467 results on '"Eddy, Sean"'
Search Results
2. An atlas of healthy and injured cell states and niches in the human kidney.
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Lake, Blue, Menon, Rajasree, Winfree, Seth, Hu, Qiwen, Ferreira, Ricardo, Kalhor, Kian, Barwinska, Daria, Otto, Edgar, Ferkowicz, Michael, Diep, Dinh, Plongthongkum, Nongluk, Knoten, Amanda, Urata, Sarah, Mariani, Laura, Naik, Abhijit, Eddy, Sean, Zhang, Bo, Wu, Yan, Salamon, Diane, Williams, James, Wang, Xin, Balderrama, Karol, Hoover, Paul, Murray, Evan, Marshall, Jamie, Noel, Teia, Vijayan, Anitha, Hartman, Austin, Chen, Fei, Waikar, Sushrut, Rosas, Sylvia, Wilson, Francis, Palevsky, Paul, Kiryluk, Krzysztof, Sedor, John, Toto, Robert, Parikh, Chirag, Kim, Eric, Satija, Rahul, Greka, Anna, Macosko, Evan, Kharchenko, Peter, Gaut, Joseph, Hodgin, Jeffrey, Eadon, Michael, Dagher, Pierre, El-Achkar, Tarek, Kretzler, Matthias, Jain, Sanjay, and Zhang, Kun
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Humans ,Cell Nucleus ,Gene Expression Profiling ,Kidney ,Kidney Diseases ,Transcriptome ,Single-Cell Analysis ,Case-Control Studies ,Imaging ,Three-Dimensional - Abstract
Understanding kidney disease relies on defining the complexity of cell types and states, their associated molecular profiles and interactions within tissue neighbourhoods1. Here we applied multiple single-cell and single-nucleus assays (>400,000 nuclei or cells) and spatial imaging technologies to a broad spectrum of healthy reference kidneys (45 donors) and diseased kidneys (48 patients). This has provided a high-resolution cellular atlas of 51 main cell types, which include rare and previously undescribed cell populations. The multi-omic approach provides detailed transcriptomic profiles, regulatory factors and spatial localizations spanning the entire kidney. We also define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive (successful or maladaptive repair), transitioning and degenerative states. Molecular signatures permitted the localization of these states within injury neighbourhoods using spatial transcriptomics, while large-scale 3D imaging analysis (around 1.2 million neighbourhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways that are relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents a comprehensive benchmark of cellular states, neighbourhoods, outcome-associated signatures and publicly available interactive visualizations.
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- 2023
3. Mammalian cells repress random DNA that yeast transcribes
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Eddy, Sean R.
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- 2024
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4. Identification of kidney cell types in scRNA-seq and snRNA-seq data using machine learning algorithms
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Tisch, Adam, Madapoosi, Siddharth, Blough, Stephen, Rosa, Jan, Eddy, Sean, Mariani, Laura, Naik, Abhijit, Limonte, Christine, McCown, Philip, Menon, Rajasree, Rosas, Sylvia E., Parikh, Chirag R., Kretzler, Matthias, Mahfouz, Ahmed, and Alakwaa, Fadhl
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- 2024
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5. Elevated Exposure to Air Pollutants Accelerates Primary Glomerular Disease Progression
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Troost, Jonathan P., D’Souza, Jennifer, Buxton, Miatta, Kshirsagar, Abhijit V., Engel, Lawrence S., O’Lenick, Cassandra R., Smoyer, William E., Klein, Jon, Ju, Wenjun, Eddy, Sean, Helmuth, Margaret, Mariani, Laura H., Kretzler, Matthias, and Trachtman, Howard
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- 2024
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6. The association of low birthweight and prematurity on outcomes in children and adults with nephrotic syndrome-a NEPTUNE cohort study
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Hingorani, Sangeeta, Gibson, Keisha L., Xie, Yuping, Wang, Yujie, Eddy, Sean, Hartman, John, and Sampson, Matthew
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Birth weight, Low -- Health aspects ,Nephrotic syndrome -- Care and treatment -- Patient outcomes ,Infants (Premature) -- Health aspects ,Health - Abstract
Background In single-center studies, both preterm birth and low birth weight (LBW) are associated with worse outcomes in childhood nephrotic syndrome. Using the Nephrotic Syndrome Study Network (NEPTUNE) observational cohort, we tested the hypothesis that in patients with nephrotic syndrome, hypertension, proteinuria status, and disease progression would be more prevalent and more severe in subjects with LBW and prematurity singly or in combination (LBW/prematurity). Methods Three hundred fifty-nine adults and children with focal segmental glomerulosclerosis (FSGS) or minimal change disease (MCD) and available birth history were included. Estimated glomerular filtration rate (eGFR) decline and remission status were primary outcomes, and secondary outcomes were kidney histopathology, kidney gene expression, and urinary biomarkers. Logistic regression was used to identify associations with LBW/prematurity and these outcomes. Results We did not find an association between LBW/prematurity and remission of proteinuria. However, LBW/prematurity was associated with greater decline in eGFR. This decline in eGFR was partially explained by the association of LBW/prematurity with APOL1 high-risk alleles, but the association remained after adjustment. There were no differences in kidney histopathology or gene expression in the LBW/prematurity group compared to normal birth weight/term birth. Conclusion LBW and premature babies who develop nephrotic syndrome have a more rapid decline in kidney function. We did not identify clinical or laboratory features that distinguished the groups. Additional studies in larger groups are needed to fully ascertain the effects of (LBW) and prematurity alone or in combination on kidney function in the setting of nephrotic syndrome., Author(s): Sangeeta Hingorani [sup.1] , Keisha L. Gibson [sup.2] , Yuping Xie [sup.3] , Yujie Wang [sup.4] , Sean Eddy [sup.4] , John Hartman [sup.4] , Matthew Sampson [sup.5] [sup.6] [...]
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- 2023
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7. Interferon-γ induces combined pyroptotic angiopathy and APOL1 expression in human kidney disease
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Juliar, Benjamin A., Stanaway, Ian B., Sano, Fumika, Fu, Hongxia, Smith, Kelly D., Akilesh, Shreeram, Scales, Suzie J., El Saghir, Jamal, Bhatraju, Pavan K., Liu, Esther, Yang, Johnson, Lin, Jennie, Eddy, Sean, Kretzler, Matthias, Zheng, Ying, Himmelfarb, Jonathan, Harder, Jennifer L., and Freedman, Benjamin S.
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- 2024
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8. Unbiased kidney-centric molecular categorization of chronic kidney disease as a step towards precision medicine
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Reznichenko, Anna, Nair, Viji, Eddy, Sean, Fermin, Damian, Tomilo, Mark, Slidel, Timothy, Ju, Wenjun, Henry, Ian, Badal, Shawn S., Wesley, Johnna D., Liles, John T., Moosmang, Sven, Williams, Julie M., Quinn, Carol Moreno, Bitzer, Markus, Hodgin, Jeffrey B., Barisoni, Laura, Karihaloo, Anil, Breyer, Matthew D., Duffin, Kevin L., Patel, Uptal D., Magnone, Maria Chiara, Bhat, Ratan, and Kretzler, Matthias
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- 2024
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9. Precision Medicine in Nephrology: An Integrative Framework of Multidimensional Data in the Kidney Precision Medicine Project
