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Organoid single cell profiling identifies a transcriptional signature of glomerular disease.

Harder JL, Menon R, Otto EA, Zhou J, Eddy S, Wys NL, O'Connor C, Luo J, Nair V, Cebrian C, Spence JR, Bitzer M, Troyanskaya OG, Hodgin JB, Wiggins RC, Freedman BS, Kretzler M; European Renal cDNA Bank (ERCB); Nephrotic Syndrome Study Network (NEPTUNE).

JCI Insight. 2019 Jan 10;4(1). pii: 122697. doi: 10.1172/jci.insight.122697. [Epub ahead of print]


The Pfam protein families database in 2019.

El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer ELL, Hirsh L, Paladin L, Piovesan D, Tosatto SCE, Finn RD.

Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432. doi: 10.1093/nar/gky995.


Hydroxypropyl-β-cyclodextrin protects from kidney disease in experimental Alport syndrome and focal segmental glomerulosclerosis.

Mitrofanova A, Molina J, Varona Santos J, Guzman J, Morales XA, Ducasa GM, Bryn J, Sloan A, Volosenco I, Kim JJ, Ge M, Mallela SK, Kretzler M, Eddy S, Martini S, Wahl P, Pastori S, Mendez AJ, Burke GW, Merscher S, Fornoni A.

Kidney Int. 2018 Dec;94(6):1151-1159. doi: 10.1016/j.kint.2018.06.031. Epub 2018 Oct 6.


Faculty Beliefs about Intelligence Are Related to the Adoption of Active-Learning Practices.

Aragón OR, Eddy SL, Graham MJ.

CBE Life Sci Educ. 2018 Sep;17(3):ar47. doi: 10.1187/cbe.17-05-0084.


JAK-STAT signaling is activated in the kidney and peripheral blood cells of patients with focal segmental glomerulosclerosis.

Tao J, Mariani L, Eddy S, Maecker H, Kambham N, Mehta K, Hartman J, Wang W, Kretzler M, Lafayette RA.

Kidney Int. 2018 Oct;94(4):795-808. doi: 10.1016/j.kint.2018.05.022. Epub 2018 Aug 6.


An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome.

Gillies CE, Putler R, Menon R, Otto E, Yasutake K, Nair V, Hoover P, Lieb D, Li S, Eddy S, Fermin D, McNulty MT; Nephrotic Syndrome Study Network (NEPTUNE), Hacohen N, Kiryluk K, Kretzler M, Wen X, Sampson MG.

Am J Hum Genet. 2018 Aug 2;103(2):232-244. doi: 10.1016/j.ajhg.2018.07.004. Epub 2018 Jul 26.


Recent Research in Science Teaching and Learning.

Eddy SL.

CBE Life Sci Educ. 2018 Sep;17(3):fe7. doi: 10.1187/cbe.18-04-0056. No abstract available.


The trade-off between graduate student research and teaching: A myth?

Shortlidge EE, Eddy SL.

PLoS One. 2018 Jun 25;13(6):e0199576. doi: 10.1371/journal.pone.0199576. eCollection 2018.


HMMER web server: 2018 update.

Potter SC, Luciani A, Eddy SR, Park Y, Lopez R, Finn RD.

Nucleic Acids Res. 2018 Jul 2;46(W1):W200-W204. doi: 10.1093/nar/gky448.


Group I introns are widespread in archaea.

Nawrocki EP, Jones TA, Eddy SR.

Nucleic Acids Res. 2018 Sep 6;46(15):7970-7976. doi: 10.1093/nar/gky414.


Reading Quizzes Improve Exam Scores for Community College Students.

Pape-Lindstrom P, Eddy S, Freeman S.

CBE Life Sci Educ. 2018 Jun;17(2):ar21. doi: 10.1187/cbe.17-08-0160.


Metabolic pathways and immunometabolism in rare kidney diseases.

