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Carl de Boer

@carldeboer.bsky.social
569 followers 187 following 118 posts

Associate Professor, UBC school of Biomedical Engineering. Trying to enable personalized medicine by solving gene regulatory code.

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Reposted by Carl de Boer
Ben de Bivort @debivort.bsky.social · 22/09/2026
Hello friends, the Harvard Life Science departments have banded together to hire a new colleague working at the intersection of Life Sciences and AI. Could be primarily an experimentalist, or could be primarily a compute/theorist. academicpositions.harvard.edu/postings/16773
academicpositions.harvard.edu
Tenure-Track Professor in Life Science and AI
The Life Sciences Departments in Harvard Faculty of Arts and Sciences seek to recruit a tenure-track professor whose research is at the interface of AI and life sciences, from methodological developme...
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Maitreya Dunham @maitreya.bsky.social · 24/09/2026
Exciting news: @uwgenome.bsky.social will be hiring for two tenure-track faculty positions this year, one open rank and one assistant professor. Both are “Genome Sciences” interpreted broadly so we welcome applicants working in a variety of fields and methods. Ad will be out shortly.
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Carl de Boer @carldeboer.bsky.social · 23/09/2026
Depressing to see all the AI generated grad school applications. These slop grenades waste our time and even if "successful" (getting a position) it will be a terrible match since the applicant was actually the AI. If I wanted a lab full of AI researchers, no people would be needed.
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Arnaud Krebs @arnaudkr.bsky.social · 21/09/2026
We are recruiting! Wet&Dry either combined or separate. If you are excited about gene regulation, new methods in genomics and AI-based interpretation! Talk to us!
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Keystone Symposia @keystonesymposia.bsky.social · 16/09/2026
Are you a postdoc or early-career scientist? The Keystone Symposia Fellows Program may be for you. Career development. SAB meetings with leaders in your field. 1:1 mentorship. A community of Fellows committed to each other's growth. Applications close in 2 weeks on Sept. 28.
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Vijay Ramani @vram142.bsky.social · 14/09/2026
Everything you wanted to know about single-molecule epigenomics but were too afraid to ask! Wonderful to co-write (h/t ENORMOUS lift by @arnaudkr.bsky.social) this primer on our nascent field. Also, a 💯 example of wonderful colleagues building something *together*, not in competition =)
nature.com
A practical guide to studying genome function using single-molecule genomics
Nature Reviews Molecular Cell Biology - Single-molecule genomics methods are used to study the activity of regulatory factors on individual DNA molecules genome-wide, thereby enabling...
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Wendy Bickmore @wbickmor.bsky.social · 08/09/2026
It was great working with students Kun and Ryan and @hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers. www.nature.com/articles/s41...
nature.com
Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics
This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...
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Nozomu Yachie @nzmyachie.bsky.social · 04/09/2026
Maybe it’s time to say goodbye to UMAP and other low-dimensional embeddings (at least in many single-cell analyses). We developed MILK to encode single-cell populations into tree representations at unprecedented scales. www.biorxiv.org/content/10.6... Here’s what MILK is: 🧵
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Emma Dann @emmamarydann.bsky.social · 28/08/2026
Our work on systematic perturb-seq of primary human T cells is now out in Cell 🎉 www.cell.com/cell/fulltex... It's been a privilege to work with @ronghuizhu.bsky.social between @jkpritch.bsky.social @marsonlab.bsky.social labs, with a dream-team of co-authors ❤️ Highlights in preprint thread👇
cell.com
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
A dynamic atlas of gene regulation was generated by perturbing every expressed gene across 22 million primary human CD4+ T cells under resting conditions and following re-stimulation. The resulting ma...
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Fred Hutch @fredhutch.org · 15/08/2026
🔬 Fred Hutch Cancer Center is hiring an Assistant or Associate Professor in the Basic Sciences Division @basicsci.fredhutch.org. Join a world-class research community in Seattle and help advance discoveries in fundamental biology. Apply: apply.interfolio.com/190640
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Carl de Boer @carldeboer.bsky.social · 10/08/2026
Watched this develop over the years and it is super cool!
