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Shyamal

@shyamalm.bsky.social
154 followers 104 following 17 posts

Assistant Professor | U Mich

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ChimeraX @chimerax.ucsf.edu · 25/09/2026
Make natural language requests to ChimeraX with the new Pellaeon plugin developed by Yam Amir that works with many free and paid large language models. Get Pellaeon using ChimeraX menu Tools / More Tools.... cxtoolshed.rbvi.ucsf.edu/apps/chimera...
PAR1 molecular structure shown in ChimeraX using Pellaeon chat bot.
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Cathy Spangler @cathyspangler.bsky.social · 22/09/2026
I'm excited to share our new preprint, where we show that fine-tuning gold nanoparticle conjugation to different Fab structural elements can produce powerful, rigidly coupled, labeling tools for in-situ cryo-ET. Take a look if you want to see an AuNP in an EM map!🔬🧠 www.biorxiv.org/content/10.6...
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Higor Rosa @hvdrosa.bsky.social · 17/09/2026
IMOD models, eLab/paper notes, "that feature in that one tomo"... keeping track across 1000s of #CryoET tomograms was hard! TOMATO puts tomos and notes in one place. Combine it with LLMs and it's an awesome base for building more: morphometrics, contactomes, anything turning visuals into numbers! 🥳😍
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Rachel Mellwig @rachelmellwig.bsky.social · 16/09/2026
Come learn about in-situ CLEM in beautiful Heidelberg! Registration closes October 25th, don’t miss out! @events.embl.org
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Alan Brown @alanbrownhms.bsky.social · 10/09/2026
Millions of beating cilia keep airways clean. At the base of each is the transition zone (TZ), a gate that controls which proteins enter and leave. In our paper out today in Science, we used cryo-FIB-ET to image the TZ inside human airway cells www.science.org/doi/10.1126/...
science.org
In situ structure of the human ciliary transition zone links linker defects to primary ciliary dyskinesia
The ciliary transition zone (TZ) regulates ciliary proteome composition, yet its molecular architecture, protein content, and contribution to motile ciliopathies remain poorly defined. We applied in situ cryo-electron tomography and subtomogram averaging ...
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Anthony Vecchiarelli @cellforganized.bsky.social · 26/08/2026
My MCDB Dept is hiring, again! Assistant Professor Faculty Search. Please Repost! Applications Due Oct 1st We welcome applications from all areas of cellular/molecular biology in prokaryotes, plants, and animals. More information can be found HERE: jobs.sciencecareers.org/job/679540/a...
jobs.sciencecareers.org
Assistant Professor - Ann Arbor, Michigan job with University of Michigan - Molecular, Cellular and Developmental Biology | 679540
UNIVERSITY OF MICHIGAN FACULTY POSITION IN CELL & MOLECULAR BIOLOGY AND RELATED FIELDS   The Department of Molecular, Cellular, and Developmental B...
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Andrea Musacchio @andrea-musacchio.bsky.social · 26/08/2026
Several mice, rabbits, sheeps, and donkeys indicted after the companies involved rejected all allegations of wrongdoing… reeserichardson.blog/2026/08/25/a...
reeserichardson.blog
At least 15 companies are selling antibodies using faked validation data
Popular vendors’ catalogs feature more than 18,000 manipulated images
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UC Berkeley MCB @berkeleymcb.bsky.social · 14/08/2026
MCB is hiring Assistant Professors across 3 divisions!: 🧪BBS: aprecruit.berkeley.edu/JPF05483 🧬GGED: aprecruit.berkeley.edu/JPF05481 🦠IMM: aprecruit.berkeley.edu/JPF05486 🗓️ Application Deadline: October 19, 2026 🔗 Click the links or scan the QR codes to learn more and apply
MCB is hiring 3 Assistant Professor positions across 3 divisions: 

Biochemistry, Biophysics and Structural Biology (BBS); Genetics, Genomics, Evolution, and Development (GGED); and Immunology and Molecular Medicine (IMM)

