-
Notifications
You must be signed in to change notification settings - Fork 21
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #5637 from openjournals/joss.06129
Merging automatically
- Loading branch information
Showing
6 changed files
with
1,075 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,326 @@ | ||
<?xml version="1.0" encoding="UTF-8"?> | ||
<doi_batch xmlns="http://www.crossref.org/schema/5.3.1" | ||
xmlns:ai="http://www.crossref.org/AccessIndicators.xsd" | ||
xmlns:rel="http://www.crossref.org/relations.xsd" | ||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
version="5.3.1" | ||
xsi:schemaLocation="http://www.crossref.org/schema/5.3.1 http://www.crossref.org/schemas/crossref5.3.1.xsd"> | ||
<head> | ||
<doi_batch_id>20240717081112-408074357331fb39ed9fca0bf14b1a0226239117</doi_batch_id> | ||
<timestamp>20240717081112</timestamp> | ||
<depositor> | ||
<depositor_name>JOSS Admin</depositor_name> | ||
<email_address>[email protected]</email_address> | ||
</depositor> | ||
<registrant>The Open Journal</registrant> | ||
</head> | ||
<body> | ||
<journal> | ||
<journal_metadata> | ||
<full_title>Journal of Open Source Software</full_title> | ||
<abbrev_title>JOSS</abbrev_title> | ||
<issn media_type="electronic">2475-9066</issn> | ||
<doi_data> | ||
<doi>10.21105/joss</doi> | ||
<resource>https://joss.theoj.org</resource> | ||
</doi_data> | ||
</journal_metadata> | ||
<journal_issue> | ||
<publication_date media_type="online"> | ||
<month>07</month> | ||
<year>2024</year> | ||
</publication_date> | ||
<journal_volume> | ||
<volume>9</volume> | ||
</journal_volume> | ||
<issue>99</issue> | ||
</journal_issue> | ||
<journal_article publication_type="full_text"> | ||
<titles> | ||
<title>dms-viz: Structure-informed visualizations for deep | ||
mutational scanning and other mutation-based datasets</title> | ||
</titles> | ||
<contributors> | ||
<person_name sequence="first" contributor_role="author"> | ||
<given_name>William W.</given_name> | ||
<surname>Hannon</surname> | ||
<ORCID>https://orcid.org/0000-0002-6014-4749</ORCID> | ||
</person_name> | ||
<person_name sequence="additional" | ||
contributor_role="author"> | ||
<given_name>Jesse D.</given_name> | ||
<surname>Bloom</surname> | ||
<ORCID>https://orcid.org/0000-0003-1267-3408</ORCID> | ||
</person_name> | ||
</contributors> | ||
<publication_date> | ||
<month>07</month> | ||
<day>17</day> | ||
<year>2024</year> | ||
</publication_date> | ||
<pages> | ||
<first_page>6129</first_page> | ||
</pages> | ||
<publisher_item> | ||
<identifier id_type="doi">10.21105/joss.06129</identifier> | ||
</publisher_item> | ||
<ai:program name="AccessIndicators"> | ||
<ai:license_ref applies_to="vor">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
<ai:license_ref applies_to="am">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
<ai:license_ref applies_to="tdm">http://creativecommons.org/licenses/by/4.0/</ai:license_ref> | ||
</ai:program> | ||
<rel:program> | ||
<rel:related_item> | ||
<rel:description>Software archive</rel:description> | ||
<rel:inter_work_relation relationship-type="references" identifier-type="doi">10.5281/zenodo.12693853</rel:inter_work_relation> | ||
</rel:related_item> | ||
<rel:related_item> | ||
<rel:description>GitHub review issue</rel:description> | ||
<rel:inter_work_relation relationship-type="hasReview" identifier-type="uri">https://github.com/openjournals/joss-reviews/issues/6129</rel:inter_work_relation> | ||
</rel:related_item> | ||
</rel:program> | ||
<doi_data> | ||
<doi>10.21105/joss.06129</doi> | ||
<resource>https://joss.theoj.org/papers/10.21105/joss.06129</resource> | ||
<collection property="text-mining"> | ||
<item> | ||
