Excited to share our preprint! “Genome-scale base editing reveals the functional effects of variants in yeast” Using high-throughput base editing, we measured the growth effects of 308,461 variants, identifying 18,009 with significant effects. #Genomics #CRISPR 1/8 www.biorxiv.org/content/10.6...

Genome-scale base editing reveals the functional effects of variants in yeast

Genome sequencing has catalogued vast genetic diversity, but the functional consequences of most variants remain unknown. Here, we used genome-scale CRISPR base editing to measure the growth effects o...

biorxiv.org

I had to teach Claude how to use a stopwatch. "Check the time twice and subtract." Then it gave a confident explanation for why it failed — which was itself just more pattern matching. Wrote it up: "Pattern Matching Is Not Thinking." drive.google.com/file/d/1Y5sT...

Zara Weinberg passed away earlier this week. She joined my lab earlier this year when her postdoc lab formally closed. She was a brilliant scientist, supportive mentor, dear friend, avid music fan, rabid believer in public transit, open science champion, and above all just an amazing human.

Incredible. We should be investing MORE in science, not less.

#TheLastOfUs: A fungus that actually infects the human brain 🧠 A recent #G3journal paper from @hitenmadhani.bsky.social and team presents a valuable auxin-inducible genetic toolkit for conditional mutation in the fungal pathogen Cryptococcus neoformans, which can cause meningitis: buff.ly/rIkC09R

When should adaptation arise from a polygenic response versus few large effect changes? https://www.biorxiv.org/content/10.1101/2025.05.15.654234v1

Our authors can freely speculate the meaning and implications of their data in our new section: 💡 Ideas and Speculation 💡 buff.ly/0I8lpwz

Here is a link to 60 Minutes NIH segment... www.cbsnews.com/news/scienti...

Scientists fear Trump administration cuts to NIH could impact the health of Americans for generations

Former National Institutes of Health Director Dr. Francis Collins, who abruptly left his NIH research lab in February, fears aggressive downsizing could impact Americans' health.

cbsnews.com

Psychedelics reduce fear by targeting immune cells that modulate brain cells This Nature paper uses a combination of genomic & behavioural screens to show that astrocytes in the amygdala limit stress-induced fear behaviour through epidermal growth factor receptor 🧪 www.nature.com/articles/s41...

Psychedelic control of neuroimmune interactions governing fear - Nature

Inflammatory monocytes in the brain meninges promote stress-induced fear behaviour, and the pathways involved can be modulated using psychedelic compounds.

nature.com

Good. But stay wary www.politico.com/news/2025/04...

Trump administration reverses abrupt terminations of foreign students’ US visa registrations

DOJ announced the reversal in federal court after weeks of intense scrutiny by courts and dozens of restraining orders issued by judges.

politico.com

Happy to join a few thousand friends in midtown today. Free Mahmoud Free Rumeysa Free Kilmar and everyone at Cecot Due process No kings

A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin

A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin

Skribbe et al. comprehensively mapped transcription factor interaction networks in S. pombe through proteomics and chromatin profiling. Their study offers invaluable resources, including an endogenously tagged transcription factor strain library and the TFexplorer web tool, which enables user-friendly exploration of the interactions revealed.

dlvr.it

Antifungal drug discovery gets an interesting and unexpected shot of good news:

A New Type of Antifungal

science.org

A slight modification to the standard yeast lithium acetate transformation protocol increases transformation efficiency substantially. Basically, 2 fold increase if you resuspend in 2M sorbitol after heat shock, and an additive increase with some sorbitol during heat shock.

Enhancing Yeast Transformation: Achieving up to a Tenfold Increase Through a Single Adjustment in the Lithium Acetate–Polyethylene Glycol Method

In red are the proposed improvements to the classical yeast transformation protocol.

onlinelibrary.wiley.com

I believe we have breaking news in Inside Medicine. I spoke to a member of the FDA vaccine committee who confirmed that the meeting to decide the 2025-2026 flu shot composition was abruptly canceled today. My on-the-record Q&A with the FDA advisor: insidemedicine.substack.com/p/scoop-fda-...

Scoop: FDA vaccine meeting abruptly canceled. Meeting was to determine 2025-2026 influenza vaccine composition.

