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xiuqichen.bsky.social

@xiuqichen.bsky.social
190 followers 316 following 50 posts

Postdoctoral researcher at TU Delft. Trying to sequence proteins with #nanopore

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xiuqichen.bsky.social @xiuqichen.bsky.social · 23/06/2026
😂 Good satire doesn't deviate far from reality. Prompt engineering is also engineering now ⚙️
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Nature Biotechnology @natbiotech.nature.com · 18/03/2026
Single-molecule peptide sequencing through reverse translation of peptides into DNA - @bioe-stanford.bsky.social go.nature.com/4sRPr2K
go.nature.com
Single-molecule peptide sequencing through reverse translation of peptides into DNA - Nature Biotechnology
Peptides are sequenced by converting each amino acid into amplifiable DNA barcodes.
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Current Biology @currentbiology.bsky.social · 04/02/2026
This is who runs this account
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Karolin Luger @nucleosomepolice.bsky.social · 03/02/2026
pdb101.rcsb.org/motm/314 histones outside of the eukaryotic domain are the 'molecule of the month'! nice!
pdb101.rcsb.org
PDB101: Molecule of the Month: Histones Across the Tree of Life
Uncovering the evolutionary diversity of histones
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Sonja Schmid @scisonja.bsky.social · 23/01/2026
WE ARE #HIRING: [reposting=👌 🙏 ] 2 funded positions for #nanopore related projects @unibas.ch 🇨🇭: 1️⃣ #PhD Candidate in Single-Molecule Biophysics using Nanopore Trapping. 2️⃣ #PhD Candidate in Microplastic Detection Using Micropores and Microfluidics. More info: schmid.chemie.unibas.ch/en/join-us-1/
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David Balchin @davidbalchin.bsky.social · 19/01/2026
Our latest cotranslational folding story is now published @cp-molcell.bsky.social. Really cool (I think) new ideas about how exactly the ribosome directs folding and assembly to make sure complicated proteins mature efficiently in cells. www.cell.com/molecular-ce...
cell.com
The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis
Large oligomeric proteins constitute a major fraction of proteomes, but are difficult to refold in vitro, raising the question of how cells direct their biogenesis. Roeselová and Shivakumaraswamy et a...
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xiuqichen.bsky.social @xiuqichen.bsky.social · 19/01/2026
Perceptions can be often misleading
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Cees Dekker @ceesdekker.bsky.social · 09/01/2026
Latest #CDlab paper on nanopore protein sequencing now published in JACS: pubs.acs.org/doi/full/10.... Here, Justas Ritmejeris, Xiuqi Chen, collaborator Bauke Albada, and me developed a conjugation chemistry strategy for nanopore sequencing of natural peptides!
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Alice Ting @aliceyting.bsky.social · 08/01/2026
Can we design mutations that bias proteins towards desired conformational states? Today in @science.org, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations.
science.org
Computational design of conformation-biasing mutations to alter protein functions
Conformational biasing (CB) is a rapid and streamlined computational method that uses contrastive scoring by inverse folding models to predict protein variants biased toward desired conformational sta...
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Tim @timisstuck.bsky.social · 23/12/2025
Giving the gift of negative data 🥰 Since I joined @lsajournal.org I have handled several stellar manuscripts that report null results. These papers do very well and reviewers almost always appreciate them! Thanks @rockefeller.edu news team for the article! www.rockefeller.edu/news/38829-t...
rockefeller.edu
The value of publishing negative data - News
Scientific journals love news-worthy results. Editors want to publish studies with novel data that scientists will eagerly read and cite in their own work. Because of this desire for novelty, studies ...
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xiuqichen.bsky.social @xiuqichen.bsky.social · 03/01/2026
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xiuqichen.bsky.social @xiuqichen.bsky.social · 18/12/2025
Quite unhinged format 🤯
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Job Dekker @jobdekker.bsky.social · 17/12/2025
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists! www.nature.com/articles/s41...
nature.com
An integrated view of the structure and function of the human 4D nucleome - Nature
The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...
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Cees Dekker @ceesdekker.bsky.social · 13/11/2025
Latest #CDlab paper on nanopore protein sequencing on @biorxivpreprint.bsky.social: www.biorxiv.org/cgi/content/... Here, Justas Ritmejeris, @xiuqichen.bsky.social, collaborator @albadalab.bsky.social and me developed a conjugation chemistry strategy for nanopore sequencing of natural peptides!
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Sonja Schmid @scisonja.bsky.social · 10/11/2025
