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Ilya Flyamer

@phlya.bsky.social
795 followers 273 following 52 posts

Postdoc in Luca Giorgetti lab, FMI Chromatin, Hi-C, gene regulation Co-organizer of Sci.STEPS mentoring program

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Reposted by Ilya Flyamer
Duncan Sproul @sproullab.bsky.social · 14/09/2026
🚨 #Postdoc position open. Want to understand non-canonical #epigenetic regulation of mammalian transcription? Come work @uoe-igc.bsky.social in Edinburgh! We’re looking for a motivated & collaborative colleague with a strong track record. 📅 14 October 2026 📢 Please share Apply here 👇
elxw.fa.em3.oraclecloud.com
Post-Doctoral Research Associate
An exciting postdoctoral position is available to research the role of epigenetic marks in gene regulation.
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Anton Goloborodko @golobor.bsky.social · 03/09/2026
1/ out in @science.org! We found a new asymmetry in large-scale chromosome structure: sister chromatids are shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! A close collaboration w/ @gerlichlab.bsky.social , led by @flaviacorsi.bsky.social www.science.org/doi/10.1126/...
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Ilya Flyamer @phlya.bsky.social · 02/09/2026
Huge congratulations, Marlies!🎉
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Reese Richardson @reeserichardson.bsky.social · 25/08/2026
A massive update: At least ~15 companies~ are selling scientists antibodies using faked validation data. We've documented 18,000+ manipulated images on 17,000+ products sold by leading laboratory suppliers including Thermo Fisher, Abcam, Santa Cruz Biotechnology, Millipore Sigma and Bio-Techne. 1/🧵
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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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Darío Lupiáñez @dariloops.bsky.social · 21/07/2026
🚨 Job Alert - Please share 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab at @cabd-upo-csic.bsky.social is expanding! ✅ 4 years fully funded PhD position 💻🧪 Experimental or computational backgrounds welcome 👇 Details below #PhDPosition #PhDOpportunity #AcademicJobs
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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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FMI science @fmiscience.bsky.social · 13/07/2026
📢 We’re hiring a Cloud Platform Engineer to drive FMI’s transition to a modern hybrid cloud architecture. Help build the infrastructure supporting 20 research groups, advanced technology platforms and large-scale biomedical data analysis. Apply by August 31 at www.fmi.ch/education-ca...
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Marieke Oudelaar @mariekeoudelaar.bsky.social · 07/07/2026
We are looking for someone to lead the new Facility for Protein Biochemistry & Biophysics at the MPI of Immunobiology and Epigenetics in Freiburg — please spread the word and apply if you are interested!
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Ilya Flyamer @phlya.bsky.social · 05/06/2026
This is appalling. Of course it's no surprise that many commercial antibodies are trash, but fake western blots at this scale are a new low, and from a company with such enormous resources.
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Ilya Flyamer @phlya.bsky.social · 28/05/2026
Congratulations Marieke! Happy for you and glad you'll be close by 😀
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Marieke Oudelaar @mariekeoudelaar.bsky.social · 26/05/2026
📣 Preprint alert! We developed a method to analyze concurrent interactions between multiple chromatin regions at single alleles at sub-nucleosome resolution (multi-way Micro-Capture-C, mwMCC) & used this to study structural synergy within super-enhancers. 1/14 www.biorxiv.org/content/10.6...
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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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Elias Friman @eliasfriman.bsky.social · 11/05/2026
Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/ www.biorxiv.org/content/10.6...
biorxiv.org
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bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 09/05/2026
Cohesin bridging as a physical principle of enhancer-promoter communication www.biorxiv.org/content/10.64898/20…
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Wendy Bickmore @wbickmor.bsky.social · 08/05/2026
Although cohesin-sensitive, long-range enhancer activation is equivalent in nature to proximal activation. Cooperativity can arise from different levels of activation inputs operating on a non-linear response function. @eliasfriman.bsky.social @uoe-igc.bsky.social www.biorxiv.org/content/10.6...
