Data availability statement extraction
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Training data and model checkpoints for DAS extraction
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10.34133_2022_9870149.pdf
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Code Availability. The source codes for our CS framework are
available at https://github.com/bianzhiyu/ContinuityScaling.
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Additional Points Code Availability. The source codes for our CS framework are available at https://github.com/bianzhiyu/ContinuityScaling .
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10.1088_1361-6501_ad180c.pdf
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Data availability statementThe data cannot be made publicly available upon publication because they are owned by a third party and the terms of use prevent public distribution. The data that support the findings of this study are available upon reasonable request from the authors.
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Data availability statement The data cannot be made publicly available upon publication because they are owned by a third party and the terms of use prevent public distribution. The data that support the findings of this study are available upon reasonable request from the authors.
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10.1038_s41467-022-30406-4.pdf
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Data availability The cryo-EM particle stacks, maps and models generated in this study have been deposited in EMPIAR image archive, EMDB database and the Protein Data Bank, respectively, under accession codes EMPIAR-10969, EMD-25757 and PDB-7T9G) for VcINDY-Na+ (300 mM) structure and under accession codes EMPIAR-10970, EMD-25756 and PDB-7T9F) for VcINDY-Ch+ structure. Source Data for Fig. 4 are available with the paper.
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Data availability The cryo-EM particle stacks, maps and models generated in this study have been deposited in EMPIAR image archive, EMDB database and the Protein Data Bank, respectively, under accession codes EMPIAR-10969, EMD-25757 and PDB-7T9G ) for VcINDY-Na + (300 mM) structure and under accession codes EMPIAR-10970, EMD- 25756 and PDB-7T9F ) for VcINDY-Ch + structure. Source Data for Fig. 4 are available with the paper.
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10.1085/jgp.202012858
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10.1007_s13280-020-01405-w.pdf
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10.1088_1361-6595_ad03bd.pdf
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Data availability statementThe data cannot be made publicly available upon publication because no suitable repository exists for hosting data in this field of study. The data that support the findings of this study are available upon reasonable request from the authors.
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Data availability statement The data cannot be made publicly available upon publication because no suitable repository exists for hosting data in this field of study. The data that support the findings of this study are available upon reasonable request from the authors.
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10.1265_ehpm.22-00245.pdf
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Availability of data and material The datasets generated and/or analyzed during the current study are not publicly available because the study involves human participants with a nondisclosure provision of individual data stated in the written informed consent in order to prevent compromise of study participants’ privacy but are available from the corresponding author upon reasonable request.
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Availability of data and material The datasets generated and/or analyzed during the current study are not publicly available because the study involves human participants with a nondisclosure provision of individual data stated in the written informed consent in order to prevent compromise of study participants' privacy but are available from the corresponding author upon reasonable request.
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10.1088_1402-4896_ad0bb9.pdf
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Data availability statementThe data cannot be made publicly available upon publication because they are owned by a third party and the terms of use prevent public distribution. The data that support the findings of this study are available upon reasonable request from the authors.
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Data availability statement The data cannot be made publicly available upon publication because they are owned by a third party and the terms of use prevent public distribution. The data that support the findings of this study are available upon reasonable request from the authors.
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10.1016_j.isci.2020.100959.pdf
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DATA AND CODE AVAILABILITY
RNA-seq data have been deposited in NCBI’s Gene Expression Omnibus (GEO). The accession number for
the RNA-seq data reported in this paper is GEO: GSE145495.
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DATA AND CODE AVAILABILITY RNA-seq data have been deposited in NCBI's Gene Expression Omnibus (GEO). The accession number for the RNA-seq data reported in this paper is GEO: GSE145495.
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10.7554_elife.85878.pdf
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Data availabilityAll data generated or analyzed in this study are included in the manuscript and supporting files. Source data files have been provided for Figure 1b, Figure 1c, Figure 1f, Figure 1g, Figure 1-figure supplement 2a-c, Figure 2b, Figure 2g, Figure 2-figure supplement 1a-f, Figure 3a, Figure 3c, Figure 3e, Figure 3h, Figure 3 supplement 1b-c, Figure 4a, Figure 4b, Figure 4e, Figure 4f, Figure 4h, Figure 4i, Figure 4-figure supplement 1a-b, Figure 4-figure supplement 2a, Figure 5b.
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Data availability All data generated or analyzed in this study are included in the manuscript and supporting files. Source data files have been provided for Figure 1b , Figure 1c, Figure 1f, Figure 1g, Figure 1-figure supplement 2a-c, Figure 2b, Figure 2g, Figure 2-figure supplement 1a-f, Figure 3a, Figure 3c, Figure 3e, Figure 3h, Figure 3 supplement 1b-c, Figure 4a, Figure 4b, Figure 4e, Figure 4f, Figure 4h, Figure 4i, Figure 4-figure supplement 1a-b, Figure 4-figure supplement 2a, Figure 5b.
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10.1371_journal.pntd.0009424.pdf
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Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
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10.7554_elife.85521.pdf
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Data availability Figure 3—source data 1, Figure 5—source data 1, Figure 6—source data 1, and Figure 7—source data 1 contain the numerical and statistical data used to generate the figures. The confocal imaging dataset is available at Brain Image Library under DOI https://doi.org/10.35077/g.933.
