CUT&ID does Genomics+Proteomics in one shot via the fusion protein Lazarus Out @narjournal.bsky.social Unstoppable @annanordin.bsky.social is thinker+executor Get in touch if you wish to try it—plasmid soon @addgene.bsky.social 🙏 @liu.se @scilifelab.se @kawresearch.bsky.social @cancerfonden

Claudio Cantù@claudiocantu81.bsky.social · 10mo ago

Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample? Yes, one can. with CUT&ID ✂️🪪 Spearheaded — singlehandedly — by @annanordin.bsky.social No need of transgenesis, cloning and overexpression. Check it out, it's fast and its works.

New from @daspliceisright.bsky.social www.biorxiv.org/content/10.6...

The strength of a gene's first 5' splice site is a key determinant of its expression

The control of gene expression is central to cellular physiology and to various biotechnological applications. In higher eukaryotes, synthesis of most messenger RNAs involves removal of introns during...

biorxiv.org

Happy to finally announce my tool Nailpolish 💅. Feedback and suggestions are very welcome and encouraged!

Nadia Davidson@nadia-davidson.bsky.social · 2d ago

Introducing Nailpolish 💅 by @oyc.id.au & @jw-tan.bsky.social. It deduplicates long-reads with UMIs via consensus calling to cut errors, shorturl.at/F9pV6. It works reference-free i.e. pre-alignment and is written in rust for speed. Applicable to any long-read experiment with UMIs. Feedback welcome!

🧬 Highly related @natgenet.nature.com paper from @binzmit.bsky.social group, using nucleosome-resolution chromatin modeling: Euchromatin forms condensed domains with short active regions on the surface www.nature.com/articles/s41... Congratulations! 🎉

Euchromatin forms condensed domains with short active regions on the surface - Nature Genetics

Simulations integrating micro-C and imaging data provide a coherent view of chromatin organization from nucleosomes to clutches to domains, revealing that most regions form compact domains but short r...

nature.com

Kazuhiro Maeshima@kazu-maeshima.bsky.social · 3w ago

Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)

A new publicly available single-cell atlas of the human prefrontal cortex was made from 6.3 million nuclei across 1,494 donors, ranging from before birth to more than 100 years. By @siddhantpusdekar.bsky.social www.thetransmitter.org/transcriptom...

Prefrontal cortex has three transcriptomic acts

Various genes show distinct exits and entrances with age in the open- source dataset, the largest of its kind to date.

thetransmitter.org

If you are curious about quantitative and predictive cell date decisions landscapes but our 14 figure paper seemed just a bit daunting, have a look at James' linked summary.

James Briscoe@jamesbriscoe.bsky.social · last wk.

Our latest paper on building models of cell fate decisions -with David Rand, Marine Fontaine & @joadelas.bsky.social- combines developmental biology, dynamical systems theory and bioinformatics. I wrote a short piece to summarise it & explain ideas behind the approach briscoelab.org/blog-quantif...

Paper 2: A cryo-EM structure of Pol λ in the short-range synaptic complex shows how Pol λ and PNKP coordinate end processing — clearing blocked ends and gaps before ligation. Led by Alex Vogt, with the Kunkel, Pedersen, Tomkinson & Lees-Miller labs. nature.com/articles/s41467-026-77503-2

Cool new results and a stunning animation!

Yuan He@yuanhejhu.bsky.social · last wk.

A big week for the lab! Two new papers on how cells repair DNA double-strand breaks: one on getting NHEJ started in chromatin, one on processing the ends before ligation. Years of work by a fantastic team.

It's here! new preprint: Gravlax, an annotation-independent molecular evidence archive for scRNA-seq. A count matrix freezes one annotation. Molecules never change. Instead, gravlax keeps the evidence. Requantify, query, and discover under any annotation. 🧵 www.biorxiv.org/content/10.6...

