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PKA-independent vasopressin signaling in renal collecting duct.

Datta A, Yang CR, Limbutara K, Chou CL, Rinschen MM, Raghuram V, Knepper MA.

FASEB J. 2020 Mar 26. doi: 10.1096/fj.201902982R. [Epub ahead of print]


CRISPR-Cas9/phosphoproteomics identifies multiple noncanonical targets of myosin light chain kinase.

Isobe K, Raghuram V, Krishnan L, Chou CL, Yang CR, Knepper MA.

Am J Physiol Renal Physiol. 2020 Mar 1;318(3):F600-F616. doi: 10.1152/ajprenal.00431.2019. Epub 2020 Jan 6.


Prioritizing Functional Goals as We Rebuild the Kidney.

Humphreys BD, Knepper MA.

J Am Soc Nephrol. 2019 Dec;30(12):2287-2288. doi: 10.1681/ASN.2019101051. Epub 2019 Nov 1. No abstract available.


PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities.

Saethang T, Hodge K, Yang CR, Zhao Y, Kimkong I, Knepper MA, Pisitkun T.

Bioinformatics. 2019 Dec 15;35(24):5313-5314. doi: 10.1093/bioinformatics/btz568.


Phosphoproteomic identification of vasopressin V2 receptor-dependent signaling in the renal collecting duct.

Deshpande V, Kao A, Raghuram V, Datta A, Chou CL, Knepper MA.

Am J Physiol Renal Physiol. 2019 Oct 1;317(4):F789-F804. doi: 10.1152/ajprenal.00281.2019. Epub 2019 Jul 17.


Renal-Tubule Epithelial Cell Nomenclature for Single-Cell RNA-Sequencing Studies.

Chen L, Clark JZ, Nelson JW, Kaissling B, Ellison DH, Knepper MA.

J Am Soc Nephrol. 2019 Aug;30(8):1358-1364. doi: 10.1681/ASN.2019040415. Epub 2019 Jun 28. No abstract available. Erratum in: J Am Soc Nephrol. 2019 Dec;30(12):2475.


RNA-Seq and protein mass spectrometry in microdissected kidney tubules reveal signaling processes initiating lithium-induced nephrogenic diabetes insipidus.

Sung CC, Chen L, Limbutara K, Jung HJ, Gilmer GG, Yang CR, Lin SH, Khositseth S, Chou CL, Knepper MA.

Kidney Int. 2019 Aug;96(2):363-377. doi: 10.1016/j.kint.2019.02.015. Epub 2019 Mar 4.


Representation and relative abundance of cell-type selective markers in whole-kidney RNA-Seq data.

Clark JZ, Chen L, Chou CL, Jung HJ, Lee JW, Knepper MA.

Kidney Int. 2019 Apr;95(4):787-796. doi: 10.1016/j.kint.2018.11.028. Epub 2019 Feb 27.


Phosphorylation Changes in Response to Kinase Inhibitor H89 in PKA-Null Cells.

Limbutara K, Kelleher A, Yang CR, Raghuram V, Knepper MA.

Sci Rep. 2019 Feb 26;9(1):2814. doi: 10.1038/s41598-019-39116-2.


Modulation of Cl- signaling and ion transport by recruitment of kinases and phosphatases mediated by the regulatory protein IRBIT.

Vachel L, Shcheynikov N, Yamazaki O, Fremder M, Ohana E, Son A, Shin DM, Yamazaki-Nakazawa A, Yang CR, Knepper MA, Muallem S.

Sci Signal. 2018 Oct 30;11(554). pii: eaat5018. doi: 10.1126/scisignal.aat5018.


From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology.

Rinschen MM, Limbutara K, Knepper MA, Payne DM, Pisitkun T.

Physiol Rev. 2018 Oct 1;98(4):2571-2606. doi: 10.1152/physrev.00057.2017. Review.


Proteomic determination of the lysine acetylome and phosphoproteome in the rat native inner medullary collecting duct.

