Skip to content

Commit

Permalink
Merge pull request #6331 from openjournals/joss.07385
Browse files Browse the repository at this point in the history 
Merging automatically
  • Loading branch information
@editorialbot
editorialbot authored Jan 12, 2025
2 parents 8b34411 + 82b66f2 commit 565ff73
Show file tree
Hide file tree
Showing 3 changed files with 959 additions and 0 deletions.
283 changes: 283 additions & 0 deletions joss.07385/10.21105.joss.07385.crossref.xml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,283 @@
<?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>20250112234821-477467422a6f45290bd892052cbf964506c032d0</doi_batch_id>
<timestamp>20250112234821</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>01</month>
<year>2025</year>
</publication_date>
<journal_volume>
<volume>10</volume>
</journal_volume>
<issue>105</issue>
</journal_issue>
<journal_article publication_type="full_text">
<titles>
<title>delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition</title>
</titles>
<contributors>
<person_name sequence="first" contributor_role="author">
<given_name>Brice</given_name>
<surname>Letcher</surname>
<affiliations>
<institution><institution_name>Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR 5239, Inserm U1293, University Claude Bernard Lyon 1, Lyon, France</institution_name></institution>
</affiliations>
<ORCID>https://orcid.org/0000-0002-8921-6005</ORCID>
</person_name>
</contributors>
<publication_date>
<month>01</month>
<day>12</day>
<year>2025</year>
</publication_date>
<pages>
<first_page>7385</first_page>
</pages>
<publisher_item>
<identifier id_type="doi">10.21105/joss.07385</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.14526258</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/7385</rel:inter_work_relation>
</rel:related_item>
</rel:program>
<doi_data>
<doi>10.21105/joss.07385</doi>
<resource>https://joss.theoj.org/papers/10.21105/joss.07385</resource>
<collection property="text-mining">
<item>
<resource mime_type="application/pdf">https://joss.theoj.org/papers/10.21105/joss.07385.pdf</resource>
</item>
</collection>
</doi_data>
<citation_list>
<citation key="bleties:2021">
<article_title>BleTIES: annotation of natural genome editing in ciliates using long read sequencing</article_title>
<author>Seah</author>
<journal_title>Bioinformatics</journal_title>
<issue>21</issue>
<volume>37</volume>
<doi>10.1093/bioinformatics/btab613</doi>
<issn>1367-4803</issn>
<cYear>2021</cYear>
<unstructured_citation>Seah, B. K. B., &amp; Swart, E. C. (2021). BleTIES: annotation of natural genome editing in ciliates using long read sequencing. Bioinformatics, 37(21), 3929–3931. https://doi.org/10.1093/bioinformatics/btab613</unstructured_citation>
</citation>
<citation key="parties:2015">
<article_title>ParTIES: a toolbox for Paramecium interspersed DNA elimination studies</article_title>
<author>Denby Wilkes</author>
<journal_title>Bioinformatics</journal_title>
<issue>4</issue>
<volume>32</volume>
<doi>10.1093/bioinformatics/btv691</doi>
<issn>1367-4803</issn>
<cYear>2015</cYear>
<unstructured_citation>Denby Wilkes, C., Arnaiz, O., &amp; Sperling, L. (2015). ParTIES: a toolbox for Paramecium interspersed DNA elimination studies. Bioinformatics, 32(4), 599–601. https://doi.org/10.1093/bioinformatics/btv691</unstructured_citation>
</citation>
<citation key="sigar:2020">
<article_title>SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping</article_title>
<author>Feng</author>
<journal_title>Genome Biology and Evolution</journal_title>
<issue>10</issue>
<volume>12</volume>
<doi>10.1093/gbe/evaa147</doi>
<issn>1759-6653</issn>
<cYear>2020</cYear>
<unstructured_citation>Feng, Y., Beh, L. Y., Chang, W.-J., &amp; Landweber, L. F. (2020). SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping. Genome Biology and Evolution, 12(10), 1711–1718. https://doi.org/10.1093/gbe/evaa147</unstructured_citation>
</citation>
<citation key="adfinder:2020">
<article_title>ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data</article_title>
<author>Zheng</author>
<journal_title>Bioinformatics</journal_title>
<issue>12</issue>
<volume>36</volume>
<doi>10.1093/bioinformatics/btaa226</doi>
<issn>1367-4803</issn>
<cYear>2020</cYear>
<unstructured_citation>Zheng, W., Chen, J., Doak, T. G., Song, W., &amp; Yan, Y. (2020). ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data. Bioinformatics, 36(12), 3632–3636. https://doi.org/10.1093/bioinformatics/btaa226</unstructured_citation>
