Sign in

Mark Frank

@markfrankbio.bsky.social
480 followers 610 following 58 posts

Postdoctoral Scholar in the Barad Lab at Oregon Health and Science University, where I study cytoskeletal remodeling in response to intracellular infection using Cryo-electron tomography. Out of lab, cat dad to Pepper. Views are my own.

PostsRepliesMedia
Mark Frank @markfrankbio.bsky.social · 25/09/2026
These photos of Pepper are too good to wait for #Caturday
Pepper, a young black cat, sits on a grey blanket and looks at the camera. Pepper, a young black cat, is seen looking on; his attention drawn. Pepper, a young black cat, sits at the base of his scratching post.
071
Reposted by Mark Frank
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! 🥳😍
0187
Mark Frank @markfrankbio.bsky.social · 09/09/2026
This is such a horrendously bad upgrade cycle for iPhone users. iPhone Duo is cool, but who wants to pay $2,000 for a phone that folds? Pro models get price increase, existing models get price increase, no base model for non-techies? #AppleEvent
010
Reposted by Mark Frank
Edward T Eng @edwardteng.bsky.social · 21/08/2026
The next #CryoEM Current Practices Webinar will be a career panel with former users and trainees of the nIH sponsored national cryoEM service centers 8/27/2026 at 12 PM ET / 9AM PT Registration is at no-cost, but sign-up is required: us02web.zoom.us/webinar/regi...
073
Reposted by Mark Frank
Dr. Roberta Dollinger @robertadolling1.bsky.social · 20/08/2026
Check out our new paper! We did Cryo-EM on native Pol II elongation complexes isolated from Drosophila embryos. This was an incredible collaboration across multiple labs and is now available for your perusal. 👇 www.nature.com/articles/s41...
nature.com
1114
Reposted by Mark Frank
Ben Barad @baradlab.com · 27/07/2026
Do any of the CryoET national centers have SPACEtomo set up for users? I've got several montaging and/or bigsmall projects I'd like to try but we have no support for either at PNCC. #teamtomo
072
Reposted by Mark Frank
Ryan Hylton @rkhylton.bsky.social · 27/07/2026
One cell, one tomogram! Our montage tomography workflow, MOSAIC, is out in Structure, and MontageMaker is on GitHub! MOSAIC: www.cell.com/structure/fu... MontageMaker: github.com/MPI-Dortmund... Big thanks to @maikaboiero.bsky.social, Adriana Prajica, Gavin Rice, and @raunser-lab.bsky.social!
15621
Reposted by Mark Frank
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.
25212
Mark Frank @markfrankbio.bsky.social · 19/06/2026
Pepper learned how to get on top of the refrigerator this morning. #blackcat
000
Mark Frank @markfrankbio.bsky.social · 16/06/2026
I am currently working through a STOPGAP tutorial for #CryoET. I am using UCSF Chimera to pick the particles now and I get this warning about the impending loss of support in future macOS versions.
100
Reposted by Mark Frank
Danielle Grotjahn @nanigrotjahn.bsky.social · 16/06/2026
Cryo-ET is often framed as a tool for in situ protein structure. But what if the real revolution is contextualization? I explore how #teamtomo is redefining what "local" means in organelle biology, revealing membrane states rather than just protein structures. tinyurl.com/localmembrane
sciencedirect.com
Think globally, act locally: Redefining organellar membrane environments through cryo-electron tomography
Early enthusiasm for the “cellular revolution” in cryo-electron tomography (cryo-ET) was largely driven by the promise of resolving protein structures…
26323
Reposted by Mark Frank
Connor Garrels @garrels.bsky.social · 01/06/2026
Very excited about our new work highlighting the role of lipids in mediating multi-channel assemblies of Cx-46/50!
0166
Reposted by Mark Frank
Carter Lab @carter-lab.bsky.social · 24/03/2026
Excited to share our work on the structure and function of cytoplasmic lattices within mouse embryos. A collaborative effort with @niakanlab.bsky.social and work led by @kashishsingh.bsky.social and @inaharasimov.bsky.social . It is now out on BioRxiv: www.biorxiv.org/content/10.6...
620684
Reposted by Mark Frank
SBGrid Consortium @sbgrid.bsky.social · 13/03/2026
New Title Alert: easymode- a collection of general pretrained networks for cellular cryoET. Learn more here: buff.ly/mLbcUbZ #SBGrid #SBGridSoftware
buff.ly
easymode
0156
Mark Frank @markfrankbio.bsky.social · 13/03/2026
It's Friday the 13th, which means it is a black cat appreciation day! #BlackCat
Pepper, an 8-month old black cat, gazes longingly into the camera as he begs to be fed on the morning of Friday, March 13, 2026.
010
Mark Frank @markfrankbio.bsky.social · 06/03/2026
Just here to pay my regular #CatTax by sharing some photos of Pepper from this past week. #CatsofBlueSky
030
Mark Frank @markfrankbio.bsky.social · 16/02/2026
Enjoying a work from home day with Pepper. #Cat #Cattree
Pepper, a black kitten, lays on a cat tree.
