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Irene Farabella

@iosonoirene.bsky.social
432 followers 922 following 7 posts

💻 🧬 3D genome & RNA lovers Group Leader at Center for Human Technologies, Italian Institute of Technology | CDA @ArmeniseHarvard

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Reposted by Irene Farabella
Rob Klose @robklose.bsky.social · 30/09/2026
Come join us April 2027 for the next instalment of the EMBL Chromatin and Epigenetics meeting. Great invited speakers and lots of talks selected from abstracts! It will be a fantastic meeting (despite the egregious nucleosome images...)
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Anders Sejr Hansen @andersshansen.bsky.social · 28/09/2026
Very nice new paper from Paggi, Long, Zhang using physical modeling of RCMC data to reconstruct physical structures of euchromatin at the nucleosome scale: Euchromatin forms condensed domains and E-P interactions largely occur on the surface! www.nature.com/articles/s41...
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Daniel Jost - Physical Biology of Chromatin group @djost-physbiol.bsky.social · 21/09/2026
Look at this masterpiece from @aurelepiazza.bsky.social lab. Happy to have been part of this story. Congrats to all the team !
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Nezar Abdennur @nvictus.bsky.social · 19/09/2026
The 4DN Center for 3D Structure and Physics of the Genome proudly presents: "Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation". www.biorxiv.org/content/10.6...
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Molecular Cell @cp-molcell.bsky.social · 18/09/2026
HoT auto-blinking probes enable real-time, super-resolution chromatin imaging in live cells and tissues
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HoT auto-blinking probes enable real-time, super-resolution chromatin imaging in live cells and tissues
Wang et al. introduce HoTs, self-blinking DNA probes for live-cell super-resolution chromatin imaging. Compatible with both STORM and MINFLUX microscopy, HoTs capture chromatin organization across live cells, animal tissues, and clinical tumor samples, opening new opportunities for studying genome architecture in health and disease.
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Anders Sejr Hansen @andersshansen.bsky.social · 07/09/2026
Enhancer–promoter proximity predicts transcriptional competence but not transcriptional output in the Drosophila brain arxiv.org/pdf/2609.03058
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Philippe Batut @philippebatut.bsky.social · 10/09/2026
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇
science.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 08/09/2026
Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)
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Weizmann Institute of Science @weizmann.ac.il · 31/08/2026
We, the Weizmann Institute of Science community, deeply mourn the passing of Prof. Ada Yonath - Nobel Laureate and a Model of Scientific Perseverance. May her memory be a blessing. bit.ly/ada-yonath-eng
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Job Dekker @jobdekker.bsky.social · 24/08/2026
How do nuclear compartments form inside cell nuclei? We show RNA glues certain loci together to form a nuclear compartment. This involves special GC-rich regions of highly expressed genes that also associate with nuclear speckles, but interactions between these loci are independent of speckles!
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Teif lab @teiflab.bsky.social · 26/07/2026
Woolfe et al, 2026. Decoding the mystery of ultra-conservation in developmental enhancers: a role for nucleosome positioning, DNA structure and transcription factor binding www.biorxiv.org/content/10.6... ▶️conserved non-coding elements ... favor nucleosome occupancy at their borders
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Anders Sejr Hansen @andersshansen.bsky.social · 25/07/2026
Very interesting study showing that active non-equilibrium fluctuations are required to explain chromatin organization at the 10-100kb scale:
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Valentina Baderna @valentinabaderna.bsky.social · 08/04/2025
Happy to share the latest story from @arnaudkr.bsky.social's lab @embl.org! With @guidobarzaghi.bsky.social, we used Single Molecule Footprinting to quantify how often chromatin is accessible at enhancers after TF and chromatin environment changes! Check our preprint bit.ly/3XQMFxN + thread ⬇️ 1/11
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Guido Barzaghi @guidobarzaghi.bsky.social · 11/08/2026
📄 That's a wrap 📄 we're excited to share that the latest from @arnaudkr.bsky.social 's lab and Judith Zaugg's lab is at last online at doi.org/10.1038/s415.... Many thanks to my co-first @valentinabaderna.bsky.social and to @embl.org for the wonderful research environment.
doi.org
Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency - Nature Genetics
This study uses single-molecule footprinting to quantify chromatin accessibility at enhancers and promoters in mouse embryonic stem cells and to dissect the contributions of transcription factor bindi...
