Justin Daho Lee

(1/8)🧵Excited to share our preprints on fast and sensitive multi-color H2O2 sensors, with a wide range of applications! @uwberndtlab @UWMolES @UWBioE @NAPECenter oROS-G(green direct response) biorxiv.org/content/10.110… oROS-HT(far-red inverse response): biorxiv.org/content/10.110…

Nobel Laureate David Baker on the phone with fellow awardees Demis Hassabis and John Jumper. The trio discussed how their teams have inspired one another and what the future may hold.

Our paper "The landscape of biomedical research" is out in @Patterns_CP! Great job by @ritagonmar. cell.com/patterns/fullt… Amazing interactive explorer by @benmschmidt from @nomic_ai: static.nomic.ai/pubmed.html For details see my original Twitter thread: twitter.com/hippopedoid/st….

#Cellpose remains the state-of-the-art for cellular segmentation. See our new paper, in response to Ma et al, Nat Methods 2024. Paper: biorxiv.org/content/10.110… Leaderboard results ⬇️⬇️⬇️

(1/5) Attention, Cellular Imaging Enthusiasts! Thrilled to share that our Analysis "The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions" has been published in Nature Methods (@NatureMethods) 🎉🎉🎉 Cell segmentation is a critical component of microscopy image analysis, but existing algorithms are often specialized for particular types of images or demand users to manually set hyper-parameters, posing challenges for biologists without a strong computational background. To address these issues, we organized an international challenge at NeurIPS 2022 to promote the development of novel cell segmentation methods that excel across a wide array of microscopy images, imaging platforms, and tissue types. 🌐 Homepage: uni-cellseg.github.io 📄 Paper: nature.com/articles/s4159… 🔬Data: neurips22-cellseg.grand-challenge.org/dataset/ 🏅Competition website: neurips22-cellseg.grand-challenge.org 👇 👇👇👇

Ending my several year long Twitter (X?) hiatus to celebrate my first-first author paper, out today in @NatComputSci!

Protein sequences from certain species (e.g. humans, mice, and E. coli) have systematically higher likelihoods than others! Further, we find that this bias can be detrimental for some protein design applications. 2/

Our (news&) views on new monomeric StayGold variants can be accessed here: rdcu.be/dBbnS I hope you enjoy reading it!

💡 FRETpredict is published 💡 We developed code to enable easy calculation of FRET efficiencies from large conformational ensembles using rotamer libraries for many common linker-dye pairs. 📜 doi.org/10.1038/s42003… 💾 github.com/KULL-Centre/_2… 🖥️ github.com/KULL-Centre/FR…

This week, we released a groundbreaking 160 entries from time-resolved #CryoEM capturing G protein activation by a #GPCR. It’s the largest data set from a single publication and describes the order of events driving G protein activation upon GTP binding!

Much improved review on conformational entropy from @fraser_lab and me. Despite the entropy loss during folding, proteins retain substantial conformational entropy as they fluctuate between conformations in their native state. chemrxiv.org/engage/chemrxi…

Latest from our conformational ensemble prediction pipeline with modified AlphaFold2: This is NOT a trajectory from MD! It took two hours to predict this conformational ensemble using one GPU. The experimentally-resolved energy barrier for this transition is > 15 kcal/mol

What does it take for an ‘AlphaFold Moment’ in functional protein engineering and design? go.nature.com/4bLthb0

#Cellpose 3! Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p biorxiv.org/content/10.110…

It's really hard for me to state in words how important I think these two sister Perspectives are for the future of bioimage analysis. Kudos to all the authors on their extraordinary efforts. It's been a fun ride handling these papers.

8/8 These are only a few examples of how oROS sensors can be utilized! Please visit bioRxiv for more including neuropharmacology of analgesics, cardiac biology, and astrocytic mechanisms of AD, thanks to our wonderful collaborators! @CJustinLee1 @ChavkinLab @pmjboyle @profnance

7/8 Co-expression of the outer PM-anchored oROS-HT with cytosolic oROS-G in HEK293 demonstrated how the oROS can aid in delineating peroxide topology in oxidative stress models by re-highlighting the potential significance of PM NOX-sourced peroxide in response to menadione.

(1/8)🧵Excited to share our preprints on fast and sensitive multi-color H2O2 sensors, with a wide range of applications! @uwberndtlab @UWMolES @UWBioE @NAPECenter oROS-G(green direct response) biorxiv.org/content/10.110… oROS-HT(far-red inverse response): biorxiv.org/content/10.110…