Acadia Kocher
@shesacadiak.bsky.social
Postdoc with Bas van Steensel @nkinl.bsky.social
PhD in @noonanlab.bsky.social
Gene regulation, genomics, chromatin, evolution
PhD in @noonanlab.bsky.social
Gene regulation, genomics, chromatin, evolution
Reposted by Acadia Kocher
SAVE THE DATE! Stoked to organize the 2026 Santa Cruz Developmental Biology Meeting with @rashmi-priya.bsky.social, @lowelab.bsky.social, and Shelbi Russell. Come learn about Biomedicine, Biomechanics, and the Biosphere, August 24-28, 2026. Registration dates, etc., coming soon! Please RT
November 19, 2025 at 8:23 PM
SAVE THE DATE! Stoked to organize the 2026 Santa Cruz Developmental Biology Meeting with @rashmi-priya.bsky.social, @lowelab.bsky.social, and Shelbi Russell. Come learn about Biomedicine, Biomechanics, and the Biosphere, August 24-28, 2026. Registration dates, etc., coming soon! Please RT
Reposted by Acadia Kocher
Out in Cell Genomics: A comprehensive analysis of the cell-type-specific effects of CHD8 loss of function on gene expression in the embryonic and juvenile mouse cortex. Thread 🧵:
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
Cell-type-specific dysregulation of gene expression due to Chd8 haploinsufficiency during mouse cortical development
Yim et al. use single-cell transcriptomics to elucidate the molecular outcomes of
Chd8 haploinsufficiency in the mouse cortex. Their results provide insight into dynamic,
cell-type-biased transcriptio...
www.cell.com
September 23, 2025 at 5:18 PM
Out in Cell Genomics: A comprehensive analysis of the cell-type-specific effects of CHD8 loss of function on gene expression in the embryonic and juvenile mouse cortex. Thread 🧵:
www.cell.com/cell-genomic...
www.cell.com/cell-genomic...
Reposted by Acadia Kocher
✨Exciting news: the main story of my PhD is out in Science!
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene
Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...
www.science.org
September 19, 2025 at 2:09 PM
✨Exciting news: the main story of my PhD is out in Science!
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Reposted by Acadia Kocher
Have you ever wondered how the exact location of a gene affects it's activity?
The main story of my PhD deals with exactly that question, and is now published in Science! ✨
www.science.org/doi/10.1126/...
My amazing co-author and friend @mathiaseder.bsky.social summarized the highlights for you
The main story of my PhD deals with exactly that question, and is now published in Science! ✨
www.science.org/doi/10.1126/...
My amazing co-author and friend @mathiaseder.bsky.social summarized the highlights for you
September 19, 2025 at 2:22 PM
Have you ever wondered how the exact location of a gene affects it's activity?
The main story of my PhD deals with exactly that question, and is now published in Science! ✨
www.science.org/doi/10.1126/...
My amazing co-author and friend @mathiaseder.bsky.social summarized the highlights for you
The main story of my PhD deals with exactly that question, and is now published in Science! ✨
www.science.org/doi/10.1126/...
My amazing co-author and friend @mathiaseder.bsky.social summarized the highlights for you
Reposted by Acadia Kocher
Very proud of our paper on "scrambling-by-hopping" LADs, which was just published: www.nature.com/articles/s41.... Congrats to Lise Dauban and the rest of the team – this was a real tour-de-force!
September 2, 2025 at 5:26 PM
Very proud of our paper on "scrambling-by-hopping" LADs, which was just published: www.nature.com/articles/s41.... Congrats to Lise Dauban and the rest of the team – this was a real tour-de-force!
Reposted by Acadia Kocher
Interactions between the genome and the nuclear lamina are multivalent and cooperative
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Interactions between the genome and the nuclear lamina are multivalent and cooperative - Nature Structural & Molecular Biology
Using a transposon-based approach to create a set of large genomic rearrangements, Dauban et al. demonstrate that interactions of lamina-associated domains with the nuclear lamina involve multiple con...
www.nature.com
September 1, 2025 at 11:21 PM
Interactions between the genome and the nuclear lamina are multivalent and cooperative
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Acadia Kocher
My feather cell type paper is finally out! doi.org/10.1111/ede.... We’ve packed a ton of stuff into this paper but I’ll go through some highlights in this thread!
