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Nessim Louafi

@nesslfy.bsky.social
161 followers 226 following 4 posts

PhD Student in Luca Giorgetti's Lab (@lucagiorgetti.bsky.social) - Genome architecture - Microscopy - Image analysis - Biophysics

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Reposted by Nessim Louafi
Timothée Lionnet @successprocess.bsky.social · 11/09/2026
Sharing ZATELLITE 🛰️ - a tool to visualize and manipulate repetitive loci in living cells using designer zinc fingers tinyurl.com/ZATELLITE led by Nestor Saiz, collab with Marcus Noyes, @teresadavoli.bsky.social, @glennislogsdon.bsky.social, @liamholt.bsky.social & @jefboeke.bsky.social (1/n)
principle of ZATELLITE: synthetic Zinc Fingers are fused to a fluorescent protein and targeted to repetitive endogenous sequences - this ensures damage-free tagging, which is not the case with dCas9
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 28/07/2026
Thank you @natgenet.nature.com for this nice Research Briefing www.nature.com/articles/s41... on our recent paper reporting live-cell measurements of Sox2 promoter bursting kinetics when varying its genomic distance from the SCR enhancer 👉 www.nature.com/articles/s41...
nature.com
The genomic position of an enhancer modulates bursting dynamics of the cognate promoter - Nature Genetics
We show that, in a genomic locus with minimal complexity, the distance between promoter and enhancer modulates the frequency of clustered transcriptional bursts. Thus, besides the nucleotide sequence,...
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 15/07/2026
Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:
doi.org
Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature Genetics
Tünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...
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Anders Sejr Hansen @andersshansen.bsky.social · 22/06/2026
(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 23/06/2026
Impressive and exciting new work by @andersshansen.bsky.social @leonidmirny.bsky.social @zechnerlab.bsky.social labs Live imaging of a synthetic enhancer-promoter system leads estimates of physical range of E-P communication + evidence for time-gated productive E-P encounters on the >1s timescale.
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Anton Goloborodko @golobor.bsky.social · 13/05/2026
our field may finally be cracking the puzzle of cohesin loop extrusion's role in enhancer! Careful biophysical measurements, engineered loci, and first-principle biophysical thinking are a powerful combo. An overview of Nora/Mirny lab's preprint+important context by @lucagiorgetti.bsky.social
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 13/05/2026
Beautiful new study from @elphegenoralab.bsky.social and Leonid Mirny's lab: Cohesin-bridged encounters mediate enhancer-promoter communication, predicting how enhancer effect scales with genomic distance and - for the first time - how CTCF sites modulate enhancer-promoter communciation! 🧵 below
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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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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 23/04/2026
📖 The final version of our paper is out in press Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption authors.elsevier.com/a/1m%7EU03vV... or www.cell.com/molecular-ce...
cell.com
Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption
Shah, Tortora, et al. show that cells can dial the rate of cohesin loop extrusion by balancing the relative dosage of NIPBL and PDS5. Their models provide a quantitative mechanistic basis for the gene...
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FMI science @fmiscience.bsky.social · 19/02/2026
💫 We're hiring! The Computational Biology Facility is looking for a Computational Proteomics Scientist to collaborate on cutting-edge proteomics projects, develop new analytical approaches, and publish impactful research. Apply by April 12 at: www.fmi.ch/education-ca...
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FMI science @fmiscience.bsky.social · 12/02/2026
🚀 We’re hiring! The Structural Biology Platform is seeking a Project Leader to advance cryo-electron tomography and expand capabilities at the FMI. Join a vibrant research community at the interface of structural biology, cell biology & disease mechanisms. Apply at: www.fmi.ch/education-ca...
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FMI science @fmiscience.bsky.social · 04/12/2025
📢 Please help spread the word: We’re hiring a Head of Student & Postdoc Affairs to coordinate our international PhD program, provide guidance & career counseling, lead training programs, collaborate on EDI initiatives, and manage alumni relations. Apply at www.fmi.ch/education-ca...
