Kristin Knouse

New preprint on technologies to scale up CRISPR screens.

We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.

We also introduce an approach for cloning lentiviral libraries with billions of elements.

a close up of a white axolotl with pink ears standing on a rock . ALT: a close up of a white axolotl with pink ears standing on a rock .

Axolotls are famous for regenerating limbs. Turns out they can also regenerate their thymus—and that may show us how to someday to the same. That story and more of the best from @science.org and science in this edition of #ScienceAdviser: www.science.org/content/arti... 🧪

ACOG reaffirms that acetaminophen is safe for managing pain and fever during pregnancy. No reputable studies support suggestions like those in HHS’s recent announcement linking acetaminophen use in pregnancy to autism; in fact, high-quality studies show no such risk. https://bit.ly/47Wxc59

depmap miner logo

The Garnett Lab is excited to launch DepMap Miner, a new tool to explore cancer dependency data!
Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models.

Start mining data now: dataminer.depmap.sanger.ac.uk

The dynamics of centromere assembly and disassembly during quiescence Quiescence is a state in which cells undergo a prolonged proliferative arrest while maintaining their capacity to reenter the cell cycle. Here, we analyze entry and exit from quiescence, focusing on h...

New preprint! Graduate student Océane Marescal leverages quiescence - proliferative hibernation - to reveal unexpected dynamics for “constitutively”-localized centromere proteins. To understand the logic of cell division, you need to consider non-dividing cells.

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

Balancing off-target and on-target considerations for optimized Cas9 CRISPR knockout library design The continued development of high-dimensional CRISPR screen readouts, such as single-cell RNA sequencing and high-content imaging, necessitates compact libraries to enable functional interrogation at ...

Doomscrolling pause to chat CRISPR libraries! Preprint describes our new, data-driven approach to combine on-target and off-target predictions much more intelligently for *selecting* guides, which we use to develop our newest Cas9 knockout library, Jacquere. Thread: www.biorxiv.org/content/10.1...

Lab retreat 2025 was a reel good time!

Side by side headshots of Sourav Ghosh and Kotaro Tomuro, winners of the 2025 Angelika Amon Young Scientist Award

Congrats to Sourav Ghosh (@souravsgw.bsky.social) of IIT Bombay
& Kotaro Tomuro of RIKEN and The University of Tokyo - our 2025 Amon Young Scientist Award winners! They present Nov 6, 10 a.m. at the Koch Institute. MIT community & Amon Lab alumni welcome. buff.ly/nzhbwPp

Breaking the rules of cell biology: Lessons from the liver's exceptional regenerative capacity | Molecular Biology of the Cell The inability of most human organs to regenerate themselves after injury underlies the lifelong morbidity of numerous diseases. As we continue to seek solutions for these intractable conditions, the l...

Our liver can completely regenerate itself in a matter of days! Excited to share this perspective on how the liver breaks the rules of cell biology to accomplish this exceptional feat and how this could unlock regenerative capacity in other organs.

www.molbiolcell.org/doi/10.1091/...

graph of NIH basisfor new drugs

A pie graph worth keeping in mind as the NIH budget plummets jamanetwork.com/journals/jam... for 356 new FDA drugs approved

RNA-binding proteins and glycoRNAs form domains on the cell surface for cell-penetrating peptide entry Mammalian cells present RNA-binding proteins on the cell surface that form clustered domains containing glycoRNAs.

Excited to share the work of Jonathan Perr where he uncovered a surprisingly common feature of cell surfaces - the presentation and clustering of RNA binding proteins with #glycoRNA.

Critically support by #NIH @cp-cell.bsky.social www.cell.com/cell/abstrac...

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage Naqvi et al. reveal how DNA sequence determines the chromatin response to transcription factor (TF) dosage changes. By combining deep learning and chemical genetics, they uncover specific sequence fea...

Excited to share the peer-reviewed version of our paper on predicting the chromatin response to TF dosage using transfer learning

www.cell.com/cell-genomic...

A roadmap toward genome-wide CRISPR screening throughout the organism Genome-wide CRISPR screening in the organism has tremendous potential to answer long-standing questions of physiology and disease; however, technical limitations have prevented its broad application. ...

Can we perform genome-wide screens in any cell type in the body?! Excited to share our roadmap for leveraging advances in sgRNA delivery, library design, and phenotypic selection to enable unprecedented genetic dissection of organismal physiology and disease.

www.cell.com/cell-genomic...

SLC25A38 is required for mitochondrial pyridoxal 5’-phosphate (PLP) accumulation Nature Communications - Pyridoxal 5’-phosphate (PLP, vitamin B6) is crucial for various metabolic processes. Here, the authors identified SLC25A38 as a key regulator of mitochondrial PLP...

Here is a quick thread to promote my research! After years of dedicated research, I'm thrilled to share our article just published at Nature Communications :)

www.nature.com/articles/s41...

#metabolism #CRISPRscreens #mitochondria

Viral Vectors can be difficult to use, but Addgene's Viral Vectors 101 eBook can help! Our second edition has helpful content, useful images, and increased accessibility for all. Find it here: www.addgene.org/educ...

Preprint alert!! How zonated hepatocytes adapt to changes in lipid influx due to fasting or a Western diet (WD). We developed a microscopy-based phenotyping method called single-cell phenomics (scPhenomics) to measure the features of mitochondria and lipid droplets (LDs).

How did we get here, with a prominent anti-vaxxer nominated to lead Health and Human Services, with its $1.7T budget?

Much of it can be traced to this retracted 1998 paper, falsely linking the measles, mumps and rubella (MMR) vaccine to autism. 1/3

CRISPR and Beyond 2025

Join us for the 6th CRISPR and Beyond Conference on 2-4 April 2025!🧬 A must-attend event for researchers in high-throughput screening and #GeneEditing, exploring emerging technologies and models. #CRISPR25

👉Programme and registration: bit.ly/3Amz34N

57 | George Church and shooting for the stars Night Science · Episode

If you don't fit in, that could actually be your biggest advantage for having new ideas. ADHD, dyslexia, narcolepsy, etc.. anything that makes you different is of tremendous value when it comes to being creative.
open.spotify.com/episode/1b1k...

We are privileged to continue honoring Angelika’s inspiring legacy of mentorship and discovery with the third annual Angelika Amon Young Scientist Award! Please encourage PhD students outside the US who embody her infectious passion for biology to apply!

ki.mit.edu/events/prize...

The Campus Wars Aren’t About Gender … Are They? Recent Ivy League dramas have made women leaders in academia wonder how far they’ve really come.

“Underlying all the conversations…the most unanswerable question of all: Would a man have been treated the same way?”

Thank you @kzernike for this important and timely piece highlighting the biases faced by women and other underrepresented leaders.

www.nytimes.com/2024/01/28/u...

Happy Halloween from the Knouse Lab, where we’re always down for a good mystery!