Add documentation for applications of Casanovo

docs/applications.md

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+# Applications of Casanovo
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+De novo peptide sequencing has diverse applications in proteomics ranging from antibody sequencing to paleoproteomics. Here are some papers that use Casanovo for de novo sequencing in different domains:
+
+- **[Cryo-EM reveals that cardiac IGLV6-derived AL fibrils can be polymorphic](https://doi.org/10.1101/2024.12.04.626857)** Casanovo is used to de novo sequence fibrils, i.e. antibody light chain aggregates.
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+- **[Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly](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.
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+- **[Giant genes are rare but implicated in cell wall degradation by predatory bacteria](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.
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+- **[De novo assembled databases enable species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition](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.
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+- **[Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases](https://doi.org/10.1101/2024.11.11.622451)** Casanovo is used to profile the sequence diversity of circulating monoclonal antibody repertoire.
+stable isotope probing.

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 of Casanovo <applications.md>
 Citing <cite.md>
 Contributing <CONTRIBUTING.md>
 Code of Conduct <CODE_OF_CONDUCT.md>