Grayson PC, Eddy S, Taroni JN, Lightfoot YL, Mariani L, Parikh H, Lindenmeyer MT, Ju W, Greene CS, Godfrey B, Cohen CD, Krischer J, Kretzler M, Merkel PA; Vasculitis Clinical Research Consortium, the European Renal cDNA Bank cohort, and the Nephrotic Syndrome Study Network.

Ann Rheum Dis. 2018 Aug;77(8):1226-1233. doi: 10.1136/annrheumdis-2017-212935. Epub 2018 May 3.


Urinary epidermal growth factor predicts renal prognosis in antineutrophil cytoplasmic antibody-associated vasculitis.

Wu L, Li XQ, Goyal T, Eddy S, Kretzler M, Ju WJ, Chen M, Zhao MH.

Ann Rheum Dis. 2018 Sep;77(9):1339-1344. doi: 10.1136/annrheumdis-2017-212578. Epub 2018 May 3.


FAR2 is associated with kidney disease in mice and humans.

Backer G, Eddy S, Sheehan SM, Takemon Y, Reznichenko A, Savage HS, Kretzler M, Korstanje R.

Physiol Genomics. 2018 Aug 1;50(8):543-552. doi: 10.1152/physiolgenomics.00118.2017. Epub 2018 Apr 13.


A Small-Molecule Inhibitor of Human DNA Polymerase η Potentiates the Effects of Cisplatin in Tumor Cells.

Zafar MK, Maddukuri L, Ketkar A, Penthala NR, Reed MR, Eddy S, Crooks PA, Eoff RL.

Biochemistry. 2018 Feb 20;57(7):1262-1273. doi: 10.1021/acs.biochem.7b01176. Epub 2018 Jan 30.


Subcutaneous implantable cardioverter defibrillator (S-ICD) shocks in a patient with a left ventricular assist device.

Saini H, Saini A, Leffler J, Eddy S, Ellenbogen KA.

Pacing Clin Electrophysiol. 2018 Mar;41(3):309-311. doi: 10.1111/pace.13273. Epub 2018 Feb 2. No abstract available.


Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.

Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI.

Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342. doi: 10.1093/nar/gkx1038.


Student perception of group dynamics predicts individual performance: Comfort and equity matter.

Theobald EJ, Eddy SL, Grunspan DZ, Wiggins BL, Crowe AJ.

PLoS One. 2017 Jul 20;12(7):e0181336. doi: 10.1371/journal.pone.0181336. eCollection 2017.


Values Affirmation Intervention Reduces Achievement Gap between Underrepresented Minority and White Students in Introductory Biology Classes.

Jordt H, Eddy SL, Brazil R, Lau I, Mann C, Brownell SE, King K, Freeman S.

CBE Life Sci Educ. 2017 Fall;16(3). pii: ar41. doi: 10.1187/cbe.16-12-0351.


Gene Evolution: Getting Something from Nothing.

Weisman CM, Eddy SR.

Curr Biol. 2017 Jul 10;27(13):R661-R663. doi: 10.1016/j.cub.2017.05.056.


Reintroducing the Current Insights Feature.

Gouvea J, Eddy SL.

CBE Life Sci Educ. 2017 Summer;16(2). pii: fe3. doi: 10.1187/cbe.17-03-0053. No abstract available.


Identification and Characterization of a Class of MALAT1-like Genomic Loci.

Zhang B, Mao YS, Diermeier SD, Novikova IV, Nawrocki EP, Jones TA, Lazar Z, Tung CS, Luo W, Eddy SR, Sanbonmatsu KY, Spector DL.

Cell Rep. 2017 May 23;19(8):1723-1738. doi: 10.1016/j.celrep.2017.05.006.


ASPECT: A Survey to Assess Student Perspective of Engagement in an Active-Learning Classroom.

Wiggins BL, Eddy SL, Wener-Fligner L, Freisem K, Grunspan DZ, Theobald EJ, Timbrook J, Crowe AJ.