Genetic Characterization of the Cell Types in Developing Feathers, and the Evolution of Feather Complexity
We used single cell sequencing to investigate the cell types of developing chicken feathers. From these data, we are able to describe the transcriptional profile of feather cell types, look at their ....
doi.org
August 26, 2025 at 5:24 PM
My feather cell type paper is finally out! doi.org/10.1111/ede.... We’ve packed a ton of stuff into this paper but I’ll go through some highlights in this thread!
Reposted by Acadia Kocher
The Vlaming lab is expanding! If you are or know a good prospective PhD student, excited about studying transcription, please (suggest them to) apply here: www.uu.nl/en/organisat...
My biased opinion: exciting topic, super nice colleagues, and great research environment in a lovely city.
My biased opinion: exciting topic, super nice colleagues, and great research environment in a lovely city.
PhD position in Gene Regulation
Are you excited about studying the crucial process of transcription? Join our supportive, young and growing team!
www.uu.nl
August 15, 2025 at 10:22 AM
The Vlaming lab is expanding! If you are or know a good prospective PhD student, excited about studying transcription, please (suggest them to) apply here: www.uu.nl/en/organisat...
My biased opinion: exciting topic, super nice colleagues, and great research environment in a lovely city.
My biased opinion: exciting topic, super nice colleagues, and great research environment in a lovely city.
Reposted by Acadia Kocher
Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts
Enhancers are non-coding cis-regulatory elements that control the expression of distally located genes in a tissue- and time-specific manner. Recent studies indicate that enhancers can differ in their...
www.biorxiv.org
August 11, 2025 at 2:56 PM
Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Acadia Kocher
In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11
Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression
Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting o...
www.science.org
July 4, 2025 at 11:00 AM
In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11
Reposted by Acadia Kocher
Our review "Predicting gene expression from DNA sequence using deep learning models" is finally out! 🤗
Predicting gene expression from DNA sequence using deep learning models go.nature.com/3F8r0Li #Review by Lucía Barbadilla-Martínez, Noud Klaassen, Bas van Steensel & Jeroen de Ridder @nkinl.bsky.social @umcutrecht.bsky.social
Predicting gene expression from DNA sequence using deep learning models - Nature Reviews Genetics
Barbadilla-Martínez et al. review recent progress in deep-learning-based sequence-to-expression models, which predict gene expression levels solely from DNA sequence. These models are providing new in...
go.nature.com
May 14, 2025 at 3:43 PM
Our review "Predicting gene expression from DNA sequence using deep learning models" is finally out! 🤗
Reposted by Acadia Kocher
Predicting gene expression from DNA sequence using deep learning models go.nature.com/3F8r0Li #Review by Lucía Barbadilla-Martínez, Noud Klaassen, Bas van Steensel & Jeroen de Ridder @nkinl.bsky.social @umcutrecht.bsky.social
Predicting gene expression from DNA sequence using deep learning models - Nature Reviews Genetics
Barbadilla-Martínez et al. review recent progress in deep-learning-based sequence-to-expression models, which predict gene expression levels solely from DNA sequence. These models are providing new in...
go.nature.com
May 14, 2025 at 7:41 AM
Predicting gene expression from DNA sequence using deep learning models go.nature.com/3F8r0Li #Review by Lucía Barbadilla-Martínez, Noud Klaassen, Bas van Steensel & Jeroen de Ridder @nkinl.bsky.social @umcutrecht.bsky.social
Reposted by Acadia Kocher
There is still time to submit an abstract! The deadline is now extended to May 14.
Like regulatory genomics? Don’t miss this very fun meeting! May 7 is the deadline for early registration and abstract submission www.asbmb.org/meetings-eve...
Evolution and core processes in gene expression
June 26–29, 2025 | Kansas City, Mo.
www.asbmb.org
May 9, 2025 at 7:33 PM
There is still time to submit an abstract! The deadline is now extended to May 14.