Hyndman KA, Yang CR, Jung HJ, Umejiego EN, Chou CL, Knepper MA.

Physiol Genomics. 2018 Sep 1;50(9):669-679. doi: 10.1152/physiolgenomics.00029.2018. Epub 2018 Jun 22.


Urinary Proteome Analysis Identified Neprilysin and VCAM as Proteins Involved in Diabetic Nephropathy.

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.

J Diabetes Res. 2018 Apr 29;2018:6165303. doi: 10.1155/2018/6165303. eCollection 2018.


Genome-Wide Mapping of DNA Accessibility and Binding Sites for CREB and C/EBPβ in Vasopressin-Sensitive Collecting Duct Cells.

Jung HJ, Raghuram V, Lee JW, Knepper MA.

J Am Soc Nephrol. 2018 May;29(5):1490-1500. doi: 10.1681/ASN.2017050545. Epub 2018 Mar 23.


AbDesigner3D: a structure-guided tool for peptide-based antibody production.

Saethang T, Hodge K, Kimkong I, Payne DM, Knepper MA, Pisitkun T.

Bioinformatics. 2018 Jun 15;34(12):2158-2160. doi: 10.1093/bioinformatics/bty055.


Reply to Edemir: Physiological regulation and single-cell RNA sequencing.

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.

Proc Natl Acad Sci U S A. 2018 Jan 16;115(3):E351-E352. doi: 10.1073/pnas.1720333115. Epub 2018 Jan 8. No abstract available.


Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq.

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.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9989-E9998. doi: 10.1073/pnas.1710964114. Epub 2017 Oct 31.


Identification of UT-A1- and AQP2-interacting proteins in rat inner medullary collecting duct.

Chou CL, Hwang G, Hageman DJ, Han L, Agrawal P, Pisitkun T, Knepper MA.

Am J Physiol Cell Physiol. 2018 Jan 1;314(1):C99-C117. doi: 10.1152/ajpcell.00082.2017. Epub 2017 Oct 18.


Systems-level identification of PKA-dependent signaling in epithelial cells.

Isobe K, Jung HJ, Yang CR, Claxton J, Sandoval P, Burg MB, Raghuram V, Knepper MA.

Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):E8875-E8884. doi: 10.1073/pnas.1709123114. Epub 2017 Oct 2.


Single-tubule RNA-Seq uncovers signaling mechanisms that defend against hyponatremia in SIADH.

Lee JW, Alsady M, Chou CL, de Groot T, Deen PMT, Knepper MA, Ecelbarger CM.

Kidney Int. 2018 Jan;93(1):128-146. doi: 10.1016/j.kint.2017.06.008. Epub 2017 Aug 23.


Expression and functional implications of the renal apelinergic system in rodents.

O'Carroll AM, Salih S, Griffiths PR, Bijabhai A, Knepper MA, Lolait SJ.

PLoS One. 2017 Aug 17;12(8):e0183094. doi: 10.1371/journal.pone.0183094. eCollection 2017.


Dynamic regulation of lysine acetylation: the balance between acetyltransferase and deacetylase activities.

Hyndman KA, Knepper MA.

Am J Physiol Renal Physiol. 2017 Oct 1;313(4):F842-F846. doi: 10.1152/ajprenal.00313.2017. Epub 2017 Jul 12. Review.


Vasopressin-induced serine 269 phosphorylation reduces Sipa1l1 (signal-induced proliferation-associated 1 like 1)-mediated aquaporin-2 endocytosis.

Wang PJ, Lin ST, Liu SH, Kuo KT, Hsu CH, Knepper MA, Yu MJ.

J Biol Chem. 2017 May 12;292(19):7984-7993. doi: 10.1074/jbc.M117.779611. Epub 2017 Mar 23.


Identification of β-catenin-interacting proteins in nuclear fractions of native rat collecting duct cells.

Hwang JR, Chou CL, Medvar B, Knepper MA, Jung HJ.

Am J Physiol Renal Physiol. 2017 Jul 1;313(1):F30-F46. doi: 10.1152/ajprenal.00054.2017. Epub 2017 Mar 15.