</citation>
<citation key="Boveri1887">
<article_title>Über differenzierung der zellkerne während der furchung des eies von ascaris megalocephala</article_title>
<author>Boveri</author>
<journal_title>Anatomischer Anzeiger</journal_title>
<volume>2</volume>
<cYear>1887</cYear>
<unstructured_citation>Boveri, T. (1887). Über differenzierung der zellkerne während der furchung des eies von ascaris megalocephala. Anatomischer Anzeiger, 2, 688–693.</unstructured_citation>
</citation>
<citation key="Beermann1977">
<article_title>The diminution of heterochromatic chromosomal segments in cyclops (crustacea, copepoda)</article_title>
<author>Beermann</author>
<journal_title>Chromosoma</journal_title>
<issue>4</issue>
<volume>60</volume>
<doi>10.1007/BF00292858</doi>
<issn>1432-0886</issn>
<cYear>1977</cYear>
<unstructured_citation>Beermann, S. (1977). The diminution of heterochromatic chromosomal segments in cyclops (crustacea, copepoda). Chromosoma, 60(4), 297–344. https://doi.org/10.1007/BF00292858</unstructured_citation>
</citation>
<citation key="Yu1991">
<article_title>Developmentally programmed healing of chromosomes by telomerase in tetrahymena</article_title>
<author>Yu</author>
<journal_title>Cell</journal_title>
<issue>4</issue>
<volume>67</volume>
<doi>10.1016/0092-8674(91)90077-c</doi>
<issn>0092-8674</issn>
<cYear>1991</cYear>
<unstructured_citation>Yu, G.-L., &amp; Blackburn, E. H. (1991). Developmentally programmed healing of chromosomes by telomerase in tetrahymena. Cell, 67(4), 823–832. https://doi.org/10.1016/0092-8674(91)90077-c</unstructured_citation>
</citation>
<citation key="Dedukh2021">
<article_title>Delete and survive: Strategies of programmed genetic material elimination in eukaryotes</article_title>
<author>Dedukh</author>
<journal_title>Biological Reviews</journal_title>
<issue>1</issue>
<volume>97</volume>
<doi>10.1111/brv.12796</doi>
<issn>1469-185X</issn>
<cYear>2021</cYear>
<unstructured_citation>Dedukh, D., &amp; Krasikova, A. (2021). Delete and survive: Strategies of programmed genetic material elimination in eukaryotes. Biological Reviews, 97(1), 195–216. https://doi.org/10.1111/brv.12796</unstructured_citation>
</citation>
<citation key="Drotos2022">
<article_title>Throwing away DNA: Programmed downsizing in somatic nuclei</article_title>
<author>Drotos</author>
<journal_title>Trends in Genetics</journal_title>
<issue>5</issue>
<volume>38</volume>
<doi>10.1016/j.tig.2022.02.003</doi>
<issn>0168-9525</issn>
<cYear>2022</cYear>
<unstructured_citation>Drotos, K. H. I., Zagoskin, M. V., Kess, T., Gregory, T. R., &amp; Wyngaard, G. A. (2022). Throwing away DNA: Programmed downsizing in somatic nuclei. Trends in Genetics, 38(5), 483–500. https://doi.org/10.1016/j.tig.2022.02.003</unstructured_citation>
</citation>
<citation key="Bailey2015">
<article_title>The MEME suite</article_title>
<author>Bailey</author>
<journal_title>Nucleic Acids Research</journal_title>
<issue>W1</issue>
<volume>43</volume>
<doi>10.1093/nar/gkv416</doi>
<issn>1362-4962</issn>
<cYear>2015</cYear>
<unstructured_citation>Bailey, T. L., Johnson, J., Grant, C. E., &amp; Noble, W. S. (2015). The MEME suite. Nucleic Acids Research, 43(W1), W39–W49. https://doi.org/10.1093/nar/gkv416</unstructured_citation>
</citation>
<citation key="Betermier2023">
<article_title>Programmed chromosome fragmentation in ciliated protozoa: Multiple means to chromosome ends</article_title>
<author>Bétermier</author>
<journal_title>Microbiology and Molecular Biology Reviews</journal_title>
<issue>4</issue>
<volume>87</volume>
<doi>10.1128/mmbr.00184-22</doi>
<issn>1098-5557</issn>
<cYear>2023</cYear>
<unstructured_citation>Bétermier, M., Klobutcher, L. A., &amp; Orias, E. (2023). Programmed chromosome fragmentation in ciliated protozoa: Multiple means to chromosome ends. Microbiology and Molecular Biology Reviews, 87(4). https://doi.org/10.1128/mmbr.00184-22</unstructured_citation>
</citation>
<citation key="Estrem2023">
<article_title>Programmed DNA elimination in the parasitic nematode ascaris</article_title>
<author>Estrem</author>
<journal_title>PLOS Pathogens</journal_title>
<issue>2</issue>
<volume>19</volume>
<doi>10.1371/journal.ppat.1011087</doi>
<issn>1553-7374</issn>
<cYear>2023</cYear>
