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Hepatocyte-Specific Ablation or Whole-Body Inhibition of Xanthine Oxidoreductase in Mice Corrects Obesity-Induced Systemic Hyperuricemia Without Improving Metabolic Abnormalities.

Harmon DB, Mandler WK, Sipula IJ, Dedousis N, Lewis SE, Eckels JT, Du J, Wang Y, Huckestein BR, Pagano PJ, Cifuentes-Pagano E, Homanics GE, Van't Erve TJ, Stefanovic-Racic M, Jurczak MJ, O'Doherty RM, Kelley EE.

Diabetes. 2019 Jun;68(6):1221-1229. doi: 10.2337/db18-1198. Epub 2019 Apr 1.


Extracellular Vesicles Secreted in Response to Cytokine Exposure Increase Mitochondrial Oxygen Consumption in Recipient Cells.

Russell AE, Jun S, Sarkar S, Geldenhuys WJ, Lewis SE, Rellick SL, Simpkins JW.

Front Cell Neurosci. 2019 Feb 14;13:51. doi: 10.3389/fncel.2019.00051. eCollection 2019.


Apollo: Democratizing genome annotation.

Dunn NA, Unni DR, Diesh C, Munoz-Torres M, Harris NL, Yao E, Rasche H, Holmes IH, Elsik CG, Lewis SE.

PLoS Comput Biol. 2019 Feb 6;15(2):e1006790. doi: 10.1371/journal.pcbi.1006790. eCollection 2019 Feb.


C-H Functionalization of Commodity Polymers.

Williamson JB, Lewis SE, Johnson RR 3rd, Manning IM, Leibfarth FA.

Angew Chem Int Ed Engl. 2019 Jun 24;58(26):8654-8668. doi: 10.1002/anie.201810970. Epub 2019 Mar 26. Review.


Use of Metatarsophalangeal Joint Dorsal Subluxation in the Diagnosis of Plantar Plate Rupture.

Bergeron MC, Ferland J, Malay DS, Lewis SE, Burkmar JA, Giovinco NA.

J Foot Ankle Surg. 2019 Jan;58(1):27-33. doi: 10.1053/j.jfas.2018.06.007. Epub 2018 Nov 15.


Gradual common carotid artery occlusion as a novel model for cerebrovascular Hypoperfusion.

Quintana DD, Ren X, Hu H, Engler-Chiurazzi EB, Rellick SL, Lewis SE, Povroznik JM, Simpkins JW, Alvi M.

Metab Brain Dis. 2018 Dec;33(6):2039-2044. doi: 10.1007/s11011-018-0312-5. Epub 2018 Sep 28.


Model organism data evolving in support of translational medicine.

Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C.

Lab Anim (NY). 2018 Oct;47(10):277-289. doi: 10.1038/s41684-018-0150-4. Epub 2018 Sep 17. Review.


Best practice data life cycle approaches for the life sciences.

Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV.

Version 2. F1000Res. 2017 Aug 31 [revised 2018 Jan 1];6:1618. doi: 10.12688/f1000research.12344.2. eCollection 2017.


Self-assembly and surface behaviour of pure and mixed zwitterionic amphiphiles in a deep eutectic solvent.

Sanchez-Fernandez A, Moody GL, Murfin LC, Arnold T, Jackson AJ, King SM, Lewis SE, Edler KJ.

Soft Matter. 2018 Jul 4;14(26):5525-5536. doi: 10.1039/c8sm00755a.


Understanding the uncertainty of estimating herbicide and nutrient mass loads in a flood event with guidance on estimator selection.

Novic AJ, Ort C, O'Brien DS, Lewis SE, Davis AM, Mueller JF.

Water Res. 2018 Apr 1;132:99-110. doi: 10.1016/j.watres.2017.12.055. Epub 2017 Dec 27.


Enantioselective transformation of fluoxetine in water and its ecotoxicological relevance.

Andrés-Costa MJ, Proctor K, Sabatini MT, Gee AP, Lewis SE, Pico Y, Kasprzyk-Hordern B.

Sci Rep. 2017 Nov 17;7(1):15777. doi: 10.1038/s41598-017-15585-1.


Azulene-boronate esters: colorimetric indicators for fluoride in drinking water.

López-Alled CM, Sanchez-Fernandez A, Edler KJ, Sedgwick AC, Bull SD, McMullin CL, Kociok-Köhn G, James TD, Wenk J, Lewis SE.

Chem Commun (Camb). 2017 Nov 21;53(93):12580-12583. doi: 10.1039/c7cc07416f.


Sperm DNA fragmentation testing is the way forward.

Lewis SEM.

Transl Androl Urol. 2017 Sep;6(Suppl 4):S331. doi: 10.21037/tau.2017.08.07. No abstract available.


Electronic effects on a one-pot aromatization cascade involving alkynyl-Prins cyclization, Friedel-Crafts alkylation and dehydration to tricyclic benzo[f]isochromenes.

Hinkle RJ, Chen Y, Nofi CP, Lewis SE.