020
Mark Frank @markfrankbio.bsky.social · 07/02/2026
Happy #Caturday.
Pepper, a black kitten, sits contently on the bed next to a stuffed animal as he receives affection.
061
Mark Frank @markfrankbio.bsky.social · 05/02/2026
Got Pepper's collar back on him last night. Snapped this photo as he played with his toy. Only time will tell if the collar stays on! #NewCoverImage #CatsofBluesky
040
Reposted by Mark Frank
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
13815
Mark Frank @markfrankbio.bsky.social · 29/01/2026
My buddy. #Cats
Pepper, a six-month-old black cat, curled up against the arm of his owner.
030
Mark Frank @markfrankbio.bsky.social · 27/01/2026
New mug from my mother to commemorate my becoming a cat dad. #catdad #coffee
010
Reposted by Mark Frank
Bina Singh @binasingh.bsky.social · 23/01/2026
Our paper is finally out! I’m proud to share this collaborative work using FIB milling and cryo-electron tomography to study tick-borne flavivirus replication. Thanks to all co-authors and collaborators — great teamwork #CryoET #ElectronTomography #Virology #Flavivirus #Microscopy #StructuralBiology
0165
Mark Frank @markfrankbio.bsky.social · 12/01/2026
It’s been an adventure this weekend. On Saturday I adopted this little guy at the Oregon Humane Society and have been working on getting him settled. He is shy, but he has a very loud purr when he gets his neck pets and scratches. He also loves Churus! Say hello to Pepper! #Cats #SpecialRescue
Pepper, a six-month-old black domestic short hair, looks out from his carrier at the viewer with his golden yellow eyes.
020
Reposted by Mark Frank
Danielle Grotjahn @nanigrotjahn.bsky.social · 06/01/2026
#teamtomo gets another quantitative cell biology tool! We extend our Surface Morphometrics pipeline to measure membrane thickness. Alongside many biological findings, we show that our 3D measurements closely match in vitro vesicle measurements from 2D EM (collab w/Neal Waxham and Fred Heberle).
15916
Reposted by Mark Frank
Fei Dong @daydreamerscent.bsky.social · 08/01/2026
By leveraging in situ cryo-ET, Tian et al. obtained high-resolution, #3D views of the native #ultrastructure of intact hippocampal #synapses. See here: doi.org/10.1007/s122...
0103
Reposted by Mark Frank
Ben Barad @baradlab.com · 08/01/2026
Happy new year #teamtomo! We've resumed our OHSU tomo journal club, and this year I am going to be sharing it on bluesky. This week we did a roundtable, where attendees each brought a paper and did a 3-5 minute discussion of what they thought was cool about it. Here are the papers they discussed!
1195
Reposted by Mark Frank
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
13111
Mark Frank @markfrankbio.bsky.social · 25/12/2025
May your holidays have the joy of a cat in an empty box on Christmas. #HappyHolidays #Christmas
Oreo, a black and white bicolor cat, in an empty Amazon box on Christmas morning.
010
Reposted by Mark Frank
Biomedical Picture of the Day BPoD @bpodaily.bsky.social · 28/10/2025
In the Ring: Details of the bacterial cell division structure the Z-ring revealed using cryo-ET 📷 Adrián Merino-Salomón et al @mpibiochem.bsky.social in @elife.bsky.social ➡️ bpod.org.uk/archive/2025... with John Ankers
0112
Mark Frank @markfrankbio.bsky.social · 30/10/2025
I am so grateful Apple brought Preview to the iPad on OS 26. It has made being without my MacBook for the week so much easier. The iPad is still not a laptop replacement, but it has gotten much closer to that recently.
000
Reposted by Mark Frank
Meng-meng Fu @mengmengfu.bsky.social · 13/10/2025
Excited to share our preprint on cytoskeletal organization in astrocytes! biorxiv.org/content/10.110… Postdoc @mewynne759 looked at microtubules, IFs/GFAP & actin along long elaborate processes. Wonderful to collaborate w postdoc @dharshinigopal & @NogalesLab on cryo-ET 🤓 1/x
biorxiv.org
3338
Reposted by Mark Frank
joe dobbs @joedobbs.bsky.social · 15/10/2025
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️ www.biorxiv.org/content/10.1... #teamtomo
Figure 1 from the preprint
811935
Mark Frank @markfrankbio.bsky.social · 27/09/2025
Meanwhile in “war ravaged Portland.” #PDX
Morris Bridge on a sunny Fall day.
011
Reposted by Mark Frank
Jeff Martin @jeff.cuchazinteractive.org · 19/08/2025
Woo! My lab's Nature Protocols paper is out today. In a nutshell, the protocol shows how to use our Cryo-ET software to solve high-res protein structures. I don't think any of the other authors are here, but congrats to Hsuan-Fu, Ye, and Wendy for all of their work! www.nature.com/articles/s41...
nature.com
In situ structure determination of conformationally flexible targets using nextPYP - Nature Protocols
The procedure for nextPYP facilitates the end-to-end processing of cryoelectron tomography data for high-resolution structure determination and conformational variability analysis.
