Carl de Boer
@carldeboer.bsky.social
Assistant Professor, UBC school of Biomedical Engineering. Trying to enable personalized medicine by solving gene regulatory code.
Reposted by Carl de Boer
I'm guest-editing a collection on "Enhancer-promoter interactions" at Genome Biology. Please send us your exciting stories!
link.springer.com/collections/...
link.springer.com/collections/...
Enhancer-promoter interactions
Genome Biology is calling for submissions to our Collection on enhancer-promoter interactions.
Enhancer–promoter interactions are central to the regulation ...
link.springer.com
November 25, 2025 at 10:55 AM
I'm guest-editing a collection on "Enhancer-promoter interactions" at Genome Biology. Please send us your exciting stories!
link.springer.com/collections/...
link.springer.com/collections/...
Reposted by Carl de Boer
We are looking for a postdoctoral fellow to work on induced proximity 🤜🤛 and functional genomics! Join our team in Toronto 🇨🇦 to tackle major challenges in oncology and neurodegeneration. www.nature.com/naturecareer...
POSTDOCTORAL FELLOW - Toronto (City), Ontario (CA) job with Taipale Lab, Donnelly Centre, University of Toronto | 12849004
The Taipale lab in the Donnelly CCBR and University of Toronto is looking for a highly motivated Postdoctoral Fellow
www.nature.com
November 19, 2025 at 5:51 PM
We are looking for a postdoctoral fellow to work on induced proximity 🤜🤛 and functional genomics! Join our team in Toronto 🇨🇦 to tackle major challenges in oncology and neurodegeneration. www.nature.com/naturecareer...
Reposted by Carl de Boer
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 Carl de Boer
Our new preprint is online! Viruses, bacteria and parasites use effector proteins to evade immunity and rewire host cell pathways. Together with @AlexanderStark8, we wondered if we could systematically map what these effectors, regardless of their origin, do in human cells. 1/8
www.biorxiv.org
November 18, 2025 at 3:57 PM
Our new preprint is online! Viruses, bacteria and parasites use effector proteins to evade immunity and rewire host cell pathways. Together with @AlexanderStark8, we wondered if we could systematically map what these effectors, regardless of their origin, do in human cells. 1/8
Reposted by Carl de Boer
(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.
srsr(at)parl.gc.ca if you want to let the committee know your thoughts... Picard could have written the email I sent to them last weekend.
November 4, 2025 at 2:19 PM
srsr(at)parl.gc.ca if you want to let the committee know your thoughts... Picard could have written the email I sent to them last weekend.
Reposted by Carl de Boer
Please 🔁! #MASSIV will be held in Vancouver from January 19-22, 2026. 4-day meeting on #synbio x #tissueengineering.
Some trainee-focused events. >50 talks (10 from abstracts), posters, panel & publishing insights sessions.
www.massivconference.com
Abstract deadline: Nov 14
Some trainee-focused events. >50 talks (10 from abstracts), posters, panel & publishing insights sessions.
www.massivconference.com
Abstract deadline: Nov 14
October 25, 2025 at 4:21 PM
Please 🔁! #MASSIV will be held in Vancouver from January 19-22, 2026. 4-day meeting on #synbio x #tissueengineering.
Some trainee-focused events. >50 talks (10 from abstracts), posters, panel & publishing insights sessions.
www.massivconference.com
Abstract deadline: Nov 14
Some trainee-focused events. >50 talks (10 from abstracts), posters, panel & publishing insights sessions.
www.massivconference.com
Abstract deadline: Nov 14
Reposted by Carl de Boer
Please RP! A 4-day synbio and tissue engineering conference #MASSIV to transform biology and medicine together.
Couldn't list all amazing speakers, so please check out this 👉https://www.massivconference.com/
Poster due is Nov 7, but will be extended.
With @stemcellnetwork.ca and JST.
Couldn't list all amazing speakers, so please check out this 👉https://www.massivconference.com/
Poster due is Nov 7, but will be extended.
With @stemcellnetwork.ca and JST.
October 18, 2025 at 5:50 PM
Please RP! A 4-day synbio and tissue engineering conference #MASSIV to transform biology and medicine together.
Couldn't list all amazing speakers, so please check out this 👉https://www.massivconference.com/
Poster due is Nov 7, but will be extended.
With @stemcellnetwork.ca and JST.
Couldn't list all amazing speakers, so please check out this 👉https://www.massivconference.com/
Poster due is Nov 7, but will be extended.
With @stemcellnetwork.ca and JST.
Reposted by Carl de Boer
How much hands-on lab expertise gets lost? We developed a multimodal AI agent that turns videos into protocols and detects procedural errors. Making science accessible. Great collaboration with #Google.
