Nick Ingolia

2025 MCB Outstanding Postdoc Award recipients

Congrats to our 2025 MCB Outstanding Postdoc Award recipients who are being honored for their excellence in research, leadership, and service! 👏🎉Erin Doherty @erinedoherty.bsky.social, Kevin Eislmayr, Naohiro Kuwayama, & Joseph Lobel
mcb.berkeley.edu/news-and-eve...

Protein language models reveal evolutionary constraints on synonymous codon choice Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...

This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...

The Em Dash Responds to the AI Allegations “In recent months, a curious fixation has emerged in corners of academia: the em dash. More specifically, the apparent moral panic around how it is...

"Writers have been using me long before the advent of AI. I am the punctuation equivalent of a cardigan—beloved by MFA grads, used by editors when it’s actually cold, and worn year-round by screenwriters. I am not new here."

Smallpox inoculation was practiced throughout the 1700s; George Washington mandated this life-saving measure for the whole Continental Army in 1777. It was supplanted by the first-ever vaccine in 1796, a huge breakthrough supported by government grants in the UK. Just randomly on my mind.

This is awful and stupid, I'm sorry.

A screenshot of the termination notice showing "Outstanding Investigator Grants"

A screenshot of the termination notice with "This award is terminated effective the date of this award, due to unsafe antisemitic actions that suggest the institution lacks concern for the safety and wellbeing of Jewish students." highlighted

Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab

Not about Chicago, but you might appreciate:
bsky.app/profile/moti...

Opinion | Science Suffers With Trump’s Funding Freeze America’s scientific enterprise demands reliable stewardship, not destabilizing political intervention.

My father-in-law, Jack Strominger, and I wrote a letter to the @wsj.com editor about the current threats to science due to Trump's funding freeze. Please repost! www.wsj.com/opinion/scie...

I was stunned by this work from Kathleen Collins' lab (Berkeley) when I heard her present this at a FASEB meeting!

What a crazy innovative idea: Adapting the R2 retrotransposon to efficiently insert any custom transgene directly into RIBOSOMAL DNA ARRAYS! 🤯🤯🤯

The applications are endless....

I’m hoping you fine tune a version for long-form Italian poetry

Analyses of translation factors Dbp1 and Ded1 reveal the cellular response to heat stress to be separable from stress granule formation Kuwayama and Powers et al. reveal differences in function for two related RNA remodelers. Dbp1 is poor at stimulating translation, but, when expressed instead of Ded1, it prevents cells from halting growth upon heat stress. This depends on a short disordered Ded1 region but not stress granule formation or reduced translation.

Great work from Gloria Brar’s group on the role of paralogous RNA helicases in the heat shock response. Surprising increase in growth at high temperature and impact of a short motif! Also important implications of the role of biomolecular condensation. Awesome www.cell.com/cell-reports...

Could you add me? I think I fit the profile...

Phosphorylation-dependent tuning of mRNA deadenylation rates mRNA decay is a major determinant of gene regulation that is controlled through shortening of mRNA poly(A) tails by the Ccr4-Not complex. The specificity of deadenylation can be mediated through RNA a...

New work from the lab!
James Stowell led this project showing the importance of multivalency and phospho-regulation in mRNA decay. This has many parallels with other mechanisms in gene expression.

biorxiv.org/cgi/content/...

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Did you know the genome might have hidden protein-coding genes?

In the years since the Human Genome Project, research has been tied to a set of 20,000 protein-coding genes. But the ‘dark genome’ has ‘dark proteins’ lurking in plain sight.

🧪
💻 + 🧬
🔎 microproteins

www.biorxiv.org/content/10.1...

CRISPRi with barcoded expression reporters dissects regulatory networks in human cells bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Exciting work from Jinyoung Kim and Nick Ingolia enabling pooled CRISPRi screens in human cells by barcoded RNA readout. www.biorxiv.org/content/10.1...

"Sensitive Compartmented Urination Facility"

Codon optimality modulates protein output by tuning translation initiation bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Spurred on by ribosome profiling and other cool methods, translation elongation has grown into a whole field with new surprises all the time (and new relevance for vaccine mRNAs!). Here’s our latest on why synonymous codons aren’t all the same. (Thread) www.biorxiv.org/content/10.1...

Short tandem repeats bind transcription factors to tune eukaryotic gene expression Transcription factors directly bind repetitive sequences that need not resemble known motifs.

Check out our paper and the accompanying perspective by Kuhlman published today in Science about the surprising role of short tandem repeats in regulating eukaryotic transcription!

www.science.org/doi/10.1126/...

www.science.org/doi/10.1126/...

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