Spiritual Bypass, but with GPUs
The "Machinal Bypass," when AI becomes a shortcut around the work that makes us human, and why some tasks should feel a little hard....
UltraMarathonRT: When Your Reverse Transcription Must Go Long
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We predict that the transcript abundance from the gene we are knocking down will (checks notes) decrease
The problem with gene-wise characterization of genetic interventions...
Countable Labs: New Approach to Enumerating DNA
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Mean squared error for estimates of differential expression
Bias-variance tradeoffs for virtual cell evals are weird...
Bell Labs Wasn't Built in a Day. Or Two Years.
<div>Rome is famous for persisting for centuries - and having not been built in a day. If you go there, then one of the most magnificent sites is the most famous sporting arena in the world, the Flavi...
Reviving BETA for Python 3: Integrating ChIP-seq and RNA-seq to Predict TF Targets
<p>I started to learn bioinformatics because I needed to analyze public ChIP-seq data in 2012. That’s how I got to know <a href="https://liulab-dfci.github.io/" target="_blank">Shirley Liu&rsquo...
Nineteen
If I had been more atop things, I would have written this just under a week ago, on the nineteenth anniversary of my starting to write in this space. That's a milestone, and actually writing somethin...
Traitors null hypothesis
<p>The rest of the UK and I have been watching <a href="https://www.bbc.co.uk/iplayer/episodes/m002csng/the-celebrity-traitors" rel="noopener noreffer " target="_blank">the Celebrity Traitors</a> over...
Understanding prcomp() center and scale Arguments for Single-Cell RNA-seq PCA
<p>During my work with single-cell RNA-seq data, I’ve often encountered confusion about PCA and specifically when to use the <code>center</code> and <code>scale</code> arguments in R’s <code>prcomp()<...