911 research outputs found
Scaling up qualitative data: with Professor Ken Benoit
No full textProfessor Benoit is the Principal Investigator in an ERC funded project QUANTESS developing innovative methods for the quantitative analysis of textual data in the social sciences. He is the co-author with Paul Nulty of the R software package for text analysis “quanteda”, and working on a book Quantitative Text Analysis Using R covering methods for managing, processing, and analysing textual data using the R programming language. He has taught quantitative text analysis extensively and has published research in this area targeting both methodology and political science applications
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>
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>
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>
Thesium philosophicarum fasciculus
No full textquem ... praeside ... Io. Friderico Benoit ... publicè tutabitur Ioh. Rodolphus Kochius, HBernas, phil. stud. author & respondens, ad diem 5. Martii ...Diss. Hohe Schule Bern, 171
Fables de La Fontaine: Une Anthologie proposée par Benoit Marchon
No full textHere are forty-three fables presented by an artist I have enjoyed twice elsewhere. The book's unusual shape (6½ x 10¾) is the first clue that it is going to present traditional material in a fresh way. Almost every presentation involves two pages and clever positioning of a few key images. GA (10-11) presents an ant with a sack of grain on his back marching across the page above a grasshopper moving upwards with a guitar on his back: character, load, and direction are all different. FC presents a cheese with its owner's name struck through and changed from Corbeau to Renard (12-13). WS shows a stork with a scissors for a head beside an x-ray of a wolf's digestive tract with the bone lodged down the throat (22-23). The spilt milk of MM is blotting out drawings of hens, pig, and cow (30-31). The surreal style fits the approach perfectly. Sometimes I have no idea why an object is presented the way Jarrie presents it; other times it is perfect. The bull in OF holds the frog by a tether as though the latter were a helium-filled balloon (32-33). Maybe best of all is The Rat and the Elephant (50-51). The elephant is segmented to make room for the text. Between the elephant's legs, mostly hidden from us, a cat reaches out a paw for the minuscule rat under the elephant's big belly. For sheer fun, try The Lion Defeated by a Man (78-79). The book has a place-holding ribbon, a short life of both La Fontaine and of Jarrie, and a helpful glossary of unusual language in the fables. This book fulfills its rear cover's promise of a fresh entry into a fabulous zoological park. Bravo, Jarrie!This is a hardbound book (hard cover)Language note: FrenchJean de La Fontaine; Benoit Marcho
L’écriture impliquée: nouvelle forme de l’engagement littéraire chez fatou diome, Léonora Miano et Marie Ndiaye
No full textMade available in DSpace on 2018-09-04T20:36:43Z (GMT). No. of bitstreams: 2
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Previous issue date: 2018-04-18Embargo set by: Seth Robbins for item 107270
Lift date: 2020-09-04T20:37:00Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 107270
Lift date: 2020-09-04T20:42:08Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemCette thèse propose d’expliciter les manières dont l’implication se manifeste dans les textes de Fatou Diome, Léonora Miano et Marie NDiaye. Dans un contexte français de résurgence de l’engagement littéraire, elle exprime des manières d’intervenir par l’écriture sur des problèmes sociaux ou politiques qui traversent la société. L’originalité de notre thèse tient à l’intérêt d’avoir privilégié le contexte d’écriture de ces auteures. En effet, la critique des littératures africaines francophones lie l’émergence de nouvelles formes d’écriture, à partir de années quatre-vingt, à la présence des auteurs de cette littérature dans un espace qui n’est plus africain mais essentiellement parisien. Le choix de l’implication nous permet d’inscrire les écrivaines choisies pour notre analyse dans un lieu témoin de pratiques d’écritures nouvelles qui montrent des préoccupations qui ne sont plus uniquement d’ordre esthétique.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2020-05-01The student, Malyoune Benoit, accepted the attached license on 2018-04-18 at 07:03.The student, Malyoune Benoit, submitted this Dissertation for approval on 2018-04-18 at 07:11.This Dissertation was approved for publication on 2018-04-18 at 17:39.DSpace SAF Submission Ingestion Package generated from Vireo submission #12334 on 2018-08-31 at 17:20:24U of I Only Restriction Lifted for Item 107270 on 2020-09-05T09:15:26Z
L'étude des cadastres antiques : à propos d'Olbia de Provence
No full textThe study of antique cadastres : namely about Olbia in Provence
The knowledge about the way land is occupied, as well in uran as rural areas, gain increasing importance with the actual approach to antique societies. The study of Greek and Roman cadastres in the Mediterrannean contour concern also Southern Gaul, not without arising problems of method about their identification, their restitution and their dating. Starting from his recent cadastral analysis of the territory surrounding the Marseilles foundation at Olbia. J. Benoit remains reserved about the reliability, the limits, even the dangers of the diverse techniques of investigation generally in practice.
