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    Lewis, Suzanna

    TitleComputer Staff Scientist
    SchoolLawrence Berkeley National Lab
    DepartmentEnviron Genomics & Systems Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-7508
    vCardDownload vCard

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Lewis S. The Vision and Challenges of the Gene Ontology. Methods Mol Biol. 2017; 1446:291-302. PMID: 27812951.
        View in: PubMed
      2. Feuermann M, Gaudet P, Mi H, Lewis S, Thomas PD. Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes. Database (Oxford). 2016; 2016. PMID: 28025345.
        View in: PubMed
      3. 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 S, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2017 Jan 04; 45(D1):D712-D722. PMID: 27899636.
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      4. Buttigieg PL, Pafilis E, Lewis S, Schildhauer MP, Walls RL, Mungall CJ. The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. J Biomed Semantics. 2016 Sep 23; 7(1):57. PMID: 27664130.
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      5. 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 S, Groza T, Valentini G, Robinson PN. A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. Am J Hum Genet. 2016 Sep 01; 99(3):595-606. PMID: 27569544; PMCID: PMC5011059 [Available on 03/01/17].
      6. 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 S, Hochheiser H, Groza T, Smedley D, Robinson PN, Mungall CJ, Haendel MA. Navigating the Phenotype Frontier: The Monarch Initiative. Genetics. 2016 Aug; 203(4):1491-5. PMID: 27516611; PMCID: PMC4981258 [Available on 08/01/17].
      7. Yachdav G, Wilzbach S, Rauscher B, Sheridan R, Sillitoe I, Procter J, Lewis S, Rost B, Goldberg T. MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinformatics. 2016 Nov 15; 32(22):3501-3503. PMID: 27412096.
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      8. Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis S, Stein L, Holmes IH. JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol. 2016 Apr 12; 17:66. PMID: 27072794; PMCID: PMC4830012.
      9. 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, Gabaldón T, Lewis S, Thomas PD, Sonnhammer E, Dessimoz C. Standardized benchmarking in the quest for orthologs. Nat Methods. 2016 May; 13(5):425-30. PMID: 27043882; PMCID: PMC4827703 [Available on 10/04/16].
      10. 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 S, Mabee PM. Emerging semantics to link phenotype and environment. PeerJ. 2015; 3:e1470. PMID: 26713234; PMCID: PMC4690371.
      11. Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN, Lewis S, Haendel MA. Use of model organism and disease databases to support matchmaking for human disease gene discovery. Hum Mutat. 2015 Oct; 36(10):979-84. PMID: 26269093.
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      12. Yachdav G, Goldberg T, Wilzbach S, Dao D, Shih I, Choudhary S, Crouch S, Franz M, García A, García LJ, Grüning BA, Inupakutika D, Sillitoe I, Thanki AS, Vieira B, Villaveces JM, Schneider MV, Lewis S, Pettifer S, Rost B, Corpas M. Anatomy of BioJS, an open source community for the life sciences. Elife. 2015 Jul 08; 4. PMID: 26153621; PMCID: PMC4495654.
      13. Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis S, Gabaldón T. Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream. Genome Biol Evol. 2015 Jul 01; 7(7):1988-99. PMID: 26133389; PMCID: PMC4524488.
      14. 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 S, Haendel MA, Parkinson H, Robinson PN. The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. Am J Hum Genet. 2015 Jul 02; 97(1):111-24. PMID: 26119816; PMCID: PMC4572507.
      15. Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis S, Robinson PN, Smedley D. Disease insights through cross-species phenotype comparisons. Mamm Genome. 2015 Oct; 26(9-10):548-55. PMID: 26092691; PMCID: PMC4602072.
      16. Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis S, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database (Oxford). 2015; 2015:bav043. PMID: 25957950; PMCID: PMC4425939.
      17. Deans AR, Lewis S, 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. Finding our way through phenotypes. PLoS Biol. 2015 Jan; 13(1):e1002033. PMID: 25562316; PMCID: PMC4285398.
      18. Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall CJ, Lewis S, Ott CE, Bauer S, Schofield PN, Mundlos S, Spielmann M, Robinson PN. Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol. 2014 Sep 04; 15(9):423. PMID: 25315429; PMCID: PMC4180961.
