cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.35092/yhjc.11400969.v1
title: Training Set of Mutated Minimal Peptides Screened by NCI Surgery Branch for Reactivity Against TIL

description: Mutated Minimal Peptides from the training set described in the manuscript titled "Development of a model for ranking candidate HLA class I neoantigens based upon datasets of known neoepitopes"
DOI: 10.35092/yhjc.11400972
title: Training Nmers randomly subsampled to reduce expression bias

description: Mutated Nmers from the balanced training set described in the manuscript titled "A machine learning model for ranking candidate HLA class I neoantigens based on known neoepitopes from multiple human tumor types". These Nmers have been randomly selected to reduce the expression bias in the data amongst the screened nmers
DOI: 10.35092/yhjc.11400972.v1
title: Training Set of Long Peptides Screened by NCI Surgery Branch for Reactivity Against TIL

description: Mutated Nmers from the training set described in the manuscript titled "Development of a model for ranking candidate HLA class I neoantigens based upon datasets of known neoepitopes"
DOI: 10.35092/yhjc.11400975
title: Training Mmps randomly subsampled to reduce expression bias

description: Mmps derived from the Nmers in the balanced training set in the manuscript titled "A machine learning model for ranking candidate HLA class I neoantigens based on known neoepitopes from multiple human tumor types". The nmers in the balanced training set were randomly selected from each decile in the full training data to reduce the expression bias in the data amongst the screened nmers<br>
DOI: 10.35092/yhjc.11400975.v1
title: All Mutated Minimal Peptides Screened by the NCI Surgery Branch for Reactivity Against TIL

description: All Mutated minimal peptides used to split into training and validation sets as described in the manuscript titled "Development of a model for ranking candidate HLA class I neoantigens based upon datasets of known neoepitopes"
DOI: 10.35092/yhjc.11400978
title: Validation Set of Long Peptides Screened by NCI Surgery Branch for Reactivity Against TIL

description: Mutated Nmers from the Validation set described in the manuscript titled "Development of a model for ranking candidate HLA class I neoantigens based upon datasets of known neoepitopes"
DOI: 10.35092/yhjc.11400978.v1
title: Validation Set of Long Peptides Screened by NCI Surgery Branch for Reactivity Against TIL

description: Mutated Nmers from the Validation set described in the manuscript titled "Development of a model for ranking candidate HLA class I neoantigens based upon datasets of known neoepitopes"
DOI: 10.35092/yhjc.11400981
title: Validation Set of Mutated Minimal Peptides Screened by NCI Surgery Branch for Reactivity Against TIL

description: Mutated Minimal peptides from the Validation set described in the manuscript titled "Development of a model for ranking candidate HLA class I neoantigens based upon datasets of known neoepitopes"
DOI: 10.35092/yhjc.11400981.v1
title: Validation Set of Mutated Minimal Peptides Screened by NCI Surgery Branch for Reactivity Against TIL

description: Mutated Minimal peptides from the Validation set described in the manuscript titled "Development of a model for ranking candidate HLA class I neoantigens based upon datasets of known neoepitopes"
DOI: 10.35092/yhjc.11400984
title: Test Set of Long Peptides Screened by NCI Surgery Branch for Reactivity Against TIL

description: Mutated Nmers From the Test set described in the manuscript titled "A machine learning model for ranking candidate HLA class I neoantigens based on known neoepitopes from multiple human tumor types"
DOI: 10.35092/yhjc.11400984.v1
title: Test Set of Long Peptides Screened by NCI Surgery Branch for Reactivity Against TIL

description: Mutated Nmers From the Test set described in the manuscript titled "Development of a model for ranking candidate HLA class I neoantigens based upon datasets of known neoepitopes"
DOI: 10.35092/yhjc.11400987
title: Test Set of Mutated Minimal Peptides screened by NCI Surgery Branch for Reactivity Against TIL

description: Mutated Minimal Peptides From the Test set described in the manuscript titled "A machine learning model for ranking candidate HLA class I neoantigens based on known neoepitopes from multiple human tumor types"
DOI: 10.35092/yhjc.11400987.v1
title: Test Set of Mutated Minimal Peptides screened by NCI Surgery Branch for Reactivity Against TIL

description: Mutated Minimal Peptides From the Test set described in the manuscript titled "Development of a model for ranking candidate HLA class I neoantigens based upon datasets of known neoepitopes"
DOI: 10.35092/yhjc.11441001.v1
title: SBCapSeq Protocol manuscript files for 'Quantifying tumor heterogeneity, clonal dynamics, and cancer driver gene evolution from Sleeping Beauty transposon mutagenesis models using SBCapSeq'