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Lake, Blue, Zhang, Kun, Lecker, Stewart, Morales, Alexander, Bogen, Steve, Amodu, Afolarin A., Beck, Laurence, Henderson, Joel, Ilori, Titlayo, Maikhor, Shana, Onul, Ingrid, Schmidt, Insa, Verma, Ashish, Waikar, Sushrut, Yadati, Pranav, Yu, Guanghao, Colona, Mia R., McMahon, Gearoid, Hacohen, Nir, Greka, Anna, Hoover, Paul J., Marshall, Jamie L., Aulisio, Mark, Bush, William, Chen, Yijiang, Crawford, Dana, Madabhushi, Anant, Viswanathan, Vidya S., Bush, Lakeshia, Cooperman, Leslie, Gadegbeku, Crystal, Herlitz, Leal, Jolly, Stacey, Nguyen, Jane, O’Malley, Charles, O’Toole, John, Palmer, Ellen, Poggio, Emilio, Spates-Harden, Kassandra, Sedor, John, Sendrey, Dianna, Taliercio, Jonathan, Appelbaum, Paul, Balderes, Olivia, Barasch, Jonathan, Berroue, Cecilia, Bomback, Andrew, Canetta, Pietro A., D’Agati, Vivette, Kiryluk, Krzysztof, Kudose, Satoru, Mehl, Karla, Sabatello, Maya, Shang, Ning, de Pinho Gonçalves, Joana, Lardenoije, Roy, Migas, Lukasz, Van de Plas, Raf, Rennke, Helmut, Azeloglu, Evren, Campbell, Kirk, Coca, Steven, He, Cijang, He, John, Iyengar, Srinivas Ravi, Lefferts, Seanee, Nadkarni, Girish, Patel, Marissa, Tokita, Joji, Ward, Stephen, Xiong, Yuguang, Verdoes, Abraham, Sabo, Angela, Barwinska, Daria, Gisch, Debora Lidia, Williams, James, Kelly, Katherine, Dunn, Kenneth, Asghari, Mahla, Eadon, Michael, Ferkowicz, Michael, Dagher, Pierre, Ferreira, Ricardo Melo, Winfree, Seth, Bledsoe, Sharon, Wofford, Stephanie, El-Achkar, Tarek, Sutton, Timothy, Bowen, William, Cheng, Ying-Hua, Slade, Austen, Record, Elizabeth, Cheng, Yinghua, Borner, Katy, Herr, Bruce, Jain, Yashvardhan, Quardokus, Ellen, Atta, Mohamed, Bernard, Lauren, Menez, Steven, Parikh, Chirag, Corona Villalobos, Celia Pamela, Wang, Ashley, Wen, Yumeng, Xu, Alan, Chen, Sarah, Donohoe, Isabel, Johansen, Camille, Rosas, Sylvia, Sun, Jennifer, Ardayfio, Joseph, Bebiak, Jack, Campbell, Taneisha, Fox, Monica, Knight, Richard, Koewler, Robert, Pinkeney, Roy, Saul, John, Shpigel, Anna, Prasad, Pottumarthi, Madhavan, Sethu M., Parikh, Samir, Rovin, Brad, Shapiro, John P., Anderton, Christopher, Lukowski, Jessica, Pasa-Tolic, Ljiljana, Velickovic, Dusan, Oliver, George, Mao, Weiguang, Sealfon, Rachel, Troyanskaya, Olga, Pollack, Ari, Goltsev, Yury, Ginley, Brandon, Anjani, Kavya, Laszik, Zoltan G., Mukatash, Tariq, Nolan, Garry, Beyda, David, Bracamonte, Erika, Brosius, Frank, Campos, Baltazar, Marquez, Nicole, Mendoza, Katherine, Scott, Raymond, Thajudeen, Bijin, Tsosie, Rebecca, Woodhead, Gregory, Saunders, Milda, Alloway, Rita R., Lee, Paul J., Rike, Adele, Shi, Tiffany, Woodle, E. Steve, Bjornstad, Petter, Hsieh, Elena, Kendrick, Jessica, Pyle, Laura, Thurman, Joshua, Vinovskis, Carissa, Wrobel, Julia, Lucarelli, Nicholas, Sarder, Pinaki, Bui, James, Carmona-Powell; Ron Gaba, Eunice, Kelly, Tanika, Lash, James, Meza, Natalie, Redmond, Devona, Renteria, Amada, Ricardo, Ana, Setty, Suman, Srivastava, Anand, Alakwaa, Fadhl, Ascani, Heather, Balis, Ul, Bitzer, Markus, Blanc, Victoria, Bonevich, Nikki, Conser, Ninive, Demeke, Dawit, Dull, Rachel, Eddy, Sean, Frey, Renee, Hartman, John, He, Yongqun Oliver, Hodgin, Jeffrey, Kretzler, Matthias, Lienczewski, Chrysta, Luo, Jinghui, Mariani, Laura, McCown, Phillip, Menon, Rajasree, Nair, Viji, Otto, Edgar, Reamy, Rebecca, Rose, Michael, Schaub, Jennifer, Steck, Becky, Wright, Zachary, Coleman, Alyson, Henderson-Brown; Jerica Berge, Dorisann, Caramori, Maria Luiza, Adeyi, Oyedele, Nachman, Patrick, Safadi, Sami, Flanagan, Siobhan, Ma, Sisi, Klett, Susan, Wolf, Susan, Harindhanavudhi, Tasma, Rao, Via, Bream, Peter, Froment, Anne, Kelley, Sara, Mottl, Amy, Chaudhury; Evan Zeitler, Prabir Roy, Bender, Filitsa, Elder, Michele, Gilliam, Matthew, Hall, Daniel E., Kellum, John A., Murugan, Raghavan, Palevsky, Paul, Rosengart, Matthew, Tan, Roderick, Tublin, Mitchell, Winters, James, Bansal, Shweta, Montellano, Richard, Pamreddy, Annapurna, Sharma, Kumar, Venkatachalam, Manjeri, Ye, Hongping, Zhang, Guanshi, Basit, Mujeeb, Cai, Qi, Hendricks, Allen, Hedayati, Susan, Kermani, Asra, Lee, Simon C., Ma, Shihong, Miller, Richard Tyler, Moe, Orson W., Park, Harold, Patel, Jiten, Pillai, Anil, Sambandam, Kamalanathan, Torrealba, Jose, Toto, Robert D., Vazquez, Miguel, Wang, Nancy, Wen, Natasha, Zhang, Dianbo, Alpers, Charles, Berglund, Ashley, Berry, Brooke, Blank, Kristina, Brown, Keith, Carson, Jonas, Daniel, Stephen, de Boer, Ian H., Dighe, Ashveena L., Dowd, Frederick, Grewenow, Stephanie M., Himmelfarb, Jonathan, Hoofnagle, Andrew, Jefferson, Nichole, Larson, Brandon, Limonte, Christine, McClelland, Robyn, Mooney, Sean, Nam, Yunbi, Park, Christopher, Phuong, Jimmy, Rezaei, Kasra, Roberts, Glenda, Sarkisova, Natalya, Shankland, Stuart, Snyder, Jaime, Stutzke, Christy, Tuttle, Katherine, Wangperawong, Artit, Wilcox, Adam, Williams, Kayleen, Young, Bessie, Allen, Jamie, Caprioli, Richard M., de Caestecker, Mark, Djambazova, Katerina, Dufresne, Martin, Farrow, Melissa, Fogo, Agnes, Sharman, Kavya, Spraggins, Jeffrey, Basta, Jeannine, Conlon, Kristine, Diettman, Sabine M., Gaut, Joseph, Kaushal, Madhurima, Jain, Sanjay, Knoten, Amanda, Minor, Brittany, Nwanne, Gerald, Vijayan, Anitha, Zhang, Bo, Arora, Tanima, Cantley, Lloyd, Victoria Castro, Angela M., Kakade, Vijayakumar, Moeckel, Gilbert, Moledina, Dennis, Shaw, Melissa, Wilson, Francis P., El-Achkar, Tarek M., and Eadon, Michael T.
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- 2024
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10. ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events
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Richardson, Mary O. and Eddy, Sean R.
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- 2023
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11. An integrated organoid omics map extends modeling potential of kidney disease
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Lassé, Moritz, El Saghir, Jamal, Berthier, Celine C., Eddy, Sean, Fischer, Matthew, Laufer, Sandra D., Kylies, Dominik, Hutzfeldt, Arvid, Bonin, Léna Lydie, Dumoulin, Bernhard, Menon, Rajasree, Vega-Warner, Virginia, Eichinger, Felix, Alakwaa, Fadhl, Fermin, Damian, Billing, Anja M., Minakawa, Akihiro, McCown, Phillip J., Rose, Michael P., Godfrey, Bradley, Meister, Elisabeth, Wiech, Thorsten, Noriega, Mercedes, Chrysopoulou, Maria, Brandts, Paul, Ju, Wenjun, Reinhard, Linda, Hoxha, Elion, Grahammer, Florian, Lindenmeyer, Maja T., Huber, Tobias B., Schlüter, Hartmut, Thiel, Steffen, Mariani, Laura H., Puelles, Victor G., Braun, Fabian, Kretzler, Matthias, Demir, Fatih, Harder, Jennifer L., and Rinschen, Markus M.
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- 2023
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12. Molecular Signatures of Glomerular Neovascularization in a Patient with Diabetic Kidney Disease
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Ferkowicz, Michael J., Verma, Ashish, Barwinska, Daria, Melo Ferreira, Ricardo, Henderson, Joel M., Kirkpatrick, Mary, Silva, Paolo S., Steenkamp, Devin W., Phillips, Carrie L., Waikar, Sushrut S., Sutton, Timothy A., Lake, Blue, Zhang, Kun, Lecker, Stewart, Morales, Alexander, Stillman, Isaac, Bogen, Steve, Amodu, Afolarin A., Beck, Laurence, Henderson, Joel, Ilori, Titlayo, Maikhor, Shana, Onul, Ingrid, Schmidt, Insa, Verma, Ashish, Waikar, Sushrut, Yadati, Pranav, Yu, Guanghao, Colona, Mia R., McMahon, Gearoid, Weins, Astrid, Hacohen, Nir, Greka, Anna, Hoover, Paul J., Marshall, Jamie L., Aulisio, Mark, Bush, William, Chen, Yijiang, Crawford, Dana, Madabhushi, Anant, Viswanathan, Vidya S., Bush, Lakeshia, Cooperman, Leslie, Gadegbeku, Crystal, Herlitz, Leal, Jolly, Stacey, Nguyen, Jane, O’Malley, Charles, O’Toole, John, Palmer, Ellen, Poggio, Emilio, Spates-Harden, Kassandra, Sedor, John, Sendrey, Dianna, Taliercio, Jonathan, Appelbaum, Paul, Balderes, Olivia, Barasch, Jonathan, Berroue, Cecilia, Bomback, Andrew, Canetta, Pietro A., D’Agati, Vivette, Kiryluk, Krzysztof, Kudose, Satoru, Mehl, Karla, Sabatello, Maya, Shang, Ning, Varela, German, de Pinho Gonçalves, Joana, Lardenoije, Roy, Migas, Lukasz, Van de Plas, Raf, Barisoni, Laura, Rennke, Helmut, Azeloglu, Evren, Campbell, Kirk, Coca, Steven, He, Cijang, He, John, Iyengar, Srinivas Ravi, Lefferts, Seanee, Nadkarni, Girish, Patel, Marissa, Tokita, Joji, Ward, Stephen, Xiong, Yuguang, Verdoes, Abraham, Sabo, Angela, Barwinska, Daria, Gisch, Debora Lidia, Williams, James, Kelly, Katherine, Dunn, Kenneth, Asghari, Mahla, Eadon, Michael, Ferkowicz, Michael, Dagher, Pierre, Ferreira, Ricardo Melo, Winfree, Seth, Bledsoe, Sharon, Wofford, Stephanie, El-Achkar, Tarek, Sutton, Timothy, Bowen, William, Cheng, Ying-Hua, Slade, Austen, Record, Elizabeth, Cheng, Yinghua, Borner, Katy, Herr, Bruce, Jain, Yashvardhan, Quardokus, Ellen, Atta, Mohamed, Bernard, Lauren, Menez, Steven, Parikh, Chirag, Corona Villalobos, Celia Pamela, Wang, Ashley, Wen, Yumeng, Xu, Alan, Chen, Sarah, Donohoe, Isabel, Johansen, Camille, Rosas, Sylvia, Sun, Jennifer, Ardayfio, Joseph, Bebiak, Jack, Brown, Keith, Campbell, Taneisha, Fox, Monica, Hayashi, Lynda, Jefferson, Nichole, Richard Knight, Jennifer Jones, Koewler, Robert, Pinkeney, Roy, Saul, John, Shpigel, Anna, Stutzke, Christy, Prasad, Pottumarthi, Madhavan, Sethu M., Parikh, Samir, Rovin, Brad, Shapiro, John P., Anderton, Christopher, Lukowski, Jessica, Pasa-Tolic, Ljiljana, Velickovic, Dusan, Oliver, George, Mao, Weiguang, Sealfon, Rachel, Troyanskaya, Olga, Wong, Aaron, Pollack, Ari, Goltsev, Yury, Ginley, Brandon, Lutnick, Brendon, Anjani, Kavya, Laszik, Zoltan G., Mukatash, Tariq, Nolan, Garry, Beyda, David, Bracamonte, Erika, Brosius, Frank, Campos, Baltazar, Marquez, Nicole, Mendoza, Katherine, Scott, Raymond, Thajudeen, Bijin, Tsosie, Rebecca, Woodhead, Gregory, Saunders, Milda, Alloway, Rita R., Lee, Paul J., Rike, Adele, Shi, Tiffany, Woodle, E. Steve, Bjornstad, Petter, Hsieh, Elena, Kendrick, Jessica, Pyle, Laura, Thurman, Joshua, Vinovskis, Carissa, Wrobel, Julia, Lucarelli, Nicholas, Sarder, Pinaki, Bui, James, Carmona-Powell, Eunice, Gaba, Ron, Kelly, Tanika, Lash, James, Meza, Natalie, Redmond, Devona, Renteria, Amada, Ricardo, Ana, Setty, Suman, Srivastava, Anand, Alakwaa, Fadhl, Ascani, Heather, Balis, Ul, Bitzer, Markus, Blanc, Victoria, Bonevich, Nikki, Conser, Ninive, Demeke, Dawit, Dull, Rachel, Eddy, Sean, Frey, Renee, Hartman, John, He, Yongqun Oliver, Hodgin, Jeffrey, Kretzler, Matthias, Lienczewski, Chrysta, Luo, Jinghui, Mariani, Laura, McCown, Phillip, Menon, Rajasree, Nair, Viji, Otto, Edgar, Reamy, Rebecca, Rose, Michael, Schaub, Jennifer, Steck, Becky, Wright, Zachary, Coleman, Alyson, Henderson-Brown, Dorisann, Berge, Jerica, Caramori, Maria Luiza, Adeyi, Oyedele, Nachman, Patrick, Safadi, Sami, Flanagan, Siobhan, Ma, Sisi, Klett, Susan, Wolf, Susan, Harindhanavudhi, Tasma, Rao, Via, Bream, Peter, Froment, Anne, Kelley, Sara, Mottl, Amy, Roy-Chaudhury, Prabir, Zeitler, Evan, Bender, Filitsa, Elder, Michele, Gilliam, Matthew, Hall, Daniel E., Kellum, John A., Murugan, Raghavan, Palevsky, Paul, Rosengart, Matthew, Tan, Roderick, Tublin, Mitchell, Winters, James, Bansal, Shweta, Montellano, Richard, Pamreddy, Annapurna, Sharma, Kumar, Venkatachalam, Manjeri, Ye, Hongping, Zhang, Guanshi, Basit, Mujeeb, Cai, Qi, Hendricks, Allen, Hedayati, Susan, and Asra