Org Biomol Chem. 2017 Sep 20;15(36):7584-7593. doi: 10.1039/c7ob01412k.


Monitoring Herbicide Concentrations and Loads during a Flood Event: A Comparison of Grab Sampling with Passive Sampling.

Novic AJ, O'Brien DS, Kaserzon SL, Hawker DW, Lewis SE, Mueller JF.

Environ Sci Technol. 2017 Apr 4;51(7):3880-3891. doi: 10.1021/acs.est.6b02858. Epub 2017 Mar 10.


Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.

Feuermann M, Gaudet P, Mi H, Lewis SE, Thomas PD.

Database (Oxford). 2016 Dec 26;2016. pii: baw155. doi: 10.1093/database/baw155. Print 2016.


The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA.

Nucleic Acids Res. 2017 Jan 4;45(D1):D712-D722. doi: 10.1093/nar/gkw1128. Epub 2016 Nov 29.


Identification of protein changes in human spermatozoa throughout the cryopreservation process.

Bogle OA, Kumar K, Attardo-Parrinello C, Lewis SE, Estanyol JM, Ballescà JL, Oliva R.

Andrology. 2017 Jan;5(1):10-22. doi: 10.1111/andr.12279. Epub 2016 Nov 17.


Hyaluronic Acid Binding Sperm Selection for assisted reproduction treatment (HABSelect): study protocol for a multicentre randomised controlled trial.

Witt KD, Beresford L, Bhattacharya S, Brian K, Coomarasamy A, Cutting R, Hooper R, Kirkman-Brown J, Khalaf Y, Lewis SE, Pacey A, Pavitt S, West R, Miller D, Cutting R.

BMJ Open. 2016 Oct 7;6(10):e012609. doi: 10.1136/bmjopen-2016-012609. Erratum in: BMJ Open. 2017 Jun 26;7(6):e012609corr1.


The Vision and Challenges of the Gene Ontology.

Lewis SE.

Methods Mol Biol. 2017;1446:291-302.


Use of the Phadebas amylase test to assess the presence of rodent saliva.

Prakash A, Lewis SE, Hickman DL.

Lab Anim (NY). 2016 Oct 20;45(11):433-434. doi: 10.1038/laban.1134. No abstract available.


Structure-activity studies of non-steroid analogues structurally-related to neuroprotective estrogens.

Qian M, Engler-Chiurazzi EB, Lewis SE, Rath NP, Simpkins JW, Covey DF.

Org Biomol Chem. 2016 Oct 18;14(41):9790-9805.


The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.

Buttigieg PL, Pafilis E, Lewis SE, Schildhauer MP, Walls RL, Mungall CJ.

J Biomed Semantics. 2016 Sep 23;7(1):57.


A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.

Smedley D, Schubach M, Jacobsen JOB, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington NL, McMurry JA, Haendel MA, Mungall CJ, Lewis SE, Groza T, Valentini G, Robinson PN.

Am J Hum Genet. 2016 Sep 1;99(3):595-606. doi: 10.1016/j.ajhg.2016.07.005. Epub 2016 Aug 25.


Navigating the Phenotype Frontier: The Monarch Initiative.

McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Xuan JN, Shefchek K, Vasilevsky NA, Yuan Z, Lewis SE, Hochheiser H, Groza T, Smedley D, Robinson PN, Mungall CJ, Haendel MA.

Genetics. 2016 Aug;203(4):1491-5. doi: 10.1534/genetics.116.188870.


MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis SE, Rost B, Goldberg T.

Bioinformatics. 2016 Nov 15;32(22):3501-3503. Epub 2016 Jul 13.


Pesticide Behavior, Fate, and Effects in the Tropics: An Overview of the Current State of Knowledge.

Lewis SE, Silburn DM, Kookana RS, Shaw M.

J Agric Food Chem. 2016 May 25;64(20):3917-24. doi: 10.1021/acs.jafc.6b01320. Epub 2016 May 13.


Langmuir monolayers composed of single and double tail sulfobetaine lipids.

Hazell G, Gee AP, Arnold T, Edler KJ, Lewis SE.

J Colloid Interface Sci. 2016 Jul 15;474:190-8. doi: 10.1016/j.jcis.2016.04.020. Epub 2016 Apr 26.


JBrowse: a dynamic web platform for genome visualization and analysis.

Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, Holmes IH.

Genome Biol. 2016 Apr 12;17:66. doi: 10.1186/s13059-016-0924-1.


Standardized benchmarking in the quest for orthologs.

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.

Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4.


Mitochondrial Impairment in Cerebrovascular Endothelial Cells is Involved in the Correlation between Body Temperature and Stroke Severity.

Hu H, Doll DN, Sun J, Lewis SE, Wimsatt JH, Kessler MJ, Simpkins JW, Ren X.

Aging Dis. 2016 Jan 2;7(1):14-27. doi: 10.14336/AD.2015.0906. eCollection 2016 Jan.


