Jonathan Froehlich
@jjfroehlich.bsky.social
Postdoc // gene regulation, genomics, synbio, stem cells, c. elegans // with @eddaschulz @molgen.mpg.de previously @n_rajewsky @mdc-bimsb //
Reposted by Jonathan Froehlich
📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
November 27, 2025 at 1:17 PM
📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
www.cell.com/cell/fulltex...
Key findings in a thread (1/6):
Reposted by Jonathan Froehlich
Anthony A. Hyman will become EMBL’s next Director General.
He joins EMBL from @mpi-cbg.de in Dresden. He is also Professor of Molecular Biology @tudresden.bsky.social, and was a group leader at EMBL Heidelberg from 1993 to 1999.
www.embl.org/news/people-...
He joins EMBL from @mpi-cbg.de in Dresden. He is also Professor of Molecular Biology @tudresden.bsky.social, and was a group leader at EMBL Heidelberg from 1993 to 1999.
www.embl.org/news/people-...
November 27, 2025 at 1:02 PM
Anthony A. Hyman will become EMBL’s next Director General.
He joins EMBL from @mpi-cbg.de in Dresden. He is also Professor of Molecular Biology @tudresden.bsky.social, and was a group leader at EMBL Heidelberg from 1993 to 1999.
www.embl.org/news/people-...
He joins EMBL from @mpi-cbg.de in Dresden. He is also Professor of Molecular Biology @tudresden.bsky.social, and was a group leader at EMBL Heidelberg from 1993 to 1999.
www.embl.org/news/people-...
Reposted by Jonathan Froehlich
#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
November 24, 2025 at 4:57 PM
#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨🔬 Built by a researcher — for researchers!
👉 Check it out at opencloning.org
Reposted by Jonathan Froehlich
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
RNA polymerase II coordinates histone deacetylation at active promoters
Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.
www.science.org
February 12, 2025 at 9:21 PM
Unpause! I'm super happy to now be able to share the published version of our paper at Science Advances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
www.science.org/doi/10.1126/...
Reposted by Jonathan Froehlich
Reposted by Jonathan Froehlich
Image screening is going to fail. We need audit trails for data provenance.
I tried an even harder example on Gemini Pro image generation and this is quite scary/amazing. I asked for a microscopy image of around 20 HeLa cells, GFP tagged 20% nuclear, 10% membrane, +1 nuclear staining, + overlap. Image below and prompt in the following post.
November 22, 2025 at 4:21 PM
Image screening is going to fail. We need audit trails for data provenance.
Reposted by Jonathan Froehlich
1/6 We are hiring!!! 🐣🐣🐣
Fully funded postdoc position in my group!
humantechnopole.it/en/research-...
Fully funded postdoc position in my group!
humantechnopole.it/en/research-...
Legnini Group - Human Technopole
Laboratory for Molecular and Systems Biology of RNA The Legnini Group at Human Technopole combines molecular and systems biology approaches to study gene regulation. We use synthetic biology and opt...
humantechnopole.it
November 6, 2025 at 5:43 PM
1/6 We are hiring!!! 🐣🐣🐣
Fully funded postdoc position in my group!
humantechnopole.it/en/research-...
Fully funded postdoc position in my group!
humantechnopole.it/en/research-...
Reposted by Jonathan Froehlich
Students applying for grad school, or reaching out to professors. I have an important piece of advice for you: STOP DOING THIS 👇 (a thread) #STEM #PhD #gradschool #academictips
November 21, 2025 at 9:53 PM
Students applying for grad school, or reaching out to professors. I have an important piece of advice for you: STOP DOING THIS 👇 (a thread) #STEM #PhD #gradschool #academictips
Reposted by Jonathan Froehlich
How the genes plasmids carry affect their hosts has been well studied, but this smaller scale of evolution has proven much tougher despite decades of theory. Plasmids are small and replication is fast and hard to measure. 2/
November 20, 2025 at 9:42 PM
How the genes plasmids carry affect their hosts has been well studied, but this smaller scale of evolution has proven much tougher despite decades of theory. Plasmids are small and replication is fast and hard to measure. 2/
Reposted by Jonathan Froehlich
what is your #1 most important rule about concise science writing?
November 20, 2025 at 1:00 AM
what is your #1 most important rule about concise science writing?
Reposted by Jonathan Froehlich
(3) Described as “futility theorem” in the 2000s, it’s hard to map functional low-affinity motifs based on low PWM match scores, yet some low-affinity motifs have crucial phenotypic consequences in vivo.
What then makes low-affinity motifs important for enhancer regulation?
What then makes low-affinity motifs important for enhancer regulation?
November 19, 2025 at 8:57 PM
(3) Described as “futility theorem” in the 2000s, it’s hard to map functional low-affinity motifs based on low PWM match scores, yet some low-affinity motifs have crucial phenotypic consequences in vivo.
What then makes low-affinity motifs important for enhancer regulation?
What then makes low-affinity motifs important for enhancer regulation?
