Evan Seitz

Which mutations rewire function of regulatory DNA? Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models. Led by @EESetiz 1/N 🧵👇

At @iclr_conf and interested in AI x Bio? Come see new work by the Koo Lab! 1. Oral presentation at @gembioworkshop by Evan Seitz (@EESeitz) on SEAM a method to decode the mechanistic impact of genetic variation on regulatory sequences with deep learning! openreview.net/forum?id=PtjMe…

Very proud that SQUID is now published in Nature Machine Intelligence! @NatMachIntell View only link (no subscription needed): rdcu.be/dLuZe Full link (w/ subscription): nature.com/articles/s4225… @EESeitz @jbkinney @TheDMMcC (Thanks to reviewers for feedback)

In genomic deep learning, the trends right now are to build bigger models that consider longer sequence contexts. While predictions are more powerful, their scale makes them difficult to interpret. To address this gap, we have developed CREME. Paper: biorxiv.org/content/10.110… 1/N

Excited to share new work on "Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models” led by @EESeitz, jointly advised by me and @jbkinney and in collab with @TheDMMcC Paper: biorxiv.org/content/10.110… Docs: squid-nn.readthedocs.io

@crescalantelab Thanks Carlos!

@EESeitz Congratulations, looks like a must read.

Thesis published: Analysis of Conformational Continuum and Free-energy Landscapes from Manifold Embedding of Single-particle Cryo-EM Ensembles of Biomolecules doi.org/10.7916/4n0v-w…

@jeebu9 @adesgeorges Thank you, Jeevan!

@cryoET Thanks Ed!!

@deswastik @FrankLabCUMC Thank you Swastik!

@EESeitz @FrankLabCUMC Congratulations, Evan!

I'm happy to announce the release of the ManifoldEM Python (beta) software suite, available at github.com/evanseitz/Mani…, featuring many interactive tools to help researchers explore highly heterogeneous cryo-EM data sets. #CryoEM #ManifoldEM

We've released a new paper exploring manifold analysis of cryo-EM data: biorxiv.org/content/10.110…

@bj_charles @UCSFChimeraX @ZhongingAlong @joachimfrank This is an interesting idea to create plugins to work in ChimeraX. As for #ManifoldEM, we are currently working to make public a comprehensive user interface, which includes visualization of intermediate and final outputs, hopefully later this year. @bj_charles @joachimfrank

Hoping @UCSFChimeraX is working with / focusing on integrating newer EM analyses into chimera for beautiful (and hugely helpful) visualisations. Difficult task no doubt, but desperately need plugins to explore #cryoDRGN, #3DVA and #ManifoldEM results. @ZhongingAlong @joachimfrank

New paper -- A simulation of cryo-EM images from a continuously varying structure: biorxiv.org/content/10.110…

Read about our latest #research on #cryoEM #Biology #protein, published with @SpringerNature in @naturemethods. Read here: nature.com/articles/s4159…

I just uploaded “Introduction to Electric Fields” to #Vimeo: vimeo.com/237845454