Peter

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

It's what you do what actually have a greater value regarding your goal

Controversial take: apart of prototyping code much faster and doing translation between programming languages, the greatest benefit of LMM-based "AIs" (i.e. chatbots) comes from deeply thinking about an issue, writing with care, and actively discussing.

"Iterative prompting" >> the answer you get

Congrats, Julia!!! Happy to see [part of] your work out as a preprint 🥳

The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩...

🔗 doi.org/10.64898/202...

Apply to become a Preprint Editor Development

We are inviting experienced researchers to apply to become Preprint Editors, a new type of editorial role responsible for handling our 'In preprints' articles and forging links with preprint literature. #prepints

Learn more and apply before 30 March 2026:
journals.biologists.com/dev/pages/pr...

After years of work, the centerpiece of my PhD is published in @natmethods.nature.com! Read it to learn about the biophysical insights we can get from single-cell data!

But first, I would like to talk a bit about RNA velocity and normalization. 1/

Benchmarking computational tools for locus-specific analysis of transposable elements in single-cell RNA-seq datasets https://www.biorxiv.org/content/10.64898/2026.02.26.708244v1

Charting single-cell lineages with synthetic and natural barcodes Nature Reviews Genetics, Published online: 27 February 2026; doi:10.1038/s41576-026-00943-5In this Review, Rodriguez-Fraticelli and Parreno discuss advances in single-cell lineage-tracing methods and how their application to diverse biological processes, such as development, ageing and cancer, is challenging prevailing views and providing new insights.

New online! Charting single-cell lineages with synthetic and natural barcodes

Charting single-cell lineages with synthetic and natural barcodes - Nature Reviews Genetics In this Review, Rodriguez-Fraticelli and Parreno discuss advances in single-cell lineage-tracing methods and how their application to diverse biological processes, such as development, ageing and canc...

INTERESTED IN SINGLE-CELL LINEAGE TRACING?

Check our new review @naturerevgenet.bsky.social from the @alejofraticelli.bsky.social lab 🎉🎉

nature.com/articles/s41...

With Victoria Parreno, we tried to update the modern manual for genetic tracing and clonal analysis.

Read link: rdcu.be/e50gy

Concurrent L1 retrotransposition events promote reciprocal translocations in human tumorigenesis LINE-1 (L1) retrotransposition generates somatic genomic variation in human cancer, but short-read sequencing has limited our understanding of its structural consequences and dynamics. Using long-read...

Today in
@science.org:
We are pleased to present our last work entitled:
"Concurrent L1 retrotransposition events promote reciprocal translocations in human tumorigenesis"
by Zumalave et al.
www.science.org/doi/10.1126/...

When I think on the timescale of days and weeks, progress can be frustratingly slow.

Shifting to the timescale of years, the progress is spectacular: Often faster than expected.

Living through the arc of technology development has been awesome.

The best is yet to come 🚀

🚨 NEW
@FraticelliLab
PREPRINT JUST WENT LIVE

biorxiv.org/content/10.6...

Here, we describe PLSTCs, Soluplus-based expansion cultures of primary mouse *Acute Myeloid Leukemia* Stem Cells. And then we use LARRY barcoding to identify drivers of leukemogenicity and drug resistance!

Leukemia stem cell expansion cultures reveal clonal drivers of leukemogenesis and therapy response https://www.biorxiv.org/content/10.64898/2026.02.24.707683v1

A new preprint our from our collaboration with Celine Vallot's teams and the single cell facilities that we are codirecting. Pushing the bundaries of single cell cut&tag. www.biorxiv.org/content/10.6...

I was wondering if `cellstates` would perform closer to multimodal metacells or very similar to `SuperCell`, on RNA alone. Thanks!

I've found `cellstates` (and `bonsai`) by @erikvannimwegen.bsky.social to be very useful and robust. In their benchmarking (fig.2b @ Grobecker et al. PLoS Comp Bio'24), one of the modes in which they use `SuperCell` performs very similar to `cellstates`.

2/3

Congratulations, David & team.

I think it's very cool how you show that multimodal metacells outperform unimodal metacells. Do you think it would make sense to include `cellstates` into your comparison? For the RNA layer, I mean.

1/3

Happy to share the beautiful manuscript of Leonard Herault: www.biorxiv.org/content/10.6...

Can you expand your thoughts about how or which tech seems the most promising to you?

We recently updated our paper demonstrating evidence of off-target probe binding affecting the 10x Genomics Xenium spatial transcriptomics platform with key clarifications, new quantifications, and approaches for evaluating custom gene panels: biorxiv.org/content/10.1...

🧵👇1/n

Do you want to pursue your ideas in computational biology independently, running your group in @embl.org‘s uniquely collaborative environment, beside world’s most comprehensive biomolecular data resources @ebi.embl.org in Genome Campus next to @sangerinstitute.bsky.social?
Apply to join us & share 🙏

Modeling the evolutionary dynamics of clonal hematopoiesis

doi.org/10.1038/s415...
t.co/ZDzi6BCqGW

Annotating genomes at increased scale and resolution Nature Reviews Genetics, Published online: 17 February 2026; doi:10.1038/s41576-026-00937-3In this Review, Ji et al. overview how rapidly advancing experimental and computational methods are enabling improved and automated annotation of gene structure and function, providing researchers with genome annotation resources of unprecedented scale and resolution.

New online! Annotating genomes at increased scale and resolution

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

This is a fascinating paper that reveals defined and clear mechanism for a phenomenon that for some seemed unbelievable- the up regulation of genes paralogous to those with specific types of inactivating mutations. This is called transcriptional adaptation 1/ www.science.org/doi/10.1126/...

Can we accurately map cell family trees using mtDNA? Excited to share MitoDrift, a high-precision single-cell lineage inference tool, enabling reliable mapping of lineage history to cell phenotypes. doi.org/10.64898/202...
Joint with @gaoteng.bsky.social. @bloodgenes.bsky.social @jswlab.bsky.social🧵

A key point: development is *constructive*. The full information about the final product is not contained in the genome. The developing organism accretes information as it builds itself.

fastdemux: Robust SNP-based demultiplexing of single-cell population genomics data https://www.biorxiv.org/content/10.64898/2026.02.10.705082v1

🚨 New preprint alert!

DNMT1 is often elevated in cancer, but its direct impact on DNA methylation regulation has been hard to isolate in tumours full of confounding processes.

Using a clean genetic system in mESCs, we asked:
What does excess DNMT1 by itself do to the methylome?
Let’s dive in 🧵
1/9

DEPower: approximate power analysis with DESeq2 https://www.biorxiv.org/content/10.64898/2026.02.05.704084v1