Elzo de Wit lab @ NKI
@dewitlab.bsky.social
Computational & Genomics Lab studying 3D genome function and dynamics @ Netherlands Cancer Institute
Pinned
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
doi.org
(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🧵:
Reposted by Elzo de Wit lab @ NKI
Apply for the Ascona workshop "Statistical and AI methods for multi-modal multi-scale modeling of biological systems", 28 Jun-3 Jul 2026 on Monte Verità, Lago Maggiore at the foot of the Swiss Alps.
ascona2026.sciencesconf.org
ascona2026.sciencesconf.org
January 15, 2026 at 4:16 PM
Apply for the Ascona workshop "Statistical and AI methods for multi-modal multi-scale modeling of biological systems", 28 Jun-3 Jul 2026 on Monte Verità, Lago Maggiore at the foot of the Swiss Alps.
ascona2026.sciencesconf.org
ascona2026.sciencesconf.org
Reposted by Elzo de Wit lab @ NKI
Start your independent as an ELISIR fellow right after your PhD, in one of the most terrific places in Europe !
January 14, 2026 at 1:13 PM
Start your independent as an ELISIR fellow right after your PhD, in one of the most terrific places in Europe !
Reposted by Elzo de Wit lab @ NKI
🧬 We’re #Hiring a #Bioinformatician/ Computational Biologist!
#Single-cell genomics, #Epigenomics & #3Dgenome biology in #Zebrafish #DevBio 🐟
📍 @cabd-upo-csic.bsky.social, CABD, Seville (Spain)
🕒 Full-time, 3-year position (start March 2026)
📅 Apply by Feb 15, 2026
👉 drive.google.com/file/d/1M8rp...
#Single-cell genomics, #Epigenomics & #3Dgenome biology in #Zebrafish #DevBio 🐟
📍 @cabd-upo-csic.bsky.social, CABD, Seville (Spain)
🕒 Full-time, 3-year position (start March 2026)
📅 Apply by Feb 15, 2026
👉 drive.google.com/file/d/1M8rp...
Job offer 2026.pdf
drive.google.com
January 12, 2026 at 3:57 PM
🧬 We’re #Hiring a #Bioinformatician/ Computational Biologist!
#Single-cell genomics, #Epigenomics & #3Dgenome biology in #Zebrafish #DevBio 🐟
📍 @cabd-upo-csic.bsky.social, CABD, Seville (Spain)
🕒 Full-time, 3-year position (start March 2026)
📅 Apply by Feb 15, 2026
👉 drive.google.com/file/d/1M8rp...
#Single-cell genomics, #Epigenomics & #3Dgenome biology in #Zebrafish #DevBio 🐟
📍 @cabd-upo-csic.bsky.social, CABD, Seville (Spain)
🕒 Full-time, 3-year position (start March 2026)
📅 Apply by Feb 15, 2026
👉 drive.google.com/file/d/1M8rp...
Reposted by Elzo de Wit lab @ NKI
We’re hiring!
@jcellsci.bsky.social is looking for a Reviews Editor to join the team. This is a fantastic opportunity for someone who loves #cellbiology and wants to stay connected with the field. A great chance to work for an organisation that believes in helping the community!
Details below👇
@jcellsci.bsky.social is looking for a Reviews Editor to join the team. This is a fantastic opportunity for someone who loves #cellbiology and wants to stay connected with the field. A great chance to work for an organisation that believes in helping the community!
Details below👇
Journal of Cell Science @jcellsci.bsky.social is recruiting an enthusiastic and motivated Reviews Editor. An exciting opportunity for a talented scientific editor to make a contribution to an important journal in the field of #cellbiology. Deadline 2 Feb.
More at: www.biologists.com/about-us/wor...
More at: www.biologists.com/about-us/wor...
Work for us
Working for us We’re always looking for talented and motivated people to work as part of our close-knit team. Roles range from editorial to production, marketing to event co-ordination, HR to accounts...
www.biologists.com
January 9, 2026 at 10:13 AM
We’re hiring!
@jcellsci.bsky.social is looking for a Reviews Editor to join the team. This is a fantastic opportunity for someone who loves #cellbiology and wants to stay connected with the field. A great chance to work for an organisation that believes in helping the community!
Details below👇
@jcellsci.bsky.social is looking for a Reviews Editor to join the team. This is a fantastic opportunity for someone who loves #cellbiology and wants to stay connected with the field. A great chance to work for an organisation that believes in helping the community!
Details below👇
Reposted by Elzo de Wit lab @ NKI
International Genome Dynamics course in Institut Curie-Paris (April 8-15), experimental and computational methods in multiomics,with a #TE centered session.
Free registration, until Jan 15th
Don’t miss it!
👉https://training.institut-curie.org/courses/Genome-Dynamics-2026
@institutcurie.bsky.social
Free registration, until Jan 15th
Don’t miss it!
👉https://training.institut-curie.org/courses/Genome-Dynamics-2026
@institutcurie.bsky.social
January 9, 2026 at 10:54 AM
International Genome Dynamics course in Institut Curie-Paris (April 8-15), experimental and computational methods in multiomics,with a #TE centered session.
