Tag: Zenodo

Tempo and drivers of plant diversification in the European mountain system

Hughes, C. E. & Atchinson, G. W. The ubiquity of alpine plant radiations: from the Andes to the Hengduan Mountains. N. Phytol. 207, 275–282 (2015). Article  Google Scholar  Rahbek, C. et al. Humboldt’s enigma: what causes global patterns of mountain biodiversity? Science 365, 1108–1113 (2019). ADS  CAS  PubMed  Article  Google…

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ZC2 RNAseq | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.6412442 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg)](https://doi.org/10.5281/zenodo.6412442) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg :target: doi.org/10.5281/zenodo.6412442 HTML <a href=”https://doi.org/10.5281/zenodo.6412442″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6412442.svg Target URL doi.org/10.5281/zenodo.6412442 Read more here: Source link

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AxelRosendahlHuber/Genotoxin_assay: Archiving code and data: Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.6424654 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6424654.svg)](https://doi.org/10.5281/zenodo.6424654) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6424654.svg :target: doi.org/10.5281/zenodo.6424654 HTML <a href=”https://doi.org/10.5281/zenodo.6424654″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6424654.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6424654.svg Target URL doi.org/10.5281/zenodo.6424654 Read more here: Source link

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Accurate assembly of multi-end RNA-seq data with Scallop2

Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010). Article  Google Scholar  Guttman, M. et al. Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28,…

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Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages

Díaz, S. et al. Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES, 2019). Fisher, R. A. The correlation between relatives on the supposition of Mendelian inheritance. Earth Environ. Sci. Trans. R. Soc. Edinb. 52,…

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Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM

Wu, W. et al. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin. Microbiol. Rev. 32, e00115–18 (2019). Yong, D. et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14…

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Xena TCGA TARGET TCGx RNAseq Data

Zenodo DOI Badge DOI 10.5281/zenodo.6323594 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg)](https://doi.org/10.5281/zenodo.6323594) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg :target: doi.org/10.5281/zenodo.6323594 HTML <a href=”https://doi.org/10.5281/zenodo.6323594″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.6323594.svg Target URL doi.org/10.5281/zenodo.6323594 Read more here: Source link

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METASnake: a Snakemake workflow to facilitate…

Introduction As sequencing technology has become cheaper and more readily accessible, the need for the increased computational capacity to process these data has become apparent. In particular, high-throughput sequencing has been particularly useful when applied to the field of metagenomics. Substantial effort has been devoted to developing software and computational…

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Accelerating minimap2 for long-read sequencing applications on modern CPUs

Chaisson, M. J. et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat. Commun. 10, 1–16 (2019). Article  Google Scholar  Conesa, A. et al. A survey of best practices for RNA-seq data analysis. Genome Biol. 17, 1–19 (2016). Article  Google Scholar  Beyter, D. et al. Long-read sequencing of…

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Multi-ancestry eQTL meta-analysis of human brain identifies candidate causal variants for brain-related traits

1. Jansen, I. E. et al. Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat. Genet. 51, 404–413 (2019). CAS  PubMed  PubMed Central  Google Scholar  2. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed…

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Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….

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scikit-survival | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5831584 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg)](https://doi.org/10.5281/zenodo.5831584) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg :target: doi.org/10.5281/zenodo.5831584 HTML <a href=”https://doi.org/10.5281/zenodo.5831584″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg Target URL doi.org/10.5281/zenodo.5831584 Read more here: Source link

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intermine/intermine: InterMine 5.0.6 | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5827966 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg)](https://doi.org/10.5281/zenodo.5827966) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg :target: doi.org/10.5281/zenodo.5827966 HTML <a href=”https://doi.org/10.5281/zenodo.5827966″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg Target URL doi.org/10.5281/zenodo.5827966 Read more here: Source link

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Decoding gene regulation in the fly brain

1. Li, H. et al. Classifying Drosophila olfactory projection neuron subtypes by single-cell RNA sequencing. Cell 171, 1206–1220 (2017). CAS  PubMed  PubMed Central  Google Scholar  2. Davie, K. et al. A single-cell transcriptome atlas of the aging Drosophila brain. Cell 174, 982–998 (2018). CAS  PubMed  PubMed Central  Google Scholar  3….

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Bacting | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5506884 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5506884.svg)](https://doi.org/10.5281/zenodo.5506884) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5506884.svg :target: doi.org/10.5281/zenodo.5506884 HTML <a href=”https://doi.org/10.5281/zenodo.5506884″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5506884.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5506884.svg Target URL doi.org/10.5281/zenodo.5506884 Read more here: Source link

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The population frequency of human mitochondrial DNA variants is highly dependent upon mutational bias

Abstract Next-generation sequencing can quickly reveal genetic variation potentially linked to heritable disease. As databases encompassing human variation continue to expand, rare variants have been of high interest, since the frequency of a variant is expected to be low if the genetic change leads to a loss of fitness or…

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Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Significance Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is…

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