
Uthsav Chitra
@uthsavc
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Incoming Assistant Professor @JHUCompSci | Postdoc @Schmidt_Center @broadinstitute | PhD @PrincetonCS | computational biology + ML
Cambridge, MA
Joined September 2018
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).
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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!
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I am so deeply grateful for the support of many mentors and role models throughout the application process — there are too many to tag here, but thank you all 🙏 . (Also grateful for the @HDSIUCSD Rising Stars in Data Science workshop which pushed me to apply this cycle!).
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RT @Schmidt_Center: 🎉Congrats!.🥇@uthsavc: Mapping the topography of spatial gene expression with interpretable deep learning.🥈Anurendra Kum….
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RT @TravisEGibson: Congrats Youn! and team, . @lab_berger @HultgrenLab @broadinstitute @mit @GeorgKGerber1 @BrighamWomens @MGBResearchNews….
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RT @sebacultrera: Excited to share our latest preprint, introducing the hierarchical cross-entropy (HCE) loss — a simple change that consis….
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RT @rohitsingh8080: I met @uthsavc at RECOMB '22. We got lunch and talked science. His GASTON work (RECOMB '24), with its isodepth, was th….
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RT @rohitsingh8080: At RECOMB-Seq, I will be presenting GLACIER, with @uthsavc and my trainees Prannav and @hliang74 , where we introduce S….
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RT @fabian_theis: 2/ Here, wanted to highlight interesting approach from Bonnie Berger’s lab @MIT, velorama @CellSystemsCP. It goes the oth….
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RT @Schmidt_Center: Congratulations to @Schmidt_Center postdoc @uthsavc and team on their preprint, which introduces GASTON-Mix, an unsuper….
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RT @henrismitch: 🚀 introducing fastppm: turbocharging tumor phylogeny reconstruction from bulk DNA-seq! we develop a new technique, tree-st….
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@benjraphael @henrismitch informed me that the NCI workshop where we developed these ideas is now canceled thanks to the @realDonaldTrump @elonmusk NIH freeze 🙁.
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Finally, if you've gotten this far: this work builds on our earlier work with @Cong992 using *complex analysis* (conformal mapping) to model spatial gradients. Check it out!.
Spatial transcriptomics meets complex analysis – our new method Belayer models spatial gene expression in layered tissues, now published in @CellSystemsCP. Work led by @Cong992 and @uthsavc with Shirley Zhang. 1/6
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Check out the paper for more details and neat biological applications! For example, modeling spatial gradients → much more accurate SVG identification. Thanks to great collaborators @BrianJohnArnold @koheisanno @hrksrkr @Cong992 Sereno @benjraphael 🙂
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GASTON algorithm is quite natural: parametrize functions h,d with neural nets and learn from data. Fun back-story: @benjraphael and I derived most of this model at the bar near an NCI workshop 🥂😅
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