BBS application link: https://aprecruit.berkeley.edu/JPF05483

GGED application link: https://aprecruit.berkeley.edu/JPF05481

IMM application link: https://aprecruit.berkeley.edu/JPF05486
Assistant Professor of Immunology and Molecular Medicine (IMM). IMM application link: https://aprecruit.berkeley.edu/JPF05486Assistant Professor of Biochemistry, Biophysics and Structural Biology (BBS). BBS application link: https://aprecruit.berkeley.edu/JPF05483Assistant Professor of Genetics, Genomics, Evolution, and Development (GGED). GGED application link: https://aprecruit.berkeley.edu/JPF05481
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Alexis Rohou @alexisrohou.bsky.social · 12/08/2026
Come work with us at Genentech. We do drug discovery, pretty cutting edge cryoEM/ET stuff, and always learn a lot together. Any questions or recommendations, do let me know.
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Kathiravan Ezhilan @kathiravan-ezhilan.bsky.social · 16/07/2026
In #cryoET, separating closely apposed membrane segmentations into distinct labels can be difficult. Small artefacts may connect otherwise separate membranes, requiring tedious slice-by-slice correction. To address this, @jasmred.bsky.social and I developed MemSplit, a napari based workflow.
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Ben Barad @baradlab.com · 08/07/2026
My personal summer of code continues with another ChimeraX plugin - this time, MorphometricsX! Load quantified meshes from morphometrics (or pycurv) in ChimeraX with color-by-quantification and display alongside tomos and particles. Coming to the toolshed soon! #teamtomo github.com/baradlab/mor...
Screenshot of MorphometricsX rendering mitochondrial membrane surfaces in chimera with color-by-quantification.
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Seychelle Vos @voslab.org · 01/07/2026
Your cryo-EM work deserves to be seen 🔬 Submit your poster or talk abstract for the annual New England cryo-EM symposium by July 15th. The meeting will be held September 8th at MIT. This is the place to be if you are doing structural biology in the Northeast! Register: cryoem.mit.edu/2026-ne-cryo...
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Silvia Ramundo @sramundo.bsky.social · 24/06/2026
1/7 New preprint: we found that Chlamydomonas carries a giant and unexpectedly elaborate chloroplast RNA polymerase with 12 previously unknown subunits, overturning the idea that the complexity of this organellar enzyme emerged during plant terrestrialization! www.biorxiv.org/content/10.6...
biorxiv.org
The structure of a 2-MDa chloroplast RNA polymerase reveals unexpected evolutionary complexity
Transcription in chloroplasts depends on the Plastid-Encoded RNA polymerase (PEP), a bacterial-derived enzyme whose catalytic core remains encoded by the highly reduced genome inherited from the cyano...
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Veijo Salo @veijosalo.bsky.social · 23/06/2026
How does a cell remodel the ER membrane into a lipid droplet? Excited to share our new bioRxiv preprint, where we find that regulated opening of the seipin ring defines a functional ER–lipid droplet interface — and identify SMLR1 as a regulator of this transition. www.biorxiv.org/content/10.6...
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Ben Barad @baradlab.com · 13/06/2026
I had such a fun time teaching at the U Michigan Cryo-ET Course this week! I taught quantitative ultrastructure analysis and we made cool figures like these! My course materials are at baradlab.com/michigan_tutorial for anyone to try. Workflow include mesh refinement and thickness measurement!
ChimeraX/ArtiaX visualization showing mitochondria-associated ribosomes connecting drives reduced IMM-OMM spacing in yeast.Surforama depiction of mitochondrial outer membrane shows membrane-associated ribosomes.
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Da-Neng Wang @danengw.bsky.social · 11/06/2026
Very sad to learn that Steve White has passed away.
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Christine Mayr @christinemayr.bsky.social · 08/06/2026
Finally out in @Cellcellpress! Proteins with long IDRs are prone to misfolding during protein synthesis. This is prevented by mRNA 3′UTRs that act as mRNA-based IDR chaperones. www.cell.com/cell/fulltex...
cell.com
mRNA 3′ UTRs chaperone intrinsically disordered regions to control protein activity
Highly conserved mRNA 3′ UTRs act as co-translational chaperones for intrinsically disordered regions (IDRs), preventing inter-domain misfolding and enabling biogenesis of fully active proteins.
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Reese Richardson @reeserichardson.bsky.social · 05/06/2026
The Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)
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Ben Cooper @bfcoop.bsky.social · 02/06/2026
I've just released a small open-source utility for RELION users: relion_tracker. RELION stores a lot of useful information in the *_optimiser.star files, but I often found myself repeatedly grepping STAR files to see how metrics were changing across iterations.
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The bumbling biochemist (Bri Bibel) @bumblingbiochemist.bsky.social · 23/05/2026
Long shot, but, with lots of labs turning from crystallography to cryo-EM I’m wondering if anyone knows of labs potentially looking to offload some of their old crystallography supplies to a PUI with potential screening hits and really eager students but nothing to harvest with, etc.?
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Alan Brown @alanbrownhms.bsky.social · 22/05/2026
