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    Mungall, Chris

    TitleComputer Scientist
    SchoolLawrence Berkeley National Lab
    DepartmentEnviron Genomics & Systems Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-4170
    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. Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. Nat Genet. 2017 Jun 26. PMID: 28650483.
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      2. Osumi-Sutherland D, Courtot M, Balhoff JP, Mungall C. Dead simple OWL design patterns. J Biomed Semantics. 2017 Jun 05; 8(1):18. PMID: 28583177.
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      3. Holmes IH, Mungall C. BioMake: a GNU Make-compatible utility for declarative workflow management. Bioinformatics. 2017 May 09. PMID: 28486579.
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      4. Mungall C, 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. 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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      5. Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MW, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JO, Groza T, Smedley D, Mungall C, Haendel M, Robinson PN. The Human Phenotype Ontology in 2017. Nucleic Acids Res. 2017 Jan 04; 45(D1):D865-D876. PMID: 27899602.
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      6. Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest AR, Kasukawa T, Kawaji H. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Res. 2016 Oct 27. PMID: 27794045.
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      7. Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y. Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. Nucleic Acids Res. 2016 Oct 12. PMID: 27733503.
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      8. Links AE, Draper D, Lee E, Guzman J, Valivullah Z, Maduro V, Lebedev V, Didenko M, Tomlin G, Brudno M, Girdea M, Dumitriu S, Haendel MA, Mungall C, Smedley D, Hochheiser H, Arnold AM, Coessens B, Verhoeven S, Bone W, Adams D, Boerkoel CF, Gahl WA, Sincan M. Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience. Front Med (Lausanne). 2016; 3:39. PMID: 27785453.
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      9. Buttigieg PL, Pafilis E, Lewis SE, Schildhauer MP, Walls RL, Mungall C. 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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      10. Hill DP, D'Eustachio P, Berardini TZ, Mungall C, Renedo N, Blake JA. Modeling biochemical pathways in the gene ontology. Database (Oxford). 2016; 2016. PMID: 27589964.
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      11. Smedley D, Schubach M, Jacobsen JO, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington NL, McMurry JA, Haendel MA, Mungall C, Lewis SE, 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 1; 99(3):595-606. PMID: 27569544.
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      12. Dumontier M, Gray AJ, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall C, Rietveld L, Wimalaratne SM, Yamaguchi A. The health care and life sciences community profile for dataset descriptions. PeerJ. 2016; 4:e2331. PMID: 27602295.
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      13. 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 C, Haendel MA. Navigating the Phenotype Frontier: The Monarch Initiative. Genetics. 2016 Aug; 203(4):1491-5. PMID: 27516611.
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      14. Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall C. The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J Biomed Semantics. 2016; 7(1):44. PMID: 27377652.
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      15. Bolleman JT, Mungall C, Strozzi F, Baran J, Dumontier M, Bonnal RJ, Buels R, Hoehndorf R, Fujisawa T, Katayama T, Cock PJ. FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. J Biomed Semantics. 2016; 7:39. PMID: 27296299.
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      16. Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall C, Mooney SD, Su AI, Wu C. High-performance web services for querying gene and variant annotation. Genome Biol. 2016; 17(1):91. PMID: 27154141.
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      17. Druzinsky RE, Balhoff JP, Crompton AW, Done J, German RZ, Haendel MA, Herrel A, Herring SW, Lapp H, Mabee PM, Muller HM, Mungall C, Sternberg PW, Van Auken K, Vinyard CJ, Williams SH, Wall CE. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PLoS One. 2016; 11(2):e0149102. PMID: 26870952.
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      18. Manda P, Mungall C, Balhoff JP, Lapp H, Vision TJ. INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Pac Symp Biocomput. 2016; 21:132-43. PMID: 26776180.
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      19. Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall C, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. Emerging semantics to link phenotype and environment. PeerJ. 2015; 3:e1470. PMID: 26713234.
