Elzo de Wit lab @ NKI
@dewitlab.bsky.social
📤 634
📥 252
📝 59
Computational & Genomics Lab studying 3D genome function and dynamics @ Netherlands Cancer Institute
pinned post!
(1/n) Excited to present the latest work from the de Wit lab, where we identify and characterise loop extrusion-mediated fountains in mammalian genomes using acute depletion of 3D genome regulators:
doi.org/10.1093/nar/...
. A Bluetorial🧵:
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Extrusion fountains are restricted by WAPL-dependent cohesin release and CTCF barriers
Abstract. Interphase chromosomes are mainly shaped by loop extrusion and compartmentalisation mechanisms. However, their temporal component and cause-effec
https://doi.org/10.1093/nar/gkaf549
4 months ago
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Elzo de Wit lab @ NKI
Rada-Iglesias Lab
3 days ago
We recently reported that promoter competition can contribute to the robust insulation of gene regulatory domains (
www.nature.com/articles/s41...
). We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇
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Elzo de Wit lab @ NKI
Max Delbrück Center
about 1 month ago
🚀 WE ARE HIRING 3️⃣ Independent Group Leaders for
#mdcBerlin's
new cutting-edge Bioengineering Cluster within our Biomedical Engineering Program. Lead cutting-edge research at the interface of biology, engineering, and medicine in Berlin. 👉 Apply now:
www.mdc-berlin.de/career/jobs/...
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Elzo de Wit lab @ NKI
Rob Klose
4 days ago
Awesome stuff James and team! Thanks for giving
@edimitrova.bsky.social
and I the opportunity to contribute.
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Exciting work from Hangpeng and James! Very nice explainer. Happy to have been able to contribute.
add a skeleton here at some point
4 days ago
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Elzo de Wit lab @ NKI
Wout Oosterheert
13 days ago
Are you excited to uncover the molecular mechanisms of actin filament assemblies that drive cell migration using cryo-EM? Only 1.5 week to apply for this exciting PhD position in my newly established lab at the Netherlands Cancer Institute in Amsterdam:
www.werkenbijavl.nl/vacatures/ph...
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PhD Student – Structural Biology of Actin Filament Assemblies | Werken bij AVL
https://www.werkenbijavl.nl/vacatures/phd-student-structural-biology-of-actin-filament-assemblies-to-understand-cell-migration/
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Elzo de Wit lab @ NKI
Maxim Greenberg
12 days ago
Spread the word! There is a professor position opening at our University
@upcite.bsky.social
. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!
add a skeleton here at some point
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Elzo de Wit lab @ NKI
Bruno Di Stefano
12 days ago
1/ Excited to share our new study with
@brumbaugh-lab.bsky.social
, out in
@natbiotech.nature.com
! P-bodies selectively sequester RNAs encoding cell fate regulators, often from the preceding developmental stage. Releasing these RNAs can drive changes in cell identity. 🧵
www.nature.com/articles/s41...
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Selective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature Biotechnology
Stem cell differentiation is controlled by manipulating RNA condensates.
https://www.nature.com/articles/s41587-025-02853-z
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Elzo de Wit lab @ NKI
Marieke Oudelaar
13 days ago
Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs:
www.embopress.org/doi/full/10....
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Elzo de Wit lab @ NKI
Anders Sejr Hansen
20 days ago
Our collab w. V Goel,
@nicholas-aboreden.bsky.social
, J Jusuf, G Blobel, L Mirny,
@irate-physicist.bsky.social
out in
@natsmb.nature.com
www.nature.com/articles/s41...
Was co-submitted with
@allanaschooley.bsky.social
@jobdekker.bsky.social
whose paper should also come out soon Brief thread 👇
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Elzo de Wit lab @ NKI
Rob Klose
23 days ago
Come join us in Geneva for everything epigenetics and gene regulation. It will be a great meeting! Please repost!
www.keystonesymposia.org/conferences/...
