David M. McCandlish

Special issue of GENETICS on fitness landscapes just announced! Edited by me and @skryazhi, submissions due March 18: doi.org/10.1093/geneti…

Have been talking this up at meetings all summer so excited to see the manuscript out!

The method accounts for any global non-linearity so that the results only reflect specific rather than non-specific epistasis

Haven't been on here much lately, but wanted to recommend this new pre-print from my former post-doc @keitokiddo 's group! They use a new trick based on modified transformers to provide the first estimate of the extent of higher-order epistasis in full length proteins

Excited to share new work on "Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models” led by @EESeitz, jointly advised by me and @jbkinney and in collab with @TheDMMcC Paper: biorxiv.org/content/10.110… Docs: squid-nn.readthedocs.io

CSHL’s Zachary Lippman and @TheDMMcC teamed up to decipher the unpredictability of natural and engineered mutations in tomatoes. Their work may help scientists navigate evolution and genome editing. 🍅 cshl.edu/you-say-genome…

(1/5) new: A critique of the "isotropic variation" critique The short version is in the first 4 minutes (full version is 40 min) What is the "isotropic variation" critique? What does it get right, or wrong? #popgen #mutation #evolution youtube.com/watch?v=RBALnz…

I tweeted about this earlier. Fig 2s shows a negative correlation between fitness effect and mut rate @BryanGitschlag @TheDMMcC et al have a theory for how a joint mutation-selection process can induce such correlations. Just came out here: journals.uchicago.edu/doi/10.1086/72…

CSHL is hiring Faculty at all career stages, in the area of Cancer Biology!Come join me and my amazing colleagues! Application deadline is November 15th. RT and check the link for more info 👇🏼 apply.interfolio.com/129695

Reminder: Comp neuro faculty job applications are due Sept 1, 2023 (if you are planning to submit later, please let me know). cshl.edu/about-us/caree… Enjoy the view of Freeman!

In new study, we develop rigorous method to jointly analyze deep mutational scanning of different protein homologs or conditions We use it to identify mutations w effects on spike-mediated viral entry that differ by >1,000-fold among #SARSCoV2 strains. biorxiv.org/content/10.110…

New preprint! Really happy with how this turned out. Hana knocked it out of the park. Colab with @cmarti_ga and @TheDMMcC biorxiv.org/cgi/content/sh…

Mutation, Randomness and Evolution is coming out in paperback this fall To check if you already have access via your university, visit the web page at OUP using the uni's proxy server All of the figures from the book are available on the OUP web site global.oup.com/academic/produ…

✴️Looking for a Research Technician to help me out @Imperial_AID @ImperialInfect in London. Let’s explore antibiotic resistance in pathogenic bacteria using deep mutational scanning 🧬🦠🧫 = 🤩 Please share and RT! Deadline 14/06 👇 imperial.ac.uk/jobs/descripti…

I am excited to present my work with @TheDMMcC on our attempt to understand complex genotype-phenotype maps tomorrow at #BoG23. I will show some cool genotype-phenotype maps with up to 16 million genotypes and explain how we can actually visualize and interpret them

OBS #Genomics Seminar on #MAVE 📅 Thu, April 11, 10 am ET 🎤 @mseumaar (@IBECBarcelona) 📝 An atlas of #amyloid aggregation 🎤 @AmmarTareen1 (@CSHL) 📝 MAVE-NN: learning genotype-phenotype maps from MAVE 👉 Register: us02web.zoom.us/meeting/regist… #openscience

Published version of the paper Arlin is referring to at: royalsocietypublishing.org/doi/10.1098/rs…