iiinova — where your digital self keeps evolving

Reposted by William J Nicolas

Alexis Rohou @alexisrohou.bsky.social · 10/09/2026

Genentech Structural Biology is hiring a Principal Scientist - please share! We're looking for someone with expertise in solving structures and in computational techniques related to dynamics - MD, ensemble modeling, ensemble docking, and/or related methods.

careers.gene.com

Principal Scientist, Structural Biology in South San Francisco, California, United States of America | Research & Development at Genentech

Apply for Principal Scientist, Structural Biology job with Genentech in South San Francisco, California, United States of America. Research & Development at Genentech

168

Reposted by William J Nicolas

Structura Biotechnology @structurabio.bsky.social · 30/07/2026

🔬 Cryo-EM Reveals the Molecular Machinery of Tubulin Assembly In a recent study from @ucdavis.bsky.social, #cryoEM and #CryoSPARC were used to uncover the molecular mechanism underlying α/β-tubulin biogenesis! Read more on the latest CyoSPARC blog 👉 cryosparc.com/blog/tubulin

1126

Reposted by William J Nicolas

Allegretti Lab @matteoall.bsky.social · 27/05/2026

We're happy to announce our new preprint! 🐸 easymode: general pretrained networks for cellular cryo-ET. Segment ~20 cellular features – ribosomes, microtubules, mitochondria, nuclei & more – with zero model training. 🔗 doi.org/10.64898/202... 🧵👇

116755

Reposted by William J Nicolas

Oli Clarke @olibclarke.bsky.social · 19/05/2026

Added user defined coloring to coot1-trimmings - color by charge, residue type, density fit, etc. Only for latest commit of coot1 (--HEAD with homebrew); relies on a recent bugfix in coot1. github.com/olibclarke/c...

0153

Reposted by William J Nicolas

Hanjin Liu @liu-hanjin.bsky.social · 09/05/2026

Job navigation in table view, searchable tags, 3D mesh optimized for masks, and many more features! 👉👉👉 github.com/hanjinliu/hi... Let's make our RELION directory a better place.

03815

William J Nicolas @wjnicol.bsky.social · 09/05/2026

Thanks to @uermel.bsky.social from the @biohub.org for helping me upload my unpublished tomograms from my time at Caltech. FIB milled and cryosectionned Arabidopsis cells and Pollen tubes (thread 🧵).

151

Reposted by William J Nicolas

Ben Engel @cellarchlab.com · 03/05/2026

MissAlignment is here to align all our Bananas🍌 and Birds🦅 into beautiful Pineapples🍍 ...Did that make sense? Either way, read Dimitry's thread🧵 for a vivid visual demonstration. This new software cooks! Look how crispy it made the #ChlamyDataset nucleosome👇. #TeamTomo is hitting escape velocity 🚀 🧪

0414

Reposted by William J Nicolas

Andy Bell @bell.bz · 29/04/2026

“vibe code cleanup specialist” is probably a good way of landing freelance gigs at the moment

641523161

Reposted by William J Nicolas

Danielle Grotjahn @nanigrotjahn.bsky.social · 24/03/2026

Fun collaboration with the Herzik lab! Very cool to see #TeamTomo + STA directly capture the effects of the AWI at the single-particle level. we know it’s happening, but it’s striking to see it so clearly!

1295

Reposted by William J Nicolas

Sjors Scheres @sjorsscheres.bsky.social · 18/03/2026

We're excited to announce the beta-release of #RELION-5.1! 🥳 This release has important updates on our #amyloid processing pipeline, as described in this preprint: doi.org/10.64898/202... There are also some tweaks for #teamtomo. #OpenSoftwareAcceleratesScience

314947

Reposted by William J Nicolas

Alexis Rohou @alexisrohou.bsky.social · 07/02/2026

More evidence also that the federal administration is NOT pursuing actual criminal activity- they have forced out the very prosecutors who were working on the social services fraud cases that had been the proclaimed casus belli for sending federal forces to MN.

142

Reposted by William J Nicolas

Alexis Rohou @alexisrohou.bsky.social · 02/02/2026

So many lucid points below. Incl on how to think abt free speech issues brought up by backlash on campuses when illiberal right-wingers are invited to speak. Also, and this has agitated me since Jan 2025: those who railed against cancel culture seem at ease with state-enforced speech restrictions.

popehat.com

How "Free Speech Culture" Is Killing Free Speech: Part One

Blurring The Lines Between Official Censorship And Individual Criticism Built The Intellectual Foundation For Trump's Assault On Free Expression

111

Reposted by William J Nicolas

Oli Clarke @olibclarke.bsky.social · 26/09/2025

Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup). A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.

