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Integrating multi-omics datasets to infer phenotype-specific driver genes, regulatory interactions and drug response

Award Number: R35GM133657
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

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PROJECT SUMMARY My lab’s research goal is to develop open source integrative computational tools that perform secondary analysis of publicly available multi-omics biological, clinical and environmental exposure datasets to infer context-specific regulatory interactions and modules, and to predict disease associated genes and patient-specific drug response. With the recent advances in high-throughput technologies in biology, the cost of data generation has reduced tremendously, which enabled the generation of vast amounts of multi-omics datasets such as gene expression, microRNA expression, copy number alteration, and DNA methylation. Numerous international and national consortiums have been established to generate these multi-omics datasets to study regulatory elements in DNA, disease and healthy tissues, epigenetic signatures, and drug responses. Furthermore, ongoing large initiatives such as UK Biobank, Million Records Project, and the All of Us research program will bring vast amounts of multi-omics datasets from millions of individuals. Consequently, there is a tremendous need for scalable methods that can integrate different layers of multi-omics datasets across millions of individuals from different backgrounds. These methods would produce valuable insights into human diseases and pave the way towards precision medicine. My research program is devoted to utilizing these multi-omics datasets cost effectively by developing open-source innovative and integrative computational resources. My lab has been successful in developing open source integrative computational methods to integrate such datasets to infer gene regulatory interactions and modules and to predict disease drivers. In the next five years, we aim to extend our recent and ongoing work to infer context-specific regulatory interactions and modules, and to predict disease associated genes and patient- specific drug response. We will integrate various types of heterogenous multi-omics datasets to build integrative and scalable computational tools. The computational tools we develop through this research will enable us to elucidate the genetic and epigenetic architecture of regulatory interactions and drug response and discover novel disease associated genes. Our tools will be applicable for any disease type and will enable researchers to leverage publicly available multi- omics datasets to their full extent and pave the road towards precision medicine. Through this research program, I will create research opportunities for graduate and undergraduate students particularly those from under-represented groups.


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: 2023 ( Subtotal = $678,989 )
2023	2023	UNIVERSITY OF NORTH TEXAS	1155 UNION CIR #305250	DENTON	TX	76203	DENTON	USA	Biomedical Research and Research Training	001	6	7/20/2023	NON-COMPETING CONTINUATION	$349,691
2023	2023	UNIVERSITY OF NORTH TEXAS	1155 UNION CIR #305250	DENTON	TX	76203	DENTON	USA	Biomedical Research and Research Training	000	5	5/16/2023	SUPPLEMENT FOR EXPANSION	$8,825
2023	2023	UNIVERSITY OF NORTH TEXAS	1155 UNION CIR #305250	DENTON	TX	76203	DENTON	USA	Biomedical Research and Research Training	002	6	8/2/2023	SUPPLEMENT FOR EXPANSION	$320,473
														Subtotal = $678,989

Issue Date FY: 2022 ( Subtotal = $461,066 )
2022	2022	UNIVERSITY OF NORTH TEXAS	1155 UNION CIR #305250	DENTON	TX	76203	DENTON	USA	Biomedical Research and Research Training	001	5	9/19/2022	SUPPLEMENT FOR EXPANSION	$111,375
2022	2022	UNIVERSITY OF NORTH TEXAS	1155 UNION CIR #305250	DENTON	TX	76203	DENTON	USA	Biomedical Research and Research Training	000	5	7/11/2022	NON-COMPETING CONTINUATION	$349,691
														Subtotal = $461,066

Issue Date FY: 2021 ( Subtotal = $314,703 )
2021	2021	UNIVERSITY OF NORTH TEXAS	1155 UNION CIR #305250	DENTON	TX	76203	DENTON	USA	Biomedical Research and Research Training	002	4	7/7/2021	NON-COMPETING CONTINUATION	$342,307
2021	2020	UNIVERSITY OF NORTH TEXAS	1155 UNION CIR #305250	DENTON	TX	76203	DENTON	USA	Biomedical Research and Research Training	005	3	7/11/2021	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$345,476
2021	2020	UNIVERSITY OF NORTH TEXAS	1155 UNION CIR #305250	DENTON	TX	76203	DENTON	USA	Biomedical Research and Research Training	001	3	12/29/2020	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$149,597
2021	2020	MARQUETTE UNIVERSITY	915 W WISCONSIN AVE RM 175	MILWAUKEE	WI	53233	MILWAUKEE	USA	Biomedical Research and Research Training	004	2	7/11/2021	NON-COMPETING CONTINUATION	-$186,791
2021	2020	MARQUETTE UNIVERSITY	915 W WISCONSIN AVE RM 175	MILWAUKEE	WI	53233	MILWAUKEE	USA	Biomedical Research and Research Training	000	2	12/28/2020	NON-COMPETING CONTINUATION	-$177,201
2021	2019	MARQUETTE UNIVERSITY	915 W WISCONSIN AVE RM 175	MILWAUKEE	WI	53233	MILWAUKEE	USA	Biomedical Research and Research Training	003	1	7/11/2021	NEW	-$158,685
														Subtotal = $314,703

Issue Date FY: 2020 ( Subtotal = $363,992 )
2020	2020	MARQUETTE UNIVERSITY	915 W WISCONSIN AVE RM 175	MILWAUKEE	WI	53233	MILWAUKEE	USA	Biomedical Research and Research Training	000	2	6/10/2020	NON-COMPETING CONTINUATION	$363,992
														Subtotal = $363,992

Issue Date FY: 2019 ( Subtotal = $341,867 )
2019	2019	MARQUETTE UNIVERSITY	915 W WISCONSIN AVE RM 175	MILWAUKEE	WI	53233	MILWAUKEE	USA	Biomedical Research and Research Training	000	1	7/30/2019	NEW	$341,867
														Subtotal = $341,867

Grand Total All Awards = $2,160,617

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Integrating multi-omics datasets to infer phenotype-specific driver genes, regulatory interactions and drug response

Award Number: R35GM133657

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

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