Josh Brickman

Thanks Chris - hope to chat later

Looking forward to Naama Barkai's visit tomorrow - all in copenhagen interested in biological specificity should come to hear her talk tomorrow!!!!

Contributions from our side, Martin Proks @nazsalehin.bsky.social and Madeleine Linneberg-Agerholm, whose original in vitro finding are validated in this paper - journals.biologists.com/dev/article/...

Our model suggests that a few cells can partially differentiate, forming early endoderm that still expresses some epiblast markers - this could be due to the differences in timing of the two binary cell fate choices in preimplantation development between mouse and human.

Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing - Nature Methods This Resource uses deep learning-based tools to build a dynamic transcriptomic reference for mouse and human preimplantation development.

We used our deep learning models that were originally published in www.nature.com/articles/s41...

Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst - Nature Communications The authors show human embryo lineage specification in the blastocyst is driven by differential FGF/ERK signaling, which segregates yolk sac-fated hypoblast and embryonic epiblast. They establish naïv...

Very happy to see this nice collaboration with @niakanlab.bsky.social bear fruit. Beautiful work by @clairesimon.bsky.social culturing human embryos in the presence of FGF/ERK stimulation/inhibition. www.nature.com/articles/s41...

Back from the ISDB,
Clearly my presence in the lab was missed!

Why combat aging with enhancers at 11? Why not just make 10 louder? It wouldn't be 11. For transcription, all the other processes (translation, splicing etc) are on ten, on ten, etc…where do they go? For Enhancers, everything on ten, the transcription factors deacetylate and go one higher, 11.

Thanks for that !

nf-core/marsseq: systematic preprocessing pipeline for MARS-seq experiments AbstractMotivation. Single sequencing technology (scRNA-seq) enables the study of gene regulation at a single cell level. Although many sc-RNA-seq protocol

Another chapter from Martin Proks PhD. The first chapter in our nf-core saga and a new pipeline for MARS-seq! academic.oup.com/bioinformati...

Very nice paper - all principles at the heart of molecular biology although the logic with which evolution implements them was a mystery.

Alba Redo Riveiro - an amazing PhD student. One chapter in her PhD is described here. It was a great paper and a very long evolving story - www.cell.com/stem-cell-re...

reNEW CEO named Fellow of the Royal Society reNEW CEO named Fellow of the Royal Society

Very excited to see Melissa elected to the Royal Society. Nice triumph for old school developmental biology entering the modern world of translation. Way to go Melissa!!!!
renew.ku.dk/latest-news/...

And wait to you see the accompanying image that goes to 11!

And here I was thinking I need to modernize my references with Taylor - perhaps the Last Dance is further away then we think!

Junior Group Leader (Associate Professor) in Stem Cell Medicine

Two days left to apply to do fantastic science in a great place - come join us as a new group leader at reNEW - employment.ku.dk/faculty/?sho...

This enhanced or deteriorating ratio of epigenetic signals may also underpin aging. Amazing work by Robert Bone @alboo87
, @molly_lowndes
and Collaborators @treebak
and Michael Nielsen, all of @LabBrickman
in @reNEW_Global
@UCPH_health

Imagine you take your grandparents to a crowded restaurant, they complain they can’t hear you both because you aren’t speaking loud enough, and that there is too much noise.

SIRT1 in turn, turns up the signal to noise ratios at the level of enhancer regulation, with 14K enhancers become 4K very effective enhancers.

Super ESCs, rejuvenated ESCs, enhanced lipid metabolism leads to elevated NAD and activated SIRT1

Essentially, we tried giving cells their own variation on Ozempic…Galactose. In the case of ESCs, we bypass the brain and substitute galactose for glucose the media…they become super stem cells.

Altering metabolism programs cell identity via NAD+-dependent deacetylation | The EMBO Journal imageimageHow alterations in cell metabolism translate into specific developmental gene programs remains a major question. This study shows that forcing OXPHOS metabolism reprograms mouse embryonic stem cells (ESCs) to a more inner cell mass (ICM)-...

How does metabolism act through generic chromatin modifiers promote specific cellular states? Simultaneous modification of transcription factors and chromatin, enhancing epigenetic signal to noise ratios.
www.embopress.org/doi/full/10....

Altering metabolism programs cell identity via NAD+-dependent deacetylation
@josh-brickman.bsky.social et al show enforced OXPHOS dependence in embryonic stem cells drives deacetylation of essential transcription factors & inner-cell-mass-like gene expression
www.embopress.org/doi/full/10....

Really looking forward to a day in Sheffield - one of the first places
In the world to work with human pluripotent cells!

PRC2 promotes canalisation during endodermal differentiation Author summary Embryogenesis requires a tightly coordinated programme of cellular expansion and specialisation to gives rise to all of the cell- and tissue-types of the developing organism. In mammals...

PRC2 promotes canalisation during endodermal differentiation

journals.plos.org/plosgenetics...

@Robertillingwo7 @wbickmor.bsky.social
@josh-brickman.bsky.social

What does PRC2 do? It keeps the differentiation train on the rails, insuring lineage fidelity!

Transcription ahead of chromatin regulation?
Activation in endoderm occurs prior to K27me3 removal, plus much more. A tribute to our amazing collaborators
@wbickmor.bsky.social and the amazing Rob Illingworth, without whom this data would have gathered dust!

journals.plos.org/plosgenetics...

PRC2 rocks - and preserves lineage fidelity

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning - Nature Communications Functional chromatin changes occur at different scales. Here, the authors introduce ChromatinHD, a method that characterises differential and predictive chromatin accessibility changes in a scale-adap...

Superb work by Wouter @Zouters & @OlgaPushkarev developing ChromatinHD, two scale-adaptive #machinelearning models & interpretation tools that use #scRNAseq + #scATACseq data to better understand how chromatin accessibility relates to gene expression doi.org/10.1038/s414...

Happy 2025 everyone 🎆 !

In the next few weeks we will start advertising for PhD students and/or post docs. We are looking for two people to join our group, one focused in pancreatic organoids and the other to join our computational team. DM if you are interested in coming to @ucph.bsky.social