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Selin Jessa

@selinjessa.bsky.social

920 followers 1.3K following 39 posts

(she/her) Computational biologist and post-doc scientist in the Greenleaf and Kundaje labs at Stanford. Interested in understanding how cells know what to become (transcription factors, gene regulation, dev bio, open science) www.selinjessa.com

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Selin Jessa @selinjessa.bsky.social · May 3

Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️

Dissecting regulatory syntax in human development with scalable multiomics and deep learning

Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...

www.biorxiv.org

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Jacob Schreiber @jmschreiber91.bsky.social · 1d

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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Mark Peifer (He, him) @peiferlabunc.bsky.social · 2d

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-...

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Julius Brennecke @juliusbrennecke.bsky.social · 3d

The Vienna BioCenter PhD Program application deadline is approaching: October 10!

Join one of Europe’s premier life science campuses, home to cutting-edge research across all areas of biology.
Apply and start your scientific journey in Vienna!

training.vbc.ac.at/phd-program/

#PhD #LifeSciences

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ralucagordan.bsky.social @ralucagordan.bsky.social · 5d

I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...

DNA mutagenesis driven by transcription factor competition with mismatch repair

Competition between transcription factors and mismatch repair machinery drives localized hypermutation at regulatory elements, with implications for cancer and genome evolution.

www.cell.com

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Raquel Fueyo @fueyoraquel.bsky.social · 7d

Today in @nature.com, we present our work leveraging functional genomics and human blastoids to uncover a human-specific mechanism in preimplantation development driven by the endogenous retrovirus HERVK.
Special thanks to the reviewers whose comments improved our manuscript a lot! rdcu.be/eI3tD

A human-specific regulatory mechanism revealed in a pre-implantation model

Nature - Genetic manipulation of blastoids reveals the role of recently emerged transposable elements and genes in human development.

rdcu.be

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Wolfgang Huber @wkhuber.bsky.social · 9d

Do you like theoretical biology, mathematical&conceptual modelling and want to apply yourself to cutting-edge research at all levels of biology, from molecules to ecosystems?

Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

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Canadian Epigenetics @ceehrc.bsky.social · 9d

FINAL REGISTRATION DEADLINE!

Last day to register for the CEEHRC Annual Meeting is FRIDAY, OCTOBER 10!

Abstracts still being accepted for the poster sessions.

Speaker lineup and other details can be found at event.fourwaves.com/...

#epigenetics #epigenomics #ceehrc

CEEHRC 11th Annual Canadian Conference on Epigenetics

Fourwaves - CEEHRC 11th Annual Canadian Conference on Epigenetics

event.fourwaves.com

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Miriam B. Goodman, PhD @wormsense.bsky.social · Sep 6

Please help me to celebrate Mei Zhen, an innovator and tremendous collaborator, named to the Royal Society of Canada Academy of Science on September 4, 2025

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Jan Żylicz @jzylicz.bsky.social · 20d

Genes are not On/Off switches. In a new preprint we show that HDAC3 is key to establish correct transcriptional dose in development. Gr8 work from N. Stamidis @ucph.bsky.social and collab. @jamiehackett.bsky.social @gregersenlab.bsky.social . Huge thx to all authors! www.biorxiv.org/content/10.1...

HDAC3 prevents enhancer hyperactivation to enable developmental transitions

Dynamic gene regulation requires precise cooperation between transcription factors and chromatin modifiers at regulatory elements to achieve not only activation or repression, but also appropriate tra...

www.biorxiv.org

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Aurelie Hintermann @aurhin.bsky.social · 21d

Are digits modified fins, or evolutionary innovations? Read how we tackled this old question from a new angle🧪
A story with @chasebolt.bsky.social, @homeobox.bsky.social and myself, coordinated by @denisduboule.bsky.social from @college-de-france.fr and published in @nature.com today!
#InHoxWeTrust

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Axel Visel @axelvisel.bsky.social · Aug 21

Postdoc opportunity with @tomasbruna.bsky.social here at @jgi.doe.gov @berkeleylab.lbl.gov:

Develop, benchmark, and apply Plant Genomic Language Models (gLMs) 🌿🧬💻

jobs.lbl.gov/jobs/computa...

#AI #PlantGenomics #gLMs #Postdoc

Graphic announcing a Computational Postdoctoral Fellow position. Text: Computational Postdoctoral Fellow – Plant Genomic Language Models (gLMs). JGI is seeking a Computational Postdoctoral Fellow to join a funded project at Berkeley Lab’s Joint Genome Institute applying genomic language models (gLMs) to unlock new biological insights in plants. Join one of the world’s leading genomics facilities to pioneer AI applications in plant biology, with access to cutting-edge computational resources and diverse genomic datasets. This project will focus on developing and exploring applications of gLMs to plant genomes, from identifying novel regulatory elements to revealing evolutionary patterns across species, with particular interest in cross-species and data-limited scenarios. In this role, you will design tasks and datasets to test and extend gLM capabilities, apply models to generate new biological hypotheses, and share findings through high-impact publications and presentations.

