Publications

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MAnuscripts

Insa M. Schmidt, Mia R. Colona, Bryan R. Kestenbaum, Leonidas G. Alexopoulos, Ragnar Palsson, Anand Srivastava, Jing Liu, Isaac E. Stillman, Helmut G. Rennke, Vishal S. Vaidya, Haojia Wu, Benjamin D. Humphreys, Sushrut S. Waikar, for the Kidney Precision Medicine Project (KPMP)13
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Cadherin-11, Sparc-related modular calcium binding protein-2, and Pigment epithelium-derived factor are promising non-invasive biomarkers of kidney fibrosis
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Kidney International
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S0085-2538(21)00505-6
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DOI: https://doi.org/10.1016/j.kint.2021.04.037
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PMID: 34051265
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PMCID: PMC8384690
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May 26, 2021
Yi Zheng, Clarissa A. Cassol, Saemi Jung, Divya Veerapaneni, Vipul C. Chitalia, Kevin Ren, Shubha S. Bellur, Peter Boor, Laura M. Barisoni, Sushrut S. Waikar, Margrit Betke, Vijaya B. Kolachalama
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Deep learning-driven quantification of interstitial fibrosis in digitized kidney biopsies
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The American Journal of Pathology
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May-2021
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DOI:https://doi.org/10.1016/j.ajpath.2021.05.005
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PMID: 34033750
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May 21, 2021
Steven Menez, Wenjun Ju, Rajasree Menon, Dennis G. Moledina, Heather Thiessen Philbrook, Eric McArthur, Yaqi Jia, Wassim Obeid, Sherry G. Mansour, Jay L. Koyner, Michael G. Shlipak, Steven G. Coca, Amit X. Garg, Andrew S. Bomback, John A. Kellum, Matthias Kretzler, and Chirag R. Parikh,for the Translational Research Investigating Biomarker Endpoints in AKI (TRIBE-AKI) Consortium and the Kidney Precision Medicine Project
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Urinary EGF and MCP-1 and risk of CKD after cardiac surgery
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Journal of Clinical Investigation
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6(11):e147464
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DOI: https://doi.org/10.1172/jci.insight.147464
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PMID: 33974569
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PMCID: PMC8262289
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May 11, 2021
Ian H. de Boer, Charles E. Alpers, Evren U. Azeloglu, Ulysses G.J. Balis, Jonathan M. Barasch, Laura Barisoni, Kristina N. Blank, Andrew S. Bomback, Keith Brown, Pierre C. Dagher, Ashveena L. Dighe, Michael T. Eadon, Tarek M. El-Achkar, Joseph P. Gaut, Nir Hacohen, Yongqun He, Jeffrey B. Hodgin, Sanjay Jain, John A. Kellum, Krzysztof Kiryluk, Richard Knight, Zoltan G. Laszik, Chrysta Lienczewski, Laura H. Mariani, Robyn L. McClelland, Steven Menez, Dennis G. Moledina, Sean D. Mooney, John F. O’Toole, Paul M. Palevsky, Chirag R. Parikh, Emilio D. Poggio, Sylvia E. Rosas, Matthew R. Rosengart, Minnie M. Sarwal, Jennifer A. Schaub, John R. Sedor, Kumar Sharma, Becky Steck, Robert D. Toto, Olga G. Troyanskaya, Katherine R. Tuttle, Miguel A. Vazquez, Sushrut S. Waikar, Kayleen Williams, Francis Perry Wilson, Kun Zhang, Ravi Iyengar, Matthias Kretzler and Jonathan Himmelfarb; for the Kidney Precision Medicine Project
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Rationale and design of the Kidney Precision Medicine Project
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Kidney International
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VOLUME 99, ISSUE 3, P498-510
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DOI:https://doi.org/10.1016/j.kint.2020.08.039
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PMID: 33637194
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PMCID: PMC8330551
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March 1, 2021
Katherine R. Tuttle, Jack Bebiak, Keith Brown, Catherine Campbell, Ashveena Dighe, Lynda Hyashi, Nichole Jefferson, Glenda V. Roberts, Christy Stutzke, Richard Knight for the Kidney Precision Medicine Project
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Patient perspectives and involvement in precision medicine research
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Kidney International
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VOLUME 99, ISSUE 3, P511-514
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DOI:https://doi.org/10.1016/j.kint.2020.10.036
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PMID: 33637195
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March 1, 2021
Eadon MT, Lampe S, Baig MM, Collins KS, Melo Ferreira R, Mang H, Cheng YH, Barwinska D, El-Achkar TM, Schwantes-An TH, Winfree S, Temm CJ, Ferkowicz MJ, Dunn KW, Kelly KJ, Sutton TA, Moe SM, Moorthi RN, Phillips CL, Dagher PC; for the Kidney Precision Medicine Project
