Epithelial Systems Biology Laboratory  
  Research   People   Publications   Join   Contact  

Click here for 12 most cited papers by Mark Knepper.

Recent Publications


473. Isobe K, Raghuram V, Krishnan L, Chou C-L, Yang C-R, Knepper MA. CRISPR-Cas9/Phosphoproteomics Identifies Multiple Non-canonical Targets of Myosin Light Chain Kinase. Am J Physiol Renal Physiol. 2019. (in press) PMID: 31904282.

472. Humphreys BD, Knepper MA. Prioritizing Functional Goals as We Rebuild the Kidney. J Am Soc Nephrol. 2019; 30:2287-2288 PMID: 31676726.

471. Deshpande V, Kao A, Raghuram V, Datta A, Chou CL, Knepper MA. Phosphoproteomic identification of vasopressin V2 receptor-dependent signaling in the renal collecting duct. Am J Physiol Renal Physiol. 2019; 317: F789-F804 PMID: 31313956.  

470. Saethang T, Hodge K, Yang CR, Zhao Y, Kimkong I, Knepper MA, Pisitkun T. PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities. Bioinformatics. 2019; pii: btz568. PMID: 31318409.

469.  Chen L, Clark JZ, Nelson JW, Kaissling B, Ellison DH, Knepper MA. Renal-tubule epithelial cell nomenclature for single-cell RNA-sequencing studies. J Am Soc Nephrol. 2019; 30: 1358-1364. PMID: 31253652.

468.  Sung CC, Chen L, Limbutara K, Jung HJ, Gilmer GG, Yang CR, Lin SH, Khositseth  S, Chou CL, Knepper MA. RNA-Seq and protein mass spectrometry in microdissected kidney tubules reveal signaling processes initiating lithium-induced nephrogenic diabetes insipidus. Kidney Int. 2019; 96: 363-377 PMID: 31146973.

467.  Wang H, Morris RG, Knepper MA, Zhou X. Sickle cell disease up-regulates vasopressin, aquaporin 2, urea transporter A1, Na-K-Cl cotransporter 2, and epithelial Na channels in the mouse kidney medulla despite compromising urinary concentration ability. Physiol Rep. 2019; 7:e14066. PMID: 31033226;  

466.  Clark JZ, Chen L, Chou CL, Jung HJ, Lee JW, Knepper MA. Representation and relative abundance of cell-type selective markers in whole-kidney RNA-Seq data.  Kidney Int. 2019; 95: 787-796. PMID: 30826016.

465.  Limbutara K, Kelleher A, Yang CR, Raghuram V, Knepper MA. Phosphorylation Changes in Response to Kinase Inhibitor H89 in PKA-Null Cells. Sci Rep. 2019; 9:2814. PMID: 30808967.

464.  Vachel L, Shcheynikov N, Yamazaki O, Fremder M, Ohana E, Son A, Shin DM, Yamazaki-Nakazawa A, Yang CR, Knepper MA, Muallem S. Modulation of Cl- signaling and ion transport by recruitment of kinases and phosphatases mediated by the regulatory protein IRBIT. Sci Signal. 2018;11 pii: eaat5018. PMID: 30377224.

463.  Medvar B, Sarkar A, Knepper M, Pisitkun T. Sequence-based searching of custom proteome and transcriptome databases. Physiol Rep. 2018 ;6:e13846 PMID: 30230259.

462. Rinschen MM, Limbutara K, Knepper MA, Payne DM, Pisitkun T. From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology. Physiol Rev. 2018; 98: 2571-2606.  Review.  PMID: 30182799.

461.  Gilmer GG, Deshpande VG, Chou CL, Knepper M. Flow resistance along the rat renal tubule. Am J Physiol Renal Physiol. 2018; 315: F1398-F1405 PMID: 30089029.

