We have developed software for phosphoproteomic site-assignment and for clustering of dynamic data. We have also developed and published software to aid in the design of peptide-directed and fusion protein-directed antibodies called NHLBI-AbDesigner (http://helixweb.nih.gov/AbDesigner/). A paper describing this tool and illustrating its use has been published (Pisitkun et al. PMID: 21956165). A second paper describing its application to development of antibodies for several glomerular marker proteins has also been published (Pisitkun et al. PMID: 25328345). NHLBI-AbDesigner is currently utilized by many commercial antibody production companies. An expansion of AbDesigner is under development. We have also developed software called PhosphoLogo to produce sequence logos from phosphoproteomic data. Current efforts are aimed at the development of practical tools for application of Bayesian statistical approaches, data-mining approaches, and structural equation modeling to large-scale physiological data. A list of available software programs can be found at http://helixweb.nih.gov/ESBL/. We have also developed several databases of proteomic and transcriptomic data to be used in kidney research (http://helixweb.nih.gov/ESBL/Database/index.html). Tools are under development for cross-referencing these databases for studies in integrative biology that are based on the Big Data concept.

Project Start
Project End
Budget Start
Budget End
Support Year
5
Fiscal Year
2015
Total Cost
Indirect Cost
Name
U.S. National Heart Lung and Blood Inst
Department
Type
DUNS #
City
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Zip Code
Hyndman, Kelly A; Yang, Chin-Rang; Jung, Hyun Jun et al. (2018) Proteomic determination of the lysine acetylome and phosphoproteome in the rat native inner medullary collecting duct. Physiol Genomics 50:669-679
Jung, Hyun Jun; Raghuram, Viswanathan; Lee, Jae Wook et al. (2018) Genome-Wide Mapping of DNA Accessibility and Binding Sites for CREB and C/EBP? in Vasopressin-Sensitive Collecting Duct Cells. J Am Soc Nephrol 29:1490-1500
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Isobe, Kiyoshi; Jung, Hyun Jun; Yang, Chin-Rang et al. (2017) Systems-level identification of PKA-dependent signaling in epithelial cells. Proc Natl Acad Sci U S A 114:E8875-E8884
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Hwang, Jacqueline R; Chou, Chung-Lin; Medvar, Barbara et al. (2017) Identification of ?-catenin-interacting proteins in nuclear fractions of native rat collecting duct cells. Am J Physiol Renal Physiol 313:F30-F46
Chen, Lihe; Lee, Jae Wook; Chou, Chung-Lin et al. (2017) Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq. Proc Natl Acad Sci U S A 114:E9989-E9998
Xue, Zhe; Chen, Jia-Xu; Zhao, Yue et al. (2017) Data integration in physiology using Bayes' rule and minimum Bayes' factors: deubiquitylating enzymes in the renal collecting duct. Physiol Genomics 49:151-159

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