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Marc A. Marti-Renom @mamartirenom.bsky.social · 08/08/2026
🚨the latest from the lab! 😃👇🏻 www.science.org/doi/10.1126/...
science.org
3D genome organization in tissue regeneration involves long-range chromatin loops
Chromosome conformation analysis in Drosophila wing discs reveals the requirement of specific meta-loops during regeneration.
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
Our latest is now out in @nataging.nature.com giving reason to celebrate! Led by talented Spiros Palikyras, it improves our preprint (posted 2 years ago!) dissecting the mechanism and functional consequences of CTCF clustering upon senescence commitment of human cells. www.nature.com/articles/s43...
nature.com
Senescent cells cluster CTCF on nuclear speckles to instruct an alternative splicing program - Nature Aging
Palikyras and colleagues investigate chromatin reorganization upon senescence induction, reporting that components of nuclear speckles coordinate chromatin rewiring and a senescence-associated splicin...
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Anders Sejr Hansen @andersshansen.bsky.social · 23/07/2026
Masahiro and I were fortunate to contribute some RCMC analyses to this beautiful paper from Koska and Wysocka that comprehensively dissects the determinants of promoter competition: www.nature.com/articles/s41...
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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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Elzo de Wit lab @ NKI @dewitlab.bsky.social · 06/07/2026
(1/10) The majority of human genetic variation is located in non-coding regions. The great challenge of the post-genomic era is to assign function to these variants. We reasoned that combining haplotyping with allele-specific multiomics can help pinpoint the functional ones: rdcu.be/fgr5W. A thread:
rdcu.be
Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning
Nature Communications - How non-coding mutations in DNA contribute to phenotypes is a largely unresolved question. Here the authors integrate personal genomics and machine learning to identify...
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Peter Ly @peterlylab.bsky.social · 19/05/2026
Excited to share our latest paper! We found that large pieces of the human genome can transfer between cells upon direct contact, endowing recipient cells with heritable phenotypic changes. @cp-cell.bsky.social (1/7) www.cell.com/cell/fulltex...
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Jorge Trojanowski @jorgetrojanowski.bsky.social · 27/04/2026
1/ ProPER - Our novel ligation-free proximity detection method for efficient multiplexed imaging of molecular interactions in situ. Among other things we use it to image the life cycle of RNA molecules and resolve differential kinetics of gene expression steps. New preprint: doi.org/10.64898/202...
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 13/05/2026
Our preprint on how variant U1 snRNAs control transcriptional and splicing homeostasis of hiPSCs is now officially out in @natcomms.nature.com and accessible via this link: www.nature.com/articles/s41... This has been the culmination of our work as part of the SPP1935 program funded by @dfg.de 1/n
nature.com
Variant U1 snRNAs contribute to cell cycle and differentiation control of human iPS cells - Nature Communications
Stem cell identity and differentiation require precise gene regulation, yet key regulatory components remain poorly understood. Here, the authors show that variant U1 snRNAs have distinct and essentia...
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Heilemann Lab @heilemannlab.bsky.social · 28/11/2025
We developed a 'smart STED microscope' to detect rare objects/events in cells, and unraveled the 3D morphology of a nuclear membraneless organelle (paraspeckle). Amazing collaboration with Sjoerd Stallinga, Bernd Rieger (TU Delft) and @mixmue.bsky.social 🙏 (1/3) www.nature.com/articles/s41...
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Daniel Jost - Physical Biology of Chromatin group @djost-physbiol.bsky.social · 23/12/2025
🚨Our work on the impact of DNA replication on 3D genome is out in Genome Biology: replication-dependent loop extrusion by sister-forks, wave of replication, no evidence for large-scale replication factory. Great collab with @aurelepiazza.bsky.social. More here: link.springer.com/article/10.1...
link.springer.com
Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes - Genome Biology
Genome Biology - Although significant progress has been made in our understanding of DNA replication and spatial chromosome organization in eukaryotes, how they interplay remains elusive. In...
