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OLOGRAM: Determining significance of total overlap length between genomic regions sets

<span title="2019-11-05">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Here, we introduce OLOGRAM, which performs overlap statistics between sets of genomic regions described in BEDs or GTF.  ...  It uses Monte Carlo simulation, taking into account both the distributions of region and inter-region lengths, to fit a negative binomial model of the total overlap length.  ...  To determine whether two such sets have a functional relationship, a typical approach is to look for significant co-localization by assessing the statistical significance of the amount of overlap between  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btz810">doi:10.1093/bioinformatics/btz810</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31688931">pmid:31688931</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dpriypfrjvayrmjqw7fk3lvjmq">fatcat:dpriypfrjvayrmjqw7fk3lvjmq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201104204749/https://hal-amu.archives-ouvertes.fr/hal-02383808/document" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f9/84/f9840905f832690dfe9a619f0bea97ae7c331b8e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btz810"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

OLOGRAM-MODL: mining enriched n-wise combinations of genomic features with Monte Carlo and dictionary learning

Quentin Ferré, Cécile Capponi, Denis Puthier
<span title="2021-10-04">2021</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dhm4lwu4tvbf5dklpg7zonzosa" style="color: black;">NAR Genomics and Bioinformatics</a> </i> &nbsp;
We introduce OLOGRAM-MODL, which considers overlaps between n ≥ 2 sets of genomic regions, and computes their statistical mutual enrichment by Monte Carlo fitting of a Negative Binomial distribution, resulting  ...  A suitable way to infer such functional associations between them is to study the overlaps of the corresponding genomic regions.  ...  between n ≥ 2 sets of genomic regions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nargab/lqab114">doi:10.1093/nargab/lqab114</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34988437">pmid:34988437</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8693575/">pmcid:PMC8693575</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dljyvm6mrrarnfn7grom54g73m">fatcat:dljyvm6mrrarnfn7grom54g73m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220103104043/https://watermark.silverchair.com/lqab114.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAsswggLHBgkqhkiG9w0BBwagggK4MIICtAIBADCCAq0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMPDaDkdbQS0vze4uWAgEQgIICfr_ieEXWtjgstbpJKRF7qJDmNe3qjHHe4gFhbHroVhNjr7ilIusce3XVUvbZRcTPTyB8y0ZyzcScA_SvwajlTXXisQ7JDQgx735oKmAav7YklQF0GbfkrAlgCHggHCaJAlKv8hXDkQ2-tmru72aJ84L8k6i6izqPdh82jpX3vgbEw_LQZCS9TeFOlThPW6Vjqwx6jWJdAUvBBshqV_y47tW3XzLjA4qKK-A5OJ0GiCRVmKLr15d_zITZPPYLgQ-OO4y04yRA3LYCRfxWMJ6wbXXVSjRHaiZr-ta43Gnxne3KsTd2TdMM_9gvS6ExYtb1TPfCjJV8NPGGQqYfkY6wbYdBKW9Cd0AF4tdo_Ew4nsAqMcyR78Pr8X806AjahqYKwZfp6HldUGzJH0GkGChbfQR-YGGw48gTSkD3VhMYtafcypa_vDd1zQVSb7ryhY_uraibweIFZKRdiEMWcHRKxEjEUHEbkYl78J1SNkFyThcC7Ofd2PilCbXOpfKBuQ3YqDbQf8DXGOcyDDKaR7gUdoA8Qx928rwvu1GrR0UkY2GEWXLBRPnfstmWzgbJodpul7uoNVtKH1RgkN2T67XjV9ruw0fvUBY0AsiJIIJ3J8a0qD4WIahLUt89cK7PGUUs4J6gHLZ4a1rj1rLlWMaiISezYJvgzOg82VyCbuiCvF5JoNnSOjP-Jn6pvdTBLib2rPh6DNagtyPaGaK6deqLAA4G-miY-jkM2HIs_0LrhHGLYA9vcqrB2XQ6PF1D_4Io8oQj8M8-RaWPOsx_dncdSNJ9CZEifw51I5Nc14WAcv2fQIZQtWavZjoGHHbWlVaxLJBI5zWyw3GVP2eUuNdr" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/01/6a/016a053ec938e2f7b9abf83cea1652a93f1a6e22.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nargab/lqab114"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8693575" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Tissue-specific transcription factor target identification in the Caenorhabditis elegans epidermis using targeted DamID [article]