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Clinical, histopathologic and molecular features of idiopathic and diabetic nodular mesangial sclerosis in humans
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Nephrol Dial Transplant
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DOI: 10.1093/ndt/gfaa331
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PMID: 33537765
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February 4, 2021
Tarek M. El-Achkar*, Michael T Eadon, Rajasree Menon, Blue B. Lake, Tara K. Sigdel, Theodore Alexandrov, Samir Parikh, Guanshi Zhang, Dejan Dobib, Kenneth W. Dunn, Edgar A. Otto, Christopher R. Anderton, Jonas M. Carson, Jinghui Luo, Chris Park, Habib Hamidi, Jian Zhou, Paul Hoover, Andrew Schroeder, Marianinha Joanes, Evren U. Azeloglu, Rachel Sealfon, Seth Winfree, Becky Steck, Yongqun He, Vivette Denise D'Agati, Ravi Iyengar, Olga G Troyanskaya, Laura Barisoni, Joseph Gaut, Kun Zhang, Zoltan Laszik, Brad Rovin, Pierre C Dagher, Kumar Sharma, Minnie Sarwal, Jeffrey B. Hodgin, Charles E. Alpers, Matthias Kretzer, Sanjay Jain*, and For the Kidney Precision Medicine Project
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A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: Guidelines from the Kidney Precision Medicine Project
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Physiological Genomics
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2021/01/11 Vol. 53, No. 1
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DOI: https://doi.org/10.1152/physiolgenomics.00104.2020
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PMID: 33197228
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PMCID: PMC7847045
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January 11, 2021
Michael J. Ferkowicz, Seth Winfree, Angela R. Sabo, Malgorzata M. Kamocka, Suraj Khochare, Daria Barwinska, Michael T. Eadon, Ying-Hua Cheng, Carrie L. Phillips, Timothy A. Sutton, Katherine J. Kelly, Pierre C. Dagher, Tarek M. El-Achkar & Kenneth W. Dunn for the Kidney Precision Medicine Project
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Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline
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Nature: Laboratory Investigations
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06 January 2021
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DOI: https://doi.org/10.1038/s41374-020-00518-w
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PMID: 33408350
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PMCID: PMC8363780
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January 6, 2021
Katherine R. Tuttle, Richard Knight, Paul S. Appelbaum, Tanima Arora, Shweta Bansal, Jack Bebiak, Keith Brown, Catherine Campbell, Leslie Cooperman, Celia P. Corona-Villalobos, Ashveena Dighe, Ian H. de Boer, Daniel E. Hall, Nichole Jefferson, Stacey Jolly, Asra Kermani, Simon C. Lee, Karla Mehl, Raghavan Murugan, Glenda V. Roberts, Sylvia E. Rosas, Jonathan Himmelfarb, R. Tyler Miller and for the Kidney Precision Medicine Project
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Integrating Patient Priorities with Science by Community Engagement in the Kidney Precision Medicine Project
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CJASN
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November 2020, CJN.10270620
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DOI: https://doi.org/10.2215/CJN.10270620
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PMID: 33257411
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PMCID: PMC8092068
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November 1, 2020
Rajasree Menon, PhD, Edgar A. Otto, PhD, Rachel Sealfon, PhD, Viji Nair, MS, Aaron K. Wong, PhD, Chandra L. Theesfeld, PhD, Xi Chen, PhD, Yuan Wang, MA, Avinash S. Boppana, Jinghui Luo, PhD, Yingbao Yang, MD, PhD, Peter M. Kasson, MD, PhD, Jennifer A. Schaub, MD, Celine C. Berthier, PhD, Sean Eddy, PhD, Chrysta C. Lienczewski, BS, Bradley Godfrey, PhD, Susan L. Dagenais, PhD, Ryann Sohaney, DO, John Hartman, BS, Damian Fermin, PhD, Lalita Subramanian, PhD, MPH, Helen C. Looker, MBBS, Jennifer L. Harder, MD, Laura H. Mariani, MD, MS, Jeffrey B. Hodgin, MD, PhD, Jonathan Z. Sexton, PhD, Christiane E. Wobus, PhD, Abhijit S. Naik, MD, MPH, Robert G. Nelson, MD, PhD, Olga G. Troyanskaya, PhD, Matthias Kretzler, MD
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SARS-CoV-2 receptor networks in diabetic and COVID-19 associated kidney disease
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Kidney International
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2020 Oct 07
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DOI: https://doi.org/10.1016/j.kint.2020.09.015
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PMID: 32511461
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PMCID: PMC7241118
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October 7, 2020
Emilio D. Poggio, Robyn L. McClelland, Kristina N. Blank, Spencer Hansen, Shweta Bansal, Andrew S. Bomback, Pietro A. Canetta, Pascale Khairallah, Krzysztof Kiryluk, Stewart H. Lecker, Gearoid M. McMahon, Paul M. Palevsky, Samir Parikh, Sylvia E. Rosas, Katherine Tuttle, Miguel A. Vazquez, Anitha Vijayan, Brad H. Rovin and for the Kidney Precision Medicine Project
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Systematic Review and Meta-Analysis of Native Kidney Biopsy Complications
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CJASN
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October 2020, CJN.04710420
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DOI: https://doi.org/10.2215/CJN.04710420
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PMID: 33060160
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PMCID: PMC7646247
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October 1, 2020
Tara K. Sigdel, Paul D. Piehowski, Sudeshna Roy, Juliane Liberto, Joshua R. Hansen, Adam C. Swensen, Rui Zhao, Ying Zhu, Priyanka Rashmi, Andrew Schroeder, Izabella Damm, Swastika Sur, Jinghui Luo, Yingbao Yang, Wei-Jun Qian, Minnie M. Sarwal and the Kidney Precision Medicine Project (KPMP)
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Near-Single-Cell Proteomics Profiling of the Proximal Tubular and Glomerulus of the Normal Human Kidney
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Frontiers in Medicine
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17 Sept 2020
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DOI: https://doi.org/10.3389/fmed.2020.00499
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PMID: 33072769
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PMCID: PMC7533534
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September 17, 2020
Ong E, Wang LL, Schaub J, O’Toole J, Steck B, Rosenberg AZ, Dowd F, Hansen J, Barisoni L, Jain S, de Boer IH, Valerius MT, Waikar SS, Park C, Crawford DC, Alexandrov T, Anderton CR, Stoeckert C, Weng C, Diehl AD, Mungall CJ, Haendel M, Robinson PB, Himmelfarb J, Iyengar R, Kretzler M, Mooney S, He Y, and the Kidney Precision Medicine Project
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Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project
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Nature Reviews Nephrology
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16 September 2020
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DOI: 10.1038/s41581-020-00335-w
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PMID: 32939051
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PMCID: PMC8012202
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September 16, 2020
Jessica K. Lukowski, Annapurna Pamreddy, Dusan Velickovic, Guanshi Zhang, Ljiljana Pasa-Tolic, Theodore Alexandrov, Kumar Sharma, Christopher R. Anderton*, and the Kidney Precision Medicine Project
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Storage Conditions of Human Kidney Tissue Sections Affect Spatial Lipidomics Analysis Reproducibility
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J. Am. Soc. Mass Spectrom
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September 8, 2020
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DOI: https://doi.org/10.1021/jasms.0c00256
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PMID: 32897710
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PMCID: PMC8162764
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September 8, 2020
Keith D. Brown, Catherine Campbell & Glenda V. Roberts
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Precision medicine in kidney disease: the patient’s view
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Nat Rev Nephr
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2020 Aug 08
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DOI: 10.1038/s41581-020-0319-0
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PMID: 32760017
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PMCID: PMC7404073
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August 8, 2020
Rajasree Menon, Edgar A. Otto, Paul Hoover, Sean Eddy, Laura Mariani, Bradley Godfrey, Celine C. Berthier, Felix Eichinger, Lalita Subramanian, Jennifer Harder, Wenjun Ju, Viji Nair, Maria Larkina, Abhijit S. Naik, Jinghui Luo, Sanjay Jain, Rachel Sealfon, Olga Troyanskaya, Nir Hacohen, Jeffrey B. Hodgin, Matthias Kretzler, Kidney Precision Medicine Project (KPMP), and Nephrotic Syndrome Study Network (NEPTUNE)
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Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker
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JCI Insight
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2020 Mar 26;5(6):e133267
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DOI: 10.1172/jci.insight.133267
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PMID: 32107344
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PMCID: PMC7213795
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March 26, 2020
Dušan Veličković, Guanshi Zhang, Dejan Bezbradica, Arunima Bhattacharjee, Ljiljana Paša-Tolić, Kumar Sharma, Theodore Alexandrov, Christopher R. Anderton*, and KPMP Consortium
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Response Surface Methodology as a New Approach for Finding Optimal MALDI Matrix Spraying Parameters for Mass Spectrometry Imaging
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J Am Soc Mass Spec
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2020 Feb 06;31(3):508-516
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DOI: 10.1021/jasms.9b00074
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PMID: 32126772
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PMCID: PMC7293970
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February 6, 2020
Beatriz Desanti De Oliveira, Katherine Xu, Tian H. Shen, Miriam Callahan, Krzysztof Kiryluk, Vivette D. D’Agati, Nicholas P. Tatonetti, Jonathan Barasch & Prasad Devarajan
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Molecular Nephrology: Types of Acute Tubular Injury
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Nat Rev Nephrol
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2019 Oct;15(10):599-612
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DOI: 10.1038/s41581-019-0184-x
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PMID: 31439924
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PMCID: PMC7303545
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October 1, 2019
Blue B. Lake, Song Chen, Masato Hoshi, Nongluk Plongthongkum, Diane Salamon, Amanda Knoten, Anitha Vijayan, Ramakrishna Venkatesh, Eric H. Kim, Derek Gao, Joseph Gaut, Kun Zhang & Sanjay Jain
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A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys
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Nat Commun
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2019 Jun 27;10(1):2832
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DOI: 10.1038/s41467-019-10861-2
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PMID: 31249312
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PMCID: PMC6597610
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June 27, 2019
Paul L. Kimmel, Nichole Jefferson, Jenna M. Norton and Robert A. Star
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How Community Engagement is Enhancing NIDDK Research
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Clin J Am Soc Nephrol
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2019 May 7;14(5):768-770
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DOI: 10.2215/CJN.14591218
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PMID: 30917992
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PMCID: PMC6500937
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May 7, 2019
Brad P. Dieter, Radica Z. Alicic, and Katherine R. Tuttle
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GLP-1 Receptor Agonists in Diabetic kidney Disease: From the Patient-Side to the Bench-Side
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Am J Physiol Renal Physiol
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2018 Dec 1;315(6):F1519-F1525
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DOI: 10.1152/ajprenal.00211.2018
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PMID: 30110568
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PMCID: PMC6337002
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December 1, 2018
Krzysztof Kiryluk, Andrew Bomback, Yim-Ling Cheng, Pablo G. Camara, Raul Rabadan, Peter Sims, and Jonathan Barasch
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Precision Medicine for Acute Kidney Injury (AKI): Redefining AKI by Agnostic Kidney Tissue Interrogation and Genetics
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Semin Nephrol
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2018 Jan;38(1):40-51
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DOI: 10.1016/j.semnephrol.2017.09.006
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PMID: 29291761
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PMCID: PMC5753434
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January 1, 2018
Blue B. Lake, Rajasree Menon, Seth Winfree, Qiwen Hu, Ricardo Melo Ferreira, Kian Kalhor, Daria Barwinska, Edgar A. Otto, Michael Ferkowicz, Dinh Diep, Nongluk Plongthongkum, Amanda Knoten, Sarah Urata, Abhijit S. Naik, Sean Eddy, Bo Zhang ,Yan Wu, Diane Salamon, James C. Williams, Xin Wang, Karol S. Balderrama, Paul Hoover, Evan Murray, Anitha Vijayan, Fei Chen, Sushrut S. Waikar, Sylvia Rosas, Francis P. Wilson, Paul M. Palevsky, Krzysztof Kiryluk, John R. Sedor, Robert D. Toto, Chirag Parikh, Eric H. Kim, Evan Z. Macosko, Peter V. Kharchenko, Joseph P. Gaut, Jeffrey B. Hodgin, Michael T. Eadon, Pierre C. Dagher, Tarek M. El-Achkar, Kun Zhang, Matthias Kretzler, Sanjay Jain, for the KPMP consortium
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An atlas of healthy and injured cell states and niches in the human kidney
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bioRxiv