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Data availability Figure 3 -source data 1, Figure 5 -source data 1, Figure 6 -source data 1, and Figure 7 -source data 1 contain the numerical and statistical data used to generate the figures. The confocal imaging dataset is available at Brain Image Library under DOI https://doi.org/10.35077/g.933 . The following dataset was generated:
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10.1371_journal.pone.0258085.pdf
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Data Availability Statement Due to legal and participants confidentiality, data will only be available upon request. The data underlying the results presented in the study are available from Shenzhen Luohu Disease Prevention and Control Center via contacting Weihong Chen, director of Shenzhen Luohu Disease Prevention and Control Center, at 1433529760@qq.com.
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Due to legal and participants confidentiality, data will only be available upon request. The data underlying the results presented in the study are available from Shenzhen Luohu
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10.1371_journal.ppat.1011871.pdf
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Data Availability Statement: Raw and processed RNA-sequencing data can be accessed from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database under accession number GSE212205.
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Raw and processed RNA-sequencing data can be accessed from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database under accession number GSE212205.
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10.1371_journal.pcbi.1011196.pdf
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Data Availability Statement Data can be found in the following doi: https://doi.org/10.6084/m9.figshare.21938651.v1.
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Data can be found in the following 10.6084/m9. figshare.21938651.v1 .
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10.1126_sciadv.adf9336.pdf
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Data and materials availability: All DNA constructs (table S2) and cell lines (table S3) are available from M.B.E. or through the Addgene repository under a material transfer agreement with California Institute of Technology. All data generated and all the computational and data analysis and modeling codes used in the current study are available at data.caltech.edu/records/0sdrn-73r13. All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.
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10.1088_1361-6579_ad0f70.pdf
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Data availability statementThe data cannot be made publicly available upon publication because they contain commercially sensitive information. The data that support the findings of this study are available upon reasonable request from the authors.
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Data availability statement The data cannot be made publicly available upon publication because they contain commercially sensitive information. The data that support the findings of this study are available upon reasonable request from the authors.
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10.1093_molbev_msad069.pdf
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Data availability No new data were generated in support of this research. TE models were deposited in the DFAM database.
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Data availability No new data were generated in support of this research. TE models were deposited in the DFAM database.
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10.1088_2752-5295_acf4b5.pdf
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Data availability statementThe data that support the findings of this study are openly available in the Harvard Dataverse at https://doi.org/10.7910/DVN/2UT4GM (Hauer 2023).
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Data availability statement The data that support the findings of this study are openly available in the Harvard Dataverse at https://doi. org/10.7910/DVN/2UT4GM (Hauer 2023) .
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10.1371_journal.pbio.3000080.pdf
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Data Availability Statement The data for individual figures are available as Excel files (labeled, e.g., S1 Data) with links in the relevant figure captions. The full listing of these data files can be found following the captions for supplementary figures, as well as in the Excel file DataFileListings.xlsx. In addition, the full data are available. The corresponding author (Aniruddha Das) will maintain the data at Columbia University until publication. Once published, all datasets will be shared openly with qualified scientists. Access will be granted by request to the corresponding author. It will be our intent to collaborate with individuals who contact us about sharing the data. But if that is not possible or does not make sense, then we will simply provide the data to them. Because of the large size of the optical imaging and electrode recording data, it might not be possible to keep it online. Hence, it will also be distributed (upon request) as a DVD box set for a nominal fee (sufficient to cover the costs of the DVDs, the time for a lab technician to burn the discs, and shipping expenses).
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The data for individual figures are available as Excel files (labeled, e.g., S1 Data) with links in the relevant figure captions. The full listing of these data files can be found following the captions for supplementary figures, as well as in the Excel file DataFileListings.xlsx. In addition, the full data are available. The corresponding author (Aniruddha Das) will maintain the data at Columbia University until all datasets will be shared openly with qualified scientists. Access will be granted by request to the corresponding
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10.1021_acssynbio.1c00142.pdf
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10.1088_2632-2153_ad0e17.pdf
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Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
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Data availability statement All data that support the findings of this study are included within the article (and any supplementary files).
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10.1186_s12875-019-0972-1.pdf
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Availability of data and materials Table 1 provides a list of the 26 included papers and Additional file 1 shows the database search strategy.
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Availability of data and materials Table 1 provides a list of the 26 included papers and Additional file 1 shows the database search strategy.
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10.1186_s13059-023-02963-4.pdf
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Availability of data and materials The results published here are in part based upon data generated by the TCGA Research Network (https://www.cancer.gov/tcga), METABRIC (https://ega-archive.org/studies/EGAS00000000083), MSK-IMPACT (https://www.mskcc.org/msk-impact) or deposited at cBioPortal (https://www.cbioportal.org/). The following expression datasets from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) have also been employed: GSE114012 [48], GSE131594 [45], GSE137912 [12], GSE152699 [49], GSE75367 [47], GSE83142 [46], GSE93991 [44], GSE134836 [13], GSE134838 [13], GSE134839 [13], GSE124854 [93], GSE135215 [94], GSE99116 [93], GSE178839 [149], GSE149224 [100], GSE139944 [102], GSE191127 [150], GSE109211 [151], GSE50509 [152], GSE65185 [153], GSE66399 [154], GSE68871 [155] and GSE99898 [156]. The GEO datasets employed in the analyses are summarised in Additional file 1: Tables S2 and S3. All codes developed for the purpose of this study can be found at the following repository, released under a GNU General Public License v3.0 at github: https://github.com/secrierlab/CancerG0Arrest [157] and Zenodo (doi: 10.5281/zenodo.7840672) [158].
