Add documentation for applications of Casanovo (#418)

* Add Casanovo applications page

* Index Casanovo applications

* Minor edits

* Shorten index title

* Add citation details and contact method

* Sentences on separate lines

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Co-authored-by: Wout Bittremieux <[email protected]>

docs/applications.md

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+# Applications of Casanovo
+
+_De novo_ peptide sequencing has diverse applications in proteomics, ranging from antibody sequencing to paleoproteomics.
+You can find some papers that use Casanovo for _de novo_ sequencing in different domains below.
+Contact us with your applications of Casanovo to feature your research on this page by opening a Github issue [here](https://github.com/Noble-Lab/casanovo/issues/new) with a link to the paper and a one-sentence description of how Casanovo is being used.
+
+- **[Comprehensive evaluation of peptide _de novo_ sequencing tools for monoclonal antibody assembly (Beslic et al., *Briefings in Bioinformatics*, 2023)](https://doi.org/10.1093/bib/bbac542)**: Casanovo is used to _de novo_ sequence monoclonal antibodies and shown to outperform other _de novo_ sequencing tools.
+- **[Giant genes are rare but implicated in cell wall degradation by predatory bacteria (West-Roberts et al., *bioRxiv*, 2023)](https://doi.org/10.1101/2023.11.21.568195)**: Casanovo is used to _de novo_ sequence giant proteins with up to 85,804 amino acids in a metagenomic setting.
+- **[Cryo-EM reveals that cardiac IGLV6-derived AL fibrils can be polymorphic (Bassett et al., *bioRxiv*, 2024)](https://doi.org/10.1101/2024.12.04.626857)**: Casanovo is used to _de novo_ sequence fibrils, i.e. antibody light chain aggregates.
+- **[_De novo_ assembled databases enable species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition (Klaes et al., *bioRxiv*, 2024)](https://doi.org/10.1101/2024.11.25.625156)**: Casanovo is used to _de novo_ sequence microbial peptides to enable species-specific protein-based stable isotope probing.
+- **[Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases (Chernigovskaya et al., *bioRxiv*, 2024)](https://doi.org/10.1101/2024.11.11.622451)**: Casanovo is used to profile the sequence diversity of circulating monoclonal antibody repertoire.
+
+Last updated on December 14, 2024.

docs/index.md

@@ -23,6 +23,7 @@ Getting Started <getting_started.md>
 File Formats <file_formats.md>
 Nextflow Workflow <nextflow.md>
 FAQs <faq.md>
+Applications <applications.md>
 Citing <cite.md>
 Contributing <CONTRIBUTING.md>
 Code of Conduct <CODE_OF_CONDUCT.md>