Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.
The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...
Figure 1 shows they key result
“I’m grateful to be included in a journal with such a strong legacy in defining and advancing the field of cell biology.”— Dr. Danielle Grotjahn (@nanigrotjahn.bsky.social). JCB is where the world meets your research. Learn more. hubs.la/Q0442hKP0
RNA-specific local translation is patterned by condensates for multinucleate cell growth
www.nature.com/articles/s41...
Cells come in many shapes and sizes, with diverse physiological functions. But how do #organelles and their interaction networks remodel during #differentiation of stem cells into different cell types? Here’s what we discovered about neuronal differentiation: 1/13
I am excited to share the main piece of work from my PhD! In this paper, we investigated the propensities of distinct transcripts in associating with biomolecular condensates, mainly focusing on how heat-induced mRNAs escape condensation and are properly translated.
www.biorxiv.org/content/10.6...
@science.org Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation | Science www.science.org/doi/10.1126/...
From MBoC… A systematic comparison of auxin-inducible degradation tools in yeast identifies optimal component combinations for fast, efficient protein depletion with low basal effects. https://www.molbiolcell.org/doi/10.1091/mbc.E25-12-0571
If you are looking for a distraction, this seems cool. Sticky ends++. If it works as advertised, seems like it could be a game-changer.
www.nature.com/articles/s41...
Our newest paper is out where we investigate how exogenous RNA triggers innate immune responses, such as PKR activation and stress granule assembly. rnajournal.cshlp.org/content/earl...
The Murphy Lab did our annual retreat this week. This year's theme was using AI (what it's good and bad for). I wanted to be open-minded to make sure we are not missing something we should be using it for, so we did a few exercises to test, and had presentations.
New preprint from my lab!!!
We took advantage of the MitoTag mouse line to study what mRNAs associate with mitochondria in axons in vivo, and we were in for a surprise! Other than our favorite Pink1, mainly cytoskeletal mRNAs hitch a ride and pave the way for axon growth. shorturl.at/rYe1U
How do cells assess mtDNA quality?
Local ATP and membrane-potential gradients reflect mtDNA integrity and drive intracellular purifying selection.
We introduce FAST, a scalable mtDNA QC assay in S. cerevisiae.
Great collaboration with the Schmoller Lab.
journals.plos.org/plosgenetics...
🧬⚡
Happy to share that the our manuscript "Cyclin CLB2 mRNA localization and protein synthesis link cell cycle progression to bud growth" is now finally out in its final form @natcomms.nature.com
www.nature.com/articles/s41...
Below a short🧵 with the key findings!
Really thrilled to have our work on mitochondrial presequence strength out today @jcb.org. We establish quantitative parameters to better define "strong" and "weak" presequences both in vitro and in vivo. This work was spearheaded by the ever talented Youmian Yan, a BBSB graduate student in my lab.
From the mukherjilab.com Mitochondrial position responds to glucose stimulation in a model of the pancreatic beta cell: Biophysical Journal www.cell.com/biophysj/ful...
⚡️Mitochondria make ATP, the energy that powers life. But in neurons, with axons up to a meter long, how do these tiny power plants stay functional in the right places? We went looking. 1/n www.biorxiv.org/content/10.6...
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
New paper from @zhixingchen2.bsky.social's lab!
It turns out that, in addition to its very low phototoxicity, PKmito Deep Red (PKMDR) directly reports on mitochondrial membrane potential (MMP) in live cells through its lifetime!
www.nature.com/articles/s41...
Excited to share that this work is now published in its final form!
link.springer.com/article/10.1...
A mechanism for controlling mRNA localization to neuronal projections:
Daniel Dominguez, Matthew Taliaferro @jmtali.bsky.social and collaborators implicated ALS-linked TDP-43 as inhibitor of mRNA accumulation in neurites, possibly by promoting their decay
link.springer.com/article/10.1...
Holy cow the Zhou lab at UCLA is cooking with Isonet 2 - www.biorxiv.org/content/10.6...
Averaging-free direct visualization of ribosome translational state! #teamtomo #cryoet
Announcing the 2026 edition of the EMBO workshop on RNA localization and local translation! This meeting will be held June 30 - July 4 near Porto, Portugal. Come for exciting updates in the field from both established investigators and trainees. See the link below for details!
What an honor to see @attychang.bsky.social’s work featured in @jcb.org The Year in Cell Biology 2025 collection! Even more special that it coincides with my first #cellbio2025 conference 🙂
s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social
#teamtomo #cellbio25
Our paper is out studying premature aging (a hallmark of Down syndrome) in aneuploid yeast. Who knew part of the problem is in Ribosome Quality Control. Congrats to Leah Escalante for leading this tour de force.
journals.plos.org/plosbiology/...
@attychang.bsky.social, @nanigrotjahn.bsky.social et al. show that cytoplasmic #ribosomes on #mitochondria alter the local membrane environment for protein import. rupress.org/jcb/article/...
📕 From The Year In Cell Biology: rupress.org/jcb/collecti...
#CellBio2025
ANOTHER PAPER from Yi Liu's lab. This one is a bit crazy - codon effects on mRNA translation happens at the initiation step and requires looping - viruses don't circularize their mRNAs and thus evade the requirement for common codons to have efficient mRNA translation.
www.nature.com/articles/s41...
Oxidative phosphorylation complexes contain subunits encoded by both the nuclear and mitochondrial genomes. How do cells coordinate the synthesis and assembly of these complexes at the inner membrane? We teamed up with Martin Ott (@mitolab.bsky.social) to address this in two recent papers.
Our study on the molecular function of translational activators for mitochondrial protein synthesis is published:
rdcu.be/eSWxT
A great collaboration with @stirlingchurchman.bsky.social and @sshaolab.bsky.social with structural work from our @pelleeas.bsky.social
Funded by @kawresearch.bsky.social
🚀 Postdoc opportunity!
The Kapahi Lab at Buck Institute for Research on Aging is hiring two postdoctoral researchers to lead cutting-edge studies on how nutrient signaling and circadian rhythms influence neurodegeneration & aging — combining fly, worm, and mammalian models with genomics. 📈
👉
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
