Sunday, June 29, 2025 6/29/2025

Computational methods for studying single-cell 3D genome

Award Number: R01HG012303
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 02/11/2022
PERIOD OF PERFORMANCE END DATE: 01/31/2026

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Computational methods for studying single-cell 3D genome - PROJECT SUMMARY The three-dimensional (3D) genome organization in the nucleus is of vital importance to genome function. The vast majority of the existing 3D genome studies, however, are based on population-based assays that are unable to unveil the functional roles of 3D genome structures at single-cell resolution in complex tissues. Recent advent in single-cell Hi-C (scHi-C) technologies has enabled genomic mapping of chromatin interactions in individual cells, but the analysis of scHi-C data remains a significant challenge. In particular, computational methods that can effectively analyze scHi-C data to extract multiscale 3D genome features are significantly lacking, limiting our ability to reveal the variability of structure and function connections in heterogeneous cell populations. The overall objective of this proposal is to develop state-of-the-art computational tools for scHi-C data analysis that effectively identify multiscale single-cell 3D genome features and connect them to genome function. Specifically, we will (1) develop algorithms for scHi-C data processing and imputation to delineate multiscale 3D genome features; (2) develop computational methods to connect 3D genome structure and function in heterogeneous cell population; and (3) develop an integrative visualization platform to navigate single-cell 3D genome organization. The methods developed in this project can be applied to all types of scHi-C data generated by different single-cell chromatin interaction assays to reveal 3D genome features at multiple scales, quantifying their variability and predicting their functional outcomes. The new tools and resources from this project will be publicly accessible through our new visualization platform that provides integrative and interactive navigation of scHi-C data and other data types. Overall, our project will greatly facilitate the use of scHi-C data by the broad scientific community and be of high value to a diverse group of biomedical researchers.


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: 2025 ( Subtotal = $540,909 )
2025	2025	CARNEGIE MELLON UNIVERSITY	5000 FORBES AVE	PITTSBURGH	PA	15213	ALLEGHENY	USA	Human Genome Research	001	4	4/24/2025	NON-COMPETING CONTINUATION	$54,091
2025	2025	CARNEGIE MELLON UNIVERSITY	5000 FORBES AVE	PITTSBURGH	PA	15213	ALLEGHENY	USA	Human Genome Research	000	4	1/23/2025	NON-COMPETING CONTINUATION	$486,818
														Subtotal = $540,909

Issue Date FY: 2024 ( Subtotal = $532,931 )
2024	2024	CARNEGIE MELLON UNIVERSITY	5000 FORBES AVE	PITTSBURGH	PA	15213	ALLEGHENY	USA	Human Genome Research	000	3	1/24/2024	NON-COMPETING CONTINUATION	$489,426
2024	2024	CARNEGIE MELLON UNIVERSITY	5000 FORBES AVE	PITTSBURGH	PA	15213	ALLEGHENY	USA	Human Genome Research	001	3	6/12/2024	NON-COMPETING CONTINUATION	$43,505
														Subtotal = $532,931

Issue Date FY: 2023 ( Subtotal = $544,905 )
2023	2023	CARNEGIE MELLON UNIVERSITY	5000 FORBES AVE	PITTSBURGH	PA	15213	ALLEGHENY	USA	Human Genome Research	001	2	3/2/2023	NON-COMPETING CONTINUATION	$54,491
2023	2023	CARNEGIE MELLON UNIVERSITY	5000 FORBES AVE	PITTSBURGH	PA	15213	ALLEGHENY	USA	Human Genome Research	000	2	1/30/2023	NON-COMPETING CONTINUATION	$490,414
														Subtotal = $544,905

Issue Date FY: 2022 ( Subtotal = $557,604 )
2022	2022	CARNEGIE MELLON UNIVERSITY	5000 FORBES AVE	PITTSBURGH	PA	15213	ALLEGHENY	USA	Human Genome Research	001	1	8/29/2022	NEW	$55,760
2022	2022	CARNEGIE MELLON UNIVERSITY	5000 FORBES AVE	PITTSBURGH	PA	15213	ALLEGHENY	USA	Human Genome Research	000	1	2/11/2022	NEW	$501,844
														Subtotal = $557,604

Grand Total All Awards = $2,176,349

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Computational methods for studying single-cell 3D genome

Award Number: R01HG012303

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 02/11/2022

PERIOD OF PERFORMANCE END DATE: 01/31/2026

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