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Dominika Borek

@dmborek.bsky.social
288 followers 917 following 16 posts

Scientist

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Reposted by Dominika Borek
Bodega Cats @bodegacats.bsky.social · 05/10/2026
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emilyriehl.bsky.social @emilyriehl.bsky.social · 25/09/2026
I was part of a group that met last week to try to propose recommended changes to the structure of math PhD programs in an age of AI. Our report, together with a collection of related resources, is now available here: cmsa.fas.harvard.edu/aimathphd_su...
cmsa.fas.harvard.edu
Summit on PhD Math Education in the Age of AI - CMSA
On September 17–18, 2026 a group of 24 mathematicians met at Harvard to grapple with the changing landscape for mathematics PhD programs in the age of AI. We produced recommendations given […]
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Structural Biology @actacrystd.iucr.org · 22/09/2026
SURFER is a lightweight, GPU-accelerated extension for UCSF ChimeraX that enables rapid semantic differentiation of membrane or membrane-mimic density from macromolecular signal #CryoEM #Segmentation #Membrane doi.org/10.1107/S205...
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American Society for Cell Biology @ascbiology.bsky.social · 11/08/2026
Congratulations to Matt Welch of UC Berkeley, recipient of the 2026 Sandra Masur Senior Leadership Award for outstanding scientific achievement and leadership in mentoring the next generation of scientists. www.ascb.org/society-news/ascb-anno…
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ContempraInn 🌹 @contemprainn.bsky.social · 08/08/2026
Hi it’s International Cat Day Today
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Lior Pachter @lpachter.bsky.social · 30/07/2026
One of the major pains of academia is having to click through labyrinths of webpages to submit papers. Now, thanks to Joe Rich (and AI), problem solved! His tool is called PaperPush and is available at github.com/pachterlab/p... It's super easy to use! 1/🧵
github.com
GitHub - pachterlab/paperpush
Contribute to pachterlab/paperpush development by creating an account on GitHub.
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Bodega Cats @bodegacats.bsky.social · 23/07/2026
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Ján Bíňovský @jbinovsky.bsky.social · 02/07/2026
🔥My first (co)first-author paper is out🔥 The surfaces of Gram+ and Gram- bacteria are markedly different from each other. How are phages equipped to breach the Gram+ envelope❓ 💡We report a baseplate structure uniquely adapted to infect Gram+ S. aureus. A 🧵⬇️ 1/8 #phagesky #cryoEM 🧪
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Arjen Jakobi @cryotud.bsky.social · 20/07/2026
The LocScale 2.0 and SURFER papers are now both published in final form. LocScale 2.0: www.nature.com/articles/s41... SURFER: onlinelibrary.wiley.com/iucr/doi/10.... Led by @alok-bharadwaj.bsky.social with contributions of former MSc/Bsc students Reinier de Bruin and Lotte Veerbeek.
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Bui Lab @McGill @builab.bsky.social · 20/07/2026
Interested in 3D-printed models of cryo-EM grids, autogrid and cryo-FIB for visual teaching/decoration. Download our model and print: makerworld.com/en/models/30... Designed in Blender by Khan Bao, an undergrad in the lab.
makerworld.com
Cryo-EM Grids for Teaching - Free 3D Print Model - MakerWorld
Download this free 3D print file designed by CiliaBuilder. EM Grid Scaled ModelScaled up and simplified 3D model of EM grids and autogrids for demonstration of preparation process and milling. Content...
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Shicheng Guo @shihcheng.bsky.social · 20/07/2026
Explore new insights! Cryo-EM reveals how S961 and Ins-AC-S2 disrupt insulin signaling by binding the receptor's site 1 and site 2, unlike S597, which activates it. PMID:42265100, Nat Commun 2026, @NatureComms doi.org/10.1038/s41467-026-73851-1 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
doi.org
Structural basis of insulin receptor antagonism by bivalent site 1-site 2 ligands S961 and Ins-AC-S2 | Nature Communications
Congenital hyperinsulinism is a rare genetic disease characterized by overproduction of insulin. One class of potential treatments is insulin receptor antagonists like S961 and Ins-AC-S2, which comprise segments for binding each of the two insulin-binding sites (site 1 and site 2) on the receptor. Notably, S597 – containing the same receptor binding segments as S961 but in the opposite order (site 2-site 1) – is an insulin receptor agonist rather than an antagonist. Using cryo-EM, we show how both S961 and Ins-AC-S2 bind an inactive conformation of the receptor, thereby explaining their antagonism. Furthermore, our structures reveal how agonist vs. antagonist activity is influenced by the order of site 1- and site 2-binding modules in bivalent ligands. Additionally, we show subtle differences between the receptor-binding mechanisms of S961 and Ins-AC-S2, which include displacement or engagement of αCT, and a binding interface between the Ins-AC-S2 insulin and the receptor FnIII-2/inser
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cryoEM papers @cryoempapers.bsky.social · 15/07/2026
Cryo-electron tomography reveals OmpB is required for the Rickettsia parkeri S-layer pubmed.ncbi.nlm.nih.gov/42441324/ #cryoEM
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Bodega Cats @bodegacats.bsky.social · 14/07/2026
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Bodega Cats @bodegacats.bsky.social · 13/07/2026
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Bodega Cats @bodegacats.bsky.social · 13/07/2026
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Bodega Cats @bodegacats.bsky.social · 03/07/2026
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Bodega Cats @bodegacats.bsky.social · 02/07/2026
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 27/06/2026
Part 2 may be of most use to experienced users of AlphaFold and related programs. It covers the origin of the AF scores in benchmarking protein structure prediction (GDT-TS, LDDT, TM score) and the AF versions of these scores (pLDDT, PAE, ipTM, ipSAE, LIS). www.youtube.com/watch?v=WW_X...
youtube.com
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 27/06/2026
I gave a workshop on AlphaFold & related programs @ the University of Utah. Part 1 covers protein structure prediction before/after AlphaFold & deep learning neural networks. Part 2 covers the math behind the scores. Part 3 covers PyMOL & the webservers. youtube.com/@rolanddunbr...
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Bodega Cats @bodegacats.bsky.social · 26/06/2026
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Wieczorek Lab @mike-wieczorek.bsky.social · 23/06/2026
