Biomedical Informatics & Genomics Grants

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Ongoing Research Support 

1.NIH R01AR069055
PI: Deng, Hong-Wen

Title: Decoding methylation mediated epigenomic contributions to male osteoporosis

Goal: To identify and characterize differentially methylated regions (DMRs) in monocytes at the whole genome level for BMD and osteoporosis variation in males.

2.NIH U19AG055373
PI: Deng, Hong-Wen

Title: Trans-omics integration of multi-omics studies for male osteoporosis

Goal: To comprehensively investigate male osteoporosis risk factors simultaneously at the genome, transcriptome, and epigeno levels in males, while considering environmental factors. 

3. NIH U19AG055373-05S1
PI: Deng, Hong-Wen

Title: Trans-omics integration of multi-omics studies for osteoporosis: administrative supplement for COVID-19 studies

Goal: To identify specific extrinsic (e.g., diet, lifestyle, medication) and intrinsic (e.g., gene expression and serum metabolites) factors contributing to individual variation in COVID-19 susceptibility, severity, and outcomes 

4. NIH U19AG055373-8797
PI: Deng, Hong-Wen

Title: Genome wide sequencing for osteoporosis risk genes in males

Goal: To identify potential functional DNA sequence variants, in particular those rare and structural variants, for male BMD, and to assess their sex/ethnicity generality/specificity and their ultimate importance to the most devastating clinical outcome of OP - osteoporotic hip fracture (HF). 

5. NIH U19AG055373-8795
PI: Zhao, Lan-Juan

Title: Core B: clinical core

Goal: To recruit 300 male human subjects (200 Caucasians and 100 African Americans, AA) for Projects 2 & 3 and offer expertise and support for clinical, translational and human study aspects of this P01 application. 

6. NIHU19AG055373-8796
PI: Wang, Yu-Ping

Title: Core C: biostatistics and bioinformatics core

Goal: To serve as a backbone support resource for experimental design refinement, data quality control, management, integration, analyses and interpretation, and serve as a synergizer to foster data and information exchange and collaboration for individual projects/cores in the PPG. 

7. NIH U19AG055373-8799
PI: Shen, Hui

Title: Analysis of methylome for osteoporosis risk in males

Goal: To identify and characterize, at the epigenome-wide level, differentially methylated regions (DMRs) in PBMs associated with osteoporosis risk in Caucasian males; and ascertain the DNA methylation mediated epigenetic mechanisms of osteoporosis.

8. NIHR56MH124925
PI: Wang, Yu-Ping

Title: Integration of brain imaging and multi-omics data for improved diagnosis and prediction of mental disorders

Goal: To lead to better differentiation of mental disorders with overlapping symptomatology and more accurate prediction of clinical outcomes and lay the groundwork for personalized care of psychiatric disorders by targeting their specific genetic make-ups and evaluating the effects of medical treatments.  

9. NIH R01AG061917
PI: Zhao, Qi; Shen, Hui
09/01/2019 – 04/30/2024

Title: Identification of metabolomic profiles for sarcopenia traits in older whites and blacks

Goal: To use the cutting-edge metabolomics approach (a high-throughput method for testing metabolites in biofluids) to systematically discover novel metabolic pathways for the pathogenesis of sarcopenia.  

10. NIH U01HG008657
PI: Jarvik, Gail Pairitzo; Crosslin, David

Title: eMERGE IV Northwest: A partnership to evaluate the use of genomic information in the health care of diverse participants

Goal: To investigate the implementation of 15 “genomic risk assessment” (GRA) scores in a network-wide set of diverse participants.

11. NIH R01GM118470
PI: Liu, Xiaowen; Ning, Xia; Sun; Liangliang

Title: Computational tools for proteoform identification by Top-Downdata independent acquisition mass spectrometry.

Goal: To propose new algorithms and machine learning models and develop the first software package for proteoform identification by TD-DIA-MS.

12. NIH R01CA247863
PI: Sun; Liangliang; Hummon, Amanda B; Liu, Xiaowen

Title: Quantitative top-down proteomics of human colorectal cancer cells and tumors

Goal: To develop new analytical tools to boost the sensitivity and scale of top-down proteomics and enable large-scale and quantitative top-down proteomics of CRC cells before and after metastasis as well as CRC tumors from patients with Lynch Syndrome.

Completed Research Support

1. NIH R01MH107354
PI: Wang, Yu-Ping
09/24/2015 – 06/30/2021

Title: Integration of fMRI imaging, genomics, network and biological knowledge

Goal: To develop novel computational approaches to correlate and integrate fMRI imaging with genomic data while incorporate biological knowledge and their interaction networks for the detection of biomarkers; and to apply/validate the detected biomarkers for the identification of risk genes/gene modules and for the improved diagnosis of subtle patient subgroups.

2. NIH R01MH104680
PI: Wang, Yu-Ping; Calhoun, Vince D & Deng, Hong-Wen

Title: Integration of brain imaging with genomic and epigenomic data

Goal: To develop integrative approaches for the detection of biomarkers from multiscale genomic and imaging data, so that multiple mental illnesses such as schizophrenia (SC), Unipolar (UD) and bipolar (BI) disorder can be better identified.  

3. NIH R01GM109068
PI: Wang, Yu-Ping
09/17/2014 – 08/31/2019

Title: Integration of multiscale genomic data for comprehensive analysis of complex dise

Goal: To tackle significant bioinformatics challenges by developing innovative integration approaches such as sparse models by considering the specific features of multiscale genomic data and apply such approaches to the diagnosis (e.g., identification of genes) and prediction of risks to complex diseases (e.g., osteoporosis). 

