Mathematical biologist, assistant professor Cold Spring Harbor Laboratory
Huntington, NY
Joined December 2016
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Special issue of GENETICS on fitness landscapes just announced!
Edited by me and @skryazhi, submissions due March 18:
doi.org/10.1093/genetics/iya…
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
Very excited to share our preprint @PalashSethi6 "Importance of higher-order epistasis in large protein sequence-function relationships" biorxiv.org/content/10.1101/…
The method accounts for any global non-linearity so that the results only reflect specific rather than non-specific epistasis
David M. McCandlish retweeted
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/10.1101/…
Docs: squid-nn.readthedocs.io
David M. McCandlish retweeted
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-edit…
David M. McCandlish retweeted
(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=RBALnzsz…
David M. McCandlish retweeted
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…
📢Clonal hematopoiesis driven by mCAs📢What fitness effects do mCAs confer to our blood cells?🩸 How often do they occur? Does an mCA’s fitness correlate with blood cancer risk?🔎Read mine & @jrblundell's latest paper @NatureGenet to find out (& more!):👉🔗rdcu.be/dlRRr
David M. McCandlish retweeted
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
David M. McCandlish retweeted
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/careers/fa…
Enjoy the view of Freeman!
Faculty job alert! CSHL is hiring a faculty position in computational neuroscience, broadly defined. Deadline to apply is Sept 1, 2023 (the earlier the better).
cshl.edu/about-us/careers/fa…
Yes, I snapped this view today, a 1 min walk from your new office!
David M. McCandlish retweeted
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/10.1101/…
David M. McCandlish retweeted
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/shor…
David M. McCandlish retweeted
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/prod…
David M. McCandlish retweeted
✴️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/descript…
ALT Streptococcus pyogenes on a blood agar
ALT Hammersmith Campus, Imperial College London
David M. McCandlish retweeted
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/regi…
#openscience
Published version of the paper Arlin is referring to at: royalsocietypublishing.org/d…
Re-upping my previous thread on mutation bias and the predictability of adaptation, our contribution to the new #PhilTransB issue on predicting #Evolution
David M. McCandlish retweeted
Our lastest #popgen piece features work of @BryanGitschlag & @theDMMcC (theory), Alej Cano & @joshualevipayne (data, simulations)
Mutation rates (u) matter so, rather than a distribution of fitness effects (DFE), we focus on a joint dist of u and s
1/?
biorxiv.org/content/10.1101/…