description: Supplementary datasets and other information accompanying manuscript: Quantifying tumor heterogeneity, clonal dynamics, and cancer driver gene evolution from Sleeping Beauty transposon mutagenesis models using SBCapSeq by Karen M. Mann Ana M. Contreras-Sandoval, Liliana Guzman-Rojas, Justin Y. Newberg, Amanda L. Meshey, Devin J. Jones, Felipe Amaya-Manzanares, Neal G. Copeland, Nancy A. Jenkins, and Michael B. Mann.<br><br>SBCapSeq is a transposon-based liquid-phase capture experimental and bioinformatic workflow optimized for Ion Torrent sequencing. SBCaptureSeq permits selective, semi-quantitative, and scalable deep sequencing of Sleeping Beauty transposon insertion sites from adaptor-ligated, barcoded Ion Torrent libraries created from populations of cells (bulk specimens) and single cells from both tumor and non-tumor genomes. This protocol includes detailed procedures for genomic DNA isolation, library preparation, capture hybridization, target sequence enrichment, sequencing, and data analysis. The SBCapSeq method, which takes about 7–10 days to perform, permits semi-quantitative sequencing and has been specifically optimized for Sleeping Beauty transposon mutagenesis genetic studies.<br>
DOI: 10.35092/yhjc.11441130
title: Supplementary Tables1-43 for 'Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression'

description: Supplementary Tables for manuscript: Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression. Aziz Aiderus, Justin Y. Newberg, Liliana Guzman-Rojas, Ana M. Contreras-Sandoval, Amanda L. Meshey, Devin J. Jones, Felipe Amaya-Manzanares, Roberto Rangel, Jerrold M. Ward, Song-Choon Lee, Kenneth Hon-Kim Ban, Keith Rogers, Susan M. Rogers, Luxmanan Selvanesan, Leslie A. McNoe, Neal G. Copeland, Nancy A. Jenkins, Kenneth Y. Tsai, Michael A. Black, Karen M. Mann, and Michael B. Mann
DOI: 10.35092/yhjc.11441130.v1
title: Supplementary Tables1-43 for 'Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression'

description: Supplementary Tables for manuscript: Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression. Aziz Aiderus, Justin Y. Newberg, Liliana Guzman-Rojas, Ana M. Contreras-Sandoval, Amanda L. Meshey, Devin J. Jones, Felipe Amaya-Manzanares, Roberto Rangel, Jerrold M. Ward, Song-Choon Lee, Kenneth Hon-Kim Ban, Keith Rogers, Susan M. Rogers, Luxmanan Selvanesan, Leslie A. McNoe, Neal G. Copeland, Nancy A. Jenkins, Kenneth Y. Tsai, Michael A. Black, Karen M. Mann, and Michael B. Mann
DOI: 10.35092/yhjc.11606319
title: Effects of Remote Limb Ischemic Conditioning on muscle strength in healthy young adults: A randomized controlled trial

description: This is the data from a clinical trial that assessed the effects of remote limb ischemic conditioning on muscle strength in healthy young adults. The data includes demographic details, ischemic conditioning parameters, and strength measures.<br> ClinicalTrials.gov Identifier: NCT03512028<br>
DOI: 10.35092/yhjc.11606319.v1
title: Effects of Remote Limb Ischemic Conditioning on muscle strength in healthy young adults: A randomized controlled trial

description: This is the data from a clinical trial that assessed the effects of remote limb ischemic conditioning on muscle strength in healthy young adults. The data includes demographic details, ischemic conditioning parameters, and strength measures.<br> ClinicalTrials.gov Identifier: NCT03512028<br>
DOI: 10.15156/bio/sh1229240.08fu
title: SH1229240.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1229241.08fu
title: SH1229241.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1229242.08fu
title: SH1229242.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/th028936
title: TH028936
title: Steinernematidae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.15156/bio/th028937
title: TH028937
title: Strongylidae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.15156/bio/th028938
title: TH028938
title: Strongyloididae

