faculty

Manu Setty

msetty@fredhutch.org
Assistant Professor

Fred Hutch

Computational Biology

Developmental Biology, Stem Cells & Aging

Gene Expression, Cell Cycle & Chromosome Biology

Computational modeling of lineage decision mechanisms using single-cell data

Faculty Contact Information

Research Summary

We are a multi-disciplinary research group investigating the mechanisms of lineage decisions and cell-fate choices. We approach this fundamental problem by developing computational algorithms that model high-throughput single-cell genomics data using a broad array of machine learning techniques. We strongly believe in collaborative science and work in close conjunction with our collaborators in all aspects spanning experimental design of data collection, data analysis and modeling, and validation experiments.

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&query_key=1&WebEnv=MCID_5f9778cc76cf6355aa5a355f&retmode=json
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Publications

The following publications were retrieved from PubMed:

Perspectives on ENCODE.

ENCODE Project Consortium., Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM.

Nature. 2020 Jul; 7818(583)693-698

Regenerative lineages and immune-mediated pruning in lung cancer metastasis.

Laughney AM, Hu J, Campbell NR, Bakhoum SF, Setty M, Lavallée VP, Xie Y, Masilionis I, Carr AJ, Kottapalli S, Allaj V, Mattar M, Rekhtman N, Xavier JB, Mazutis L, Poirier JT, Rudin CM, Pe'er D, Massagué J.

Nat Med. 2020 Feb; 2(26)259-269

Author Correction: Characterization of cell fate probabilities in single-cell data with Palantir.

Setty M, Kiseliovas V, Levine J, Gayoso A, Mazutis L, Pe'er D.

Nat Biotechnol. 2019 Oct; 10(37)1237

The emergent landscape of the mouse gut endoderm at single-cell resolution.

Nowotschin S, Setty M, Kuo YY, Liu V, Garg V, Sharma R, Simon CS, Saiz N, Gardner R, Boutet SC, Church DM, Hoodless PA, Hadjantonakis AK, Pe'er D.

Nature. 2019 May; 7756(569)361-367

Negative Co-stimulation Constrains T Cell Differentiation by Imposing Boundaries on Possible Cell States.

Wei SC, Sharma R, Anang NAS, Levine JH, Zhao Y, Mancuso JJ, Setty M, Sharma P, Wang J, Pe'er D, Allison JP.

Immunity. 2019 Apr 16; 4(50)1084-1098.e10

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