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Page 1
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.
Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW Jr, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA. Green RE, et al. Among authors: armstrong j. Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449. Epub 2014 Dec 11. Science. 2014. PMID: 25504731 Free PMC article.
Comparative assembly hubs: web-accessible browsers for comparative genomics.
Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B. Nguyen N, et al. Among authors: armstrong j. Bioinformatics. 2014 Dec 1;30(23):3293-301. doi: 10.1093/bioinformatics/btu534. Epub 2014 Aug 18. Bioinformatics. 2014. PMID: 25138168 Free PMC article.
The UCSC Genome Browser database: 2015 update.
Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. Rosenbloom KR, et al. Among authors: armstrong j. Nucleic Acids Res. 2015 Jan;43(Database issue):D670-81. doi: 10.1093/nar/gku1177. Epub 2014 Nov 26. Nucleic Acids Res. 2015. PMID: 25428374 Free PMC article.
Building a pan-genome reference for a population.
Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Nguyen N, et al. Among authors: armstrong j. J Comput Biol. 2015 May;22(5):387-401. doi: 10.1089/cmb.2014.0146. Epub 2015 Jan 7. J Comput Biol. 2015. PMID: 25565268 Free PMC article.
Long-read sequence assembly of the gorilla genome.
Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin CS, Eichler EE. Gordon D, et al. Among authors: armstrong j. Science. 2016 Apr 1;352(6281):aae0344. doi: 10.1126/science.aae0344. Science. 2016. PMID: 27034376 Free PMC article.
Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.
Rice ES, Kohno S, John JS, Pham S, Howard J, Lareau LF, O'Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN 2nd, Gresham C, McCarthy F, Kern C, Haan D, Phan T, Schmidt C, Sanford JR, Ray DA, Paten B, Guillette LJ Jr, Green RE. Rice ES, et al. Among authors: armstrong j. Genome Res. 2017 May;27(5):686-696. doi: 10.1101/gr.213595.116. Epub 2017 Jan 30. Genome Res. 2017. PMID: 28137821 Free PMC article.
A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0).
Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes IT, Armstrong J, Laayouni H, Gordon D, Huddleston J, Garcia Perez R, Povolotskaya I, Serres Armero A, Gómez Garrido J, Ho D, Ribeca P, Alioto T, Green RE, Paten B, Navarro A, Betranpetit J, Herrero J, Eichler EE, Sharp AJ, Feuk L, Warren WC, Marques-Bonet T. Kuderna LFK, et al. Among authors: armstrong j. Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix098. Gigascience. 2017. PMID: 29092041 Free PMC article.
High-resolution comparative analysis of great ape genomes.
Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE. Kronenberg ZN, et al. Among authors: armstrong j. Science. 2018 Jun 8;360(6393):eaar6343. doi: 10.1126/science.aar6343. Science. 2018. PMID: 29880660 Free PMC article.
Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.
Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. Fiddes IT, et al. Among authors: armstrong j. Genome Res. 2018 Jul;28(7):1029-1038. doi: 10.1101/gr.233460.117. Epub 2018 Jun 8. Genome Res. 2018. PMID: 29884752 Free PMC article.
2,601 results