CBE Life Sci Educ. 2017 Summer;16(2). pii: ar32. doi: 10.1187/cbe.16-08-0244.


Olfactory effects of a hypervariable multicomponent pheromone in the red-legged salamander, Plethodon shermani.

Wilburn DB, Doty KA, Chouinard AJ, Eddy SL, Woodley SK, Houck LD, Feldhoff RC.

PLoS One. 2017 Mar 30;12(3):e0174370. doi: 10.1371/journal.pone.0174370. eCollection 2017.


A Guide for Graduate Students Interested in Postdoctoral Positions in Biology Education Research.

Aikens ML, Corwin LA, Andrews TC, Couch BA, Eddy SL, McDonnell L, Trujillo G.

CBE Life Sci Educ. Winter 2016;15(4). pii: es10.


A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs.

Rivas E, Clements J, Eddy SR.

Nat Methods. 2017 Jan;14(1):45-48. doi: 10.1038/nmeth.4066. Epub 2016 Nov 7.


Human Translesion Polymerase κ Exhibits Enhanced Activity and Reduced Fidelity Two Nucleotides from G-Quadruplex DNA.

Eddy S, Tillman M, Maddukuri L, Ketkar A, Zafar MK, Eoff RL.

Biochemistry. 2016 Sep 20;55(37):5218-29. doi: 10.1021/acs.biochem.6b00374. Epub 2016 Sep 7.


Local TNF causes NFATc1-dependent cholesterol-mediated podocyte injury.

Pedigo CE, Ducasa GM, Leclercq F, Sloan A, Mitrofanova A, Hashmi T, Molina-David J, Ge M, Lassenius MI, Forsblom C, Lehto M, Groop PH, Kretzler M, Eddy S, Martini S, Reich H, Wahl P, Ghiggeri G, Faul C, Burke GW 3rd, Kretz O, Huber TB, Mendez AJ, Merscher S, Fornoni A.

J Clin Invest. 2016 Sep 1;126(9):3336-50. doi: 10.1172/JCI85939. Epub 2016 Aug 2.


Cognitive Difficulty and Format of Exams Predicts Gender and Socioeconomic Gaps in Exam Performance of Students in Introductory Biology Courses.

Wright CD, Eddy SL, Wenderoth MP, Abshire E, Blankenbiller M, Brownell SE.

CBE Life Sci Educ. 2016 Summer;15(2). pii: ar23. doi: 10.1187/cbe.15-12-0246.


Epigenomic landscapes of retinal rods and cones.

Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J.

Elife. 2016 Mar 7;5:e11613. doi: 10.7554/eLife.11613.


Males Under-Estimate Academic Performance of Their Female Peers in Undergraduate Biology Classrooms.

Grunspan DZ, Eddy SL, Brownell SE, Wiggins BL, Crowe AJ, Goodreau SM.

PLoS One. 2016 Feb 10;11(2):e0148405. doi: 10.1371/journal.pone.0148405. eCollection 2016.


The Pfam protein families database: towards a more sustainable future.

Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A.

Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85. doi: 10.1093/nar/gkv1344. Epub 2015 Dec 15.


Parameterizing sequence alignment with an explicit evolutionary model.

Rivas E, Eddy SR.

BMC Bioinformatics. 2015 Dec 10;16:406. doi: 10.1186/s12859-015-0832-5.


Caution, Student Experience May Vary: Social Identities Impact a Student's Experience in Peer Discussions.

Eddy SL, Brownell SE, Thummaphan P, Lan MC, Wenderoth MP.

CBE Life Sci Educ. 2015 Winter;14(4):ar45. doi: 10.1187/cbe.15-05-0108.


The Dfam database of repetitive DNA families.

Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ.

Nucleic Acids Res. 2016 Jan 4;44(D1):D81-9. doi: 10.1093/nar/gkv1272. Epub 2015 Nov 26.


Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates.

Chen X, Jung S, Beh LY, Eddy SR, Landweber LF.

