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479 results for “genomic evolution”
Data from: Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.
Data and code for "Genomic–transcriptomic evolution in lung cancer and metastasis"
<p>Processed data and code to generate all main figures and extended data figures for the manuscript "Genomic–transcriptomic evolution in lung cancer and metastasis" (transcriptomics_scripts_data_20230330.zip) as well as data and code to run the ensemble machine learning classifier to predict metastatic potential (pred_met_2023.zip).</p>
Data from: A genome for gnetophytes and early evolution of seed plants
Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes. Comparative analysis of the G. montanum genome with other gymnosperm genomes unveiled some remarkable and distinctive genomic features, such as a diverse assemblage of retrotransposons with evidence for elevated frequencies of elimination rather than accumulation, considerable differences in intron architecture, including both length distribution and proportions of (retro) transposon elements, and distinctive patterns of proliferation of functional protein domains. Furthermore, a few gene families showed Gnetum-specific copy number expansions (for example, cellulose synthase) or contractions (for example, Late Embryogenesis Abundant protein), which could be connected with Gnetum's distinctive morphological innovations associated with their adaptation to warm, mesic environments. Overall, the G. montanum genome enables a better resolution of ancestral genomic features within seed plants, and the identification of genomic characters that distinguish Gnetum from other gymnosperms.
Longitudinal Assessment of Genomic Alterations and Clonal Evolution in ALK-positive NSCLC (Galileo Project)
ClinicalTrials.gov study NCT06234579. IPD Sharing: NO. Countries: 1. Publications: 0.
Genomic Evolution of Metastasis in Gastric Cancer
ClinicalTrials.gov study NCT05061082. IPD Sharing: NO. Countries: 1. Publications: 0.
A Genomic Analysis of Evolution of Epithelia Ovarian Tumors
ClinicalTrials.gov study NCT03742388. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Centromere evolution in Brachypodium genomes with different polyploid levels
GEO Series GSE157143. Brachypodium distachyon; Brachypodium hybridum; Brachypodium stacei. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Reorganization of 3D Genome Structure May Contribute to Gene Regulatory Evolution in Primates
GEO Series GSE122520. Homo sapiens; Pan troglodytes. 8 samples. Type: Other.
Longitudinal Genome Wide Analysis of Chronic Lymphocytic Leukemia Reveals Complex Evolution of Clonal Architecture at Disease Progression and at the Time of Relapse
GEO Series GSE30217. Homo sapiens. 54 samples. Type: Genome variation profiling by genome tiling array.
Evolution of genome architecture in Archaea: spontaneous generation of a new chromosome in Haloferax volcanii by homologous recombination
GEO Series GSE108201. Haloferax volcanii. 4 samples. Type: Other.
Comparative genomic analyses of the human NPHP1 locus reveal complex genomic architecture and its regional evolution in primates
GEO Series GSE73962. Papio anubis; Macaca mulatta; Gorilla gorilla; Pongo abelii; Homo sapiens; Pan troglodytes. 32 samples. Type: Genome variation profiling by genome tiling array.
The consequences of rapid mating system evolution in crucifer genomes
GEO Series GSE45518. Capsella rubella; Capsella grandiflora. 18 samples. Type: Expression profiling by high throughput sequencing.
Data from: A genome for gnetophytes and early evolution of seed plants
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Data from: Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits
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Data from: Monophyletic origin and evolution of the largest crucifer genomes
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Data from: Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats
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Epigenomic maps of the rainbow trout reveal epiQTL signatures of genetic selection and regulatory elements involved in controlling gene expression and genome evolution
GEO Series GSE245212. Oncorhynchus mykiss. 78 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes
GEO Series GSE198194. Isoetes sinensis. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Comparative 3D genomic architectures elucidate the function of the adaptive human-specific inversions in human brain evolution
GEO Series GSE213693. Macaca mulatta; Homo sapiens. 2 samples. Type: Other.
Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes
GEO Series GSE198196. Isoetes sinensis. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
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.