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Benoit Bruneau @benoitbruneau.bsky.social · Aug 20

New preprint from the lab just dropped! Our continued partnership with Irfan Kathiriya from @ucsanfrancisco.bsky.social on gene regulatory networks in atrial disease modeling using iPS cells
www.biorxiv.org/content/10.1...

Reduced TBX5 dosage undermines developmental control of atrial cardiomyocyte identity in a model of human atrial disease

There is evidence for a shared genetic basis of atrial septal defects (ASDs) and atrial fibrillation (AF), but it remains unclear how genetic susceptibility leads to these distinct human atrial diseas...

www.biorxiv.org

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María Mariner @mariamafau.bsky.social · Jul 24

Thrilled to share the story stemming from my PhD!
We used mESC neural differentiation, genome editing and bulk & single-cell approaches to uncover how ZIC2 controls early neural fate by playing a dual and sequential regulatory role as a promiscous pioneer and a selective lineage-specific activator.

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The Lewis Lab @peterlewislab.bsky.social · Jul 23

We are excited to share our new preprint demonstrating that nucleic acid interactions with SUZ12 constrain PRC2 activity, establishing a kinetic buffer essential for targeted gene silencing and revealing vulnerabilities in diffuse midline gliomas.
www.biorxiv.org/content/10.1...

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H. Courtney Hodges @hodgeshc.bsky.social · Jul 22

How do chromatin remodelers use #IDRs to find TF binding partners? In our new Molecular Cell paper, we show that β-catenin is an adaptor that links SWI/SNF (cBAF) subunit ARID1A with binding partners via IDR-domain interactions.
www.cell.com/molecular-ce...

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Caleb Lareau @caleblareau.bsky.social · Jul 22

Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1...

Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/

the treasure trove of all sequencing datasets

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Doug Fowler @dougfowler.bsky.social · Jul 21

Interested in using functional data to understand clinical variants? Been hunting for a good review of the topic? We just wrote one! rdcu.be/exaEU

Multiplexed assays of variant effect for clinical variant interpretation

Nature Reviews Genetics - Multiplexed assays of variant effect (MAVEs) are highly scalable experimental approaches used to generate functional data for genetic variants. In this Review, McEwen et...

www.nature.com

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Li Zhao @lizhao.bsky.social · Jul 15

Our latest paper is out: rdcu.be/ev6Ym — one of my favorite projects. It began about 8 years ago when Nobel laureate Torsten Wiesel asked me: what transcription factors regulate new genes? I had no idea then. Now we have some answers.

Gene regulatory networks and essential transcription factors for de novo-originated genes

Nature Ecology & Evolution - A combination of computational methods applied to single-cell RNA sequencing data and genetic experiments shows that a small number of transcription factors are...

rdcu.be

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Jonathan Pritchard @jkpritch.bsky.social · Jul 7

Staff scientist position (computational):

I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs

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Vicki Metzis @vmetzis.bsky.social · Jun 27

Paper alert! I am really pleased to share the final version of the work led by Irène Amblard in the team on a regulatory switch controlling Cdx2 expression during posterior body development! #regulatorylogic #devbio @mrc-lms.bsky.social @imperialmed.bsky.social

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Žiga Avsec @avsecz.bsky.social · Jun 25

Thanks to the large consortia like ENCODE, FANTOM5, GTEx, 4DNucleome for generating key training data. And finally, thanks to numerous researchers developing inspiring DNA sequence-to-function models, informative evaluations, and interpretation tools.

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Žiga Avsec @avsecz.bsky.social · Jun 25

Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind

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Anshul Kundaje @anshulkundaje.bsky.social · Jun 25

This a really exciting leap forward for genomic sequence to activity gene regulation models. It is a genuine improvement over pretty much all SOTA models spanning a wide range of regulatory, transcriptional and post-transcriptional processes. 1/

Žiga Avsec @avsecz.bsky.social · Jun 25

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Anshul Kundaje @anshulkundaje.bsky.social · Jun 19

@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/

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Pooja Kathail @poojakathail.bsky.social · Nov 20

Super excited to share our review on genomic deep learning models for non-coding variant effect prediction, with Ayesha Bajwa and Nilah Ioannidis. We’d like this review to be a useful resource, and welcome any feedback, comments, or questions! 1/4

arxiv.org/abs/2411.11158

Leveraging genomic deep learning models for non-coding variant effect prediction

The majority of genetic variants identified in genome-wide association studies of complex traits are non-coding, and characterizing their function remains an important challenge in human genetics. Gen...

arxiv.org

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