description: Here we present the novel 'taxon hypothesis' (TH) concept to accommodate fungal 'species hypothesis' (SH) into existing classification frameworks for taxonomic communication. As supplied with Digital Object Identifiers (DOIs), THs are flexible in time and enable direct cross-communication of higher level taxa along with evolving classification schemes. Every TH includes given number of SHs and consequently fixed number of fungal rDNA ITS sequences. DNA sequences generated by High-throughput or Sanger sequencing studies and identified against UNITE SHs will be automatically assigned to THs as well.
DOI: 10.35092/yhjc.10324874
title: Eye tracking data for typically developing participants for "Distinct neural mechanisms of social orienting and mentalizing revealed by independent measures of neural and eye movement typicality"

description: Eye movement data, before any preprocessing, from typically developing participants while watching 24 short movie (14s long) movie clips.<br>Dataset structure is participants x movie x direction (horizontal, vertical) x time (sampled at 1000Hz).<br><br>See collection for related datasets: https://doi.org/10.35092/yhjc.c.4741556<br>See publication for details: Ramot, M., Walsh, C., Reimann, G.E., & Martin, A. Distinct neural mechanisms of social orienting and mentalizing revealed by independent measures of neural and eye movement typicality. Commun Biol 3, 48 (2020). https://doi.org/10.1038/s42003-020-0771-1<br>
DOI: 10.35092/yhjc.10324874.v1
title: Eye tracking data for typically developing participants for "Distinct neural mechanisms of social orienting and mentalizing revealed by independent measures of neural and eye movement typicality"

description: Eye movement data, before any preprocessing, from typically developing participants while watching 24 short movie (14s long) movie clips.<br>Dataset structure is participants x movie x direction (horizontal, vertical) x time (sampled at 1000Hz).<br><br>See collection for related datasets: https://doi.org/10.35092/yhjc.c.4741556<br>See publication for details: Ramot, M., Walsh, C., Reimann, G.E., & Martin, A. Distinct neural mechanisms of social orienting and mentalizing revealed by independent measures of neural and eye movement typicality. Commun Biol 3, 48 (2020). https://doi.org/10.1038/s42003-020-0771-1<br>
DOI: 10.35092/yhjc.10688180
title: fMRI dataset for "Distinct neural mechanisms of social orienting and mentalizing revealed by independent measures of neural and eye movement typicality"

description: fMRI dataset for 63 typically developing participants and 36 participants with ASD while watching a 9.5 minute movie clip inside the scanner.<br>Multi data EPI with 3 echos and anatomical MPRAGE are provided for each participant.<br>See collection for related datasets: https://doi.org/10.35092/yhjc.c.4741556<br>See publication for details: Ramot, M., Walsh, C., Reimann, G.E., & Martin, A. Distinct neural mechanisms of social orienting and mentalizing revealed by independent measures of neural and eye movement typicality. Commun Biol 3, 48 (2020). https://doi.org/10.1038/s42003-020-0771-1<br>
DOI: 10.35092/yhjc.10688180.v1
title: fMRI dataset for "Distinct neural mechanisms of social orienting and mentalizing revealed by independent measures of neural and eye movement typicality"

description: fMRI dataset for 63 typically developing participants and 36 participants with ASD while watching a 9.5 minute movie clip inside the scanner.<br>Multi data EPI with 3 echos and anatomical MPRAGE are provided for each participant.<br>See collection for related datasets: https://doi.org/10.35092/yhjc.c.4741556<br>See publication for details: Ramot, M., Walsh, C., Reimann, G.E., & Martin, A. Distinct neural mechanisms of social orienting and mentalizing revealed by independent measures of neural and eye movement typicality. Commun Biol 3, 48 (2020). https://doi.org/10.1038/s42003-020-0771-1<br>
DOI: 10.35092/yhjc.11349710
title: Datasets to reproduce Figures 1-3 and associated Extended Data Figures

description: The CHI, HIPC-I (Stanford and Yale), Emory, Yellow fever and SLE data sets used in the study. Unpack this file to your working directory and keep the directory structure. The R codes can be downloaded from github (https://github.com/kotliary/baseline) into the R directory.<br>This item is a part of the collection: https://doi.org/10.35092/yhjc.c.4753772<br><b>If you use our data (including CITE-seq data) or code for your work please cite the following publication</b>:Kotliarov, Y., Sparks, R. et al. Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus. Nat. Med. DOI: https://doi.org/10.1038/s41591-020-0769-8 (2020)<br><b>Abstract</b><br>Responses to vaccination and to diseases vary widely across individuals, which may be partly due to baseline immune variations. Identifying such baseline predictors and their biological basis are of broad interest given their potential importance for cancer immunotherapy, disease outcomes, vaccination and infection responses. Here we uncover baseline blood transcriptional signatures predictive of antibody responses to both influenza and yellow fever vaccinations in healthy subjects. These same signatures evaluated at clinical quiescence are correlated with disease activity in systemic lupus erythematosus patients with plasmablast-associated flares. CITE-seq profiling of 82 surface proteins and transcriptomes of 53,201 single cells from healthy high and low influenza-vaccination responders revealed that our signatures reflect the extent of activation in a plasmacytoid dendritic cell—Type I IFN—T/B lymphocyte network. Our findings raise the prospect that modulating such immune baseline states may improve vaccine responsiveness and mitigate undesirable autoimmune disease activities.<br><br><b>General contact</b>: John Tsang (john.tsang@nih.gov)<b>Questions about software/code</b>: Yuri Kotliarov (yuri.kotliarov@nih.gov)<br>
DOI: 10.35092/yhjc.11530191
title: RNAseq data of CD20+CD38++ and other B cell subsets sorted from healthy donors