<unstructured_citation>Estrem, B., &amp; Wang, J. (2023). Programmed DNA elimination in the parasitic nematode ascaris. PLOS Pathogens, 19(2), e1011087. https://doi.org/10.1371/journal.ppat.1011087</unstructured_citation>
</citation>
<citation key="Rey2023">
<article_title>Programmed DNA elimination in mesorhabditis nematodes</article_title>
<author>Rey</author>
<journal_title>Current Biology</journal_title>
<issue>17</issue>
<volume>33</volume>
<doi>10.1016/j.cub.2023.07.058</doi>
<issn>0960-9822</issn>
<cYear>2023</cYear>
<unstructured_citation>Rey, C., Launay, C., Wenger, E., &amp; Delattre, M. (2023). Programmed DNA elimination in mesorhabditis nematodes. Current Biology, 33(17), 3711–3721.e5. https://doi.org/10.1016/j.cub.2023.07.058</unstructured_citation>
</citation>
<citation key="GonzalezdelaRosa2020">
<article_title>A telomere-to-telomere assembly of oscheius tipulae and the evolution of rhabditid nematode chromosomes</article_title>
<author>Gonzalez de la Rosa</author>
<journal_title>G3 Genes|Genomes|Genetics</journal_title>
<issue>1</issue>
<volume>11</volume>
<doi>10.1093/g3journal/jkaa020</doi>
<issn>2160-1836</issn>
<cYear>2020</cYear>
<unstructured_citation>Gonzalez de la Rosa, P. M., Thomson, M., Trivedi, U., Tracey, A., Tandonnet, S., &amp; Blaxter, M. (2020). A telomere-to-telomere assembly of oscheius tipulae and the evolution of rhabditid nematode chromosomes. G3 Genes|Genomes|Genetics, 11(1). https://doi.org/10.1093/g3journal/jkaa020</unstructured_citation>
</citation>
<citation key="Dockendorff2022">
<article_title>The nematode oscheius tipulae as a genetic model for programmed DNA elimination</article_title>
<author>Dockendorff</author>
<journal_title>Current Biology</journal_title>
<issue>23</issue>
<volume>32</volume>
<doi>10.1016/j.cub.2022.10.043</doi>
<issn>0960-9822</issn>
<cYear>2022</cYear>
<unstructured_citation>Dockendorff, T. C., Estrem, B., Reed, J., Simmons, J. R., Zadegan, S. B., Zagoskin, M. V., Terta, V., Villalobos, E., Seaberry, E. M., &amp; Wang, J. (2022). The nematode oscheius tipulae as a genetic model for programmed DNA elimination. Current Biology, 32(23), 5083–5098.e6. https://doi.org/10.1016/j.cub.2022.10.043</unstructured_citation>
</citation>
<citation key="DTOL2022">
<article_title>Sequence locally, think globally: The darwin tree of life project</article_title>
<author>Blaxter</author>
<journal_title>Proceedings of the National Academy of Sciences</journal_title>
<issue>4</issue>
<volume>119</volume>
<doi>10.1073/pnas.2115642118</doi>
<issn>1091-6490</issn>
<cYear>2022</cYear>
<unstructured_citation>Blaxter, M., Mieszkowska, N., Di Palma, F., Holland, P., Durbin, R., Richards, T., Berriman, M., Kersey, P., Hollingsworth, P., Wilson, W., Twyford, A., Gaya, E., Lawniczak, M., Lewis, O., Broad, G., Howe, K., Hart, M., Flicek, P., &amp; Barnes, I. (2022). Sequence locally, think globally: The darwin tree of life project. Proceedings of the National Academy of Sciences, 119(4). https://doi.org/10.1073/pnas.2115642118</unstructured_citation>
</citation>
<citation key="EBGP2022">
<article_title>The earth BioGenome project 2020: Starting the clock</article_title>
<author>Lewin</author>
<journal_title>Proceedings of the National Academy of Sciences</journal_title>
<issue>4</issue>
<volume>119</volume>
<doi>10.1073/pnas.2115635118</doi>
<issn>1091-6490</issn>
<cYear>2022</cYear>
<unstructured_citation>Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, M. L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S.-M., Chen, L., Childers, A. K., Coddington, J. A., … Zhang, G. (2022). The earth BioGenome project 2020: Starting the clock. Proceedings of the National Academy of Sciences, 119(4). https://doi.org/10.1073/pnas.2115635118</unstructured_citation>
</citation>
<citation key="ZenodoData2024">
<article_title>Dataset supporting the tool ’delfies: A python package for the detection of DNA breakpoints with neo-telomere addition’</article_title>
<author>Letcher</author>
<doi>10.5281/zenodo.14101797</doi>
<cYear>2024</cYear>
<unstructured_citation>Letcher, B. (2024). Dataset supporting the tool ’delfies: A python package for the detection of DNA breakpoints with neo-telomere addition’. Zenodo. https://doi.org/10.5281/zenodo.14101797</unstructured_citation>
</citation>
</citation_list>
</journal_article>
</journal>
</body>
</doi_batch>
Binary file added joss.07385/10.21105.joss.07385.pdf
View file
Binary file not shown.
Loading

0 comments on commit 565ff73

Please sign in to comment.