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Availability of data and materials The results published here are in part based upon data generated by the TCGA Research Network ( https:// www. cancer. gov/ tcga ), METABRIC ( https:// ega-archi ve. org/ studi es/ EGAS0 00000 00083 ), MSK-IMPACT ( https:// www. mskcc. org/ msk- impact ) or deposited at cBioPortal ( https:// www. cbiop ortal. org/ ). The following expression datasets from the Gene Expression Omnibus (GEO, https:// www. ncbi. nlm. nih. gov/ geo/ ) have also been employed: GSE114012 [48] , GSE131594 [45] , GSE137912 [12] , GSE152699 [49] , GSE75367 [47] , GSE83142 [46] , GSE93991 [44] , GSE134836 [13] , GSE134838 [13] , GSE134839 [13] , GSE124854 [93] , GSE135215 [94] , GSE99116 [93] , GSE178839 [149], GSE149224 [100], GSE139944 [102], GSE191127 [150], GSE109211 [151], GSE50509 [152], GSE65185 [153], GSE66399 [154], GSE68871 [155] and GSE99898 [156]. The GEO datasets employed in the analyses are summarised in Additional file 1: Tables S2 and S3 . All codes developed for the purpose of this study can be found at the following repository, released under a GNU General Public License v3.0 at github: https:// github. com/ secri erlab/ Cance rG0Ar rest [157] and Zenodo (doi: 10. 5281/ zenodo. 78406 72 ) [158].
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10.1371_journal.pone.0261071.pdf
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Data Availability Statement Data are available from the Zenodo database (DOI: 10.5281/zenodo.5774499).
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Data are available from the Zenodo database (DOI: 10.5281/zenodo. 5774499 ).
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10.1186_s12866-023-02901-1.pdf
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Data AvailabilityRaw sequences from this study are available and were deposited in the European Nucleotide Archive (ENA) with bio project accession PRJEB56537 in the ENA bio project database: https://www.ebi.ac.uk/ena/browser/view/PRJEB56537.
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Data Availability Raw sequences from this study are available and were deposited in the European Nucleotide Archive (ENA) with bio project accession PRJEB56537 in the ENA bio project database: https://www.ebi.ac.uk/ena/browser/view/ PRJEB56537 .
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10.1371_journal.pone.0244053.pdf
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Data Availability Statement The data are accessible via Dataverse (https://doi.org/10.7910/DVN/8ZVOKW).
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The data are accessible via Dataverse ( https://doi.org/10.7910/ DVN/8ZVOKW ).
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10.1371_journal.pone.0250044.pdf
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Data Availability Statement Data are available here: Wall, Kristin, 2021, "Replication Data for: "Etiologies of genital inflammation and ulceration in symptomatic Rwandan men and women responding to radio promotions of free screening and treatment services"", https://doi.org/10.7910/DVN/CFX6UU, Harvard Dataverse.
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Data are available here: Wall, Kristin,
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10.1126_sciadv.abn5709.pdf
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Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Code for analyzing mechano-NPS data is archived at Zenodo (https://doi.org/10.5281/zenodo.7884859). Requests for strain CA846 can be submitted through the Caenorhabditis Genetics Center at https://cgc.umn.edu/strain/WH257. Strain CA1728 [mjl-1(tm1651)] can be requested from the National Bioresource Project (https://shigen.nig.ac.jp/c.elegans/). Requests for strains generated in this study should be submitted to C.L. or A.F.D.
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10.1126_sciadv.ade1817.pdf
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Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. All transcriptome data are available at the Gene Expression Omnibus (GEO) repository under the accession number GSE198939. Raw data from all experiments are available at zenodo.org under the following DOI: 10.5281/zenodo.7654968. All strains are available at CGC under https://cgc.umn.edu/.
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10.1073_pnas.2301985120.pdf
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Data, Materials, and Software Availability Cryo-EM density maps of the KCNQ1 channel with the voltage sensor in the up, intermediate, and down conformation have been deposited in the electron microscopy data bank under accession codes EMD-40508 (70), EMD-40509 (71), and EMD-40510 (72), respectively. Atomic coordinates of the KCNQ1 channel with the voltage sensor in the up, intermediate, and down conformation have been deposited in the protein data bank under accession codes 8SIK (73), 8SIM (74), and 8SIN (75), respectively.
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10.1002_advs.202200181.pdf
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Data Availability Statement
The data that support the findings of this study are available from the cor-
responding authors upon reasonable request.
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Data Availability Statement The data that support the findings of this study are available from the corresponding authors upon reasonable request.
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10.1371_journal.pone.0257328.pdf
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Data Availability Statement LANYERO, HINDUM (2021), Validity of caregivers’ reports on prior use of antibacterials in children under five years presenting to health facilities in Gulu, northern Uganda, Dryad, Dataset, https://doi.org/10.5061/dryad.sj3tx9642.
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10.3389_fpsyt.2022.1086038.pdf
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Data availability statement The datasets presented in this article are not readily available because ethics approval did not include public data sharing. Requests to access the datasets should be directed to the corresponding author.