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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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Job Dekker @jobdekker.bsky.social · 22/12/2025
Exciting new paper out! @allanaschooley.bsky.social and Sergey Venev led this project that let to the discovery of two chromosome folding programs: one inherited via mitotic chromosomes and one mitotic inherited through the cytoplasm! www.nature.com/articles/s41...
nature.com
Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm - Nature Cell Biology
Schooley et al. find that mitotically bookmarked loci drive a transient chromosome folding state during G1 entry that is subsequently modulated by factors inherited through the cytoplasm.
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BioExcel CoE @bioexcelcoe.bsky.social · 12/09/2025
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
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Eric Joyce @ericjoyce.bsky.social · 14/08/2025
🚨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...
biorxiv.org
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 ...
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Molecular Systems Biology @molsystbiol.org · 15/05/2025
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....
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Siyuan (Steven) Wang @sstevenwang.bsky.social · 19/08/2025
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
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Ting Wu Lab @tingwu-lab.bsky.social · 13/08/2025
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.
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Guy Nir @guynir.bsky.social · 16/06/2025
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...
biorxiv.org
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EMBL @embl.org · 01/08/2025
🌐 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...
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
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Eileen Furlong @eileen-furlong.bsky.social · 30/07/2025
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...
embl.wd103.myworkdayjobs.com
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...
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ME Torres-Padilla @metorrespadilla.bsky.social · 12/06/2025
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 :) 🙂
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Nature Methods @natmethods.nature.com · 29/04/2025
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...
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Lars Velten @larsplus.bsky.social · 08/05/2025
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... 🧵
cell.com
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...
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Irene Farabella @iosonoirene.bsky.social · 08/05/2025
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 👏🏻👏🏻
expeciallyianakim.bsky.social
Bluesky
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Nature Methods @natmethods.nature.com · 11/04/2025
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...
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Nature Methods @natmethods.nature.com · 11/04/2025
Read the News & Views highlighting this cool work here! www.nature.com/articles/s41...
nature.com
Pooled CRISPR screening with optical sequencing reveals regulators of 3D chromatin organization - Nature Methods
The Perturb-Tracing approach represents a significant step forward in our ability to perform pooled loss-of-function perturbations to identify regulators of 3D genome organization across multiple leng...
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Irene Farabella @iosonoirene.bsky.social · 12/04/2025
Bravo to all !! Definitely in my reading list for the weekend !!
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Job Dekker @jobdekker.bsky.social · 11/04/2025
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:
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Marc A. Marti-Renom @mamartirenom.bsky.social · 08/04/2025
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
cnag.eu
PhD Student - Structural Genomics Team (HoloGen Project) | CNAG, Centro Nacional de Análisis Genómico
MPORTANT MOBILITY RULE FOR THIS POSITION The MSCA mobility rule applies to this position: the applicant must not have resided or carried out their main activity (e.g., studies, work, research) in Spai...
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Maya Voichek @mayavoichek.bsky.social · 17/03/2025
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 🧵👇
Drosophila follicle showing retrotransposons (pink & yellow) expressed in somatic cells infecting the oocyte
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Irene Farabella @iosonoirene.bsky.social · 02/04/2025
Just apply! Amazing Lab ☺️
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Marc A. Marti-Renom @mamartirenom.bsky.social · 29/03/2025
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
cnag.eu
PhD Student - Structural Genomics Team (HoloGen Project) | CNAG, Centro Nacional de Análisis Genómico
MPORTANT MOBILITY RULE FOR THIS POSITION The MSCA mobility rule applies to this position: the applicant must not have resided or carried out their main activity (e.g., studies, work, research) in Spai...
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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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EMBL Events @events.embl.org · 01/04/2025
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
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Irene Farabella @iosonoirene.bsky.social · 01/04/2025
🧬 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
tinyurl.com
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...
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