325 research outputs found
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments
No full text<p><strong>ReMap</strong> is a large scale integrative analysis of DNA-binding experiments for <a href="https://remap.univ-amu.fr/about_hsap_page">Homo sapiens</a>, <a href="https://remap.univ-amu.fr/about_mmus_page">Mus musculus</a>, <a href="https://remap.univ-amu.fr/about_dmel_page">Drosophila melanogaster</a> and <a href="https://remap.univ-amu.fr/about_atha_page">Arabidopsis thaliana</a> transcriptional regulators. The catalogues are the results of the manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources (GEO, ENCODE, ENA).</p>
<p><strong>ReMap</strong> (<a href="https://remap.univ-amu.fr/" target="_blank" rel="noopener">https://remap.univ-amu.fr</a>) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative anlysis of DNA-binding experiments in Human, Mouse, Fly and <em>Arabidopsis thaliana</em> for hundreds of transcription factors and regulators. In this 2022 update, we have uniformly processed >11 000 DNA-binding sequencing datasets from public sources across four species. The updated Human regulatory atlas includes 8103 datasets covering a total of 1210 transcriptional regulators (TRs) with a catalog of 182 million (M) peaks, while the updated Arabidopsis atlas reaches 4.8M peaks, 423 TRs across 694 datasets. Also, this ReMap release is enriched by two new regulatory catalogs for <em>Mus musculus</em> and <em>Drosophila melanogaster</em>. First, the Mouse regulatory catalog consists of 123M peaks across 648 TRs as a result of the integration and validation of 5503 ChIP-seq datasets. Second, the <em>Drosophila melanogaster</em> catalog contains 16.6M peaks across 550 TRs from the integration of 1205 datasets. The four regulatory catalogs are browsable through track hubs at UCSC, Ensembl and NCBI genome browsers. Finally, ReMap 2022 comes with a new Cis Regulatory Module identification method, improved quality controls, faster search results, and better user experience with an interactive tour and video tutorials on browsing and filtering ReMap catalogs.</p>
<p>We thank our users for past and future feedback to make ReMap useful for the community. The ReMap team welcomes your feedback on the catalogs, use of the website and use of the downloadable files. Please contact <a href="mailto:[email protected]" target="">[email protected]</a> for development requests.</p>
<p><em>Reference: </em></p>
<p><em>ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments </em><br><em>Fayrouz Hammal, Pierre de Langen, Aurélie Bergon, Fabrice Lopez, Benoit Ballester</em><br><em>Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D316–D325, </em><br><em><a href="https://doi.org/10.1093/nar/gkab996" target="_blank" rel="noopener">https://doi.org/10.1093/nar/gkab996</a></em></p>
La estructura narrativa del Don Juan de Torrente Ballester
No full textLa voz narrativa de Don Juan caracterizada por su pasividad, permite que Leporello sea un
personaje narrador indirecto que estructura la novela. Torrente Ballester adoptó este punto
de vista narrativo, con sus ventajas y desventajas, para lograr verosimilitud tanto frente a la
identidad de Leporello como a las experiencias del narrador pasivo. Todo ello da pie a un
juego literario en el que el autor ofrece su propia versión del mito de Don Juan.The narrative voice of Don Juan is characterized by its passivity, and this allows Leporello
to be an indirect narrator and organize the novel. Torrente Ballester adopted this style of
narration, with its advantages and disadvantages, to achieve the credibility of, for example,
the nature of Leporello or the experiences of the passive narrator. All this gives rise to a
literary game in which the author offers his own version of the myth of Don Jua
MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data
No full text<p>This repository contains the data required to run the example notebooks and to reproduce the figures from the paper : </p>
<div>
<div><strong>MUFFIN : A suite of tools for the analysis of functional sequencing d</strong>ata</div>
</div>
<div><em>Pierre de Langen, Benoit Ballester</em></div>
<div>bioRxiv 2023.12.11.570597; doi: <a href="https://doi.org/10.1101/2023.12.11.570597" target="_blank" rel="noopener">https://doi.org/10.1101/2023.12.11.570597</a></div>
<div> </div>
<div>Source code is located here :</div>
<div><a href="https://github.com/pdelangen/Muffin" target="_blank" rel="noopener">https://github.com/pdelangen/Muffin</a></div>
<div> </div>
<ul>
<li><strong>10k_pbmc_gene/ </strong>contains the data for 10k pbmc dataset in standard 10x sparse count table format.</li>
<li><strong>genome_annot/</strong> contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)</li>
<li><strong>GO_files/</strong> contains gene set information retrieved from the g:ProfileR website.</li>