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
In labs, hands-on expertise is often lost because it's not written down. We leverage multimodal AI agents to capture & share expertise by analyzing video and speech to generate protocols, detect errors, and guide researchers. #AI #TeamMassSpec
📄 Preprint: doi.org/10.1101/2025... 1/🧵
📄 Preprint: doi.org/10.1101/2025... 1/🧵
Multimodal AI agents for capturing and sharing laboratory practice
We present a multimodal AI laboratory agent that captures and shares tacit experimental practice by linking written instructions with hands-on laboratory work through the analysis of video, speech, an...
doi.org
October 9, 2025 at 10:54 AM
How much hands-on lab expertise gets lost? We developed a multimodal AI agent that turns videos into protocols and detects procedural errors. Making science accessible. Great collaboration with #Google.
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
Reposted by Carl de Boer
Which mutations rewire function of regulatory DNA?
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
October 9, 2025 at 12:03 PM
Which mutations rewire function of regulatory DNA?
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.
Led by @EESetiz
1/N 🧵👇
Reposted by Carl de Boer
Open rank tenure-track position in comp bio at the University of Montreal. Great environment, great position. @futurepislack.bsky.social
medecine.umontreal.ca/wp-content/u...
medecine.umontreal.ca/wp-content/u...
medecine.umontreal.ca
October 3, 2025 at 9:24 PM
Open rank tenure-track position in comp bio at the University of Montreal. Great environment, great position. @futurepislack.bsky.social
medecine.umontreal.ca/wp-content/u...
medecine.umontreal.ca/wp-content/u...
Reposted by Carl de Boer
We have space for two postdoctoral fellows in the Taipale Lab at the @sangerinstitute.bsky.social. This is a core-funded open position! Come with your ideas and interests and we can develop a project together.
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
Postdoctoral Fellow - Gene Regulation and Functional Genomics
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
sanger.wd103.myworkdayjobs.com
September 25, 2025 at 10:58 AM
We have space for two postdoctoral fellows in the Taipale Lab at the @sangerinstitute.bsky.social. This is a core-funded open position! Come with your ideas and interests and we can develop a project together.
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
sanger.wd103.myworkdayjobs.com/en-US/Wellco...
Reposted by Carl de Boer
Excited to finally present the lab's latest work in defining candidate causal genetic variants that drive autoimmune diseases and their effects on primary human T cell expression and function! www.nature.com/articles/s41...
Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks - Nature Genetics
Massively parallel reporter assay in primary human CD4+ T cells and bulk and single-cell CRISPR-interference screens identify candidate causal variants linked to autoimmune disease risk that modulate ...
www.nature.com
September 18, 2025 at 8:50 PM
Excited to finally present the lab's latest work in defining candidate causal genetic variants that drive autoimmune diseases and their effects on primary human T cell expression and function! www.nature.com/articles/s41...
Reposted by Carl de Boer
"We propose a model in which TF binding is not determined by individual binding sites, but rather by the sum of multiple, overlapping binding sites."
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
September 3, 2025 at 8:57 PM
"We propose a model in which TF binding is not determined by individual binding sites, but rather by the sum of multiple, overlapping binding sites."
www.nature.com/articles/s41...
www.nature.com/articles/s41...
New preprint from the lab 🎉 on the evolution of gene regulatory network complexity, where we tested whether sexual recombination promotes more complex GRNs using biochemically-inspired evolutionary simulations 🧐. Bluetorial from 1st author @chapelmadison.bsky.social 👇
1/ Why are eukaryotic gene regulatory networks (GRNs) so much more complex than prokaryotic ones?
In our new preprint, we investigated the role that recombination – a key step in eukaryotic reproductive strategies – plays in this problem! www.biorxiv.org/content/10.1...
In our new preprint, we investigated the role that recombination – a key step in eukaryotic reproductive strategies – plays in this problem! www.biorxiv.org/content/10.1...
Evolutionary simulations reveal role for genomic recombination in the evolution of gene regulatory network complexity and robustness
The gene regulatory networks (GRNs) of eukaryotes are dramatically more complex than the GRNs of prokaryotes, but we lack a complete picture of the selective pressures that have shaped this difference...
www.biorxiv.org
September 4, 2025 at 12:37 AM
New preprint from the lab 🎉 on the evolution of gene regulatory network complexity, where we tested whether sexual recombination promotes more complex GRNs using biochemically-inspired evolutionary simulations 🧐. Bluetorial from 1st author @chapelmadison.bsky.social 👇
Reposted by Carl de Boer
Defence spending must include health spending too www.theglobeandmail.com/gift/2109fef...