Reposted by Jonathan Froehlich
Good to see the peer reviewed version of this in print
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program operates across the vertebrate nervous system to control neural cell diversity
www.cell.com/developmenta...
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program operates across the vertebrate nervous system to control neural cell diversity
www.cell.com/developmenta...
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
Zhang et al. identify a global temporal chromatin program that operates across the
developing vertebrate nervous system to control neural cell diversity. This mechanism,
which involves Nr6a1 and NFIA/...
www.cell.com
November 18, 2025 at 8:59 AM
Good to see the peer reviewed version of this in print
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program operates across the vertebrate nervous system to control neural cell diversity
www.cell.com/developmenta...
The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program operates across the vertebrate nervous system to control neural cell diversity
www.cell.com/developmenta...
Reposted by Jonathan Froehlich
(1/13) Excited to share the outcome of the IBIS Challenge! The IBIS challenge united dozens of teams across the world in tackling the problem of modeling transcription factor (TF) binding specificity using a diverse collection of experimental datasets for understudied human TFs.
November 18, 2025 at 10:55 PM
(1/13) Excited to share the outcome of the IBIS Challenge! The IBIS challenge united dozens of teams across the world in tackling the problem of modeling transcription factor (TF) binding specificity using a diverse collection of experimental datasets for understudied human TFs.
Reposted by Jonathan Froehlich
check out my journal club on the seminal discovery of local translation in neurons (Kang & Schuman. 1996), and more recently, its activity in neocortex neurodevelopment (Pilaz...Silver. 2023).
cheers to the @erin-schuman.bsky.social & @debbysilver.bsky.social labs!
www.nature.com/articles/s41...
cheers to the @erin-schuman.bsky.social & @debbysilver.bsky.social labs!
www.nature.com/articles/s41...
The on-site, on-demand, neuronal gene machine - Nature Reviews Neuroscience
In this Journal Club, Matthew Kraushar discusses a study published in 1996 that found a role for local protein translation in hippocampal synaptic plasticity.
www.nature.com
November 18, 2025 at 6:35 PM
check out my journal club on the seminal discovery of local translation in neurons (Kang & Schuman. 1996), and more recently, its activity in neocortex neurodevelopment (Pilaz...Silver. 2023).
cheers to the @erin-schuman.bsky.social & @debbysilver.bsky.social labs!
www.nature.com/articles/s41...
cheers to the @erin-schuman.bsky.social & @debbysilver.bsky.social labs!
www.nature.com/articles/s41...
Reposted by Jonathan Froehlich
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...
www.biorxiv.org
November 19, 2025 at 8:57 PM
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Reposted by Jonathan Froehlich
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Dissecting regulatory syntax in human development with scalable multiomics and deep learning
Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...
www.biorxiv.org
May 3, 2025 at 6:27 PM
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Reposted by Jonathan Froehlich
We used model interpretation techniques (DeepLIFT/SHAP & TF-MoDISco) to score the contribution of every nucleotide to accessibility, and discover recurrent patterns of sequences predictive of local chromatin accessibility - and these patterns turned out to primarily resemble TF binding motifs!
May 3, 2025 at 6:27 PM
We used model interpretation techniques (DeepLIFT/SHAP & TF-MoDISco) to score the contribution of every nucleotide to accessibility, and discover recurrent patterns of sequences predictive of local chromatin accessibility - and these patterns turned out to primarily resemble TF binding motifs!
Reposted by Jonathan Froehlich
In one year, I genetically engineered the boring Arabidopsis into a beautiful ornamental flower 🧬🌹
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
December 12, 2024 at 11:24 AM
In one year, I genetically engineered the boring Arabidopsis into a beautiful ornamental flower 🧬🌹
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Here is how and why I gave this model organism a visual upgrade 🧵(1/7)
Reposted by Jonathan Froehlich
1/n Very excited to share our recent paper published on
@ScienceAdvances
where we dissect the gene regulatory landscape guiding mouse sex determination!
science.org/doi/10.1126/...
A huge well done to @IsabelleStevant.genomic.social.ap.brid.gy, Meshi and Elisheva who spearhead this project!
@ScienceAdvances
where we dissect the gene regulatory landscape guiding mouse sex determination!
science.org/doi/10.1126/...
A huge well done to @IsabelleStevant.genomic.social.ap.brid.gy, Meshi and Elisheva who spearhead this project!
The gene regulatory landscape driving mouse gonadal supporting cell differentiation
Multiomics analysis revealed the regulatory elements and transcription factors responsible for gonadal sex determination.
science.org
July 27, 2025 at 6:04 AM
1/n Very excited to share our recent paper published on
@ScienceAdvances
where we dissect the gene regulatory landscape guiding mouse sex determination!
science.org/doi/10.1126/...
A huge well done to @IsabelleStevant.genomic.social.ap.brid.gy, Meshi and Elisheva who spearhead this project!
@ScienceAdvances
where we dissect the gene regulatory landscape guiding mouse sex determination!
science.org/doi/10.1126/...