New preprint! In collaboration with the Steinmetz Lab at PSI we report cryo-EM structures of microtubules at up to 1.9 Å (!) resolution & in different nucleotide state mimics, suggesting a mechanism for lattice-induced GTP hydrolysis and why it leads to catastrophe: tinyurl.com/7cjrf863
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Bodega Cats @bodegacats.bsky.social · 22/06/2026
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Bodega Cats @bodegacats.bsky.social · 17/06/2026
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Dominika Borek @dmborek.bsky.social · 16/06/2026
Cryo-electron tomography reveals OmpB is required for the Rickettsia parkeri S-layer doi.org/10.17912/mic...
doi.org
Cryo-electron tomography reveals OmpB is required for the Rickettsia parkeri S-layer | microPublication
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Dominika Borek @dmborek.bsky.social · 15/06/2026
New paper: www.nature.com/articles/s41... ! We finally get to see native chlamydial MOMP by cryo-EM: a trimer with three β-barrels topped by a folded antigenic cap. It is strange, beautiful, and full of clues for vaccine design. [1/5]
MOMP structure
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Bodega Cats @bodegacats.bsky.social · 11/06/2026
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Elias Spiliotis @septinlab.bsky.social · 05/06/2026
Sick!
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Bodega Cats @bodegacats.bsky.social · 04/06/2026
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Cedric Feschotte @cedricfeschotte.bsky.social · 29/05/2026
📣 POSTDOC position available in the Feschotte Lab at Cornell to work on #TRANSPOSONS! More details below. Pls send informal application or inquiry ASAP by DM or email to cf458_at_cornell.edu. Pls spread the word 🙏 #TEsky www.thefeschottelabatcornell.com
thefeschottelabatcornell.com
The Feschotte Lab at Cornell
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cryoEM papers @cryoempapers.bsky.social · 29/05/2026
Context matters: A view on metadata analysis in cryo-electron tomography pubmed.ncbi.nlm.nih.gov/42202749/ #cryoEM
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cryoEM papers @cryoempapers.bsky.social · 27/05/2026
The evolving role of structural biology in pharma: integration of X-ray crystallography, cryo-electron microscopy and beyond pubmed.ncbi.nlm.nih.gov/42189178/ #cryoEM
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Bodega Cats @bodegacats.bsky.social · 24/05/2026
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Molecular Cell @cp-molcell.bsky.social · 24/05/2026
Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis
dlvr.it
Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis
The roles of water molecules in transcription have long been overlooked due to resolution limitations. Li et al. resolve high-resolution cryo-EM structures of RNA polymerase II and visualize previously undetected water molecules. These waters play essential roles in RNA polymerase II catalysis and in mediating interactions within the transcription machinery.
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bioRxivpreprint @biorxivpreprint.bsky.social · 11/05/2026
A multi-species toolkit of TOP2 hypercleavage mutants for studying topoisomerase II-mediated DNA damage www.biorxiv.org/content/10.64898/20…
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cryoEM papers @cryoempapers.bsky.social · 10/05/2026
Rational acquisition of laboratory equipment: an accurate mathematical model to estimate the trade-offs in shared and nonshared equipment pubmed.ncbi.nlm.nih.gov/42099227/ #cryoEM
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cryoEM papers @cryoempapers.bsky.social · 10/05/2026
AAA+ protein unfoldases-the Moirai of the proteome pubmed.ncbi.nlm.nih.gov/42099002/ #cryoEM
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Dimitry Tegunov @dtegunov.bsky.social · 03/05/2026
We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better. Preprint: www.biorxiv.org/content/10.6... Code: github.com/warpem/miss-... 🧶 Thread:
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Bodega Cats @bodegacats.bsky.social · 30/04/2026
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Martin Pacesa @martinpacesa.bsky.social · 29/04/2026
I am happy to share a review I recently wrote on the design of peptide binders. It gives an overview of experimentally validated tools and discusses the challenges of why peptide design is more difficult than the design of classical protein binders. www.chimia.ch/chimia/artic...
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Helena Watson @helenawatson.bsky.social · 25/04/2026
BIGSMALL is now implemented in SPACEtomo. Setup is easy: - define low mag parameters with SerialEM Search preset - add LM + HM targets in the same beam-shift group - acquire! (5/6)
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Helena Watson @helenawatson.bsky.social · 25/04/2026
Preprint 🧵! I’m really excited to introduce BIGSMALL, an interleaved multi-magnification cryo-ET scheme bridging molecular and cellular scales in a single acquisition! BIGSMALL = 𝐁road 𝐈nformation 𝐆athering 𝐒trategy by 𝐌ultiscale 𝐀cquisition of lame𝐋𝐋a www.biorxiv.org/content/10.6... (1/6)
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 21/04/2026
cryoAgent: An agentic workflow for robust and adaptive end-to-end cryo-EM image processing www.biorxiv.org/content/10.64898/20…
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qiangguo.bsky.social @qiangguo.bsky.social · 21/04/2026
The peer reviewed version is out. Our study suggests this process is not limited to a single dimer architecture: we identified an additional dimeric arrangement, pointing to greater structural diversity in stress-induced ribosome hibernation-like states. doi.org/10.1093/nar/...
doi.org
rRNA expansion segments mediate ribosome dimerization as a conserved stress response
Abstract. Inhibition of messenger RNA translation is a common feature in proteostatic stress cellular responses. Puromycin, a widely used compound for stud
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cryoEM papers @cryoempapers.bsky.social · 18/04/2026
VitriFlex: An Open-Source, Modular, and Customizable Robotic Platform for Cryo-EM Grid Preparation pubmed.ncbi.nlm.nih.gov/41993429/ #cryoEM
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Jason Rasgon @vectorgen.bsky.social · 17/04/2026
WAT www.science.org/doi/10.1126/...
science.org
Science | AAAS
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Oli Clarke @olibclarke.bsky.social · 10/04/2026
Friday scripting - made a little CS-tools script to visualize the results of per-particle defocus refinement (here with the vault particle). The bottom panel is supposed to be a pseudo-tomo view looking in the plane of the ice layer; min_ice is the inferred ice thickness based on the mask extent
Visualization of per-particle defocus changes; top panel shows a micrograph of the vault particle, with circular markers showing the change in defocus vs Patch CTF, with both size & color indicating the magnitude & direction of the defocus change. 