Free registration, until Jan 15th
Don’t miss it!
👉https://training.institut-curie.org/courses/Genome-Dynamics-2026
@institutcurie.bsky.social
Free registration, until Jan 15th
Don’t miss it!
👉https://training.institut-curie.org/courses/Genome-Dynamics-2026
@institutcurie.bsky.social
Reposted by Elzo de Wit lab @ NKI
Planning to apply to the @scilifelab.se DDLS Research School Postdoc Call 2026?
Our lab will be happy to host prospective computational postdocs at @ki.se Karolinska Institutet / @scilifelab.se .
#Postdoc #ComputationalBiology #RNA #InfectionBiology #AntimicrobialResistance #Bioinformatics
Our lab will be happy to host prospective computational postdocs at @ki.se Karolinska Institutet / @scilifelab.se .
#Postdoc #ComputationalBiology #RNA #InfectionBiology #AntimicrobialResistance #Bioinformatics
DDLS Research School Postdoc call 2026
Call for Academic and Industrial Postdoctoral Fellowships in Data-Driven Life Science 2026 Generic Description of the DDLS Postdoc Program The SciLifeLab and Wallenberg National Program for Data-Drive...
www.scilifelab.se
January 8, 2026 at 3:39 PM
Planning to apply to the @scilifelab.se DDLS Research School Postdoc Call 2026?
Our lab will be happy to host prospective computational postdocs at @ki.se Karolinska Institutet / @scilifelab.se .
#Postdoc #ComputationalBiology #RNA #InfectionBiology #AntimicrobialResistance #Bioinformatics
Our lab will be happy to host prospective computational postdocs at @ki.se Karolinska Institutet / @scilifelab.se .
#Postdoc #ComputationalBiology #RNA #InfectionBiology #AntimicrobialResistance #Bioinformatics
Reposted by Elzo de Wit lab @ NKI
Reading “The 5 stages of the ‘enshittification’ of academic publishing”
theconversation.com/the-5-stages...
theconversation.com/the-5-stages...
The 5 stages of the ‘enshittification’ of academic publishing
Academic publishing now shows the same decline that has hit social media and online marketplaces.
theconversation.com
January 7, 2026 at 9:32 AM
Reading “The 5 stages of the ‘enshittification’ of academic publishing”
theconversation.com/the-5-stages...
theconversation.com/the-5-stages...
Reposted by Elzo de Wit lab @ NKI
DNA sequence quantitatively encodes CTCF-binding affinity at genome scale https://www.biorxiv.org/content/10.64898/2026.01.05.696797v1
January 6, 2026 at 7:31 AM
DNA sequence quantitatively encodes CTCF-binding affinity at genome scale https://www.biorxiv.org/content/10.64898/2026.01.05.696797v1
Reposted by Elzo de Wit lab @ NKI
🌱 As of Jan 1, I started as Assistant Professor at UMC Utrecht – Center for Molecular Medicine.
Very grateful to @dewitlab.bsky.social and @jopkind.bsky.social and to the many other people who supported me along the way.
I’ll be launching the lab soon, focusing on Chromatin Systems Biology.
Very grateful to @dewitlab.bsky.social and @jopkind.bsky.social and to the many other people who supported me along the way.
I’ll be launching the lab soon, focusing on Chromatin Systems Biology.
January 2, 2026 at 1:56 PM
🌱 As of Jan 1, I started as Assistant Professor at UMC Utrecht – Center for Molecular Medicine.
Very grateful to @dewitlab.bsky.social and @jopkind.bsky.social and to the many other people who supported me along the way.
I’ll be launching the lab soon, focusing on Chromatin Systems Biology.
Very grateful to @dewitlab.bsky.social and @jopkind.bsky.social and to the many other people who supported me along the way.
I’ll be launching the lab soon, focusing on Chromatin Systems Biology.
Reposted by Elzo de Wit lab @ NKI
December 23, 2025 at 9:34 AM
Reposted by Elzo de Wit lab @ NKI
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology
Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.
www.nature.com
December 22, 2025 at 11:45 AM
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Elzo de Wit lab @ NKI
@science.org Chromatin buffers torsional stress during transcription | Science www.science.org/doi/10.1126/...
Chromatin buffers torsional stress during transcription
During eukaryotic transcription, Pol II must overcome nucleosome obstacles and, because of DNA’s helical structure, must also rotate relative to DNA, generating torsional stress. However, there is lim...
www.science.org
December 19, 2025 at 10:31 PM
@science.org Chromatin buffers torsional stress during transcription | Science www.science.org/doi/10.1126/...
Reposted by Elzo de Wit lab @ NKI
As 2025 comes to a close, my university (Dalhousie U in Halifax, Canada) is recruiting faculty, including outstanding early career researchers, and Canada Research Chairs. Applications are due January 19 2026 (was just notified today!). Please repost.
