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Today is the last day of Alec Plotkin ‘a rotation with us and Justin Milner . 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!

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

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 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

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…

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

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 Jolene Ranek arxiv.org/abs/2207.00584

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…

.haidyi and Jolene Ranek are in Chicago ACM BCB to present their new papers! 🙂🎉 CytoEMD presented by haidyi : dl.acm.org/doi/10.1145/35… Distribution-preserving sketching presented by Jolene Ranek : dl.acm.org/doi/10.1145/35…

Very proud of Jolene Ranek 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… . 🥳

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 Genome Biology! Biggest thank you to Natalie Stanley Purvis Lab 😊 genomebiology.biomedcentral.com/articles/10.11…

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

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)

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

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! 🧠

Our 🪐SATURN method is now out in Nature Methods! 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.

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'.

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