<li><strong>immune_chip/ </strong>contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.</li>
<li><strong>tcga_atac/</strong> contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.</li>
<li><strong>muffin_apptainer.img</strong> is a singularity/apptainer image file which contains the muffin package.</li>
</ul>
<div> </div>
Albada dels estudis folklòrics valencians: a propòsit de la relació entre Francesc Martínez i Martínez i Adolf Salvà i Ballester
No full textSi l’obra de Francesc Martínez i Martínez va ser el primer treball “veritablement folklòric” en l’àmbit cultural valencià, la relació entre aquest autor i Adolf Salvà i Ballester constitueix l’origen d’una primera tradició en els estudis folklòrics valencians, amb interaccions, correccions, ampliacions, discussions, propostes i col·laboracions. Així ho demostren els documents que l’autor dona a conéixer i estudia en aquest article.Francesc Martínez i Martínez is the first researcher “really folkloric” in Valencian culture. The relationship between this author and Adolf Salvà i Ballester constitutes the first tradition in Valencian folk studies: with interactions, corrections, extensions, discussions, proposals and collaborations. The documents that the author discloses and studies in this paper demonstrate this
MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data
No full text<p>This repository contains the data required to run the example notebooks and to reproduce the figures from the paper : </p>
<div>
<div><strong>MUFFIN : A suite of tools for the analysis of functional sequencing data</strong></div>
</div>
<div><em>Pierre de Langen, Benoit Ballester</em></div>
<div>bioRxiv 2023.12.11.570597; doi: <a href="https://doi.org/10.1101/2023.12.11.570597" target="_blank" rel="noopener">https://doi.org/10.1101/2023.12.11.570597</a></div>
<div> </div>
<div>Source code is located here :</div>
<div><a href="https://github.com/pdelangen/Muffin" target="_blank" rel="noopener">https://github.com/pdelangen/Muffin</a></div>
<div> </div>
<ul>
<li><strong>10k_pbmc_gene/ </strong>contains the data for 10k pbmc dataset in standard 10x sparse count table format.</li>
<li><strong>genome_annot/</strong> contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)</li>
<li><strong>GO_files/</strong> contains gene set information retrieved from the g:ProfileR website.</li>
<li><strong>immune_chip/ </strong>contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.</li>
<li><strong>tcga_atac/</strong> contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.</li>
<li><strong>scATAC/</strong> contains the cell barcode-genomic region ATAC tag count table, as well as the barcode metadata and the 10k pbmc dataset pre-analyzed in h5 AnnData format.</li>
</ul>
<div> </div>
MUFFIN : A suite of tools for the analysis of functional sequencing data - Example input data
No full text<p>This repository contains the data required to run the example notebooks and to reproduce the figures from the paper : </p>
<div>
<div><strong>MUFFIN : A suite of tools for the analysis of functional sequencing data</strong></div>
</div>
<div><em>Pierre de Langen, Benoit Ballester</em></div>
<div>bioRxiv 2023.12.11.570597; doi: <a href="https://doi.org/10.1101/2023.12.11.570597" target="_blank" rel="noopener">https://doi.org/10.1101/2023.12.11.570597</a></div>
<div> </div>
<div>Source code is located here :</div>
<div><a href="https://github.com/pdelangen/Muffin" target="_blank" rel="noopener">https://github.com/pdelangen/Muffin</a></div>
<div> </div>
<ul>
<li><strong>10k_pbmc_gene/ </strong>contains the data for 10k pbmc dataset in standard 10x sparse count table format.</li>
<li><strong>genome_annot/</strong> contains gencode v38 and chromosomes for the human (used for gene set enrichment analyses)</li>
<li><strong>GO_files/</strong> contains gene set information retrieved from the g:ProfileR website.</li>
<li><strong>immune_chip/ </strong>contains the data required to re-run the ChIP-seq analyses, it will require to also launch the dl_data.smk to retrieve the data from ENCODE.</li>
<li><strong>tcga_atac/</strong> contains the sample-genomic region ATAC tag count table, as well as the sample metadata and a gene set file of cancer hallmark genes.</li>
<li><strong>scATAC/</strong> contains the cell barcode-genomic region ATAC tag count table, as well as the barcode metadata and the 10k pbmc dataset pre-analyzed in h5 AnnData format.</li>
</ul>
<div> </div>
Albada dels estudis folklòrics valencians: a propòsit de la relació entre Francesc Martínez i Martínez i Adolf Salvà i Ballester
