From 980570bf9a44805a10a22f0e06b5fe15cf54f5fc Mon Sep 17 00:00:00 2001 From: Melih Yilmaz <32707537+melihyilmaz@users.noreply.github.com> Date: Wed, 11 Dec 2024 20:19:13 +0300 Subject: [PATCH 1/6] Add Casanovo applications page --- docs/applications.md | 14 ++++++++++++++ 1 file 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..a63a1098 --- /dev/null +++ b/docs/applications.md @@ -0,0 +1,14 @@ +# 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: + +- **[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. + +- **[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. + +- **[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. From c74efcfd929981c4bf52b170b77d18f327bfe593 Mon Sep 17 00:00:00 2001 From: Melih Yilmaz <32707537+melihyilmaz@users.noreply.github.com> Date: Wed, 11 Dec 2024 20:20:36 +0300 Subject: [PATCH 2/6] Index Casanovo applications --- docs/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/index.md b/docs/index.md index f6f54dd7..e091bf3e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -23,6 +23,7 @@ Getting Started File Formats Nextflow Workflow FAQs +Applications of Casanovo Citing Contributing Code of Conduct From e15d85b03c58570adb5e754a183d958db5185e93 Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Fri, 13 Dec 2024 12:33:23 +0100 Subject: [PATCH 3/6] Minor edits --- docs/applications.md | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/docs/applications.md b/docs/applications.md index a63a1098..2ae39427 100644 --- a/docs/applications.md +++ b/docs/applications.md @@ -1,14 +1,13 @@ # 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. From c727a8ccaaf8722ec90020899b961098d7fd112b Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Fri, 13 Dec 2024 12:33:53 +0100 Subject: [PATCH 4/6] Shorten index title --- docs/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.md b/docs/index.md index e091bf3e..a6adc917 100644 --- a/docs/index.md +++ b/docs/index.md @@ -23,7 +23,7 @@ Getting Started File Formats Nextflow Workflow FAQs -Applications of Casanovo +Applications Citing Contributing Code of Conduct From 15b0c0a3b073cb8b32d2e60adfc431f295abbb13 Mon Sep 17 00:00:00 2001 From: Melih Yilmaz <32707537+melihyilmaz@users.noreply.github.com> Date: Sat, 14 Dec 2024 08:34:36 +0300 Subject: [PATCH 5/6] Add citation details and contact method --- docs/applications.md | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/docs/applications.md b/docs/applications.md index 2ae39427..3c3c780e 100644 --- a/docs/applications.md +++ b/docs/applications.md @@ -1,13 +1,16 @@ # 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. 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 here by simplying 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. -- **[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 (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. -- **[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 (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. -- **[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. +- **[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](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 (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](https://doi.org/10.1101/2024.11.11.622451)**: Casanovo is used to profile the sequence diversity of circulating monoclonal antibody repertoire. +- **[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 From b10084275943237f3c87aae3a9fcd2d153f18a7c Mon Sep 17 00:00:00 2001 From: Wout Bittremieux Date: Mon, 16 Dec 2024 16:24:01 +0100 Subject: [PATCH 6/6] Sentences on separate lines --- docs/applications.md | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/docs/applications.md b/docs/applications.md index 3c3c780e..8d5c0cec 100644 --- a/docs/applications.md +++ b/docs/applications.md @@ -1,16 +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 here by simplying 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. +_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 +Last updated on December 14, 2024.