Friday, September 19, 2025 9/19/2025

Bayesian Differential Causal Network and Clustering Methods for Single-Cell Data

Award Number: R01GM148974
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/21/2022
PERIOD OF PERFORMANCE END DATE: 08/31/2026

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Bayesian Differential Causal Network and Clustering Methods for Single-Cell Data - PROJECT SUMMARY (See instructions): The emergence of single-cell RNA-sequencing (scRNA-seq) techniques has motivated many computational methods to study gene regulation and cell differentiation at the single-cell level. However, to improve the translational value of scRNA-seq, new methods are required to comparatively study the molecular differences between normal and pathological cells/tissues, and between control and case/treatment groups. The vast majority of existing network and clustering models have focused on scRNA-seq data generated under one experimental condition. Moreover, most existing scRNA-seq network models are correlative in nature and do not infer causality. What remains lacking are rigorous statistical methods for inference of differential causal gene regulation and cell composition in response to experimental interventions. There is, therefore, a critical need to develop novel methodologies for identifying the effects of experimental interventions on causal gene regulatory relationships and cell differentiation by jointly modeling scRNA-seq data across experimental groups. Without such tools, mechanistically understanding gene regulatory activities and cell differentiation will likely remain difficult. Our overall objective is to design and validate Bayesian network and clustering models for identifying differential causal gene regulatory networks and cell composition for scRNA-seq data generated under different experimental conditions. To achieve the overall objective, three specific aims will be pursued: Aim 1: Develop a differential zero-inflated negative binomial Bayesian network model to construct differential cell-type-specific causal gene regulatory networks under two experimental conditions. Aim 2: Develop a trajectory-dependent directed cyclic graph model to construct cell-specific causal networks with feedback loops and monitor its structural changes with cell development. Aim 3: Develop a scalable Bayesian semiparametric differential clustering method to discover differential cell composition and cell-type-specific marker genes that are shared and/or unique to each experimental group.


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 = $297,934 )
2025	2025	TEXAS A & M UNIVERSITY	400 HARVEY MITCHELL PKY S STE 300	COLLEGE STATION	TX	77845	BRAZOS	USA	Biomedical Research and Research Training	000	4	8/16/2025	NON-COMPETING CONTINUATION	$297,934
														Subtotal = $297,934

Issue Date FY: 2024 ( Subtotal = $297,934 )
2024	2024	TEXAS A & M UNIVERSITY	400 HARVEY MITCHELL PKY S STE 300	COLLEGE STATION	TX	77845	BRAZOS	USA	Biomedical Research and Research Training	000	3	9/6/2024	NON-COMPETING CONTINUATION	$297,934
														Subtotal = $297,934

Issue Date FY: 2023 ( Subtotal = $297,934 )
2023	2023	TEXAS A & M UNIVERSITY	400 HARVEY MITCHELL PKY S STE 300	COLLEGE STATION	TX	77845	BRAZOS	USA	Biomedical Research and Research Training	000	2	9/12/2023	NON-COMPETING CONTINUATION	$297,934
														Subtotal = $297,934

Issue Date FY: 2022 ( Subtotal = $304,449 )
2022	2022	TEXAS A & M UNIVERSITY	400 HARVEY MITCHELL PKY S STE 300	COLLEGE STATION	TX	77845	BRAZOS	USA	Biomedical Research and Research Training	000	1	9/20/2022	NEW	$304,449
														Subtotal = $304,449

Grand Total All Awards = $1,198,251

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Bayesian Differential Causal Network and Clustering Methods for Single-Cell Data

Award Number: R01GM148974

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 09/21/2022

PERIOD OF PERFORMANCE END DATE: 08/31/2026

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