Defence spending must include health spending too
Biotech investment can deliver on Canada’s NATO commitments, protect citizens and drive economic growth
www.theglobeandmail.com
September 2, 2025 at 1:24 PM
Defence spending must include health spending too www.theglobeandmail.com/gift/2109fef...
Reposted by Carl de Boer
Excited to share our new review on AI-driven protein design - from its origins to today’s breakthroughs, methods, potential, and challenges ahead !
www.cell.com/structure/fu...
www.cell.com/structure/fu...
Code to complex: AI-driven de novo binder design
In this review, Fox et al. discuss how artificial intelligence has transformed our
ability to design new-to-nature proteins that bind target proteins with high affinity
and specificity. The authors de...
www.cell.com
September 2, 2025 at 10:51 AM
Excited to share our new review on AI-driven protein design - from its origins to today’s breakthroughs, methods, potential, and challenges ahead !
www.cell.com/structure/fu...
www.cell.com/structure/fu...
Reposted by Carl de Boer
New preprint from the lab: Dr. Daniela James led an effort to improve the ChIP-exo protocol for high-res protein-DNA interactions. Particularly focused on optimizing for use in mammalian cells and making the protocol compatible with newer Illumina sequencers.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells
By combining chromatin immunoprecipitation (ChIP) with an exonuclease digestion of protein-bound DNA fragments, ChIP-exo characterizes genome-wide protein-DNA interactions at near base-pair resolution...
www.biorxiv.org
August 23, 2025 at 7:16 PM
New preprint from the lab: Dr. Daniela James led an effort to improve the ChIP-exo protocol for high-res protein-DNA interactions. Particularly focused on optimizing for use in mammalian cells and making the protocol compatible with newer Illumina sequencers.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Carl de Boer
Thrilled to share the second half of my PhD work here!
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
August 22, 2025 at 7:50 PM
Thrilled to share the second half of my PhD work here!
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
Reposted by Carl de Boer
This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇
August 18, 2025 at 1:00 PM
This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇
Reposted by Carl de Boer
New paper from our lab on synthetic genome work in yeast is out - Iterative SCRaMbLE for Engineering Synthetic Genome Modules and Chromosomes. Exciting project led by Jane (Xinyu) Lu in our group, now online. t.co/0LuGwgAWlA
https://www.nature.com/articles/s41467-025-62356-y
t.co
August 11, 2025 at 12:36 PM
New paper from our lab on synthetic genome work in yeast is out - Iterative SCRaMbLE for Engineering Synthetic Genome Modules and Chromosomes. Exciting project led by Jane (Xinyu) Lu in our group, now online. t.co/0LuGwgAWlA
Reposted by Carl de Boer
To all post-docs: The Genome Biology dept @embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Group Leader - Genome Biology Unit
Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...
embl.wd103.myworkdayjobs.com
July 30, 2025 at 1:41 PM
To all post-docs: The Genome Biology dept @embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
SOOOO MANY GENOMICS MODELSSSS! 😱 Often unclear which is best since they benchmark differently! In this preprint, we introduce GAME, a new framework that utilizes APIs to enable sustainable, uniform model evaluation so we can see which is actually best for each task. doi.org/10.1101/2025...
July 11, 2025 at 7:34 AM
SOOOO MANY GENOMICS MODELSSSS! 😱 Often unclear which is best since they benchmark differently! In this preprint, we introduce GAME, a new framework that utilizes APIs to enable sustainable, uniform model evaluation so we can see which is actually best for each task. doi.org/10.1101/2025...
Reposted by Carl de Boer
CloneSelect published in Nature Biotechnology
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
A multi-kingdom genetic barcoding system for precise clone isolation - Nature Biotechnology
A barcoded CRISPR base editing system isolates target clones from complex mammalian, yeast and bacterial populations.
www.nature.com
May 21, 2025 at 1:56 PM
CloneSelect published in Nature Biotechnology
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
Reposted by Carl de Boer
🎉 This paper has been a long time and a labour of love (and hardship) for multiple group members, but, finally: we MPRA'ed 25k introgressed variants (Denisovan and Neanderthal) segregating at allele frequencies > 0.15 in humans today to evaluate their potential to regulate gene expression.
Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans https://www.biorxiv.org/content/10.1101/2025.05.04.652069v1
May 5, 2025 at 2:43 AM
🎉 This paper has been a long time and a labour of love (and hardship) for multiple group members, but, finally: we MPRA'ed 25k introgressed variants (Denisovan and Neanderthal) segregating at allele frequencies > 0.15 in humans today to evaluate their potential to regulate gene expression.