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Reposted by Willow Coyote-Maestas

Camille Moore @camille-moore.bsky.social · 6d

Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization.
www.science.org/doi/10.1126/...

ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes

Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...

www.science.org

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Willow Coyote-Maestas @willowcoyote.bsky.social · Sep 8

I love writing spontaneous and unsolicited reviews. I would be thrilled folks did it to me too! I think it gets the heart of what we do science for - giving and getting feedback to get closer to the ‘truth’! Otherwise why post a preprint if you don’t want people to read and respond?

James Fraser @fraserlab.com · Sep 8

Why hasn't Preprint Peer Review caught on more?

I discovered a small, but simple reason - authors are missing out on the JOY of getting feedback because they aren't notified when feedback occurs.

more in thread below!

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Seth Shipman @seth-shipman.bsky.social · Sep 8

Check out MitoScribe in our new preprint led by Linhan Wang: www.biorxiv.org/content/10.1...

It's an analog molecular recorder that uses neutral base edits to the mitochondrial genome to store information about historical signaling in a cell. Single cell resolution at scale (see next post)!

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Willow Coyote-Maestas @willowcoyote.bsky.social · Aug 26

Congrats! So well deserved!

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Joslynn Lee, Ph.D. @theoreticalfun.bsky.social · Aug 26

1st day of classes went well for this associate professor! I’ll ride this tenure/promotion wave for another week.

I’m teaching a new chemical biology class this semester. Excited to bring computational chemistry topics & hands-on activities in the computer lab.

Also still masking this semester!

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Guillaume Diss @guillaumediss.bsky.social · Aug 25

Latest pre-print from our lab is out. Great work by @alexbendel.bsky.social and team.

Full deep mutational scan of an entire human protein interaction domain family

2M quantitative measurement of protein-protein interaction -> deep learning model to predict PPI from sequence

More details 👇

Alexandra Bendel @alexbendel.bsky.social · Aug 25

I am happy to finally share this preprint of my PhD project in @guillaumediss.bsky.social lab at the FMI in Basel.
We used ddPCA to map the genetic architecture of the entire human bZIP interaction network.

www.biorxiv.org/content/10.1...

Thanks to all our co-authors for the great collaboration!

The genetic architecture of the human bZIP family

Generative biology holds the promise to transform our ability to design and understand living systems by creating novel proteins, pathways, and organisms with tailored functions that address challenge...

www.biorxiv.org

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Marissa Scavuzzo she/her @marissascavuzzo.bsky.social · Aug 25

Congrats Kevin Allan, Jesse Zhan, @tymillerlab.bsky.social, @tesarlab.bsky.social, et al

It was fun to do some super-resolution microscopy to help look into how a cell matures, all while sending a lot of spooky faces to Paul and Kevin since, unlike these Sox6 ko cells, I have yet to mature 😱😱😱😱😱

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Alexandra Bendel @alexbendel.bsky.social · Aug 25

I am happy to finally share this preprint of my PhD project in @guillaumediss.bsky.social lab at the FMI in Basel.
We used ddPCA to map the genetic architecture of the entire human bZIP interaction network.

www.biorxiv.org/content/10.1...

Thanks to all our co-authors for the great collaboration!

The genetic architecture of the human bZIP family

Generative biology holds the promise to transform our ability to design and understand living systems by creating novel proteins, pathways, and organisms with tailored functions that address challenge...

www.biorxiv.org

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Reposted by Willow Coyote-Maestas

Joslynn Lee, Ph.D. @theoreticalfun.bsky.social · Aug 13

I got to share a bit about Indigenous values in chemistry on this pod! Thanks @nature for the feature and joining some an amazing list of ChangeMakers!

Nature @nature.com · Aug 12

Latest from the Nature Careers Podcast 🔊 How Indigenous values permeate my chemistry teaching and research

go.nature.com/45KuNsB

How Indigenous values permeate my chemistry teaching and research

Joslynn Lee describes why she seeks to bridge the Native American worldview with Western science.

go.nature.com

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Tadashi Fukami @fukamit.bsky.social · Aug 6

Assistant Professor position in Traditional Ecological Knowledge at Stanford University. Applications due Sept 30, 2025

facultypositions.stanford.edu/en-us/job/49...

Stanford | Faculty Positions: Details - Assistant Professor in Traditional Ecological Knowledge

facultypositions.stanford.edu

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Nature Methods @natmethods.nature.com · Aug 4

ProDomino is a machine learning-based method that predicts domain insertion sites and helps guide the engineering of functional multi-domain proteins.

www.nature.com/articles/s41...

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Willow Coyote-Maestas @willowcoyote.bsky.social · Aug 4

Awesome work from @jingyour.bsky.social, @hjp.bsky.social and a lil bit us!

New stats framework for mutational scanswhere we measure multiple phenotypes like expression & activity. Jingyou is able to pull out immediately patterns that took us otherwise weeks to months data digging. Amazing work!