<resource mime_type="application/pdf">https://joss.theoj.org/papers/10.21105/joss.06129.pdf</resource> | ||
</item> | ||
</collection> | ||
</doi_data> | ||
<citation_list> | ||
<citation key="bloomFitnessEffectsMutations2023"> | ||
<article_title>Fitness effects of mutations to SARS-CoV-2 | ||
proteins</article_title> | ||
<author>Bloom</author> | ||
<journal_title>Virus Evolution</journal_title> | ||
<issue>2</issue> | ||
<volume>9</volume> | ||
<doi>10.1093/ve/vead055</doi> | ||
<issn>2057-1577</issn> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Bloom, J. D., & Neher, R. A. | ||
(2023). Fitness effects of mutations to SARS-CoV-2 proteins. Virus | ||
Evolution, 9(2), vead055. | ||
https://doi.org/10.1093/ve/vead055</unstructured_citation> | ||
</citation> | ||
<citation key="bobyOpenScienceDiscovery2023"> | ||
<article_title>Open Science Discovery of Potent Non-Covalent | ||
SARS-CoV-2 Main Protease Inhibitors</article_title> | ||
<author>Boby</author> | ||
<doi>10.1101/2020.10.29.339317</doi> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Boby, M. L., Fearon, D., Ferla, M., | ||
Filep, M., Koekemoer, L., Robinson, M. C., The COVID Moonshot | ||
Consortium, Chodera, J. D., Lee, A. A., London, N., von Delft, A., & | ||
von Delft, F. (2023). Open Science Discovery of Potent Non-Covalent | ||
SARS-CoV-2 Main Protease Inhibitors (p. 2020.10.29.339317). bioRxiv. | ||
https://doi.org/10.1101/2020.10.29.339317</unstructured_citation> | ||
</citation> | ||
<citation key="dadonaitePseudovirusSystemEnables2023"> | ||
<article_title>A pseudovirus system enables deep mutational | ||
scanning of the full SARS-CoV-2 spike</article_title> | ||
<author>Dadonaite</author> | ||
<journal_title>Cell</journal_title> | ||
<issue>6</issue> | ||
<volume>186</volume> | ||
<doi>10.1016/j.cell.2023.02.001</doi> | ||
<issn>1097-4172</issn> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Dadonaite, B., Crawford, K. H. D., | ||
Radford, C. E., Farrell, A. G., Yu, T. C., Hannon, W. W., Zhou, P., | ||
Andrabi, R., Burton, D. R., Liu, L., Ho, D. D., Chu, H. Y., Neher, R. | ||
A., & Bloom, J. D. (2023). A pseudovirus system enables deep | ||
mutational scanning of the full SARS-CoV-2 spike. Cell, 186(6), | ||
1263–1278.e20. | ||
https://doi.org/10.1016/j.cell.2023.02.001</unstructured_citation> | ||
</citation> | ||
<citation key="espositoMaveDBOpensourcePlatform2019"> | ||
<article_title>MaveDB: An open-source platform to distribute | ||
and interpret data from multiplexed assays of variant | ||
effect</article_title> | ||
<author>Esposito</author> | ||
<journal_title>Genome Biology</journal_title> | ||
<issue>1</issue> | ||
<volume>20</volume> | ||
<doi>10.1186/s13059-019-1845-6</doi> | ||
<issn>1474-760X</issn> | ||
<cYear>2019</cYear> | ||
<unstructured_citation>Esposito, D., Weile, J., Shendure, | ||
J., Starita, L. M., Papenfuss, A. T., Roth, F. P., Fowler, D. M., & | ||
Rubin, A. F. (2019). MaveDB: An open-source platform to distribute and | ||
interpret data from multiplexed assays of variant effect. Genome | ||
Biology, 20(1), 223. | ||
https://doi.org/10.1186/s13059-019-1845-6</unstructured_citation> | ||
</citation> | ||
<citation key="fowlerAtlasVariantEffects2023"> | ||
<article_title>An Atlas of Variant Effects to understand the | ||
genome at nucleotide resolution</article_title> | ||
<author>Fowler</author> | ||
<journal_title>Genome Biology</journal_title> | ||
<issue>1</issue> | ||
<volume>24</volume> | ||
<doi>10.1186/s13059-023-02986-x</doi> | ||
<issn>1474-760X</issn> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Fowler, D. M., Adams, D. J., Gloyn, | ||
A. L., Hahn, W. C., Marks, D. S., Muffley, L. A., Neal, J. T., Roth, F. | ||