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Alejandro Montenegro @aemonten.bsky.social · 05/08/2026
"Here we describe a systematic effort (‘Codebook’) to determine the sequence specificity of 332 putative and poorly characterized human TFs." www.nature.com/articles/s41...
nature.com
An expanded codebook of human transcription factor DNA-binding specificity - Nature
Results from a panel of assays that analyse different aspects of DNA sequence specificity reveal more than 100 new motifs to aid the characterization of putative human transcription factors.
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Centre de Regulació Genòmica (CRG) @crg.eu · 03/06/2026
Congratulations to CRG's @benlehner.bsky.social on receiving the 2026 Premio Rei Jaume I for Biomedical Research. The award recognises his pioneering discoveries on genetic variation, evolution and disease, helping transform our understanding of biology and human health. #genomics #genetics #CRG
Ben Lehner at the CRG
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Jay Shendure @jshendure.bsky.social · 30/07/2026
New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...
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Lior Pachter @lpachter.bsky.social · 30/07/2026
One of the major pains of academia is having to click through labyrinths of webpages to submit papers. Now, thanks to Joe Rich (and AI), problem solved! His tool is called PaperPush and is available at github.com/pachterlab/p... It's super easy to use! 1/🧵
github.com
GitHub - pachterlab/paperpush
Contribute to pachterlab/paperpush development by creating an account on GitHub.
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Jenny Chen @jennychen.bsky.social · 29/07/2026
The Chen Lab @ EMBL Rome (current population: 1) is hiring! Looking for an experimental Lab Manager w/ a PhD and experience in molecular bio and mouse-based neuro research. Apply if you like: mouse behaviors, high-throughput sequencing, good coffee & ancient history tinyurl.com/48h66vfh
tinyurl.com
Lab Manager
The European Molecular Biology Laboratory (EMBL) is one of the world’s leading life science research organizations. With sites across Europe, EMBL fosters an international, collaborative, and inclusiv...
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Albert Blanch-Asensio @ablanchasensio.bsky.social · 20/07/2026
The STRAIGHT-IN (Dual) kit is now available via @addgene.bsky.social! 🧬 A complete 24-plasmid toolkit for installing up to two orthogonal CLYBL landing pads, DASIT-based enrichment without FACS, and efficient large DNA integration in human cells. Link: www.addgene.org/kits/gallowa... 🧵
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 19/07/2026
scWeave: A deep learning model that bidirectionally translates between gene expression and chromatin structure at single cell resolution www.biorxiv.org/content/10.64898/20…
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FragileNucleosome @fnucleosome.bsky.social · 17/06/2026
We just started our summer break, but we're also planning our September-December seminar schedule! If you have an exciting chromatin/transcription story that will be ready for the spotlight by then, use the survey below to nominate yourself to give a #FNucleosome talk 🧬🧬 forms.gle/1EKYN2Nt79ar...
forms.gle
Application to speak in the Fragile Nucleosome series
Thank you for your interest in our seminar series! We use a variety of different session formats but, in general, trainees can plan for a ~15 min talk + 5min Q/A and PIs can plan for a ~25min talk +...
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Richard Sever @richardsever.bsky.social · 06/07/2026
“move from preprint to peer-reviewed publication leaves the central claims of most abstracts intact, indicating preprints are a reliable source…papers that were never posted as preprints were retracted at roughly twice the rate of those that were…” www.biorxiv.org/content/10.6...
biorxiv.org
Tracking claim changes from preprint to publication across 72,644 biomedical studies using large language models
Preprints now disseminate a large share of biomedical research before peer review. Because they have not yet passed peer review, some scientists regard preprint claims as unverified or potentially unr...
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Carl de Boer @carldeboer.bsky.social · 20/06/2026
This year, mostly same content, I gave students mini Chocolate bars to complete the survey in class. No conditions for how they rated the class and honor system that they completed survey at all. Way better ratings than previous years.
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Nature Biotechnology @natbiotech.nature.com · 11/06/2026
Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT -@rongfan8.bsky.social @yaleschoolofmed.bsky.social www.nature.com/articles/s41...
nature.com
Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT - Nature Biotechnology
In vivo CRISPR genetic perturbations are spatially mapped at scale.