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Anton Goloborodko @golobor.bsky.social · 06/05/2026
how does loop extrusion and chromatid cohesion interact in interphase? Find out in our latest collaboration with Gerlich lab | | | vvv
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MC Gambetta @mcgambetta.bsky.social · 04/05/2026
Hello all, our lab is recruiting a PhD candidate to study how 3D genome folding impacts gene regulation in development. We're located at the Center for Integrative Genomics department of the University of Lausanne, Switzerland. Please email me if interested. #PhDPosition, #PhDOpportunity
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FMI science @fmiscience.bsky.social · 04/05/2026
Spread the word: We’re hiring a Director of Operations to lead scientific support at the FMI. This senior role enables cutting-edge research by partnering with scientists, overseeing technology platforms, ensuring safety & compliance, and representing the FMI externally: www.fmi.ch/education-ca...
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Max Planck Institute of Immunobiology and Epigenetics @mpi-ie.bsky.social · 27/03/2026
🚨 Postdoc in 3D genome architecture – join the @jumanaaha.bsky.social lab at the MPI-IE, Freiburg (🇩🇪) The wonderful lab of Jumana AlHaj Abed is pushing the limits of how chromosomes fold and interaction – and we need someone who can code, image, & think across scales. Apply here: s.gwdg.de/9c8838
Illustration of a fly and cellular structures connected by red and black thread-like lines inside a circle with a blue dot labeled 'TF' and text 'AlHaj Abed LAB' and 'Postdoctoral Researcher (m/w/d) Max Planck Institute of Immunobiology & Epigenetics'Text listing tasks in AlHaj Abed lab including Hi-C and Micro-C analysis, adapting multi-way contact genomic tools for Drosophila, building visualization framework for Pore-C data, image analysis, and programming in R and/or PythonText listing reasons to appreciate the Max Planck Institute in Freiburg including collaborative culture, core facilities, grants, scientific network, international diversity, public benefits, family support, relocation service, social life, and location, with a website linkLogo of the Max Planck Society; below text inviting to join the AlHaj Abed Lab with application deadline April 8, 2026, and a project website URL
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Ilya Flyamer @phlya.bsky.social · 25/03/2026
Partially it digests itself, what's left will be inactivated by high salt and/or ethanol washes. (Probably it's not even necessary and just direct SPRI bead purification would work, library prep is not so sensitive to some protein contaminants). I just prefer it over alcohol precipitation...
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Ilya Flyamer @phlya.bsky.social · 25/03/2026
Maybe just digest with ProtK and then AMPure beads? Unless you have very short fragments, at high ratio it should work well imo.
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Noura Maziak @nmaziak.bsky.social · 10/03/2026
Excited to share my PhD work! The question: How is genome organization established? Here, we developed a low-input Micro-C method, Pico-C, and used it to map chromatin architecture across early stages of fly development. Here’s a quick Blue-torial 🙂 (1/n) www.nature.com/articles/s41...
nature.com
Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila - Nature Genetics
Pico-C, a low-input Micro-C approach, reveals that dynamic three-dimensional genome folding precedes zygotic genome activation in Drosophila.
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Wendy Bickmore @wbickmor.bsky.social · 05/03/2026
Delighted to see this published: H3K115 acetylation is associated with fragile nucleosomes at CpG island promoters and active regulatory sites. Great work from all contributors; Yatendra Kumar, @illingworth-lab.bsky.social @eliasfriman.bsky.social @helink.bsky.social doi.org/10.7554/eLif...
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Darío Lupiáñez @dariloops.bsky.social · 06/03/2026
🚨 Job Alert - Please share! 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab at @cabd-upo-csic.bsky.social is expanding! We’re recruiting: ✅ PhD students ✅ Postdocs 💻🧪 Experimental or computational backgrounds welcome 👇 Details below
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Ilya Flyamer @phlya.bsky.social · 03/03/2026
Marimo? There is an extension for VS Code, I think it should work just like Jupyter notebooks in this regard... I have been meaning to set it up too, looks cool
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Claudia Keller Valsecchi @kellervalsecchi.bsky.social · 02/03/2026
Our Lab is searching a postdoc for an exciting ERC-funded project that will start this summer. Apply if you’re passionate about multi-omics, cutting-edge computational approaches, and exploring biological questions across the animal 🪼 🪱 🐞 🦎 🦋 🕷️ tree of life www.biozentrum.unibas.ch/open-positio...
biozentrum.unibas.ch
Postdoctoral Researcher (ERC-funded project)
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Ilya Flyamer @phlya.bsky.social · 24/02/2026
Congrats Noura! 🎉
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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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Job Dekker @jobdekker.bsky.social · 03/02/2026
Terrific paper on a new chromosomal compartment where extensive loop extrusion isolates domains from other such domains
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Aleksandra Galitsyna @agalicina.bsky.social · 26/01/2026
Have you wondered how the rules of chromatin folding have evolved? Well, this task is not easy to formalize. But here is our take on it: train species-specific DNA-to-chromatin encoder, apply to DNA of unseen species, and build chromatin rules-based tree of life. Have a look: doi.org/10.1093/nar/...