Roflumilast and aquaporin-2 regulation in rat renal inner medullary collecting duct.

Umejiego EN, Wang Y, Knepper MA, Chou CL.

Physiol Rep. 2017 Jan;5(2). pii: e13121. doi: 10.14814/phy2.13121.


Data integration in physiology using Bayes' rule and minimum Bayes' factors: deubiquitylating enzymes in the renal collecting duct.

Xue Z, Chen JX, Zhao Y, Medvar B, Knepper MA.

Physiol Genomics. 2017 Mar 1;49(3):151-159. doi: 10.1152/physiolgenomics.00120.2016. Epub 2016 Dec 30.


From 20th century metabolic wall charts to 21st century systems biology: database of mammalian metabolic enzymes.

Corcoran CC, Grady CR, Pisitkun T, Parulekar J, Knepper MA.

Am J Physiol Renal Physiol. 2017 Mar 1;312(3):F533-F542. doi: 10.1152/ajprenal.00601.2016. Epub 2016 Dec 14.


Serine/threonine phosphatases and aquaporin-2 regulation in renal collecting duct.

LeMaire SM, Raghuram V, Grady CR, Pickering CM, Chou CL, Umejiego EN, Knepper MA.

Am J Physiol Renal Physiol. 2017 Jan 1;312(1):F84-F95. doi: 10.1152/ajprenal.00455.2016. Epub 2016 Oct 26.


Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin.

Sandoval PC, Claxton JS, Lee JW, Saeed F, Hoffert JD, Knepper MA.

Sci Rep. 2016 Oct 11;6:34863. doi: 10.1038/srep34863.


BIG: a large-scale data integration tool for renal physiology.

Zhao Y, Yang CR, Raghuram V, Parulekar J, Knepper MA.

Am J Physiol Renal Physiol. 2016 Oct 1;311(4):F787-F792. doi: 10.1152/ajprenal.00249.2016. Epub 2016 Jun 8.


Comprehensive database of human E3 ubiquitin ligases: application to aquaporin-2 regulation.

Medvar B, Raghuram V, Pisitkun T, Sarkar A, Knepper MA.

Physiol Genomics. 2016 Jul 1;48(7):502-12. doi: 10.1152/physiolgenomics.00031.2016. Epub 2016 May 13.


Deubiquitylation of Protein Cargo Is Not an Essential Step in Exosome Formation.

Huebner AR, Cheng L, Somparn P, Knepper MA, Fenton RA, Pisitkun T.

Mol Cell Proteomics. 2016 May;15(5):1556-71. doi: 10.1074/mcp.M115.054965. Epub 2016 Feb 16.


Peptide Labeling Using Isobaric Tagging Reagents for Quantitative Phosphoproteomics.

Cheng L, Pisitkun T, Knepper MA, Hoffert JD.

Methods Mol Biol. 2016;1355:53-70. doi: 10.1007/978-1-4939-3049-4_4.


Proteomic profiling of nuclear fractions from native renal inner medullary collecting duct cells.

Pickering CM, Grady C, Medvar B, Emamian M, Sandoval PC, Zhao Y, Yang CR, Jung HJ, Chou CL, Knepper MA.

Physiol Genomics. 2016 Feb;48(2):154-66. doi: 10.1152/physiolgenomics.00090.2015. Epub 2015 Oct 27.


Deep proteomic profiling of vasopressin-sensitive collecting duct cells. II. Bioinformatic analysis of vasopressin signaling.

Yang CR, Raghuram V, Emamian M, Sandoval PC, Knepper MA.

Am J Physiol Cell Physiol. 2015 Dec 15;309(12):C799-812. doi: 10.1152/ajpcell.00214.2015. Epub 2015 Aug 26.


Deep proteomic profiling of vasopressin-sensitive collecting duct cells. I. Virtual Western blots and molecular weight distributions.

Yang CR, Tongyoo P, Emamian M, Sandoval PC, Raghuram V, Knepper MA.

