Publications

Cloudy with a chance of Peptides
nf-encyclopedia: An Open-Source Proteomics Pipeline
Building Spectral Libraries from DIA Mass Spec Data
Calibration Curves for Assessing Quantitative Proteomics
Quantification of Transcription Factors and Nuclear Proteins
Semisupervised Machine Learning for Sensitive Open Modification Spectral Library Searching
The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data
De novo mass spectrometry peptide sequencing with a transformer model
Sequence-to-sequence translation from mass spectra to peptides with a transformer model
Evaluating proteomics imputation methods with improved criteria
Quantification of Transcription Factors and Nuclear Proteins