Josh Brickman
@josh-brickman.bsky.social
Developmental and Stem Cell Biologist, interested in all things gene regulation. Transcription, lineage specification, potency and plasticity.
Looking forward to Naama Barkai's visit tomorrow - all in copenhagen interested in biological specificity should come to hear her talk tomorrow!!!!
August 12, 2025 at 7:19 AM
Looking forward to Naama Barkai's visit tomorrow - all in copenhagen interested in biological specificity should come to hear her talk tomorrow!!!!
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...
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...
www.nature.com
August 11, 2025 at 1:38 PM
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!
Clearly my presence in the lab was missed!
June 24, 2025 at 11:03 AM
Back from the ISDB,
Clearly my presence in the lab was missed!
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.
Issue 11
N&V: fibroblast dynamics during mammary oncogenesis
RIPK1 oligomers at core of CD95 necrosomes
Autophagosomes as hub for AKAP regulation of neuronal PKA
Centipede neurotoxin reveals new mode of Nav channel modulation
Cover: @josh-brickman.bsky.social et al
www.embopress.org/toc/14602075...
N&V: fibroblast dynamics during mammary oncogenesis
RIPK1 oligomers at core of CD95 necrosomes
Autophagosomes as hub for AKAP regulation of neuronal PKA
Centipede neurotoxin reveals new mode of Nav channel modulation
Cover: @josh-brickman.bsky.social et al
www.embopress.org/toc/14602075...
June 2, 2025 at 1:10 PM
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.
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...
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
academic.oup.com
May 25, 2025 at 12:21 PM
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.
Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵
Design principles of cell-state-specific enhancers in hematopoiesis
Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread
dual activator-repressor function of transcription factors (TFs) and enables the model-guided
design of cell-state-sp...
www.cell.com
May 25, 2025 at 12:20 PM
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...
May 22, 2025 at 1:43 PM
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...
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/...
renew.ku.dk/latest-news/...
reNEW CEO named Fellow of the Royal Society
reNEW CEO named Fellow of the Royal Society
renew.ku.dk
May 20, 2025 at 10:05 AM
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/...
renew.ku.dk/latest-news/...
And here I was thinking I need to modernize my references with Taylor - perhaps the Last Dance is further away then we think!
Congrats Josh! Was just thinking of you while listening to this new Mekons session. Your ##PaperThemeTune can be the first track: it lacks chromatin, but does contain an age-appropriate dose of nostalgia... www.bbc.co.uk/sounds/play/...
Riley & Coe - Mekons live in session! - BBC Sounds
Marc is joined by legendary punk rockers Mekons live from the BBC's Maida Vale studios.
www.bbc.co.uk
May 9, 2025 at 12:48 AM
And here I was thinking I need to modernize my references with Taylor - perhaps the Last Dance is further away then we think!
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...
Junior Group Leader (Associate Professor) in Stem Cell Medicine
employment.ku.dk
May 7, 2025 at 1:01 PM
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...
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....
www.embopress.org/doi/full/10....
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)-...
www.embopress.org
April 25, 2025 at 3:26 PM
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....
www.embopress.org/doi/full/10....
Reposted by Josh Brickman
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....
@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....
April 25, 2025 at 3:10 PM
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....
@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!
In the world to work with human pluripotent cells!
Today we welcome Josh Brickman @josh-brickman.bsky.social from reNEW at the University of Copenhagen, who will present his work on transcription factors and cellular memory.
Alfred Denny Conference Room, 1 pm. All welcome!
Host: Anestis Tsakiridis @tsakiridis.bsky.social
Alfred Denny Conference Room, 1 pm. All welcome!
Host: Anestis Tsakiridis @tsakiridis.bsky.social
March 3, 2025 at 8:06 AM
Really looking forward to a day in Sheffield - one of the first places
In the world to work with human pluripotent cells!
In the world to work with human pluripotent cells!
Reposted by Josh Brickman
PRC2 promotes canalisation during endodermal differentiation
journals.plos.org/plosgenetics...
@Robertillingwo7 @wbickmor.bsky.social
@josh-brickman.bsky.social
journals.plos.org/plosgenetics...
@Robertillingwo7 @wbickmor.bsky.social
@josh-brickman.bsky.social
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...
journals.plos.org
February 2, 2025 at 2:02 PM
PRC2 promotes canalisation during endodermal differentiation
journals.plos.org/plosgenetics...
@Robertillingwo7 @wbickmor.bsky.social
@josh-brickman.bsky.social
journals.plos.org/plosgenetics...
@Robertillingwo7 @wbickmor.bsky.social
@josh-brickman.bsky.social
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...
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...
February 2, 2025 at 1:48 PM
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...
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...
Reposted by Josh Brickman
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 🎆 !
Happy 2025 everyone 🎆 !
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...
doi.org
January 6, 2025 at 2:05 PM
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 🎆 !
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
January 14, 2025 at 8:27 AM
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
Reposted by Josh Brickman
We have an amazing programme with fantastic speakers! @chribue.bsky.social @wbickmor.bsky.social @robklose.bsky.social @mariekeoudelaar.bsky.social @eileen-furlong.bsky.social @josh-brickman.bsky.social @parinazmehdipour.bsky.social @edchuong.bsky.social @jorge-ferrer.bsky.social @helink.bsky.social
January 6, 2025 at 2:58 PM
We have an amazing programme with fantastic speakers! @chribue.bsky.social @wbickmor.bsky.social @robklose.bsky.social @mariekeoudelaar.bsky.social @eileen-furlong.bsky.social @josh-brickman.bsky.social @parinazmehdipour.bsky.social @edchuong.bsky.social @jorge-ferrer.bsky.social @helink.bsky.social
Browsing through the literature as things calm down, thinking about posting now that the twittersphere has turned blue, I discover the next step change in chromatin analysis....an incredible data deluge!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
December 23, 2024 at 3:42 PM
Browsing through the literature as things calm down, thinking about posting now that the twittersphere has turned blue, I discover the next step change in chromatin analysis....an incredible data deluge!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Embryologists from
Amager Hvidovre Hospital visiting Brickman and @jzylicz.bsky.social labs learning about stem cell based embryo models!
Amager Hvidovre Hospital visiting Brickman and @jzylicz.bsky.social labs learning about stem cell based embryo models!
December 20, 2024 at 1:15 PM
Embryologists from
Amager Hvidovre Hospital visiting Brickman and @jzylicz.bsky.social labs learning about stem cell based embryo models!
Amager Hvidovre Hospital visiting Brickman and @jzylicz.bsky.social labs learning about stem cell based embryo models!