A huge well done to @IsabelleStevant.genomic.social.ap.brid.gy, Meshi and Elisheva who spearhead this project!
Reposted by Jonathan Froehlich
This is such an interesting paper. Why? Because the binding of transcription factor (TF) proteins to DNA governs how our genes are turned on/off/up/down, & so is the primary issue for how our genes work in development and how our cells respond to just about anything.🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Multiple overlapping binding sites determine transcription factor occupancy - Nature
A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create ov...
www.nature.com
October 30, 2025 at 11:04 PM
This is such an interesting paper. Why? Because the binding of transcription factor (TF) proteins to DNA governs how our genes are turned on/off/up/down, & so is the primary issue for how our genes work in development and how our cells respond to just about anything.🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Jonathan Froehlich
Our paper on LARGE-scale benchmarking of motif discovery tools is published! nature.com/articles/s42...
It was a long, 7 years long journey, which coordinated efforts of 50+ researchers, proud to be on of them.
More results from Codebook about poorly studied TFs are coming soon.
It was a long, 7 years long journey, which coordinated efforts of 50+ researchers, proud to be on of them.
More results from Codebook about poorly studied TFs are coming soon.
November 17, 2025 at 10:44 AM
Our paper on LARGE-scale benchmarking of motif discovery tools is published! nature.com/articles/s42...
It was a long, 7 years long journey, which coordinated efforts of 50+ researchers, proud to be on of them.
More results from Codebook about poorly studied TFs are coming soon.
It was a long, 7 years long journey, which coordinated efforts of 50+ researchers, proud to be on of them.
More results from Codebook about poorly studied TFs are coming soon.
Reposted by Jonathan Froehlich
📣 SAVE THE DATE
Next X-inactivation meeting in Sapporo, Japan, 19-23 October 2026. Visit x-inactivation-meeting.org to join our mailing list. 🧬 speakers @dandergassen.bsky.social @marnieblewitt.bsky.social @heard65.bsky.social @crougeulle.bsky.social @sexchrlab.bsky.social @zhouqi1982.bsky.social
Next X-inactivation meeting in Sapporo, Japan, 19-23 October 2026. Visit x-inactivation-meeting.org to join our mailing list. 🧬 speakers @dandergassen.bsky.social @marnieblewitt.bsky.social @heard65.bsky.social @crougeulle.bsky.social @sexchrlab.bsky.social @zhouqi1982.bsky.social
November 17, 2025 at 11:39 AM
📣 SAVE THE DATE
Next X-inactivation meeting in Sapporo, Japan, 19-23 October 2026. Visit x-inactivation-meeting.org to join our mailing list. 🧬 speakers @dandergassen.bsky.social @marnieblewitt.bsky.social @heard65.bsky.social @crougeulle.bsky.social @sexchrlab.bsky.social @zhouqi1982.bsky.social
Next X-inactivation meeting in Sapporo, Japan, 19-23 October 2026. Visit x-inactivation-meeting.org to join our mailing list. 🧬 speakers @dandergassen.bsky.social @marnieblewitt.bsky.social @heard65.bsky.social @crougeulle.bsky.social @sexchrlab.bsky.social @zhouqi1982.bsky.social
Reposted by Jonathan Froehlich
The recent openRxiv meeting was a chance to present a vision for the future: a network of organizations working together to improve science communication and an ‘article of the future’ that is a constellation of linked web objects.
openrxiv.org/openrxiv-day/
openrxiv.org/openrxiv-day/
November 13, 2025 at 7:14 PM
The recent openRxiv meeting was a chance to present a vision for the future: a network of organizations working together to improve science communication and an ‘article of the future’ that is a constellation of linked web objects.
openrxiv.org/openrxiv-day/
openrxiv.org/openrxiv-day/
Reposted by Jonathan Froehlich
New preprint!
It turns out you can integrate arrays with super high efficiency using PhiC31.
www.biorxiv.org/content/10.1...
It turns out you can integrate arrays with super high efficiency using PhiC31.
www.biorxiv.org/content/10.1...
High-efficiency targeted integration of extrachromosomal arrays in C. elegans using PhiC31 integrase
Extrachromosomal arrays are unique chromosome-like structures created from DNA injected into the C. elegans germline. Arrays are easy to create and allow for high expression of multiple transgenes. Th...
www.biorxiv.org
November 13, 2025 at 2:59 AM
New preprint!
It turns out you can integrate arrays with super high efficiency using PhiC31.
www.biorxiv.org/content/10.1...
It turns out you can integrate arrays with super high efficiency using PhiC31.
www.biorxiv.org/content/10.1...
Reposted by Jonathan Froehlich
Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - @jshendure.bsky.social @troymcdiarmid.bsky.social @uwgenome.bsky.social go.nature.com/49eTPCu
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - Nature Biotechnology
Prime editing in mammalian cells benefits from a comprehensive list of genetic parts.
go.nature.com
November 12, 2025 at 6:06 PM
Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com