Dalhousie University is recruiting up to 30 tenure and tenure-track faculty positions
Backed by the Government of Canada’s $1.7 billion Global Impact+ Research Talent Initiative, Dalhousie University is undertaking one of the most ambitious research-leader recruitment efforts in its hi...
www.dal.ca
December 19, 2025 at 8:17 PM
As 2025 comes to a close, my university (Dalhousie U in Halifax, Canada) is recruiting faculty, including outstanding early career researchers, and Canada Research Chairs. Applications are due January 19 2026 (was just notified today!). Please repost.
Reposted by Elzo de Wit lab @ NKI
My lab is hiring a postdoc (ERC funded)! If you're interested, get in touch!
December 18, 2025 at 8:36 AM
My lab is hiring a postdoc (ERC funded)! If you're interested, get in touch!
It was a pleasure to write this News & Views article for the 4D Nucleome flagship article: www.nature.com/articles/d41...
With great editorial support from @hollyasmith.bsky.social!
Read the 4D Nucleome paper here: www.nature.com/articles/s41...
With great editorial support from @hollyasmith.bsky.social!
Read the 4D Nucleome paper here: www.nature.com/articles/s41...
Systematic maps reveal how human chromosomes are organized
Our genomes are highly structured, which facilitates gene regulation. An ambitious project has catalogued the organization of DNA in the nuclei of human cells.
www.nature.com
December 17, 2025 at 10:16 PM
It was a pleasure to write this News & Views article for the 4D Nucleome flagship article: www.nature.com/articles/d41...
With great editorial support from @hollyasmith.bsky.social!
Read the 4D Nucleome paper here: www.nature.com/articles/s41...
With great editorial support from @hollyasmith.bsky.social!
Read the 4D Nucleome paper here: www.nature.com/articles/s41...
Reposted by Elzo de Wit lab @ NKI
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
An integrated view of the structure and function of the human 4D nucleome - Nature
The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...
www.nature.com
December 17, 2025 at 8:59 PM
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Elzo de Wit lab @ NKI
Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample?
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
December 13, 2025 at 7:00 AM
Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample?
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
Yes, one can. with CUT&ID ✂️🪪
Spearheaded — singlehandedly — by @annanordin.bsky.social
No need of transgenesis, cloning and overexpression.
Check it out, it's fast and its works.
Reposted by Elzo de Wit lab @ NKI
An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
SET1/MLL complexes control transcription independently of H3K4me3
Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein comp...
www.biorxiv.org
December 11, 2025 at 6:09 AM
An early Christmas present for those interested in chromatin and transcription! Fantastic work from @au-ho-yu.bsky.social and @aleksszczurek.bsky.social . Thanks to Inge and Michiel for their help. Please repost!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Elzo de Wit lab @ NKI
Reminder: Tomorrow is VGZT day! 🚀
Don’t miss great talks from
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
Don’t miss great talks from
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
Join us next week for another round of inspiring VGZT talks! 🤩
🗓️ Thursday, December 4th
⏰ 9:30 PST / 12:30 EST / 17:30 UTC / 17:30 GMT / 18:30 CET
Our speakers are
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
See you next week 👋
🗓️ Thursday, December 4th
⏰ 9:30 PST / 12:30 EST / 17:30 UTC / 17:30 GMT / 18:30 CET
Our speakers are
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
See you next week 👋
December 3, 2025 at 7:48 AM
Reminder: Tomorrow is VGZT day! 🚀
Don’t miss great talks from
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
Don’t miss great talks from
👉 Luca Braccioli (@bracciolilab.bsky.social)
👉 Komal Makwana (on X: @Komal_Makwana4)
Reposted by Elzo de Wit lab @ NKI
Apply for our Pathway to Independence (PI) programme, supporting postdocs in #devbio and #stemcell research during the transition to their first group leader position: www.biologists.com/grants/devel...
Application deadline: 2 February 2026.
Application deadline: 2 February 2026.
December 2, 2025 at 2:53 PM
Apply for our Pathway to Independence (PI) programme, supporting postdocs in #devbio and #stemcell research during the transition to their first group leader position: www.biologists.com/grants/devel...
Application deadline: 2 February 2026.
Application deadline: 2 February 2026.
Reposted by Elzo de Wit lab @ NKI
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
Reposted by Elzo de Wit lab @ NKI
We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth.
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
December 2, 2025 at 2:18 PM
We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth.
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Reposted by Elzo de Wit lab @ NKI
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
November 27, 2025 at 9:59 PM
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function
now revised and journal accepted at www.science.org/doi/10.1126/...
🧵👇
Reposted by Elzo de Wit lab @ NKI
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 Elzo de Wit lab @ NKI
Very pleased to share our latest paper published in Cell:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants
BRAIN-MAGNET, a convolutional neural network trained on 148,198 functionally tested
non-coding regulatory elements, predicts enhancer activity directly from DNA sequence
and identifies nucleotides ess...
www.cell.com
November 20, 2025 at 9:38 AM
Very pleased to share our latest paper published in Cell:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings:
BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants: Cell www.cell.com/cell/fulltex...
@cellpress.bsky.social, @cp-cell.bsky.social, @ruizhideng.bsky.social #enhancer
here is a thread about our findings: