Selin Jessa

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...

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!)

JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models Abstract. JASPAR (https://jaspar.elixir.no/) is an open-access database that has provided high-quality, manually curated, and non-redundant DNA binding pro

From @damlaob.bsky.social & colleagues in @narjournal.bsky.social #NARDatabaseIssue | #JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models | #Bioinformatics #Genomics #Database #OpenScience #TFBS 🧬 🖥️🧪🔓
⬇️
academic.oup.com/nar/advance-...

Topoisomerase IIb binding delineates localized mutational processes and driver mutations in cancer genomes - Nature Communications Topoisomerases resolve topological DNA stress via double-strand breaks and are established targets of cancer chemotherapies. Here, the authors link genomic binding of TOP2B with localized mutational p...

⚠️New study: we mapped DNA-binding of topoisomerase TOP2B in cancer, uncovering surprising hotspots of DNA damage. TOP2B, normally essential for DNA stress relief, can act as a double-edged sword. co-led by @LiisUuskula @ChristianLee, out now @natcomms.nature.com www.nature.com/articles/s41... [1/7]

📣 I hereby make my Bluesky debut to announce that our work linking DNA binding affinities and kinetics 𝘪𝘯 𝘷𝘪𝘵𝘳𝘰 and 𝘪𝘯 𝘷𝘪𝘷𝘰 for the human transcription factor KLF1 just got published in Cell! @cp-cell.bsky.social

www.cell.com/cell/fulltex...

Key findings in a thread (1/6):

Canadian Bioinformatics Hub Conference 2026. May 27-29, 2026, MaRS Discovery District, Toronto, Canada. Nominate Outstanding Contributors to Canada's Bioinformatics Community! Help us recognize the researchers and community builders shaping the future of bioinformatics in Canada! CBHC 2026 is accepting nominations for awards celebrating innovation, leadership, inclusivity, and trainee excellence across the BCBDS community. Eligible nominees include trainees, early-career, and mid-career professionals. Self-nominations welcome!

The Canadian Bioinformatics Hub is accepting applications for their recognition awards. Three awards are available: CBH Research & Innovation Award, Francis Ouellette Community Award, and CBH Impact Trainee Award. Apply by Dec 8, 2025: www.iscb.org/cbhc2026/cal...

How do genetic association studies rank genes? Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.

@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪

www.nature.com/articles/d41...

Data Scientist in Sutton | The Institute of Cancer Research View details and apply for this Data Scientist vacancy in Sutton. Salary : Salary range £39,805 to £53,500 (Dependent on experience ) Reporting to: Professor Trevor Gra...

Calling cancer data scientists! 📊 💽 🧮
We have a number of open positions in our core facility @icr.ac.uk These are bioinformatician staff scientist like roles to work on exciting single cell, spatial & other genomics data from across our Institute. A PhD is required. jobs.icr.ac.uk/vacancies/13...

✨ I’m looking for PhD students in machine learning who are passionate about applying AI to biomedicine to join my lab at the University of Cambridge.✨

More info: www.cruk.cam.ac.uk/vacancies/cr...

Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”

shorturl.at/H3Qww

This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.

Bluetorial below.

Excited to share Nona: a unifying multimodal masking framework for functional genomics.

Models for DNA have evolved along separate paths: sequence-to-function (AlphaGenome), language models (Evo2), and generative models (DDSM).

Can these be unified under a single paradigm? 1/15

Design principles of cell-state-specific enhancers in hematopoiesis Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread dual activator-repressor function of transcription factors (TFs) and enables the model-guided design of cell-state-sp...

Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis
🧬🩸 screen of fully synthetic enhancers in blood progenitors
🤖 AI that creates new cell state specific enhancers
🔍 negative synergies between TFs lead to specificity!
www.cell.com/cell/fulltex...
🧵

GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.

Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....

genzplyr is dplyr, but bussin fr fr no cap.

Base-resolution deep learning improves functional annotation of off-target sites overlying a cCRE. c) Overview of deep-learning workflow. A ChromBPNet model is trained on ATAC-seq data to predict accessibility in 1,000 bp windows using 2,114 bp local DNA sequence as input. Models are interpreted by DeepLIFT to derive base-resolution scores representing contribution to accessibility. Editing windows from beCasKAS can be overlaid, with or without an observed mutation. d) First track: Predicted accessibility profile at off-target locus for chr6:39263686 A>G edit compared to the reference genome, using T-cell ChromBPNet model. Second track: JASPAR CORE 2024 motifs and base-resolution DeepLIFT contribution scores within the 150-bp ATAC-seq summit. Third track: Contribution scores of unedited (reference) sequence. Last track: Contribution scores after in silico chr6:39263686 A>G edit is performed. e) Crystal structure of c-Fos/c-Jun:DNA complex (PDB: 1FOS). The A>G edit within the editing window is colored in yellow and the target DNA strand has DeepLIFT contribution scores overlaid. Total RNA-seq quantifications of FOS and JUN expression in activated T-cells is also shown (in TPM units, Transcripts Per Million).

And then we stratified off-target base edits in non-coding loci based on their predicted consequences on the epigenome. In a case study, an intergenic off-target edit overlaps multiple motifs - our models predict that it specifically disrupts an AP-1 site. Much more in the paper, check out Tong's 🧵!