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- 2024
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13. Participant Experience with Protocol Research Kidney Biopsies in the Kidney Precision Medicine Project
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Victoria-Castro, Angela M., Corona-Villalobos, Celia P., Xu, Alan Y., Onul, Ingrid, Huynh, Courtney, Chen, Sarah W., Ugwuowo, Ugochukwu, Sarkisova, Natalya, Dighe, Ashveena L., Blank, Kristina N., Blanc, Victoria M., Rose, Michael P., Himmelfarb, Jonathan, de Boer, Ian H., Tuttle, Katherine R., Roberts, Glenda V., Alexandrov, Theodore, Alloway, Rita R., Alpers, Charles E., Amodu, Afolarin A., Anderton, Christopher R., Anjani, Kavya, Appelbaum, Paul, Ardayfio, Joseph, Arora, Tanima, Ascani, Heather, El-Achkar, Tarek M., Aulisio, Mark, Azeloglu, Evren U., Balderes, Olivia, Balis, Ulysses G.J., Bansal, Shweta, Barasch, Jonathan M., Bansal, Shweta, Barkell, Alex, Barwinska, Daria, Basit, Mujeeb, Basta, Jeanine, Bebiak, Jack, Beck, Laurence H., Bender, Filitsa, Berglund, Ashley, Bernard, Lauren, Berrouet, Cecilia, Berry, Brooke, Bjornstad, Petter M., Blanc, Victoria M., Blank, Kristina N., Bledsoe, Sharon, Boada, Patrick, Bogen, Steve, Bomback, Andrew S., Bonevich, Nikole, Borner, Katy, Brown, Keith, Bueckle, Andreas, Burg, Ashley R., Burgess, Adam, Bush, Lakeshia, Bush, William S., Campbell, Catherine E., Campbell, Taneisha, Canetta, Pietro A., Cantley, Lloyd G., Caprioli, Richard M., Carson, Jonas, Chen, Sarah, Chen, Yijiang M., Cheng, Yinghua, Cimino, Jim, Colona, Mia R., Conser, Ninive C., Cooperman, Leslie, Crawford, Dana C., DʼAgati, Vivette D., Dagher, Pierre C., Daniel, Stephen, Daratha, Kenn, de Boer, Ian H., Diettman, Sabine M., Dighe, Ashveena L., Donohoe, Isabel, Dowd, Frederick, Dunn, Kenneth W., Eadon, Michael T., Eddy, Sean, Elder, Michele M., Ferkowicz, Michael J., Frey, Renee, Gadegbeku, Crystal A., Gaut, Joseph P., Gilliam, Matthew, Ginley, Brandon, Gisch, Debora, Goltsev, Yury, Gonzalez-Vicente, Agustin, Greka, Anna, Grewenow, Stephanie M., Hacohen, Nir, Hall, Daniel E., Hansen, Jens, Hayashi, Lynda, He, Cijang, He, Yougqun, Hedayati, S. Susan, Henderson, Joel M., Hendricks, Allen H., Herlitz, Leal, Herr, Bruce W., Himmelfarb, Jonathan, Hodgin, Jeffrey B., Hoofnagle, Andrew N., Hoover, Paul J., Ilori, Titlayo, Iyengar, Ravi, Jain, Sanjay, Jain, Yashvardhan, Janowczyk, Andrew, Jefferson, Nichole, Johansen, Camille, Jolly, Stacey, Kakade, Vijaykumar R., Kellum, John A., Kelly, Katherine J., Kermani, Asra, Kiryluk, Krzysztof, Knight, Richard, Koewler, Robert, Kretzler, Matthias, Kudose, Satoru, Lake, Blue B., Larson, Brandon, Laszik, Zoltan G., Lecker, Stewart H., Lee, Paul J., Lee, Simon C., Lienczewski, Chrysta, Limonte, Christine, Lu, Christopher Y., Lucarelli, Nicholas, Lukowski, Jessica, Luo, Jinghui, Lutnick, Brendon, Ma, Shihong, Madabhushi, Anant, Madhavan, Sethu M., Maikhor, Shana, Mariani, Laura H., Marshall, Jamie L., McClelland, Robyn L., McMahon, Gearoid M., Mehl, Karla, Ferreira, Ricardo Melo, Menez, Steven, Menon, Rajasree, Miller, R. Tyler, Moe, Orson W., Moledina, Dennis, Montellano, Richard, Mooney, Sean D., Morales, Martha Catalina, Mukatash, Tariq, Murugan, Raghavan, Nam, Yunbi, Nguyen, Jane, Nolan, Garry, Oʼtoole, John, Oliver, George (Holt), Onul, Ingrid, Otto, Edgar, Palevsky, Paul M., Palmer, Ellen, Pamreddy, Annapurna, Parikh, Chirag R., Parikh, Samir, Park, Christopher, Park, Harold, Pasa-Tolic, Ljiljana, Patel, Jiten, Patterson, Nathan, Phuong, Jim, Pillai, Anil, Pinkeney, Roy, Poggio, Emilio, Pollack, Ari, Prasad, Pottumarthi, Pyle, Laura, Quardokus, Ellen M., Randhawa, Parmjeet, Rauchman, Michael I., Record, Elizabeth, Rennke, Helmut, Rezaei, Kasra, Rike, Adele, Rivera, Marcelino, Roberts, Glenda V., Rosas, Sylvia E., Rosenberg, Avi, Rosengart, Matthew, Rovin, Brad, Roy, Neil, Sabatello, Maya, Sambandam, Kamalanathan, Sarder, Pinaki, Sarkisova, Natalya, Sarwal, Minnie, Saul, John, Schaub, Jennifer, Schmidt, Insa, Sealfon, Rachel, Sedor, John, Sendrey, Dianna, Shang, Ning, Shankland, Stuart, Shapiro, John P., Sharma, Kumar, Sharman, Kavya, Shaw, Melissa M., Shi, Tiffany, Shpigel, Anna, Sigdel, Tara, Slade, Austen, Snyder, Jamie, Spates-Harden, Kassandra, Spraggins, Jeffrey M., Srivastava, Anand, Steck, Becky, Stillman, Isaac, Stutzke, Christy, Su, Jing, Sun, Jennifer, Sutton, Timothy A., Taliercio, Jonathan, Tan, Roderick, Torrealba, Jose, Toto, Robert D., Troyanskaya, Olga, Tublin, Mitchell, Tuttle, Katherine R., Ugwuowo, Ugochukwu, Valerius, M. Todd, Van de Plas, Raf, Varela, German, Vazquez, Miguel, Velickovic, Dusan, Venkatachalam, Manjeri, Verma, Ashish, Victoria-Castro, Angela M., Vijayan, Anitha, Corona-Villalobos, Celia P., Vinovskis, Carissa, Viswanathan, Vidya S., Vita, Tina, Waikar, Sushrut, Wang, Ashley, Wang, Ruikang, Wang, Nancy, Weins, Astrid, Wen, Natasha, Wen, Yumeng, Wilcox, Adam, Williams, James C., Jr., Kayleen Williams, Williams, Mark, Wilson, Francis P., Winfree, Seth, Winters, James, Wofford, Stephanie, Wong, Aaron, Woodle, E. Steve, Xiong, Yuguang, Xu, Alan, Yadati, Pranav, Ye, Hongping, Yu, Guanghao, Zhang, Dianbo, Zhang, Guanshi, and Zhang, Kun
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- 2024
- Full Text
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14. Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis
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Mariani, Laura H., Eddy, Sean, AlAkwaa, Fadhl M., McCown, Phillip J., Harder, Jennifer L., Nair, Viji, Eichinger, Felix, Martini, Sebastian, Ademola, Adebowale D., Boima, Vincent, Reich, Heather N., El Saghir, Jamal, Godfrey, Bradley, Ju, Wenjun, Tanner, Emily C., Vega-Warner, Virginia, Wys, Noel L., Adler, Sharon G., Appel, Gerald B., Athavale, Ambarish, Atkinson, Meredith A., Bagnasco, Serena M., Barisoni, Laura, Brown, Elizabeth, Cattran, Daniel C., Coppock, Gaia M., Dell, Katherine M., Derebail, Vimal K., Fervenza, Fernando C., Fornoni, Alessia, Gadegbeku, Crystal A., Gibson, Keisha L., Greenbaum, Laurence A., Hingorani, Sangeeta R., Hladunewich, Michelle A., Hodgin, Jeffrey B., Hogan, Marie C., Holzman, Lawrence B., Jefferson, J. Ashley, Kaskel, Frederick J., Kopp, Jeffrey B., Lafayette, Richard A., Lemley, Kevin V., Lieske, John C., Lin, Jen-Jar, Menon, Rajarasee, Meyers, Kevin E., Nachman, Patrick H., Nast, Cynthia C., O’Shaughnessy, Michelle M., Otto, Edgar A., Reidy, Kimberly J., Sambandam, Kamalanathan K., Sedor, John R., Sethna, Christine B., Singer, Pamela, Srivastava, Tarak, Tran, Cheryl L., Tuttle, Katherine R., Vento, Suzanne M., Wang, Chia-shi, Ojo, Akinlolu O., Adu, Dwomoa, Gipson, Debbie S., Trachtman, Howard, and Kretzler, Matthias
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- 2023
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15. A Participant-Centered Approach to Understanding Risks and Benefits of Participation in Research Informed by the Kidney Precision Medicine Project
