المؤلفون: Chatrikhi, Rakesh, Mallory, Michael J, Gazzara, Matthew R, Agosto, Laura M, Zhu, Wandi S, Litterman, Adam J, Ansel, K Mark, Lynch, Kristen W

المصدر: Cell Reports. 28(11)

مصطلحات موضوعية: Biochemistry and Cell Biology, Biological Sciences, Human Genome, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, 3' Untranslated Regions, CELF Proteins, Cell Line, Tumor, Cleavage And Polyadenylation Specificity Factor, Enhancer Elements, Genetic, Gene Expression Regulation, Humans, Introns, Nerve Tissue Proteins, Polyadenylation, Protein Binding, RNA Splicing Factors, RNA-Binding Proteins, RNA-Seq, Repressor Proteins, Signal Transduction, Splicing Factor U2AF, Transcriptome, 3′ UTR, APA, CELF2, CFIm25, CstF64, polyadenylation, Medical Physiology, Biological sciences

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/4qg7j0txTest

المؤلفون: Bryce-Smith, Sam, Burri, Dominik, Gazzara, Matthew R., Herrmann, Christina J., Danecka, Weronika, Fitzsimmons, Christina M., Wan, Yuk Kei, Zhuang, Farica, Fansler, Mervin M., Fernández, José M., Ferret, Meritxell, Gonzalez-Uriarte, Asier, Haynes, Samuel, Herdman, Chelsea, Kanitz, Alexander, Katsantoni, Maria, Marini, Federico, McDonnel, Euan, Nicolet, Ben, Poon, Chi-Lam, Rot, Gregor, Schärfen, Leonard, Wu, Pin-Jou, Yoon, Yoseop, Barash, Yoseph, Zavolan, Mihaela

مصطلحات موضوعية: benchmarking, alternative polyadenylation, RNA-seq, bioinformatics, community initiative

العلاقة: https://zenodo.org/record/8290349Test; https://doi.org/10.5281/zenodo.8290349Test; oai:zenodo.org:8290349

الإتاحة: https://doi.org/10.5281/zenodo.8290349Test
https://doi.org/10.1101/2023.06.23.546284Test
https://doi.org/10.5281/zenodo.8290348Test
https://zenodo.org/record/8290349Test

المؤلفون: Vaquero-Garcia, Jorge, Aicher, Joseph K., Jewell, San, Gazzara, Matthew R., Radens, Caleb M., Jha, Anupama, Green, Christopher J., Norton, Scorr S., Lahens, Nicholas F., Grant, Gregory R., Barash, Yoseph

العلاقة: https://zenodo.org/record/7508064Test; https://doi.org/10.5281/zenodo.7508064Test; oai:zenodo.org:7508064

الإتاحة: https://doi.org/10.5281/zenodo.7508064Test
https://doi.org/10.5281/zenodo.7508063Test
https://zenodo.org/record/7508064Test

المؤلفون: Bryce-Smith, Sam, Burri, Dominik, Gazzara, Matthew R., Herrmann, Christina J., Danecka, Weronika, Feranandez, José M., Ferret, Meritxell, Gonzalez Uriarte, Asier

المساهمون: Barcelona Supercomputing Center

مصطلحات موضوعية: Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, RNA sequence, Computational biology, Benchmarking, (alternative) polyadenylation, Bioinformatics, RNA-seq, Community initiative, Bioinformàtica

وصف الملف: application/pdf

العلاقة: https://rnajournal.cshlp.org/content/29/12/1839.fullTest; info:eu-repo/grantAgreement/EC/H2020/871075/EU/Connect and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services/ELIXIR-CONVERGE; All code and metrics for the project are publicly available at https://github.com/iRNA-COSI/APAevalTest. Unless otherwise stated, publicly available containers (e.g., from the Biocontainers project; Da Veiga Leprevost et al. 2017) were utilized for execution workflows. In a few cases, we generated custom-built docker images. These are hosted at https://hub.docker.com/u/apaevalTest. The most informative metrics for all challenges of the identification and absolute quantification events are stored in the OpenEBench database (https://openebench.bsc.es/benchmarking/OEBC007/eventsTest), where the results can be visualized and further explored. All data sets used in this study are publicly available. For SRA accessions and download links, see Supplemental Table S1. Annotation files, input ground truth and RNA-seq files, code for figure plotting, and other data to reproduce or supplement this analysis have been deposited in a Zenodo repository available at https://doi.org/10.5281/zenodo.8290348Test.; Bryce-Smith, S. [et al.]. Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data. "RNA", 2023; http://hdl.handle.net/2117/402125Test

الإتاحة: https://doi.org/10.1261/rna.079849.123Test
https://doi.org/10.5281/zenodo.8290348Test
http://hdl.handle.net/2117/402125Test

المؤلفون: Agosto, Laura M., Mallory, Michael J., Ferretti, Max B., Blake, Davia, Krick, Keegan S., Gazzara, Matthew R., Garcia, Benjamin A., Lynch, Kristen W.

