David M. McCandlish

Mathematical biologist, assistant professor Cold Spring Harbor Laboratory

[David M. McCandlish @TheDMMcC]

Special issue of GENETICS on fitness landscapes just announced!

Edited by me and @skryazhi, submissions due March 18:
https://t.co/Q2p1clcic9

[David M. McCandlish @TheDMMcC]

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

[David M. McCandlish @TheDMMcC]

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

[JuannanZhou @keitokiddo]

Very excited to share our preprint @PalashSethi6 "Importance of higher-order epistasis in large protein sequence-function relationships" https://t.co/PZI2cht54x

[David M. McCandlish @TheDMMcC]

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

[Peter Koo @pkoo562]

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: https://t.co/dC8slzHIvr
Docs: https://t.co/R0AF6ZgdAr

[Cold Spring Harbor Laboratory @CSHL]

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. 🍅
https://t.co/GmP6HHd3nA

[Arlin @ArlinStoltzfus]

(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

https://t.co/cNYrsDS4zV

[Arlin @ArlinStoltzfus]

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:
https://t.co/4IVdgMZGy1

[Camila dos Santos @caoresco]

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 👇🏼 https://t.co/78UgDgU3au

[Benjamin Cowley @BenjoCowley]

Reminder: Comp neuro faculty job applications are due Sept 1, 2023 (if you are planning to submit later, please let me know).

https://t.co/I0PS3sQtQU

Enjoy the view of Freeman!

[Bloom Lab @jbloom_lab]

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.

https://t.co/LR9JiFfN3q

[Joshua L. Payne @joshualevipayne]

New preprint!

Really happy with how this turned out. Hana knocked it out of the park. Colab with @cmarti_ga and @TheDMMcC

https://t.co/cWIcnQjHeo

[Arlin @ArlinStoltzfus]

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

https://t.co/s537xui8yM

[Valerie Soo @Valerie__Soo]

✴️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 👇
https://t.co/fClgwNKhzB

[Carlos Martí @cmarti_ga]

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

[Open Box Science @OpenBoxSci]

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: https://t.co/GFZjmPujI2

#openscience

[David M. McCandlish @TheDMMcC]

Published version of the paper Arlin is referring to at: https://t.co/6rPhUcc7vF

[Arlin @ArlinStoltzfus]

Re-upping my previous thread on mutation bias and the predictability of adaptation, our contribution to the new #PhilTransB issue on predicting #Evolution