Genome Biol Evol. 2015 Sep 2;7(10):2859-70. doi: 10.1093/gbe/evv172.


Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.

Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker JR, Nathans J.

Neuron. 2015 Jun 17;86(6):1369-84. doi: 10.1016/j.neuron.2015.05.018.


PORTAAL: A Classroom Observation Tool Assessing Evidence-Based Teaching Practices for Active Learning in Large Science, Technology, Engineering, and Mathematics Classes.

Eddy SL, Converse M, Wenderoth MP.

CBE Life Sci Educ. 2015 Summer;14(2):14:ar23. doi: 10.1187/cbe.14-06-0095. Epub 2015 Jun 1.


A high-enrollment course-based undergraduate research experience improves student conceptions of scientific thinking and ability to interpret data.

Brownell SE, Hekmat-Scafe DS, Singla V, Chandler Seawell P, Conklin Imam JF, Eddy SL, Stearns T, Cyert MS.

CBE Life Sci Educ. 2015 Summer;14(2):14:ar21. doi: 10.1187/cbe.14-05-0092. Epub 2015 Jun 1.


HMMER web server: 2015 update.

Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR.

Nucleic Acids Res. 2015 Jul 1;43(W1):W30-8. doi: 10.1093/nar/gkv397. Epub 2015 May 5.


Evidence for the kinetic partitioning of polymerase activity on G-quadruplex DNA.

Eddy S, Maddukuri L, Ketkar A, Zafar MK, Henninger EE, Pursell ZF, Eoff RL.

Biochemistry. 2015 May 26;54(20):3218-30. doi: 10.1021/acs.biochem.5b00060. Epub 2015 May 11.


Homology searches for structural RNAs: from proof of principle to practical use.

Eddy SR.

RNA. 2015 Apr;21(4):605-7. doi: 10.1261/rna.050484.115. No abstract available.


Bioavailability of everolimus administered as a single 5 mg tablet versus five 1 mg tablets: a randomized, open-label, two-way crossover study of healthy volunteers.

Thudium K, Gallo J, Bouillaud E, Sachs C, Eddy S, Cheung W.

Clin Pharmacol. 2015 Jan 22;7:11-7. doi: 10.2147/CPAA.S73472. eCollection 2015.


Rfam 12.0: updates to the RNA families database.

Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D130-7. doi: 10.1093/nar/gku1063. Epub 2014 Nov 11.


The Werner syndrome protein limits the error-prone 8-oxo-dG lesion bypass activity of human DNA polymerase kappa.

Maddukuri L, Ketkar A, Eddy S, Zafar MK, Eoff RL.

Nucleic Acids Res. 2014 Oct 29;42(19):12027-40. doi: 10.1093/nar/gku913. Epub 2014 Oct 7.


Reply to Hora: Meta-analytic techniques are designed to accommodate variation in implementation.

Freeman S, Eddy SL, Jordt H, Smith MK, Wenderoth MP.

Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):E3025. No abstract available.


Gender gaps in achievement and participation in multiple introductory biology classrooms.

Eddy SL, Brownell SE, Wenderoth MP.

CBE Life Sci Educ. 2014 Fall;13(3):478-92. doi: 10.1187/cbe.13-10-0204. Erratum in: CBE Life Sci Educ. 2014 Winter;13(4):738.


Getting under the hood: how and for whom does increasing course structure work?

Eddy SL, Hogan KA.

CBE Life Sci Educ. 2014 Fall;13(3):453-68. doi: 10.1187/cbe.14-03-0050.


Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.

Eddy SR.

Annu Rev Biophys. 2014;43:433-56. doi: 10.1146/annurev-biophys-051013-022950. Review.


Active learning increases student performance in science, engineering, and mathematics.

Freeman S, Eddy SL, McDonough M, Smith MK, Okoroafor N, Jordt H, Wenderoth MP.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8410-5. doi: 10.1073/pnas.1319030111. Epub 2014 May 12.

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