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Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities | Keystone Symposia
Join us at the Keystone Symposia on Epigenetics and Gene Regulation in Health and Disease: Linking Basic Mechanisms with Therapeutic Opportunities, March 2026, in Geneva, with field leaders!
https://www.keystonesymposia.org/conferences/conference-listing/meeting/C12026
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Elzo de Wit lab @ NKI
Rob Klose
23 days ago
We are recuiting two new Associate Professors here in Oxford Biochemistry. Come join us! Reach out to me if you have any questions. Please repost!
tinyurl.com/mr3m7bd3
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Elzo de Wit lab @ NKI
Ed Banigan
23 days ago
Excited to share our paper on dynamics of microcompartments during M-to-G1 is now published in
@natsmb.nature.com
www.nature.com/articles/s41...
Compared to biorxiv, published includes new analysis from James Jusuf and Viraat Goel (from
@andersshansen.bsky.social
lab) on transcriptional spiking
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The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project! If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
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Characterization of induced cohesin loop extrusion trajectories in living cells
Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...
https://rdcu.be/eLiT5
24 days ago
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Elzo de Wit lab @ NKI
Daniel Ibrahim
24 days ago
What is a promoter? And how does it work? We very happy to share our latest work trying to understand enhancer-promoter compatibility. I am very excited about the results of
@blanka-majchrzycka.bsky.social
, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
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Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
https://www.biorxiv.org/content/10.1101/2025.10.14.682013v1
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Elzo de Wit lab @ NKI
Stephan Gruber
25 days ago
And also the bacterial telomere protection paper by Maya, Nicolas, & Ania is out:
doi.org/10.1038/s443...
Great experience with
@reviewcommons.org
&
@embojournal.org
Feels just right to have the manuscript reviewed without having to target a specific journal from the start.
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Elzo de Wit lab @ NKI
Wout Oosterheert
28 days ago
Very excited that my final postdoctoral work is now online in Cell
@cellpress.bsky.social
.
www.sciencedirect.com/science/arti...
Using 16 (!) cryo-EM structures, we uncovered how the three proteins coronin, cofilin and AIP1 work together to rapidly disassemble actin filaments.
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Elzo de Wit lab @ NKI
Di Jiang
28 days ago
Last week
@science.org
mRNA initiation and termination are spatially coordinated | Science
www.science.org/doi/10.1126/...
from
@anafiszbein.bsky.social
@athmapai.bsky.social
et al.
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Elzo de Wit lab @ NKI
Daniel Durocher
29 days ago
9 days to go: * 2 x open positions! * Exceptional environment, competitive start-up package * University of Toronto appointments * Toronto has great (and peaceful) quality of life!
add a skeleton here at some point
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Elzo de Wit lab @ NKI
James Briscoe
about 1 month ago
The
@crick.ac.uk
is recruiting Early Career Group Leaders - Lab set-up, research costs, salaries for up to 5 researchers - Support for up to 12 years - Access to our core facilities - Competitive salary - Fantastic colleagues - All areas of biology Deadline 27 Nov
www.crick.ac.uk/careers-stud...
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Early career group leaders
We appoint researchers from across biology and biomedicine to set up their first groups at the Crick.
https://www.crick.ac.uk/careers-study/faculty/early-career-group-leaders
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Elzo de Wit lab @ NKI
Naomi Moris
about 1 month ago
The Crick is looking for new junior group leaders! Any postdocs or early career researchers wanting to be our colleagues should apply 👍
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Elzo de Wit lab @ NKI
Carl Zimmer
about 1 month ago
Today my
@nytimes.com
colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link:
nyti.ms/3IWXbiE
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https://nyti.ms/3IWXbiE
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Elzo de Wit lab @ NKI
Arnau Sebé-Pedrós
about 1 month ago
A thoughtful and beautifully written
@quantamagazine.bsky.social
article about genome regulatory innovation at the origin of animals. Featuring some of our work and highlighting key open questions. Thanks to
@philipcball.bsky.social
for this fantastic piece.