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Teif lab @teiflab.bsky.social · 12/06/2026
Great preprint by @vram142.bsky.social & Co www.biorxiv.org/content/10.6... "fiber homotypy," where chromatin fibers with similar nucleosome spacing interact more frequently in 3D --> Related to our previous "nucleosome homology recognition" in chromatin royalsocietypublishing.org/rsif/article...
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Carl de Boer @carldeboer.bsky.social · 12/06/2026
Brutal IP burn: "You have ordinary skill in the art."
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Carl de Boer @carldeboer.bsky.social · 10/06/2026
We had similar findings (not emphasized in the publication) in our study of variant characterization at TNFAIP3. Different "monocyte" cell lines looked very distinct. "B cell" lines looked very distinct. Cell lines are often bad proxies for primary cells in terms of gene regulation.
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 02/06/2026
Gigabase-scale deletion scanning of the human genome www.biorxiv.org/content/10.64898/20…
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Carl de Boer @carldeboer.bsky.social · 30/05/2026
Understanding where genomics models work and fail will be critical to their successful deployment. Meta models can tell us this, and give some insight into failure modes. 3/3 for @muntakimrafi.bsky.social this week. CSHL AIxBIO to boot (sorry to miss!) What a week!
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Carl de Boer @carldeboer.bsky.social · 29/05/2026
Which active learning methods are best for genomics models? See Rafi's thread on our recent preprint, below. www.biorxiv.org/content/10.6... Rafi is having a good week - he's got one more preprint to post!
biorxiv.org
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Carl de Boer @carldeboer.bsky.social · 28/05/2026
There is widespread homology across our genomes. How does this impact genomics models? Major update to our preprint! 🎉 We tested more models and more tasks; the overall findings were robust, but one conclusion on how future models should be trained differs⚠️ www.biorxiv.org/content/10.1...
biorxiv.org
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 27/05/2026
gRely: Relyability for genome trained sequence-to-expression models www.biorxiv.org/content/10.64898/20…
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Avantika Lal @avantikalal.bsky.social · 27/05/2026
Our Decima paper is now published in Nature Methods! Full text: rdcu.be/fkASS. Decima can predict gene expression in specific cell types and cell states from DNA sequence. I would say more but @drkbio.bsky.social and Johannes Linder wrote this great news & views: www.nature.com/articles/s41...
rdcu.be
Decoding sequence determinants of gene expression in diverse cellular and disease states
Nature Methods - Decima learns to predict cell-type-specific gene expression based on DNA sequences, contributing to the analysis of gene regulation and design of context-specific regulatory elements.
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Andrew Pruszynski @andpru.bsky.social · 14/05/2026
CIHR has launched a trial ballon that suggests shifting to one competition a year. This is the worst idea I have heard in a long time. The only benefit is making top-line success rates look better than they are. Keep it as is, do in-person reviews, and keep the pain in the open.
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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 13/05/2026
Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇
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Carl de Boer @carldeboer.bsky.social · 19/05/2026
I think the LLMs finally found me. Got like 5 review requests this weekend.
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James Prendergast @jprendergast.bsky.social · 13/05/2026
🚨 New preprint! How does noncoding variation drive complex traits? We built a massive atlas of cattle regulatory variants (>150k emVars!) and directly tested them in both bovine AND human cells. 🐄🧬🚶‍♂️ Read it here: www.biorxiv.org/content/10.6...
Schema of approach for mapping regulatory elements and variants in cattle and testing their cross-species activity in human cells.
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Carl de Boer @carldeboer.bsky.social · 14/05/2026
I think both journals and authors vastly underestimate the reputational harm that comes from sending bad papers out for review. Demonstrates disrespect for our time, and poor judgement. I remember it next time I am asked to review, and will rethink submitting to that journal.
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Rebecca Shapiro @shapirorebecca.bsky.social · 12/05/2026
It's been a long time coming to finally see this in print! While not the first paper from my lab, it is one of the very first projects we started working on from day 1 links.springernature.com/f/a/1IP7gCfA...
links.springernature.com
Pooled CRISPRi screening reveals fungal-specific drug target candidates - Nature Microbiology
This study presents a pooled CRISPRi screening approach in Candida albicans to investigate essential genes at scale, revealing environment- and strain-dependent gene sensitivities and conserved vulner...