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Alexandrov, Theodore, Alpers, Charles E., Anderton, Christopher R., Ardayfio, Joseph, Arora, Tanima, El-Achkar, Tarek M., Azeloglu, Evren U., Balderes, Olivia, Balis, Ulysses G.J., Bansal, Shweta, Barasch, Jonathan M., Barwinska, Daria, Bebiak, Jack, Blanc, Victoria M., Blank, Kristina N., Bomback, Andrew S., Brown, Keith D., Bush, William S., Campbell, Taneisha, Canetta, Pietro A., Carson, Jonas, Cooperman, Leslie, Crawford, Dana C., D’Agati, Vivette D., Dagher, Pierre C., Daniel, Stephen, Dowd, Frederick, Dunn, Kenneth W., Eadon, Michael T., Eddy, Sean, Elder, Michele M., Ferkowicz, Michael J., Gaut, Joe P., Goltsev, Yury, Gonzalez-Vicente, Agustin, Hacohen, Nir, Hansen, Jens, Hayashi, Lynda, He, Oliver, He, Cijang, Hedayati, S. Susan, Herlitz, Leal, Hodgin, Jeffrey B., Hoofnagle, Andrew N., Hoover, Paul J., Iyengar, Ravi, Jain, Sanjay, Jefferson, Nichole, Jolly, Stacey, Kellum, John A., Kelly, Katherine J., Kermani, Asra, Kiryluk, Krzysztof, Koewler, Robert, Kretzler, Matthias, Lake, Blue B., Laszik, Zoltan G., Lecker, Stewart H., Lee, Simon C., Lienczewski, Chrysta, Lu, Christopher Y., Mariani, Laura H., McClelland, Robyn L., McMahon, Gearoid M., Menez, Steven, Menon, Rajasree, Miller, Tyler, Moe, Orson W., Moledina, Dennis, Mooney, Sean D., Nguyen, Jane, Nolan, Garry, Oliver, George, Otto, Edgar, Palevsky, Paul M., Palmer, Ellen, Pamreddy, Annapurna, Parikh, Chirag R., Parikh, Samir, Park, Christopher, Park, Harold, Pasa-Tolic, Ljiljana, Pinkeney, Roy, Poggio, Emilio, Randhawa, Parmjeet, Rennke, Helmut, Roberts, Glenda V., Rosenberg, Avi, Rosengart, Matthew, Rovin, Brad, Roy, Neil, Sambandam, Kamalanathan, Sarwal, Minnie, Saul, John, Schaub, Jennifer, Sealfon, Rachel, Shang, Ning, Shankland, Stuart, Sharma, Kumar, Shpigel, Anna, Sigdel, Tara, Steck, Becky, Stillman, Isaac, Stutzke, Edith Christine, Sutton, Timothy A., Torrealba, Jose, Toto, Robert D., Troyanskaya, Olga, Tublin, Mitchell, Ugwuowo, Ugochukwu, Vazquez, Miguel, Velickovic, Dusan, Venkatachalam, Manjeri, Vijayan, Anitha, Corona-Villalobos, Celia P., Wang, Nancy, Weins, Astrid, Wilcox, Adam, Williams, Kayleen, Williams, Mark, Wilson, Francis P., Winfree, Seth, Xiong, Yuguang, Zhang, Kun, Zhang, Guanshi, Butler, Catherine R., Appelbaum, Paul S., Ascani, Heather, Aulisio, Mark, Campbell, Catherine E., de Boer, Ian H., Dighe, Ashveena L., Hall, Daniel E., Himmelfarb, Jonathan, Knight, Richard, Mehl, Karla, Murugan, Raghavan, Rosas, Sylvia E., Sedor, John R., O’Toole, John F., Tuttle, Katherine R., Waikar, Sushrut S., and Freeman, Michael
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- 2022
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16. Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes
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Weisman, Caroline M., Murray, Andrew W., and Eddy, Sean R.
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- 2022
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17. Quantification of Glomerular Structural Lesions: Associations With Clinical Outcomes and Transcriptomic Profiles in Nephrotic Syndrome
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Dell, K., Sedor, J., Schachere, M., Negrey, J., Lemley, K., Lim, E., Srivastava, T., Garrett, A., Sethna, C., Laurent, K., Canetta, P., Pradhan, A., Greenbaum, L., Wang, C., Kang, C., Adler, S., LaPage, J., Athavale, A., Itteera, M., Atkinson, M., Boynton, S., Fervenza, F., Hogan, M., Lieske, J., Chernitskiy, V., Kaskel, F., Ross, M., Flynn, P., Kopp, J., Blake, J., Trachtman, H., Zhdanova, O., Modersitzki, F., Vento, S., Bray, M., Kelton, M., Cooper, A., Lafayette, R., Mehta, K., Gadegbeku, C., Quinn-Boyle, S., Hladunewich, M., Reich, H., Ling, P., Romano, M., Fornoni, A., Bidot, C., Kretzler, M., Gipson, D., Williams, A., LaVigne, J., Derebail, V., Gibson, K., Cole, E., Ormond-Foster, J., Holzman, L., Meyers, K., Kallem, K., Swenson, A., Sambandam, K., Wang, Z., Rogers, M., Jefferson, A., Hingorani, S., Tuttle, K., Lin, J.J., Barisoni, L., Bixler, J., Desmond, H., Eddy, S., Fermin, D., Gillespie, B., Kurtz, V., Larkina, M., Lavigne, J., Li, S., Lienczewski, C.C., Liu, J., Mainieri, T., Mariani, L., Sampson, M., Smith, A., Zee, J., Avila-Casado, Carmen, Bagnasco, Serena, Gaut, Joseph, Hewitt, Stephen, Hodgin, Jeff, Lemley, Kevin, Mariani, Laura, Palmer, Matthew, Rosenberg, Avi, Royal, Virginie, Thomas, David, Zee, Jarcy, Barisoni, Laura, Nast, Cynthia, Hodgin, Jeffrey B., Mariani, Laura H., Liu, Qian, Smith, Abigail R., Eddy, Sean, Hartman, John, Hamidi, Habib, Gaut, Joseph P., Palmer, Matthew B., Nast, Cynthia C., Chang, Anthony, Gillespie, Brenda W., Kretzler, Matthias, and Holzman, Lawrence B.
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- 2022
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18. Urine Single-Cell RNA Sequencing in Focal Segmental Glomerulosclerosis Reveals Inflammatory Signatures
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Latt, Khun Zaw, Heymann, Jurgen, Jessee, Joseph H., Rosenberg, Avi Z., Berthier, Celine C., Arazi, Arnon, Eddy, Sean, Yoshida, Teruhiko, Zhao, Yongmei, Chen, Vicky, Nelson, George W., Cam, Margaret, Kumar, Parimal, Mehta, Monika, Kelly, Michael C., Kretzler, Matthias, Ray, Patricio E., Moxey-Mims, Marva, Gorman, Gregory H., Lechner, Brent L., Regunathan-Shenk, Renu, Raj, Dominic S., Susztak, Katalin, Winkler, Cheryl A., and Kopp, Jeffrey B.
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- 2022
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19. 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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Knight, Richard, Lecker, Stewart H., Stillman, Isaac, Bogen, Steve, Amodu, Afolarin A., Ilori, Titlayo, Maikhor, Shana, Schmidt, Insa M., Beck, Laurence H., Henderson, Joel M., Onul, Ingrid, Verma, Ashish, McMahon, Gearoid M., Valerius, M. Todd, Waikar, Sushrut, Weins, Astrid, Colona, Mia R., Greka, Anna, Hacohen, Nir, Hoover, Paul J., Marshall, Jamie L., Aulisio, Mark, Chen, Yijiang M., Janowczyk, Andrew, Jayapandian, Catherine, Viswanathan, Vidya S., Bush, William S., Crawford, Dana C., Madabhushi, Anant, Bush, Lakeshia, Cooperman, Leslie, Gonzalez-Vicente, Agustin, Herlitz, Leal, Jolly, Stacey, Nguyen, Jane, O’toole, John, Palmer, Ellen, Poggio, Emilio, Sedor, John, Sendrey, Dianna, Spates-Harden, Kassandra, Taliercio, Jonathan, Bjornstad, Petter M., Pyle, Laura, Vinovskis, Carissa, Appelbaum, Paul, Balderes, Olivia, Barasch, Jonathan M., Bomback, Andrew S., Canetta, Pietro A., D’Agati, Vivette D., Kiryluk, Krzysztof, Kudose, Satoru, Mehl, Karla, Shang, Ning, Bansal, Shweta, Alexandrov, Theodore, Rennke, Helmut, El-Achkar, Tarek M., Barwinska, Daria, Bledso, Sharon, Borner, Katy, Bueckle, Andreas, Cheng, Yinghua, Dagher, Pierre C., Dunn, Kenneth W., Eadon, Michael T., Ferkowicz, Michael J., Herr, Bruce W., Kelly, Katherine J., Ferreira, Ricardo Melo, Quardokus, Ellen M., Record, Elizabeth, Rivera, Marcelino, Su, Jing, Sutton, Timothy A., Williams, James C., Jr., Winfree, Seth, Jain, Yashvardhan, Menez, Steven, Parikh, Chirag R., Rosenberg, Avi, Corona-Villalobos, Celia P., Wen, Yumeng, Johansen, Camille, Rosas, Sylvia E., Roy, Neil, Sun, Jennifer, Williams, Mark, Azeloglu, Evren U., Hansen, Jens, He, Cijang, Iyengar, Ravi, Xiong, Yuguang, Prasad, Pottumarthi, Srivastava, Anand, Madhavan, Sethu M., Parikh, Samir, Rovin, Brad, Shapiro, John P., Anderton, Christopher R., Lukowski, Jessica, Pasa-Tolic, Ljiljana, Velickovic, Dusan, Oliver, George (Holt), Ardayfio, Joseph, Bebiak, Jack, Brown, Keith, Campbell, Taneisha, Campbell, Catherine E., Hayashi, Lynda, Jefferson, Nichole, Roberts, Glenda V., Saul, John, Shpigel, Anna, Stutzke, Christy, Koewler, Robert, Pinkeney, Roy, Sealfon, Rachel, Troyanskaya, Olga, Wong, Aaron, Tuttle, Katherine R., Pollack, Ari, Goltsev, Yury, Ginley, Brandon, Lucarelli, Nicholas, Lutnick, Brendon, Sarder, Pinaki, Lake, Blue B., Zhang, Kun, Boada, Patrick, Laszik, Zoltan G., Nolan, Garry, Anjani, Kavya, Sarwal, Minnie, Mukatash, Tariq, Sigdel, Tara, Alloway, Rita R., Burg, Ashley R., Lee, Paul J., Rike, Adele, Shi, Tiffany, Woodle, E. Steve, Ascani, Heather, Balis, Ulysses G.J., Blanc, Victoria M., Conser, Ninive C., Eddy, Sean, Frey, Renee, He, Yougqun, Hodgin, Jeffrey B., Kretzler, Matthias, Lienczewski, Chrysta, Luo, Jinghui, Mariani, Laura H., Menon, Rajasree, Otto, Edgar, Schaub, Jennifer, Steck, Becky, Elder, Michele M., Gilliam, Matthew, Hall, Daniel E., Murugan, Raghavan, Palevsky, Paul M., Randhawa, Parmjeet, Rosengart, Matthew, Tublin, Mitchell, Vita, Tina, Winters, James, Kellum, John A., Alpers, Charles E., Berglund, Ashley, Berry, Brooke, Blank, Kristina N., Carson, Jonas, Daniel, Stephen, De Boer, Ian H., Dighe, Ashveena L., Dowd, Frederick, Grewenow, Stephanie M., Himmelfarb, Jonathan, Hoofnagle, Andrew N., Limonte, Christine, McClelland, Robyn L., Mooney, Sean D., Rezaei, Kasra, Shankland, Stuart, Snyder, Jamie, Wang, Ruikang, Wilcox, Adam, Williams, Kayleen, Park, Christopher, Montellano, Richard, Pamreddy, Annapurna, Sharma, Kumar, Venkatachalam, Manjeri, Ye, Hongping, Zhang, Guanshi, Basit, Mujeeb, Hedayati, S. Susan, Kermani, Asra, Lee, Simon C., Lu, Christopher Y., Miller, R. Tyler, Moe, Orson W., Patel, Jiten, Pillai, Anil, Sambandam, Kamalanathan, Torrealba, Jose, Toto, Robert D., Vazquez, Miguel, Wang, Nancy, Wen, Natasha, Zhang, Dianbo, Park, Harold, Caprioli, Richard M., Patterson, Nathan, Sharman, Kavya, Spraggins, Jeffrey M., Van de Plas, Raf, Basta, Jeanine, Diettman, Sabine M., Gaut, Joseph P., Jain, Sanjay, Rauchman, Michael I., Vijayan, Anitha, Cantley, Lloyd G., Kakade, Vijaykumar R., Moledina, Dennis, Shaw, Melissa M., Ugwuowo, Ugochukwu, Wilson, Francis P., Arora, Tanima, Kestenbaum, Bryan R., Alexopoulos, Leonidas G., Palsson, Ragnar, Liu, Jing, Stillman, Isaac E., Rennke, Helmut G., Vaidya, Vishal S., Wu, Haojia, Humphreys, Benjamin D., and Waikar, Sushrut S.
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- 2021
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20. Annexin A1 alleviates kidney injury by promoting the resolution of inflammation in diabetic nephropathy
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Wu, Liang, Liu, Changjie, Chang, Dong-Yuan, Zhan, Rui, Sun, Jing, Cui, Shi-He, Eddy, Sean, Nair, Viji, Tanner, Emily, Brosius, Frank C., Looker, Helen C., Nelson, Robert G., Kretzler, Matthias, Wang, Jian-Cheng, Xu, Ming, Ju, Wenjun, Zhao, Ming-Hui, Chen, Min, and Zheng, Lemin
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- 2021
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21. SGLT2 inhibitors mitigate kidney tubular metabolic and mTORC1 perturbations in youth-onset type 2 diabetes
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Schaub, Jennifer A., AlAkwaa, Fadhl M., McCown, Phillip J., Naik, Abhijit S., Nair, Viji, Eddy, Sean, Menon, Rajasree, Otto, Edgar A., Demeke, Dawit, Hartman, John, Fermin, Damian, O'Connor, Christopher L., Subramanian, Lalita, Bitzer, Markus, Harned, Roger, Ladd, Patricia, Pyle, Laura, Pennathur, Subramaniam, Inoki, Ken, Hodgin, Jeffrey B., Brosius, Frank C., III, Nelson, Robert G., Kretzler, Matthias, and Bjornstad, Petter
- Subjects
Hypoglycemic agents -- Usage -- Physiological aspects ,Type 2 diabetes -- Drug therapy -- Complications and side effects ,Pediatric research ,Diabetic nephropathies -- Risk factors -- Development and progression -- Prevention ,Health care industry - Abstract
The molecular mechanisms of sodium-glucose cotransporter-2 (SGLT2) inhibitors (SGLT2i) remain incompletely understood. Single-cell RNA sequencing and morphometric data were collected from research kidney biopsies donated by young persons with type 2 diabetes (T2D), aged 12 to 21 years, and healthy controls (HCs). Participants with T2D were obese and had higher estimated glomerular filtration rates and mesangial and glomerular volumes than HCs. Ten T2D participants had been prescribed SGLT2i (T2Di[+]) and 6 not (T2Di[-]). Transcriptional profiles showed SGLT2 expression exclusively in the proximal tubular (PT) cluster with highest expression in T2Di(-) patients. However, transcriptional alterations with SGLT2i treatment were seen across nephron segments, particularly in the distal nephron. SGLT2i treatment was associated with suppression of transcripts in the glycolysis, gluconeogenesis, and tricarboxylic acid cycle pathways in PT, but had the opposite effect in thick ascending limb. Transcripts in the energy-sensitive mTORC1-signaling pathway returned toward HC levels in all tubular segments in T2Di(+), consistent with a diabetes mouse model treated with SGLT2i. Decreased levels of phosphorylated S6 protein in proximal and distal tubules in T2Di(+) patients confirmed changes in mTORC1 pathway activity. We propose that SGLT2i treatment benefits the kidneys by mitigating diabetes-induced metabolic perturbations via suppression of mTORC1 signaling in kidney tubules., Introduction The incedence of youth-onset type 2 diabetes (T2D) is rapidly rising among children and adolescents globally (1). It is associated with a more severe clinical course than youth-onset type [...]
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- 2023
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22. SARS-CoV-2 receptor networks in diabetic and COVID-19–associated kidney disease
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Menon, Rajasree, Otto, Edgar A., Sealfon, Rachel, Nair, Viji, Wong, Aaron K., Theesfeld, Chandra L., Chen, Xi, Wang, Yuan, Boppana, Avinash S., Luo, Jinghui, Yang, Yingbao, Kasson, Peter M., Schaub, Jennifer A., Berthier, Celine C., Eddy, Sean, Lienczewski, Chrysta C., Godfrey, Bradley, Dagenais, Susan L., Sohaney, Ryann, Hartman, John, Fermin, Damian, Subramanian, Lalita, Looker, Helen C., Harder, Jennifer L., Mariani, Laura H., Hodgin, Jeffrey B., Sexton, Jonathan Z., Wobus, Christiane E., Naik, Abhijit S., Nelson, Robert G., Troyanskaya, Olga G., and Kretzler, Matthias
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- 2020
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23. Urinary Epidermal Growth Factor as a Marker of Disease Progression in Children With Nephrotic Syndrome
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Gipson, Debbie S., Trachtman, Howard, Waldo, Anne, Gibson, Keisha L., Eddy, Sean, Dell, Katherine M., Srivastava, Tarak, Lemley, Kevin V., Greenbaum, Larry A., Hingorani, Sangeeta, Meyers, Kevin E., Kaskel, Frederick J., Reidy, Kimberly J., Sethna, Christine B., Tran, Cheryl L., Wang, Chia-shi, Tuttle, Katherine R., Oh, Gia, Neu, Alicia M., Brown, Elizabeth, Lin, Jen-Jar, Yee, Jennifer Lai, Roth, Therese M., Troost, Jonathan P., Gillespie, Brenda W., Sampson, Matthew G., Kretzler, Matthias, and Ju, Wenjun
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- 2020
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24. Epigenomic landscapes of retinal rods and cones.
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Mo, Alisa, Luo, Chongyuan, Davis, Fred P, Mukamel, Eran A, Henry, Gilbert L, Nery, Joseph R, Urich, Mark A, Picard, Serge, Lister, Ryan, Eddy, Sean R, Beer, Michael A, Ecker, Joseph R, and Nathans, Jeremy
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Animals ,Mice ,Histones ,Transcription Factors ,DNA ,Gene Expression Profiling ,Epigenesis ,Genetic ,Methylation ,Retinal Rod Photoreceptor Cells ,Retinal Cone Photoreceptor Cells ,DNA methylation ,chromatin ,evolutionary biology ,genomics ,mouse ,neuroscience ,retinal development ,retinal photoreceptors ,transcription factors ,Epigenesis ,Genetic ,Biochemistry and Cell Biology - Abstract
Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide patterns of DNA methylation and chromatin accessibility in mouse rods and cones and correlate differences in these features with gene expression, histone marks, transcription factor binding, and DNA sequence motifs. Loss of NR2E3 in rods shifts their epigenomes to a more cone-like state. The data further reveal wide differences in DNA methylation between retinal photoreceptors and brain neurons. Surprisingly, we also find a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin. Many of these regions exhibit hallmarks of regulatory regions that were active earlier in neuronal development, suggesting that these regions could remain undermethylated due to the highly compact chromatin in mature rods. This work defines the epigenomic landscapes of rods and cones, revealing features relevant to photoreceptor development and function.
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- 2016
25. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain
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Mo, Alisa, Mukamel, Eran A, Davis, Fred P, Luo, Chongyuan, Henry, Gilbert L, Picard, Serge, Urich, Mark A, Nery, Joseph R, Sejnowski, Terrence J, Lister, Ryan, Eddy, Sean R, Ecker, Joseph R, and Nathans, Jeremy
- Subjects
Genetics ,Biotechnology ,Human Genome ,Neurosciences ,Underpinning research ,1.1 Normal biological development and functioning ,Neurological ,Animals ,Cell Nucleolus ,Chromatin Immunoprecipitation ,DNA Methylation ,Epigenomics ,Gene Expression Profiling ,Gene Expression Regulation ,Developmental ,Green Fluorescent Proteins ,Mice ,Mice ,Transgenic ,Microtubule-Associated Proteins ,Neocortex ,Nerve Tissue Proteins ,Neurons ,Proto-Oncogene Proteins c-myc ,Psychology ,Cognitive Sciences ,Neurology & Neurosurgery - Abstract
Neuronal diversity is essential for mammalian brain function but poses a challenge to molecular profiling. To address the need for tools that facilitate cell-type-specific epigenomic studies, we developed the first affinity purification approach to isolate nuclei from genetically defined cell types in a mammal. We combine this technique with next-generation sequencing to show that three subtypes of neocortical neurons have highly distinctive epigenomic landscapes. Over 200,000 regions differ in chromatin accessibility and DNA methylation signatures characteristic of gene regulatory regions. By footprinting and motif analyses, these regions are predicted to bind distinct cohorts of neuron subtype-specific transcription factors. Neuronal epigenomes reflect both past and present gene expression, with DNA hyper-methylation at developmentally critical genes appearing as a novel epigenomic signature in mature neurons. Taken together, our findings link the functional and transcriptional complexity of neurons to their underlying epigenomic diversity.
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- 2015
26. MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease
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Taroni, Jaclyn N., Grayson, Peter C., Hu, Qiwen, Eddy, Sean, Kretzler, Matthias, Merkel, Peter A., and Greene, Casey S.
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- 2019
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27. Hydroxypropyl-β-cyclodextrin protects from kidney disease in experimental Alport syndrome and focal segmental glomerulosclerosis
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Mitrofanova, Alla, Molina, Judith, Varona Santos, Javier, Guzman, Johanna, Morales, Ximena A., Ducasa, G. Michelle, Bryn, Jonathan, Sloan, Alexis, Volosenco, Ion, Kim, Jin-Ju, Ge, Mengyuan, Mallela, Shamroop K., Kretzler, Matthias, Eddy, Sean, Martini, Sebastian, Wahl, Patricia, Pastori, Santiago, Mendez, Armando J., Burke, George W., Merscher, Sandra, and Fornoni, Alessia
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- 2018
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28. JAK-STAT signaling is activated in the kidney and peripheral blood cells of patients with focal segmental glomerulosclerosis
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Tao, Jianling, Mariani, Laura, Eddy, Sean, Maecker, Holden, Kambham, Neeraja, Mehta, Kshama, Hartman, John, Wang, Weiqi, Kretzler, Matthias, and Lafayette, Richard A.
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- 2018
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29. An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome
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Sedor, John, Dell, Katherine, Schachere, Marleen, Lemley, Kevin, Whitted, Lauren, Srivastava, Tarak, Haney, Connie, Sethna, Christine, Grammatikopoulos, Kalliopi, Appel, Gerald, Toledo, Michael, Greenbaum, Laurence, Wang, Chia-shi, Lee, Brian, Adler, Sharon, Nast, Cynthia, LaPage, Janine, Athavale, Ambarish, Neu, Alicia, Boynton, Sara, Fervenza, Fernando, Hogan, Marie, Lieske, John C., Chernitskiy, Vladimir, Kaskel, Frederick, Kumar, Neelja, Flynn, Patricia, Kopp, Jeffrey, Castro-Rubio, Eveleyn, Blake, Jodi, Trachtman, Howard, Zhdanova, Olga, Modersitzki, Frank, Vento, Suzanne, Lafayette, Richard, Mehta, Kshama, Gadegbeku, Crystal, Johnstone, Duncan, Cattran, Daniel, Hladunewich, Michelle, Reich, Heather, Ling, Paul, Romano, Martin, Fornoni, Alessia, Barisoni, Laura, Bidot, Carlos, Kretzler, Matthias, Gipson, Debbie, Williams, Amanda, Pitter, Renee, Nachman, Patrick, Gibson, Keisha, Grubbs, Sandra, Froment, Anne, Holzman, Lawrence, Meyers, Kevin, Kallem, Krishna, Cerecino, Fumei, Sambandam, Kamal, Brown, Elizabeth, Johnson, Natalie, Jefferson, Ashley, Hingorani, Sangeeta, Tuttle, Kathleen, Curtin, Laura, Dismuke, S., Cooper, Ann, Freedman, Barry, Lin, Jen Jar, Gray, Stefanie, Barisoni, Larua, Gillespie, Brenda, Mariani, Laura, Sampson, Matthew G., Song, Peter, Troost, Johnathan, Zee, Jarcy, Herreshoff, Emily, Kincaid, Colleen, Lienczewski, Chrysta, Mainieri, Tina, Abbott, Kevin, Roy, Cindy, Urv, Tiina, Brooks, John, Gillies, Christopher E., Putler, Rosemary, Menon, Rajasree, Otto, Edgar, Yasutake, Kalyn, Nair, Viji, Hoover, Paul, Lieb, David, Li, Shuqiang, Eddy, Sean, Fermin, Damian, McNulty, Michelle T., Hacohen, Nir, Kiryluk, Krzysztof, and Wen, Xiaoquan
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- 2018
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30. Circular Box C/D RNAs in Pyrococcus furiosus
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Starostina, Natalia G., Marshburn, Sarah, Johnson, L. Steven, Eddy, Sean R., Terns, Rebecca M., Terns, Michael P., and Doolittle, W. Ford
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- 2004
31. Gene Evolution: Getting Something from Nothing
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Weisman, Caroline M. and Eddy, Sean R.
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- 2017
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32. Identification and Characterization of a Class of MALAT1-like Genomic Loci
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Zhang, Bin, Mao, Yuntao S., Diermeier, Sarah D., Novikova, Irina V., Nawrocki, Eric P., Jones, Tom A., Lazar, Zsolt, Tung, Chang-Shung, Luo, Weijun, Eddy, Sean R., Sanbonmatsu, Karissa Y., and Spector, David L.
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- 2017
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33. Noncoding RNA Genes Identified in AT-Rich Hyperthermophiles
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Klein, Robert J., Misulovin, Ziva, and Eddy, Sean R.
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- 2002
34. Rationale and design of the Nephrotic Syndrome Study Network (NEPTUNE) Match in glomerular diseases: designing the right trial for the right patient, today
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Massengill, Susan, Lo, Layla, Dell, Katherine, O’Toole, John, Sedor, John, Martin, Blair, Macumber, Ian, Sharma, Silpa, Srivastava, Tarak, Markus, Kelsey, Sethna, Christine, Vento, Suzanne, Canetta, Pietro, Olabisi, Opeyemi, Gbadegesin, Rasheed, Smith, Maurice, Greenbaum, Laurence, Wang, Chia-shi, Yun, Emily, Adler, Sharon, LaPage, Janine, Amarah, Amatur, Itteera, Mathew, Atkinson, Meredith, Williams, Miahje, Lieske, John, Hogan, Marie, Fervenza, Fernando, Selewski, David, Alston, Cheryl, Reidy, Kim, Ross, Michael, Kaskel, Frederick, Flynn, Patricia, Malaga-Dieguez, Laura, Zhdanova, Olga, Pehrson, Laura Jane, Miranda, Melanie, Almaani, Salem, Roberts, Laci, Lafayette, Richard, Dave, Shiktij, Lee, Iris, Shah, Shweta, Batla, Sadaf, Reich, Heather, Hladunewich, Michelle, Ling, Paul, Romano, Martin, Brakeman, Paul, Dylewski, James, Rogers, Nathan, McCarthy, Ellen, Creed, Catherine, Fornoni, Alessia, Bandes, Miguel, Kretzler, Matthias, Mariani, Laura, Modi, Zubin, Williams, A., Ni, Roxy, Nachman, Patrick, Rheault, Michelle, Kowalski, Amy, Rauwolf, Nicolas, Derebail, Vimal, Gibson, Keisha, Froment, Anne, Kelley, Sara, Holzman, Lawrence, Meyers, Kevin, Kallem, Krishna, Edwards, Aliya, Sharma, Samin, Roehm, Elizabeth, Sambandam, Kamalanathan, Brown, Elizabeth, Hellewege, Jamie, Jefferson, Ashley, Hingorani, Sangeeta, Tuttle, Katherine, Manahan, Linda, Pao, Emily, Kuykendall, Kelli, Lin, Jen Jar, Dharnidharka, Vikas, Gillespie, Brenda, Salmon, Eloise, Trachtman, Howard, Mainieri, Tina, Alter, Gabrielle, Arbit, Michael, Desmond, Hailey, Eddy, Sean, Fermin, Damian, Ju, Wenjun, Larkina, Maria, Lienczewski, Chrysta, Scherr, Rebecca, Troost, Jonathan, Williams, Amanda, Zhai, Yan, Kincaid, Colleen, Li, Shengqian, Li, Shannon, Gadegbeku, Crystal, Barisoni, Laura, Sampson, Matthew G., Smith, Abigail, Zee, Jarcy, Avila-Casado, Carmen, Bagnasco, Serena, Bu, Lihong, Caltharp, Shelley, Cassol, Clarissa, Demeke, Dawit, Hassler, Jared, Herlitz, Leal, Hewitt, Stephen, Hodgin, Jeff, Holanda, Danni, Kambham, Neeraja, Lemley, Kevin, Messias, Nidia, Mikhailov, Alexei, Moreno, Vanessa, Najafian, Behzad, Palmer, Matthew, Rosenberg, Avi, Royal, Virginie, Sekulik, Miroslav, Stokes, Barry, Thomas, David, Wu, Ming, Yamashita, Michifumi, Yin, Hong, Zuo . Cochairs, Yiqin, Nast, Cynthia, Williams, Amanda L., Mariani, Laura H., Ascani, Heather K., Uhlmann, Wendy R., Spino, Cathie, Holzman, Lawrence B., Sedor, John R., Subramanian, Lalita, Lienczewski, Chrysta C., Manieri, Tina, Roberts, Scott J., and Gipson, Debbie S.
- Published
- 2024
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35. Homologs of Small Nucleolar RNAs in Archaea
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Omer, Arina D., Lowe, Todd M., Russell, Anthony G., Ebhardt, Holger, Eddy, Sean R., and Dennis, Patrick P.
- Published
- 2000
36. A Computational Screen for Methylation Guide snoRNAs in Yeast
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Lowe, Todd M. and Eddy, Sean R.
