Irene Farabella

4️⃣ Featuring the fourth of our showcase projects

Upgrading GROMACS to handle billion-atom systems and enhancing I/O performance and precision, making the first-ever whole-cell simulation possible ➡️ bioexcel.eu/uw67

#MolecularDynamics #GROMACS #ComputationalBiology

Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen The nuclear periphery is a key site for heterochromatin organization in eukaryotic cells, where lamina-associated domains (LADs) promote transcriptional repression and genome stability. Despite their ...

🚨New preprint from the lab🚨
🧬 What keeps certain chromatin domains anchored at the nuclear periphery? Our new genome-wide HiDRO screen uncovers a key role for RNA-binding protein hnRNPK.
www.biorxiv.org/content/10.1...

Extensive differences observed in 3D genome structure between homologous heterozygous chromosomes revealed by Genome Architecture Mapping #GAM in the @apombo1.bsky.social lab ➡️ www.embopress.org/doi/full/10....

Glad to share our latest publication in Nature Genetics: Tracing the evolution of single-cell 3D genomes in Kras-driven cancers. In this work, we generated the first single-cell 3D genome atlases of any cancer using any technique. 1/12

What better way to launch our new account with the publication of @jmstein.bsky.social latest paper from the lab! 🧪 Check out the 🧵 below to learn more about tkPAINT and how we use it to image proteins, DNA, and RNA in the nucleus using DNA-PAINT.

Our new preprint is out on bioRxiv! We show that restoring rigidity sensing via Tpm2.1 is not enough to trigger anoikis in cancer cells, thanks to compensatory AKT signaling and cell–cell adhesion.
With Anat, Nehal, and in memory of Mike Sheetz. www.biorxiv.org/content/10.1...

Caption+Credit: EMBL’s AI Strategy aims to transform life sciences by integrating AI across research areas like genomics, drug discovery, and imaging. Creative team/ EMBL

🌐 EMBL’s new initiative is set to transform life science research through full AI integration – from genomics to drug discovery.

💡 Funding from the Hector Foundation is dedicated to attracting interdisciplinary talent, boosting infrastructure, training, & innovation.

www.embl.org/news/connect...

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...

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...

Are you @ the late stages of your postdoc ? Want to pursue a PI career ?

Then this 👇👇 is for you ! Apply for a spot @ our Talent Forum
www.helmholtz-munich.de/en/stem-cell...

Peer-networking / Career orientation and more !!!

Please distribute :) 🙂

New from the Dai and Li labs: Meta-learning-empowered reflective lattice light-sheet virtual structured illumination microscopy (Meta-rLLS-VSIM) offers near-isotropic resolution for fast and versatile super-resolution imaging of subcellular dynamics www.nature.com/articles/s41...

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...
🧵

Check this out! 👇🏻👇🏻
Amazing work on regulatory element evolution .. Bravo to all involved @arnausebe.bsky.social @mamartirenom.bsky.social but
expecially @ianakim.bsky.social … she is a star 👏🏻👏🏻

Perturb-tracing integrates CRISPR screening with barcode readout and chromatin tracing for loss-of-function screens, facilitating the study of chromatin folding regulators.

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

Read the News & Views highlighting this cool work here!

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

Bravo to all !! Definitely in my reading list for the weekend !!

Excited to share our latest work on how cells fold their genomes, and build mitotic chromosomes! Out in Science today!

Lots of interesting results and proposals for those interested in loop extrusion, and chromosomes!

With @golobor.bsky.social, Leonid Mirny, Bill Earnshaw labs.

See thread below:

Looking for a PhD in sunny Barcelona? ☀️🔬
Our team is hiring a PhD student for the @hologen.bsky.social
project!

📅 Deadline: *Apr 20*
⚠️ READ THE MOBILITY RULE FOR THIS POSITION
🔁 Please, spread the word

All the info here 👉 www.cnag.eu/jobs/phd-stu...

#PhDlife #Genomics #HoloGen #Barcelona

Drosophila follicle showing retrotransposons (pink & yellow) expressed in somatic cells infecting the oocyte

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇

gracias Marc :)

Just apply! Amazing Lab ☺️

Looking for a PhD in sunny Barcelona? ☀️🔬
Our team is hiring a PhD student for the @hologen.bsky.social project!

📅 Deadline: Apr 20
⚠️ READ THE MOBILITY RULE FOR THIS POSITION
🔁 Please, spread the word

All the info here 👉 www.cnag.eu/jobs/phd-stu...

#PhDlife #Genomics #HoloGen #Barcelona

Celebrating 10 years of our lab with a new preprint:
www.biorxiv.org/content/10.1...
How does enhancer location within a TAD control transcriptional bursts from a cognate promoter?
Experiments by Jana Tünnermann and modelling by Gregory Roth

It's Day 2 of #EMBLAIOneHealth! 🎉

Today, participants heard a keynote from Giorgio Metta (Italian Institute of Technology (IIT), Italy) on artificial intelligence in RNA interactions, disease prediction, and therapeutic design.

📷 EMBL Photolab: Stuart Ingham

Postdoc in Genomic Data Science Commitment & contract: Post Doc 1 year collaboration contract, renewable Location: Centre for Human Technologies – Genoa At the Italian Institute of Technology (IIT), we are committed to advancing h...

🧬 We’re hiring a Postdoc in Genomic Data Science @IITalk! Join us to explore 3D genome architecture and RNAs using imaging, genomics & ML 💻🔬🐠
💼 Up to €45k/year
✅ PhD + Python/ML skills
➕ Experience with omics, imaging, or modelling = plus
📍 Genoa 🌊☀️
📧 irene.farabella@iit.it
🔗 tinyurl.com/6z52jhr9

🚨🚨 MEGA JOB ALERT 🚨🚨
Independent Group Leader Positions in Computational Biology @humantechnopole.bsky.social!

Are you ready to start your own lab? Do you know someone who is? Repost this + share with everyone who might want to know about it. Thanks!!! 🙏

More details below... check it out! 🧵 1/3

We often speak about chromatin as being accessible or inaccessible, but what does it mean? We wrote a short review on this, 🔬 focused:

sciencedirect.com/science/arti...

A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab

@marcelonollmann
for their help as editors.

🚨🚨🚨

If you're a bioinformatician who loves:

🧬 #SingleCell #LongReadSequencing & #AlternativeSplicing
🚀 Collaborating and travelling

Apply to work with us at the spectacular BIMSB (@mdc-berlin.bsky.social) in Berlin + @upf.edu-@crg.eu in Barcelona. Qs: www.transdevolab.com

Please RT! 🙏

Sub-cellular Imaging of the Entire Protein-Coding Human Transcriptome (18933-plex) on FFPE Tissue Using Spatial Molecular Imaging Single-cell RNA-seq revolutionized single-cell biology, by providing a complete whole transcriptome view of individual cells. Regrettably, this was accomplished only for individual, tissue-dissociated...

💥🚀

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

Like ‘old Twitter’: The scientific community finds a new home on Bluesky After recent changes to Elon Musk’s X, a gradual migration turns into a stampede

The sky is the limit again!
www.science.org/content/arti...