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Manu Setty -- Computational modelling of lineage decision mechanisms using single-cell data

Patterned pufferfish scales demonstrating a Turing pattern in the natural world
Dates:22 March 2021
Times:16:00 - 17:00
What is it:Seminar
Organiser:Department of Mathematics
Who is it for:University staff, External researchers, Current University students
Speaker:Manu Setty
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  • Mathematics in the life sciences
  • Department of Mathematics

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  • In category "Seminar"
  • In group "(Maths) Mathematics in the life sciences "
  • In group "(Maths) Maths seminar series"
  • By Department of Mathematics

(via Zoom) Join us for this seminar by Manu Setty (Fred Hutch, WA, USA) as part of the North West Seminar Series in Mathematical Biology and Data Sciences. Details of the full series can be found here https://www.cms.livjm.ac.uk/APMSeminar/

Please contact carl.whitfield@manchester.ac.uk or igor.chernyavsky@manchester.ac.uk for the zoom link, or sign up to the mailing list.

Abstract: How a cell decides its lineage is a long-standing and enigmatic question in molecular biology. Single-cell technologies offer unprecedented scale and resolution to study the cellular differentiation process and enable the alignment of cells into a unified trajectory representing their developmental progression. I will describe Palantir, the first single-cell trajectory detection algorithm to view the differentiation process as a probabilistic change in cell potential. Palantir models differentiation as a Markov process to compute the lineage biases and differentiation potential, a measure of plasticity, for all cells. Palantir modeling enables an accurate identification of lineage decision regions and associated gene expression and regulatory dynamics. I will then describe our study to characterize the spatial and temporal trajectories of mouse endoderm development. Combining Palantir modeling with a large-scale single-cell data, we uncovered an unexpected plasticity of embryonic epiblast cells to differentiate to the surrounding extra-embryonic endoderm at implantation and the concomitant emergence of the spatial signal in the endoderm. Our analysis further demonstrated the convergence of embryonic definitive and extra-embryonic visceral endoderm cells into spatially organized organ territories in the gut-tube at mid-gestation.

To subscribe to the mailing list for this event series, please send an e-mail with the phrase “subscribe math-lifesci-seminar” in the message body to listserv@listserv.manchester.ac.uk

Speaker

Manu Setty

Role: Assistant Prof

Organisation: Fred Hutchinson Cancer Centre

  • https://www.fredhutch.org/en/faculty-lab-directory/setty-manu.html

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Carl Whitfield

carl.whitfield@manchester.ac.uk

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