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3,650 results for “antibody”
AntiRef: reference clusters of human antibody sequences
<p><strong>Motivation:</strong> Biases in the human antibody repertoire result in publicly available antibody sequence datasets containing many duplicate or highly similar sequences. These redundant sequences are a barrier to rapid similarity searches and reduce the efficiency with which these datasets can be used to train statistical or machine learning models of human antibodies. Identity-based clustering provides a solution, however, the extremely large size of available antibody repertoire datasets make such clustering operations computationally intensive and potentially out of reach for many scientists and researchers who would benefit from such data.</p> <p><strong>Results:</strong> AntiRef (Antibody Reference Clusters), which is modeled after UniRef, provides clustered datasets of filtered human antibody sequences. Starting from a dataset of ~335M unique, full-length, productive human antibody sequences from the Observed Antibody Space repository, several AntiRef cluster sets were generated. Due to the modular nature of recombined antibody genes, the clustering thresholds used by UniRef (100, 90 and 50 percent identity) to cluster general protein sequences are suboptimal for antibody clustering. AntiRef provides reference antibody sequence datasets clustered at a range of relevant identity thresholds: 100, 99, 98, 96, 94, 92 and 90 percent. AntiRef90, which uses the lowest clustering threshold of any AntiRef dataset, is roughly one-third the size of the filtered input dataset and less than half the size of the non-redundant AntiRef100.</p> <p><strong>Datasets:</strong> AntiRef comprises a series of datasets, each representing one of several clustering thresholds. AntiRef datasets were generated by a nested clustering procedure similar to UniRef which, proceeding in order of decreasing stringency, clusters the representative sequences from the preceding round of clustering. AntiRef datasets can be found at the following links:</p> <ul> <li><a href="https://doi.org/10.5281/zenodo.7474657">AntiRef100</a>: representative sequences resulting from clustering all filtered AntiRef input sequences at 100% identity.</li> <li><a href="https://doi.org/10.5281/zenodo.7475961">AntiRef99</a>: representative sequences resulting from clustering AntiRef100 at 99% identity.</li> <li><a href="https://doi.org/10.5281/zenodo.7476040">AntiRef98</a>: representative sequences resulting from clustering AntiRef99 at 98% identity.</li> <li><a href="https://doi.org/10.5281/zenodo.7487182">AntiRef96</a>: representative sequences resulting from clustering AntiRef98 at 96% identity.</li> <li><a href="https://doi.org/10.5281/zenodo.7487199">AntiRef94</a>: representative sequences resulting from clustering AntiRef96 at 94% identity.</li> <li><a href="https://doi.org/10.5281/zenodo.7487264">AntiRef92</a>: representative sequences resulting from clustering AntiRef94 at 92% identity.</li> <li><a href="https://doi.org/10.5281/zenodo.7487298">AntiRef90</a>: representative sequences resulting from clustering AntiRef92 at 90% identity.</li> </ul> <p><strong>Files:</strong> The following files are included in the primary AntiRef data repository:</p> <ul> <li><em>antiref_cluster-manifest.csv.gz:</em> A compressed CSV file containing the cluster assignments for every sequence in the AntiRef input dataset. For each AntiRef round, cluster names correspond to the sequence ID of the representative sequence (as determined by MMSeqs2). The nested clustering process conserves cluster names between iterations, meaning the clustering lineage of any sequence can easily be traced across all AntiRef datasets.</li> <li><em>download_heavy.txt</em>: A plain text file (generated by the <a href="http://opig.stats.ox.ac.uk/webapps/oas/">Observed Antibody Space</a>) containing the commands necessary to download all antibody heavy chain sequences used to create AntiRef.</li> <li><em>download_light.txt:</em> A plain text file (generated by the <a href="http://opig.stats.ox.ac.uk/webapps/oas/">Observed Antibody Space</a>) containing the commands necessary to download all antibody light chain sequences used to create AntiRef.</li> </ul> <p><strong>Code:</strong> All code used to generate AntiRef (data download, filtering, and clustering) is available under the MIT license on <a href="http://www.github.com/briney/antiref">GitHub</a>.</p>
Dataset for the Moesin antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Moesin protein, encoded by the MSN gene. The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.4724169">https://doi.org/10.5281/zenodo.4724169</a>).</em></p>
Dataset for the Midkine antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterization antibodies for the Midkine protein, encoded by the MDK gene. The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.5644321">https://doi.org/10.5281/zenodo.5644321</a>), and published on F1000Research (<a href="https://doi.org/10.12688/f1000research.130587.4">https://doi.org/10.12688/f1000research.130587.4</a></em><em>).</em></p>
Dataset for the Secreted frizzled-related protein 1 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Secreted frizzled-related protein 1 protein, encoded by the SFRP1 gene. The original study is also available on Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.6370454">https://doi.org/10.5281/zenodo.6370454</a>).</em></p>
