Congrats to Gina (the smart one in the family) for receiving the NIDAnews travel award! asam.org/membership/asa…

Big thanks to Michael Lidsky, MD, FACS for the great mentorship and Society of Surgical Oncology for the opportunity!

Interesting new from Corri Sept Martin Aryee et al. combines MNase HiChIP for CTCF with new FactorFinder algorithm to profile 3D interactions conditional on CTCF being bound.

Nice insights in loop extrusion from the perspective of CTCF-anchored cohesin

biorxiv.org/content/10.110…

Our newest pre-print from the Wood lab is now up on bioRxiv! Super fun collaborative effort led by Duke MSTP candidate Christian Cerda-Smith.

Integrative PTEN Enhancer Discovery Reveals a New Model of Enhancer Organization biorxiv.org/content/10.110…

Super cool example of using genomics to inform conservation efforts to save endangered species! rdcu.be/dkD8Q

I've been thinking about compassion and pediatricians.

There's an idea that pediatricians are 'softer' than internal medicine docs because we take care of kids. And kids are cute! Funny! Sticky! 1/

Extraordinary claims require extraordinary evidence. In our new nature paper, Darrin Schultz Darrin Schultz used the position of genes on chromosomes to show that ctenophores (comb jellies) not sponges are the sister-group to all other animals. nature.com/articles/s4158…

This is a really well done python reimplementation of DESeq2 and apeglm, I’ve checked the code closely. Nice work Boris Muzellec Maria Teleńczuk et al

Tweetorial time! We Recursion mapped consequences of #CRISPR screening of >17K human genes, found a systematic bias confounding all CRISPR screens, traced its molecular cause, and propose a debiasing algorithm.

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent immune response against a distant tumor. Y. Erin Chen, MD PhD led the charge w/ help from Djenet Bousbaine, Alessandra S. Veinbachs, Belkaid Lab. Science Magazine 1/26
science.org/doi/10.1126/sc…

Hack-a-thon but it’s just people setting up their python environments for 48 hours

Okay! Here it is! all 15 years of the K99/R00 grant mechanism (2007-2022). Only K99s that successfully transferred to R00. File is too large for Twitter. I have a zoom-in-able SVG on my lab website:

sites.uab.edu/tyrrelllab/abo…

bioRxiv: biorxiv.org/content/10.110…

Out today and freely available, a tool many in the image analysis community have been waiting for!

PyImageJ: A library for integrating ImageJ and Python

Kevin Eliceiri UW LOCI (Eliceiri lab) 𝙲𝚞𝚛𝚝𝚒𝚜 𝚁𝚞𝚎𝚍𝚎𝚗 (@[email protected]) Beth Cimini Lab 🔬💻 📊 Anne Carpenter, PhD

nature.com/articles/s4159…

Lots of interesting stats to digest here. R01 and R35 submission and success from 2019-2021 at NIGMS.
loop.nigms.nih.gov/2022/08/applic…

i’ve been asked to give my take on IRA so here it is: the bill contains some very good, very needed investments: in renewable energy, in a green bank, in electrifying key tech in homes, in credits for EV purchases, etc.

it also weds those investments to very major harms 1/

“Mathematicians are a lot like artists in that really we’re looking for beauty” A wonderful profile of Fields Medal winner June Huh. quantamagazine.org/june-huh-high-…

In the wake of the ruling, AAP will continue to support our chapters as states consider policies affecting access to abortion care, and pediatricians will continue to support our patients. Full statement: aap.org/en/news-room/n… 3/3

My thoughts on the Supreme Court's decision to overturn Roe v. Wade.

Remember: NIH modular grant budgets have not been adjusted for inflation in >20 years. We have ~40% less purchasing power with them now, than we did 20 years ago.

There is no industry on planet Earth that can survive like that, and it is reflected in salaries.

Analysis of #scRNAseq requires constant, tedious, interaction with genomics databases. To facilitate querying from Ensembl et al., Laura Luebbert developed gget:
biorxiv.org/content/10.110… (code @ github.com/pachterlab/gget).
gget has many uses; a 🧵on the its amazing versatility: 1/