P., Rubin, A. F., Starita, L. M., & Hurles, M. E. (2023). An Atlas | ||
of Variant Effects to understand the genome at nucleotide resolution. | ||
Genome Biology, 24(1), 147. | ||
https://doi.org/10.1186/s13059-023-02986-x</unstructured_citation> | ||
</citation> | ||
<citation key="fowlerDeepMutationalScanning2014"> | ||
<article_title>Deep mutational scanning: A new style of | ||
protein science</article_title> | ||
<author>Fowler</author> | ||
<journal_title>Nature Methods</journal_title> | ||
<issue>8</issue> | ||
<volume>11</volume> | ||
<doi>10.1038/nmeth.3027</doi> | ||
<issn>1548-7105</issn> | ||
<cYear>2014</cYear> | ||
<unstructured_citation>Fowler, D. M., & Fields, S. | ||
(2014). Deep mutational scanning: A new style of protein science. Nature | ||
Methods, 11(8), 801–807. | ||
https://doi.org/10.1038/nmeth.3027</unstructured_citation> | ||
</citation> | ||
<citation key="hiltonDmsviewInteractiveVisualization2020"> | ||
<article_title>Dms-view: Interactive visualization tool for | ||
deep mutational scanning data</article_title> | ||
<author>Hilton</author> | ||
<journal_title>Journal of Open Source | ||
Software</journal_title> | ||
<issue>52</issue> | ||
<volume>5</volume> | ||
<doi>10.21105/joss.02353</doi> | ||
<issn>2475-9066</issn> | ||
<cYear>2020</cYear> | ||
<unstructured_citation>Hilton, S. K., Huddleston, J., Black, | ||
A., North, K., Dingens, A. S., Bedford, T., & Bloom, J. D. (2020). | ||
Dms-view: Interactive visualization tool for deep mutational scanning | ||
data. Journal of Open Source Software, 5(52), 2353. | ||
https://doi.org/10.21105/joss.02353</unstructured_citation> | ||
</citation> | ||
<citation key="liDeepMutationalScanning2023"> | ||
<article_title>Deep mutational scanning reveals the | ||
functional constraints and evolutionary potential of the influenza A | ||
virus PB1 protein</article_title> | ||
<author>Li</author> | ||
<doi>10.1101/2023.08.27.554986</doi> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Li, Y., Arcos, S., Sabsay, K. R., te | ||
Velthuis, A. J. W., & Lauring, A. S. (2023). Deep mutational | ||
scanning reveals the functional constraints and evolutionary potential | ||
of the influenza A virus PB1 protein (p. 2023.08.27.554986). bioRxiv. | ||
https://doi.org/10.1101/2023.08.27.554986</unstructured_citation> | ||
</citation> | ||
<citation key="matreyekMultiplexAssessmentProtein2018"> | ||
<article_title>Multiplex assessment of protein variant | ||
abundance by massively parallel sequencing</article_title> | ||
<author>Matreyek</author> | ||
<journal_title>Nature Genetics</journal_title> | ||
<issue>6</issue> | ||
<volume>50</volume> | ||
<doi>10.1038/s41588-018-0122-z</doi> | ||
<issn>1546-1718</issn> | ||
<cYear>2018</cYear> | ||
<unstructured_citation>Matreyek, K. A., Starita, L. M., | ||
Stephany, J. J., Martin, B., Chiasson, M. A., Gray, V. E., Kircher, M., | ||
Khechaduri, A., Dines, J. N., Hause, R. J., Bhatia, S., Evans, W. E., | ||
Relling, M. V., Yang, W., Shendure, J., & Fowler, D. M. (2018). | ||
Multiplex assessment of protein variant abundance by massively parallel | ||
sequencing. Nature Genetics, 50(6), 874–882. | ||
https://doi.org/10.1038/s41588-018-0122-z</unstructured_citation> | ||
</citation> | ||
<citation key="radfordMappingNeutralizingSpecificity2023"> | ||
<article_title>Mapping the neutralizing specificity of human | ||
anti-HIV serum by deep mutational scanning</article_title> | ||
<author>Radford</author> | ||
<journal_title>Cell Host & Microbe</journal_title> | ||
<issue>7</issue> | ||
<volume>31</volume> | ||
<doi>10.1016/j.chom.2023.05.025</doi> | ||
<issn>1934-6069</issn> | ||
<cYear>2023</cYear> | ||
