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Chris Jackson

@cajackson.org
481 followers 2K following 363 posts

Systems biology

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Chris Jackson @cajackson.org · 26/08/2026
Don't think this guy would sign a letter for me if I got fired for teaching about climate change tbh
Throughout this time, Kalkstein tried to get a letter to Defense Secretary Pete Hegseth through his chain of command, but Sussman, who shared the letter with Stars and Stripes, said it never left campus. The professor argued that exaggerated positions of climate change made under President Joe Biden politicized the field, “making it difficult to separate fact from fiction.”
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Chris Jackson @cajackson.org · 07/02/2026
Book cover for Ethan of Athos by Lois McMaster Bujold
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Chris Jackson @cajackson.org · 01/11/2023
This is a pretty good firing offense by itself
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Chris Jackson @cajackson.org · 26/09/2023
And cause it's interpretable, we can backpropagate the prediction error for the entire transcriptome to the transcription factor layer and figure out which TFs we're mispredicting (could continue fine-tuning the model this way, too). We explicitly measure that error in the context of TF activity.
Backpropagated error to the transcription factor layer from observed TF deletions
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Chris Jackson @cajackson.org · 26/09/2023
It worked really nicely, with some biological constraints the decomposition is nice and clean, and you can find clear differences in decay vs transcription regulation
Plotting RNA velocity, transcription rate, and decay rate over time
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Chris Jackson @cajackson.org · 26/09/2023
In order to make this work, we had to estimate RNA velocity and then break it out into separately modeled decay rates and transcription rates (so that changing TFs only changes transcription and not any other process).
Deep learning models for decay rate and transcription rate
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Chris Jackson @cajackson.org · 26/09/2023
We used that data to train a model, which takes proliferative cells and predicts the entire transcriptome as it responds to rapamycin.
Heatmaps comparing observed to predicted transcriptomes
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Chris Jackson @cajackson.org · 26/09/2023
We put together a single-cell training data set from yeast cells that are continually sampled for single-cell sequencing, which gives a beautiful time-dependent transcriptome curve.
Single cell continuous sampling UMAP plots
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Chris Jackson @cajackson.org · 26/09/2023
Q: Can we make a general-purpose model of gene regulation? A tool where you can make changes to regulation and see what happens, or take observed effects and figure out what the cause is.
Computational biology model schematic
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Chris Jackson @cajackson.org · 22/09/2023
🤔
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