From 5d06beae748fcd2aca5be049adfd0e47947aaf37 Mon Sep 17 00:00:00 2001 From: Melih Yilmaz <32707537+melihyilmaz@users.noreply.github.com> Date: Mon, 16 Dec 2024 18:24:41 +0300 Subject: [PATCH] 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 --------- Co-authored-by: Wout Bittremieux --- docs/applications.md | 13 +++++++++++++ docs/index.md | 1 + 2 files changed, 14 insertions(+) create mode 100644 docs/applications.md diff --git a/docs/applications.md b/docs/applications.md new file mode 100644 index 00000000..8d5c0cec --- /dev/null +++ b/docs/applications.md @@ -0,0 +1,13 @@ +# 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. diff --git a/docs/index.md b/docs/index.md index f6f54dd7..a6adc917 100644 --- a/docs/index.md +++ b/docs/index.md @@ -23,6 +23,7 @@ Getting Started File Formats Nextflow Workflow FAQs +Applications Citing Contributing Code of Conduct