<unstructured_citation>Radford, C. E., Schommers, P., | ||
Gieselmann, L., Crawford, K. H. D., Dadonaite, B., Yu, T. C., Dingens, | ||
A. S., Overbaugh, J., Klein, F., & Bloom, J. D. (2023). Mapping the | ||
neutralizing specificity of human anti-HIV serum by deep mutational | ||
scanning. Cell Host & Microbe, 31(7), 1200–1215.e9. | ||
https://doi.org/10.1016/j.chom.2023.05.025</unstructured_citation> | ||
</citation> | ||
<citation key="roseNGLViewerWebbased2018"> | ||
<article_title>NGL viewer: Web-based molecular graphics for | ||
large complexes</article_title> | ||
<author>Rose</author> | ||
<journal_title>Bioinformatics (Oxford, | ||
England)</journal_title> | ||
<issue>21</issue> | ||
<volume>34</volume> | ||
<doi>10.1093/bioinformatics/bty419</doi> | ||
<issn>1367-4811</issn> | ||
<cYear>2018</cYear> | ||
<unstructured_citation>Rose, A. S., Bradley, A. R., | ||
Valasatava, Y., Duarte, J. M., Prlic, A., & Rose, P. W. (2018). NGL | ||
viewer: Web-based molecular graphics for large complexes. Bioinformatics | ||
(Oxford, England), 34(21), 3755–3758. | ||
https://doi.org/10.1093/bioinformatics/bty419</unstructured_citation> | ||
</citation> | ||
<citation key="starrDeepMutationalScanning2020"> | ||
<article_title>Deep Mutational Scanning of SARS-CoV-2 | ||
Receptor Binding Domain Reveals Constraints on Folding and ACE2 | ||
Binding</article_title> | ||
<author>Starr</author> | ||
<journal_title>Cell</journal_title> | ||
<issue>5</issue> | ||
<volume>182</volume> | ||
<doi>10.1016/j.cell.2020.08.012</doi> | ||
<issn>1097-4172</issn> | ||
<cYear>2020</cYear> | ||
<unstructured_citation>Starr, T. N., Greaney, A. J., Hilton, | ||
S. K., Ellis, D., Crawford, K. H. D., Dingens, A. S., Navarro, M. J., | ||
Bowen, J. E., Tortorici, M. A., Walls, A. C., King, N. P., Veesler, D., | ||
& Bloom, J. D. (2020). Deep Mutational Scanning of SARS-CoV-2 | ||
Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding. | ||
Cell, 182(5), 1295–1310.e20. | ||
https://doi.org/10.1016/j.cell.2020.08.012</unstructured_citation> | ||
</citation> | ||
<citation key="starrProspectiveMappingViral2021"> | ||
<article_title>Prospective mapping of viral mutations that | ||
escape antibodies used to treat COVID-19</article_title> | ||
<author>Starr</author> | ||
<journal_title>Science (New York, N.Y.)</journal_title> | ||
<issue>6531</issue> | ||
<volume>371</volume> | ||
<doi>10.1126/science.abf9302</doi> | ||
<issn>1095-9203</issn> | ||
<cYear>2021</cYear> | ||
<unstructured_citation>Starr, T. N., Greaney, A. J., | ||
Addetia, A., Hannon, W. W., Choudhary, M. C., Dingens, A. S., Li, J. Z., | ||
& Bloom, J. D. (2021). Prospective mapping of viral mutations that | ||
escape antibodies used to treat COVID-19. Science (New York, N.Y.), | ||
371(6531), 850–854. | ||
https://doi.org/10.1126/science.abf9302</unstructured_citation> | ||
</citation> | ||
<citation key="yuBiophysicalModelViral2022"> | ||
<article_title>A biophysical model of viral escape from | ||
polyclonal antibodies</article_title> | ||
<author>Yu</author> | ||
<journal_title>Virus Evolution</journal_title> | ||
<issue>2</issue> | ||
<volume>8</volume> | ||
<doi>10.1093/ve/veac110</doi> | ||
<issn>2057-1577</issn> | ||
<cYear>2022</cYear> | ||
<unstructured_citation>Yu, T. C., Thornton, Z. T., Hannon, | ||
W. W., DeWitt, W. S., Radford, C. E., Matsen, F. A., & Bloom, J. D. | ||
(2022). A biophysical model of viral escape from polyclonal antibodies. | ||
Virus Evolution, 8(2), veac110. | ||
https://doi.org/10.1093/ve/veac110</unstructured_citation> | ||
</citation> | ||
</citation_list> | ||
</journal_article> | ||
</journal> | ||
</body> | ||
</doi_batch> |
Binary file not shown.
Oops, something went wrong.