One, perhaps two, of our postdocs are moving on to faculty positions this year (more news soon!). While they're truly irreplaceable, it does mean that we have openings for new members to join our team studying #cilia. If interested, please apply: academicpositions.harvard.edu/postings/15526
Advert for postdoctoral positions at Harvard Medical School studying cilia
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Reese Richardson @reeserichardson.bsky.social · 21/05/2026
@johanduchene.bsky.social @sholtodavid.bsky.social Spent the last hour looking, found ten more apparently manipulated Western blots in Thermo Fisher's antibody verification data (across eight different catalogued products). Thread below. www.thermofisher.com/antibody/pro...
Apparent manipulation in the antibody verification data in Thermo Fisher's online catalog
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Shyamal @shyamalm.bsky.social · 14/05/2026
A huge milestone for the lab! The first Ph.D. from the lab, Dr. Jaimin Rana. In keeping with my training and German tradition, he received a Doktorhut! Jaimin graduates with 2 first-author manuscripts (one more to come soon) and 5 additional manuscripts in which he is a contributing author.
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Dawid Zyla @dzyla.bsky.social · 07/05/2026
Measles is coming back. Until now, we didn't know how human antibodies actually recognize and neutralize the virus. No structure of either measles surface protein bound to a human antibody had ever been reported. We set out to change that.
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Gregor Weiss @weiss-lab.bsky.social · 22/04/2026
New preprint 🚀 ❄️ We developed Autogrid-compatible HPF planchettes that enable direct freezing of clipped EM grids and streamline integration with cryo-FIB workflows ✔️ improved grid stability ✔️ reduced handling ✔️ robust vitrification (🦠 🧫 🧠) A step toward routine HPF for complex samples #teamtomo
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Utz Ermel @uermel.bsky.social · 20/04/2026
Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines. 🧵👇 doi.org/10.1002/pro.70578
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Tomas Pascoa @tomaspascoa.bsky.social · 14/04/2026
1/ Excited to share our preprint! 🥳 Degradation of aromatic compounds, including BTEX pollutants, requires highly endergonic aromatic ring reduction. Using #cryoEM and in situ #cryoET, we show how BCRII couples electron bifurcation modules in one giant redox machine www.biorxiv.org/content/10.6...
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Caitie McCafferty @computingcaitie.bsky.social · 08/04/2026
I am excited to share our most recent work collaborating with @centriolelab.bsky.social and @stearnslab.bsky.social to look at the ciliary base of mammalian multiciliated cells w/ cryo-ET, XL/MS, and U-ExM www.biorxiv.org/content/10.6...
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bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 07/04/2026
Molecular architecture of the ciliary base in mammalian multiciliated cells www.biorxiv.org/content/10.64898/20…
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U-M Life Sciences Institute @umlifesciences.bsky.social · 31/03/2026
The LSI labs of David H. Sherman and Filipa Pereira have teamed up to boost bacterial production of a long-elusive compound, leading to a potential new treatment for drug-resistant malaria. Read more: research.umich.edu/research-sto...
Filipa Pereira working with LSI lab members.
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bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 28/03/2026
Neurodegeneration risk variants promote lysosomal TMEM106B fibrilaccumulation www.biorxiv.org/content/10.64898/20…
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Shyamal @shyamalm.bsky.social · 28/03/2026
Excited to share this collaborative work with Ward and Petrucelli Labs! We show that two major genetic risk factors for #neurodegeneration and cognitive decline converge on TMEM106B fibrils accumulating within lysosomes. A LOT of work packed in here 🧠🔬 Preprint: www.biorxiv.org/content/10.6...
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Cell Biology J-Club @cellclub.bsky.social · 20/03/2026
www.nature.com/articles/s41...
nature.com
Visualizing suborganellar lipid distribution using correlative light and electron microscopy - Nature Cell Biology
Lennartz et al. introduce a correlative light and electron microscopy workflow, Lipid-CLEM, combining near-native lipid probes and on-section labelling via click chemistry. Lipid-CLEM quantitatively a...
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 11/03/2026
Holy smoke. What ultimately happened???
Image from their link showing evidence of fabricated references
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SwiftOnSecurity @swiftonsecurity.com · 02/03/2026
Remember that everyone you meet is fighting their own battle, sometimes with amino acids
I fucking hate proline so fucking much it's the worst amino acid it's so fucking stupid it's incapable of being fucking normal so it forms an ugly ass ring with itself with its own fucking nitrogen cuz it's a loser fucking amino acid I hate it so much I'd rather cut off my right tit than have to ever draw a mechanism with proline ever again
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Anthony Schuller @aschuller17.bsky.social · 24/02/2026
Incredibly proud of our small but mighty team at Interdict Bio as we bring the interdictor modality closer to the clinic! Check out our first publication that lays the foundation for context-dependent translation modulators as a therapeutic approach for cancer! www.nature.com/articles/s41...
nature.com
Context-dependent translation inhibition as a cancer therapeutic modality - Nature Communications
