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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
About me
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Posts
Future Blog Post
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Blog Post number 4
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Blog Post number 3
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Blog Post number 2
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Blog Post number 1
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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
modelangelo
ModelAngelo is an automated cryo-EM atomic model building software. It is free and available for everyone to use on Github. You can find the pre-print on arXiv. If you have an interesting use case, and especially if you have good resolution maps with unknown protein sequences, please reach out to me! In the future, this page will include a fully worked through tutorial along with example output. For now, you can enjoy this picture of ModelAngelo’s output on PHFs.
portfolio
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publications
ChainGAN: A sequential approach to GANs
Appears on arXiv
DeepConsensus: using the consensus of features from multiple layers to attain robust image classification
Appears on arXiv
An Inductive Bias for Distances: Neural Nets that Respect the Triangle Inequality
Published in ICLR 2020
Sparse Fourier Backpropagation in Cryo-EM Reconstruction
Published in NeurIPS 2022
Fast protein structure searching using structure graph embeddings
Published in Machine Learning for Structural Biology Workshop, NeurIPS 2022
A graph neural network approach to automated model building in cryo-EM maps
Published in Machine Learning for Structural Biology Workshop, NeurIPS 2022
A graph neural network approach to automated model building in cryo-EM maps
Published in ICLR 2023
Automated model building and protein identification in cryo-EM maps
Published in Nature
talks
Automated model building in cryo-EM maps using equivariant graph neural networks
Published:
Gave a talk describing my PhD project on using equivariant graph neural networks to do automated model building. This was at the Swiss Equivariant Learning Workshop.
ModelAngelo: Automated atomic model building and protein sequence discovery for cryo-EM maps
Published:
Seminar about ModelAngelo for the Molecular Biophysics Stockholm group at SciLifeLab, Stockholm.
ModelAngelo: Automated atomic model building and protein sequence discovery for cryo-EM maps
Published:
ModelAngelo talk for the SBGrid webinar series. Recording available in the link. This talk included some practical information for running the program as well as the methods details.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
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