Tag: Zenodo
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria
Miyakawa, T., Matsuzawa, H., Matsuhashi, M. & Sugino, Y. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112, 950–958 (1972). Article CAS PubMed PubMed Central Google Scholar Ayala, J. A., Garrido, T., De Pedro,…
Population-level variation in enhancer expression identifies disease mechanisms in the human brain
Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). PubMed Central Article CAS Google Scholar Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS PubMed PubMed Central …
Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation
Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018). CAS PubMed PubMed Central Google Scholar Yizhak, K. et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science 364, eaaw0726 (2019). CAS PubMed PubMed Central Google Scholar Yokoyama, A….
Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data
Visscher, P. M. et al. 10 years of GWAS discovery: biology, function, and translation. Am. J. Hum. Genet. 101, 5–22 (2017). CAS PubMed PubMed Central Article Google Scholar Hekselman, I. & Yeger-Lotem, E. Mechanisms of tissue and cell-type specificity in heritable traits and diseases. Nat. Rev. Genet. 21, 137–150 (2020)….
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…
ZC2 RNAseq | Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.6412442 Markdown [](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
AxelRosendahlHuber/Genotoxin_assay: Archiving code and data: Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.6424654 Markdown [](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
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,…
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,…
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…
Xena TCGA TARGET TCGx RNAseq Data
Zenodo DOI Badge DOI 10.5281/zenodo.6323594 Markdown [](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
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…
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…
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…
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….
scikit-survival | Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.5831584 Markdown [](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
intermine/intermine: InterMine 5.0.6 | Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.5827966 Markdown [](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
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….
Bacting | Zenodo
Zenodo DOI Badge DOI 10.5281/zenodo.5506884 Markdown [](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
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…
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…
