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87 results for “human assemblies”
Recent and rapid assembly of an island species–area relationship threatened by human disturbance
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Data for: Endo-lysosomal assembly variations among Human Leukocyte Antigen class I (HLA-I) allotypes
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De novo genome assembly of human cell line CHM13 nanopore ultra-long reads using Shasta
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Eigen scores for human genome assembly GRCh38 Part 1 (Chr12 - Chr22)
<p>Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike many existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations.</p>
Eigen scores for human genome assembly GRCh38 Part 2 (Chr6 - Chr11)
<p>Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike many existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations.</p>
Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features"
<p>Data for "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features" (submitted to Nature Communications)</p>
Data from: Contrasting trait assembly patterns in plant and bird communities along environmental and human-induced land-use gradients
Human-driven environmental changes can induce marked shifts in the functional structure of biological communities with possible repercussion on important ecosystem functions and services. At the same time it remains unclear to which extent these changes may differently affect various types of organisms. We investigated species richness and community functional structure of species assemblages at the landscape scale (1km2 plots) for two contrasting model taxa, i.e., plants (producers and sessile organisms) and birds (consumers and mobile organisms), along topography, climate, landscape heterogeneity, and land-use (agriculture and urbanization) gradients in a densely populated region of Switzerland. Our study revealed that agricultural and urban land uses drove marked shifts in the functional structure of biological communities compared to changes along climate and topography gradients, especially for plants, while for birds these changes were comparable. Agricultural and urban land uses enhanced divergence in traits related to resource use for birds (diet and nesting), growth forms, dispersal, and reproductive traits for plants, while it induced convergence in vegetative plant traits (plant height and leaf dry matter content). These results suggest that contrasting assembly patterns may arise within and across taxonomic groups along the same environmental gradients as result of distinct underlying processes and 'organism-specific' environmental perceptions. Our results further suggest a potential homogenization of biological communities, as well as low functional diversity and redundancy levels of bird assemblages in our human-dominated study region. This might potentially compromise the maintenance of key ecological processes under future environmental changes.
Data from: Assembling a species–area curve through colonization, speciation and human-mediated introduction
Aim: The fundamental biogeographical processes of colonization, speciation and extinction shape island biotas in space–time. On oceanic islands, area and isolation affect these processes and resulting biodiversity patterns. In the Anthropocene, a new human-mediated colonization dynamic is altering insular ecosystems world-wide. Here, we test predictions about the roles of archipelago area and isolation in structuring ant diversity patterns through effects on both natural and anthropogenic biogeographical processes. Location: Tropical Pacific islands. Methods: We compiled a comprehensive data set of ant faunal compositions across tropical Pacific archipelagos. Using regression analysis we evaluated the bivariate and interactive effects of area and isolation on the number of colonizing lineages, native species, endemic species, exotic species and total richness in the archipelago. Results: There is a strong species–area effect and a much more modest isolation effect on total ant species richness across the Pacific archipelagos. The number of colonizing lineages of each archipelago is strongly driven by the isolation of the archipelago. Endemic species are present in large archipelagos of low and intermediate isolation. The most remote archipelagos are nearly devoid of endemic lineages and their ant faunas are largely composed of Pacific Tramp species and exotics brought from outside the Pacific region. Main conclusions: The prominent species–area curve in Pacific ants emerged over time through multiple processes. The colonization of lineages is determined primarily by isolation, with few or no lineages reaching remote archipelagos. Cladogenesis mediates the isolation effect and increases the area effect through the differential radiation of lineages in large archipelagos. In the Anthropocene, the assembly of the species–area relationship has accelerated dramatically through human-mediated colonization. Overall, our results support a view that species–area curves reflect regulating limits on species richness that scale with area, but that multiple biogeographical processes can occur to achieve these limits.
Inversion polymorphism in a complete human genome assembly
<p>Supplementary data including code for an journal article titled 'Inversion polymorphism in a complete human genome assembly'.</p>
Data from: Assembling a species–area curve through colonization, speciation and human-mediated introduction
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Co-assembly of 98TBs of metagenomes from human gut using exascale assembler MetaHipMer
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Data from: Contrasting trait assembly patterns in plant and bird communities along environmental and human-induced land-use gradients
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Eigen scores for human genome assembly GRCh37 Part 3 (Chr9 - Chr16)
<p>Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike many existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations.</p>
Eigen scores for human genome assembly GRCh37 Part 2 (Chr4 - Chr8)
<p>Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike many existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations.</p>
MACIE scores for human genome assembly GRCh37 Part 2 (Chr4 - Chr7)
<p>MACIE (Multi-dimensional Annotation Class Integrative Estimation) is an unsupervised multivariate mixed model framework to assess multi-dimensional functional impacts for both coding and non-coding variants in the human genome. MACIE integrates a variety of functional annotations, including protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics, and estimates the joint posterior probabilities of each genetic variant being functional.</p> <p>For each non-coding and synonymous coding variant, the MACIE score is a vector of length 4, representing the estimated joint posterior probabilities of “not evolutionarily conserved and regulatory functional” (MACIE01); “evolutionarily conserved and not regulatory functional” (MACIE10); “not evolutionarily conserved and not regulatory functional” (MACIE00); “both evolutionarily conserved and regulatory functional (MACIE11). MACIE_conserved is the estimated posterior probability of “evolutionarily conserved”, which is the sum of MACIE10 and MACIE11; MACIE_regulatory is the estimated posterior probability of “regulatory functional”, which is the sum of MACIE01 and MACIE11; MACIE_anyclass is the estimated posterior probability of “evolutionarily conserved” or “regulatory functional”, which is the sum of MACIE01, MACIE10, and MACIE11.</p>
Yak k-mer dumps for partition human chrX/Y in de novo assemblies
<p>See <a href="https://github.com/lh3/yak">yak</a> for details.</p>
Data from: Wnt5a regulates the assembly of human adipose-derived stromal vascular fraction-derived microvasculatures
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Data from: Genomic characterization of large heterochromatic gaps in the human genome assembly
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RNASeq of total RNA isolated from self-assembling co-cultures of primary human hepatocytes (SACC-PHHs) mono-infected with HBV, co-infected with HBV/HDV, or uninfected at 8 and 28 days post-infection
GEO Series GSE112118. Homo sapiens; Mus musculus. 44 samples. Type: Expression profiling by high throughput sequencing.
Selective Translation Complex Profiling in yeast and human Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes [Yeast]
GEO Series GSE139130. Saccharomyces cerevisiae. 16 samples. Type: Expression profiling by high throughput sequencing; Other.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.