Genomics + immunology + ML = personalized cancer immunotherapy.
Nov 17 • 10 tweets • 4 min read
Let's say you want to publish in a top-tier journal and need to have a high accuracy predictor of something of great medical importance, such as survival of cancer patients in response to immunotherapy. The easiest route is just to cheat: (X,y).predict(X) model.fit
Since you're just memorizing the test data (or maybe a superset of it), then the predictor works better as you add more features.
Feb 25, 2022 • 19 tweets • 6 min read
Preprint live: biorxiv.org/content/10.110…
tl;dr We did not disprove the role of T-cells in clearing SARS-CoV-2 (sorry to disappoint) but we did manage to make a vaccine which induces strong but useless T-cell responses against SARS-CoV-2. Details & guess at interpretation below 1/n
Many SARS-CoV-2 vaccines present the immune system with the spike protein or the parts of the spike most vulnerable to neutralization (S1 portion or even just the RBD). This antigenic content can be made directly (protein subunit), encoded as mRNA, DNA, DNA in a virus, &c
Jun 15, 2021 • 26 tweets • 12 min read
It's been a preprint for a while but a much improved version of our paper is out in @GenomeMedicine
"Landscape and selection of vaccine epitopes in SARS-CoV-2"