Computational Tools for Proteomics

Knepper, Mark

Abstract

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. NHLBI-AbDesigner: An online tool for design of peptide-directed antibodies. American Journal of Physiology: Cell Physiology. Epub in advance of printing, 2011). We have also developed software to produce sequence logos from phosphoproteomic data called Phosphologo. A list of available software programs can be found at http://helixweb.nih.gov/ESBL/. Finally, we have maintained an improved our proteomics and transcriptomic databases. A list of these databases can be found online at http://helixweb.nih.gov/ESBL/Database/index.html.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Heart, Lung, and Blood Institute (NHLBI)
• Type: Investigator-Initiated Intramural Research Projects (ZIA)
• Project #: 1ZIAHL006129-03
• Application #: 8746685
• Support Year: 3
• Fiscal Year: 2013
• Total Cost: $350,091

Institution

• Name: National Heart, Lung, and Blood Institute

Publications

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

Lee, Jae Wook; Alsady, Mohammad; Chou, Chung-Lin et al. (2018) Single-tubule RNA-Seq uncovers signaling mechanisms that defend against hyponatremia in SIADH. Kidney Int 93:128-146

Gilmer, Gabrielle G; Deshpande, Venkatesh; Chou, Chung-Ling et al. (2018) Flow Resistance along the Rat Renal Tubule. Am J Physiol Renal Physiol :

Saethang, Thammakorn; Hodge, Kenneth; Kimkong, Ingorn et al. (2018) AbDesigner3D: a structure-guided tool for peptide-based antibody production. Bioinformatics 34:2158-2160

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

Corcoran, Callan C; Grady, Cameron R; Pisitkun, Trairak et al. (2017) From 20th century metabolic wall charts to 21st century systems biology: database of mammalian metabolic enzymes. Am J Physiol Renal Physiol 312:F533-F542

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