Reposted by Acadia Kocher
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
March 26, 2025 at 5:11 PM
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
Reposted by Acadia Kocher
Happy to present the first preprint from my lab after relocating @CHOP_Research @ChildrensPhila Here we describe gene expression at the single cell level across major milestones of human and mouse development. preprint here: https://buff.ly/3PFWNoG
January 21, 2025 at 9:38 PM
Happy to present the first preprint from my lab after relocating @CHOP_Research @ChildrensPhila Here we describe gene expression at the single cell level across major milestones of human and mouse development. preprint here: https://buff.ly/3PFWNoG
Reposted by Acadia Kocher
Together with @smandrup.bsky.social and Minna Kaikkonen we are happy to announce the 3rd Edition of the EMBO Workshop on #Enhancers and #Enhanceropathies. This time we will meet during the beautiful Danish summer (June 16-21).
Book the dates and register soon!!!
meetings.embo.org/event/25-enh...
Book the dates and register soon!!!
meetings.embo.org/event/25-enh...
Enhancer Mechanics and Enhanceropathies
Join us for the highly anticipated third EMBO workshop on Enhancer Mechanics and Enhanceropathies! Building on the success of our previous meetings in Santander (2021) and Marseilles (2023), this eve…
meetings.embo.org
January 31, 2025 at 2:35 PM
Together with @smandrup.bsky.social and Minna Kaikkonen we are happy to announce the 3rd Edition of the EMBO Workshop on #Enhancers and #Enhanceropathies. This time we will meet during the beautiful Danish summer (June 16-21).
Book the dates and register soon!!!
meetings.embo.org/event/25-enh...
Book the dates and register soon!!!
meetings.embo.org/event/25-enh...
Reposted by Acadia Kocher
Out today in Cell: a comprehensive map of Human Accelerated Region gene targets in human and chimpanzee neural stem cells. Thread:
authors.elsevier.com/a/1kWzdL7PXu...
www.cell.com/cell/fulltex...
authors.elsevier.com/a/1kWzdL7PXu...
www.cell.com/cell/fulltex...
Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment
Human accelerated regions (HARs) have been implicated in human brain evolution with
limited understanding of the biological processes they alter. This study reports that
HARs influenced brain evolutio...
www.cell.com
January 30, 2025 at 5:55 PM
Out today in Cell: a comprehensive map of Human Accelerated Region gene targets in human and chimpanzee neural stem cells. Thread:
authors.elsevier.com/a/1kWzdL7PXu...
www.cell.com/cell/fulltex...
authors.elsevier.com/a/1kWzdL7PXu...
www.cell.com/cell/fulltex...
Reposted by Acadia Kocher
My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful.
It’s available on Amazon: tinyurl.com/mx2hewen
It’s available on Amazon: tinyurl.com/mx2hewen
January 17, 2025 at 2:30 PM
My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful.
It’s available on Amazon: tinyurl.com/mx2hewen
It’s available on Amazon: tinyurl.com/mx2hewen
Reposted by Acadia Kocher
Welcome to our lab! We are no longer active on Twitter/X. New results/preprints/papers will be posted here.
January 13, 2025 at 10:17 PM
Welcome to our lab! We are no longer active on Twitter/X. New results/preprints/papers will be posted here.
Reposted by Acadia Kocher
We want to make JASPAR (jaspar.elixir.no) even better for our users! Please share your experience and help us enhance the database by taking a quick survey: nettskjema.no/a/467842.
Your insights make a difference!
Your insights make a difference!
January 8, 2025 at 4:53 PM
We want to make JASPAR (jaspar.elixir.no) even better for our users! Please share your experience and help us enhance the database by taking a quick survey: nettskjema.no/a/467842.
Your insights make a difference!
Your insights make a difference!
Reposted by Acadia Kocher
Now available as preprint:
The ENCODE 4 expanded registry of regulatory elements
- 2.35M 🧍 human cCREs
- 927k 🐭 mouse cCREs
www.biorxiv.org/content/10.1...