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Alejandro Montenegro @aemonten.bsky.social · 27/04/2026
"In this study, we present a genome-scale map of genetic interactions in the human haploid cell line HAP1, based on CRISPR-based perturbation of ∼4 million gene pairs. The resulting network comprises ∼89,000 high-confidence gene-gene interactions" doi.org/10.1016/j.ce...
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Shreyas Pai @theshreyaspai.bsky.social · 24/04/2026
Thrilled to have my first PhD paper with @mmdesai.bsky.social out! @science.org Link: www.science.org/doi/10.1126/... Thread below: #mevosky #evosky #evobio #popgen #evolsky #ecoevo #molevol
science.org
Sex decreases the pleiotropic costs of local adaptation by purging hitchhiking load
Understanding the evolutionary mechanisms that maintain sex despite its direct costs is a long-standing challenge. Previous work has shown that sexual recombination can accelerate adaptation, in part ...
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cxqiu.bsky.social @cxqiu.bsky.social · 09/04/2026
New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...
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AI x Bio Discovery @aixbiobot.bsky.social · 07/04/2026
Genetic background shapes AI-predicted variant effects [new] ...uncovering heterogeneous predictions where variants shift between pathogenic and benign outcomes across diverse genomic contexts, crucial for interpretation.
Genetic background shapes AI-predicted variant effectsFigure 1Figure 2Figure 3
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callista yee @csybio.bsky.social · 07/04/2026
It is with great sadness that I'm sharing the news that Dr. Don Moerman passed away this weekend. He was such a legend in the #Celegans and Canadian science community.
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VIB.AI @vibai.bsky.social · 03/04/2026
The @steinaerts.bsky.social lab published CREsted, an end-to-end modeling framework to 🧬 Train sequence-based enhancer models on large sc datasets 🔍 Decode enhancer logic with nucleotide-level interpretability ⚙️ Design synthetic enhancers with cell-type specificity tinyurl.com/ypurmrw5
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Kathleen Bachynski @bachynski.bsky.social · 03/04/2026
“My patient is refusing a drug studied in 170,000 people because of side effects that a 124,000-person analysis just confirmed do not exist — while injecting a compound studied in 14 humans, from unregulated sources, based on the recommendation of someone who profits from selling it.”
statnews.com
My patient would rather take a peptide than a statin. That reveals an uncomfortable truth in medicine
“The volume of evidence behind a therapy has become inversely correlated with public trust in it,” writes Vikas Patel.
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Troy McDiarmid @troymcdiarmid.bsky.social · 02/04/2026
Stoked to announce that I’m starting a lab as an Assistant Professor in the School of Biomedical Engineering and Centre for Brain Health at UBC! mcdiarmid-lab.sbme.ubc.ca Recruiting at all levels - please share the word! Cheers and happy long weekend all!
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AITHYRA Research Institute of the Austrian Academy of Sciences @aithyra.bsky.social · 26/03/2026
AITHYRA is recruiting an AI/ML STARTING PI Generative Models, Large Language Models, Agentic AI, Active & Reinforcement Learning, AI-driven Scientific Discovery & Lab Automation, ML-driven molecular simulations... Job Ad: aithyra.at/fileadmin/do... Apply by 30.4.2026 #StartingPI #AI/ML #AITHYRA
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AITHYRA Research Institute of the Austrian Academy of Sciences @aithyra.bsky.social · 26/03/2026
AITHYRA is recruiting a LIFE SCIENCE PI We are interested in research questions related to one of our four core disease areas: cancer research, immunological disorders, infectious diseases, neurodevelopment disorders. Job Ad: aithyra.at/fileadmin/do... Apply by 30.4.2026 #StartingPI #LS #AITHYRA
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Trends in Genetics @cp-trendsgenetics.bsky.social · 18/03/2026
"Beyond the baseline: mapping the context-specific regulatory landscape of disease" by Yoav Gilad and Alexis Battle authors.elsevier.com/sd/article/S...
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Carl de Boer @carldeboer.bsky.social · 18/03/2026
New preprint from our lab where we learn some interesting things about the context specificity of TFs in their regulation of gene expression by dissecting MPRA-trained sequence-expression models. Surprising guest appearance from RNA Pol III(!) Thread from 1st author @sambean12.bsky.social 👇
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