@comp_cy
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single-cell bioinformatics lab focusing on the immune system! PI: @natstann /in {@unccs,@compmedunc}.
UNC-Chapel Hill
Joined February 2021
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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/Sketch…. Give it a try! ✨ @JoleneRanek
Congratulations to Sneha for presenting her poster at the celebration for undergraduate research yesterday!
CompCy Lab @ UNC retweeted
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'.
CompCy Lab @ UNC retweeted
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.
SATURN performs cross-species integration and analysis using both single-cell gene expression and protein representations generated by protein language models. @jure @YanayRosen @mariabrbic @yusufroohani
nature.com/articles/s41592-0…
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! 🧠
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.
CompCy Lab @ UNC retweeted
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/10.1101/… 😊(1/8)
Cytocoarsening was accepted at #PSB23. Congratulations Chi-Jane and Emma. Importantly, we are going to Hawaii 🌊 :) biorxiv.org/content/10.1101/…
CompCy Lab @ UNC retweeted
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.…
CompCy Lab @ UNC retweeted
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.… . 🥳
.@haidyi1 and @JoleneRanek are in Chicago @acm_bcb to present their new papers! 🙂🎉
CytoEMD presented by @haidyi1 : dl.acm.org/doi/10.1145/35355…
Distribution-preserving sketching presented by @JoleneRanek : dl.acm.org/doi/10.1145/35355…
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/10.1101/…
CompCy Lab @ UNC retweeted
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
CompCy Lab @ UNC retweeted
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/10.1101/…
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.
Today is the last day of @alecplot ‘a rotation with us and @JJMilnerLab . He did a great job and is on the way to becoming both an expert of T-cells and graphs. What a great combo of content 🧫👨💻 :) thanks for joining us Alec!