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Ilya Flyamer @phlya.bsky.social · 24/01/2026
That sounds amazing!
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Ilya Flyamer @phlya.bsky.social · 24/01/2026
Ah wow, I'm not a protein person, but that sounds easy😅 Thanks, I'll reach out if I decide to try it!
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Ilya Flyamer @phlya.bsky.social · 24/01/2026
Well, a while ago was a few months ago... So I doubt it. Actually in this paper there is a custom more convenient version
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Ilya Flyamer @phlya.bsky.social · 24/01/2026
Yeah I wanted to try this enzyme a while ago too, saw some papers using it for ChIP or something like that... but you have to purify it yourself😅 I wish it was available commercially, I would like to try it
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 20/01/2026
Would anyone out there be able to share some Mus Spretus DNA with us? 🐀🧬 Any tissue of origin, for PCR amplification of selected genomic regions. Many thanks in advance!
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Ilya Flyamer @phlya.bsky.social · 19/12/2025
In this specific paper there is a focus on two loci, one is I think >100kb. I offered you to try modeling this data many years ago😂
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Ilya Flyamer @phlya.bsky.social · 19/12/2025
Far!
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Ilya Flyamer @phlya.bsky.social · 19/12/2025
Nuclear hormone receptor enhancers activate gene expression within like 15 min, at this sort of distance... E.g. see here, but there is a ton of literature pubmed.ncbi.nlm.nih.gov/38781242/
pubmed.ncbi.nlm.nih.gov
Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity - PubMed
How enhancers regulate their target genes in the context of 3D chromatin organization is extensively studied and models which do not require direct enhancer-promoter contact have recently emerged. Here, we use the activation of estrogen receptor-dependent enhancers in a breast cancer cell line to st …
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Duncan Sproul @sproullab.bsky.social · 08/12/2025
🚨 Want to do a #Phd using high-throughput mutagenesis and CRISPR screens to understand how gene body methylation impacts transcription in collaboration with Greg Kudla's group? Do apply, deadline in a week! www.findaphd.com/phds/project... Deadline 15th December 2025 #epigenetics Please share 🙏
findaphd.com
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FMI science @fmiscience.bsky.social · 10/11/2025
📢 Last days to apply 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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Hannah Long @hannahlong.bsky.social · 10/11/2025
📣 Paper alert! I am delighted that our paper exploring the impact of Neanderthal-derived variants on the activity of a disease-associated craniofacial enhancer has been published in Development today! journals.biologists.com/dev/article/...
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Ilya Flyamer @phlya.bsky.social · 09/11/2025
Last chance to become a mentor in Sci.STEP, the call is about to close!
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Ilya Flyamer @phlya.bsky.social · 07/11/2025
Congrats Wendy and team! Great news!
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Ilya Flyamer @phlya.bsky.social · 24/10/2025
We are looking for mentors for the Sci.STEPS program! Please apply if you want to help your junior colleagues around the globe navigate their career path in any science related field.
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Ilya Flyamer @phlya.bsky.social · 24/10/2025
Hi Marc, "minutes" is correct :) The CTCF and cohesin mediated loops, at least measured in those studies, are very stable
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Mattia Ubertini @mattiaubertini.bsky.social · 25/09/2025
If you are curious about how cohesin regulates chromosome contact dynamics and its role in enhancer-promoter communication, check out our latest work. It’s been really fun to work with @nesslfy.bsky.social and @lucagiorgetti.bsky.social. Hope you enjoy reading it!
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 24/09/2025
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication. www.biorxiv.org/content/10.1... A🧵👇
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Ilya Flyamer @phlya.bsky.social · 04/09/2025
Congrats, Charlene, amazing news!
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