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Data availability statement The datasets presented in this article are not readily available because ethics approval did not include public data sharing. Requests to access the datasets should be directed to the corresponding author. organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
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10.3390/ijerph19127064
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Data Availability Statement: The code and data underlying this article will be shared on reasonable
request to the corresponding author.
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Data Availability Statement: The code and data underlying this article will be shared on reasonable request to the corresponding author.
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10.1103_physrevb.107.094206.pdf
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10.1371_journal.ppat.1010103.pdf
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Data Availability Statement The RNA-seq datasets generated during this study are available at Bioproject accession number PRJNA742496 in the NCBI Bioproject database (http://www.ncbi.nlm.nih.gov/bioproject/742496).
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The RNA-seq datasets generated during this study are available at Bioproject accession number PRJNA742496 in the NCBI Bioproject database ( http://www.ncbi. nlm.nih.gov/bioproject/742496 ).
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10.1186_s12874-023-01902-y.pdf
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Data AvailabilityWe provide R modules as the basis for the dashboard development on GitHub (https://github.com/CTU-Basel/viewTrial). Qualitative data that supported the development of the risk assessment and study dashboard is provided in the supplementary material.
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Data Availability We provide R modules as the basis for the dashboard development on GitHub ( https://github.com/CTU-Basel/viewTrial ). Qualitative data that supported the development of the risk assessment and study dashboard is provided in the supplementary material.
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10.1093_nar_gkad331.pdf
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DATA AVAILABILITY The online resource is available without restriction at https://www.flyrnai.org/tools/pangea/.
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10.1021_acschembio.3c00413.pdf
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10.1038/s41431-022-01214-7
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10.3390_molecules24122333.pdf
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10.1093_ijrl_eeac041.pdf
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10.1371_journal.pbio.3002453.pdf
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Data Availability Statement: All data supporting the findings of this manuscript are available on the Open Science Framework at osf.io/3kyvw.
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All data supporting the findings of this manuscript are available on the Open Science Framework at osf.io/3kyvw .
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10.1186_s12874-019-0884-8.pdf
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Availability of data and materials Restrictions by the data custodians mean that the datasets are not publicly available or able to be provided by the authors. Researchers wanting to access the datasets used in this study should refer to the Centre for Health Record Linkage application process (www.cherel.org.au/apply-for-linked-data).
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10.1371_journal.pone.0229895.pdf
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Data Availability Statement All relevant data are within the manuscript.
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All relevant data are within the manuscript.
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10.1088_1361-6579_ad0426.pdf
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Data availability statementThe data cannot be made publicly available upon publication because they are not available in a format that is sufficiently accessible or reusable by other researchers. The data that support the findings of this study are available upon reasonable request from the authors.
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Data availability statement The data cannot be made publicly available upon publication because they are not available in a format that is sufficiently accessible or reusable by other researchers. The data that support the findings of this study are available upon reasonable request from the authors.
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10.1007_s00122-023-04372-4.pdf
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Data availabilityElectronic supplementary material The online version of this article (https://doi.org/xxxxx) contains supplementary material, which is available to authorized users.
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Data availability Electronic supplementary material The online version of this article ( https:// doi. org/ xxxxx ) contains supplementary material, which is available to authorized users.
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10.1017_etds.2021.165.pdf
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10.1371_journal.pone.0227230.pdf
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Data Availability Statement: All relevant data are
within the manuscript and its Supporting
Information files.
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All relevant data are within the manuscript and its Supporting Information files.
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10.1088_2634-4386_ad046d.pdf
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Data availability statementThe data that support the findings of this study are openly available (Kaiser et al 2023). The experiment code is available on https://github.com/electronicvisions/model-paper-mc-sbi.
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Data availability statement The data that support the findings of this study are openly available (Kaiser et al 2023) . The experiment code is available on https://github.com/electronicvisions/model-paper-mc-sbi .
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10.1103_physrevresearch.5.013045.pdf
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10.3390_math10224246.pdf
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Data Availability Statement: Data sharing is not applicable to this article as no datasets were
generated or analyzed during the current study.
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Data Availability Statement: Data sharing is not applicable to this article as no datasets were generated or analyzed during the current study.
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10.1186_s12889-023-16038-3.pdf
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Availability of data and materials The datasets used and analyzed during this current study are available from the corresponding author on reasonable request.
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Availability of data and materials The datasets used and analyzed during this current study are available from the corresponding author on reasonable request.
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10.1371_journal.pone.0257370.pdf
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Data Availability Statement This study was registered in the Open Science Framework Registry (https://osf.io/rqve6). The review protocol can be accessed at https://bookdown.org/MathiasHarrer/Doing_Meta_Analysis_in_R/. Data are available from the Dryad Data Repository (https://datadryad.org/stash/dataset/doi:10.6078/D10T42).
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This study was registered in the Open Science Framework Registry ( https://osf.io/rqve6 ). The review protocol can be accessed at https://bookdown.org/MathiasHarrer/ Doing_Meta_Analysis_in_R/ . Data are available from the Dryad Data Repository ( https://datadryad. org/stash/dataset/doi:10.6078/D10T42 ).
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10.1098_rsos.220808.pdf
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Data accessibility. This article has no additional data.
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Data accessibility. This article has no additional data.
