Indiana University
Bloomington, USA, Bloomington · 16 authors
Indiana University (Bloomington, USA, Bloomington): 16 authors and 22 papers in the de novo peptide sequencing catalog.
Departments
- Computer Science
- Department of Chemistry
Papers (22)
- AI proteomics: from protein identification to virtual cells (2026, Nature Methods)
- CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo (2026, bioRxiv)
- A living proteomics benchmark for comprehensive evaluation of deep learning-based de novo peptide sequencing tools (2026, Nature Methods (Registered Report))
- Improvements to Casanovo, a Deep Learning De Novo Peptide Sequencer (2025, Journal of Proteome Research)
- Improvements to CasaNovo, a deep learning de novo peptide sequencer (2025, bioRxiv)
- Foundation model for mass spectrometry proteomics (2025, arXiv)
- Deep Learning Methods for De Novo Peptide Sequencing (2024, Mass Spectrometry Reviews)
- Accounting for Digestion Enzyme Bias in Casanovo (2024, Journal of Proteome Research)
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2024, Nature Communications)
- Accurate de novo peptide sequencing using fully convolutional neural networks (2023, Nature Communications)
- Sequence-to-sequence translation from mass spectra to peptides with a transformer model (2023, bioRxiv)
- De novo mass spectrometry peptide sequencing with a transformer model (2022, ICML 2022)
- PepNet: A Fully Convolutional Neural Network for De novo Peptide Sequencing (2022, Research Square)
- De novo mass spectrometry peptide sequencing with a transformer model (2022, bioRxiv)
- Proteogenomic Analysis Unveils the HLA Class I-Presented Immunopeptidome in Melanoma and EGFR-Mutant Lung Adenocarcinoma (2021, Molecular & Cellular Proteomics)
- 2018 YPIC Challenge: A Case Study in Characterizing an Unknown Protein Sample (2019, Journal of Proteome Research)
- Constrained De Novo Sequencing of neo-Epitope Peptides Using Tandem Mass Spectrometry (2018, Lecture Notes in Computer Science)
- Investigation of VUV photodissociation propensities using peptide libraries (2011, International Journal of Mass Spectrometry)
- De NovoSequencing of Tryptic Peptides Derived fromDeinococcus radioduransRibosomal Proteins Using 157 nm Photodissociation MALDI TOF/TOF Mass Spectrometry (2010, Journal of Proteome Research)
- Peptide de Novo Sequencing Using 157 nm Photodissociation in a Tandem Time-of-Flight Mass Spectrometer (2010, Analytical Chemistry)
- Peptide de Novo Sequencing Facilitated by a Dual-Labeling Strategy (2005, Analytical Chemistry)
- Shotgun Protein Sequencing by Tandem Mass Spectra Assembly (2004, Analytical Chemistry)