I will hire a Postdoc to study the genomic determinants of tumor heterogeneity Please, get in touch if interested, or help me spread the voice @scilifelab.se @kawresearch.bsky.social @liu.se liu.se/en/research/...

The Cantù Lab - Genome Regulation in Development and Disease

The Cantù Lab at LiU is focused on one important goal: to discover the mechanisms of genome regulation that drive cell differentiation and specialization during embryonic development.

liu.se

The 4DN Center for 3D Structure and Physics of the Genome proudly presents: "Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation". www.biorxiv.org/content/10.6...

What can we learn about a single rare variant? Published today in Science: the 23andMe Research Institute and Dana-Farber studied the EGFR T790M in 10.1M 23andMe research participants. The variant has OR = 25.2 for lung cancer, rising to 61.7 in never-smokers(!). 🧵

New preprint led by Zoe Rudnick: bramble 🌿 RNA-seq quantification makes you pick a side. Align to the transcriptome and your quantifier is happy, but reads from unannotated transcripts get misassigned to annotated ones. Align to the genome and you keep discovery, but limit quantification choices.

🚨 New preprint from the Rendeiro lab! We mapped human tissue aging at single-cell resolution: 3.5 billion cells, 16 organs, 980 donors, spanning the adult lifespan. Led by @e-abila.bsky.social 📄 www.biorxiv.org/content/10.6...

🧠🧬 New from our lab! Postdoc Celeste Laureyssen ( @celestelaureyssen.bsky.social ) reviews how neuropathology-centered GWAS can sharpen our understanding of the genetics of Alzheimer’s disease and its frequent co-pathologies—moving beyond clinical diagnosis alone. link.springer.com/article/10.1...

A new era of genome-wide association studies in the field of Alzheimer’s disease and overlapping co-pathologies: lessons learned from a neuropathology-centered approach - Acta Neuropathologica

Alzheimer’s disease (AD) and overlapping pathologies represent a growing worldwide health concern. With the first disease-modifying treatments on the rise, it becomes increasingly important to move re...

link.springer.com

Everything you wanted to know about single-molecule epigenomics but were too afraid to ask! Wonderful to co-write (h/t ENORMOUS lift by @arnaudkr.bsky.social) this primer on our nascent field. Also, a 💯 example of wonderful colleagues building something *together*, not in competition =)

A practical guide to studying genome function using single-molecule genomics

Nature Reviews Molecular Cell Biology - Single-molecule genomics methods are used to study the activity of regulatory factors on individual DNA molecules genome-wide, thereby enabling...

nature.com

Our paper is out in Nature Methods! 🧑‍💻 There are 50+ methods for spatially-aware clustering on spatial transcriptomics data. How should we use them? A thread 🧵 (1/7) 📄 doi.org/10.1038/s415... #spatialtranscriptomics #bioinformatics #computationalbiology

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering - Nature Methods

Benchmarking spatially aware clustering is challenging. SACCELERATOR is an open-source, extensible framework that formalizes expert-guided spatial clustering analysis.

doi.org

Excited to share our new preprint on in situ chromatin structure of the inactive X chromosome in differentiated female mouse embryonic stem cells. www.biorxiv.org/content/10.6... 🧵1/8

Check out our new preprint on thousands of novel recursive exons in the human genome (if you don't know about recursive exons, they are pretty cool), led by PhD student David Bass @davidb256.bsky.social : www.biorxiv.org/content/10.6...

Large-scale analysis of transcript data reveals thousands of recursive splicing events in human introns

Recursive splicing (RS) is a process in which an intron is removed from a nascent RNA molecule in two or more splicing events rather than one. We introduce a novel approach for detecting recursive spl...

biorxiv.org

New Online! PRC2–RNA interactions through the lens of bioinformatics pipeline choices

PRC2–RNA interactions through the lens of bioinformatics pipeline choices

Nature Reviews Molecular Cell Biology, Published online: 11 September 2026; doi:10.1038/s41580-026-01028-1Four recent studies that have differently assessed PRC2–RNA interactions reveal key technical pitfalls underlying research in the field.

dlvr.it

Happy to share the peer-reviewed version of this manuscript now published in Bioinformatics Journal. Briefly, we developed HiCPotts, a novel method to better detect 3D DNA contacts from HiC/microC data. doi.org/10.1093/bioi... bioconductor.org/packages/HiC... For a summary, see original post.