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Elzo de Wit lab @ NKI
Emilia Dimitrova
about 1 month ago
If you are a computational biologist interested in how chromatin states are established and maintained to regulate transcription, this is the dream job for you! This will be in close collaboration with the Klose lab in Oxford and we have a lot of cool projects you can get involved in. Apply!
add a skeleton here at some point
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Elzo de Wit lab @ NKI
Bart Deplancke
about 1 month ago
🧵1/ Excited to share our new paper introducing a new
#singlecell
assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗
www.nature.com/articles/s41...
Big congrats to the entire team @EPFL & @SIAT_China
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Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics
This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.
https://www.nature.com/articles/s41588-025-02343-7
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Elzo de Wit lab @ NKI
Tung Le
about 1 month ago
Independent research fellowships leading to tenured positions at the John Innes Centre. Repost = nice. Thank you very much!!!
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Elzo de Wit lab @ NKI
Edda Schulz
about 1 month ago
⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation. 👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial
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Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology
Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.
https://www.nature.com/articles/s41594-025-01686-3
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Elzo de Wit lab @ NKI
Benoit Bruneau
about 1 month ago
awesome new work by my
@gladstoneinst.bsky.social
and
@ucsanfrancisco.bsky.social
colleagues incl
@vram142.bsky.social
on how chromatin remodelers affect mesoscale chromatin organization
www.science.org/doi/10.1126/...
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ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes
Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...
https://www.science.org/doi/10.1126/science.adr0018
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Elzo de Wit lab @ NKI
Francesca Mattiroli
about 1 month ago
Join us at the Hubrecht Institute in Utrecht to start your research group! Fantastic scientific environment, strong support, and nice colleagues :) Apply and please share broadly in your network.
add a skeleton here at some point
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Elzo de Wit lab @ NKI
Seema Sheth
about 1 month ago
Tenure-track Assistant Professor position in Bioinformatics in the Department of Biology at the University of San Francisco
usfca.wd5.myworkdayjobs.com/en-US/USF_Fu...
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Assistant Professor, Tenure-Track, Department of Biology, University of San Francisco
Job Title: Assistant Professor, Tenure-Track, Department of Biology, University of San Francisco Job Summary: The Department of Biology at the University of San Francisco invites applications for a fu...
https://usfca.wd5.myworkdayjobs.com/en-US/USF_Full-Time_Faculty/job/USF-Hilltop-Campus/Assistant-Professor--Tenure-Track--Department-of-Biology--University-of-San-Francisco_R0011691
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Elzo de Wit lab @ NKI
Bas van Steensel lab (NKI)
about 2 months ago
Our reporter hopping scaled up to thousands of integrations in a single locus, to produce high-resolution functional maps, with plenty of interesting insights:
www.science.org/doi/10.1126/...
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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...
https://www.science.org/doi/10.1126/science.ads6552
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Elzo de Wit lab @ NKI
Luca Giorgetti lab @FMI
about 2 months ago
Really excited to share our latest work led by
@mattiaubertini.bsky.social
and
@nesslfy.bsky.social
: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
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Elzo de Wit lab @ NKI
Nature Methods
about 1 month ago
scEpi2-seq: a method for simultaneous single-cell profiling of DNA methylation and histone modifications.
@jervdberg.bsky.social
@hubrechtinstitute.bsky.social
www.nature.com/articles/s41...
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Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance - Nature Methods
This work presents scEpi2-seq, a method for simultaneous single-cell profiling of DNA methylation and histone modifications, enabling direct investigation of the interplay between these two epigenomic marks.
https://www.nature.com/articles/s41592-025-02847-4
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Elzo de Wit lab @ NKI
Tobias Raisch
about 2 months ago
We just published this paper of which I am immensely proud:
www.nature.com/articles/s41...