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10.1038_s41556-023-01184-y.pdf
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Data availabilityAll data that support the findings of this study are available within the paper and its supplementary files. Sequencing data that support the findings of this study have been deposited in the Gene Expression Omnibus under accession code GSE208072. Previously published RNA-seq data from BCC, SCC and normal EpdSCs that were re-analysed here are available under accession code GSE152487. Source data are provided with this paper. All other data supporting the findings of this study are available from the corresponding author on reasonable request.Code availabilityAll bioinformatic analysis tools and pipelines used in this study are documented in the method section. Codes are available from the corresponding author upon reasonable request.
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Data availability All data that support the findings of this study are available within the paper and its supplementary files. Sequencing data that support the findings of this study have been deposited in the Gene Expression Omnibus under accession code GSE208072 . Previously published RNA-seq data from BCC, SCC and normal EpdSCs that were re-analysed here are available under accession code GSE152487 . Source data are provided with this paper. All other data supporting the findings of this study are available from the corresponding author on reasonable request. Code availability All bioinformatic analysis tools and pipelines used in this study are documented in the method section. Codes are available from the corresponding author upon reasonable request. Article https://doi.org/10.1038/s41556-023-01184-y Extended Data Fig. 1 | See next page for caption. Nature Cell Biology Article https://doi.org/10.1038/s41556-023-01184-y Materials availability. Will be provided upon request and available upon publication.
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10.1371_journal.pcbi.1011795.pdf
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Data Availability Statement: Computational code is available at https://github.com/kieran12lamb/SARS-CoV2_Mutational_Signatures GISAID data accessions are available at doi.org/10.55876/gis8.221201qs, doi.org/10.55876/gis8.230406qg and doi.org/10.55876/gis8.230406fb.
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Computational code is available at https://github.com/kieran12lamb/ SARS-CoV2_Mutational_Signatures GISAID data accessions are available at doi.org/10.55876/gis8 .
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10.1038_s41598-020-77562-5.pdf
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Data availability
All data generated and analyzed during the present study are available upon request from the corresponding
author upon reasonable request.
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Data availability All data generated and analyzed during the present study are available upon request from the corresponding author upon reasonable request. Received: 22 April 2020; Accepted: 9 November 2020
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10.1073_pnas.2304611120.pdf
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Data, Materials, and Software AvailabilityStructure factors and refined coordinates obtained from X-ray crystallography have been deposited into the Protein Data Bank (www.wwpdb.org) under PDB accession codes: 8SSP (72) (AurA-danusertib-Mb1), 8SSO (73) (AurA-danusertib-Mb2), and 8SSN (74) (Abl64–510-SKI-asciminib).
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10.1001_jamanetworkopen.2019.12416.pdf
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10.1103_physrevx.13.021007.pdf
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10.3390_biom13060952.pdf
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Data Availability Statement The data supporting this study are available from the corresponding authors upon reasonable request.
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Data Availability Statement: The data supporting this study are available from the corresponding authors upon reasonable request.
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10.1177_03010066231175014.pdf
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Data Availability: Data and scripts used to conduct this analysis can be viewed at Open Science Framework: Data and analysis for Effects of cortical distance on the Ebbinghaus and Delboeuf illusions. https://doi.org/10.17605/OSF.IO/GUHSF.
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Data Availability Data and scripts used to conduct this analysis can be viewed at Open Science Framework: Data and analysis for Effects of cortical distance on the Ebbinghaus and Delboeuf illusions. https://doi.org/10.17605/OSF.IO/ GUHSF .
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10.1038_s42003-023-04955-3.pdf
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Data availabilityThe main data supporting the results in this study are available within the paper and its Supplementary Information. Source data for all figures can be found in Supplementary Data 1. The raw and analysed datasets generated during the study are too large to be publicly shared, yet they are available for research purposes from the corresponding authors on reasonable request.
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Data availability The main data supporting the results in this study are available within the paper and its Supplementary Information. Source data for all figures can be found in Supplementary Data 1. The raw and analysed datasets generated during the study are too large to be publicly shared, yet they are available for research purposes from the corresponding authors on reasonable request.
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10.1093_jncics_pkab068.pdf
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Data Availability The data underlying this article cannot be shared publicly due to privacy restrictions of individuals that participated in the study. Aggregated, deidentified data may be shared on reasonable request to the corresponding author.
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Data Availability The data underlying this article cannot be shared publicly due to privacy restrictions of individuals that participated in the study. Aggregated, deidentified data may be shared on reasonable request to the corresponding author.
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10.1016/j.jbc.2022.102361
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Data availability
Data available upon request. Contact anthony.koleske@yale.
edu for more information.
The limited proteolysis mass spectrometry data have been
deposited to the ProteomeXchange Consortium via the PRIDE
(46) partner repository with the dataset identifier PXD034393
(http://www.ebi.ac.uk/pride).
