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I'm a bioinformatician who works with mass spectrometry data. My PhD was dedicated to developing computational methods for glycomics and glycoproteomics, finding integrated-omics strategies to dig deeper into complex biological samples. My professional work now involves using that knowledge to analyze immunopeptidomics data to help develop better cancer vaccines. :email: Email me if you want to discuss MS data processing techniques, glycoinformatics, or antigenomics

🔬 Active Projects

I'm actively working on these projects. They get updated frequently. Please contact me if you want to know more about them or if you find them useful!

  • glycresoft: A glycan and glycopeptide LC-MS/MS search engine
  • ms_deisotope: A mass spectrometry library and executable for data access, signal processing, deisotoping, and charge state deconvolution suite. Actively working to deconvolute raw ion mobility data supporting Waters Cyclic IMS and Bruker TIMS-TOF data.
  • glypy: A glycoinformatics library for reading, writing, and manipulating glycans, as well as access to glycoinformatics resources around the web.

Supporting Libraries

These libraries receive updates as needed, but their purpose is to serve my other active projects. If they look useful to you, please let me know.

  • psims: Write HUPO PSI-MS mzML and mzIdentML XML formats.
  • brainpy: A library to generate coarse theoretical isotopic patterns.
  • ms_peak_picker: A low level library for signal processing of raw mass spectra
  • glycopeptidepy: A library to model glycopeptides and how they fragment. An extension to glypy.

Joshua Klein's Projects

arcashla icon arcashla

Fast and accurate in silico inference of HLA genotypes from RNA-seq

asinclude.jl icon asinclude.jl

A small macro to make re-defining types in a REPL or IJulia Notebook possible without restarting.

autodocstring icon autodocstring

vscode extension that generates docstrings for python files

autowrap icon autowrap

Generates Python Extension modules from Cythons PXD files

brainpy icon brainpy

A Python implementation of Baffling Recursive Algorithm for Isotopic distributioN calculations

casanovo icon casanovo

De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model

cgi_examples icon cgi_examples

A set of examples using CGI to demonstrate basic techniques

comtypes icon comtypes

A pure Python, lightweight COM client and server framework, based on the ctypes Python FFI package.

cyarray icon cyarray

An exercise in templating fast, resizable arrays for Cython that incur less Python overhead than the array module and expose a pure C representation which does not require any Python interaction.

cython_pyinstaller_example icon cython_pyinstaller_example

A simple example repository describing the process of building a PyInstaller executable for a Cython-compiled program

diffanal2 icon diffanal2

A simple differential gene expression analysis pipeline

gagdecon icon gagdecon

An isotopic pattern database approach to deconvolution of low molecular weight heparins

glm icon glm

A lean, mean GLM-modeling machine in Python

glycan-distributions icon glycan-distributions

Python script and web app for generating cosine similarity and normalized Kullback-Leibler divergence for glycoproteins

glycresoft icon glycresoft

An LC-MS/MS glycan and glycopeptide search engine

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