- Published
- 1999
37. Local TNF causes NFATc1-dependent cholesterol-mediated podocyte injury
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Pedigo, Christopher E., Ducasa, Gloria Michelle, Leclercq, Farah, Sloan, Alexis, Mitrofanova, Alla, Hashmi, Tahreem, Molina-David, Judith, Ge, Mengyuan, Lassenius, Mariann I., Forsblom, Carol, Lehto, Markku, Groop, Per- Henrik, Kretzler, Matthias, Eddy, Sean, Martini, Sebastian, Reich, Heather, Wahl, Patricia, Ghiggeri, GianMarco, Faul, Christian, Burke, III, George W., Kretz, Oliver, Huber, Tobias B., Mendez, Armando J., Merscher, Sandra, and Fornoni, Alessia
- Subjects
Inflammation -- Research -- Risk factors ,Chronic diseases -- Research -- Care and treatment -- Complications and side effects ,Tumor necrosis factor -- Research -- Influence ,Apoptosis -- Analysis ,Health care industry - Abstract
High levels of circulating TNF and its receptors, TNFR1 and TNFR2, predict the progression of diabetic kidney disease (DKD), but their contribution to organ damage in DKD remains largely unknown. Here, we investigated the function of local and systemic TNF in podocyte injury. We cultured human podocytes with sera collected from DKD patients, who displayed elevated TNF levels, and focal segmental glomerulosclerosis (FSGS) patients, whose TNF levels resembled those of healthy patients. Exogenous TNF administration or local TNF expression was equally sufficient to cause free cholesteroldependent apoptosis in podocytes by acting through a dual mechanism that required a reduction in ATP-binding cassette transporter A1-mediated (ABCA1-mediated) cholesterol efflux and reduced cholesterol esterification by sterol- O-acyltransferase 1 (SOAT1). TNF-induced albuminuria was aggravated in mice with podocyte-specific ABCA1 deficiency and was partially prevented by cholesterol depletion with cyclodextrin. TNF-stimulated free cholesterol-dependent apoptosis in podocytes was mediated by nuclear factor of activated T cells 1 (NFATc1). ABCA1 overexpression or cholesterol depletion was sufficient to reduce albuminuria in mice with podocyte-specific NFATc1 activation. Our data implicate an NFATc1/ ABCA1-dependent mechanism in which local TNF is sufficient to cause free cholesterol-dependent podocyte injury irrespective of TNF, TNFR1, or TNFR2 serum levels., Introduction Chronic low-grade inflammation and elevated TNF levels have been associated with several diseases, such as rheumatoid arthritis (1), multiple sclerosis (2), and atherosclerosis (3). However, the complex nature of [...]
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- 2016
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38. Integrated single-cell sequencing and histopathological analyses reveal diverse injury and repair responses in a participant with acute kidney injury: a clinical-molecular-pathologic correlation
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Knight, Richard, Lecker, Stewart H., Stillman, Isaac, Bogen, Steve, Beck, Laurence H., Waikar, Sushrut, McMahon, Gearoid M., Weins, Astrid, Colona, Mia R., Hacohen, Nir, Hoover, Paul J., Aulisio, Mark, Bush, William S., Crawford, Dana C., O'toole, John, Poggio, Emilio, Sedor, John, Cooperman, Leslie, Jolly, Stacey, Herlitz, Leal, Nguyen, Jane, Gonzalez-Vicente, Agustin, Palmer, Ellen, Sendrey, Dianna, Vinovskis, Carissa, Bjornstad, Petter M., Appelbaum, Paul, Barasch, Jonathan M., Bomback, Andrew S., D'Agati, Vivette D., Kiryluk, Krzysztof, Mehl, Karla, Canetta, Pietro A., Shang, Ning, Balderes, Olivia, Kudose, Satoru, Bansal, Shweta, Alexandrov, Theodore, Rennke, Helmut, El-Achkar, Tarek M., Cheng, Yinghua, Dagher, Pierre C., Eadon, Michael T., Dunn, Kenneth W., Kelly, Katherine J., Sutton, Timothy A., Barwinska, Daria, Ferkowicz, Michael J., Winfree, Seth, Bledsoe, Sharon, Rivera, Marcelino, Williams, James C., Jr., Ferreira, Ricardo Melo, Parikh, Chirag R., Corona-Villalobos, Celia P., Menez, Steven, Rosenberg, Avi, Rosas, Sylvia E., Roy, Neil, Williams, Mark, Azeloglu, Evren U., He, Cijang, Iyengar, Ravi, Hansen, Jens, Xiong, Yuguang, Rovin, Brad, Parikh, Samir, Shapiro, John P., Anderton, Christopher R., Pasa-Tolic, Ljiljana, Velickovic, Dusan, Lukowski, Jessica, Oliver, George, Ardayfio, Joseph, Bebiak, Jack, Brown, Keith, Campbell, Catherine E., Saul, John, Shpigel, Anna, Stutzke, Christy, Koewler, Robert, Campbell, Taneisha, Hayashi, Lynda, Jefferson, Nichole, Roberts, Glenda V., Pinkeney, Roy, Troyanskaya, Olga, Sealfon, Rachel, Tuttle, Katherine R., Goltsev, Yury, Zhang, Kun, Lake, Blue B., Laszik, Zoltan G., Nolan, Garry, Boada, Patrick, Sarwal, Minnie, Sigdel, Tara, Lee, Paul J., Alloway, Rita R., Woodle, E. Steve, Ascani, Heather, Balis, Ulysses G.J., Hodgin, Jeffrey B., Kretzler, Matthias, Lienczewski, Chrysta, Mariani, Laura H., Menon, Rajasree, Steck, Becky, He, Yougqun, Otto, Edgar, Schaub, Jennifer, Blanc, Victoria M., Eddy, Sean, Conser, Ninive C., Luo, Jinghui, Palevsky, Paul M., Rosengart, Matthew, Kellum, John A., Hall, Daniel E., Randhawa, Parmjeet, Tublin, Mitchell, Murugan, Raghavan, Elder, Michele M., Winters, James, Alpers, Charles E., Blank, Kristina N., Carson, Jonas, De Boer, Ian H., Dighe, Ashveena L., Himmelfarb, Jonathan, Mooney, Sean D., Shankland, Stuart, Williams, Kayleen, Park, Christopher, Dowd, Frederick, McClelland, Robyn L., Daniel, Stephen, Hoofnagle, Andrew N., Wilcox, Adam, Grewenow, Stephanie M., Sharma, Kumar, Venkatachalam, Manjeri, Zhang, Guanshi, Pamreddy, Annapurna, Ye, Hongping, Montellano, Richard, Toto, Robert D., Vazquez, Miguel, Lee, Simon C., Miller, R. Tyler, Moe, Orson W., Torrealba, Jose, Wang, Nancy, Kermani, Asra, Sambandam, Kamalanathan, Park, Harold, Hedayati, S. Susan, Lu, Christopher Y., Jain, Sanjay, Vijayan, Anitha, Gaut, Joseph P., Moledina, Dennis, Wilson, Francis P., Ugwuowo, Ugochukwu, Arora, Tanima, and D’Agati, Vivette D.
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- 2022
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39. WCN24-385 PREDICTING PATIENT RESPONSE TO STANDARD-OF-CARE THERAPIES IN GLOMERULAR DISEASES
- Author
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Eddy, Sean, Helmuth, Margaret, Hartman, John, McCown, Phillip, Ju, Wenjun, Nair, Viji, Mariani, Laura, and Kretzler, Matthias
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- 2024
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- View/download PDF
40. Patient perspectives and involvement in precision medicine research
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Knight, Richard, Lecker, Stewart, Stillman, Isaac, Waikar, Sushrut, Mcmahon, Gearoid, Weins, Astrid, Short, Samuel, Hacohen, Nir, Hoover, Paul, Aulisio, Mark, Cooperman, Leslie, Herlitz, Leal, O’Toole, John, Poggio, Emilio, Sedor, John, Jolly, Stacey, Appelbaum, Paul, Balderes, Olivia, Barasch, Jonathan, Bomback, Andrew, Canetta, Pietro A., d’Agati, Vivette D., Kiryluk, Krzysztof, Kudose, Satoru, Mehl, Karla, Radhakrishnan, Jai, Weng, Chenhua, Barisoni, Laura, Alexandrov, Theodore, Ashkar, Tarek, Barwinska, Daria, Dagher, Pierre, Dunn, Kenneth, Eadon, Michael, Ferkowicz, Michael, Kelly, Katherine, Sutton, Timothy, Winfree, Seth, Menez, Steven, Parikh, Chirag, Rosenberg, Avi, Villalobos, Pam, Malik, Rubab, Fine, Derek, Atta, Mohammed, Monroy Trujillo, Jose Manuel, Slack, Alison, Rosas, Sylvia, Williams, Mark, Azeloglu, Evren, He, Cijang (John), Iyengar, Ravi, Hansen, Jens, Parikh, Samir, Rovin, Brad, Anderton, Chris, Pasa-Tolic, Ljiljana, Velickovic, Dusan, Lukowski, Jessica, Oliver, George (Holt), Ardayfio, Joseph, Bebiak, Jack, Brown, Keith, Campbell, Taneisha, Campbell, Catherine, Hayashi, Lynda, Jefferson, Nichole, Koewler, Robert, Roberts, Glenda, Saul, John, Shpigel, Anna, Stutzke, Edith Christine, Wright, Lorenda, Miegs, Leslie, Pinkeney, Roy, Sealfon, Rachel, Troyanskaya, Olga, Tuttle, Katherine, Dobi, Dejan, Goltsev, Yury, Lake, Blue, Zhang, Kun, Joanes, Maria, Laszik, Zoltan, Schroeder, Andrew, Sarwal, Minnie, Sigdel, Tara, Balis, Ulysses, Blanc, Victoria, He, Oliver, Hodgin, Jeffrey, Kretzler, Matthias, Mariani, Laura, Menon, Rajasree, Otto, Edgar, Schaub, Jennifer, Steck, Becky, Lienczewski, Chrysta, Eddy, Sean, Elder, Michele, Hall, Daniel, Kellum, John, Kruth, Mary, Murugan, Raghav, Palevsky, Paul, Randhawa, Parmjeet, Rosengart, Matthew, Sims-Lucas, Sunny, Stefanick, Mary, Stull, Stacy, Tublin, Mitchell, Alpers, Charles, de Boer, Ian, Dighe, Ashveena, Himmelfarb, Jonathan, Mcclelland, Robyn, Mooney, Sean, Shankland, Stuart, Williams, Kayleen, Blank, Kristina, Carson, Jonas, Dowd, Frederick, Drager, Zach, Park, Christopher, Sharma, Kumar, Zhang, Guanshi, Bansal, Shweta, Venkatachalam, Manjeri, Kermani, Asra, Lee, Simon, Lu, Christopher, Miller, Tyler, Moe, Orson, Park, Harold, Sambandam, Kamalanathan, Sanchez, Francisco, Torrealba, Jose, Robert, Toto, Vazquez, Miguel, Wang, Nancy, Gaut, Joe, Jain, Sanjay, Vijayan, Anitha, Luciano, Randy, Moledina, Dennis, Ugochukwu, Ugwuowo, Wilson, Francis Perry, Alfano, Sandy, Tuttle, Katherine R., Hyashi, Lynda, Roberts, Glenda V., and Stutzke, Christy