The cross-linking raw mass spectrometry data and peak lists
are available in the massIVE repository (https://massive.ucsd.
edu) with accession number: MSV000089621
Annotated spectra supporting the cross-linked identifications are published on MS-Viewer (https://msviewer.ucsf.edu/
cgi-bin/msform.cgi?form=msviewer) with the following search
keys:
Trio SR6-GEF1-WT: l4abvtas5a
|
Data availability Data available upon request. Contact anthony.koleske@yale. edu for more information. The limited proteolysis mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE (46) partner repository with the dataset identifier PXD034393 ( http://www.ebi.ac.uk/pride ). The cross-linking raw mass spectrometry data and peak lists are available in the massIVE repository ( https://massive.ucsd. edu ) with accession number: MSV000089621
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10.1038_s41586-023-06415-8.pdf
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Data availabilityDesign structures, AF2 models and experimental measurements are available at https://figshare.com/s/439fdd59488215753bc3. Cryo-EM maps and corresponding atomic models for the Influenza HA binder in Fig. 6d–h have been deposited in the PDB and the Electron Microscopy Data Bank under accession codes 8SK7 and EMDB-40557, respectively. Electron microscopy data collected for the HE0537 oligomer are available at EMDB-40602.Code availabilityCode for running RFdiffusion has been released on GitHub, free for academic, personal and commercial use at https://github.com/RosettaCommons/RFdiffusion. It is also available as a Google Colab notebook, accessible through GitHub.
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Data availability Design structures, AF2 models and experimental measurements are available at https://figshare.com/s/439fdd59488215753bc3 . Cryo-EM maps and corresponding atomic models for the Influenza HA binder in Fig. 6d -h have been deposited in the PDB and the Electron Microscopy Data Bank under accession codes 8SK7 and EMDB-40557, respectively. Electron microscopy data collected for the HE0537 oligomer are available at EMDB-40602 . Code availability Code for running RFdiffusion has been released on GitHub, free for academic, personal and commercial use at https://github.com/Rosetta- Commons/RFdiffusion . It is also available as a Google Colab notebook, accessible through GitHub.
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10.1088_1361-6501_ad0e9d.pdf
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Data availability statementThe data cannot be made publicly available upon publication because the cost of preparing, depositing and hosting the data would be prohibitive within the terms of this research project. The data that support the findings of this study are available upon reasonable request from the authors.
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Data availability statement The data cannot be made publicly available upon publication because the cost of preparing, depositing and hosting the data would be prohibitive within the terms of this research project. The data that support the findings of this study are available upon reasonable request from the authors.
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10.1371_journal.pone.0255730.pdf
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Data Availability Statement All relevant data are within the manuscript.
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All relevant data are within the manuscript.
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10.1371_journal.pbio.3002512.pdf
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Data Availability Statement: Codes and preprocessed data are available at https://osf.io/m7dta/. Note that raw SEEG and neuroimaging (T1-MPRAGE) data are protected and cannot be shared (CPP Sud-Est V, 2009-A00239-48).
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Codes and preprocessed data are available at https://osf.io/ m7dta/ . Note that raw SEEG and neuroimaging (T1-MPRAGE) data are protected and cannot be shared (CPP Sud-Est V, 2009-A00239-48).
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10.12688_f1000research.16224.3.pdf
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Data availability Pediococcus acidilactici strain DS32 16S ribosomal RNA gene, partial sequence, obtained during this study. GenBank accession number MH938236: http://identifiers.org/ncbigi/GI:1481059229.
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all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported Data availability Pediococcus acidilactici strain DS32 16S ribosomal RNA gene, partial sequence, obtained during this study. GenBank accession number MH938236: http://identifiers.org/ncbigi/ GI:1481059229 . Grant information This research was supported by Ministry of Research, Technology and Higher Education Republic of Indonesia through Master of Education Towards Doctoral Scholarship Program for Excellence Undergraduate and the support through World Class Professor Program Scheme-B No. 123.57/D2.3/KP/2018. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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10.1038_s41598-022-24860-9.pdf
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Data availability
All data presented here can be found online in Supplementary Information 1 (includes Methods S1–S6; Fig-
ures S1–S3; Tables S1–S5), and Supplementary Data S1.
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Data availability All data presented here can be found online in Supplementary Information 1 (includes Methods S1-S6; Figures S1-S3; Tables S1-S5 ), and Supplementary Data S1.
|
10.1371_journal.pone.0279220.pdf
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Data Availability Statement All relevant data are within the manuscript and its Supporting Information files. All files are available from thefigshare database (10.6084/m9.figshare.22578787 10.6084/m9.figshare.22578808).
|
All relevant data are within the manuscript and its Supporting Information files. All files are available from thefigshare database ( 10.6084/m9.figshare. 22578787 10.6084/m9.figshare.22578808 ).
|
10.1016_j.jrurstud.2023.01.003.pdf
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Data availabilityData will be made available on request.
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Data availability Data will be made available on request.
|
10.1007_s00428-018-2504-0.pdf
| null | null |
10.1088_1402-4896_ad07c3.pdf
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Data availability statementThe data cannot be made publicly available upon publication because they contain sensitive personal information. The data that support the findings of this study are available upon reasonable request from the authors.
|
Data availability statement The data cannot be made publicly available upon publication because they contain sensitive personal information. The data that support the findings of this study are available upon reasonable request from the authors.
|
10.3390_ijms241210388.pdf
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Data Availability StatementNot applicable.