4. NIH R01AR059781
PI: Deng, Hong-Wen

Title: Epigenomewide DNA methylation study for osteoporosis risk

Goal: To identify and characterize differentially methylated regions (DMRs) in monocytes at the whole genome level for BMD and osteoporosis variation.  

5. NIH R01AR050496
PI: Deng, Hong-Wen
08/01/2004- 06/30/2015

Title: Robust and powerful test of candidate genes to bone mass

Goal: To identify NOVEL osteoporosis genes, assess their sex and ethnic specificity/generality, and perform functional studies of the identified novel genes for their specific molecular functional mechanisms for BMD variation.  

6. NIH R01AR057049
PI: Deng, Hong-Wen

Title: Identification of proteins important for male osteoporosis

Goal: To identify proteins differentially expressed in BMMSCs and PBMs in men with high vs. low BMD and thus identify proteins (and their genes) associated with male osteoporosis in BMMSCs and PBMs.

7. NIH P50AR055081-1
PI: Deng, Hong-Wen

Title: Genome wide scans for female osteoporosis

Goal: To identify osteoporosis genes that are gender specific for females with lower BMD and, secondarily, to assess the gender specificity of these identified genes in male samples.  

8. NIH P50AR055081-2
PI: Deng, Hong-Wen

Title: Genomic convergence for female osteoporosis risk genes

Goal: To identify osteoporosis risk genes and their functional aspects in females and assess the female specificity of these identified genes/functions in male samples.  

9. NIH P50AR055081-3
PI: Deng, Hong-Wen

Title: Proteome-wide expression study of osteogenic cells

Goal: To identify proteins differentially expressed in BMMSCs and PBMs in women: 1) with high vs. low BMD; 2) before and after menopause, and thus identify proteins (and their genes) associated with female osteoporosis and menopause in BMMSCs and PBMs.  

10. NIH P50AR055081-9001
PI: Deng, Hong-Wen

Title: Clinical core

Goal: To recruit 160 human subjects during four years to support work in Projects 2 and 3. Steps in recruitment are: search the ORC archive; make telephone contact; schedule candidates who pass the telephone screen; if eligible, complete clinical examination and collect specimens  

11. NIH P50AR055081-9002
PI:Deng, Hong-Wen

Title: Biostatistics and bioinformatics core

Goal: To collaborate with project investigators on the experimental design issues and the design of questionnaires and forms for efficient data acquisition, entry, tracking, retrieval and transfer, etc. and to implement (and develop if necessary) efficient and high quality data entry/management database system for all individual projects and to build quality control measures into those systems.  

12. NIH R03TW008221
PI: Deng, Hong-Wen
09/01/2009 – 06/30/2013

Title: Genetics of osteoporotic fractures in Chinese

Goal: To identify the genes for hip BMD and HF in Chinese by testing in Chinese the significance of the genes associated with hip BMD in Caucasians.  

13. NIH R21LM010042
PI: Wang, Yu-Ping
07/01/2009 – 06/30/2013

Title: A new paradigm for integrated analysis of multiscale genomic imaging datasets

Goal: To provide innovative and interdisciplinary approaches that combine the latest progress in image processing, imaging database design and machine learning with the development of high resolution and high throughput molecular imaging probes in genomics.  

14. NIHRC2DE020756
PI: Liu, Yao-Zhong; Deng, Hong-Wen; Genco, Robert; Hong, Liang
09/25/2009- 01/31/2013

Title: Genome-wide association study of periodontitis

Goal: To identify genes underlying risk of periodontitis, a prevalent dental disease of significant public health burden in the US.  

15. NIH R01AG026564
PI: Deng, Hong-Wen

Title: Genomic search for bone mass QTLs

Goal: To identify genomic regions underlying BMD variation with exceptionally high power and certitude using multiple and complementary approaches.  

16. NIH R15GM088802
PI: Wang, Yu-Ping

Title: Accurate detection of chromosomal abnormalities with multi-color image processing

Goal: To develop innovative multi-spectral image processing and machine learning techniques for M-FISH image analysis so that chromosomal rearrangement detection can be made more reproducible, robust, and faster, thereby significantly increasing the ability and efficacy of this newly developed cellular imaging technique.  

17. NIH R21AG027110
PI: Deng, Hong-Wen

Title: Proteomics study of peripheral blood monocytes on osteoporosis

Goal: To identify proteins differentially expressed in PBM in females, and identify those proteins that are associated with osteoporosis and menopause in PBM  

18. NIH R01GM060402
PI: Deng, Hong-Wen
08/01/2000- 08/31/2006

Title: Characterization of deleterious genomic mutations.

Goal: To provide powerful and efficient experimental designs and statistical methods for estimating U, and the distribution of mutation effects in a broad range of taxa, and provide useful and powerful tools for empiricists to characterize deleterious genomic mutations.  

19. NIH K01AR002170
PI: Deng, Hong-Wen

Title: Genetic basis of osteoporotic fractures and bone mass

Goal: To develop approaches in molecular and genetic epidemiology to search for genes underlying complex traits and to study genotype-by-environment (GXE) interaction. 

20. NIH P01DC001813-9002
PI: Deng, Hong-Wen

Title: Core: Statistics and data management

Goal: To provide support of the project that includes software and hardware support for all data collection and entering aspects, genetic analysis aspects, and database searches.