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19,342 results for “sequence”
Scalable mixed model approaches for set-based association studies on large-scale categorical data analysis and its application to 450k exome sequencing data in UK Biobank
<p>The ongoing release of large-scale sequencing data in the UK Biobank allows for identifying associations between rare variants and complex traits. SAIGE-GENE+ is a valid approach to conducting set-based association tests for quantitative and binary traits. However, for ordinal categorical phenotypes, applying SAIGE-GENE+ with treating the trait as quantitative or binarizing the trait can cause inflated type I error rates or power loss. In this study, we propose a novel method for rare-variant association tests, POLMM-GENE, in which a proportional odds logistic mixed model was used to characterize ordinal categorical phenotypes while adjusting for sample relatedness. POLMM-GENE fully utilizes the categorical nature of phenotypes and thus can well control type I error rates while remaining powerful. In the analyses of UK Biobank 450k whole exome-sequencing data for 5 ordinal categorical traits, POLMM-GENE identified 54 gene-phenotype associations.</p>
FIGURE 1 in Additional description on morphology of the Misol snake eel from Taiwan, with four verified barcodes of life sequences
FIGURE 1. Lateral view of Yirrkala misolensis. (A) Before fixing, TOU-AE7866, 351 mm TL with broken tail, Ke-tzu-liao fish market, Kaohsiung, Taiwan. Scale represents 10 mm. The position of dorsal fin origin and vent marked with red arrows. The center is a close-up view of cephalic part (Photo by W. -C. Huang). (B) When preserved, NMMB-P12003, 486 mm TL, mature female, Dong-gang fish market, Ping-tung, Taiwan, the position of dorsal fin origin and vent marked with pins.
FIGURE 3 in Additional description on morphology of the Misol snake eel from Taiwan, with four verified barcodes of life sequences
FIGURE 3. Neighbor-joining tree based on CO1 sequences, constructed using the specimens mentioned in the present study and 1 congener from NCBI. The bar indicates the evolutionary distances which were computed using the Kimura 2-parameter method with 10,000 bootstrap-replicated.
FIGURE 2 in Additional description on morphology of the Misol snake eel from Taiwan, with four verified barcodes of life sequences
FIGURE 2. Illustration of Yirrklala misolensis, NMMB-P12003, 486 mm TL, mature female, Dong-gang fish market, Pingtung, Taiwan. (A) Lateral view of head, arrows show the position of frontal pore and supratemporal pore. (B) Dentition.
Combination of whole genome sequencing and Supervised Machine Learning provides unambiguous identification of enterohemorrhagic Escherichia coli in raw milk
<p>These dataset are used in the "rename_list_of_groups.ipynb" notebook</p>
Data set for "The effect of pulling and twisting forces on chameleon sequence peptides"
<p>Data set for the publication "The effect of pulling and twisting forces on chameleon sequence peptides"<br> <br> The data contains all energy landscapes explored, structures extracted and analysed, and the necessary utility scripts, written by James Meadows. The README details which data is in each directory. The image directory contains the disconnectivity graphs associated with this data.</p>
Aligned and curated mtDNA sequences from: Ancient DNA reveals interstadials as a driver of common vole population dynamics during the last glacial period
<p><strong><span>Aim: </span></strong><span>Many species experienced population turnover and local extinction during the Late Pleistocene. In the case of megafauna, it remains challenging to disentangle climate change and the activities of Palaeolithic hunter-gatherers as the main cause. In contrast, the impact of humans on rodent populations </span><span>is likely to be negligible. This study investigated which climatic and/or environmental factors affect the population dynamics of the common vole. </span><span>This temperate rodent is widespread across Europe and was one of the most abundant small mammal species throughout the Late Pleistocene.</span></p> <p><span><strong>Location:</strong> </span><span>Europe</span></p> <p><strong><span>Taxon: </span></strong><span>Common vole (<em>Microtus arvalis</em>)</span></p> <p><strong><span>Methods: </span></strong><span>We generated a dataset comprised of a 4.2-kb-long fragment of mitochondrial DNA (mtDNA) from 148 ancient and 51 modern specimens sampled from multiple localities across Europe and covering the last 60 thousand years (ka). We used Bayesian inference to reconstruct their phylogenetic relationships and to estimate the age of the specimens that were not directly dated.