- Published
- 2021
- Full Text
- View/download PDF
41. Rationale and design of the Kidney Precision Medicine Project
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Knight, Richard, Lecker, Stewart, Stillman, Isaac, Waikar, Sushrut, Mcmahon, Gearoid, Weins, Astrid, Short, Samuel, Hacohen, Nir, Hoover, Paul, Aulisio, Mark, Cooperman, Leslie, Herlitz, Leal, O’Toole, John, Poggio, Emilio, Sedor, John, Jolly, Stacey, Appelbaum, Paul, Balderes, Olivia, Barasch, Jonathan, Bomback, Andrew, Canetta, Pietro A., d’Agati, Vivette D., Kiryluk, Krzysztof, Kudose, Satoru, Mehl, Karla, Radhakrishnan, Jai, Weng, Chenhua, Barisoni, Laura, Alexandrov, Theodore, Ashkar, Tarek, Barwinska, Daria, Dagher, Pierre, Dunn, Kenneth, Eadon, Michael, Ferkowicz, Michael, Kelly, Katherine, Sutton, Timothy, Winfree, Seth, Menez, Steven, Parikh, Chirag, Rosenberg, Avi, Villalobos, Pam, Malik, Rubab, Fine, Derek, Atta, Mohammed, Monroy Trujillo, Jose Manuel, Slack, Alison, Rosas, Sylvia, Williams, Mark, Azeloglu, Evren, He, Cijang (John), Iyengar, Ravi, Hansen, Jens, Parikh, Samir, Rovin, Brad, Anderton, Chris, Pasa-Tolic, Ljiljana, Velickovic, Dusan, Lukowski, Jessica, Oliver, George (Holt), Ardayfio, Joseph, Bebiak, Jack, Brown, Keith, Campbell, Taneisha, Campbell, Catherine, Hayashi, Lynda, Jefferson, Nichole, Koewler, Robert, Roberts, Glenda, Saul, John, Shpigel, Anna, Stutzke, Edith Christine, Wright, Lorenda, Miegs, Leslie, Pinkeney, Roy, Sealfon, Rachel, Troyanskaya, Olga, Tuttle, Katherine, Dobi, Dejan, Goltsev, Yury, Lake, Blue, Zhang, Kun, Joanes, Maria, Laszik, Zoltan, Schroeder, Andrew, Sarwal, Minnie, Sigdel, Tara, Balis, Ulysses, Blanc, Victoria, He, Oliver, Hodgin, Jeffrey, Kretzler, Matthias, Mariani, Laura, Menon, Rajasree, Otto, Edgar, Schaub, Jennifer, Steck, Becky, Lienczewski, Chrysta, Eddy, Sean, Elder, Michele, Hall, Daniel, Kellum, John, Kruth, Mary, Murugan, Raghav, Palevsky, Paul, Randhawa, Parmjeet, Rosengart, Matthew, Sims-Lucas, Sunny, Stefanick, Mary, Stull, Stacy, Tublin, Mitchell, Alpers, Charles, de Boer, Ian, Dighe, Ashveena, Himmelfarb, Jonathan, Mcclelland, Robyn, Mooney, Sean, Shankland, Stuart, Williams, Kayleen, Blank, Kristina, Carson, Jonas, Dowd, Frederick, Drager, Zach, Park, Christopher, Sharma, Kumar, Zhang, Guanshi, Bansal, Shweta, Venkatachalam, Manjeri, Kermani, Asra, Lee, Simon, Lu, Christopher, Miller, Tyler, Moe, Orson, Park, Harold, Sambandam, Kamalanathan, Sanchez, Francisco, Torrealba, Jose, Robert, Toto, Vazquez, Miguel, Wang, Nancy, Gaut, Joe, Jain, Sanjay, Vijayan, Anitha, Luciano, Randy, Moledina, Dennis, Ugochukwu, Ugwuowo, Wilson, Francis Perry, Alfano, Sandy, de Boer, Ian H., Alpers, Charles E., Azeloglu, Evren U., Balis, Ulysses G.J., Barasch, Jonathan M., Blank, Kristina N., Bomback, Andrew S., Dagher, Pierre C., Dighe, Ashveena L., Eadon, Michael T., El-Achkar, Tarek M., Gaut, Joseph P., He, Yongqun, Hodgin, Jeffrey B., Kellum, John A., Laszik, Zoltan G., Mariani, Laura H., McClelland, Robyn L., Moledina, Dennis G., Mooney, Sean D., O’Toole, John F., Palevsky, Paul M., Parikh, Chirag R., Poggio, Emilio D., Rosas, Sylvia E., Rosengart, Matthew R., Sarwal, Minnie M., Schaub, Jennifer A., Sedor, John R., Toto, Robert D., Troyanskaya, Olga G., Tuttle, Katherine R., Vazquez, Miguel A., and Waikar, Sushrut S.
- Published
- 2021
- Full Text
- View/download PDF
42. Nucleotide Sequence of Yellow Fever Virus: Implications for Flavivirus Gene Expression and Evolution
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Rice, Charles M., Lenches, Edith M., Eddy, Sean R., Shin, Se Jung, Sheets, Rebecca L., and Strauss, James H.
- Published
- 1985
43. Genome Maps VI: Caenorhabditis Elegans
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Chalfie, Martin, Eddy, Sean, Hengartner, Michael O, Hodgkin, Jonathan, Kohara, Yuji, Waterston, Robert H., and White, John G.
- Published
- 1995
44. Artificial Mobile DNA Element Constructed from the EcoRI Endonuclease Gene
- Author
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Eddy, Sean R. and Gold, Larry
- Published
- 1992
45. Rfam 12.0: updates to the RNA families database
- Author
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Nawrocki, Eric P., Burge, Sarah W., Bateman, Alex, Daub, Jennifer, Eberhardt, Ruth Y., Eddy, Sean R., Floden, Evan W., Gardner, Paul P., Jones, Thomas A., Tate, John, and Finn, Robert D.
- Published
- 2015
- Full Text
- View/download PDF
46. Cloning and expression of PPARγ and PGC-1α from the hibernating ground squirrel, Spermophilus tridecemlineatus
- Author
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Eddy, Sean F., Morin, Jr., Pier, and Storey, Kenneth B.
- Published
- 2005
- Full Text
- View/download PDF
47. Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes
- Author
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Darnell, Jennifer C., Eddy, Sean R., Fraser, Claire E., Darnell, Robert B., Stefani, Giovanni, Mostovetsky, Olga, and Jones, Thomas A.
- Subjects
RNA -- Research ,Genetic code -- Research ,Fragile X syndrome -- Research ,Biological sciences - Abstract
A study demonstrated that the association of Fragile-X mental retardation protein (FMRP) with brain polyribosomes was abrogated by competition with the MRP kissing complex RNA, but not by high-affinity G-quartet RNAs. It was concluded that mental retardation associated with the 1304N mutation, and likely, the Fragile-X syndrome might relate to a crucial role for RNAs harboring the kissing complex motif as targets for FMRP translational regulation.
- Published
- 2005
48. Generation and annotation of the DNA sequences of human chromosomes 2 and 4
- Author
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Hillier, LaDeana W., Graves, Tina A., Fulton, Robert S., Fulton, Lucinda A., Pepin, Kymberlie H., Minx, Patrick, Wagner-McPherson, Caryn, Layman, Dan, Wylie, Kristine, Sekhon, Mandeep, Becker, Michael C., Fewell, Ginger A., Delehaunty, Kimberly D., Miner, Tracie L., Nash, William E., Kremitzki, Colin, Oddy, Lachlan, Du, Hui, Sun, Hui, Bradshaw-Cordum, Holland, Ali, Johar, Carter, Jason, Cordes, Matt, Harris, Anthony, Isak, Amber, van Brunt, Andrew, Nguyen, Christine, Du, Feiyu, Courtney, Laura, Kalicki, Joelle, Ozersky, Philip, Abbott, Scott, Armstrong, Jon, Belter, Edward A., Caruso, Lauren, Cedroni, Maria, Cotton, Marc, Davidson, Teresa, Desai, Anu, Elliott, Glendoria, Erb, Thomas, Fronick, Catrina, Gaige, Tony, Haakenson, William, Haglund, Krista, Holmes, Andrea, Harkins, Richard, Kim, Kyung, Kruchowski, Scott S., Strong, Cynthia Madsen, Grewal, Neenu, Goyea, Ernest, Hou, Shunfang, Levy, Andrew, Martinka, Scott, Mead, Kelly, McLellan, Michael D., Meyer, Rick, Randall-Maher, Jennifer, Tomlinson, Chad, Dauphin-Kohlberg, Sara, Kozlowicz-Reilly, Amy, Shah, Neha, Swearengen-Shahid, Sharhonda, Snider, Jacqueline, Strong, Joseph T., Thompson, Johanna, Yoakum, Martin, Leonard, Shawn, Pearman, Charlene, Trani, Lee, Radionenko, Maxim, Waligorski, Jason E., Wang, Chunyan, Rock, Susan M., Tin-Wollam, Aye-Mon, Maupin, Rachel, Latreille, Phil, Wendl, Michael C., Yang, Shiaw-Pyng, Pohl, Craig, Wallis, John W., Spieth, John, Bieri, Tamberlyn A., Berkowicz, Nicolas, Nelson, Joanne O., Osborne, John, Ding, Li, Meyer, Rekha, Sabo, Aniko, Shotland, Yoram, Sinha, Prashant, Wohldmann, Patricia E., Cook, Lisa L., Hickenbotham, Matthew T., Eldred, James, Williams, Donald, Jones, Thomas A., She, Xinwei, Ciccarelli, Francesca D., Izaurralde, Elisa, Taylor, James, Schmutz, Jeremy, Myers, Richard M., Cox, David R., Huang, Xiaoqiu, McPherson, John D., Mardis, Elaine R., Clifton, Sandra W., Warren, Wesley C., Chinwalla, Asif T., Eddy, Sean R., Marra, Marco A., Ovcharenko, Ivan, Furey, Terrence S., Miller, Webb, Eichler, Evan E., Bork, Peer, Suyama, Mikita, Torrents, David, Waterston, Robert H., and Wilson, Richard K.
- Subjects
Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): LaDeana W. Hillier [1]; Tina A. Graves [1]; Robert S. Fulton [1]; Lucinda A. Fulton [1]; Kymberlie H. Pepin [1]; Patrick Minx [1]; Caryn Wagner-McPherson [1]; Dan Layman [1]; [...]
- Published
- 2005
- Full Text
- View/download PDF
49. Pfam: the protein families database
- Author
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Finn, Robert D., Bateman, Alex, Clements, Jody, Coggill, Penelope, Eberhardt, Ruth Y., Eddy, Sean R., Heger, Andreas, Hetherington, Kirstie, Holm, Liisa, Mistry, Jaina, Sonnhammer, Erik L. L., Tate, John, and Punta, Marco
- Published
- 2014
- Full Text
- View/download PDF
50. Pack-MULE transposable elements mediate gene evolution in plants
- Author
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Jiang, Ning, Bao, Zhirong, Zhang, Xiaoyu, Eddy, Sean R., and Wessler, Susan R.
- Subjects
Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Ning Jiang [1, 3, 4]; Zhirong Bao [2, 3, 4]; Xiaoyu Zhang [1, 4]; Sean R. Eddy [2]; Susan R. Wessler (corresponding author) [1] Mutator -like transposable elements (MULEs) [...]
- Published
- 2004
- Full Text
- View/download PDF
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