In the study, we uncover how the enzyme MPO disassembles
#nucleosomes
in a process called NETosis, a funky mechanism of
#neutrophils
to kill
#pathogens
that you might have never heard of. Let's dive in... 🧵
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Myeloperoxidase transforms chromatin into neutrophil extracellular traps - Nature
Myeloperoxidase, a highly expressed neutrophil protein, disassembles nucleosomes, facilitating neutrophil extracellular trap (NET) formation, and binds stably to NETs extracellularly.
https://www.nature.com/articles/s41586-025-09523-9
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Elzo de Wit lab @ NKI
Polly Fordyce
about 2 months ago
Please apply to our tenure-track faculty position at
@stanford-chemh.bsky.social
! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely!
chemh.stanford.edu/opportunitie...
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Faculty Recruitment
https://chemh.stanford.edu/opportunities/faculty-recruitment
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Elzo de Wit lab @ NKI
Di Jiang
about 2 months ago
@science.org
🧬🔬Functional maps of a
#genomic
locus reveal confinement of an enhancer by its target
#gene
| Science
www.science.org/doi/10.1126/...
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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...
https://www.science.org/doi/10.1126/science.ads6552
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reposted by
Elzo de Wit lab @ NKI
about 2 months ago
✨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/...
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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...
https://www.science.org/doi/10.1126/science.ads6552
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Elzo de Wit lab @ NKI
Vijay Ramani
about 2 months ago
Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt &
@palindromephd.bsky.social
, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)
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The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers
DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...
https://www.biorxiv.org/content/10.1101/2025.09.18.677126v1
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Elzo de Wit lab @ NKI
Michelle Percharde
about 2 months ago
Come be our head of bioinformatics at
@mrc-lms.bsky.social
! Our bioinformatics team are closely involved with lots of interesting science and we love working with them. Topics inc. development, cancer, metabolism, aging, TEs (my favourite of course 😜)
#TEsky
lms.mrc.ac.uk/work/vacanci...
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Head of Bioinformatics - MRC Laboratory of Medical Sciences
We are recruiting for a Head of Bioinformatics to lead our Bioinformatics facility
https://lms.mrc.ac.uk/work/vacancies/head-of-bioinformatics/
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Elzo de Wit lab @ NKI
Bas van Steensel lab (NKI)
2 months ago
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!
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Elzo de Wit lab @ NKI
Aurelie Hintermann
about 2 months ago
Are digits modified fins, or evolutionary innovations? Read how we tackled this old question from a new angle🧪 A story with
@chasebolt.bsky.social
,
@homeobox.bsky.social
and myself, coordinated by
@denisduboule.bsky.social
from
@college-de-france.fr
and published in
@nature.com
today!
#InHoxWeTrust
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Elzo de Wit lab @ NKI
Jop Kind
about 2 months ago
1/ 🧵 I am excited to share a new preprint from our group: Single-cell Dam&T-seq during mouse corticogenesis reveals how genome–lamina interactions regulate long neuronal genes.
doi.org/10.1101/2025...
#Neurodevelopment
#Epigenetics
@hubrechtinstitute.bsky.social
@oncodeinstitute.bsky.social
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MeCP2 binding and genome–lamina reorganization precede long gene activation during mouse corticogenesis
During corticogenesis, neural gene expression is tightly coordinated by chromatin and epigenetic changes, whose misregulation can lead to neurodevelopmental disorders[1][1]–[4][2]. The role of spatial...
https://doi.org/10.1101/2025.09.01.673434
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reposted by
Elzo de Wit lab @ NKI
Sara Wickstrom
about 2 months ago
My lab
@mpi-muenster.bsky.social
is looking for a computational biologist with a passion for imaging and spatial biology. A staff scientist position with long-term perspective! Apply and spread the word 🙏
jobs.mpi-muenster.mpg.de/jobposting/0...