      19. Zemojtel T, Köhler S, Mackenroth L, Jäger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Oien NC, Schweiger MR, Krüger U, Frommer G, Fischer B, Kornak U, Flöttmann R, Ardeshirdavani A, Moreau Y, Lewis S, Haendel M, Smedley D, Horn D, Mundlos S, Robinson PN. Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Sci Transl Med. 2014 Sep 03; 6(252):252ra123. PMID: 25186178; PMCID: PMC4512639.
      20. Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis S, Giglio M. Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford). 2014; 2014. PMID: 25052702; PMCID: PMC4105709.
      21. Oellrich A, Koehler S, Washington N, Mungall C, Lewis S, Haendel M, Robinson PN, Smedley D. The influence of disease categories on gene candidate predictions from model organism phenotypes. J Biomed Semantics. 2014; 5(Suppl 1 Proceedings of the Bio-Ontologies Spec Interest G):S4. PMID: 25093073; PMCID: PMC4108905.
      22. Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis S, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics. 2014; 5:21. PMID: 25009735; PMCID: PMC4089931.
      23. Corpas M, Jimenez R, Carbon SJ, García A, Garcia L, Goldberg T, Gomez J, Kalderimis A, Lewis S, Mulvany I, Pawlik A, Rowland F, Salazar G, Schreiber F, Sillitoe I, Spooner WH, Thanki AS, Villaveces JM, Yachdav G, Hermjakob H. BioJS: an open source standard for biological visualisation - its status in 2014. F1000Res. 2014; 3:55. PMID: 25075290; PMCID: PMC4103492.
      24. Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis S. The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics. 2013 Dec 11; 4(1):43. PMID: 24330602; PMCID: PMC3904460.
      25. Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis S, Robinson PN. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014 Jan; 42(Database issue):D966-74. PMID: 24217912; PMCID: PMC3965098.
      26. Robinson PN, Köhler S, Oellrich A, Wang K, Mungall CJ, Lewis S, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D. Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res. 2014 Feb; 24(2):340-8. PMID: 24162188; PMCID: PMC3912424.
      27. Lee E, Helt GA, Reese JT, Munoz-Torres MC, Childers CP, Buels RM, Stein L, Holmes IH, Elsik CG, Lewis S. Web Apollo: a web-based genomic annotation editing platform. Genome Biol. 2013 Aug 30; 14(8):R93. PMID: 24000942; PMCID: PMC4053811.
      28. Maynard SM, Mungall CJ, Lewis S, Imam FT, Martone ME. A knowledge based approach to matching human neurodegenerative disease and animal models. Front Neuroinform. 2013; 7:7. PMID: 23717278; PMCID: PMC3653101.
      29. Smedley D, Oellrich A, Köhler S, Ruef B, Westerfield M, Robinson P, Lewis S, Mungall C. PhenoDigm: analyzing curated annotations to associate animal models with human diseases. Database (Oxford). 2013; 2013:bat025. PMID: 23660285; PMCID: PMC3649640.
      30. Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis S, Robinson PN, Mungall CJ. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res. 2013; 2:30. PMID: 24358873; PMCID: PMC3799545.1.
      31. Doelken SC, Köhler S, Mungall CJ, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S, Klopocki E, Schofield PN, Westerfield M, Robinson PN, Lewis S. Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Dis Model Mech. 2013 Mar; 6(2):358-72. PMID: 23104991; PMCID: PMC3597018.
      32. Mabee P, Deans A, Huala E, Lewis S. Phenotype Ontology Research Coordination Network meeting report: creating a community network for comparing and leveraging phenotype-genotype knowledge across species. Stand Genomic Sci. 2012 Jul 30; 6(3):440-3. PMID: 23409218; PMCID: PMC3558964.
      33. Chen CK, Mungall CJ, Gkoutos GV, Doelken SC, Köhler S, Ruef BJ, Smith C, Westerfield M, Robinson PN, Lewis S, Schofield PN, Smedley D. MouseFinder: Candidate disease genes from mouse phenotype data. Hum Mutat. 2012 May; 33(5):858-66. PMID: 22331800; PMCID: PMC3327758.
