Brief thoughts on: iNaturalist
Let me say first: I was wrong! My profile shows that I created my account at iNaturalist in August 2008, the year that the site was launched. I created a lot of accounts in those days. At the time, th...
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...
Thoughts on generative AI contributions as an Open Source project maintainer
<p>To be clear up front, these are my personal opinions right now, and while they will influence any future policy I have a hand in writing, they are not the position of the Biopython Project or the O...
Using R/anomalize to identify delays in games of Australian Rules football
In which we generate a dataset of game durations, do a little exploratory data analysis and then try to identify unusual instances and their causes. In my Twitter-whinge-post, I mentioned that one of ...
Review of Cold Spring Harbor Laboratory’s Obituary for Dr. James Watson
James Watson, who described himself as “not a racist in a conventional way”, has died at the age of 97. Below is a review of an obituary for Dr. James Watson published by Cold Spring Harbo...
RNA velocity in situ infers gene expression dynamics using spatial transcriptomics data
Introduction...
How big would ABI377 plates need to be to deliver NovaSeq X Plus output?
<p>I asked ChatGPT this question one evening and working through the session was fun. Maybe it needs more fact-checking…I know some of my readers are fastidious enough to call me out if I’...
cfDNA fragmentomics reviewed
<p>This is a fantastic and comprehensive review on Cell-free DNA fragmentomics in cancer. Out in Cancer Cell by Denis Lo et al. In this review focused on cell-free DNA (cfDNA) fragmentomics ...
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...