15725

Reposted by William J Nicolas

Ben Engel @cellarchlab.com · 20/09/2025

A molecular-resolution look into the near-native architecture of the spinach chloroplast🌱. This one was a long time in the oven, but we're happy to finally share our "version of record". What long-standing debates did we settle? Check back for a short thread🧵 on Monday. #TeamTomo #PlantScience 🧪🧶🧬🔬🌾

313446

Reposted by William J Nicolas

Sven Klumpe @svenklumpe.bsky.social · 24/08/2025

If you are thinking about the future of structural biology, we are too! Our two cents (Jürgen Plitzko and I) just got published online here: authors.elsevier.com/sd/article/S...

28827

Reposted by William J Nicolas

SBGrid Consortium @sbgrid.bsky.social · 12/08/2025

New Title Alert: AITom- an open-source platform for AI driven cellular electron cryo-tomography analysis. Learn more here: buff.ly/LLGhjvY #SBGrid #SBGridSoftware #StructuralBiology

buff.ly

Research

Xu Lab of Computational Biology

044

Reposted by William J Nicolas

Marcel Dickmanns | 🌿❄️🔬 @madic.bsky.social · 26/07/2025

New preprint: In situ Architecture of #Plasmodesmata. Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores. 🔗 doi.org/10.1101/2025... 🧪🧵1/n #teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM

1121778

Reposted by William J Nicolas

Marcel Dickmanns | 🌿❄️🔬 @madic.bsky.social · 19/02/2025

Our methods paper made it to bioRxiv: doi.org/10.1101/2025... Full #cryoET workflows for #plant tissues. Plus some general tricks and tweaks on serial Lift-Out and cryo-FLM. 🧪🧵1/5 #teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM #CLEM

211843

Reposted by William J Nicolas

Alexis Rohou @alexisrohou.bsky.social · 17/07/2025

Outstanding work from Christine, Stan and the whole team on this beautiful story. Wow.

051

Reposted by William J Nicolas

Oli Clarke @olibclarke.bsky.social · 09/07/2025

Neural net picker with a truly general model - no per dataset training required (at least if it works as advertised). Want to try this on some messy/mixed samples where other approaches struggle!

162

Reposted by William J Nicolas

Alexey Amunts @amunts.bsky.social · 23/06/2025

Running Phenix and stuck? Now you can ask the new Phenix chatbot anything from the 600-page tutorial about how to run any program. Big thanks to Tom Willinger for making this happen! Try it out: phenix-online.org/version_docs...

12810

Reposted by William J Nicolas

Alister Burt @alisterburt.bsky.social · 12/06/2025

And it’s done! Thanks to everyone who came out for the first edition of FrostByte, our event for the local computational cryo-EMers in the Bay Area ❄️ Special thanks to @joshdcryoem.bsky.social and Ariana Peck for help organizing 🙏

1232

Reposted by William J Nicolas

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 09/06/2025

This paper combines two sort-of-crazy (in the best sense) approaches in cryoEM sample preparation: (1) Native, soft-landing electrospray ion beam deposition, followed by (2) deposition of amorphous ice, and reheating and freezing by laser flash melting. Has potential for time-resolved studies.

03612

Reposted by William J Nicolas

Paul Byrne @theplanetaryguy.com · 23/05/2025

This is a view from the surface of Comet 67P. The busy particles in the foreground are cosmic rays or bits of dust and ice. The dots moving in the background are stars.

315116732157

Reposted by William J Nicolas

Yi-Wei Chang @yiweichang.bsky.social · 15/05/2025

Excited to share our new @science.org paper! Led by postdocs Ruchao Peng and Xin Xu, we used cryo-EM/ET to reveal the influenza ribonucleoprotein complex structure and its strand-sliding mechanism for RNA synthesis, paving the way for new antivirals. www.science.org/doi/10.1126/...

science.org

Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesis

Influenza viruses replicate and transcribe their genome in the context of a conserved ribonucleoprotein (RNP) complex. By integrating cryo–electron microscopy single-particle analysis and cryo–electro...

712356

Reposted by William J Nicolas

Morgridge Institute for Research @morgridgeinstitute.bsky.social · 14/05/2025

Mass Spec + lasers + cryoEM = COOL SCIENCE! New research from @coonlab.bsky.social and the Grant Lab combines mass spec to land proteins on TEM grids, a laser to restore protein structure, and cryoEM imaging and analysis to produce 3D reconstructions. www.mcponline.org/article/S153...

mcponline.org

Laser-Induced Rehydration of Cryo-Landed Proteins Restores Native Structure

The use of native mass spectrometry (MS) to land biological molecules for subsequent cryogenic electron microscopy (cryoEM) imaging and three-dimensional reconstruction has gained momentum in recent y...