المساهمون: National Institutes of Health, National Science Foundation

المصدر: Cell Reports ; volume 42, issue 3, page 112273 ; ISSN 2211-1247

مصطلحات موضوعية: General Biochemistry, Genetics and Molecular Biology

الإتاحة: https://doi.org/10.1016/j.celrep.2023.112273Test
https://api.elsevier.com/content/article/PII:S221112472300284X?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S221112472300284X?httpAccept=text/plainTest

المؤلفون: Vaquero-Garcia, Jorge, Aicher, Joseph K., Jewell, San, Gazzara, Matthew R., Radens, Caleb M., Jha, Anupama, Norton, Scott S., Lahens, Nicholas F., Grant, Gregory R., Barash, Yoseph

المساهمون: U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development, U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute, Blavatnik Family Foundation, U.S. Department of Health & Human Services | NIH | National Institute on Aging, U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences, U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine

المصدر: Nature Communications ; volume 14, issue 1 ; ISSN 2041-1723

مصطلحات موضوعية: General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary

الإتاحة: https://doi.org/10.1038/s41467-023-36585-yTest
https://www.nature.com/articles/s41467-023-36585-y.pdfTest
https://www.nature.com/articles/s41467-023-36585-yTest

المؤلفون: Blake, Davia^1,2 (AUTHOR), Gazzara, Matthew R.^1,3 (AUTHOR), Breuer, Isabel^1,4 (AUTHOR), Ferretti, Max¹ (AUTHOR), Lynch, Kristen W.^1,2,3,4 (AUTHOR) klync@pennmedicine.upenn.edu

المصدر: Scientific Reports. 5/14/2024, Vol. 14 Issue 1, p1-14. 14p.

مصطلحات موضوعية: *T cells, *RNA-binding proteins, *CELL proliferation

المؤلفون: Blake, Davia, Radens, Caleb M, Ferretti, Max B, Gazzara, Matthew R, Lynch, Kristen W

المساهمون: National Institute of General Medical Sciences

المصدر: eLife ; volume 11 ; ISSN 2050-084X

الإتاحة: https://doi.org/10.7554/elife.80953Test
https://cdn.elifesciences.org/articles/80953/elife-80953-v2.pdfTest
https://cdn.elifesciences.org/articles/80953/elife-80953-v2.xmlTest
https://elifesciences.org/articles/80953Test

المؤلفون: Grgic, Olja, Gazzara, Matthew R., Chesi, Alessandra, Medina-Gomez, Carolina, Cousminer, Diana L., Mitchell, Jonathan A., Prijatelj, Vid, de Vries, Jard, Shevroja, Enisa, McCormack, Shana E., Kalkwarf, Heidi J., Lappe, Joan M., Gilsanz, Vicente, Oberfield, Sharon E., Shepherd, John A., Kelly, Andrea, Mahboubi, Soroosh, Faucz, Fabio R., Feelders, Richard A., de Jong, Frank H., Uitterlinden, Andre G., Visser, Jenny A., Ghanem, Louis R., Wolvius, Eppo B., Hofland, Leo J., Stratakis, Constantine A., Zemel, Babette S., Barash, Yoseph, Grant, Struan F.A., Rivadeneira, Fernando

المصدر: Grgic , O , Gazzara , M R , Chesi , A , Medina-Gomez , C , Cousminer , D L , Mitchell , J A , Prijatelj , V , de Vries , J , Shevroja , E , McCormack , S E , Kalkwarf , H J , Lappe , J M , Gilsanz , V , Oberfield , S E , Shepherd , J A , Kelly , A , Mahboubi , S , Faucz , F R , Feelders , R A , de Jong , F H , Uitterlinden , A G , Visser ....

وصف الملف: application/pdf

الإتاحة: https://doi.org/10.1038/s42003-021-02774-yTest
https://pure.eur.nl/en/publications/087a3c84-a690-4612-ac66-b3cd9ff70fb8Test
https://pure.eur.nl/ws/files/43409547/CYP11B1_variants_influence_skeletal_maturation_via_alternative_splicing.pdfTest
http://www.scopus.com/inward/record.url?scp=85118643896&partnerID=8YFLogxKTest

المؤلفون: Le, Trang T., Himmelstein, Daniel S., Hippen, Ariel A., Gazzara, Matthew R., Greene, Casey S.

المساهمون: Gordon and Betty Moore Foundation

المصدر: Cell Systems ; volume 12, issue 9, page 900-906.e5 ; ISSN 2405-4712

مصطلحات موضوعية: Cell Biology, Histology, Pathology and Forensic Medicine

الإتاحة: https://doi.org/10.1016/j.cels.2021.07.007Test
https://api.elsevier.com/content/article/PII:S2405471221002854?httpAccept=text/xmlTest
https://api.elsevier.com/content/article/PII:S2405471221002854?httpAccept=text/plainTest