CompCy Lab @ UNC

Dealing with too many cells across multi-sample single-cell data? We developed a sketching approach based on Kernel Herding to downsample data, specifically optimized to maintain frequencies across all cell-types. Code: github.com/CompCy-lab/Ske…. Give it a try! ✨ @JoleneRanek

Congratulations to Sneha for presenting her poster at the celebration for undergraduate research yesterday!

Exciting week! 🎉 Next Monday, Sneha will defend her honors thesis 'Deciphering the Microglia Transcriptome: Unraveling the Consequences of Early Life Stress and Aging'. Next Tuesday Haidong will defend his PhD 'Set-based modeling and applications in single-cell bioinformatics'.

Our 🪐SATURN method is now out in @naturemethods! SATURN paves the way for universal cell embeddings, enabling integration of datasets across different species 🐒🐁🧍🐟🐸 Using protein language models, we encode biological meaning of genes in scRNA-seq datasets.

Congratulations to our two amazing rotons Luvna and Yu-Chen for great rotations and for getting the neuroimmune and microglia projects going in the lab! 🧠

@DhuviKarthikey1 @alecplot @JJMilnerLab Nice, thanks Dhuvi for the photo!

@alecplot @comp_cy @JJMilnerLab I was gonna say…back to RCR for you sir

Congratulations @alecplot for winning a best poster award at data science day for work predicting CD8 T-cell fates with @JJMilnerLab :) Truthfully, this a picture from last week, but is the same poster. Great job Alec.

Super excited to introduce DELVE (github.com/jranek/delve), an unsupervised feature selection method for improving inference of developmental or disease trajectories from noisy single-cell data: biorxiv.org/content/10.110… 😊(1/8)

@TonyCulos It’s okay Tony. It’s more fun to be solving impactful problems 🤩

Cytocoarsening was accepted at #PSB23. Congratulations Chi-Jane and Emma. Importantly, we are going to Hawaii 🌊 :) biorxiv.org/content/10.110…

Have you ever wondered if you could leverage RNA velocity data to better resolve biological trajectories or disease phenotypes? Delighted to share that our benchmarking study is out today in @GenomeBiology! Biggest thank you to @natstann @purvislab 😊 genomebiology.biomedcentral.com/articles/10.11…

Very proud of @JoleneRanek as her task oriented benchmarking study for integrating RNA velocity and gene expression for trajectory inference and outcome prediction is out today in Genome Biology! genomebiology.biomedcentral.com/articles/10.11… . 🥳

.@haidyi1 and @JoleneRanek are in Chicago @acm_bcb to present their new papers! 🙂🎉 CytoEMD presented by @haidyi1 : dl.acm.org/doi/10.1145/35… Distribution-preserving sketching presented by @JoleneRanek : dl.acm.org/doi/10.1145/35…

Congratulations to Chi-Jane who led our new paper on graph coarsening approaches for single-cell data. We show that by shrinking the graph in a principled way, you can achieve similar performance in downstream bioinf tasks as if using the full graph. biorxiv.org/content/10.110…

Excited to share our new paper (to appear soon in ACM BCB!) about sketching single-cell data. 😀 Specifically, our sketches preserve cell population frequencies and of course rare populations ;), led by Vishal and @JoleneRanek arxiv.org/abs/2207.00584

Most recent lab photo a few weeks ago 😀 so lucky to work with the best students! 🥰

The influx of single-cell data is staggering—not just in volume but in its multiple modalities. How can we optimally combine these modalities to make biologically meaningful predictions? (1/7) biorxiv.org/content/10.110…

Happy to share our new work in collaboration with Junier Oliva and lead by Siyuan Shan on encoding and featurizing cellular landscapes with random Fourier features and kernel mean embeddings! ✨ arxiv.org/abs/2201.07322

Happy Holidays to all! Grateful for support from students, collaborators, colleagues and mentors in our first 11 months. :) Wishing you lots of CyTOF in 2022.

Happy thanksgiving! 🥗🥑 thankful for students and collaborators, and CyTOF 💛