Uthsav Chitra
@uthsavc
Incoming Assistant Professor @JHUCompSci | Postdoc @Schmidt_Center @broadinstitute | PhD @PrincetonCS | computational biology + ML
New life update! 🎆 🎓 This Fall, I will be joining the Department of Computer Science at Johns Hopkins University (@JHUCompSci) as an Assistant Professor, with an affiliation at the new Data Science and AI Institute (@HopkinsDSAI).
Congrats to Ben Langmead on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational & life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access & use DNA sequencing data. 🧬
🎉Congrats! 🥇@uthsavc: Mapping the topography of spatial gene expression with interpretable deep learning 🥈Anurendra Kumar: CellWHISPER: Inference of contact-mediated cell-sell signaling 🥉@xinhez: An AI-Cyborg System for Adaptive Intelligent Modulation of Organoid Maturation
Presenting at #ISMBECCB2025 tomorrow! GASTON-Mix, a unified model of spatial gradients and domains in spatial 'omics data. 11:20am UK time at RegSys Also recruiting students for my new lab at @JHUCompSci, feel free to reach out if you want to chat
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts biorxiv.org/content/10.110… #biorxiv_bioinfo
1/6 Excited to share our latest preprint: "MORPH Predicts the Single-Cell Outcome of Genetic Perturbations Across Conditions and Data Modalities". 🔗 biorxiv.org/content/10.110… 🧵 👇 Here is what MORPH is in a nutshell!
Congrats to @gillianychu et al!!
The culmination of several PhD years — today LAML is published! LAML infers max likelihood time-resolved cell lineage trees from dynamic lineage tracing data accurately and efficiently. Thanks to @benjraphael for his guidance! genomebiology.biomedcentral.com/articles/10.11…
The White House Vision for Dismantling Science in One Simple Plot open.substack.com/pub/joshuaswei…
Congrats Youn! and team, @lab_berger @HultgrenLab @broadinstitute @mit @GeorgKGerber1 @BrighamWomens @MGBResearchNews @harvardmed @AshleeMEarl
"Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain" - Kim et al. rdcu.be/ekTwf
Excited to share our latest preprint, introducing the hierarchical cross-entropy (HCE) loss — a simple change that consistently improves performance in atlas-scale cell type annotation models. doi.org/10.1101/2025.0…
I met @uthsavc at RECOMB '22. We got lunch and talked science. His GASTON work (RECOMB '24), with its isodepth, was the missing piece for applying our DAG Granger Causality (RECOMB '23) to spatial settings. And thus GLACIER got going, led by Prannav Shankar and @hliang74!
At RECOMB-Seq, I will be presenting GLACIER, with @uthsavc and my trainees Prannav and @hliang74 , where we introduce Spatial Granger Causal inference: decoding the drivers of tissue topology. It's a lovely RECOMB-to-RECOMB story, will tweet more soon. biorxiv.org/content/10.110…
2/ Here, wanted to highlight interesting approach from Bonnie Berger’s lab @MIT, velorama @CellSystemsCP. It goes the other way than regvelo, essentially leverages dynamics to infer regulatory interactions from single cell transcriptome and velocities, see cell.com/cell-systems/a…
Congratulations to @Schmidt_Center postdoc @uthsavc and team on their preprint, which introduces GASTON-Mix, an unsupervised deep learning approach for more accurately inferring spatial domains and gradients of gene expression: biorxiv.org/content/10.110… @broadinstitute
🚀 introducing fastppm: turbocharging tumor phylogeny reconstruction from bulk DNA-seq! we develop a new technique, tree-structured dual dynamic programming, to obtain 50-450x speedups for an important tumor phylogeny regression problem. check it out: biorxiv.org/content/10.110….