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      20. Bone WP, Washington NL, Buske OJ, Adams DR, Davis J, Draper D, Flynn ED, Girdea M, Godfrey R, Golas G, Groden C, Jacobsen J, Köhler S, Lee EM, Links AE, Markello TC, Mungall C, Nehrebecky M, Robinson PN, Sincan M, Soldatos AG, Tifft CJ, Toro C, Trang H, Valkanas E, Vasilevsky N, Wahl C, Wolfe LA, Boerkoel CF, Brudno M, Haendel MA, Gahl WA, Smedley D. Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genet Med. 2016 Jun; 18(6):608-17. PMID: 26562225.
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      21. Robinson PN, Mungall C, Haendel M. Capturing phenotypes for precision medicine. Cold Spring Harb Mol Case Stud. 2015 Oct; 1(1):a000372. PMID: 27148566.
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      22. Buske OJ, Schiettecatte F, Hutton B, Dumitriu S, Misyura A, Huang L, Hartley T, Girdea M, Sobreira N, Mungall C, Brudno M. The Matchmaker Exchange API: Automating Patient Matching Through the Exchange of Structured Phenotypic and Genotypic Profiles. Hum Mutat. 2015 Oct; 36(10):922-7. PMID: 26255989.
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      23. Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall C, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery. Hum Mutat. 2015 Oct; 36(10):915-21. PMID: 26295439.
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      24. Mungall C, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN, Lewis SE, 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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      25. 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 C, Lewis SE, Haendel MA, Parkinson H, Robinson PN. The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. Am J Hum Genet. 2015 Jul 2; 97(1):111-24. PMID: 26119816.
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      26. Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall C, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D. Disease insights through cross-species phenotype comparisons. Mamm Genome. 2015 Oct; 26(9-10):548-55. PMID: 26092691.
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      27. Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall C, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C. Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015 Feb 27; 347(6225):1010-4. PMID: 25678556.
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      28. 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 C, 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.
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      29. Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall C, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, 't Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol. 2015; 16(1):22. PMID: 25723102.
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      30. Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall C. TermGenie - a web-application for pattern-based ontology class generation. J Biomed Semantics. 2014; 5:48. PMID: 25937883.
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      31. Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall C, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res. 2015 Jan 28; 43(Database issue):D1071-8. PMID: 25348409.
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      32. Thacker RW, Díaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall C. The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. J Biomed Semantics. 2014; 5(1):39. PMID: 25276334.
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      33. Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, Haendel M, Washington NL, Smedley D, Mungall C, Lewis SE, 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; 15(9):423. PMID: 25315429.
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      34. Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall C, Carey TE, States DJ, Athey BD, He Y. CLO: The cell line ontology. J Biomed Semantics. 2014; 5:37. PMID: 25852852.
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      35. Dahdul WM, Cui H, Mabee PM, Mungall C, Osumi-Sutherland D, Walls RL, Haendel MA. Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. J Biomed Semantics. 2014; 5:34. PMID: 25140222.
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      36. Chibucos MC, Mungall C, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M. Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford). 2014; 2014. PMID: 25052702.
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      37. Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall C, O'Donovan C, Apweiler R, Huntley RP. Representing kidney development using the gene ontology. PLoS One. 2014; 9(6):e99864. PMID: 24941002.
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      38. Oellrich A, Koehler S, Washington N. 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.
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      39. Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall C. A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics. 2014; 15(1):155. PMID: 24885854.
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      40. 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 SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall C. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics. 2014; 5:21. PMID: 25009735.
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      41. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27; 507(7493):462-70. PMID: 24670764.
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      42. Buttigieg PL, Morrison N, Smith B, Mungall C, Lewis SE. The environment ontology: contextualising biological and biomedical entities. J Biomed Semantics. 2013; 4(1):43. PMID: 24330602.
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      43. Köhler S, Doelken SC, Mungall C, 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, Vooren SV, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, Leeuw Nd, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014 Jan 1; 42(1):D966-74. PMID: 24217912.
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      44. Robinson PN, Köhler S, Oellrich A. Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res. 2014 Feb; 24(2):340-8. PMID: 24162188.
