Uthsav Chitra
@uthsavc
Assistant Professor of Computer Science, Johns Hopkins University @JHUCompSci @HopkinsDSAI working on computational genomics + ML
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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).
The Department of Computer Science is pleased to welcome 9 new tenure-track faculty to its ranks this academic year! Featuring @anand_bhattad, @uthsavc, @zihyunchiu, @krisgligoric, @murat_kocaoglu_, @_ziyang_, @tizianopiccardi, @yaxingyao, & @zakynthinou: cs.jhu.edu/news/nine-new-…
Unique Molecular Identifiers (UMIs) in RNA-seq are supposed to be… unique. But what if they don’t have to be? In our new preprint w/ Dylan Agyemang + @rafalab, we show that UMIs can be shorter—if you use the right estimator. 1/12
TissueMosaic is a super cool method for contrastive ST analysis with lots of rigorous benchmarking -- congrats @SandeepKambham2 et al!!
TissueMosaic, our method to study how changes in tissue structure across conditions affect cell-intrinsic function, is now out @CellSystemsCP! cell.com/cell-systems/f…
#HopkinsDSAI welcomes 22 new faculty members, who join more than 150 DSAI faculty members across @JohnsHopkins in advancing the study of data science, machine learning, and #AI and translation to a range of critical and emerging fields. ai.jhu.edu/news/data-scie…
Should you take an SVD before or after integrating your data? Our new preprint derives some surprising insights using tools from Random Matrix Theory. With @PhillipNicol, @rafalab, and Rong Ma. arxiv.org/pdf/2507.22170 (1/n)
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. 🧬
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! 🥇@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
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…
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