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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 27/11/2025
Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀 Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function now revised and journal accepted at www.science.org/doi/10.1126/... 🧵👇
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Luca Costa @costaluca.bsky.social · 25/11/2025
We are hiring a 2-year postdoctoral researcher to join our Membrane Biophysics team at the CBS in Montpellier. Join us to reinvent Atomic Force Microscopy to image the most common interface on our planet: the surface of water @membranesbiophy.bsky.social @cbsmontpellier.bsky.social
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Center for Structural Biology (CBS Montpellier) @cbsmontpellier.bsky.social · 08/11/2025
In two weeks, our #qbio #Master students learned to build, from drawing to full realization, their own : confocal FCS, TIRF microscope, and optical tweezers setup ! This is hand-on #microscopy ! Interested ? Join the qbio master next year at the Montpellier University ! qbio.umontpellier.fr
Picture of a student's made TIRF microscopePicture of a student's made optical tweezers microscopePicture of a student's made confocal FCS microscope
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Center for Structural Biology (CBS Montpellier) @cbsmontpellier.bsky.social · 05/11/2025
Postdoctoral position in the team of Alessandro Barducci in the CBS, focusing on multiscale simulations of RNA-driven condensates, with applications in synthetic biology. More information : www.cbs.cnrs.fr/images/jobs/... The position is expected to start in early 2026, with some flexibility.
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FMI science @fmiscience.bsky.social · 26/09/2025
📢 Spread the word: Applications are now open for our #PhD and #MDPhD programs! Become part of Basel, Europe’s #LifeScience hub, and grow in a dynamic, international, and supportive community. Apply by Nov 15: www.fmi.ch/education-ca...
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Nessim Louafi @nesslfy.bsky.social · 25/09/2025
Very excited to share my PhD project! With @mattiaubertini.bsky.social in @lucagiorgetti.bsky.social we combined polymer simulation and super resolution live-cell imaging to study the dynamics of encounter of distant loci in the genome.
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FMI science @fmiscience.bsky.social · 12/09/2025
📣The Turco group is seeking a computational biologist to analyze large omics datasets. Work on cutting-edge 3D organoid models of the human placenta and be embedded in our Computational Biology Platform (part of @sib.swiss). Apply here: www.fmi.ch/education-ca...
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Julia Batki @juliabatki.bsky.social · 14/09/2025
I am excited to announce that we are looking for a Lab Manager @fmiscience.bsky.social in Basel. If you want to be part of a growing team investigating development and tissue formation, and are enthusiastic about helping set up a new lab, please check out the role: www.fmi.ch/education-ca...
fmi.ch
Friedrich Miescher Institute, open position
Friedrich Miescher Institute, open position
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FMI science @fmiscience.bsky.social · 08/09/2025
🚨 We're hiring, please share! The FMI seeks a tenure-track Group Leader (Assistant Prof) in Structural Biology 🔬 Innovative scientists in genome regulation, RNA metabolism, or protein homeostasis—especially using cutting-edge approaches—apply now at www.fmi.ch/education-ca...
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Magdalena Solyga @solygamagda.bsky.social · 19/08/2025
A new preprint from our lab with @zelechowski.bsky.social & @georgkeller.bsky.social ! Using wireless EEG + VR, we recorded visuomotor mismatch responses in freely moving humans. Huge thanks to all participants, Keller Lab members and FMI facilities! Read more: www.biorxiv.org/content/10.1...
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Elphege Nora Lab at UCSF @elphegenoralab.bsky.social · 16/08/2025
New preprint with @gfudenberg.bsky.social We find the rate of cohesin loop extrusion in cells is set by NIPBL dosage and tunes many aspects of chromosome folding. This provides a molecular basis for NIPBL haploinsufficiency in humans. 🧵👇 www.biorxiv.org/content/10.1...
biorxiv.org
NIPBL dosage shapes genome folding by tuning the rate of cohesin loop extrusion
Cohesin loop extrusion is a major driver of chromosome folding, but how its dynamics are controlled to shape the genome remains elusive. Here we disentangle the contributions of the cohesin cofactors ...