No full textSi l’obra de Francesc Martínez i Martínez va ser el primer treball “veritablement folklòric” en l’àmbit cultural valencià, la relació entre aquest autor i Adolf Salvà i Ballester constitueix l’origen d’una primera tradició en els estudis folklòrics valencians, amb interaccions, correccions, ampliacions, discussions, propostes i col·laboracions. Així ho demostren els documents que l’autor dona a conéixer i estudia en aquest article.Francesc Martínez i Martínez is the first researcher “really folkloric” in Valencian culture. The relationship between this author and Adolf Salvà i Ballester constitutes the first tradition in Valencian folk studies: with interactions, corrections, extensions, discussions, proposals and collaborations. The documents that the author discloses and studies in this paper demonstrate this.Aquest article s’emmarca en una línia d’investigació que ha rebut finançament del Ministeri de Ciència, Innovació i Universitats a través del projecte PGC2018-093993-B-I00 (MCIU/AEI/FEDER, UE)
Gonzalo Torrente Ballester entre las aulas y el periódico
No full textThis article analyzes the vision in educational matters of Gonzalo Torrente Ballester, one of whose main occupations and vocations was that of teaching. To do this, the focus will be on a series of articles that this author wrote in the newspaper Faro de Vigo between 1965 and 1966. It is intended to study, on the one hand, his journalistic facet, and on the other, his teaching spirit. The aspects treated will include from the pedagogical method that, according to these texts, guided the teaching of the writer, to its position about the curricula of the time, the formation and the conditions of the teacher or the concept of education aimed at their ideals.Este artículo analiza la visión en materia educativa de Gonzalo Torrente Ballester, una de cuyas principales ocupaciones y vocaciones fue la de la docencia. Para ello, se pondrá el foco en una serie de columnas que este autor escribió en el diario Faro de Vigo entre los años 1965 y 1966. Se pretende con ello estudiar,
por un lado, su faceta periodística, y por otro, su espíritu docente. Los aspectos tratados comprenderán desde el método pedagógico que, según se puede intuir a la luz de estos textos, guiaba la docencia del escritor, hasta su posición respecto a los planes de estudio de la época, la formación y las condiciones del profesorado o el concepto general de educación al que apuntaban sus ideales
Transición sociopolítica y transición personal: intrahistoria y discurso en Off-side, de Gonzalo Torrente Ballester
No full textThe early sixties were decisive in the life of the writer GonzaloTorrente Ballester. This article examines some of the life circumstances of the author and his correspondence with the intra-history reflected in the novel Off-side trying to show that treatment of a subject and the use of new or renewed discursive strategies that involve the abandonment of worn formulas, the writer is definitely free from limiting labels and manages, through fiction, to reveal their true ideological position.Los primeros años sesenta del siglo XX fueron decisivos en la vida y la obra del escritor español Gonzalo Torrente Ballester. Este artículo examina algunas de las circunstancias vitales del autor y su correspondencia con la intrahistoria plasmada en la novela Off-side pretendiendo mostrar que, con el tratamiento de un tema y la utilización de nuevas o renovadas estrategias discursivas que suponen el abandono de gastadas fórmulas, el escritor se libera definitivamente de limitadoras etiquetas y logra, a través de la ficción, poner de manifiesto su verdadera posición ideológica
Causal Viscous Universe in Sáez-Ballester Theory
No full textIn this work the authors examine the dynamics of viscous Universe in Sáez-Ballester theory of gravity. The solutions of the Friedmann-Robertson-Walker (FRW) field equations have been derived within the framework of full causal theories presented by Israel and Stewart (1979) using simple parametrization of scale factor a(t), i.e. power law relation a(t)=a_{0}t^{\alpha} and exponential law a(t)=b_{0}e^{\beta t}. The power law cosmological model shows that the Universe transitioned from early cosmic deceleration to the present cosmic acceleration and the exponential cosmological model shows the accelerated expansion of the Universe. It has been discovered that as time passes, energy density and viscosity decrease while temperature rises. The behaviour of the cosmological parameters such as the Hubble parameter, energy density, pressure, coefficient of viscosity and state-finder parameter have been presented graphically.The presentation of the authors' names and (or) special characters in the title of the pdf file of the accepted manuscript may differ slightly from what is displayed on the item page. The information in the pdf file of the accepted manuscript reflects the original submission by the author
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