Hi everyone,

open.substack.com

Despite court order, NIH grants remain frozen. Newly awarded grants, grants with fundable scores, & funds for a new budget cycle of a current project are all *FROZEN*🥶 and not being released. US research is being choked to death & is on life support right now www.motherjones.com/politics/202...

NIH is again throttling research funding in defiance of a federal court order

A freeze on "new and continuation awards" will "remain in place" pending DEI review, states a new internal memo.

motherjones.com

Roche's SBX sequencing by expansion - preprint out! www.biorxiv.org/content/10.1...

Good lord

WESA@wesa.fm · 2y ago

The University of Pittsburgh confirmed Friday that there would be no new Ph.D. offers of admission while Pitt works to understand how reduced federal aid could impact the institution.

Almost all grant-review meetings still suspended at the NIH -- the Trump administration is exploiting a loophole to keep a funding freeze in place, leaving researchers in limbo. @maxkozlov.bsky.social reports for @nature.com www.nature.com/articles/d41...

Revealed: NIH research grants still frozen despite lawsuits challenging Trump order

The Trump administration is exploiting a loophole to keep a funding freeze in place, leaving researchers in limbo.

nature.com

Biomedical graduate admissions paused or cut back as some universities respond to Trump orders on research - STAT apple.news/APlQhGHRrSfy...

Graduate student admissions paused and cut back as universities react to Trump orders on research — STAT

Acceptances for biomedical graduate students and postdoctoral scholars are being cut back at some universities and medical centers across the country as many grapple with the potential impact of the T...

apple.news

a grim but essential read, if you care about American science the system was already under stress from underfunding over many years (nominal increases were sub-inflationary) but this is a sudden and severe shock to the system

Usha Lee McFarling@usha.bsky.social · 2y ago

NEW: Trump actions on science may affect a generation as pauses + cuts in graduate admissions begin. “We had just flown them out, we told them we love you, we want to admit you, and then everything just stopped." "It's freezing everybody into inaction." www.statnews.com/2025/02/19/t...

Distinct explanations underlie gene-environment interactions in the UK Biobank. www.cell.com/ajhg/abstrac...

Distinct explanations underlie gene-environment interactions in the UK Biobank

The role of gene-environment (GxE) interaction in disease and complex trait architectures is widely hypothesized but currently unknown. Here, we apply three statistical approaches to quantify and dist...

cell.com

Insufficient evidence for a severe bottleneck in humans during the Early to Middle Pleistocene transition academic.oup.com/mbe/advance-...

Insufficient evidence for a severe bottleneck in humans during the Early to Middle Pleistocene transition

Abstract. A recently proposed model suggests a severe bottleneck in the panmictic ancestral population of modern humans during the Early to Middle Pleistoc

academic.oup.com

A big loss and very bad sign for NIH, folks

Science Magazine@science.org · 2y ago

Lawrence Tabak, longtime principal deputy director of the National Institutes of Health, has abruptly resigned—surprising even his own lab staff and the broader community. scim.ag/4hR40OE

I would expect to see this at every research institute until there's clarity on funding and budgets.

Roland Hatzenpichler@environmicrobio.bsky.social · 2y ago

I was told today that we cannot proceed with two planned faculty hires bc of lack of $ (startups are funded through IDCs). We had interviewed people, etc. All for nothing.

NEW: approximately 330 National Cancer Institute probationary employees will be fired this afternoon. That’s a bit less than 10% of its entire staff.

Scoop: The databases powering DOGE.gov are insecure, and people outside the government have already pushed their own updates to the site to prove it: www.404media.co/anyone-can-p...

Anyone Can Push Updates to the DOGE.gov Website

"THESE 'EXPERTS' LEFT THEIR DATABASE OPEN."

404media.co

Biopharma companies and CEOs are keeping their heads down at their own peril. They should speak up about what’s happening to the NIH and other science agencies before it’s too late. Silence gives consent. And no one should consent to this.

Stand Up And Be Counted

science.org

Trump & Musk are making massive cuts to the National Institutes of Health. I know there is a lot going on right now, but this is one of worst things they have done so far, will affect cancer research and trials, the search for cures, innovation and competitiveness, our universities. Your lives.