Inside a zone where cadastre is established, to the North of Olbia, J. Benoit has dissociated the area situated to the North- North-East of the antique settlement. After a critical interpretation and Mediterranean wide comparaisons, the author delimits an area relatively restricted (750 acres), spreading from the sea to the mountain, regulated by a rectangular module 105x52,5 m. This cadastre most probably established on the basic mesure of a foot of 29,6 cm, could belong to a periode of Greek colonization (middle of the fourth - beginning of the first century B. C).La connaissance des modes de l'occupation des sols, tant urbaine que rurale, prend de plus en plus d'importance dans l'approche actuelle des sociétés antiques. L'étude des cadastrations grecques et romaines du pourtour méditerranéen concerne également le Midi gaulois, non sans poser plusieurs problèmes de méthode pour leur identification, leur restitution et leur datation. Partant de ses récentes analyses sur la cadastration du territoire alentour de la fondation massaliote d'Olbia, J. Benoit s'interroge, en premier lieu, sur la fiabilité, les limites, voire les dangers des diverses techniques d'investigation généralement usitées.
A l'intérieur d'une zone cadastrée au Nord d'Olbia, J. Benoit dissocie celle située au Nord-Nord-Est de l'agglomération antique. Après une interprétation critique et des comparaisons méditerranéennes, l'auteur délimite une aire relativement réduite (305 ha), s'étalant entre mer et montagne, rythmée selon un module rectangulaire de 105 x 52,5 m. Ce cadastre, très probablement édifié sur la mesure d'un pied de 29,6 cm, pourrait se rapporter à l'époque de colonisation grecque (milieu du IVème - début du Ier s. av. J.-C).Benoit Jean. L'étude des cadastres antiques : à propos d'Olbia de Provence. In: Documents d'Archéologie Méridionale, vol. 8, 1985. pp. 25-48
Solving eigenvalue response matrix equations with nonlinear techniques
No full textThis paper presents new algorithms for use in the eigenvalue response matrix method (ERMM) for reactor eigenvalue problems. ERMM spatially decomposes a domain into independent nodes linked via boundary conditions approximated as truncated orthogonal expansions, the coefficients of which are response functions. In its simplest form, ERMM consists of a two-level eigenproblem: an outer Picard iteration updates the k-eigenvalue via balance, while the inner λ -eigenproblem imposes neutron balance between nodes. Efficient methods are developed for solving the inner λ-eigenvalue problem within the outer Picard iteration. Based on results from several diffusion and transport benchmark models, it was found that the Krylov-Schur method applied to the λ -eigenvalue problem reduces Picard solver times (excluding response generation) by a factor of 2–5. Furthermore, alternative methods, including Picard acceleration schemes, Steffensen’s method, and Newton’s method, are developed in this paper. These approaches often yield faster k-convergence and a need for fewer k-dependent response function evaluations, which is important because response generation is often the primary cost for problems using responses computed online (i.e., not from a precomputed database). Accelerated Picard iteration was found to reduce total computational times by 2–3 compared to the unaccelerated case for problems dominated by response generation. In addition, Newton’s method was found to provide nearly the same performance with improved robustness
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