Nick Ingolia
@nickingolia.bsky.social
Translation and RNA Biology • Comprehensive and high-throughput experiments
Professor, Molecular and Cell Biology, UC Berkeley
Professor, Molecular and Cell Biology, UC Berkeley
Reposted by Nick Ingolia
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...
mcb.berkeley.edu/news-and-eve...
September 30, 2025 at 5:38 PM
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...
mcb.berkeley.edu/news-and-eve...
Reposted by Nick Ingolia
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...
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...
www.biorxiv.org
August 7, 2025 at 8:29 AM
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...
Reposted by Nick Ingolia
"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."
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...
buff.ly
July 17, 2025 at 6:20 PM
"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."
Reposted by Nick Ingolia
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.
June 9, 2025 at 10:51 PM
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.
Reposted by Nick Ingolia
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
May 13, 2025 at 11:37 PM
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
Reposted by Nick Ingolia
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...
Opinion | Science Suffers With Trump’s Funding Freeze
America’s scientific enterprise demands reliable stewardship, not destabilizing political intervention.
www.wsj.com
April 21, 2025 at 6:21 PM
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...
Reposted by Nick Ingolia
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....
What a crazy innovative idea: Adapting the R2 retrotransposon to efficiently insert any custom transgene directly into RIBOSOMAL DNA ARRAYS! 🤯🤯🤯
The applications are endless....
Transgenes are inserted into human cells by 2-RNA delivery of a retroelement protein and template go.nature.com/3utPERu
rdcu.be/d8LVW
rdcu.be/d8LVW
Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci - Nature Biotechnology
Transgenes are inserted into human cells by 2-RNA delivery of a retroelement protein and template.
go.nature.com
February 5, 2025 at 10:55 PM
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....
What a crazy innovative idea: Adapting the R2 retrotransposon to efficiently insert any custom transgene directly into RIBOSOMAL DNA ARRAYS! 🤯🤯🤯
The applications are endless....
Reposted by Nick Ingolia
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...
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.
www.cell.com
December 18, 2024 at 3:10 AM
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...
Reposted by Nick Ingolia
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/...
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/...
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...
biorxiv.org
October 21, 2024 at 1:11 AM
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/...
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/...
Reposted by Nick Ingolia
1/
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...
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...
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
www.biorxiv.org
September 10, 2024 at 3:30 PM
1/
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...
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...
Reposted by Nick Ingolia
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...
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
www.biorxiv.org
September 8, 2024 at 4:30 AM
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...
Reposted by Nick Ingolia
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...
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
www.biorxiv.org
November 29, 2023 at 7:07 AM
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...
Reposted by Nick Ingolia
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/...
A thread (1/11):
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
A thread (1/11):
Short tandem repeats bind transcription factors to tune eukaryotic gene expression
Transcription factors directly bind repetitive sequences that need not resemble known motifs.
www.science.org
September 21, 2023 at 7:54 PM
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/...
A thread (1/11):
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
A thread (1/11):