Led by @moorejille.bsky.social, this preprint summarizes data and analyses generated by hundreds of contributors across ENCODE 4
The ENCODE 4 expanded registry of regulatory elements
- 2.35M 🧍 human cCREs
- 927k 🐭 mouse cCREs
www.biorxiv.org/content/10.1...
Led by @moorejille.bsky.social, this preprint summarizes data and analyses generated by hundreds of contributors across ENCODE 4
January 8, 2025 at 8:35 PM
Now available as preprint:
The ENCODE 4 expanded registry of regulatory elements
- 2.35M 🧍 human cCREs
- 927k 🐭 mouse cCREs
www.biorxiv.org/content/10.1...
Led by @moorejille.bsky.social, this preprint summarizes data and analyses generated by hundreds of contributors across ENCODE 4
The ENCODE 4 expanded registry of regulatory elements
- 2.35M 🧍 human cCREs
- 927k 🐭 mouse cCREs
www.biorxiv.org/content/10.1...
Led by @moorejille.bsky.social, this preprint summarizes data and analyses generated by hundreds of contributors across ENCODE 4
Reposted by Acadia Kocher
How to test the functional impact of non-coding variants in vivo? We developed a new method called dual-enSERT, which can quantitatively compare the effects of enhancer variants in live mouse embryos in under two weeks. www.nature.com/articles/s41... 1/n
January 6, 2025 at 2:55 PM
How to test the functional impact of non-coding variants in vivo? We developed a new method called dual-enSERT, which can quantitatively compare the effects of enhancer variants in live mouse embryos in under two weeks. www.nature.com/articles/s41... 1/n
Reposted by Acadia Kocher
40 years ago all of Genbank was published in print form by NAR. The same format today would require over 4 light seconds of shelf space. To a year of progress in 2025.
December 29, 2024 at 9:50 AM
40 years ago all of Genbank was published in print form by NAR. The same format today would require over 4 light seconds of shelf space. To a year of progress in 2025.
Reposted by Acadia Kocher
Please check out our new paper showing that the supposed looping factor ZNF143 has no role in chromatin looping: www.cell.com/molecular-ce...
And also check out the companion paper from @andersshansen.bsky.social: www.cell.com/molecular-ce...
And also check out the companion paper from @andersshansen.bsky.social: www.cell.com/molecular-ce...
ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF
ZNF143 has been implicated in gene activation and chromatin looping. Magnitov et al. show that ZNF143 has no general looping factor activity and explain why this function has been misattributed. Instead, ZNF143 regulates transcription of nuclear-encoded mitochondrial genes, ensuring energy homeostasis, proliferation, and differentiation potential of stem cells.
www.cell.com
December 20, 2024 at 4:22 PM
Please check out our new paper showing that the supposed looping factor ZNF143 has no role in chromatin looping: www.cell.com/molecular-ce...
And also check out the companion paper from @andersshansen.bsky.social: www.cell.com/molecular-ce...
And also check out the companion paper from @andersshansen.bsky.social: www.cell.com/molecular-ce...
Reposted by Acadia Kocher
How do 250k regulatory sequences coordinate 15k genes in mammalian development?
Just out: A genomic evidence board to decode the chaos by mapping enhancer-gene interactions across embryonic mouse tissues
New resource with Miao Yu, Ming Hu, Bing Ren, and more.
www.nature.com/articles/s41...
Just out: A genomic evidence board to decode the chaos by mapping enhancer-gene interactions across embryonic mouse tissues
New resource with Miao Yu, Ming Hu, Bing Ren, and more.
www.nature.com/articles/s41...
December 17, 2024 at 2:36 PM
How do 250k regulatory sequences coordinate 15k genes in mammalian development?
Just out: A genomic evidence board to decode the chaos by mapping enhancer-gene interactions across embryonic mouse tissues
New resource with Miao Yu, Ming Hu, Bing Ren, and more.
www.nature.com/articles/s41...
Just out: A genomic evidence board to decode the chaos by mapping enhancer-gene interactions across embryonic mouse tissues
New resource with Miao Yu, Ming Hu, Bing Ren, and more.
www.nature.com/articles/s41...