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Yasemin Baris

@yaseminbaris1.bsky.social
395 followers 351 following 3 posts

Wellcome Trust Early Career Fellow @The Francis Crick Institute @Yardimci_Lab I Ph.D. @MRC_LMB @Yeeles_Lab @Cambridge_Uni / DNA replication &replication stress enthusiast 🧬

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Reposted by Yasemin Baris
Achilles Kapanidis @achilleskap.bsky.social · 13/10/2026
Super-excited 🤪 for SPIN-seq! Congrats to Jagadish, Becky, and team! We link the worlds of single-molecule kinetics 🔬 and single-molecule sequencing 🧬 - on the *same* single molecules, surface and instrument! Single-molecule phenotyping + in situ sequencing = SPIN-Seq. www.nature.com/articles/s41...
nature.com
Unraveling single-molecule reactions via multiplexed in-situ DNA sequencing - Nature Communications
The authors develop SPIN-Seq, a method that directly links the sequence of individual DNA molecules to their functional behavior, revealing how DNA sequence impacts protein-DNA interactions and the ki...
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Reposted by Yasemin Baris
Lopes_Lab @lopeslab.bsky.social · 25/09/2026
Working with a great team to organize @keystoneSymposia.bsky.social DNA Replication: Pathway Crosstalk Shaping Physiology and Disease, this April! Join us to explore emerging research in London! keysym.us/KSDNA27 #KSDNA27
keysym.us
DNA Replication: Pathway Crosstalk Shaping Physiology and Disease | Keystone Symposia
Join us at the Keystone Symposia on DNA Replication: Pathway Crosstalk Shaping Physiology and Disease, April 2027, in London, with field leaders!
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Reposted by Yasemin Baris
Lopes_Lab @lopeslab.bsky.social · 16/09/2026
Thrilled to share a new important study from the lab, published today in @nature.com, showing how cohesin mediates efficient replication fork plasticity and stress response, using its loop extrusion activity to promote 3D contacts on replicating DNA: www.nature.com/articles/s41...
nature.com
Cohesin reshapes replication fork contacts to aid fork slowing and reversal - Nature
Cohesin-mediated loop extrusion limits sister-fork coupling and tethers nearby replication forks under replication stress, promoting fork reversal and slowing fork progression to safeguard genome...
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Reposted by Yasemin Baris
Sami Chaaban @sami-c.bsky.social · 10/09/2026
Excited to share that the Chaaban Lab will be opening in January at the Crick!
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Reposted by Yasemin Baris
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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Reposted by Yasemin Baris
The EMBO Journal @embojournal.org · 27/08/2026
Do chemotherapeutic nucleoside analogues inhibiting isolated DNA polymerase also act on whole replisomes? @harryorrin.bsky.social & @yeeles-lab.bsky.social reveal tolerance via replisome plasticity, with lagging-strand Pol δ taking over leading strand synthesis link.springer.com/article/10.1...
link.springer.com
Response of the replisome to araA and araC suggests a mechanism for arabinosyl nucleoside tolerance - The EMBO Journal
Arabinosyl (ara) nucleoside analogues such as vidarabine (araA) and cytarabine (araC) are antimetabolites known to inhibit DNA polymerases in isolation. However, their effects on DNA synthesis catalys...
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Reposted by Yasemin Baris
MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 27/08/2026
Kelly Nguyen, Group Leader in the LMB’s Structural Studies Division, has been awarded the 2027 Francis Crick Medal and Lecture from @royalsociety.org. Read more about @kellythd-nguyen.bsky.social’s research on telomerase here: mrclmb.ac.uk/news-events/... #LMBNews
Kelly Nguyen, smiling with a blurred background
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Reposted by Yasemin Baris
Hasan Yardimci @hyardimci.bsky.social · 20/08/2026
Delighted to share our latest publication, a collaborative work with @hanasedlackova.bsky.social and @puckknipscheer.bsky.social. Grateful to everyone who contributed to this project. www.cell.com/cell-reports...
cell.com
FANCJ and RTEL1 facilitate pre-replication complex disassembly following replisome collision
Cameron et al. show that dormant pre-replication complexes are removed upon collision with replication forks in Xenopus egg extracts. They identify FANCJ and RTEL1 as key factors in this process and s...
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Reposted by Yasemin Baris
Basil Greber @bjgreber.bsky.social · 24/07/2026
Happy that our most recent paper on nucleotide excision repair mechanisms has now been published in Science Advances. This project was led by @natalia-mg.bsky.social and @callumhaste.bsky.social and focused on visualising early steps of the NER process by #cryoEM. www.science.org/doi/10.1126/...
science.org
Visualization of stepwise derepression of TFIIH in global genome nucleotide excision repair
Cryogenic electron microscopy captures nucleotide excision repair complexes assembling on damaged DNA templates.
