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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. Here are some papers that use Casanovo for de novo sequencing in different domains:
+_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.
+- **[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.
 
-- **[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.
+- **[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.
 
-- **[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.
+- **[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.
 
-- **[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.
+- **[_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.
 
-- **[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.
+- **[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.