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Data Availability Statement: Not applicable.
|
10.1038_s41467-021-27769-5.pdf
|
Data availability
The data and code underlying Fig. 2a, c, d are provided in the github repository https://
github.com/ClaMtnez/Ocean_tags. The data underlying Figs. 3, 4 & 5 and
Supplementary Figs. 1, 4 & 5 are provided as a Supplementary Data Files. The sequence
data generated in this study have been deposited in the EMBL Nucleotide Sequence
Database (ENA) database under Bioproject PRJEB35712 (metagenomic and
metatranscriptomic raw reads, metagenomic and metatranscriptomic assemblies,
metagenomic assembled genomes, and single-cell amplified genomes) and in the NCBI
Sequence Read Archive (SRA) under Bioproject PRJNA593264 (16S rRNA gene
amplicon reads). The following public databases were used in this study: Swiss-Prot
database, https://www.uniprot.org/, release-2018_10; Genome Taxonomy Database,
https://gtdb.ecogenomic.org/, release 80; SILVA non-redundant SSU Ref database,
https://www.arb-silva.de/, v.138; UniRef 100 VIROME database, http://
virome.dbi.udel.edu; Greening lab metabolic marker gene database, https://doi.org/
10.26180/c.5230745; CAZyme HMM database, https://bcb.unl.edu/dbCAN2/, v.8.0; Pfam
HMM database, http://pfam.xfam.org/, release 32.0; and TIGRFAM HMM database,
https://www.ncbi.nlm.nih.gov/genome/annotation_prok/tigrfams/, release 15.0
|
Data availability The data and code underlying Fig. 2a , c, d are provided in the github repository https:// github.com/ClaMtnez/Ocean_tags . The data underlying Figs. 3 , 4 & 5 and Supplementary Figs. 1, 4 & 5 are provided as a Supplementary Data Files. The sequence data generated in this study have been deposited in the EMBL Nucleotide Sequence Database (ENA) database under Bioproject PRJEB35712 (metagenomic and metatranscriptomic raw reads, metagenomic and metatranscriptomic assemblies, metagenomic assembled genomes, and single-cell amplified genomes) and in the NCBI Sequence Read Archive (SRA) under Bioproject PRJNA593264 (16S rRNA gene amplicon reads). The following public databases were used in this study: Swiss-Prot database, https://www.uniprot.org/ , release-2018_10; Genome Taxonomy Database, https://gtdb.ecogenomic.org/ , release 80; SILVA non-redundant SSU Ref database, https://www.arb-silva.de/ , v.138; UniRef 100 VIROME database, http:// virome.dbi.udel.edu ; Greening lab metabolic marker gene database, https://doi.org/ 10.26180/c.5230745 ; CAZyme HMM database, https://bcb.unl.edu/dbCAN2/ , v.8.0; Pfam HMM database, http://pfam.xfam.org/ , release 32.0; and TIGRFAM HMM database, https://www.ncbi.nlm.nih.gov/genome/annotation_prok/tigrfams/ , release 15.0
|
10.1371_journal.pone.0240176.pdf
|
Data Availability Statement All relevant data are within the manuscript and its Supporting Information files.
|
All relevant data are within the manuscript and its Supporting Information files.
|
10.1073_pnas.2220576120.pdf
|
Data, Materials, and Software Availability Sequencing data is available at National Center for Biotechnology Information Gene Expression Omnibus under accession GSE214456 (52). All other data are included in the manuscript and/or SI Appendix.
| null |
10.1088_1748-3190_ad00a2.pdf
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Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
|
Data availability statement All data that support the findings of this study are included within the article (and any supplementary files).
|
10.1093_nar_gkad633.pdf
|
Data AvailabilityAnalyses and data acquisition codes are upload on lab GitHub account and archived in Zenodo with the following doi. Additionally, raw data that support our findings have been uploaded and archived in Zenodo, corresponding to each individual figure.GitHub: https://github.com/Ha-SingleMoleculeLabAnalyses, data acquisition codes, and raw data are archived in Zenodo:Raw data analysis DOI: 10.5281/zenodo.4925617Data acquisition DOI: 10.5281/zenodo.4925630Raw data DOI: 10.5281/zenodo.8088172
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Data acquisition DOI: 10.5281 / zenodo.4925630 Raw data DOI: 10.5281 / zenodo.8088172
|
10.1186_s12872-022-02488-x.pdf
|
Availability of data and materials The data that support the findings of this study are available from the National Health Insurance Service in the Republic of Korea, but restrictions apply to the availability of these data, which were used under license for the current study and so are not publicly available. Data are, however, available from the authors upon reasonable request and with permission from the National Health Insurance Service.
|
Availability of data and materials The data that support the findings of this study are available from the National Health Insurance Service in the Republic of Korea, but restrictions apply to the availability of these data, which were used under license for the current study and so are not publicly available. Data are, however, available from the authors
|
10.1088_1402-4896_ad075b.pdf
|
Data availability statementAll data that support the findings of this study are included within the article (and any supplementary files).
|
Data availability statement All data that support the findings of this study are included within the article (and any supplementary files).
|
10.1103_physrevd.106.012002.pdf
| null | null |
10.1057_s41287-023-00576-y.pdf
| null | null |
10.1038_s41467-022-35112-9.pdf
|
Data availability
Data from this study is available at https://zenodo.org/badge/
latestdoi/566835035.
Code availability
The version of the model code used in this study is tagged as release
v1.0 and is available at https://zenodo.org/badge/latestdoi/566835035.