Dataset for the Transmembrane protein 106B antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Transmembrane protein 106B protein, encoded by the TEM106b gene. The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.7459629">https://doi.org/10.5281/zenodo.7459629</a>).</em></p>
Dataset for the TDP-43 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing antibodies for the TDP-43 protein. The study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.7249802">https://doi.org/10.5281/zenodo.7249802</a>).</em></p>
Dataset for the Profilin-1 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Profilin-1 protein. The study is available on Zenodo (<a href="https://doi.org/10.5281/zenodo.7249258">https://doi.org/10.5281/zenodo.7249258</a>).</em></p>
Dataset for the Ubiquilin-2 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Ubiquilin-2 protein. The study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.7459541">https://doi.org/10.5281/zenodo.7459541</a>).</em></p>
Dataset for the Sequestosome-1 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Sequestosome-1 protein. The study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.4818440">https://doi.org/10.5281/zenodo.4818440</a>).</em></p>
Dataset for Superoxide dismutase 1 Cu/Zn (SOD1) antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Superoxide dismutase 1 Cu/Zn (SOD1) protein. The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.5061103">https://doi.org/10.5281/zenodo.5061103</a>).</em></p>
Dataset for Optineurin antibody screening study
<p>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Optineurin protein. The study is available on Zenodo (https://doi.org/10.5281/zenodo.4730992).</p>
Dataset for the hVPS35 antibody screening study
<p>This project contains the following underlying data included in a study aiming at characterizing antibodies for the hVPS35 protein. The study is available on Zenodo (https://doi.org/10.5281/zenodo.7671730).</p>
Dataset for the TIA1 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing antibodies for the TIA1 protein, encoded by the TIA1 gene. The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.7671718">https://doi.org/10.5281/zenodo.7671718</a>).</em></p>
Dataset for the Apolipoprotein E antibody screning study
<p>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Apolipoprotein E protein. The study is available on Zenodo (https://doi.org/10.5281/zenodo.7249055).</p>
[Dataset] Pattern and repeatability of ascarid-specific antigen excretion through chicken faeces, and the diagnostic accuracy of copro-antigen measurements as compared with McMaster egg counts and plasma and egg yolk antibody measurements in laying hens
<p>Comprehensive data examining the pattern and repeatability of ascarid-specific antigen excretion in chicken faeces and the diagnostic accuracy of copro-antigen measurements compared to McMaster egg counts and antibody measurements in laying hens.</p> <p>The dataset consists of observations and measurements obtained from a controlled study involving laying hens infected with mixed <em>Ascaridia galli</em> and<em> Heterakis gallinarum</em>. A total of 179 individual hens were monitored between wpi 2 and 18 and their fecal samples/blood samples were collected at specific time points. Faecel samples were repeatedly collected four(4) consecutive times in one wpi.Hence antigen measurements is 4 X 179 = 716 measurements</p>
Dataset for the Amyloid-beta precursor protein antibody screening study
<p>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Amyloid-beta precursor protein. The study is available on Zenodo (https://doi.org/10.5281/zenodo.7971926).</p>
Dataset for the Charged multivesicular body protein 2b antibody screening study
<p>This project contains the following underlying data included in a study which characterized antibodies for Charged multivesicular body protein 2b. The study is available on Zenodo (https://doi.org/10.5281/zenodo.6370501).</p>
Dataset for the Ras-related protein Rab5A antibody screening study
<p>This project contains the underlying data included in a study which characterized eleven commercially-available antibodies for Ras-related protein Rab5A. The study is also available on Zenodo (https://doi.org/10.5281/zenodo.8356241).</p>
Dataset for the Rab-1A and Rab-1B antibody screening study
<p>This project contains the underlying data included in a study which characterized twelve commercially-available antibodies for the two Rab1 isoforms, Rab-1A and Rab-1B. Seven antibodies were intended to target Rab-1A and five antibodies intended to target Rab-1B. The study is also available on Zenodo (https://doi.org/10.5281/zenodo.8356353).</p>
Dataset SeBluCo study: SARS-CoV-2-antibodies among German blood donors 2020 – 2022, a repetitive cross-sectional study
<p>The dataset is the result of a repetitive cross-sectional study in 28 regions in Germany on SARS-CoV-2 antibodies in residual samples of blood donors from April 2020 to April 2021, September 2021 and April/May 2022. These data were used to aide in monitoring the pandemic in Germany. Data were completely anonymised at the site of sample collection. Serological test results are accompanied by demographic data including sex, age and area of residence (assigned a level two Nomenclature des Unités Territoriales Statistiques (NUTS2)). </p><p>The file contains data (sheet "data") as well as the description of variable content and coding (sheet "variables").</p>
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International Brain Laboratory public data
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OpenNeuro
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