Erythroblast ChromBPNet model predicts impact of known therapeutic CRISPR target (exagamglogene autotemcel, Casgevy) on accessibility a) Schematic of Casgevy mechanism. BCL11A represses fetal hemoglobin in adulthood. Disruption of a BCL11A enhancer reactivates fetal hemoglobin. b) Observed ATAC and predicted accessibility from ChromBPNet BCL11A intron, for T-cells (this study) and erythroblasts 48. c) Predicted accessibility for chr2 60495264: T>C edit and reference sequence in erythroblasts, along with DeepLIFT contribution scores. d) Predicted accessibility of chr2 60495267: T>C edit and reference sequence in erythroblasts. The ABE8e edit window is derived from the highest efficiency gRNA sg1620

We then used sequence-to-activity deep learning models, to predict effects of non-coding edits on TF binding and chromatin accessibility. We first show that a ChromBPNet model can predict the same GATA site disruption mechanism exploited by the FDA-approved Casgevy medicine, specifically in T cells:

A highlight of my summer was this collab w/
@twangmdphd.bsky.social ! CRISPR base editors are driving several clinical trials, but it's hard to quantify off-target edits and their effects. Tong developed a sequencing assay to identify off-targets *in primary cells* 🧬🖥️🧪 #genomics #chromatin #CRISPR

And then we stratified off-target base edits in non-coding loci based on their predicted consequences on the epigenome. We show a case study of an intergenic off-target edit overlapping multiple motifs. Our models predict that it disrupts an AP-1 site. So much more in the paper, check out Tong's 🧵!

We then used sequence-to-activity deep learning models, to predict effects of non-coding edits on TF binding and chromatin accessibility. We first show that a ChromBPNet model can predict the same GATA site disruption mechanism exploited by the FDA-approved Casgevy medicine, specifically in T cells:

Specificity, length and luck drive gene rankings in association studies - Nature Genetic association tests prioritize candidate genes based on different criteria.

How do GWAS and rare variant burden tests rank gene signals?

In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!

🧬🧪🧵

www.nature.com/articles/s41...

📢 Open Call! The Max Perutz Labs invite applications for a Tenure-Track Professorship in Genome Biology. We are particularly interested in researchers investigating the molecular and biophysical mechanisms underlying genome function and regulation. More details ➡️ tinyurl.com/3t7vvdct

Molecular determinants underlying functional divergence of TBP homologs The TATA-box binding protein (TBP) is a highly conserved basal transcription factor and a core component of the pre-initiation complex (PIC) for all three eukaryotic RNA polymerases (RNA Pols). Despit...

How does a “universal” transcription factor evolve to do species-specific jobs?
Our new preprint reveals how divergence in TBP’s domains shapes transcriptional specialization across eukaryotes.

Read it here 👉

www.biorxiv.org/content/10.1...

#MolecularEvolution #Transcription

Hierarchical lineage architecture of human and avian spinal cord revealed by single-cell genomic barcoding The formation of neural circuits depends on the precise spatial and temporal organisation of neuronal populations during development. In the vertebrate spinal cord, progenitors are patterned into mole...

Thrilled to share my main postdoc work with @jamesbriscoe.bsky.social

We used genomic barcoding + scRNAseq in chick & human embryos to reveal a lineage architecture that reshapes how we understand neural tube development & cell fate decisions
🧵👇

www.biorxiv.org/content/10.1...

Looking forward, I am launching my lab in the @mitkochinstitute.bsky.social and IMES at @mit.edu, and will continue studying how the unique regulatory landscape of ecDNA enables tumor evolution. We're looking for creative scientists to push this frontier - if you're interested, get in touch!

Enhancer activation from transposable elements in extrachromosomal DNA - Nature Cell Biology Kraft, Murphy, Jones et al. identify extrachromosomal DNA (ecDNA)-interacting elements (EIEs) enriched for transposable elements within ecDNA in colorectal cancer cells. They show that EIE 14 integrat...

Delighted to share our new study in @natcellbio.nature.com showing that the unique epigenetic landscape of ecDNA can enable the oncogenic enhancer activation of transposable elements! This was a great collaboration with @katerinakraft.bsky.social and @sedonamurphy.bsky.social. tinyurl.com/mwfbu4w4

The Skok Lab is recruiting an experienced computational scientist to lead single-molecule epigenomic and 3D genome analysis. We integrate long-read sequencing with Hi-C/Hi-ChIP, scmulti-omics, and machine-learning to explore chromatin topology, and gene regulation.

[2026] – Endogenous retroviruses in human embryogenesis

My lab is seeking two PhD candidates to investigate the function and regulation of endogenous retroviruses in the early stages of human development 🦠👩‍🔬. Apply through the International Max Planck Research School (IMPRS) program: www.molgen.mpg.de/IMPRS/applic.... www.molgen.mpg.de/5094682/Fuey...

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...

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...

Postdoctoral Scientist - Zhang Lab Primary Work Address: One Shields Avenue, Davis, CA, 95616 Current HHMI Employees, click here to apply via your Workday account. The Howard Hughes Medical Institute (HHMI) advances the discovery and s...

🚨 We are recruiting postdocs! If you're interested in reproductive, stem cell/developmental biology, and/or women's health, please apply! 📝 Please repost! 🚩
More info here: hhmi.wd1.myworkdayjobs.com/en-US/Extern...

(1/4) New Pre-print! 🌟
Embryonic development is usually seen as a continuous process, yet some embryos can pause their development to survive harsh conditions, a phenomenon known as diapause. How this pausing is actively maintained has remained a mystery.

Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!

The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.

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Faculty positions in animal morphogenesis that may be filled at the Assistant or Associate Professor level in one of my favorite Departments" Cell and Systems Biology at the University of Toronto. 1/n
jobs.utoronto.ca/job/Toronto-...
jobs.utoronto.ca/job/Toronto-...