (re-) analysis of data."],["dc.identifier.doi","10.1093/bioinformatics/btv113"],["dc.identifier.gro","3141872"],["dc.identifier.isi","000357425800020"],["dc.identifier.pmid","25701573"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2012"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1460-2059"],["dc.relation.issn","1367-4803"],["dc.title","Oasis: online analysis of small RNA deep sequencing data"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","102"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Neuroscience"],["dc.bibliographiccitation.lastpage","110"],["dc.bibliographiccitation.volume","19"],["dc.contributor.author","Halder, Rashi"],["dc.contributor.author","Hennion, Magali"],["dc.contributor.author","Vidal, Ramon O."],["dc.contributor.author","Shomroni, Orr"],["dc.contributor.author","Rahman, Raza-Ur"],["dc.contributor.author","Rajput, Ashish"],["dc.contributor.author","Centeno, Tonatiuh Pena"],["dc.contributor.author","van Bebber, Frauke"],["dc.contributor.author","Capece, Vincenzo"],["dc.contributor.author","Garcia Vizcaino, Julio C."],["dc.contributor.author","Schuetz, Anna-Lena"],["dc.contributor.author","Burkhardt, Susanne"],["dc.contributor.author","Benito, Eva"],["dc.contributor.author","Navarro Sala, Magdalena"],["dc.contributor.author","Bahari Javan, Sanaz"],["dc.contributor.author","Haass, Christian"],["dc.contributor.author","Schmid, Bettina"],["dc.contributor.author","Fischer, André"],["dc.contributor.author","Bonn, Stefan"],["dc.date.accessioned","2018-05-30T15:01:05Z"],["dc.date.available","2018-05-30T15:01:05Z"],["dc.date.issued","2016"],["dc.description.abstract","The ability to form memories is a prerequisite for an organism's behavioral adaptation to environmental changes. At the molecular level, the acquisition and maintenance of memory requires changes in chromatin modifications. In an effort to unravel the epigenetic network underlying both short- and long-term memory, we examined chromatin modification changes in two distinct mouse brain regions, two cell types and three time points before and after contextual learning. We found that histone modifications predominantly changed during memory acquisition and correlated surprisingly little with changes in gene expression. Although long-lasting changes were almost exclusive to neurons, learning-related histone modification and DNA methylation changes also occurred in non-neuronal cell types, suggesting a functional role for non-neuronal cells in epigenetic learning. Finally, our data provide evidence for a molecular framework of memory acquisition and maintenance, wherein DNA methylation could alter the expression and splicing of genes involved in functional plasticity and synaptic wiring."],["dc.identifier.doi","10.1038/nn.4194"],["dc.identifier.pmid","26656643"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/14808"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1546-1726"],["dc.title","DNA methylation changes in plasticity genes accompany the formation and maintenance of memory"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]