The Joy of Rediscovery
A key goal of science is to discover new information, and it is one of the great joys of science to believe you have done so. Sometimes it really does prove novel and interesting - an experience our ...
Video games in 2025: puzzles galore
<p>I played more games this year, particularly puzzle games. I also just bought a Switch 2, which seems good so far (nice screen).</p> <h1 id="puzzle-games">Puzzle games</h1> <h2 id="blue-prince"><em>...
Christmas dinner
<p>Mostly for personal reference for next year, here were my xmas dinner notes. I forgot about stuffing, and didn’t make yorkshire puddings properly because our main oven is broken (we have a co...
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...
Mean squared error for estimates of differential expression
Bias-variance tradeoffs for virtual cell evals are weird...
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...
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()<...
RNA velocity in situ infers gene expression dynamics using spatial transcriptomics data
Introduction...
15th Anniversary
<p>It has been 15 years since I started this blog! As typical with many of my anniversary posts, I reflect on things that I have started to do and/or have learned since the last time I wrote an annive...