Jingyou Rao @jingyour.bsky.social · Aug 4

How do we decouple the effects of two functional phenotypes in protein deep mutational scanning (DMS)?
Meet Cosmos, our new statistical framework for causal inference in multi-phenotype DMS.
www.biorxiv.org/content/10.1...
[1/n]

Cosmos: A Position-Resolution Causal Model for Direct and Indirect Effects in Protein Functions

Multi-phenotype deep mutational scanning (DMS) experiments provide a powerful means to dissect how protein variants affect different layers of molecular function, such as abundance, surface expression...

www.biorxiv.org

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Willow Coyote-Maestas @willowcoyote.bsky.social · Aug 1

So lucky to have the brilliant @jingyour.bsky.social joining the lab as a postdoc! It’s been inspiring collaborating the last couple years and I can’t wait to see the extraordinary things she’ll do :)

Jingyou Rao @jingyour.bsky.social · Jul 31

Perfect first day: receiving a set of new pipettes! Can’t wait to do more cool experiments with the lab for the next few years. @willowcoyote.bsky.social

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Harold Pimentel @hjp.bsky.social · Jul 21

Super proud of my first student, @jingyour.bsky.social! Well done! Looking forward to the amazing work you will do in the future 🥲 bsky.app/profile/jing...

Jingyou Rao @jingyour.bsky.social · Jul 21

Thrilled to share that I just successfully defended my PhD! Thanks to my committee, collaborators, and everyone who’d supported me throughout my seven years at UCLA. A special thank you to my PI Harold for his incredible mentorship! @hjp.bsky.social

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Jingyou Rao @jingyour.bsky.social · Jul 21

Thrilled to share that I just successfully defended my PhD! Thanks to my committee, collaborators, and everyone who’d supported me throughout my seven years at UCLA. A special thank you to my PI Harold for his incredible mentorship! @hjp.bsky.social

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Irene Gallego Romero @ee-reh-neh.bsky.social · Jul 11

🧪🖥️🧬 It's here!! Our second MPRA, which is totally different from the first. For starters, there's no human sequences anywhere!

Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)

bioRxiv Genomics @biorxiv-genomic.bsky.social · Jul 11

Dissecting functional regulatory convergence over 160 million years of therian evolution https://www.biorxiv.org/content/10.1101/2025.07.10.662670v1

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Judi Simcox @judisimcox.bsky.social · Jul 10

Officially tenured. Thank you to all the mentors who guided me, and to the trainees who made this possible with your ideas, hard work, and scientific joy.

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Harold Pimentel @hjp.bsky.social · Jul 2

Very excited to have this work out by @jeromics.bsky.social ! Please check it out.

I think my favorite story from the supplement is how impactful normalization can be in this context.

bsky.app/profile/jero...

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Matt Howard @matthewkhoward.bsky.social · Jun 30

Check out Jerome's paper! As we push the boundaries of DMS, it is critical that we develop robust ways to score variant effects--and he is doing just that. Excited to put this to use in our upcoming GPCR-DMS endeavors :)

Jerome @jeromics.bsky.social · Jun 30

Check out our new preprint on Lilace, a statistical tool for scoring FACS-based deep mutational scanning experiments! Lilace directly models the shift between variant fluorescence distributions and provides score uncertainty estimates to better assess reliability and reproducibility. (1/3)

Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace

Deep mutational scanning (DMS) experiments interrogate the effect of genetic variants on protein function, often using fluorescence-activated cell sorting (FACS) to quantitatively measure molecular ph...

www.biorxiv.org

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Willow Coyote-Maestas @willowcoyote.bsky.social · Jun 30

Check out @jeromics.bsky.social @hjp.bsky.socials recent facs based model for dms studies!!!

Jerome @jeromics.bsky.social · Jun 30

Check out our new preprint on Lilace, a statistical tool for scoring FACS-based deep mutational scanning experiments! Lilace directly models the shift between variant fluorescence distributions and provides score uncertainty estimates to better assess reliability and reproducibility. (1/3)

Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace

Deep mutational scanning (DMS) experiments interrogate the effect of genetic variants on protein function, often using fluorescence-activated cell sorting (FACS) to quantitatively measure molecular ph...

www.biorxiv.org

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Willow Coyote-Maestas @willowcoyote.bsky.social · Jun 3

Congrats - amazing work show a beautiful landscape of opioid receptor conformations by EM

Michael J. Robertson @biophysicsguy.bsky.social · Jun 2

Excited to share our latest preprint! We used cryoEM and MD simulations to look at the GTP-induced activation of the mu-opioid receptor-Gi complex with partial, full, & super agonists resolving the landscape of Gi activation and how its modulated by different ligands!
www.biorxiv.org/content/10.1...

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Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · May 29

This is disappointing. To understand the significance of this area for Natives, listen to this Native American Calling episode with Natives in the area describing their relationship with this land.

www.nativeamericacalling.com/tuesday-may-...

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Harold Pimentel @hjp.bsky.social · May 8

I’m super honored to be selected, and immensely grateful. Huge thanks, @hypothesisfund.bsky.social! We are looking forward to doing some fun science!

bsky.app/profile/hypo...

Hypothesis Fund @hypothesisfund.bsky.social · May 8

3/ Leveraging large population studies & small scale lab experiments, Awardee @hjp.bsky.social will integrate diverse datasets to strengthen our ability to interpret rare genetic🧬 variants in disease. 🤯

🥳 Congrats Dr. Pimentel!
🙏 #HFScout Kay Tye

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Ben Lehner @benlehner.bsky.social · May 6

Come and join us! We’re hiring a new Group Leader in Generative Biology at the @sangerinstitute.bsky.social

Building AI models or the data to train them?

Core funding of >$130M a year for a faculty of ~30.

www.nature.com/naturecareer...

acrobat.adobe.com/id/urn:aaid:...

pls RT!

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Willow Coyote-Maestas @willowcoyote.bsky.social · Apr 21

Everyone knows triplicates are the rigorous number for everything... 3 aims, 3 washes, 3 replicates, 3rd times the charm... Are you questioning the physical law of 3s?

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