I recently wrote a 1page "Highlight" article for the Swiss Journal @chimiajournal.bsky.social about the #single-molecule perspective on biomolecular dynamics and experiments: Beyond 3D Structures: New Ways to Study Biomolecular Gymnastics www.chimia.ch/chimia/artic...
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Albada Lab @albadalab.bsky.social · 10/11/2025
#paperalert Very happy to share our new paper in Chemical Science @chemicalscience.rsc.org Great work by Yuri Damen (now at BioChem in Oss), @joresfu.bsky.social, Judith Firet, and Han Zuilhof @w-u-r.bsky.social Especially for those of you who use strained alkynes in their click reactions!
pubs.rsc.org
Temperature–dependent reaction rates of quinone-alkene cycloaddition reveal that only entropy determines the rate of SPOCQ reactions
Second-order rate constants and thermodynamic activation parameters for the strain-promoted oxidation-controlled quinone (SPOCQ) click reaction of an ortho-quinone with various trans-cyclooctene and c...
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Cees Dekker @ceesdekker.bsky.social · 06/11/2025
I am thrilled with the news that our ERC Synergy proposal GeneMotors was granted!! This prestigious grant allows Leonid Mirny (MIT), Wendy Bickmore (Edinburgh), Benjamin Rowland (NKI) and me to study the DNA-looping SMC motors proteins that control our chromosomes in the next 6 years
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Svetlana Dodonova @dodonova-sveta.bsky.social · 28/10/2025
Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️ Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
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xiuqichen.bsky.social @xiuqichen.bsky.social · 28/10/2025
🤯
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xiuqichen.bsky.social @xiuqichen.bsky.social · 27/10/2025
Results from Nature’s 2025 global survey of more than 3,700 doctoral students: Supervisors who make a conscious effort to support and mentor their PhD candidates have more-satisfied students www.nature.com/articles/d41...
nature.com
What makes PhD students happy? Good supervision
Supervisors who invest in positive mentoring relationships with their PhD candidates also reap the benefits for their own research.
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Bob Johnston @bobbyjeyeguy.bsky.social · 21/10/2025
Check out our paper from @christ3na.bsky.social in G+D. DIO3, which degrades thyroid hormone/TH, is expressed in progenitors and turns off in neurons. As the progenitor:neuron ratio decreases, DIO3 decreases and TH increases, triggering photoreceptor generation. genesdev.cshlp.org/content/earl...
genesdev.cshlp.org
DIO3 coordinates photoreceptor development timing and fate stability in human retinal organoids
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
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Stephan Gruber @gruberlab.bsky.social · 09/10/2025
How do SMC complexes load onto DNA to get ready for loop extrusion? @roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸‍♂️🤸‍♂️🤸‍♂️. Check out the new paper: www.cell.com/molecular-ce...
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GIIN @genomeiinetwork.bsky.social · 30/09/2025
Next week GIIN webinar will feature @fmattiroli.bsky.social and Marco Tigano. Join us on Tuesday, October 7th at 5 PM Rome / 11 AM NYC via zoom: uniroma1.zoom.us/j/95149984403 Register here to become part of our community: docs.google.com/forms/d/e/1F...
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Francesca Mattiroli @fmattiroli.bsky.social · 28/09/2025
Join us at the Hubrecht Institute in Utrecht to start your research group! Fantastic scientific environment, strong support, and nice colleagues :) Apply and please share broadly in your network.
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Wei Chen @weichen2.bsky.social · 27/05/2025
Now published! Phosphorylation patterns modulate transient secondary structures of the intrinsically disordered CTD of RNA polymerase II www.sciencedirect.com/science/arti...
sciencedirect.com
Phosphorylation modulates secondary structure of intrinsically disorder regions in RNA polymerase II
The intrinsically disordered C-terminal domain (CTD) of RNA polymerase II contains tandem repeats with the consensus sequence YSPTSPS and coordinates …
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Nature Structural & Molecular Biology @natsmb.nature.com · 20/09/2025
ICYMI: New online: The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking
go.nature.com
The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking
Nature Structural & Molecular Biology, Published online: 19 September 2025; doi:10.1038/s41594-025-01676-5By studying dynamic folding intermediates on the human ribosome, Pellowe et al. show that newly made domains help each other to fold but do not stably interact until synthesis is complete, avoiding interdomain misfolding.
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FragileNucleosome @fnucleosome.bsky.social · 01/09/2025
We're super excited to announce the entire lineup for the Fall season of Fragile Nucleosome Seminars, starting on Sept 10th at 1200 EDT / 1600 UTC with @gracebower.bsky.social and @creminslab.bsky.social! register here for the entire series: us06web.zoom.us/webinar/regi...
Fragile Nucleosome Fall Seminars:
September 10    Grace Bower, Kvon Lab @ UC Irvine, USA
    Jennifer Phillips-Cremins, UPenn, USA