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DOI: 10.1101/2021.07.28.454201
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Supplemental materials:
Text Link
Daria Barwinska, Tarek M. El-Achkar, Ricardo Melo Ferreira, Farooq Syed, Ying-Hua Cheng, Seth Winfree, Michael J. Ferkowicz, Takashi Hato, Kimberly S. Collins, Kenneth W. Dunn, Katherine J. Kelly, Timothy A. Sutton, Brad H. Rovin5, Samir V. Parikh, Carrie L. Phillips, Pierre C. Dagher, Michael T. Eadon for the Kidney Precision Medicine Project
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Molecular characterization of the human kidney interstitium in health and disease
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Science Advances
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Vol. 7, no. 7, eabd3359
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DOI: 10.1126/sciadv.abd3359
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PMID: 33568476
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PMCID: PMC7875540
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Supplemental materials:
Text Link
Daria Barwinska1, Michael J. Ferkowicz1, Ying-Hua Cheng1, Seth Winfree1,2, Kenneth W. Dunn1, Katherine J. Kelly1, Timothy A. Sutton1, Brad H. Rovin3, Samir V. Parikh3, Carrie L. Phillips4, Pierre C. Dagher1, Tarek M. El-Achkar1, Michael T. Eadon1, For The Kidney Precision Medicine Project,
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Application of Laser Microdissection to Uncover Regional Transcriptomics in Human Kidney Tissue
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JoVE
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June 9, 2020
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DOI: 10.3791/61371
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PMID: 32597856
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PMCID: PMC8136155
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Supplemental materials:
Text Link
Jens Hansen, Rachel Sealfon, Rajasree Menon, Michael T. Eadon, Blue B. Lake, Becky Steck, Dejan Dobi, Samir Parikh, Tara K. Sidgel, Theodore Alexandrov, Andrew Schroeder, Edgar A. Otto, Christopher R. Anderton, Daria Barwinska, Guanshi Zheng, Michael P. Rose, John P. Shapiro, Dusan Velickovic, Annapurna Pamreddy, Seth Winfree, Yongqun He, Ian H. de Boer, Jeffrey B. Hodgin, Abhijit Nair, Kumar Sharma, Minnie Sarwal, Kun Zhang, Jonathan Himmelfarb, Zoltan Laszik, Brad Rovin, Pierre C. Dagher, John Cijiang He, Tarek M. El-Achkar, Sanjay Jain, Olga G. Troyanskaya, Matthias Kretzler, Ravi Iyengar, Evren U. Azeloglu, for the Kidney Precision Medicine Project Consortium
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Towards Building a Smart Kidney Atlas: Network-based integration of multimodal transcriptomic, proteomic, metabolomic and imaging data in the Kidney Precision Medicine Project
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Biorxiv [Preprint]
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2020 July 24
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DOI: 10.1101/2020.07.23.216507
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Supplemental materials:
Text Link
Andrew W. Schroeder, Swastika Sur, Priyanka Rashmi, Izabella Damm, Arya Zarinsefat, Matthias Kretzler, Jeff Hodgin, George Hartoularos, Tara Sigdel, Jimmie Chun Ye, Minnie M. Sarwal, for the Kidney Precision Medicine Project
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Novel Human Kidney Cell Subsets Identified by Mux-Seq
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BioRxiv 973925 [Preprint]
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2020 Mar 04
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DOI: 10.1101/2020.03.02.973925
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Supplemental materials:
Text Link
Tarek M. El-Achkar, Michael T. Eadon, Rajasree Menon, Blue B. Lake, Tara K. Sigdel, Theodore Alexandrov, Samir Parikh, Guanshi Zhang, Dejan Dobi, Kenneth W. Dunn, Edgar A. Otto, Christopher R. Anderton, Jonas M. Carson, Jinghui Luo, Chris Park, Habib Hamidi, Jian Zhou, Paul Hoover, Andrew Schroeder, Marianinha Joanes, Evren Azeloglu, Rachel Sealfon, Seth Winfree, Becky Steck, Yongqun He, Vivette D’Agati, Ravi Iyengar, Olga G Troyanskaya, Laura Barisoni, Joseph Gaut, Kun Zhang, Zoltan Laszik, Brad Rovin, Pierre C. Dagher, Kumar Sharma, Minnie Sarwal, Jeffrey B. Hodgin, Charles E. Alpers, Matthias Kretzler, Sanjay Jain, For the Kidney Precision Medicine Project
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A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: The Kidney Precision Medicine Project
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BioRxiv 828665 [Preprint]
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2019 Nov 06
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DOI: 10.1101/828665
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PMID: 33197228
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PMCID: PMC7847045
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Supplemental materials:
Text Link

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