Princeton beehive

Ari Gewirtz defended her impressive thesis today: "Exploring Context-Specific Expression Variation and Distal Gene Regulation via Latent Variable Models." I can't wait for her to share the last chapter on QTL mapping w/single cell data -- preprint soon! We will miss you, Ari!

@sunny_ccui, with Liz Yoo, @DidongLi, and collaborators from @PennMedicine, presented her paper 'Hierarchical Gaussian Processes and Mixtures of Experts to Model COVID-19 Patient Trajectories' last week at @PacSymBiocomp worldscientific.com/doi/abs/10.114…

Congratulations to Guillaume Martinet, PhD who successfully defended his thesis: "Invariant Mechanisms in Transfer Learning and Causal Inference: Some Theoretical Perspectives and Algorithms" on Tuesday! Great presentation, and exciting work! 🌟

Our paper “Hierarchical Gaussian Processes and Mixtures of Experts in Predicting COVID Patient Trajectories” has been accepted accepted for publication in the proceedings AND oral presentation at PSB 2022! Can’t wait to share our results with you on the Big Island 🏝️ #PSB22

Great work from @hotarcheetos in leading the project with @ras_trophysics and in the Toettcher lab members/collaborators @kazuhiroaokilab and @danielle_isakov!

Amazing collaboration with @toettch and @ras_trophysics -- can't wait for the next one!

Do you have time-series fluorescence data in which you would like to quantify signaling? Our cellular point process paper is out: pnas.org/content/118/32…

Wonderful work on best practices EHR data processing and some cool vignettes by @Aishwarya_R_M, Liz Yoo, and Jeff Soules (Flatiron), and a great collaboration with Dr. Krzysztof Laudanski (HUP). Try out COP-E-CAT if you build AI/ML methods for EHR data!

COP-E-CAT paper: dl.acm.org/doi/10.1145/34… COP-E-CAT software: github.com/eyeshoe/cop-e-… MIMIC-IV data: physionet.org/content/mimici…

Our COP-E-CAT paper and software are available! COP-E-CAT allows you to access, regularize, filter, impute, and chunk the MIMIC-IV data into regular time slices. Then you can use this EHR dataset easily in ML downstream analyses: prediction, dimension reduction, RL, etc.

@Brian_SungJoon successfully defended his thesis on Tuesday: "Analysis of Distal eQTLs across Multiple Human Tissues and Methods to Improve Their Quality" -- incredible work on trans-eQTLs and methods for discovery in the GTEx data. Congratulations, Brian!

Incredible Greg Gundersen defended his thesis today "Practical Algorithms for Latent Variable Models." His curiosity, determination, & the gradient of his trajectory will not be matched soon. The blog he wrote for his own understanding is an ML treasure: gregorygundersen.com/blog/

.@hotarcheetos Archit Verma, PhD successfully defended his thesis "Bayesian modeling of single cell data" last week. His work on models to study single cell data is phenomenal! We will miss him so much, but hope he will join us for future group retreats! Best of luck, Archit!

PhD student @andy_c_jones did so well on his generals exam on contrastive latent variable models for case-control study data. I love his collaborator slide because it shows the breadth of his work & collaborations, and also the mentoring he's involved in with amazing undergrads!

This is the work of @jordan_t_ash, Greg Darnell, and @danbmunro -- all code available at github.com/daniel-munro/i…

The ImageCCA paper is out! Seven years in the making, this work uses a convolutional autoencoder plus CCA to find associations between histopathological images and bulk gene expression data across tissues. In GTEx v6 data, we find image morphology QTLs. nature.com/articles/s4146…

The scGeneFit paper is out! Amazing collaboration with @SoledadVillar5 and @bidumit -- and an easy-to-use Python package available for marker discovery in single cell data! nature.com/articles/s4146…

Barbara was selected for the ISCB Overton Prize! She will give the Overton lecture this July at ISMB. iscb.org/ismbeccb2021-p…

Out in PLoS Comp Bio: Causal network inference from gene transcription time series data. Super excited about this work with (then) undergrad @JonathanLu11, @bidumit, and @timreddy's Lab! journals.plos.org/ploscompbiol/a…