OmniNovo
algorithm · Transformer (NAR)
OmniNovo: algorithm · Transformer (NAR). PTM-aware NAR
PTM-aware NAR
| Kind | algorithm |
| Deep learning | yes |
| Acquisition | DDA |
| Family | Transformer (NAR) |
Code
Live stars, open issues and last-push figures are on the Code activity chart.
Data
What the papers describing this method trained it on and reported its results on, as each paper states it. A version is named only where the paper names one.
Trained on
- A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermi (as deposited)
- An impaired respiratory electron chain triggers down-regulation of the energy metabolism and de-ubiquitination of solute (as deposited)
- Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation (as deposited)
- Analysis of the ubiquitin-modified proteome identifies novel host determinants of Kaposi’s sarcoma herpesvirus lytic rea (as deposited)
- Arginine methylation during transcriptional arrest (as deposited)
- BRCA1-dependent ubiquitination and phosphorylation regulates signaling events in high-grade serous ovarian cancer tissue (as deposited)
- Characterization of Arginine Methylation in Cancer Cell using LC-MS/MS (as deposited)
- Decrypting drug actions and protein modifications by dose- and time-resolved chemical proteomics (as deposited)
- High-dose oncogenic PIK3CA drives constitutive cellular stemness through increased NODAL/TGFb signaling (as deposited)
- Human Arginine Methylome - Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cel (as deposited)
- IPX001804000 (as deposited)
- Improved functional annotation of posttranslationally modified proteins (as deposited)
- Integrative phosphoproteomic analysis reveal hemostatic-endothelial signaling interplay (as deposited)
- Lztr1 loss leads to Noonan syndrome-like vascular defects by dysregulating vesicular trafficking (as deposited)
- MassIVE-KB (v1)
- MassIVE-KB (v2)
- Mutations in TRAF7 drive meningioma development by dysregulating proteostasis of the RAS-like GTPases (as deposited)
- ProMetheus: a database of hmSILAC-validated protein methylation sites (as deposited)
- Proteomics Profiling of Arginine Methylation Defines PRMT5 Substarate Specificity (as deposited)
- Quantitative phosphoproteomic analysis of acquired drug resistance to pazopanib and dasatinib (as deposited)
- Therapeutic targeting of RNA splicing catalysis through inhibition of protein arginine methylation (as deposited)
- Time-resolved analysis reveals rapid dynamics and broad scope of the CBP/p300 acetylome (as deposited)
Evaluated on
- A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermi (as deposited)
- An impaired respiratory electron chain triggers down-regulation of the energy metabolism and de-ubiquitination of solute (as deposited)
- Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation (as deposited)
- Analysis of the ubiquitin-modified proteome identifies novel host determinants of Kaposi’s sarcoma herpesvirus lytic rea (as deposited)
- Arginine methylation during transcriptional arrest (as deposited)
- BRCA1-dependent ubiquitination and phosphorylation regulates signaling events in high-grade serous ovarian cancer tissue (as deposited)
- Characterization of Arginine Methylation in Cancer Cell using LC-MS/MS (as deposited)
- DNA-PKcs kinase activity stabilizes the transcription factor Egr1 in activated immune cells (as deposited)
- Decrypting drug actions and protein modifications by dose- and time-resolved chemical proteomics (as deposited)
- Definition of aberrant MYB CBP/P300 complex in AML (as deposited)
- High-dose oncogenic PIK3CA drives constitutive cellular stemness through increased NODAL/TGFb signaling (as deposited)
- Human Arginine Methylome - Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cel (as deposited)
- IPX001804000 (as deposited)
- Identification of MRCKA as an integral component of ovarian cancer signaling and a therapeutic target (as deposited)
- Improved functional annotation of posttranslationally modified proteins (as deposited)
- InstaNovo-P FGFR2 phosphoproteomics (as deposited)
- Integrated lysine acetylation stoichiometry and proteomics analysis in human cells (as deposited)
- Integrated proteomic analysis of Tumor Necrosis Factor α and Interleukin 1 β-induced endothelial inflammation (as deposited)
- Integrative phosphoproteomic analysis reveal hemostatic-endothelial signaling interplay (as deposited)
- Lztr1 loss leads to Noonan syndrome-like vascular defects by dysregulating vesicular trafficking (as deposited)
- Mapping Ubiquitination Sites in Alzheimer’s Disease (as deposited)
- Mutations in TRAF7 drive meningioma development by dysregulating proteostasis of the RAS-like GTPases (as deposited)
- Nine-species benchmark (original (DeepNovo, 2017))
- Nine-species benchmark (revised (build not stated))
- PRMT1 controls the Senescence Associated Secretory Phenotype in Replication Stress Response (as deposited)
- Phosphoproteomic-based kinase profiling early in influenza virus infection (as deposited)
- ProMetheus: a database of hmSILAC-validated protein methylation sites (as deposited)
- Profiling of Proteome and Ubiquitome Changesin in endothelial cells in response to shear stress (as deposited)
- Proteomics Profiling of Arginine Methylation Defines PRMT5 Substarate Specificity (as deposited)
- Quantitative Analysis of Lysine Acetylation in A549 Cell Line (as deposited)
- Quantitative phosphoproteomic analysis of acquired drug resistance to pazopanib and dasatinib (as deposited)
- TBK1 interacts with tau and enhances neurodegeneration in tauopathy (as deposited)
- Therapeutic targeting of RNA splicing catalysis through inhibition of protein arginine methylation (as deposited)
- Time-resolved analysis reveals rapid dynamics and broad scope of the CBP/p300 acetylome (as deposited)
Paper describing it
- Accurate de novo sequencing of the modified proteome with OmniNovo (2025, arXiv, preprint)