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Antonio Scialdone @antonio-scialdone.bsky.social · 25/07/2025
How can we quantify cell potency from scRNAseq data? In our latest preprint, we show that intrinsic dimensionality (ID) tracks potency in single cells across reprogramming datasets, and we provide IDEAS, a Python toolkit for ID-based potency analysis: www.biorxiv.org/content/10.1...
biorxiv.org
Intrinsic dimensionality of single-cell transcriptomic data reveals potency landscapes during cell reprogramming
Cell potency, the ability of a cell to generate other cell types, is a fundamental property that drives development, regeneration, and reprogramming. Recent computational advances have en- abled estim...
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Anton Goloborodko @golobor.bsky.social · 15/07/2025
We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab. www.biorxiv.org/content/10.1... 1/
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 26/06/2025
We are looking for a research assistant to join our lab and support ongoing projects with genome engineering in mouse embryonic stem cells! Please get in touch if you are interested. www.fmi.ch/education-ca...
fmi.ch
Friedrich Miescher Institute, open position
Friedrich Miescher Institute, open position
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Florian Jug @florianjug.bsky.social · 09/06/2025
Come and work with us! Super exciting and relevant projects! Become an #AI pro and do something positive for the 🌍! 👩‍🎓 🧑‍🎓 If you know someone who might be interested… please repost and/or forward this! 🙏
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Albert Dominguez Mantes @albertdm.bsky.social · 06/06/2025
Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com! Since the pre-print, we have added many features, notably native 3D detection! @maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social Paper: rdcu.be/epIB7 (1/N)
rdcu.be
Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression
Nature Methods - Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in...
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Anders Sejr Hansen @andersshansen.bsky.social · 15/05/2025
(1/n) Thread @matteomazzocca.bsky.social @domenicnarducci.bsky.social Simon Grosse-Holz @jessematthias.bsky.social preprint Q: how does chromatin move? Using MINFLUX, SPT & SRLCI, we track chromatin dynamics across 7 orders of magnitude in time to provide answers www.biorxiv.org/content/10.1...
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Jan Funke @janfunkey.bsky.social · 18/04/2025
How can AI help you to analyze your microscopy images? Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6! Applications are due 🚨 April 30 🚨 Read on for more! 👇 www.mbl.edu/education/ad...
mbl.edu
AI@MBL: Machine Learning for Microscopy Image Analysis | Marine Biological Laboratory
The goal of this course is to familiarize researchers in the life sciences with state-of-the-art deep learning techniques for microscopy image analysis and to introduce them to tools and frameworks th...
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FMI science @fmiscience.bsky.social · 18/02/2025
📢Please share: We're now accepting applications for our #PhD and #MDPhD programs! 🧬Join us in Basel, Europe's #LifeScience hub, and unleash your potential in a vibrant, international and supportive environment. 📅Apply by May 1 at www.fmi.ch/education-ca...
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 29/03/2025
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
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Nessim Louafi @nesslfy.bsky.social · 08/03/2025
Still time to apply to this great program! (Objectively)
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FMI science @fmiscience.bsky.social · 12/02/2025
🚨Job alert: We're hiring a Data Scientist (Image Analysis) to join our Facility for Advanced Imaging & Microscopy. The facility provides cutting-edge light and electron microscopy, high-content screening, image analysis and spatial-transcriptomics services. Apply at: www.fmi.ch/education-ca...
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FMI science @fmiscience.bsky.social · 16/12/2024
📣 Please share: We’re hiring a tenure-track Group Leader in Multicellular Systems to explore the molecular and cellular mechanisms driving the formation, maintenance, or destabilization of tissues, organs and organisms. Apply at: www.fmi.ch/education-ca...
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 11/12/2024
Incredible day for the lab with @mattiaubertini.bsky.social and Verena Mutzel both being awarded EMBO fellowships to pursue their postdoctoral projects! We're so proud of them and grateful to the EMBO community for supporting our science.
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