description: The purpose of this experiment was to determine the transcriptional differences between CD19+CD20+CD38++ B cells and the total CD19+CD20+ B cell fraction in healthy human donors.<br><br>This data can be used to reproduce the results reported in Extended Data Figure 7 for the associated article.<br>This item is a part of the collection: https://doi.org/10.35092/yhjc.c.4753772<br><b>If you use our data (including CITE-seq data) or code for your work please cite the following publication</b>:Kotliarov, Y., Sparks, R. et al. Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus. Nat. Med. DOI: https://doi.org/10.1038/s41591-020-0769-8 (2020)<br><b>Abstract</b><br>Responses to vaccination and to diseases vary widely across individuals, which may be partly due to baseline immune variations. Identifying such baseline predictors and their biological basis are of broad interest given their potential importance for cancer immunotherapy, disease outcomes, vaccination and infection responses. Here we uncover baseline blood transcriptional signatures predictive of antibody responses to both influenza and yellow fever vaccinations in healthy subjects. These same signatures evaluated at clinical quiescence are correlated with disease activity in systemic lupus erythematosus patients with plasmablast-associated flares. CITE-seq profiling of 82 surface proteins and transcriptomes of 53,201 single cells from healthy high and low influenza-vaccination responders revealed that our signatures reflect the extent of activation in a plasmacytoid dendritic cell—Type I IFN—T/B lymphocyte network. Our findings raise the prospect that modulating such immune baseline states may improve vaccine responsiveness and mitigate undesirable autoimmune disease activities.<br><br><b>General contact</b>: John Tsang (john.tsang@nih.gov)<b>Questions about software/code</b>: Yuri Kotliarov (yuri.kotliarov@nih.gov)<br>
DOI: 10.35092/yhjc.11530191.v1
title: RNAseq data of CD20+CD38++ and other B cell subsets sorted from healthy donors

description: The purpose of this experiment was to determine the transcriptional differences between CD19+CD20+CD38++ B cells and the total CD19+CD20+ B cell fraction in healthy human donors.<br><br>This data can be used to reproduce the results reported in Extended Data Figure 7 for the associated article.<br>This item is a part of the collection: https://doi.org/10.35092/yhjc.c.4753772<br><b>If you use our data (including CITE-seq data) or code for your work please cite the following publication</b>:Kotliarov, Y., Sparks, R. et al. Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus. Nat. Med. DOI: https://doi.org/10.1038/s41591-020-0769-8 (2020)<br><b>Abstract</b><br>Responses to vaccination and to diseases vary widely across individuals, which may be partly due to baseline immune variations. Identifying such baseline predictors and their biological basis are of broad interest given their potential importance for cancer immunotherapy, disease outcomes, vaccination and infection responses. Here we uncover baseline blood transcriptional signatures predictive of antibody responses to both influenza and yellow fever vaccinations in healthy subjects. These same signatures evaluated at clinical quiescence are correlated with disease activity in systemic lupus erythematosus patients with plasmablast-associated flares. CITE-seq profiling of 82 surface proteins and transcriptomes of 53,201 single cells from healthy high and low influenza-vaccination responders revealed that our signatures reflect the extent of activation in a plasmacytoid dendritic cell—Type I IFN—T/B lymphocyte network. Our findings raise the prospect that modulating such immune baseline states may improve vaccine responsiveness and mitigate undesirable autoimmune disease activities.<br><br><b>General contact</b>: John Tsang (john.tsang@nih.gov)<b>Questions about software/code</b>: Yuri Kotliarov (yuri.kotliarov@nih.gov)<br>