The key innovation leading to this performance gain is the derivation of a statistical model based on the mechanism of tag cross-contamination, which accounts for both cell-bound contamination and ambient contamination.

Using negative binomial generalized linear models and expectation-maximization (EM), deMULTIplex2 probabilistically infer the sample identity of each cell, and has robust performance even with down-sampling of the cells during the model fitting.

deMULTIplex2 is provided as an open-source R package, and is optimized for speed and memory usage. Download and try it on your own data from github.com/Gartner-Lab/de…. Please let us know how it performs for you!

💧🫧What do the developing gut and water on your windshield have in common? Check out our new preprint from Zev Gartner and Ophir Klein labs to find out!🫧💧 biorxiv.org/content/10.110… More info in the🧵👇

Weird fact: Tissues have average structures that are critical to their function, yet individual cells reside in highly heterogeneous structural microenvironments. What gives? Check our pre-print: biorxiv.org/content/10.110… - with Zev Gartner and Jennifer Hu!

Want to know why tissues are fundamentally heterogeneous? Or how we can use stat mech to study cancer? If you are at #cellbio2023, please stop by my talk or poster on Tuesday Dec 5th! (pre-print link below)

Excited to share our paper mapping the interactions between colorectal carcinoma and the TME, featured in Nature Communications Editors’ Highlights (nature.com/collections/aa…) and led by Ning Li and me (my final PhD project). Check out the full paper here: nature.com/articles/s4146…

1/13 I’m thrilled to announce our comparison of the C. elegans and C. briggsae embryonic lineages by scRNA-seq, led by a talented postdoc, Chris Large, with @RupaKhanal11, Bob Waterston, @JunhyongKim and LaDeana Hillier

More amazing science with Ophir Klein lab! It's been such a pleasure to work with this team and be part of this collaboration!

Join us at #SCDB2024 to explore unifying principles in dev bio! Abstracts due JUNE 28. 18 will be picked for talks🎙️. 🙏 to sponsors Chan Zuckerberg Initiative Chan Zuckerberg Biohub Network @CompanyofBiol, we have many travel awards avail! Check out our amazing speakers & apply today! tinyurl.com/scdb24

Honored to be interviewed at #CICON24, amazing conference!!!

Happy to share our newest work, CelloType, to improve segmentation and annotation of tissue spatial omics data. twtr.to/T0m76. CelloType performs simultaneous segmentation and structure annotation using a transformer-based model.

Excited to share our latest work in Nature Cancer to get a better understanding why relapsed T-ALL is so deadly and potential target strategies, led by Jason Xu and @changya1 with members of David Teachey, @junjyang, Charles Mullighan and many great colleagues. twtr.to/foS9o.

1. Struggling to integrate single-cell datasets? Finding it hard to resolve clear differentiation trajectories? Reveal the underlying structure in your data with CONCORD.biorxiv.org/content/10.110…