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Computational image analyst (m/f/d)
The Max Planck Institute for Molecular Biomedicine in Münster, Germany, has an opening for a
https://jobs.mpi-muenster.mpg.de/jobposting/0b62e338d834d8397afd8d521e2c7996841d1f680
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Elzo de Wit lab @ NKI
Oxford Biology
about 2 months ago
Oxford Biology is growing 📢 We’re appointing 3 Associate Professors in: 🌱 Plant Sciences 🦉 Animal Behaviour 🔬 Molecular Cell Biology 3 fields. 3 opportunities. One new home for Oxford Biology. Learn more 👉
bit.ly/41S2Tc7
Apply now 👉
bit.ly/488CNW3
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Elzo de Wit lab @ NKI
Pelechano lab
about 2 months ago
We are looking for new SciLifeLab Fellows (group leaders) to join SciLifeLab and Karolinska Institutet
@ki.se
.
@scilifelab.se
is a great place to start your lab with generous funding. Deadline: 15th November. Apply and join us in beautiful
#Stockholm
#JuniorPI
ki.varbi.com/en/what:job/...
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Assistant Professor in Molecular Life Science (SciLifeLab Fellow)
Do you want to contribute to top quality medical research? Karolinska Institutet (KI) is recruiting researchers as part of the SciLifeLab Fellows program. The successful candidates will join KI and co
https://ki.varbi.com/en/what:job/jobID:844336/
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reposted by
Elzo de Wit lab @ NKI
Mark Peifer (He, him)
about 2 months ago
Thanks to journalist
@felixschmidtner.bsky.social
for bringing the plight of the key scientific database
@flybase.bsky.social
to a German/European audience
www.faz.net/aktuell/wiss...
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Die wichtigste Datenbank über die Fruchtfliege steht vor dem Aus.
Forscher weltweit sind auf eine zentrale Datenbank mit Erkenntnissen zu Drosophila angewiesen. Deren Finanzierung steht vor dem Aus. Wegen Donald Trump. Warum uns das nicht gleichgültig sein sollte.
https://www.faz.net/aktuell/wissen/die-wichtigste-datenbank-ueber-die-fruchtfliege-steht-vor-dem-aus-110676806.html
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reposted by
Elzo de Wit lab @ NKI
Jesse Veenvliet
about 2 months ago
W/ critical contributions from
@mtrani.bsky.social
, Alba Villaronga Luque,
@yonitmms.bsky.social
, Allyson Ryan, & in collab w/
@carldmodes.bsky.social
@csbdresden.bsky.social
&
@campaslab.bsky.social
@poldresden.bsky.social
. Funded by
#EICPathfinder
@ec.europa.eu
. Background thread coming soon!
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Elzo de Wit lab @ NKI
Alex Stark
about 2 months ago
Join this year's CSH Asia Systems Biology of Gene Regulation & Genome Editing meeting in beautiful Suzhou, China, Oct 20-24. Let's bring the international communities together! Abstract deadline Sept 19! Infos and registration at
csh-asia.org?content/2767
. Please repost!
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Elzo de Wit lab @ NKI
Constantin Pape
3 months ago
Join us as a colleague in Göttingen!
add a skeleton here at some point
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Elzo de Wit lab @ NKI
Wolfgang Huber
2 months ago
Join EMBL as a research group leader in AI in biology. EMBL AI is our new initiative aiming to exploit the full potential of ML/AI-based approaches to advance our understanding of the most complex system in the known universe - life on Earth.
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
(1/3)
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Elzo de Wit lab @ NKI
Carmelo Ferrai
2 months ago
6th Annual Meeting on Advances in Nuclear Topology & 3D Chromatin Architecture in Cancer. Don’t miss insights from leading experts in the field. Join us online on Nov 25, 2025—register for free:
bit.ly/chromatin-2025
#chromatin2025
bsky.app/profile/jane...
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