460. Guillén-Gómez E, Bardají-de-Quixano B, Ferrer S, Brotons C, Knepper MA, Carrascal M, Abian J, Mas JM, Calero F, Ballarín JA, Fernández-Llama P. Urinary Proteome Analysis Identified Neprilysin and VCAM as Proteins Involved in Diabetic Nephropathy. J Diabetes Res. 2018; 2018:6165303. PMID: 29854824.

459.   Briggs J, Palevsky P, Knepper M. JASN this Month: Something Old, Something New. J Am Soc Nephrol. 2018; 29:1345-1346. PMID: 29618491.

458.  Jung HJ, Raghuram V, Lee JW, Knepper MA. Genome-Wide Mapping of DNA Accessibility and Binding Sites for CREB and C/EBPβ in Vasopressin-Sensitive Collecting Duct Cells. J Am Soc Nephrol. 2018; 29:1490-1500  PMID: 29572403.

457.  Saethang T, Hodge K, Kimkong I, Payne MD, Knepper MA, Pisitkun T. AbDesigner3D: a structure-guided tool for peptide-based antibody production. Bioinformatics. 2018 [Epub ahead of print] PMID: 29408997.

456.  Chen L, Lee JW, Chou CL, Nair AV, Battistone MA, Păunescu TG, Merkulova M, Breton S, Verlander JW, Wall SM, Brown D, Burg MB, Knepper MA. Reply to Edemir: Physiological regulation and single-cell RNA sequencing. Proc Natl Acad Sci USA. 2018; 115: E351-E352. PMID: 29311339.

455.  Chou CL, Hwang G, Hageman DJ, Han L, Agrawal P, Pisitkun T, Knepper MA. Identification of UT-A1- and AQP2-interacting proteins in rat inner medullary collecting duct. Am J Physiol Cell Physiol. 2018; 314: C99-C117. PMID: 29046292.

454.  Lee JW, Alsady M, Chou CL, de Groot T, Deen PMT, Knepper MA, Ecelbarger CM. Single-tubule RNA-Seq uncovers signaling mechanisms that defend against hyponatremia in SIADH. Kidney Int. 2018; 93: 128-146. PMID: 28843412.

453.  Chen L, Lee JW, Chou CL, Nair AV, Battistone MA, Păunescu TG, Merkulova M, Breton S, Verlander JW, Wall SM, Brown D, Burg MB, Knepper MA. Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq. Proc Natl Acad Sci USA. 2017; 114: E9989-E9998.  PMID: 29089413.

452.  Isobe K, Jung HJ, Yang CR, Claxton J, Sandoval P, Burg MB, Raghuram V, Knepper MA. Systems-level identification of PKA-dependent signaling in epithelial cells. Proc Natl Acad Sci USA.  2017; 114: E8875-E8884.   PMID: 28973931.

451.  Hyndman KA, Knepper MA. Dynamic regulation of lysine acetylation: the balance between acetyltransferase and deacetylase activities. Am J Physiol Renal Physiol.  2017;313: F842-F846.   PMID: 28701313.  Review.

450. O'Carroll AM, Salih S, Griffiths PR, Bijabhai A, Knepper MA, Lolait SJ. Expression and functional implications of the renal apelinergic system in rodents. PLoS One. 2017; 12: e0183094. PMID: 28817612.

449. Wang PJ, Lin ST, Liu SH, Kuo KT, Hsu CH, Knepper MA, Yu MJ. Vasopressin-induced serine 269 phosphorylation reduces Sipa111 (signal-induced proliferation-associated 1 like 1)-mediated aquaporin-2 endocytosis. J Biol Chem. 2017; 292: 7984-7993. PMID: 28336531.

448.  Lucotte BM, Powell C, Knutson JR, Combs CA, Malide D, Yu ZX, Knepper M, Patel KD, Pielach A, Johnson E, Borysova L, Dora KA, Balaban RS. Direct visualization of the arterial wall water permeability barrier using CARS microscopy. Proc Natl Acad Sci U S A. 2017; 114:4805-4810. PMID: 28373558.

