Update and clean up of bibliography: citations updated, fixed and sor…

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galaxyproject · Jan 22, 2025 · ffa783c · ffa783c
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diff --git a/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.bib b/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.bib
@@ -14,39 +14,34 @@
 #
 # You can remove the examples below
 
-@article{Batut2018,
-  doi = {10.1016/j.cels.2018.05.012},
-  url = {https://doi.org/10.1016/j.cels.2018.05.012},
-  year = {2018},
-  month = jun,
-  publisher = {Elsevier {BV}},
-  volume = {6},
-  number = {6},
-  pages = {752--758.e1},
-  author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and
-           Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton
-           and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and
-           Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and
-           Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{i}}rez and Devon Ryan and
-           Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and
-           Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Bj\"{o}rn Gr\"{u}ning},
-  title = {Community-Driven Data Analysis Training for Biology},
-  journal = {Cell Systems}
+@article{Ayres1994,
+  title = {The Complete DNA Sequence of Autographa californica Nuclear Polyhedrosis Virus},
+  volume = {202},
+  ISSN = {0042-6822},
+  url = {http://dx.doi.org/10.1006/viro.1994.1380},
+  DOI = {10.1006/viro.1994.1380},
+  number = {2},
+  journal = {Virology},
+  publisher = {Elsevier BV},
+  author = {Ayres,  Martin D. and Howard,  Stephen C. and Kuzio,  John and Lopez-Ferber,  Miguel and Possee,  Robert D.},
+  year = {1994},
+  month = aug,
+  pages = {586–605}
 }
 
-@article{vanOers2007,
-  title = {Baculovirus Genomics},
-  volume = {8},
-  ISSN = {1389-4501},
-  url = {http://dx.doi.org/10.2174/138945007782151333},
-  DOI = {10.2174/138945007782151333},
-  number = {10},
-  journal = {Current Drug Targets},
-  publisher = {Bentham Science Publishers Ltd.},
-  author = {van Oers,  Monique and Vlak,  Just},
-  year = {2007},
-  month = oct,
-  pages = {1051–1068}
+@article{Cox2021,
+  title = {Innovations in the Insect Cell Expression System for Industrial Recombinant Vaccine Antigen Production},
+  volume = {9},
+  ISSN = {2076-393X},
+  url = {http://dx.doi.org/10.3390/vaccines9121504},
+  DOI = {10.3390/vaccines9121504},
+  number = {12},
+  journal = {Vaccines},
+  publisher = {MDPI AG},
+  author = {Cox,  Manon M. J.},
+  year = {2021},
+  month = dec,
+  pages = {1504}
 }
 
 @article{Fan2020,
@@ -63,34 +58,6 @@ @article{Fan2020
   month = sep 
 }
 
-@article{Wennmann2024,
-  title = {Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants},
-  volume = {105},
-  ISSN = {1465-2099},
-  url = {http://dx.doi.org/10.1099/jgv.0.001983},
-  DOI = {10.1099/jgv.0.001983},
-  number = {5},
-  journal = {Journal of General Virology},
-  publisher = {Microbiology Society},
-  author = {Wennmann,  J\"{o}rg T. and Lim,  Fang-Shiang and Senger,  Sergei and Gani,  Mudasir and Jehle,  Johannes A. and Keilwagen,  Jens},
-  year = {2024},
-  month = may 
-}
-
-@misc{ICTV_AcMNPV_genome_figure,
-  author = {International Committee on Taxonomy of Viruses (ICTV)},
-  title = {Genome mag of Autographa californica multiple nucleopolyhedrovirus isolate C6 (Figure 2)},
-  url = {\url{https://ictv.global/sites/default/files/inline-images/7651.ODD.Baculo.Fig2.v2.png}},
-  urldate = {2024-12-27}
-}
-
-@online{gtn-website,
-  author = {GTN community},
-  title = {GTN Training Materials: Collection of tutorials developed and maintained by the worldwide Galaxy community},
-  url = {https://training.galaxyproject.org},
-  urldate = {2021-03-24}
-}
-
 @article{Harrison2018,
   title = {ICTV Virus Taxonomy Profile: Baculoviridae},
   volume = {99},
@@ -106,29 +73,33 @@ @article{Harrison2018
   pages = {1185–1186}
 }
 
-@article{Ayres1994,
-  title = {The Complete DNA Sequence of Autographa californica Nuclear Polyhedrosis Virus},
-  volume = {202},
-  ISSN = {0042-6822},
-  url = {http://dx.doi.org/10.1006/viro.1994.1380},
-  DOI = {10.1006/viro.1994.1380},
+@article{RodrguezHernndez2023,
+  title = {Baculovirus Display of Peptides and Proteins for Medical Applications},
+  volume = {15},
+  ISSN = {1999-4915},
+  url = {http://dx.doi.org/10.3390/v15020411},
+  DOI = {10.3390/v15020411},
   number = {2},
-  journal = {Virology},
-  publisher = {Elsevier BV},
-  author = {Ayres,  Martin D. and Howard,  Stephen C. and Kuzio,  John and Lopez-Ferber,  Miguel and Possee,  Robert D.},
-  year = {1994},
-  month = aug,
-  pages = {586–605}
+  journal = {Viruses},
+  publisher = {MDPI AG},
+  author = {Rodríguez-Hernández,  Aaron Pavel and Martínez-Flores,  Daniel and Cruz-Reséndiz,  Adolfo and Padilla-Flores,  Teresa and González-Flores,  Rodrigo and Estrada,  Kenia and Sampieri,  Alicia and Camacho-Zarco,  Aldo Román and Vaca,  Luis},
+  year = {2023},
+  month = feb,
+  pages = {411}
 }
 
