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LineageDiscovery SIGNED

Laying the Biological, Computational and Architectural Foundations for Human Cell Lineage Discovery

Total Cost €

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EC-Contrib. €

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Partnership

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Project "LineageDiscovery" data sheet

The following table provides information about the project.

Coordinator
WEIZMANN INSTITUTE OF SCIENCE 

Organization address
address: HERZL STREET 234
city: REHOVOT
postcode: 7610001
website: www.weizmann.ac.il

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Israel [IL]
 Project website http://www.weizmann.ac.il/math/Shapiro/
 Total cost 2˙250˙000 €
 EC max contribution 2˙250˙000 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-ADG
 Funding Scheme ERC-ADG
 Starting year 2015
 Duration (year-month-day) from 2015-09-01   to  2020-07-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    WEIZMANN INSTITUTE OF SCIENCE IL (REHOVOT) coordinator 2˙250˙000.00

Map

 Project objective

Within a decade, advances in single-cell genomics would allow humanity to embark on a coordinated international effort to discover the human cell lineage tree. The goal of LineageDiscovery is to lay the biological, computational and architectural foundations for this envisioned project and demonstrate its feasibility and value. An organismal cell lineage tree is a rooted, labelled binary tree where nodes represent organism cells, edges represent progeny relations and labels capture cell state. The tree of an adult human has about 100 trillion nodes. Many fundamental open questions in biology and medicine are about the structure, dynamics and variance of the human cell lineage tree in development, health, ageing and disease. E.g., which cancer cells give rise to metastases? Do beta cells renew? Which progeny do brain stem cells produce in development, maintenance and ageing? LineageDiscovery is based on a decade of research on this challenge by Shapiro’s lab and others. It will develop an efficient biological-computational cell lineage discovery workflow that starts with sampled cells and ends with knowledge of their cell lineage tree; and a scalable architecture for the collaborative development and the distributed deployment of this workflow. The workflow will be based on emerging single-cell technologies and will include novel algorithms to analyse single-cell data, to reconstruct cell lineage trees, and to infer ancestral cell type and state dynamics. A programmable meta-system will be developed and used for workflow optimization and evaluation. The workflow and architecture will be deployed and tested in a broad range of proof-of-concept human cell lineage discovery experiments with self-funded collaborators. Successful execution of this research plan coupled with expected advances in single-cell genomics would establish both the feasibility and the value of the envisioned large-scale human cell lineage discovery project, ideally leading to its launch.

 Publications

year authors and title journal last update
List of publications.
2016 Tamir Biezuner, Adam Spiro, Ofir Raz, Shiran Amir, Lilach Milo, Rivka Adar, Noa Chapal-Ilani, Veronika Berman, Yael Fried, Elena Ainbinder, Galit Cohen, Haim M. Barr, Ruth Halaban, Ehud Shapiro
A generic, cost-effective, and scalable cell lineage analysis platform
published pages: 1588-1599, ISSN: 1088-9051, DOI: 10.1101/gr.202903.115
Genome Research 26/11 2019-07-05
2016 Adam Spiro, Ehud Shapiro
eSTGt: a programming and simulation environment for population dynamics
published pages: , ISSN: 1471-2105, DOI: 10.1186/s12859-016-1004-y
BMC Bioinformatics 17/1 2019-07-05
2016 Ofir Raz, Tamir Biezuner, Adam Spiro, Shiran Amir, Lilach Milo, Alon Titelman, Amos Onn, Uriel Feige, Ehud Shapiro
Short Tandem Repeat stutter model inferred from direct measurement of in vitro stutter noise
published pages: , ISSN: 0028-0836, DOI: 10.1101/065110
bioRxiv 2019-06-05
2016 Tamir Biezuner, Adam Spiro, Ofir Raz, Shiran Amir, Lilach Milo, Rivka Adar, Noa Chapal-Ilani, Veronika Berman, Yael Fried, Elena Ainbinder, Galit Cohen, Haim M. Barr, Ruth Halaban and Ehud Shapiro
A generic, cost-effective, and scalable cell lineage analysis platform
published pages: , ISSN: 1088-9051, DOI: 10.1101/gr.202903.115
Genome research 2019-06-05

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The information about "LINEAGEDISCOVERY" are provided by the European Opendata Portal: CORDIS opendata.

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