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Nitika Taneja @TanejaLab @nitikataneja.bsky.social · 01/07/2026
Very excited to share our new Nature study! We discovered that replication stress stabilizes CTCF-dependent chromatin loops enclosing stressed nascent DNA, where G9a-mediated heterochromatin protects it from nucleolytic degradation. rdcu.be/frzLg Huge thanks to all our collaborators and co-authors!
nature.com
Replication-stress-induced chromatin loops protect fork stability - Nature
Replication stress induces the formation of transient chromatin loops that enclose de novo heterochromatin-enriched stalled replication forks.
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Reposted by Yasemin Baris
David Dulin @dulinlab.bsky.social · 20/06/2026
Copy-back RNA synthesis by coronavirus polymerase requires helicase activity and is stimulated by remdesivir and molnupiravir | Science Advances www.science.org/doi/10.1126/... #Coronavirus #SARS2 #COVID19 #singlemolecule #biophysics #magnetictweezers
science.org
Copy-back RNA synthesis by coronavirus polymerase requires helicase activity and is stimulated by remdesivir and molnupiravir
Helicase-driven copy-back RNA synthesis in coronaviruses reveals how antivirals trap replication intermediates.
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Reposted by Yasemin Baris
James Dewar @jamesmdewar.bsky.social · 28/05/2026
🧬 ⛓️‍💥 Our paper is now out in @natsmb.nature.com ! We examined the fate of replication forks that collapse at single-strand DNA breaks (SSBs) in vertebrates 🐸, comparing the consequences of collapse at single vs convergent forks. www.nature.com/articles/s41...
nature.com
Distinct repair outcomes from single and convergent replication fork collapse - Nature Structural & Molecular Biology
Here the authors show that collapse of single replication forks causes recombination, end fusions or degradation but does not restart DNA synthesis. In contrast, collapse of convergent forks completes...
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Julian Sale @juliansalelab.bsky.social · 02/04/2026
A really terrific opportunity to work in a very exciting group. Strongly recommended! 👇
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Kumar Somyajit & Lab @ksomyajit.bsky.social · 29/01/2026
Dear Colleagues, Delighted to share that our first lab paper is now published in Nature.!!! 😊😊😊 We identify a previously concealed “safety limit” in DNA replication program: cells intrinsically rate-limit PCNA via PAF15, shaping strand-specific and global replication dynamics. 👉 rdcu.be/e1bBt
rdcu.be
PAF15–PCNA exhaustion governs the strand-specific control of DNA replication
Nature - PCNA–PAF15 has a key role in determining replisome dynamics during genome replication and protecting against genome instability.
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Reposted by Yasemin Baris
Hasan Yardimci @hyardimci.bsky.social · 25/11/2025
We are recruiting a postdoctoral fellow to study mechanisms of DNA replication stress using single-molecule imaging tools. If you are excited about microscopy, replisome dynamics, and genome stability, we’d love to hear from you. Application deadline: 24 December www.crick.ac.uk/careers-stud...
crick.ac.uk
Postdoctoral Fellow - H Yardimci Lab
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Reposted by Yasemin Baris
Ernst Schmid @ernstschmid.bsky.social · 12/11/2025
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
biorxiv.org
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
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Ci Ji (CJ) Lim @cijilim.bsky.social · 30/10/2025
Our paper in Science is out! @souravagrawal.bsky.social, @rlynn.bsky.social, @susvirkar.bsky.social, and the rest of the team show human RPA is a telomerase processivity factor essential for telomere maintenance. This reshapes our thinking about telomerase regulation. www.science.org/doi/10.1126/...
science.org
Human RPA is an essential telomerase processivity factor for maintaining telomeres
Telomerase counteracts telomere shortening by repeatedly adding DNA repeats to chromosome ends. We identified the replication protein A (RPA) heterotrimer as a telomerase processivity factor critical ...
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Morgan Jones @04mjone.bsky.social · 14/10/2025
An enormous thanks to @wellcometrust and everyone who’s helped along the way 📢 PhD position open now 🎓– apply here 👉 www.bioch.ox.ac.uk/supervisors-... 🧪 Postdoc adverts coming 2026!
bioch.ox.ac.uk
Supervisors and Projects
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Reposted by Yasemin Baris
Achilles Kapanidis @achilleskap.bsky.social · 16/09/2025
What controls how/when growing RNA unblocks the "door" to exit RNA polymerase? Brilliant duo Anna Wang and Abhishek Majumder led a study in my lab - now out in NAR - on this. *Sequence* matters a lot! Read on... Super smFRET/dynamics work as well. Excited! academic.oup.com/nar/article/...
