Selin Jessa

Quick Draft for Obsidian App - App Store Download Quick Draft for Obsidian by Serhii Petrenko on the App Store. See screenshots, ratings and reviews, user tips, and more apps like Quick Draft for…

On Android, I use (and love) Quick Draft for this and looks like it's on iOS as well - apps.apple.com/us/app/quick.... You can choose one or more destination notes and then share from browser, choose destination, and the link gets appended

Flyer for symposium: https://ctrlepiedit.sciencesconf.org/

Very excited to announce the FIRST symposium on epigenome editing! These tools are becoming widely used in mol bio, ag & therapy. It's time to bring leaders together to discuss this rapidly growing and exciting field. And why not in Paris! Please register & share! (1/2) ctrlepiedit.sciencesconf.org

Pls re-post: My department @oxfordbiochemistry.bsky.social are recruiting for several new faculty positions (links below). Broad search in molecular biology/biochemistry, across prokaryotes and eukaryotes. Interested in understanding life at the molecular level, this job might be for you!
1/n

A reminder that we are actively recruiting a geneticist to the Department of Genetics at Albert Einstein College of Medicine

careers-einstein.icims.com/jobs/17847/a...

In world-first, B.C. teen cured of rare genetic disease The 19-year-old, who lives in Kelowna, had been diagnosed with chronic granulomatous disease around age five, compromising his immune system

In a world first, B.C. teen cured of rare disease through gene editing treatment. Ty Sperle cured of chronic granulomatous disease with a treatment known as “prime editing,” by Brenna Owen www.theglobeandmail.com/canada/briti... via @theglobeandmail.com

📢📢📢Lectureships at Bristol!📢📢📢

We're hiring 3 x lecturers (=assistant professor) in Biological Sciences, across the discipline.

Great department, great colleagues, great building, great city

Details here:
www.bristol.ac.uk/jobs/find/de...

Research Unit Director – IRCM Cancer Research Center Job reference code: IRCM-Cancer

Principal investigator job alert @ircm.bsky.social! We are recruiting a new junior faculty member working in the field of cancer. Apply before February 22nd. Contact me if you have more questions.

www.ircm.qc.ca/en/position-...

Each summer, I lead a week-long creative retreat for environmental researchers & academics on Catalina Island. We develop your most ambitious project ideas. It's truly life-changing.

Applications for the 2026 Storymakers fellowship are now open! Deadline is Feb 1. dornsife.usc.edu/wrigley/enga...

🧬🎉Join us on Dec 17th for our last session of 2025! 🎉🧬Two fantastic talks on transcriptional regulation:
🔬JB Lalanne on developmental enhancers (and starting a lab in 2025?)
🔬 @rberrens.bsky.social on transposable elements in development
📋Register here: us06web.zoom.us/webinar/regi...

Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...

First paper from the lab is now online
@natneuro.nature.com !
We mapped injury induced enhancers in the mouse CNS and decoded their sequence architecture. Little 🧵 rdcu.be/eSQi1

Congrats!! Excited to check out the new version!

Ledidi is a DNA design method that designs *edits* to a template while explicitly minimizing the number of needed edits. This allows you to build upon informative starting material, which our genomes are full of, and simply edit in the final touches, similar to an Instagram filter or video touch-up.

Programmatic design and editing of cis-regulatory elements The development of modern genome editing and DNA synthesis has enabled researchers to edit DNA sequences with high precision but has left unsolved the problem of designing these edits. We introduce Le...

After a huge amount of work w/ @alex-stark.bsky.social's group, a new version of our Ledidi preprint is now out!

In an era of AI-designed proteins, the next leap will be controlling when, where, and how much of these proteins are expressed in living cells.

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

Causal modelling of gene effects from regulators to programs to traits - Nature Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.

Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:

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