The empty drops you threw out in your single-cell RNA sequencing analysis might be hiding mysterious things π check out our bioRxiv preprint!
The empty drops do not contain cells. Yet we can still use them to learn interesting things about biology and technology. 1/
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
Very happy to share our work with Seth Berger and UCI-GREGoR at @ajhgnews.bsky.social .
We developed and extensively evaluated a method - duoNovo - that uses long-read sequencing to detect de novo variants using *only one* biological parent. (1/n)
R package: github.com/sbergercnmc/...
Great work by Albert from my lab! Albert has a few more papers coming shortly and will be graduating soon. Then off to a PD! He is a great PD catch and you should consider him :) bsky.app/profile/albe...
The function of nuclear speckles is revealed! This is an incredibly important paper with absolutely beautiful data! Wow! www.cell.com/cell/fulltex...
New paper from my group led by @alexyfyf.bsky.social. We started with simple questions: what is the best way to do differential analysis with long-read RNA-seq without a reference genome? and are long-reads fulfilling their promise of accurate transcript reconstruction compared to short-read?
Beyond metaphor: quantitative reconstruction of Waddington's landscape and exploration of cellular behavior academic.oup.com/bib/article/... - really nice review of how big data and new computational methods and reviving an old conceptual framework
CODA enables mapping of human organs and tissues in 3D and single-cell resolution and integration with spatial transcriptomics and proteomics.
Our overall goal is revisit and expand work by Bourgery & Jacob using the most modern AI tools....it's working!
More here: www.nature.com/articles/s41...
TEExplorer: A Web Portal to Investigate TE-Epigenome Associations Across Human Cell Types https://www.biorxiv.org/content/10.64898/2026.02.18.706470v1
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...
π§΅π1/n
Allele-specific alternative polyadenylation links noncoding genetic variation to Alzheimer's disease risk https://www.biorxiv.org/content/10.64898/2026.02.13.705798v1
π₯οΈπ§¬π I am excited to share that our #omnideconv study is finally published on Genome Biology: doi.org/10.1186/s130...
Single-subject Proteomic Signatures in Alzheimers Disease Reflect Clinical Phenotypes and Distinguish Asymptomatic from Symptomatic Cases https://www.biorxiv.org/content/10.64898/2026.02.06.704408v1
New pre-print is out! We combined long- and short-read RNA sequencing in iPSC-derived excitatory neurons, astrocytes, and microglia to build a cell-type resolved atlas of NMD-sensitive alternative splicing.
www.biorxiv.org/content/10.6...
Please share: we're hiring a new tenure-track faculty member to our Department of Genetics at Albert Einstein College of Medicine.
faculty-einstein.icims.com/jobs/17847/a...
Please share this with your network: Postdoctoral position available in my group.
www.linkedin.com/jobs/view/43...
Unquestionably the result of combined effort from all current and former lab members, support from colleagues @CSU and @CU, and support from @hhmi-science.bsky.social and NIH over decades. A heartfelt π to my nominators and of course @vilcekfoundation.bsky.social.
vilcek.org/prizes/prize...
Molecular features of human pathological tau distinguish tauopathy-associated dementias www.cell.com/cell/fulltex...
We are thrilled to announce the first official release (v0.1.8) of #π―π²π±π±π²πΏ, the successor to one of our flagship tool, #π―π²π±ππΌπΌπΉπ! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
After a long review process, I'm excited that our paper is finally in print: www.cell.com/cell/fulltex...
TL;DR: We use CRISPR screens in iPSC-derived neurons to find a new tau E3 ligase and a relationship between oxidative stress, the proteasome, and tau proteolytic fragments.
More below π
CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis: @cellpress.bsky.social www.cell.com/cell/fulltex...
"we find that peripheral cancer inhibits amyloid pathology & rescues cognition via secretion of cystatin-c, which binds amyloid oligomers & activates triggering receptor expressed on myeloid cells 2 in microglia, enabling microglia to degrade the existing plaques in AD mice"
doi.org/10.1016/j.ce...
π
'Here, we systematically benchmark five commercial ST platforms (Visium v1, Visium v2/CytAssist, Visium HD, Xenium, and CosMx) using matched FFPE human tumor sections from six cancer types.'
link.springer.com/article/10.1...
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.
Preprint alert: Jiangyuan Liu developed a new workflow for chromatin loop calling across Hi-C datasets, e.g., during differentiation. Most loops are shared between datasets/cell states. Important work for all interested in chromatin loops and how to identify them!
www.biorxiv.org/content/10.6...
Congrats!!!!!
Cartoon zebrafish with green lit-up brain, in well of plate responding to hit molecule.
Drug discovery for nervous system disorders is really challenging. We think early/rapid in vivo testing with zebrafish will accelerate the drug development cycle for conserved targets. Check out our proof-of-principle pilot study and virtual drug discovery pipeline (tinyurl.com/3whr23hs). #Skytorial
Paper is here and preview is below. This is case where the long back and forth between authors and reviewers is illuminating and touches on the historical literature elifesciences.org/articles/105...
We are proud to announce a new ENCODE Registry of cCREs (candidate Cis-Regulatory Elements) track for hg38 as described in Moore et al., Nature 2026.
See our news for more: bit.ly/ucscENCODE4cCREs
TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread
