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Page 1
The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics.
Matentzoglu N, Bello SM, Stefancsik R, Alghamdi SM, Anagnostopoulos AV, Balhoff JP, Balk MA, Bradford YM, Bridges Y, Callahan TJ, Caufield H, Cuzick A, Carmody LC, Caron AR, de Souza V, Engel SR, Fey P, Fisher M, Gehrke S, Grove C, Hansen P, Harris NL, Harris MA, Harris L, Ibrahim A, Jacobsen JOB, Köhler S, McMurry JA, Munoz-Fuentes V, Munoz-Torres MC, Parkinson H, Pendlington ZM, Pilgrim C, Robb SM, Robinson PN, Seager J, Segerdell E, Smedley D, Sollis E, Toro S, Vasilevsky N, Wood V, Haendel MA, Mungall CJ, McLaughlin JA, Osumi-Sutherland D. Matentzoglu N, et al. Among authors: segerdell e. bioRxiv [Preprint]. 2024 Sep 22:2024.09.18.613276. doi: 10.1101/2024.09.18.613276. bioRxiv. 2024. PMID: 39345458 Free PMC article. Preprint.
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. Shefchek KA, et al. Among authors: segerdell e. Nucleic Acids Res. 2020 Jan 8;48(D1):D704-D715. doi: 10.1093/nar/gkz997. Nucleic Acids Res. 2020. PMID: 31701156 Free PMC article.
A unified anatomy ontology of the vertebrate skeletal system.
Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. Dahdul WM, et al. Among authors: segerdell e. PLoS One. 2012;7(12):e51070. doi: 10.1371/journal.pone.0051070. Epub 2012 Dec 10. PLoS One. 2012. PMID: 23251424 Free PMC article.
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.
Fisher ME, Segerdell E, Matentzoglu N, Nenni MJ, Fortriede JD, Chu S, Pells TJ, Osumi-Sutherland D, Chaturvedi P, James-Zorn C, Sundararaj N, Lotay VS, Ponferrada V, Wang DZ, Kim E, Agalakov S, Arshinoff BI, Karimi K, Vize PD, Zorn AM. Fisher ME, et al. Among authors: segerdell e. BMC Bioinformatics. 2022 Mar 22;23(1):99. doi: 10.1186/s12859-022-04636-8. BMC Bioinformatics. 2022. PMID: 35317743 Free PMC article.
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. Deans AR, et al. Among authors: segerdell e. PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan. PLoS Biol. 2015. PMID: 25562316 Free PMC article.
Research resources: curating the new eagle-i discovery system.
Vasilevsky N, Johnson T, Corday K, Torniai C, Brush M, Segerdell E, Wilson M, Shaffer C, Robinson D, Haendel M. Vasilevsky N, et al. Among authors: segerdell e. Database (Oxford). 2012 Mar 20;2012:bar067. doi: 10.1093/database/bar067. Print 2012. Database (Oxford). 2012. PMID: 22434835 Free PMC article.
Phenotype ontologies: the bridge between genomics and evolution.
Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M. Mabee PM, et al. Among authors: segerdell e. Trends Ecol Evol. 2007 Jul;22(7):345-50. doi: 10.1016/j.tree.2007.03.013. Epub 2007 Apr 9. Trends Ecol Evol. 2007. PMID: 17416439
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.
Sprague J, Bayraktaroglu L, Bradford Y, Conlin T, Dunn N, Fashena D, Frazer K, Haendel M, Howe DG, Knight J, Mani P, Moxon SA, Pich C, Ramachandran S, Schaper K, Segerdell E, Shao X, Singer A, Song P, Sprunger B, Van Slyke CE, Westerfield M. Sprague J, et al. Among authors: segerdell e. Nucleic Acids Res. 2008 Jan;36(Database issue):D768-72. doi: 10.1093/nar/gkm956. Epub 2007 Nov 8. Nucleic Acids Res. 2008. PMID: 17991680 Free PMC article.
Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.
James-Zorn C, Ponferrada V, Fisher ME, Burns K, Fortriede J, Segerdell E, Karimi K, Lotay V, Wang DZ, Chu S, Pells T, Wang Y, Vize PD, Zorn A. James-Zorn C, et al. Among authors: segerdell e. Methods Mol Biol. 2018;1757:251-305. doi: 10.1007/978-1-4939-7737-6_10. Methods Mol Biol. 2018. PMID: 29761462 Free PMC article.
23 results