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Developing new computational tools for spatial transcriptomics data

Award Number: R01HG011883
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/16/2021
PERIOD OF PERFORMANCE END DATE: 06/30/2026

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Developing new computational tools for spatial transcriptomics data - Project Summary Spatial transcriptomics is a groundbreaking new technology that allows measurement of gene ac- tivity in a tissue sample while mapping where the activity is occurring. It holds the promise to facilitate our understanding of spatial heterogeneity underlying essential phenotypes and diseases, such as neurodegenerative diseases and cancer. However, the development of bioinformatics infrastructures and computational tools has fallen seriously behind the technological advances. The lack of proper computational approaches presents current data analysis barriers that signiﬁcantly hinder biological investigations. The overarching goal of this proposal is to address some of the most pressing ana- lytic challenges facing proﬁling and interpreting spatial transcriptomics data, including 1) lack of robust identiﬁcation of genes with spatial expression patterns across a variety of technical platforms, 2) lack of tools to identify structures, microenvironments as well as developmental trajectory on the tissue, and 3) lack of tools that can jointly analyze spatial transcriptomic data across multiple samples and multiple data sources. In the proposal, we will work on the following aims: Aim 1. Develop nonpara- metric tools for identifying genes with spatial expression patterns. Aim 2. Develop spatially aware dimension reduction tools for detecting structures and developmental trajectories on the tissue. Aim 3. Develop integrative association tools for spatial transcriptomic analysis across multiple samples and datasets. All the methods will be implemented in user-friendly software and disseminated to the sci- entiﬁc community. Successful achievement of all aims will dramatically increase the power of spatial transcriptomics analysis, and facilitate the application of these cutting-edge technologies to transla- tional and clinical studies.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2024 ( Subtotal = $373,641 )
2024	2024	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	000	4	7/22/2024	NON-COMPETING CONTINUATION	$373,641
														Subtotal = $373,641

Issue Date FY: 2023 ( Subtotal = $381,266 )
2023	2023	UNIVERSITY OF CHICAGO	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	000	3	7/3/2023	NON-COMPETING CONTINUATION	$381,266
														Subtotal = $381,266

Issue Date FY: 2022 ( Subtotal = $381,266 )
2022	2022	UNIVERSITY OF CHICAGO, THE	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	000	2	6/27/2022	NON-COMPETING CONTINUATION	$381,266
														Subtotal = $381,266

Issue Date FY: 2021 ( Subtotal = $397,266 )
2021	2021	UNIVERSITY OF CHICAGO, THE	5801 S ELLIS AVE	CHICAGO	IL	60637	COOK	USA	Human Genome Research	000	1	9/16/2021	NEW	$397,266
														Subtotal = $397,266

Grand Total All Awards = $1,533,439

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Developing new computational tools for spatial transcriptomics data

Award Number: R01HG011883

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/16/2021

PERIOD OF PERFORMANCE END DATE: 06/30/2026

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