Manu Setty Profile
Manu Setty

@SettyM

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Assistant Professor, @fredhutch @HutchBasicSci & Translational Data Science IRC. Computational biologist | Single-cell data analysis and modeling.

Seattle, WA
Joined January 2011
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@SettyM
Manu Setty
1 year
Very excited to have Mellon out in @naturemethods today!.
@naturemethods
Nature Methods
1 year
Mellon accurately estimates cell-state densities using high-dimensional single-cell data, unveiling regulatory dynamics and mechanisms in cell differentiation. @SettyM @fredhutch
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@SettyM
Manu Setty
9 months
@KamalaHarris Incredibly easy, fast and efficient process. Thank you @KingCountyWA @kcelections !
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@SettyM
Manu Setty
9 months
My journey from south India to biomedical researcher in the United States is not too dissimilar to the one taken by @KamalaHarris mother. With deep gratitude for all the opportunities I have been provided, my vote is for respect, dignity and a new way forward.
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@SettyM
Manu Setty
9 months
16 years after arriving in the United States, I am honored and proud to cast my first vote in a Presidential election to a daugher of immigrants, @VP @KamalaHarris !
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@SettyM
Manu Setty
9 months
What happens when a high school science teacher spends her summer learning computational biology and coding basics ? Biology and Forensics teacher Dr. Rama Devagupta wrote about her experience in the Setty Lab . Check out our Hutch Teacher Fellowship Blog:
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@SettyM
Manu Setty
9 months
Are you an early career scientist who wants to pursue a research project in the lab of a Fred Hutch Computational Biologist mentor? If yes, then the #MahanFellowship is for you. Apply by Dec. 20, 2024! Learn more: 
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@SettyM
Manu Setty
10 months
RT @elhamazizi: Awesome week at Bertinoro #CompBio meeting! Exciting times for cancer evolution x tumor microenvironment! Thank you @Sohrab….
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@SettyM
Manu Setty
1 year
Join us in this exciting symposium to learn about post-doc opportunities at @HutchBasicSci.
@HutchBasicSci
Hutch Basic Sciences
1 year
Calling everyone interested in #postdoc opportunities @HutchBasicSci! . Join us at the Pathfinders: Postdoc Recruitment Symposium @FredHutch. Explore our research programs, present your work, and network with current postdocs and faculty. Apply by July 8:
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@SettyM
Manu Setty
1 year
@naturemethods Re-upping the tweetorial from our bioRxiv post here:
@SettyM
Manu Setty
2 years
Super excited to present our algorithm, Mellon for computing densities in single-cell landscapes.
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@SettyM
Manu Setty
1 year
Terrific work by @danielcjones in @EvNewell1 lab- Proseg is our go-to cell segmentation for all spatial transcriptomics data!.
@EvNewell1
Evan Newell
1 year
Using in situ spatial transcriptomics? Try Proseg, @danielcjones’s new cell segmentation method based on probabilistic and Cellular Potts modeling. Great for @vizgen_inc Merscope, @10xGenomics Xenium, and @nanostringtech CosMx data. Preprint & code: (1/n).
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@SettyM
Manu Setty
2 years
The #MahanFellowship supports young scientists in the early stages of their careers. We offer fellows a 21-month stipend as they pursue their proposed research project, alongside a mentor in one of our Herbold Computational Biologist labs. Apply today:
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@SettyM
Manu Setty
2 years
RT @cegs_ica: 1/8 Today we highlight exciting work from the @SettyM lab that introduces Mellon, a new approach for quantifying cell-state d….
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@SettyM
Manu Setty
2 years
RT @PhilippWeiler7: Say hello to CellRank 2, a unified framework for data view independent fate mapping! Have a look at our preprint on bio….
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@SettyM
Manu Setty
2 years
Deadline this Friday!.
@SettyM
Manu Setty
2 years
Calling all PhD (or equivalent) students within 2 years of graduation or who have graduated in the last year: Join us for an opportunity to visit with faculty at @FredHutch and hear about career opportunities at this world-renowned institution:
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@SettyM
Manu Setty
2 years
Mellon repository is available at and the pipeline for primed and lineage-specific peak identification (along with other utilities for ATAC metacells) is available at:
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@SettyM
Manu Setty
2 years
We have implemeneted Mellon as a general purpose Gaussian Process function estimator with a number of utilities including super-fast gene trend estimation along pseudo-time for thousands of genes.
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@SettyM
Manu Setty
2 years
Finally, Mellon is blazing fast - density for 100k cells takes only a few minutes with a (near) linear dependence of computation time on number of cells.
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@SettyM
Manu Setty
2 years
The function is also differentiable, which means we can interpolate the change in density too! The measured time points are grey lines at the bottom - all other times are interpolated densities and changes.
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@SettyM
Manu Setty
2 years
Mellon framework can be extended to infer a density function that is continuous in both cell-state and time. We use this to interpolate densities between measured time points in time-series datasets. Thanks to @MarioniLab for the repo to download data: !
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@SettyM
Manu Setty
2 years
We also developed a procedure to disentagle primed and lineage-specific peaks from single-cell ATAC data (rather than one gene score), and show that enhancer priming plays a role in driving low-density transitions.
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