Stephanie Wankowicz

Big experiments are only big if they can fail Some reflections on Arena Bioworks' unexpected wind down as a fellow institutional experimentalist

Blog post on testing out new funding mechanisms by @seemaychou.bsky.social seemay.substack.com/p/big-experi...

The Drain of Scientific Publishing The domination of scientific publishing in the Global North by major commercial publishers is harmful to science. We need the most powerful members of the research community, funders, governments and ...

Preprint 2: The Drain of Scientific Publishing arxiv.org/abs/2511.04820

Preprint 1: Hit or Miss: Understanding Emergence and Absence of Homo-oligomeric Contacts in Protein Language
Models
www.biorxiv.org/content/10.1...

@sokrypton.org

Spotify: open.spotify.com/episode/0BES...

Episode 9: I Can Do It With a Broken Grant Cycle Podcast Episode · The Tortured Proteins Department · 11/23/2025 · 1h 1m

Apple: podcasts.apple.com/us/podcast/e...

TTPD Episode 9 with @fraserlab.com: I Can Do It With a Broken Grant Cycle
(Sorry for the crappy audio in places!)

Topics: Government Shutdown/Reopening, Travels, Jane Richardson's impact (en.wikipedia.org/wiki/Jane_S....), Arena BioWorks closing, AI review tools

wankowiczlab.com/2025/11/24/T...

Actually the OPPOSITE.

Was thinking the same thing!

Congrats!

CAHRA 2025: Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms A community-wide data processing challenge for cryo-electron microscopy.

Announcing cryo-EM heterogeneity challenge #2, now dubbed the 2025 Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms (CAHRA)! Join us for a webinar next Friday (Nov 14th) to learn more. Datasets already posted here: heterogeneity.notion.site/challenge #cryoem

❤️

Zara Weinberg passed away earlier this week. She joined my lab earlier this year when her postdoc lab formally closed.
She was a brilliant scientist, supportive mentor, dear friend, avid music fan, rabid believer in public transit, open science champion, and above all just an amazing human.

The Numbers Six and Seven Are Making Life Hell for Math Teachers ‘Six seven’ sends teens into a frenzy that schools have been powerless to stop. ‘It’s like throwing catnip at cats.’

Can confirm.
www.wsj.com/lifestyle/si...

Higher education fails at collective action In the latest development in the ongoing combat between universities in the United States and the Trump administration, the Department of Education has presented them with what it calls a “compact.” I...

"It's past time to recognize that university administrators aren't going to lead the way out of this, [setting] the stage for leadership... from faculty, staff, & students, [where] most if not all progress in higher ed over the past 100 yrs has occurred."
www.science.org/doi/10.1126/...
#AcademicSky

Join our virtual info session on Nov 6, 2025, at 1 PM PT! Explore cutting-edge research in computational biology! Learn how we train future scientific leaders! Get answers to your questions about our program! Meet current students and faculty! Find out what makes a successful application! https://bmi.ucsf.edu/admissions

🚨PhD opportunity at the intersection of computation & biology! 🖥️🧬🧪
Ready to tackle complex biological problems with cutting-edge tools? The BMI PhD program @UCSF trains future leaders in comp bio, bioinformatics, & data science.
📢 Info session: 11/6 @ 1 PM PT
bmi.ucsf.edu/admissions
Learn more👇

It was such an honor for me to work with awesome colleagues Needhi Bhalla and JoAnn Trejo on this important piece 👇

Three schematic diagrams. The first illustrates selective publishing of internal resection, the second selective causal focus, and the third selective access and funding for researchers.

1. We ( @jbakcoleman.bsky.social, @cailinmeister.bsky.social, @jevinwest.bsky.social, and I) have a new preprint up on the arXiv.

There we explore how social media companies and other online information technology firms are able to manipulate scientific research about the effects of their products.

**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: pcossio@flatironinstitute.org

Experiment-guided AlphaFold3 resolves accurate protein ensembles AlphaFold3 predicts highly accurate protein structures from sequence, but tends to collapse to a single dominant conformation, even when the underlying structure is inherently heterogeneous. Moreover,...

Preprint: Experiment-guided AlphaFold3 resolves accurate protein ensembles⁠ www.biorxiv.org/content/10.1...

Episode 8: Open Science in a Changing Academic World

Spotify: open.spotify.com/episode/2kSP...
Apple: podcasts.apple.com/us/podcast/e...

TTPD #8 with @fraserlab.com: Open access, Clear science, Full hearts, Can’t lose!

We chat about the Compact for Academic Excellence in Higher Education, HHMI open access, the government shutdown, the BEAR, the Nobel Prizes, and The Life of a Showgirl! wankowiczlab.com/2025/10/23/T...

Feedback welcomed!

3) Experimental approaches for determining ensembles face major challenges, including ensemble averaging, data sparsity, and intrinsic measurement errors.

4) Standardized representations, comparison metrics, and uncertainty quantification are still lacking.

Feedback welcomed!

Updated preprint on the roadmap to predicting macromolecular ensembles with @bonomimax.bsky.social! Four key issues:
1) Structural ensembles are defined inconsistently across disciplines.
2) No single experimental technique alone can fully capture structural ensembles
arxiv.org/abs/2505.01919

From Lab to Legacy: Marnett’s Trainees Gather to Toast a Life in Science and Service In a heartwarming tribute to a remarkable career, more than 70 of his former graduate students and postdoctoral scholars recently traveled from across the globe for a three-day festivity on Oct. 3–…

🎓👏 Join us in honoring dean emeritus Larry Marnett, whose five decades of dedication to science, leadership, and mentorship was highlighted during a reunion of 70+ former trainees from around the globe.

Read more about this tribute 👉 medschool.vanderbilt.edu/basic-scienc...

Yes, that points out another challenge about these models is how they are generated and what data they are generated should lead to different interpretations.

Ensemble models can imply correlated motions, but they aren’t directly encoded. You need to derive covariance, but we could directly put this into the model (where supported by data).

Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure Traditional structural models of biomolecules typically represent only a single conformational state, even though biomolecules naturally exist in multiple states crucial for their function. Here, we p...

Fantastic question! Yes, the PDB format (multiconf and ensemble) is limited in showing correlated motion. We are working on integrating a new hierarchical encoding strategy that will help with this and is hopefully set to be approved by the mmCIF working group soon! journals.iucr.org/m/issues/202...

There are also some other great blog posts and logbooks on our initial data collections. Check out diffuse.science to see what we have been up to! @diffuseproject.bsky.social @fraserlab.com @andolab.bsky.social @nozomi-ando.bsky.social