</span></p> <p><span><strong>Results:</strong> </span><span>We estimated the time to the most recent common ancestor of all last glacial and extant common vole lineages to be 90 ka ago and the divergence of the main mtDNA lineages present in extant populations to between 55 and 40 ka ago, which is earlier than previous estimates. </span><span>We detected several lineage turnovers in Europe during the period of high climate variability at the end of Marine Isotope Stage 3 (MIS 3; 57–29 ka ago) in addition to those found previously around the Pleistocene/Holocene transition.</span><span> </span><span>In contrast, data from the Western Carpathians suggest continuity throughout the Last Glacial Maximum (LGM), even at high latitudes.</span></p> <p><strong><span>Main conclusions: </span></strong><span>The main factor affecting the common vole populations during the last glacial period was the decrease in open habitat during the interstadials, whereas </span><span>climate </span><span>deterioration </span><span>during</span><span> the LGM had little impact on population dynamics. This suggests that the rapid environmental change rather than other factors was the major force shaping the histories of the Late Pleistocene faunas.</span></p>
CRAG: De novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing
<p><strong>Supplementary dataset for the manuscript:</strong></p> <p><strong>CRAG: De novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing</strong></p> <p> Xionghui Zhou1,*, Haizi Zheng1,*, Hailu Fu1,*, Kelsey L. Dillehay McKillip2-3, Susan M. Pinney2,4, Yaping Liu1-2,5-7 #</p> <p>Affiliations:</p> <p>1 Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229</p> <p>2 University of Cincinnati Cancer Center, Cincinnati, OH 45229</p> <p>3 Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45229</p> <p>4 Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45229</p> <p>5 Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229</p> <p>6 Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229</p> <p>7 Department of Electrical Engineering and Computing Sciences, University of Cincinnati College of Engineering and Applied Science, Cincinnati, OH 45229</p> <p>* These authors contributed equally</p> <p># Email: lyping1986@gmail.com</p>
Fig. 3 in ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies
Fig. 3. Maximum likelihood trees and population structuring of Apatania (A) and Limnephilus (B) based on ddRAD SNP data.ML trees were inferred from RAxML analysis with 1,000 bootstrap replicates. The bootstrap values are indicated near the branches. Results of population STRUCTURE analyses with posterior probability plots of individual assignments to the inferred genetic clusters for K = 6 and 7 for Apatania and K = 4 for Limnephilus.
Fig. 2 in ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies
Fig. 2. Maximum likelihood trees based on mitochondrial COI sequences of Apatania (A) and Limnephilus (B). The bootstrap values are indicated near the branches (only shown for nodes supported with more than 50% of BS).
Geodetic Model of 2017 Kerman earthquake sequences estimated from joint inversion of InSAR and offset tracking techniques
<p>We upload here the inSAR and Pixel offset tracking results obtained based on Radar, Sentinel-1, PlanetScope, and Sentinel-2 satellite data. </p>
Figure 5 in Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences
Figure 5. Chronogram for major clades of Brachycera estimated by BEAST 1.8.4 based on 107-taxon_PCG_nt12 (scale on x-axis in mya). At the branching nodes, numbers show the estimated divergence times and blue bars represent the time interval for 95% probability of actual node age.
Figure 4 in Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences
Figure 4. The simplified ML tree inferred from the dataset 107-taxon_PCG_aa by using IQ-TREE, under the data partitions and best-fitting models selected by PartitionFinder 2. Node numbers show the bootstrap support values (> 50). The insect pictures are provided by Yuqiang Xi.
Figure 1 in Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences
Figure 1. Representations of previous hypotheses for the relationships among major groups of Brachycera inferred from morphologically-based or molecular studies by authors cited. A, Woodley (1989) based on morphological data; B, Wiegmann et al. (2003) based on morphological and molecular data; C, Yeates (2002) based on morphological data; D, Wiegmann et al. (2011) based on morphological and molecular data; E, Shin et al. (2018) based on molecular data; F, Bayless et al. (2021) based on molecular data.