Dimitris Katsanos, Michalis Barkoulas
<span title="2020-12-18">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We reveal direct links between these two factors and the cell differentiation programme, as well as the Wnt signalling pathway.  ...  Using a combination of TaDa and single-molecule FISH (smFISH), we refine the positions of LIN-22 and NHR-25 within the epidermal gene network.  ...  OLOGRAM: determining significance of total overlap length between genomic regions sets. Bioinformatics 36, 1920 -1922 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.12.17.423252">doi:10.1101/2020.12.17.423252</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/33abhqzbnfhyzesjbrurmqopay">fatcat:33abhqzbnfhyzesjbrurmqopay</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429023303/https://www.biorxiv.org/content/biorxiv/early/2020/12/18/2020.12.17.423252.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f1/e5/f1e5498b33e22d1293b867802b323d6ab2a7a642.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.12.17.423252"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Rapport d'activités IFB 2019-2020 [article]

Claudine Médigue, Suzanne Lauriou, Angela Saenz, Jacques Van Helden, IFB Teams
<span title="2021-08-29">2021</span> <i title="Zenodo"> Zenodo </i> &nbsp;
genomic surveillance.  ...  Equipex+ (Equipements Structurants pour la Recherche), that gathers 37 teams (IFB platforms, data centers, mesocenters and data-producing infrastructures) from 16 research organizations and 160 persons, totaling  ...  >> Detailed report of the survey  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5324333">doi:10.5281/zenodo.5324333</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/py5xp6q7ungkdevdqx25zxfwmq">fatcat:py5xp6q7ungkdevdqx25zxfwmq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210907234401/https://zenodo.org/record/5324334/files/Rapport%20IFB%202019-2020.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fe/89/fe89e044b3439f5b69cc5323f11af36be8f885f6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.5324333"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

Genetic Predisposition to the Mortality in Septic Shock Patients: From GWAS to the Identification of a Regulatory Variant Modulating the Activity of a CISH Enhancer

Florian Rosier, Audrey Brisebarre, Claire Dupuis, Sabrina Baaklini, Denis Puthier, Christine Brun, Lydie C. Pradel, Pascal Rihet, Didier Payen
<span title="2021-05-29">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
An association of 139 SNPs with death based on a false discovery rate of 5% was detected. The most significant SNPs were within the CISH gene involved in cytokine regulation.  ...  Two genome-wide association studies (GWAS) on 832 septic shock patients were performed.  ...  We thank Laurence Borge for assistance and for the use of the cell culture platform facility (CRCM U1068, Marseille).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms22115852">doi:10.3390/ijms22115852</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34072601">pmid:34072601</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lrrm37yjwbdazffghlfsqnxxii">fatcat:lrrm37yjwbdazffghlfsqnxxii</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716164238/https://hal-amu.archives-ouvertes.fr/hal-03245766/document" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/07/60/0760626056651c5f24b8eecb136390526eaed5be.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms22115852"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation

Agata Cieslak, Guillaume Charbonnier, Melania Tesio, Eve-Lyne Mathieu, Mohamed Belhocine, Aurore Touzart, Charlotte Smith, Guillaume Hypolite, Guillaume P. Andrieu, Joost H.A. Martens, Eva Janssen-Megens, Marta Gut (+8 others)
<span title="2020-07-15">2020</span> <i title="Rockefeller University Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hlxgij3xe5gajfxq2e74j7itlu" style="color: black;">Journal of Experimental Medicine</a> </i> &nbsp;
Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an integrative analysis of other hematopoietic populations.  ...  , irrespective of their activation status.  ...  Acknowledgments We thank the Cell Imaging Platform of Institut des Maladies Génétiques Imagine and the Transcriptomics and Genomics Marseille-Luminy sequencing platform.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1084/jem.20192360">doi:10.1084/jem.20192360</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32667968">pmid:32667968</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/37qbajtyvfazrbjwafa7a2dru4">fatcat:37qbajtyvfazrbjwafa7a2dru4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210804024823/https://repository.ubn.ru.nl/bitstream/handle/2066/225041/1/225041.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/96/ec/96ec762c40f0e98a315822396abd79a163ae69f9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1084/jem.20192360"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>