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Proteome Analysis of Isolated Podocytes Reveals Stress Responses in Glomerular Sclerosis.

Koehler S, Kuczkowski A, Kuehne L, Jüngst C, Hoehne M, Grahammer F, Eddy S, Kretzler M, Beck BB, Höhfeld J, Schermer B, Benzing T, Brinkkoetter PT, Rinschen MM.

J Am Soc Nephrol. 2020 Feb 11. pii: ASN.2019030312. doi: 10.1681/ASN.2019030312. [Epub ahead of print]


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

Rivas E, Clements J, Eddy SR.

Bioinformatics. 2020 Feb 7. pii: btaa080. doi: 10.1093/bioinformatics/btaa080. [Epub ahead of print]


Recent Research in Science Teaching and Learning.

Eddy SL.

CBE Life Sci Educ. 2020 Mar;19(1):fe2. doi: 10.1187/cbe.19-12-0277.


A genetic, genomic, and computational resource for exploring neural circuit function.

Davis FP, Nern A, Picard S, Reiser MB, Rubin GM, Eddy SR, Henry GL.

Elife. 2020 Jan 15;9. pii: e50901. doi: 10.7554/eLife.50901. [Epub ahead of print]


Representation learning of genomic sequence motifs with convolutional neural networks.

Koo PK, Eddy SR.

PLoS Comput Biol. 2019 Dec 19;15(12):e1007560. doi: 10.1371/journal.pcbi.1007560. eCollection 2019 Dec.


Free circular introns with an unusual branchpoint in neuronal projections.

Saini H, Bicknell AA, Eddy SR, Moore MJ.

Elife. 2019 Nov 7;8. pii: e47809. doi: 10.7554/eLife.47809.


Identification of glomerular and podocyte-specific genes and pathways activated by sera of patients with focal segmental glomerulosclerosis.

Otalora L, Chavez E, Watford D, Tueros L, Correa M, Nair V, Ruiz P, Wahl P, Eddy S, Martini S, Kretzler M, Burke GW 3rd, Fornoni A, Merscher S.

PLoS One. 2019 Oct 3;14(10):e0222948. doi: 10.1371/journal.pone.0222948. eCollection 2019.


Renal SGLT mRNA expression in human health and disease: a study in two cohorts.

Srinivasan Sridhar V, Ambinathan JPN, Kretzler M, Pyle LL, Bjornstad P, Eddy S, Cherney DZ, Reich HN; European Renal cDNA Bank (ERCB);; Nephrotic Syndrome Study Network (NEPTUNE).

Am J Physiol Renal Physiol. 2019 Nov 1;317(5):F1224-F1230. doi: 10.1152/ajprenal.00370.2019. Epub 2019 Sep 23.


Motivating Structured walking Activity in people with Intermittent Claudication (MOSAIC): protocol for a randomised controlled trial of a physiotherapist-led, behavioural change intervention versus usual care in adults with intermittent claudication.

Bearne L, Galea Holmes M, Bieles J, Eddy S, Fisher G, Modarai B, Patel S, Peacock JL, Sackley C, Volkmer B, Weinman J.

BMJ Open. 2019 Aug 24;9(8):e030002. doi: 10.1136/bmjopen-2019-030002.


Recent Research in Science Teaching and Learning.

Eddy SL.

CBE Life Sci Educ. 2019 Sep;18(3):fe5. doi: 10.1187/cbe.19-07-0132.


Defining and Measuring Students' Interest in Biology: An Analysis of the Biology Education Literature.

Rowland AA, Knekta E, Eddy S, Corwin LA.

CBE Life Sci Educ. 2019 Sep;18(3):ar34. doi: 10.1187/cbe.19-02-0037.


True Grit: Passion and persistence make an innovative course design work.

Casper AM, Eddy SL, Freeman S.

PLoS Biol. 2019 Jul 18;17(7):e3000359. doi: 10.1371/journal.pbio.3000359. eCollection 2019 Jul.


MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease.

Taroni JN, Grayson PC, Hu Q, Eddy S, Kretzler M, Merkel PA, Greene CS.

Cell Syst. 2019 May 22;8(5):380-394.e4. doi: 10.1016/j.cels.2019.04.003.


Selective dorsal rhizotomy in ambulant children with cerebral palsy: an observational cohort study.

Summers J, Coker B, Eddy S, Elstad M, Bunce C, Bourmpaki E, Pennington M, Aquilina K, Cawker S, Edwards R, Goodden J, Hawes S, McCune K, Pettorini B, Smith J, Sneade C, Vloeberghs M, Patrick H, Powell H, Verity C, Peacock JL; Selective Dorsal Rhizotomy Steering Committee.

Lancet Child Adolesc Health. 2019 Jul;3(7):455-462. doi: 10.1016/S2352-4642(19)30119-1. Epub 2019 Apr 30.


One Size Doesn't Fit All: Using Factor Analysis to Gather Validity Evidence When Using Surveys in Your Research.

Knekta E, Runyon C, Eddy S.

CBE Life Sci Educ. 2019 Mar;18(1):rm1. doi: 10.1187/cbe.18-04-0064.


Closing the Achievement Gap in a Large Introductory Course by Balancing Reduced In-Person Contact with Increased Course Structure.

Gavassa S, Benabentos R, Kravec M, Collins T, Eddy S.

CBE Life Sci Educ. 2019 Mar;18(1):ar8. doi: 10.1187/cbe.18-08-0153.


Recent Research in Science Teaching and Learning.

Eddy SL.

CBE Life Sci Educ. 2019 Mar;18(1):fe1. doi: 10.1187/cbe.18-12-0250.


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.

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