Am J Physiol Cell Physiol. 2015 Dec 15;309(12):C785-98. doi: 10.1152/ajpcell.00213.2015. Epub 2015 Aug 26.


Molecular Physiology of Water Balance.

Knepper MA, Kwon TH, Nielsen S.

N Engl J Med. 2015 Jul 9;373(2):196. doi: 10.1056/NEJMc1505505. No abstract available.


Systems biology of diuretic resistance.

Knepper MA.

J Clin Invest. 2015 May;125(5):1793-5. doi: 10.1172/JCI81505. Epub 2015 Apr 20.


Molecular physiology of water balance.

Knepper MA, Kwon TH, Nielsen S.

N Engl J Med. 2015 Apr 2;372(14):1349-58. doi: 10.1056/NEJMra1404726. Review. No abstract available.


Deep Sequencing in Microdissected Renal Tubules Identifies Nephron Segment-Specific Transcriptomes.

Lee JW, Chou CL, Knepper MA.

J Am Soc Nephrol. 2015 Nov;26(11):2669-77. doi: 10.1681/ASN.2014111067. Epub 2015 Mar 27.


Database of osmoregulated proteins in mammalian cells.

Grady CR, Knepper MA, Burg MB, Ferraris JD.

Physiol Rep. 2014 Oct 28;2(10). pii: e12180. doi: 10.14814/phy2.12180.


Integrated Design of Antibodies for Systems Biology Using Ab Designer.

Pisitkun T, Dummer P, Somparn P, Hirankarn N, Kopp JB, Knepper MA.

J Proteomics Bioinform. 2014 Mar 24;7(4):088-94.


Letter to the editor: "Systems biology versus reductionism in cell physiology".

Knepper MA, Raghuram V, Bradford D, Chou CL, Hoffert JD, Pisitkun T.

Am J Physiol Cell Physiol. 2014 Aug 1;307(3):C308-9. doi: 10.1152/ajpcell.00175.2014. No abstract available.


Four-dimensional MRI of renal function in the developing mouse.

Xie L, Subashi E, Qi Y, Knepper MA, Johnson GA.

NMR Biomed. 2014 Sep;27(9):1094-102. doi: 10.1002/nbm.3162. Epub 2014 Jul 26.


A knowledge base of vasopressin actions in the kidney.

Sanghi A, Zaringhalam M, Corcoran CC, Saeed F, Hoffert JD, Sandoval P, Pisitkun T, Knepper MA.

Am J Physiol Renal Physiol. 2014 Sep 15;307(6):F747-55. doi: 10.1152/ajprenal.00012.2014. Epub 2014 Jul 23.


Exploiting Thread-Level and Instruction-Level Parallelism to Cluster Mass Spectrometry Data using Multicore Architectures.

Saeed F, Hoffert JD, Pisitkun T, Knepper MA.

Netw Model Anal Health Inform Bioinform. 2014 Apr;3:54.


Early targets of lithium in rat kidney inner medullary collecting duct include p38 and ERK1/2.

Trepiccione F, Pisitkun T, Hoffert JD, Poulsen SB, Capasso G, Nielsen S, Knepper MA, Fenton RA, Christensen BM.

Kidney Int. 2014 Oct;86(4):757-67. doi: 10.1038/ki.2014.107. Epub 2014 Apr 30.


Use of LC-MS/MS and Bayes' theorem to identify protein kinases that phosphorylate aquaporin-2 at Ser256.

Bradford D, Raghuram V, Wilson JL, Chou CL, Hoffert JD, Knepper MA, Pisitkun T.

Am J Physiol Cell Physiol. 2014 Jul 15;307(2):C123-39. doi: 10.1152/ajpcell.00377.2012. Epub 2014 Mar 5.


PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data.

Saeed F, Pisitkun T, Hoffert JD, Rashidian S, Wang G, Gucek M, Knepper MA.

Proteome Sci. 2013 Nov 7;11(Suppl 1):S14. doi: 10.1186/1477-5956-11-S1-S14. Epub 2013 Nov 7.

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