053

Reposted by William J Nicolas

Alister Burt @alisterburt.bsky.social · 12/05/2025

In the Bay Area? Love computational cryo-EM/ET? Come join us for the first edition of FrostByte - a meeting for the local computational cryo-EM methods community! Details and registration at frostbyte-cryoem.github.io Thanks to @joshdcryoem.bsky.social and Ariana Peck for help organizing!

32311

Reposted by William J Nicolas

Philippe Van der Stappen @phaips.vd.st · 06/05/2025

Hey #TeamTomo, Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging? That's why @florentwaltz.bsky.social and I made this website! tomoguide.github.io Follow the thread 1 /🧵 #CryoET #CryoEM 🔬🧪

tomoguide.github.io

Welcome to TomoGuide

A step-by-step Cryo-ET guide

512344

Reposted by William J Nicolas

European Commission @ec.europa.eu · 05/05/2025

"Science is an investment. We will put forward a new 500 million package for 2025-2027 to support the best and the brightest researchers and scientists from Europe and around the world." — President @vonderleyen.ec.europa.eu at the ‘Choose Europe for Science' event at La Sorbonne 🇫🇷

35963301

Reposted by William J Nicolas

Kara Swisher @karaswisher.bsky.social · 29/04/2025

Jeff Bezos is a decidedly unfit owner for the Washington Post if this is all it takes to get him to fold. Profile in non courage. www.cnbc.com/2025/04/29/w...

cnbc.com

Trump complained to Bezos before Amazon said it scrapped idea to display tariff cost

Amazon founder Jeff Bezos has cozied up to President Donald Trump since the Republican won a second White House term.

48466611346

Reposted by William J Nicolas

Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 23/04/2025

Everyone please read and act! 👇

14437

Reposted by William J Nicolas

Ricardo D. Righetto @lifeonthewedge.bsky.social · 23/04/2025

We have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples! Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵 #CryoET #TeamTomo www.biorxiv.org/content/10.1...

Figure 4. MemBrain v2 end-to-end workflow detects periodic phycobilisome organization. A: Raw tomogram slice of EMD-31244. B: Out-of-the-box MemBrain-seg segmentation (light blue). C: A single membrane instance can be visualized in Surforama and manually annotated with GT phycobilisome positions (magenta). D: MemBrain-pick localizes particles (trained with data from C) on all membranes in the tomogram. E: MemBrain-stats computes Ripley’s O statistic using the positions from D with a bin size of 5nm. The distance between peaks (35 nm) was measured to estimate chain unit spacings.

37020

William J Nicolas @wjnicol.bsky.social · 22/04/2025

We are trying to contact the person in charge of processing payments for the purchase of a SHELX licence. We get no response and this is a major road block. Anyone has a responsive contact within Goettingen university that could help us? Thanks,

000

Reposted by William J Nicolas

Dare Obasanjo @carnage4life.bsky.social · 13/04/2025

We just need to turn the negative productivity of scientists at NASA and IRS auditors that DOGE fired to gainfully making shoes in Nike factories reshored from Vietnam. This is the groundbreaking economic thinking of communist purges from Mao to Pol Pot with a sprinkle of American Exceptionalism.

601481346

Reposted by William J Nicolas

Alexis Rohou @alexisrohou.bsky.social · 05/04/2025

Remember “climategate” with the email leaks? Here’s the best explanation of it, in some detail, I’ve ever come across. Great intro to climate science, and to science in general. podcasts.apple.com/us/podcast/c...

podcasts.apple.com

Story: briffa_sep98_e.pro - The File That Sparked a Storm

Podcast Episode · CoRecursive: Coding Stories · 04/02/2025 · 58m

011

Reposted by William J Nicolas

NanoImaging Services @nanoimaging.bsky.social · 03/04/2025

The third and final chapter of our webinar series “Cryo-EM: Back to Basics” is on demand. Hear from Giovanna about challenges in #cryoEM, how to overcome them. Catch all three chapters: Chapter 1: youtu.be/e8GyDe4_BAQ Chapter 2: youtu.be/2dBnPVkaoFs Chapter 3: youtu.be/kUGNSTGc8II

youtu.be

Cryo-EM: Back to Basics - Chapter 1

Rediscover the fundamentals of cryo-EM with NIS CSO, Giovanna Scapin! Join us for three engaging sessions covering Sample Preparation & Imaging, Data Process...

0105

Reposted by William J Nicolas

Martin Walsh @walshdls.bsky.social · 04/04/2025

Participants in the annual serial crystallography workshop for graduates student some funded by our @wellcometrust.bsky.social PhD program have got homework to do in the evening time …. @diamondlightsource.bsky.social @instruct-eric.bsky.social

legobox set of I24 which accordi g to google is the worlds best tuneable microfocus mx beamline in the world

13013

Reposted by William J Nicolas

Emil Gustavsson @emilgustavsson.bsky.social · 03/04/2025

Officer, I would like to report a murder

011