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      45. Druzinsky R, Mungall C, Haendel M, Lapp H, Mabee P. What is an anatomy ontology? Anat Rec (Hoboken). 2013 Dec; 296(12):1797-9. PMID: 24127438.
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      46. Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, Mungall C, Lomax J. The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. J Biomed Semantics. 2013; 4(1):20. PMID: 24093723.
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      47. Meehan TF, Vasilevsky NA, Mungall C, Dougall DS, Haendel MA, Blake JA, Diehl AD. Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics. 2013; 14:263. PMID: 24004649.
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      48. Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall C, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. BMC Genomics. 2013; 14:513. PMID: 23895341.
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      49. Maynard SM, Mungall C, Lewis SE, Imam FT, Martone ME. A knowledge based approach to matching human neurodegenerative disease and animal models. Front Neuroinform. 2013; 7:7. PMID: 23717278.
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      50. Smedley D, Oellrich A, Köhler S, Ruef B. PhenoDigm: analyzing curated annotations to associate animal models with human diseases. Database (Oxford). 2013; 2013:bat025. PMID: 23660285.
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      51. Köhler S, Doelken SC, Ruef BJ, Bauer S, Washington N, Westerfield M, Gkoutos G, Schofield P, Smedley D, Lewis SE, Robinson PN, Mungall C. Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research. F1000Res. 2013; 2. PMID: 24358873.
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      52. Aranguren ME, Fernández-Breis JT, Mungall C, Antezana E, González AR, Wilkinson MD. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. J Biomed Semantics. 2013; 4(1):2. PMID: 23286517.
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      53. Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall C, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. A unified anatomy ontology of the vertebrate skeletal system. PLoS One. 2012; 7(12):e51070. PMID: 23251424.
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      54. Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall C, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P. The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol. 2013 Feb; 54(2):e1. PMID: 23220694.
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      55. Gene Ontology annotations and resources. Nucleic Acids Res. 2013 Jan; 41(Database issue):D530-5. PMID: 23161678.
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      56. Doelken SC, Köhler S, Mungall C, Gkoutos GV, Ruef BJ, Smith C, Smedley D, Bauer S, Klopocki E, Schofield PN, Westerfield M, Robinson PN, Lewis SE. 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.
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      57. Walls RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall C, Preece J, Rensing S, Smith B, Stevenson DW. Ontologies as integrative tools for plant science. Am J Bot. 2012 Aug; 99(8):1263-75. PMID: 22847540.
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      58. Chen CK, Mungall C, Gkoutos GV, Doelken SC, Köhler S, Ruef BJ, Smith C, Westerfield M, Robinson PN, Lewis SE, Schofield PN, Smedley D. MouseFinder: Candidate disease genes from mouse phenotype data. Hum Mutat. 2012 May; 33(5):858-66. PMID: 22331800.
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      59. Osumi-Sutherland D, Reeve S, Mungall C, Neuhaus F, Ruttenberg A, Jefferis GS, Armstrong JD. A strategy for building neuroanatomy ontologies. Bioinformatics. 2012 May 1; 28(9):1262-9. PMID: 22402613.
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      60. Thomas PD, Wood V, Mungall C, Lewis SE, 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.
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      61. Mungall C, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 2012; 13(1):R5. PMID: 22293552.
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      62. Köhler S, Bauer S, Mungall C, Carletti G, Smith CL, Schofield P, Gkoutos GV, Robinson PN. Improving ontologies by automatic reasoning and evaluation of logical definitions. BMC Bioinformatics. 2011; 12:418. PMID: 22032770.
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      63. Tirmizi SH, Aitken S, Moreira DA, Mungall C, Sequeda J, Shah NH, Miranker DP. Mapping between the OBO and OWL ontology languages. J Biomed Semantics. 2011; 2 Suppl 1:S3. PMID: 21388572.
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      64. Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall C, Diehl AD. Logical development of the cell ontology. BMC Bioinformatics. 2011; 12:6. PMID: 21208450.
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