      34. Thomas PD, Wood V, Mungall CJ, Lewis S, Blake JA. On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol. 2012; 8(2):e1002386. PMID: 22359495; PMCID: PMC3280971.
      35. Mungall CJ, Torniai C, Gkoutos GV, Lewis S, Haendel MA. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012 Jan 31; 13(1):R5. PMID: 22293552.
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      36. Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S, Kephart ET, Lloyd P, Stinson EO, Washington NL, Perry MD, Ruzanov P, Zha Z, Lewis S, Stein LD, Micklem G. modMine: flexible access to modENCODE data. Nucleic Acids Res. 2012 Jan; 40(Database issue):D1082-8. PMID: 22080565; PMCID: PMC3245176.
      37. Gaudet P, Livstone MS, Lewis S, Thomas PD. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief Bioinform. 2011 Sep; 12(5):449-62. PMID: 21873635; PMCID: PMC3178059.
      38. Washington NL, Stinson EO, Perry MD, Ruzanov P, Contrino S, Smith R, Zha Z, Lyne R, Carr A, Lloyd P, Kephart E, McKay SJ, Micklem G, Stein LD, Lewis S. The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. Database (Oxford). 2011; 2011:bar023. PMID: 21856757; PMCID: PMC3170170.
      39. Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis S, Karsch Mizrachi I, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C. Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford). 2011; 2011:baq027. PMID: 21205783; PMCID: PMC3017395.
      40. Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. PMID: 21177974; PMCID: PMC3192495.
      41. Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010 Dec 24; 330(6012):1775-87. PMID: 21177976; PMCID: PMC3142569.
      42. Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis S, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C. Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 2011 Jan; 39(Database issue):D7-10. PMID: 21097465; PMCID: PMC3013734.
      43. Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis S, Ashburner M. Integrating phenotype ontologies across multiple species. Genome Biol. 2010 Jan 08; 11(1):R2. PMID: 20064205; PMCID: PMC2847714.
      44. Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 2010 Jan; 38(Database issue):D204-10. PMID: 20015972; PMCID: PMC2808919.
      45. Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis S. Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol. 2009 Nov; 7(11):e1000247. PMID: 19956802; PMCID: PMC2774506.
      46. Karp DR, Marthandan N, Marsh SG, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH. Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis. Hum Mol Genet. 2010 Feb 15; 19(4):707-19. PMID: 19933168; PMCID: PMC2807365.
      47. Gabaldón T, Dessimoz C, Huxley-Jones J, Vilella AJ, Sonnhammer EL, Lewis S. Joining forces in the quest for orthologs. Genome Biol. 2009; 10(9):403. PMID: 19785718; PMCID: PMC2768974.
      48. Lee E, Harris N, Gibson M, Chetty R, Lewis S. Apollo: a community resource for genome annotation editing. Bioinformatics. 2009 Jul 15; 25(14):1836-7. PMID: 19439563; PMCID: PMC2705230.
      49. Schober D, Smith B, Lewis S, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA. Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinformatics. 2009 Apr 27; 10:125. PMID: 19397794; PMCID: PMC2684543.
      50. Gkoutos GV, Mungall C, Dolken S, Ashburner M, Lewis S, Hancock J, Schofield P, Kohler S, Robinson PN. Entity/quality-based logical definitions for the human skeletal phenome using PATO. Conf Proc IEEE Eng Med Biol Soc. 2009; 2009:7069-72. PMID: 19964203; PMCID: PMC3398700.
      51. Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009 Jan 15; 25(2):288-9. PMID: 19033274; PMCID: PMC2639003.
      52. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 2009 Jan; 37(Database issue):D619-22. PMID: 18981052; PMCID: PMC2686536.
      53. Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis S, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 2008 Aug; 26(8):889-96. PMID: 18688244; PMCID: PMC2771753.