1247
Reposted by Mark Frank
bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 16/09/2025
Structural dynamics of mitochondrial ATP synthase in Chlamydomonas reinhardtii revealed by in situ CryoET www.biorxiv.org/content/10.1101/202…
022
Mark Frank @markfrankbio.bsky.social · 02/09/2025
I realize I don't post much, but figured I would share an update. As of today, I am officially supported by the Interdisciplinary Training in Microbial Pathogenesis and Immunology T32 Training grant.
010
Reposted by Mark Frank
OHSU Knight Cancer Institute @ohsuknight.bsky.social · 14/08/2025
"We couldn’t be more excited about the transformational potential of this work for humanity." - Phil and Penny Knight on their historic $2 billion gift to @ohsuknight.bsky.social to transform the future of cancer care and set a new standard globally. #GiveCancerHell
Interior view of a hallway at OHSU with an inspirational quote on the wall reading "Is there a higher calling than curing cancer?" and the OHSU logo displayed.
112
Mark Frank @markfrankbio.bsky.social · 29/06/2025
Took this photo of the Tilikum Bridge on my walk this morning. Beautiful weather this morning. #PDX
010
Reposted by Mark Frank
arXiv cs.CV Computer Vision and Pattern Recognition @cscv-bot.bsky.social · 27/05/2025
Gokul Adethya, Bhanu Pratyush Mantha, Tianyang Wang, Xingjian Li, Min Xu: SaSi: A Self-augmented and Self-interpreted Deep Learning Approach for Few-shot Cryo-ET Particle Detection arxiv.org/abs/2505.19948 arxiv.org/pdf/2505.19948 arxiv.org/html/2505.19948
114
Reposted by Mark Frank
David Pollock @genomesevolve.bsky.social · 19/05/2025
This is really nice CryoET work and video. paper link: 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...
053
Reposted by Mark Frank
Nature @nature.com · 07/05/2025
‘Forever chemicals’ self-assemble into stable structures resembling biological cells — a behaviour that could help to explain why they stick around for decades in the soil or groundwater go.nature.com/3F02sEd
go.nature.com
‘Forever’ molecules arrange themselves into cell-like structures
At sufficiently high concentrations, some of the compounds called per- and poly-fluoroalkyl substances self-organize into two-layered membranes.
15813
Reposted by Mark Frank
Angie Rasmussen @angierasmussen.bsky.social · 07/05/2025
I talked to @kakape.bsky.social about this for @science.org, along with many other colleagues including those with different views on regulatory oversight. We all agree: it’s too vague to be implemented, effective, or enforceable. www.science.org/content/arti...
science.org
Trump moves to tighten rules on risky research on viruses, bacteria, and toxins
Executive order on gain-of-function experiments could chill research on infectious diseases, scientists say
612856
Mark Frank @markfrankbio.bsky.social · 07/05/2025
When the White House fact sheet says manipulates "viruses and other biological agents," it reads as potentially restricting a lot more than research on viruses of pandemic potential. I am concerned in terms of how this will ultimately be interpreted into policy.
010
Reposted by Mark Frank
Ben Engel @cellarchlab.com · 07/05/2025
“The Website” is here! It can be intimidating getting into analysis of #CryoET data, and software is evolving all the time👩‍💻🚀. @phaips.vd.st & @florentwaltz.bsky.social put our lab’s workflows into an online guide. We hope this helps lower the bar to joining #TeamTomo. Feedback much appreciated! 🧪🧶🧬🔬
38720
Reposted by Mark Frank
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 Mark Frank
Enninga Lab @enningalab.bsky.social · 06/05/2025
Our latest paper is out! Congratulations to @leaswistak.bsky.social et al for this amazing #cryoET work that elucidates the initial stages of #T3SS dependent vacuolar damage during #Shigella infection. We will do a deep-dive later! journals.plos.org/plosbiology/...
journals.plos.org
The bacterial type three secretion system induces mechanoporation of vacuolar membranes
Many intracellular bacteria breach vacuolar membranes to replicate in the host cytosol, but the precise mechanisms remain unclear. This study shows that the human pathogen Shigella flexneri uses its t...
45318
Reposted by Mark Frank
Danielle Grotjahn @nanigrotjahn.bsky.social · 01/05/2025
🚨New preprint!🚨 #teamtomo We expanded Surface Morphometrics to quantify membrane thickness from cryo-ET—revealing local variation across organelles. Led by the lab’s first grad student, @mmedina300kv.bsky.social (defending Monday! 🍾) w/ @attychang.bsky.social @hamid13r.bsky.social & @tomo.science
57431
Reposted by Mark Frank
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
Reposted by Mark Frank
SBGrid Consortium @sbgrid.bsky.social · 07/04/2025
Join us April 8th for a software webinar with @alisterburt.bsky.social from @genentech.bsky.social sharing the latest on Warp. Warp Alister Burt, Ph.D., Computational Scientist, Genentech Tuesday, April 8, 2025 - 12:00pm ET Register here: buff.ly/mXUYR4A #SBGrid #Webinars #StructuralBiology
buff.ly
Webinars
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
052