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1.

An atlas of healthy and injured cell states and niches in the human kidney.

Lake, Blue B; Menon, Rajasree; Winfree, Seth; Hu, Qiwen; Melo Ferreira, Ricardo; Kalhor, Kian; Barwinska, Daria; Otto, Edgar A; Ferkowicz, Michael; Diep, Dinh; Plongthongkum, Nongluk; Knoten, Amanda; Urata, Sarah; Mariani, Laura H; Naik, Abhijit S; Eddy, Sean; Zhang, Bo; Wu, Yan; Salamon, Diane; Williams, James C; Wang, Xin; Balderrama, Karol S; Hoover, Paul J; Murray, Evan; Marshall, Jamie L; Noel, Teia; Vijayan, Anitha; Hartman, Austin; Chen, Fei; Waikar, Sushrut S; Rosas, Sylvia E; Wilson, Francis P; Palevsky, Paul M; Kiryluk, Krzysztof; Sedor, John R; Toto, Robert D; Parikh, Chirag R; Kim, Eric H; Satija, Rahul; Greka, Anna; Macosko, Evan Z; Kharchenko, Peter V; Gaut, Joseph P; Hodgin, Jeffrey B; Eadon, Michael T; Dagher, Pierre C; El-Achkar, Tarek M; Zhang, Kun; Kretzler, Matthias; Jain, Sanjay.

Nature ; 619(7970): 585-594, 2023 Jul.

Artículo en Inglés | MEDLINE | ID: mdl-37468583

2.

Mammalian cells repress random DNA that yeast transcribes.

Eddy, Sean R.

Nature ; 628(8007): 271-273, 2024 Apr.

Artículo en Inglés | MEDLINE | ID: mdl-38448526

3.

Rationale and design of the Nephrotic Syndrome Study Network (NEPTUNE) Match in glomerular diseases: designing the right trial for the right patient, today.

Trachtman, Howard; Desmond, Hailey; Williams, Amanda L; Mariani, Laura H; Eddy, Sean; Ju, Wenjun; Barisoni, Laura; Ascani, Heather K; Uhlmann, Wendy R; Spino, Cathie; Holzman, Lawrence B; Sedor, John R; Gadegbeku, Crystal; Subramanian, Lalita; Lienczewski, Chrysta C; Manieri, Tina; Roberts, Scott J; Gipson, Debbie S; Kretzler, Matthias.

Kidney Int ; 105(2): 218-230, 2024 Feb.

Artículo en Inglés | MEDLINE | ID: mdl-38245210

4.

Unbiased kidney-centric molecular categorization of chronic kidney disease as a step towards precision medicine.

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; Kretzler, Matthias.

Kidney Int ; 2024 Jan 27.

Artículo en Inglés | MEDLINE | ID: mdl-38286178

5.

Codetta: predicting the genetic code from nucleotide sequence.

Shulgina, Yekaterina; Eddy, Sean R.

Bioinformatics ; 39(1)2023 01 01.

Artículo en Inglés | MEDLINE | ID: mdl-36511586

6.

Correction: Constructing Benchmark Test Sets for Biological Sequence Analysis Using Independent Set Algorithms.

Petti, Samantha; Eddy, Sean R.

PLoS Comput Biol ; 19(3): e1010971, 2023 Mar.

Artículo en Inglés | MEDLINE | ID: mdl-36888579

7.

ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events.

Richardson, Mary O; Eddy, Sean R.

BMC Bioinformatics ; 24(1): 471, 2023 Dec 13.

Artículo en Inglés | MEDLINE | ID: mdl-38093195

8.

Precision nephrology identified tumor necrosis factor activation variability in minimal change disease and focal segmental glomerulosclerosis.

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.

Kidney Int ; 103(3): 565-579, 2023 03.

Artículo en Inglés | MEDLINE | ID: mdl-36442540

9.

Many, but not all, lineage-specific genes can be explained by homology detection failure.

Weisman, Caroline M; Murray, Andrew W; Eddy, Sean R.

PLoS Biol ; 18(11): e3000862, 2020 11.

Artículo en Inglés | MEDLINE | ID: mdl-33137085

10.

Constructing benchmark test sets for biological sequence analysis using independent set algorithms.

Petti, Samantha; Eddy, Sean R.

PLoS Comput Biol ; 18(3): e1009492, 2022 03.

Artículo en Inglés | MEDLINE | ID: mdl-35255082

11.

The association of low birthweight and prematurity on outcomes in children and adults with nephrotic syndrome-a NEPTUNE cohort study.

Hingorani, Sangeeta; Gibson, Keisha L; Xie, Yuping; Wang, Yujie; Eddy, Sean; Hartman, John; Sampson, Matthew; Cassol, Clarissa; Thomas, David; Gipson, Debbie S; Trachtman, Howard; Srivastava, Tarak; Reidy, Kimberly.