academic.oup.com
The displacement of the σ70 finger in initial transcription is highly heterogeneous and promoter-dependent
Abstract. Most bacterial sigma factors (σ) contain a highly conserved structural module, the ‘σ-finger’, which forms a loop that protrudes towards the RNA
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Reposted by Yasemin Baris
Aga Gambus @agagambus.bsky.social · 11/07/2025
Very exciting new technology manuscript from @alicepyne.bsky.social lab! High-res AFM + AI pipeline quantifies complex DNA topology. t.co/qxD7o7ASl6 Very happy to contribute with @singlemoleculenev.bsky.social plasmids replicating past barriers in Xenopus egg extract. Congratulation everyone!
t.co
https://doi.org/10.1038/s41467-025-60559-x
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Reposted by Yasemin Baris
Aga Gambus @agagambus.bsky.social · 10/07/2025
It is finally out 👍😀. Great job of the team (mostly absent from Bsky) and @m-saponaro.bsky.social CDK-driven phosphorylation of TRAIP is essential for mitotic replisome disassembly and MiDAS url: academic.oup.com/nar/article/...
academic.oup.com
CDK-driven phosphorylation of TRAIP is essential for mitotic replisome disassembly and MiDAS
Abstract. Disassembly of the replication machinery (replisome) from chromatin is an active process driven by two ubiquitin ligases Cul2LRR1 and TRAIP, whic
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Reposted by Yasemin Baris
Alessandro Costa @costalaboratory.bsky.social · 20/06/2025
Postdoc positions open in my lab (Francis Crick Institute) to study 1. initiation of DNA replication. 2. chromatin replication/epigenetic inheritance. Great for biochemists, biophysicists and cryo-EM/cryo-tomography scientists. Deadline 3 August 2025. crick.wd3.myworkdayjobs.com/External/job...
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Reposted by Yasemin Baris
Andreas Panagopoulos @apanagopoulos.bsky.social · 21/05/2025
Delighted to share that the results of my main postdoc project are now published in @nature.com 🔗 doi.org/10.1038/s415...
doi.org
Multigenerational cell tracking of DNA replication and heritable DNA damage - Nature
A multigenerational single-cell tracking approach provides a framework to dissect phenotypic plasticity at the single-cell level, offering insights into cellular processes that may resemble early even...
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Yasemin Baris @yaseminbaris1.bsky.social · 06/04/2025
Amazing work!
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Lucas Farnung @lucas.farnunglab.com · 06/04/2025
🔬 New from the Farnung Lab: We established a fully in vitro reconstituted chromatin replication system and report the first cryo-EM snapshots of the human replisome engaging nucleosomes. Brilliant work by @felixsteinruecke.bsky.social with support from @jonmarkert.bsky.social! tinyurl.com/replisome
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Andrew Deans @genomestability.bsky.social · 04/04/2025
I ❤️ this new paper on RAD52 at replication forks, just published @nature.com. Cryo-EM reveals a unique double-ring structure that blocks reversal of replication forks. www.nature.com/articles/s41...
nature.com
The RAD52 double-ring remodels replication forks restricting fork reversal - Nature
A head-to-head double-ring complex of the human multifunctional DNA repair protein RAD52 mediates protection of stalled replication forks during replication stress, protecting them from reversal by SM...
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Reposted by Yasemin Baris
Ellenberg Lab @ellenberglab.bsky.social · 24/03/2025
Our new findings on how chromosomes get ready for cell division are now published in @cellpress.bsky.social! Congratulations, Kai, @andibrunner.bsky.social and everyone else involved! 🤩 www.sciencedirect.com/science/arti...
sciencedirect.com
Nanoscale DNA tracing reveals the self-organization mechanism of mitotic chromosomes
How genomic DNA is folded during cell division to form the characteristic rod-shaped mitotic chromosomes essential for faithful genome inheritance is …
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Reposted by Yasemin Baris
Lopes_Lab @lopeslab.bsky.social · 17/03/2025
Exciting seminar series from Genome integrity italian Network (GiiN), chaired by myself and Raffaella Di Micco! Short talks (2x30’), at convenient time for EU/USA attendees. Big shots and raising stars in an expanding field. See flyers + link to receive email alerts. Please repost to your network!👇
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James Dewar @jamesmdewar.bsky.social · 10/03/2025
🧬⛓️‍ Our latest preprint examines the fate of collapsed forks in vertebrates 🐸 and our colleagues in @heathmurraylab.bsky.social asked similar questions in bacteria 🦠 to reveal how evolution shapes the response to fork collapse (see🧵) www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...
biorxiv.org
Resolution of collapsed forks is separate from completion of DNA synthesis
Replication fork collapse at single-strand DNA breaks (SSBs) poses a serious threat to genome stability. Using Xenopus egg extracts, we show that a replication fork encountering an SSB on either the l...