447.  Hwang JR, Chou CL, Medvar B, Knepper MA, Jung HJ. Identification of β-Catenin-Interacting Proteins in Nuclear Fractions of Native Rat Collecting Duct Cells. Am J Physiol Renal Physiol. 2017; 313: F30-F46. PMID: 28298358.

446.  Umejiego EN, Wang Y, Knepper MA, Chou CL. Roflumilast and aquaporin-2 regulation in rat renal inner medullary collecting duct. Physiol Rep. 2017; pii: e13121. PMID: 28108651.

445.  Xue Z, Chen JX, Zhao Y, Medvar B, Knepper MA. Data integration in physiology using Bayes' rule and minimum Bayes' factors: deubiquitylating enzymes in the renal collecting duct. Physiol Genomics. 2017; 49: 151-159.

444.   Corcoran CC, Grady CR, Pisitkun T, Parulekar J, Knepper MA. From 20th century metabolic wall charts to 21st century systems biology: database of mammalian metabolic enzymes. Am J Physiol Renal Physiol. 2017; 312: F533-F542.

443.  LeMaire S, Raghuram V, Grady CR, Pickering CM, Chou CL, Umejiego EN, Knepper MA. Serine/Threonine Phosphatases and Aquaporin-2 Regulation in Renal Collecting Duct. Am J Physiol Renal Physiol.. 2017; 312: F84-F95.

442.  Sandoval PC, Claxton JS, Lee JW, Saeed F, Hoffert JD, Knepper MA. Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin. Sci Rep. 2016; 6:34863. PMID: 27725713.

441. Zhao Y, Yang CR, Raghuram V, Parulekar J, Knepper MA. BIG: a large-scale data integration tool for renal physiology. Am J Physiol Renal Physiol. 2016; 311: F787-F792. PMID: 27279488.

440. Huebner AR, Cheng L, Somparn P, Knepper MA, Fenton RA, Pisitkun T. Deubiquitylation of Protein Cargo Is Not an Essential Step in Exosome Formation. Mol Cell Proteomics. 2016; 15: 1556-71.  PMID: 26884507. 

439.  Medvar B, Raghuram V, Pisitkun T, Sarkar A, Knepper MA. Comprehensive Database of Human E3 Ubiquitin Ligases: Application to Aquaporin-2 Regulation. Physiol Genomics. 2016, PMID: 27199454.

438.  Cheng L, Pisitkun T, Knepper MA, Hoffert JD. Peptide labeling using isobaric tagging reagents for quantitative phosphoproteomics. Methods Mol Biol. 2016; 1355:53-70. Review.

437.   Pickering CM, Grady CR, Medvar B, Emamian M, Sandoval PC, Zhao Y, Yang CR, Jung HJ, Chou CL, Knepper MA. Proteomic profiling of nuclear fractions from native renal inner medullary collecting duct cells. Physiol Genomics. 2015; physiolgenomics.00090.2015. PMID: 26508704.

436.   Lee JW, Chou CL, Knepper MA. Deep sequencing in microdissected renal tubules identifies nephron segment-specific transcriptomes. J Am Soc Nephrol. 2015; 26: 2669-77

435.   Knepper MA. Systems biology of diuretic resistance. J Clin Invest. 2015; 125:1793-5.  Comment.

434.   Knepper MA, Kwon TH, Nielsen S. Molecular physiology of water balance. N Engl J Med. 2015; 372:1349-58.  Review.

433.  Yang CR, Raghuram V, Emamian M, Sandoval PC, Knepper MA. Deep proteomic profiling of vasopressin-sensitive collecting duct cells. II. Bioinformatic analysis of vasopressin signaling. Am J Physiol Cell Physiol. 2015; 309: C799-812.

432.  Yang CR, Tongyoo P, Emamian M, Sandoval PC, Raghuram V, Knepper MA. Deep proteomic profiling of vasopressin-sensitive collecting duct cells. I. Virtual western blots and molecular weight distributions. Am J Physiol Cell Physiol. 2015; 309: C785-98.