Pediatr Nephrol ; 38(10): 3297-3308, 2023 10.

Artículo en Inglés | MEDLINE | ID: mdl-37140708

12.

Rfam 14: expanded coverage of metagenomic, viral and microRNA families.

Kalvari, Ioanna; Nawrocki, Eric P; Ontiveros-Palacios, Nancy; Argasinska, Joanna; Lamkiewicz, Kevin; Marz, Manja; Griffiths-Jones, Sam; Toffano-Nioche, Claire; Gautheret, Daniel; Weinberg, Zasha; Rivas, Elena; Eddy, Sean R; Finn, Robert D; Bateman, Alex; Petrov, Anton I.

Nucleic Acids Res ; 49(D1): D192-D200, 2021 01 08.

Artículo en Inglés | MEDLINE | ID: mdl-33211869

13.

Activation of Stimulator of IFN Genes (STING) Causes Proteinuria and Contributes to Glomerular Diseases.

Mitrofanova, Alla; Fontanella, Antonio; Tolerico, Matthew; Mallela, Shamroop; Molina David, Judith; Zuo, Yiqin; Boulina, Marcia; Kim, Jin-Ju; Santos, Javier; Ge, Mengyuan; Sloan, Alexis; Issa, Wadih; Gurumani, Margaret; Pressly, Jeffrey; Ito, Marie; Kretzler, Matthias; Eddy, Sean; Nelson, Robert; Merscher, Sandra; Burke, George; Fornoni, Alessia.

J Am Soc Nephrol ; 33(12): 2153-2173, 2022 12.

Artículo en Inglés | MEDLINE | ID: mdl-36198430

14.

Quantification of Glomerular Structural Lesions: Associations With Clinical Outcomes and Transcriptomic Profiles in Nephrotic Syndrome.

Hodgin, Jeffrey B; Mariani, Laura H; Zee, Jarcy; Liu, Qian; Smith, Abigail R; Eddy, Sean; Hartman, John; Hamidi, Habib; Gaut, Joseph P; Palmer, Matthew B; Nast, Cynthia C; Chang, Anthony; Hewitt, Stephen; Gillespie, Brenda W; Kretzler, Matthias; Holzman, Lawrence B; Barisoni, Laura.

Am J Kidney Dis ; 79(6): 807-819.e1, 2022 06.

Artículo en Inglés | MEDLINE | ID: mdl-34864148

15.

Gene expression profiles of diabetic kidney disease and neuropathy in eNOS knockout mice: Predictors of pathology and RAS blockade effects.

Eid, Stephanie A; Hinder, Lucy M; Zhang, Hongyu; Eksi, Ridvan; Nair, Viji; Eddy, Sean; Eichinger, Felix; Park, Meeyoung; Saha, Jharna; Berthier, Celine C; Jagadish, Hosagrahar V; Guan, Yuanfang; Pennathur, Subramaniam; Hur, Junguk; Kretzler, Matthias; Feldman, Eva L; Brosius, Frank C.

FASEB J ; 35(5): e21467, 2021 05.

Artículo en Inglés | MEDLINE | ID: mdl-33788970

16.

Annexin A1 alleviates kidney injury by promoting the resolution of inflammation in diabetic nephropathy.

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; Zheng, Lemin.

Kidney Int ; 100(1): 107-121, 2021 07.

Artículo en Inglés | MEDLINE | ID: mdl-33675846

17.

An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome.

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; Kretzler, Matthias; Wen, Xiaoquan; Sampson, Matthew G.

Am J Hum Genet ; 103(2): 232-244, 2018 08 02.

Artículo en Inglés | MEDLINE | ID: mdl-30057032

18.

Estimating the power of sequence covariation for detecting conserved RNA structure.

Rivas, Elena; Clements, Jody; Eddy, Sean R.

Bioinformatics ; 36(10): 3072-3076, 2020 05 01.

Artículo en Inglés | MEDLINE | ID: mdl-32031582

19.

Remote homology search with hidden Potts models.

Wilburn, Grey W; Eddy, Sean R.

PLoS Comput Biol ; 16(11): e1008085, 2020 11.

Artículo en Inglés | MEDLINE | ID: mdl-33253143

20.

The Pfam protein families database in 2019.

El-Gebali, Sara; Mistry, Jaina; Bateman, Alex; Eddy, Sean R; Luciani, Aurélien; Potter, Simon C; Qureshi, Matloob; Richardson, Lorna J; Salazar, Gustavo A; Smart, Alfredo; Sonnhammer, Erik L L; Hirsh, Layla; Paladin, Lisanna; Piovesan, Damiano; Tosatto, Silvio C E; Finn, Robert D.

Nucleic Acids Res ; 47(D1): D427-D432, 2019 01 08.

Artículo en Inglés | MEDLINE | ID: mdl-30357350

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