September 24    Ali Wilkening, Sanulli Lab @ Stanford, USA
    Juanma Schvartzman, Columbia University, USA

October 8    Sanim Rahman, Greenberg Lab @ UPenn, USA
    Alex Federation, Talus Bio, USA

October 22    Alice Laigle, Croll Lab @ University of Neuchâtel, Switzerland
    Seungsoo Kim, UC Irvine, USA

November 5    Hannah Long, University of Edinburgh, UK
    Jeff Vierstra, Altius Institute, USA

November 19    Ishtiaque Hossain, Pastor Lab @ McGill, Canada
    Sarah Teichmann, University of Cambridge, UK

December 3    María Mariner Faulí, Rada Iglesias Lab @ IBBTEC, Spain
    Jonathan Henninger, Carnegie Mellon, USA

December 17    Rebecca Berrens, Oxford University, UK
    Jean-Benoit Lalanne, University of Montreal, Canada
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Sonja Schmid @scisonja.bsky.social · 31/07/2025
💥 We have 3 positions open in my lab in Basel, Switzerland🇨🇭: #nanopores #smFRET #biomolecular #dynamics #singleMolecules We’re looking for talented & ambitious new colleagues enthusiastic about biomolecular dynamics & single-molecule tech. Please share broadly, thank you!🤝 schmid.chemie.unibas.ch
schmid.chemie.unibas.ch
Home | Research Group Schmid | University of Basel
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xiuqichen.bsky.social @xiuqichen.bsky.social · 22/08/2025
Open position in @ceesdekker.bsky.social lab! Apply if you are interested in nanopore sequencing!
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xiuqichen.bsky.social @xiuqichen.bsky.social · 13/08/2025
Come join us!
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Cees Dekker @ceesdekker.bsky.social · 13/08/2025
Building a synthetic cell together - nice common perspective written by many leading scientists who gathered in Shenzhen China for the inaugural ‘SynCell Global Summit’. Check it out in Nature Comm: www.nature.com/articles/s41...
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xiuqichen.bsky.social @xiuqichen.bsky.social · 12/08/2025
🏖️Back from an amazing vacation in 🌴Sanya🐟. Refreshed and recharged, ready to dive back to research!
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Cell Reports @cp-cellreports.bsky.social · 02/07/2025
Telomeres stall DNA loop extrusion by condensin
dlvr.it
Telomeres stall DNA loop extrusion by condensin
Analikwu et al. show that dense linear arrays of the telomeric protein Rap1 on DNA block DNA loop extrusion by condensin. Rap1-induced stalling depends on array length and protein density and leads to a local chromatin decompaction during anaphase, revealing how protein arrays can regulate SMC-driven genome organization.
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xiuqichen.bsky.social @xiuqichen.bsky.social · 24/07/2025
🤔 How do proteins fold while they're still being made? As the main project in my PhD, I developed "Arrest Peptide Profiling" to record proteins folding with as they emerge from ribosomes in living cells 🦠 - with single codon resolution! @natcomms.nature.com‬ 🧵 1/6 #ProteinFolding
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xiuqichen.bsky.social @xiuqichen.bsky.social · 21/07/2025
Really appreciate your support on this project @ceesdekker.bsky.social ! Excited to make new discoveries!
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Nature Structural & Molecular Biology @natsmb.nature.com · 21/07/2025
New online: Q&A with Francesca Mattiroli
go.nature.com
Q&A with Francesca Mattiroli
Nature Structural & Molecular Biology, Published online: 21 July 2025; doi:10.1038/s41594-025-01620-7Francesca Mattiroli leads a research group at the Hubrecht Institute in Utrecht in the Netherlands, delving into the dynamics of chromatin during DNA synthesis. Here we ask her about her research ethos, experience and interests.
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Microsoft Research @msftresearch.bsky.social · 10/07/2025
Today in the journal Science: BioEmu from Microsoft Research AI for Science. This generative deep learning method emulates protein equilibrium ensembles – key for understanding protein function at scale. www.science.org/doi/10.1126/...
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Cees Dekker @ceesdekker.bsky.social · 25/06/2025
Here's a new very exciting paper from our #CDlab: www.cell.com/cell-reports... In an exemplary in vitro/in vivo study, 1st authors ‪@btanalikwu.bsky.social‬ & Alice Deshayes showed that dense linear protein arrays (e.g. telomeres) do stop loop-extruding SMCs! Great collaboration with Marcand lab.
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Reuven Gordon @reuven-gordon.bsky.social · 28/05/2025
The energy landscape of a single disordered protein (tau) and the impact of PTMs is resolved. An important step to understanding the function and dysfunction of disordered proteins from their conformational ensemble. Not yet peer reviewed. www.biorxiv.org/content/10.1...
biorxiv.org