Necessary boundary condition files and observational data are inclu-
ded as part of the code release.
|
Data availability Data from this study is available at https://zenodo.org/badge/ latestdoi/566835035 . Code availability The version of the model code used in this study is tagged as release v1.0 and is available at https://zenodo.org/badge/latestdoi/566835035 . Necessary boundary condition files and observational data are included as part of the code release.
|
10.1016_j.celrep.2023.112408.pdf
|
Data and code availability Original small-RNA sequencing datasets are publicly available in NCBI under the accession number BioProject: PRJNA874806.
| null |
10.1088_1402-4896_ad0b51.pdf
|
Data availability statementThe data cannot be made publicly available upon publication because they are not available in a format that is sufficiently accessible or reusable by other researchers. The data that support the findings of this study are available upon reasonable request from the authors.
|
Data availability statement The data cannot be made publicly available upon publication because they are not available in a format that is sufficiently accessible or reusable by other researchers. The data that support the findings of this study are available upon reasonable request from the authors.
|
10.1103_physrevd.107.035007.pdf
| null | null |
10.1371_journal.pone.0241692.pdf
|
Data Availability Statement Data are contained within the paper.
|
Data are contained within the paper.
|
10.1021_acscentsci.3c00547.pdf
| null | null |
10.1371_journal.pclm.0000184.pdf
|
Data Availability Statement Causal loop diagrams refined during workshop discussion comprise the major data source of the study and are included in the submitted manuscript. Search terms and the extraction matrix used for the literature search to develop preliminary causal loop models are included as Supplementary material. Listing of the literature accessed and data extracted are lodged on the QMU eData repository: https://eresearch.qmu.ac.uk/handle/20.500.12289/12889.
| null |
10.1186_s12917-019-2170-8.pdf
|
Availability of data and materials The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
|
Availability of data and materials The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
|
10.1088_1402-4896_ad0a2a.pdf
|
Data availability statementThe data that support the findings of this study are openly available at the following URL/DOI: https://orcid.org/0000-0003-3389-9318.
|
Data availability statement The data that support the findings of this study are openly available at the following URL/DOI: https://orcid. org/0000-0003-3389-9318 .
|
10.1038/s41467-023-35891-9
|
Data availability
The data that support the findings of this study are available from the
corresponding authors upon request.
|
Data availability The data that support the findings of this study are available from the corresponding authors upon request.
|
10.1371_journal.pone.0262844.pdf
|
Data Availability Statement All relevant data are within the paper.
|
All relevant data are within the paper.
|
10.3389_fmicb.2021.711073.pdf
|
DATA AVAILABILITY STATEMENT
The original contributions presented in the study are included
in the article/Supplementary Material, further inquiries can be
directed to the corresponding author/s.
|
DATA AVAILABILITY STATEMENT The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author/s.
|
10.1038_s42003-021-02716-8.pdf
|
Data availabilitySeveral public databases were used in this study, including Immune Epitope Database and Analysis Resource (IEDB) (https://www.iedb.org/) for experimental measurements, UniProt (https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz) for decoy peptides, and IPD-IMGT/HLA (https://github.com/ANHIG/IMGTHLA/tree/3410) for MHC-I allele sequences. Research data files supporting this study, including the peptide-binding cleft sequence of MHC-I alleles; the training, validation, and benchmark datasets; the prediction of the validation and benchmark datasets; and the prediction of the allele expansion are available from Mendeley Data (10.17632/c249p8gdzd.3)33. Source data for all figures are provided in Supplementary Data. Code availabilityThe source code of the research and the MHCfovea’s predictor are freely available at GitHub (https://github.com/kohanlee1995/MHCfovea) and Mendeley Data33 for academic non-commercial research purposes. All source codes are based on Python (v3.6.9) and its packages, including numpy (v1.18.2), pandas (v1.0.3), scikit-learn (v0.22.2), pytorch (v1.4.0), matplotlib (v3.2.1), seaborn (v0.10.0), logomaker (v0.8). Numpy, pandas, and scikit-learn, are used for data analysis; pytorch is used for deep learning; matplotlib, seaborn, and logomaker are used for visualization. The website for the summarization of MHCfovea is available at https://mhcfovea.ailabs.tw.
|
Data availability Several public databases were used in this study, including Immune Epitope Database and Analysis Resource (IEDB) ( https://www.iedb.org/ ) for experimental measurements, UniProt ( https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/ complete/uniprot_sprot.fasta.gz ) for decoy peptides, and IPD-IMGT/HLA ( https:// github.com/ANHIG/IMGTHLA/tree/3410 ) for MHC-I allele sequences. Research data files supporting this study, including the peptide-binding cleft sequence of MHC-I alleles; the training, validation, and benchmark datasets; the prediction of the validation and benchmark datasets; and the prediction of the allele expansion are available from Mendeley Data ( https://doi.org/10.17632/c249p8gdzd.3 ) 33 . Source data for all figures are provided in Supplementary Data. Code availability The source code of the research and the MHCfovea's predictor are freely available at GitHub ( https://github.com/kohanlee1995/MHCfovea ) and Mendeley Data 33 for academic non-commercial research purposes. All source codes are based on Python (v3.6.9) and its packages, including numpy (v1.18.2), pandas (v1.0.3), scikit-learn (v0.22.2), pytorch (v1.4.0), matplotlib (v3.2.1), seaborn (v0.10.0), logomaker (v0.8). Numpy, pandas, and scikit-learn, are used for data analysis; pytorch is used for deep learning; matplotlib, seaborn, and logomaker are used for visualization. The website for the summarization of MHCfovea is available at https://mhcfovea.ailabs.tw .
|
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