Dr Radu Zabet@raduzabet.bsky.social · 4mo ago

🚨 Excited to share a new manuscript from the lab. Here, we have developed a new method, HiCPotts, to identify significant interactions in 3D chromatin data www.biorxiv.org/content/10.6...; package bioconductor.org/packages/HiC.... Big shoutout to an amazing previous PhD in the lab Godwin. 1/n

🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇

Noncoding transcription controls the developmental dynamics of long-range gene regulation

The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...

science.org

Hi friends - thanks for checking this out. The project is now available as an R package. Many improvements & better documentation. Thanks again to Srivastava, Dongze He, @robp.bsky.social, @mikelove.bsky.social, and @plbaldoni.bsky.social for all the methods & glue! github.com/sbresnahan/s...

GitHub - sbresnahan/scAmbi: Mapping Ambiguity Overdispersion Correction for scRNA-seq

Mapping Ambiguity Overdispersion Correction for scRNA-seq - sbresnahan/scAmbi

github.com

Sean Bresnahan@seantbres.bsky.social · last yr.

In bulk RNA-seq, @plbaldoni.bsky.social et al showed that correcting overdispersion (OD) from read-to-transcript mapping ambiguity improves downstream analyses. Here I extend this to scRNA-seq using @mikelove.bsky.social et al Alevin’s bootstraps to correct per-cell OD github.com/sbresnahan/O...

We're pleased to share the results of the 2026 ASHG Board Election! Congratulations to the newly elected ASHG President-Elect and four Directors, who begin their terms on Jan. 1, 2027. Thank you to all members who voted. Meet the Board: https://bit.ly/3TjJXSo

Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)

Thanks so much @zeileis.org for the {exams} #Rstats package. So powerful and well documented! www.r-exams.org Super helpful to create dynamic (individual) exercises for +200 students with automatic feedback and grading in platforms like Blackboard, Moodle...

R/exams

Automatic generation and evaluation of exams. From Markdown, LaTeX and R code to standalone documents, learning management systems and live voting.

r-exams.org

It was great working with students Kun and Ryan and @hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers. www.nature.com/articles/s41...

Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics

This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...

nature.com

Spatial-ATAC-Hi-C enables profiling chromatin accessibility and spatial organization, as shown in mouse and human brain samples. www.nature.com/articles/s41...

Spatial chromatin architecture and accessibility co-profiling of mammalian tissues - Nature Methods

Spatial-ATAC-Hi-C enables the profiling of both chromatin accessibility and organization in a spatially resolved manner, as demonstrated on mouse brain and human glioblastoma and astrocytoma samples.

nature.com

Authors of @ajhgnews.bsky.social latest article introduce IsoRanker, a long-read transcriptome sequencing-based framework that prioritizes functionally relevant variants by detecting genes and isoforms with outlier expression, allelic imbalance, and/or NMD: https://bit.ly/4ybz2ZA #ASHG

No paper from me or my lab will ever be submitted to an MDPI journal - including any of their superfluous "special issues". I will very rarely (if ever) cite MDPI papers. And I will never review for them. deevybee.blogspot.com/2024/08/gues... The same goes for FrontiersIn journals, among others.

My experience as a reviewer for MDPI

Guest post by  René Aquarius, PhD Department of Neurosurgery Radboud University Medical Center, Nijmegen, The Ne...

deevybee.blogspot.com

Brooke Fitzwater, PhD (she/her) 🐟🪱🏳️‍🌈♾️@oceanfilly.bsky.social · 10mo ago

POV: You receive an email from a predatory journal inviting you to submit