-@misc{sequence-analysis-quality-control,
-author = "Bérénice Batut and Maria Doyle and Alexandre Cormier and Anthony Bretaudeau and Laura Leroi and Erwan Corre and Stéphanie Robin and Cameron Hyde",
-	title = "Quality Control (Galaxy Training Materials)",
-	year = "",
-	month = "",
-	day = "",
-	url = "\url{https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html}",
-	note = "[Online; accessed Wed Jan 08 2025]"
+@article{vanOers2011,
+  title = {Opportunities and challenges for the baculovirus expression system},
+  volume = {107},
+  ISSN = {0022-2011},
+  url = {http://dx.doi.org/10.1016/j.jip.2011.05.001},
+  DOI = {10.1016/j.jip.2011.05.001},
+  journal = {Journal of Invertebrate Pathology},
+  publisher = {Elsevier BV},
+  author = {van Oers,  Monique M.},
+  year = {2011},
+  month = jul,
+  pages = {S3–S15}
 }
 
 @article{Wennmann2020,
@@ -144,4 +115,50 @@ @article{Wennmann2020
   year = {2020},
   month = jun,
   pages = {625}
+}
+
+@article{Wennmann2024,
+  title = {Haplotype determination of the Bombyx mori nucleopolyhedrovirus by Nanopore sequencing and linkage of single nucleotide variants},
+  volume = {105},
+  ISSN = {1465-2099},
+  url = {http://dx.doi.org/10.1099/jgv.0.001983},
+  DOI = {10.1099/jgv.0.001983},
+  number = {5},
+  journal = {Journal of General Virology},
+  publisher = {Microbiology Society},
+  author = {Wennmann,  J\"{o}rg T. and Lim,  Fang-Shiang and Senger,  Sergei and Gani,  Mudasir and Jehle,  Johannes A. and Keilwagen,  Jens},
+  year = {2024},
+  month = may 
+}
+
+@inbook{Eberle2012,
+  title = {Microbial control of crop pests using insect viruses.},
+  ISBN = {9781780640020},
+  url = {http://dx.doi.org/10.1079/9781845938086.0281},
+  DOI = {10.1079/9781845938086.0281},
+  booktitle = {Integrated pest management: principles and practice},
+  publisher = {CABI},
+  author = {Eberle,  K. E. and Jehle,  J. A. and Huber,  J.},
+  year = {2012},
+  month = jan,
+  pages = {281–298}
+}
+
+@inbook{Grzywacz2017,
+  title = {Production,  Formulation,  and Bioassay of Baculoviruses for Pest Control},
+  ISBN = {9780128035276},
+  url = {http://dx.doi.org/10.1016/B978-0-12-803527-6.00007-X},
+  DOI = {10.1016/b978-0-12-803527-6.00007-x},
+  booktitle = {Microbial Control of Insect and Mite Pests},
+  publisher = {Elsevier},
+  author = {Grzywacz,  D. and Moore,  S.},
+  year = {2017},
+  pages = {109–124}
+}
+
+@misc{ICTV_AcMNPV_genome_figure,
+  author = {International Committee on Taxonomy of Viruses (ICTV)},
+  title = {Genome mag of Autographa californica multiple nucleopolyhedrovirus isolate C6 (Figure 2)},
+  url = {\url{https://ictv.global/sites/default/files/inline-images/7651.ODD.Baculo.Fig2.v2.png}},
+  urldate = {2024-12-27}
 }
diff --git a/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.md b/topics/variant-analysis/tutorials/baculovirus-isolate-variation/tutorial.md
@@ -34,8 +34,10 @@ contributors:
 # Introduction
 
 Baculoviruses of the family *Baculoviridae* ({% cite Harrison2018 %}) are among the most intensively 
-studied viruses, not only because of their widespread application in biotechnology, medicine, and 
-agriculture ({% cite vanOers2007 %}). Like all members of the class *Naldaviricetes*, 
+studied viruses, not only because of their widespread application in biotechnology as protein expression 
+systems, medicine, and as biological insecticides ({% cite RodrguezHernndez2023 %}, 
+{% cite Cox2021 %}, {% cite Grzywacz2017 %}, {% cite Eberle2012 %}, {% cite vanOers2011 %}). 
+Like all members of the class *Naldaviricetes*, 
 baculoviruses have large circular dsDNA genomes that, in the family *Baculoviridae*, 
 range from 90 to 180 kbp and can encode up to 180 open reading frames (ORFs). 
 A detailed description of the biology of the Baculoviridae family can be found in the