The laboratory studies the molecular mechanisms of water transport in the renal collecting duct and the pathophysiology of water balance disorders. Much of the data for tthese studies comes from protein mass spectrometry and next-generation sequencing. Mass spectrometers suitable for protein mass spectrometry are rapidly improving in performance capabilities, providing more and more data for systems biology-oriented studies. However, quite often data processing tasks are rate limiting for progress in proteomics-based studies. In this project, we are developing software tools need for interpretation of the large data sets obtained. They are developed initially for our own studies but we make these tools available to other investigators. To aid in dissemination of our software, the algorithms are coded in Java, which is platform-independent, allowing the code to run on a variety of machines. In addition, where possible, we are striving to make software available online (on the World Wide Web) for execution (see In addition, proteomic investigation often requires the design and production of new antibodies. We have developed software to predict the optimal synthetic peptide sequences for production of antibodies (see The advent of next-generation sequencing has created new computational challenges that are being addressed in the laboratory.

Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
U.S. National Heart Lung and Blood Inst
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
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
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
Hyndman, Kelly A; Knepper, Mark A (2017) Dynamic regulation of lysine acetylation: the balance between acetyltransferase and deacetylase activities. Am J Physiol Renal Physiol 313:F842-F846

Showing the most recent 10 out of 72 publications