      54. Mons B, Ashburner M, Chichester C, van Mulligen E, Weeber M, den Dunnen J, van Ommen GJ, Musen M, Cockerill M, Hermjakob H, Mons A, Packer A, Pacheco R, Lewis S, Berkeley A, Melton W, Barris N, Wales J, Meijssen G, Moeller E, Roes PJ, Borner K, Bairoch A. Calling on a million minds for community annotation in WikiProteins. Genome Biol. 2008; 9(5):R89. PMID: 18507872; PMCID: PMC2441475.
      55. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis S, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008 May; 26(5):541-7. PMID: 18464787; PMCID: PMC2409278.
      56. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007 Nov; 25(11):1251-5. PMID: 17989687; PMCID: PMC2814061.
      57. Day-Richter J, Harris MA, Haendel M, Lewis S. OBO-Edit--an ontology editor for biologists. Bioinformatics. 2007 Aug 15; 23(16):2198-200. PMID: 17545183.
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      58. Thomas PD, Mi H, Lewis S. Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol. 2007 Feb; 11(1):4-11. PMID: 17208035.
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      59. Vastrik I, D'Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L. Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 2007; 8(3):R39. PMID: 17367534; PMCID: PMC1868929.
      60. Swedlow JR, Lewis S, Goldberg IG. Modelling data across labs, genomes, space and time. Nat Cell Biol. 2006 Nov; 8(11):1190-4. PMID: 17060903.
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      61. Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis S, Reese MG. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol. 2006; 7 Suppl 1:S2.1-31. PMID: 16925836; PMCID: PMC1810551.
      62. Yandell M, Mungall CJ, Smith C, Prochnik S, Kaminker J, Hartzell G, Lewis S, Rubin GM. Large-scale trends in the evolution of gene structures within 11 animal genomes. PLoS Comput Biol. 2006 Mar; 2(3):e15. PMID: 16518452; PMCID: PMC1386723.
      63. Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis S, Major F, Mathews DH, Richardson JS, Williamson JR, Westhof E. The RNA Ontology Consortium: an open invitation to the RNA community. RNA. 2006 Apr; 12(4):533-41. PMID: 16484377; PMCID: PMC1421088.
      64. Rubin DL, Lewis S, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Day-Richter J, Noy NF, Musen MA. National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. OMICS. 2006; 10(2):185-98. PMID: 16901225.
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      65. Musen MA, Lewis S, Smith B. Wrestling with SUMO and bio-ontologies. Nat Biotechnol. 2006 Jan; 24(1):21; author reply 23. PMID: 16404381; PMCID: PMC2768033.
      66. Eilbeck K, Lewis S, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 2005; 6(5):R44. PMID: 15892872; PMCID: PMC1175956.
      67. Lewis S. Gene Ontology: looking backwards and forwards. Genome Biol. 2005; 6(1):103. PMID: 15642104; PMCID: PMC549054.
      68. Eilbeck K, Lewis S. Sequence ontology annotation guide. Comp Funct Genomics. 2004; 5(8):642-7. PMID: 18629179; PMCID: PMC2447471.
      69. Mi H, Vandergriff J, Campbell M, Narechania A, Majoros W, Lewis S, Thomas PD, Ashburner M. Assessment of genome-wide protein function classification for Drosophila melanogaster. Genome Res. 2003 Sep; 13(9):2118-28. PMID: 12952880; PMCID: PMC403707.
      70. Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis S. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 2002; 3(12):RESEARCH0083. PMID: 12537572; PMCID: PMC151185.
      71. Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis S, Rubin GM, Ashburner M, Celniker SE. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 2002; 3(12):RESEARCH0084. PMID: 12537573; PMCID: PMC151186.
      72. Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis S, Richards S, Ashburner M, Hartenstein V, Celniker SE, Rubin GM. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2002; 3(12):RESEARCH0088. PMID: 12537577; PMCID: PMC151190.
      73. Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science. 2002 Oct 04; 298(5591):149-59. PMID: 12364792.
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      74. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S. The generic genome browser: a building block for a model organism system database. Genome Res. 2002 Oct; 12(10):1599-610. PMID: 12368253; PMCID: PMC187535.
      75. Ashburner M, Lewis S. On ontologies for biologists: the Gene Ontology--untangling the web. Novartis Found Symp. 2002; 247:66-80; discussion 80-3, 84-90, 244-52. PMID: 12539950.
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