Figure 3. The Bayesian tree inferred from the dataset 107 in Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences
Figure 3. The Bayesian tree inferred from the dataset 107-taxon_PCG_nt12 using PhyloBayes, under the site-heterogeneous mixture model (CAT-GTR). Node numbers show the posterior probability values (> 0.90). The insect pictures are provided by Yuqiang Xi.
Figure 2 in Phylogenetic relationships of Brachycera (Insecta: Diptera) inferred from mitochondrial genome sequences
Figure 2. The simplified ML tree inferred from the dataset 187-taxon_PCG_nt123 using IQ-TREE, under the data partitions and best-fitting models selected by PartitionFinder 2. Node numbers show the bootstrap support values (> 50). For the full tree, see Supporting Information, Fig. S3A. The insect pictures are provided by Yuqiang Xi.
Sequence data of 190 tea plantations soil microorganisms
<p>The file contains 190 clean fastq data for soil samples from 19 different types of tea plantations in two districts of Pu'er city, which designed for the study of soil bacterial communities .The tea plantations all belong to Pu'er city, Yunnan province from China.</p>
Methods for structural variant detection with long-read sequencing data
<p>SV calls from different long-read based SV callers on sequencing data. SV results evaluated in Methods for structural variant detection with long-read sequencing data.</p> <p>NA24385_Pacbio_HiFi -> HiFi_L1 in paper</p> <p>NA24385_Pacbio_MtSinai -> CLR_L1 in paper</p> <p>NA24385_Pacbio_CLR_SRX7668835 -> CLR_L2 in paper</p> <p>NA24385_Pacbio_CLR_SRX6719924 -> CLR_L3 in paper</p> <p>NA24385_ONT_Promethion -> Nano_L1 in paper</p>
Data from: Haplotype sequence collection of ABO blood group alleles by long-read sequencing reveals putative A1-diagnostic variants
<p>In the era of blood group genomics, reference collections of complete and fully-resolved blood group gene alleles have gained high importance. For most blood groups, however, such collections are currently lacking, as resolving full-length gene sequences as haplotypes (i.e. separated maternal/paternal origin) remains exceedingly difficult with both Sanger and short-read next-generation sequencing. Using the latest third-generation long-read sequencing, we generated a collection of fully-resolved sequences for all six main <em>ABO</em> allele groups: <em>ABO</em>*<em>A1</em>/<em>A2</em>/<em>B</em>/<em>O.01.01</em>/<em>O.01.02</em>/<em>O.02</em>. We selected 77 samples from an <em>ABO</em> genotype dataset (n=25,200) of serologically-typed Swiss blood donors. The entire <em>ABO</em> gene was amplified in two overlapping long-range PCRs (covering ~23.6 kb) and sequenced by long-read Oxford Nanopore sequencing. For quality validation, two samples per <em>ABO</em> group were re-sequenced using Illumina and PacBio technology. All 154 full-length <em>ABO</em> sequences were resolved as haplotypes. We observed novel, distinct sequence patterns for each <em>ABO</em> group. Most genetic diversity was found between, not within, <em>ABO</em> groups. Phylogenetic tree and haplotype network analyses highlighted distinct clades of each <em>ABO</em> group. Strikingly, our data uncovered four genetic variants putatively specific for <em>ABO</em>*<em>A1</em>, for which direct diagnostic targets are currently lacking. We validated <em>A1</em>-diagnostic potential using whole-genome data (n=4,872) of a multi-ethnic cohort. Overall, our sequencing strategy proved powerful for producing high-quality <em>ABO</em> haplotypes and holds promise for generating similar collections for other blood groups. The publicly available collection of 154 haplotypes will serve as a valuable resource for molecular analyses of <em>ABO</em>, as well as studies about the function and evolutionary history of <em>ABO</em>.</p>
Supplementary material 1 from: Conrado AC, Arruda H, Stanton DWG, James SW, Kille P, Brown G, Silva E, Dupont L, Taheri S, Morgan AJ, Simões N, Rodrigues A, Montiel R, Cunha L (2017) The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning. ZooKeys 688: 1-13. https://doi.org/10.3897/zookeys.688.13721
Inferred secondary structure of 22 tRNA genes in the mitochondrial DNA of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata). :
ScienceDex guides
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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.