Azulenesulfonium Salts: Accessible, Stable, and Versatile Reagents for Cross-Coupling.

Cowper P, Jin Y, Turton MD, Kociok-Köhn G, Lewis SE.

Angew Chem Int Ed Engl. 2016 Feb 12;55(7):2564-8. doi: 10.1002/anie.201510666. Epub 2016 Jan 14.


Emerging semantics to link phenotype and environment.

Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM.

PeerJ. 2015 Dec 14;3:e1470. doi: 10.7717/peerj.1470. eCollection 2015.


Early detection of cardiac dysfunction in the type 1 diabetic heart using speckle-tracking based strain imaging.

Shepherd DL, Nichols CE, Croston TL, McLaughlin SL, Petrone AB, Lewis SE, Thapa D, Long DM, Dick GM, Hollander JM.

J Mol Cell Cardiol. 2016 Jan;90:74-83. doi: 10.1016/j.yjmcc.2015.12.001. Epub 2015 Dec 3.


Lipopolysaccharide exacerbates infarct size and results in worsened post-stroke behavioral outcomes.

Doll DN, Engler-Chiurazzi EB, Lewis SE, Hu H, Kerr AE, Ren X, Simpkins JW.

Behav Brain Funct. 2015 Oct 13;11(1):32. doi: 10.1186/s12993-015-0077-5.


Translational Regulation of the Mitochondrial Genome Following Redistribution of Mitochondrial MicroRNA in the Diabetic Heart.

Jagannathan R, Thapa D, Nichols CE, Shepherd DL, Stricker JC, Croston TL, Baseler WA, Lewis SE, Martinez I, Hollander JM.

Circ Cardiovasc Genet. 2015 Dec;8(6):785-802. doi: 10.1161/CIRCGENETICS.115.001067. Epub 2015 Sep 16.


Use of model organism and disease databases to support matchmaking for human disease gene discovery.

Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN, Lewis SE, Haendel MA.

Hum Mutat. 2015 Oct;36(10):979-84. doi: 10.1002/humu.22857. Epub 2015 Sep 8.


Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T; Quest for Orthologs Species Tree Working Group.

Genome Biol Evol. 2015 Jul 1;7(7):1988-99. doi: 10.1093/gbe/evv121.


The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.

Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN.

Am J Hum Genet. 2015 Jul 2;97(1):111-24. doi: 10.1016/j.ajhg.2015.05.020. Epub 2015 Jun 25.


Should sperm DNA fragmentation testing be included in the male infertility work-up?

Lewis SE.

Reprod Biomed Online. 2015 Aug;31(2):134-7. doi: 10.1016/j.rbmo.2015.05.006. Epub 2015 May 15.


Disease insights through cross-species phenotype comparisons.

Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D.

Mamm Genome. 2015 Oct;26(9-10):548-55. doi: 10.1007/s00335-015-9577-8. Epub 2015 Jun 20. Review.


The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M.

Database (Oxford). 2015 May 9;2015:bav043. doi: 10.1093/database/bav043. Print 2015.


The paternal genome and the health of the assisted reproductive technology child.

Lewis SE, Kumar K.

Asian J Androl. 2015 Jul-Aug;17(4):616-22. doi: 10.4103/1008-682X.153301. Review.


Mitochondrial crisis in cerebrovascular endothelial cells opens the blood-brain barrier.

Doll DN, Hu H, Sun J, Lewis SE, Simpkins JW, Ren X.

Stroke. 2015 Jun;46(6):1681-9. doi: 10.1161/STROKEAHA.115.009099. Epub 2015 Apr 28.


Decontaminating Ebola-infected ultrasound probes.

Johnston AM, Lewis SE.

Anaesthesia. 2015 May;70(5):628-9. doi: 10.1111/anae.13060. No abstract available.


Cycloparaphenylenes and related nanohoops.

Lewis SE.

Chem Soc Rev. 2015 Apr 21;44(8):2221-304. doi: 10.1039/c4cs00366g.


Finding our way through phenotypes.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.

PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan.


Transgenic overexpression of mitofilin attenuates diabetes mellitus-associated cardiac and mitochondria dysfunction.

Thapa D, Nichols CE, Lewis SE, Shepherd DL, Jagannathan R, Croston TL, Tveter KJ, Holden AA, Baseler WA, Hollander JM.

J Mol Cell Cardiol. 2015 Feb;79:212-23. doi: 10.1016/j.yjmcc.2014.11.008. Epub 2014 Nov 22.


Deletions of chromosomal regulatory boundaries are associated with congenital disease.

Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ, Lewis SE, Ott CE, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN.

Genome Biol. 2014 Sep 4;15(9):423. doi: 10.1186/s13059-014-0423-1.


Direct core functionalisation of naphthalenediimides by iridium catalysed C-H borylation.

Lyall CL, Shotton CC, Pérez-Salvia M, Pantoş GD, Lewis SE.

Chem Commun (Camb). 2014 Nov 18;50(89):13837-40. doi: 10.1039/c4cc06522k.


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