Direct observation of conformational dynamics of intrinsically disordered proteins at the single-molecule level
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) are integral to many biological processes, including neurotransmitter regulation, microtubule regulat...
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Magdalena Skipper @magdalenaskipper.bsky.social · 26/05/2025
“Research assistants, local collaborators & community partners, esp those from the Global South, are often seen as data collectors rather than co-creators of knowledge” A great piece on inclusive authorship & the need for flexibility @lseimpactblog.bsky.social blogs.lse.ac.uk/impactofsoci...
blogs.lse.ac.uk
Why restrictive academic authorship practices perpetuate inequality - Impact of Social Sciences
Authorship plays a central role in the credibility and career progression of academics. Yet as Joseph Mellors and Stroma Cole argue, restrictive authorship practices risk perpetuating inequalities and...
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Rafeeque Mavoor @rafeequemavoor.bsky.social · 13/05/2025
🧵5 Top Free Alternatives to BioRender for Scientific Illustrations! These five websites offer free scientific illustrations for biologists. Great for presentations, research papers and other research communication needs. Save and share the post!
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Francesca Mattiroli @fmattiroli.bsky.social · 04/05/2025
Want to learn more about chromatin and its dynamics? Read this review by Charlotte and Jolijn in our lab, aimed at giving an overview on this and the ways this is dealt with during transcription, replication and damage repair. Thanks to Biochemistry for inviting us! doi.org/10.1021/acs....
doi.org
Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes
Our genome is organized into chromatin, a dynamic and modular structure made of nucleosomes. Chromatin organization controls access to the DNA sequence, playing a fundamental role in cell identity and...
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Heng Li @lh3lh3.bsky.social · 18/04/2025
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
biorxiv.org
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...
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Sergio Cruz-León @sergiocruzleon.bsky.social · 11/04/2025
Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social, @marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social 🔗 Preprint here tinyurl.com/3a74uanv
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Zach Marin @zacsimile.bsky.social · 09/04/2025
MINFLUX works well in theory, but system and sample imperfections can lead to suboptimal resolution. To address this, @jonasries.bsky.social and I developed SimuFLUX: www.biorxiv.org/content/10.1..., a realistic simulator to optimize MINFLUX experiments before samples go on the microscope.
biorxiv.org
Evaluating MINFLUX experimental performance in silico
MINFLUX is a super-resolution microscopy technique with remarkable resolution for imaging and tracking. Its optical resolution is well understood under idealized conditions, but because of system comp...
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Gerry Wright @gdwantibiotics.bsky.social · 26/03/2025
The latest discovery from the lab and great colleagues at McMaster and U Illinois, Chicago. Lariocidin, a new lasso peptide antibiotic that inhibits the ribosome. rdcu.be/efdha
rdcu.be
A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome
Nature - A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common...
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Florent Waltz @florentwaltz.bsky.social · 21/03/2025
I'm super happy that our story is now published! 📖 www.science.org/doi/10.1126/... But what changed compared to the original preprint? Also, I feel i should post Movie 1 🎥, that inspired the cover. Back when I did the original bluesky thread, movies were not available.
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University of Basel @unibas.ch · 21/03/2025
A horse’s gallop was once a blur—until film revealed its rhythm. Sonja Schmid (@scisonja.bsky.social) draws a parallel to biomolecules: only by observing them one at a time can we understand their dynamics. Her team is developing a method using nanopores that let single molecules pass through.
unibas.ch
Molecules in full gallop.
An interdisciplinary team of scientists investigates how exactly individual biomolecules move around. One of the tricks the researchers use involves tiny pores that only allow one molecule to slip thr...
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evacide @evacide.bsky.social · 19/03/2025
If you're critical of the US government and you are planning to cross the US border any time soon, today is a good day to review EFF's border search pocket guide: www.eff.org/document/eff...
eff.org
EFF Border Search Pocket Guide
border-pocket-guide-2.pdf
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