Outliers (>3sdev in the measured set) are indicated with *s.

In the lower panel, a view looking along the y-axis of the upper panel, with computed projections of the refinement mask, colored by defocus change; the patch CTF defocus for each particle is represented with a green square (in this case all the same as we used one patch).
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TJ McCorvie @allostericstate.bsky.social · 10/04/2026
Best 3D reconstruction so far from this Tundra dataset. Right shape with some hints of secondary structure. Data collected at a higher magnification will hopefully improve this. @nusbf.bsky.social #cryoEM
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Bodega Cats @bodegacats.bsky.social · 07/04/2026
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Furukawa Lab @CSHL @lab-furukawa.bsky.social · 31/03/2026
We’re hiring! Our group at CSHL has openings for postdoctoral fellows in structural biology with a focus on ion channels and receptors in neurotransmission and cancer immunology. Join and pursue unique, cross-disciplinary science to boost your career. jobrxiv.org/job/cold-spr...
jobrxiv.org
Postdoctoral Position in Membrane Protein Biology & Ion Channel Physiology
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
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TJ McCorvie @allostericstate.bsky.social · 05/04/2026
2D classes of the 58 kDa sample collected on the 100 keV Tundra TEM with a Falcon C detector at @nusbf.bsky.social @newcastleuni.bsky.social. Still much work to do to optimise the sample & data collection but its cool to see what a 100 keV TEM is capable of. #cryoEM @recon4imd.bsky.social
2D classes of a 58 kDa particle collected on a 100 kev Tundra electron microscope
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