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Reposted by Yasemin Baris
Dirk Remus @dirkremus.bsky.social · 06/03/2025
How do replisomes walk on DNA? And what happens when they run into a G-quadruplex? @sahilbatra.bsky.social and @benallwein.bsky.social provide unexpected insight in our latest paper with Richard Hite @mskcancercenter.bsky.social @science.org www.science.org/doi/10.1126/.... Congrats to all authors!
science.org
G-quadruplex–stalled eukaryotic replisome structure reveals helical inchworm DNA translocation
DNA G-quadruplexes (G4s) are non–B-form DNA secondary structures that threaten genome stability by impeding DNA replication. To elucidate how G4s induce replication fork arrest, we characterized fork ...
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Reposted by Yasemin Baris
Hasan Yardimci @hyardimci.bsky.social · 04/03/2025
A new PhD position is available in my lab to explore DNA replication mechanisms using single-molecule approaches. Apply by 19th of March: www.crick.ac.uk/careers-stud...
crick.ac.uk
Yardimci Lab | Single-molecule visualisation of the eukaryotic replication machinery
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GIIN @genomeiinetwork.bsky.social · 03/03/2025
It's time for a new exciting GIIN webinar!🧬 Tomorrow @cejkalab.bsky.social and @spanier55.bsky.social will showcase their works. Join the GIIN community tomorrow (March 4th) from 5 PM (Rome time) on Zoom uniroma1.zoom.us/j/95149984403
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Anja Groth @groth-anja.bsky.social · 26/02/2025
SAVE THE DATE! The next EMBO | EMBL Symposium on 'DNA replication and genome maintenance: from basic biology to disease' will be held October 20-23, 2026.   Organized by Helle Ulrich (IMB), Johannes Walter (Harvard) and Anja Groth (Danish Cancer Institute). www.embl.org/about/info/c...
embl.org
DNA replication and genome maintenance: from basic biology to disease
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Yasemin Baris @yaseminbaris1.bsky.social · 19/02/2025
Beautiful work!
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Reposted by Yasemin Baris
Clausen Lab @clausenlab.bsky.social · 29/01/2025
scary but fascinating - cells have a degradation pathway that hunts down C-terminal scars (amides!) on damaged proteins. just wow. chemical biology plus CRISPR at its best. big congrats to all authors! www.nature.com/articles/s41...
nature.com
C-terminal amides mark proteins for degradation via SCF–FBXO31 - Nature
SCF–FBXO31 scans proteins for C-terminal amidation and marks them for subsequent proteasomal degradation.
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FragileNucleosome @fnucleosome.bsky.social · 27/01/2025
The first seminar of 2025 is only 2 days away! Have you registered yet? us06web.zoom.us/webinar/regi...
us06web.zoom.us
Welcome! You are invited to join a webinar: Fragile Nucleosome. After registering, you will receive a confirmation email about joining the webinar.
Welcome! You are invited to join a webinar: Fragile Nucleosome. After registering, you will receive a confirmation email about joining the webinar.
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Reposted by Yasemin Baris
Nynke Dekker Lab @nynkedekkerlab.bsky.social · 12/12/2024
Opening for a senior postdoc in our single-molecule DNA replication lab! Deadline January 15, 2025!
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Reposted by Yasemin Baris
Ana Tufegdzic Vidakovic @anatv.bsky.social · 11/12/2024
The first paper from our lab is online! A wonderful collaboration with @scottbscience.bsky.social lab. We discover that Pol II is extensively regulated by Ubiquitin at the beginning of the transcription cycle! www.cell.com/molecular-ce...
cell.com
CRL3ARMC5 ubiquitin ligase and Integrator phosphatase form parallel mechanisms to control early stages of RNA Pol II transcription
Cacioppo, Gillis, Shlamovitz, Zeller, et al. show that CRL3ARMC5 ubiquitylates RNA Pol II at early stages of transcription as part of a major homeostatic RNA Pol II turnover mechanism. CRL3ARMC5 and the Integrator phosphatase act as complementary pathways, monitoring the quantity and quality of RNA Pol II complexes before they are licensed into elongation.
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Tatiana Moiseeva @tat1anamoiseeva.bsky.social · 04/12/2024
Awesome paper, I think the authors are not on Bluesky yet
nature.com
Multiple mechanisms for licensing human replication origins
Nature - Biochemical and structural studies of the loading pathway of the human MCM2–7 replicative helicase motor reveal differences from the orthologous yeast system that may increase...
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Alessandro Costa @costalaboratory.bsky.social · 27/11/2024
Our article "MCM double hexamer loading visualized with human proteins" published in Nature today! ❄️🔬🧬🎉🥳 Great collaboration with John Diffley's lab. Congratulations to Florian Weissmann, Julia Greiwe and all other authors! rdcu.be/d1F7m
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