Robust protein synthesis by the ribosome is required for rapid cancer growth. Here authors present interdictors, small molecule inhibitors of protein synthesis with context-dependent activity that inh...
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Shyamal @shyamalm.bsky.social · 17/02/2026
Graduate student Martin Fernandez just won the best poster 🏆 at the Gordon Research Conference on ‘Frontotemporal Dementia and Related Rare Dementias’ #proudPI
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Sjors Scheres @sjorsscheres.bsky.social · 16/02/2026
Please spread the word: the Structural Studies Division @mrclmb.bsky.social is looking for a new tenure-track, independent group leader with an exciting plan in any area of Structural (Molecular & Cell) biology, in discovery biology and/or methods development. 🥳 mrc.tal.net/vx/mobile-0/...
mrc.tal.net
Research Group Leader Tenure Track - Structural Studies - LMB 2775 - Medical Research Council
Location: Cambridge. Vacancy: Research Group Leader Tenure Track - Structural Studies - LMB 2775. Closing Date: 16/03/2026, 23:55
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Letters of Note @lettersofnote.com · 12/02/2026
Happy birthday to one of my favourite haters, Charles Darwin
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Ben Barad @baradlab.com · 11/02/2026
I am getting excited about teaching at this! I think we're going to do copick, membrain-seg, morphometrics, and surforama on my day!
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U-M Life Sciences Institute @umlifesciences.bsky.social · 09/02/2026
Join us this summer for U-M's 2026 #CryoET Data Processing Workshop! This four-day workshop will introduce participants to standard image processing packages and all aspects of cryo-ET data processing. Apply by March 20: myumi.ch/lsi-cryo-workshop-2026 @jbquerido.bsky.social @shyamalm.bsky.social
Cryo-electron tomogram on a navy background with text: Cryo-ET Data Processing Workshop. June 7-11, 2026
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Shyamal @shyamalm.bsky.social · 09/02/2026
Caveolins are conserved (metazoan) proteins essential for forming membrane-derived vesicles called caveolae. While evolutionarily distant caveolins have similar structures, we found they do not maintain caveolae-generating capabilities (movie). What determines this? Check out our new preprint!
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Patrick Bryant @patrickbryant1.bsky.social · 07/02/2026
Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure. We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
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Ben Barad @baradlab.com · 04/02/2026
I've been working on Surface Morphometrics for a new version (coming soon), and made some significant (AI-assisted) performance improvements, especially in pycurv (20-50x!). If you've had technical issues or just felt like it was too slow, give it another try! #teamtomo github.com/GrotjahnLab/...
github.com
GitHub - GrotjahnLab/surface_morphometrics: Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging.
Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging. - GrotjahnLab/surface_morphometrics
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Richard Sever @richardsever.bsky.social · 03/02/2026
"AI is rapidly populating medical records with synthetic content, creating a feedback loop [that] drives a rapid erosion of pathological variability and diagnostic reliability...this renders AI generated documentation clinically useless after just two generations" www.medrxiv.org/content/10.6...
medrxiv.org
AI-generated data contamination erodes pathological variability and diagnostic reliability
Generative artificial intelligence (AI) is rapidly populating medical records with synthetic content, creating a feedback loop where future models are increasingly at risk of training on uncurated AI ...
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EMBL @embl.org · 22/01/2026
EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond. We extend our deepest condolences to his family, friends, and colleagues. www.embl.org/news/people-...
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Shyamal @shyamalm.bsky.social · 20/01/2026
We are running the cryo-ET image processing workshop again this year! Come learn everything tomo: STA, segmentation, heterogeneity analysis from @baradlab.com @williamnwan.bsky.social and others! Apply!
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U-M Life Sciences Institute @umlifesciences.bsky.social · 16/01/2026
#Postdoc job opportunity: The Pereira lab at the LSI is seeking a postdoctoral researcher help develop cutting-edge experimental and computational approaches to accelerate #NaturalProduct discovery. Learn more and apply: careers.umich.edu/job_detail/2...
careers.umich.edu
RESEARCH FELLOW | U-M Careers
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Ben Barad @baradlab.com · 26/12/2025
Online today, the journal version of our ( @nanigrotjahn.bsky.social @attychang.bsky.social @mmedina300kv.bsky.social) manuscript from earlier this year describing membrane thickness measurement in cells with #teamtomo! rupress.org/jcb/article/...
rupress.org
Surface Morphometrics reveals local membrane thickness variation in organellar subcompartments | Journal of Cell Biology | Rockefeller University Press
Medina, Chang et al. introduce a new method based on the Surface Morphometrics pipeline to measure global and local thicknesses of organellar membranes fro
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Shyamal @shyamalm.bsky.social · 19/12/2025
Wow! Amazing stuff from @matteoall.bsky.social. Congratulations to all the authors involved.
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