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Results: 1 to 20 of 23

1.

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication.

Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KF, Rounsley S, Wing RA.

Nat Genet. 2014 Sep;46(9):982-8. doi: 10.1038/ng.3044. Epub 2014 Jul 27.

PMID:
25064006
2.

Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome.

Shearer LA, Anderson LK, de Jong H, Smit S, Goicoechea JL, Roe BA, Hua A, Giovannoni JJ, Stack SM.

G3 (Bethesda). 2014 May 30;4(8):1395-405. doi: 10.1534/g3.114.011197.

3.

Global genomic diversity of Oryza sativa varieties revealed by comparative physical mapping.

Wang X, Kudrna DA, Pan Y, Wang H, Liu L, Lin H, Zhang J, Song X, Goicoechea JL, Wing RA, Zhang Q, Luo M.

Genetics. 2014 Apr;196(4):937-49. doi: 10.1534/genetics.113.159970. Epub 2014 Jan 14.

4.

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds.

Singh R, Ong-Abdullah M, Low ET, Manaf MA, Rosli R, Nookiah R, Ooi LC, Ooi SE, Chan KL, Halim MA, Azizi N, Nagappan J, Bacher B, Lakey N, Smith SW, He D, Hogan M, Budiman MA, Lee EK, DeSalle R, Kudrna D, Goicoechea JL, Wing RA, Wilson RK, Fulton RS, Ordway JM, Martienssen RA, Sambanthamurthi R.

Nature. 2013 Aug 15;500(7462):335-9. doi: 10.1038/nature12309. Epub 2013 Jul 24.

5.

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.

Zuccolo A, Bowers JE, Estill JC, Xiong Z, Luo M, Sebastian A, Goicoechea JL, Collura K, Yu Y, Jiao Y, Duarte J, Tang H, Ayyampalayam S, Rounsley S, Kudrna D, Paterson AH, Pires JC, Chanderbali A, Soltis DE, Chamala S, Barbazuk B, Soltis PS, Albert VA, Ma H, Mandoli D, Banks J, Carlson JE, Tomkins J, dePamphilis CW, Wing RA, Leebens-Mack J.

Genome Biol. 2011;12(5):R48. doi: 10.1186/gb-2011-12-5-r48. Epub 2011 May 27.

6.

Long-range and targeted ectopic recombination between the two homeologous chromosomes 11 and 12 in Oryza species.

Jacquemin J, Chaparro C, Laudié M, Berger A, Gavory F, Goicoechea JL, Wing RA, Cooke R.

Mol Biol Evol. 2011 Nov;28(11):3139-50. doi: 10.1093/molbev/msr144. Epub 2011 May 25.

7.

The 19 genomes of Drosophila: a BAC library resource for genus-wide and genome-scale comparative evolutionary research.

Song X, Goicoechea JL, Ammiraju JS, Luo M, He R, Lin J, Lee SJ, Sisneros N, Watts T, Kudrna DA, Golser W, Ashley E, Collura K, Braidotti M, Yu Y, Matzkin LM, McAllister BF, Markow TA, Wing RA.

Genetics. 2011 Apr;187(4):1023-30. doi: 10.1534/genetics.111.126540. Epub 2011 Feb 14.

8.

An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research.

Febrer M, Goicoechea JL, Wright J, McKenzie N, Song X, Lin J, Collura K, Wissotski M, Yu Y, Ammiraju JS, Wolny E, Idziak D, Betekhtin A, Kudrna D, Hasterok R, Wing RA, Bevan MW.

PLoS One. 2010 Oct 18;5(10):e13461. doi: 10.1371/journal.pone.0013461.

9.

Comparative sequence analysis of the SALT OVERLY SENSITIVE1 orthologous region in Thellungiella halophila and Arabidopsis thaliana.

Nah G, Pagliarulo CL, Mohr PG, Luo M, Sisneros N, Yu Y, Collura K, Currie J, Goicoechea JL, Wing RA, Schumaker KS.

Genomics. 2009 Sep;94(3):196-203. doi: 10.1016/j.ygeno.2009.05.007. Epub 2009 May 28.

10.

Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set.

Ammiraju JS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J, Collura K, Talag J, Fan C, Goicoechea JL, Zuccolo A, Chen J, Bennetzen JL, Chen M, Jackson S, Wing RA.

Plant Cell. 2008 Dec;20(12):3191-209. doi: 10.1105/tpc.108.063727. Epub 2008 Dec 19.

11.

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza.

Kim H, Hurwitz B, Yu Y, Collura K, Gill N, SanMiguel P, Mullikin JC, Maher C, Nelson W, Wissotski M, Braidotti M, Kudrna D, Goicoechea JL, Stein L, Ware D, Jackson SA, Soderlund C, Wing RA.

Genome Biol. 2008;9(2):R45. doi: 10.1186/gb-2008-9-2-r45. Epub 2008 Feb 28.

12.

Physical and genetic structure of the maize genome reflects its complex evolutionary history.

Wei F, Coe E, Nelson W, Bharti AK, Engler F, Butler E, Kim H, Goicoechea JL, Chen M, Lee S, Fuks G, Sanchez-Villeda H, Schroeder S, Fang Z, McMullen M, Davis G, Bowers JE, Paterson AH, Schaeffer M, Gardiner J, Cone K, Messing J, Soderlund C, Wing RA.

PLoS Genet. 2007 Jul;3(7):e123.

13.

Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum.

Hass-Jacobus BL, Futrell-Griggs M, Abernathy B, Westerman R, Goicoechea JL, Stein J, Klein P, Hurwitz B, Zhou B, Rakhshan F, Sanyal A, Gill N, Lin JY, Walling JG, Luo MZ, Ammiraju JS, Kudrna D, Kim HR, Ware D, Wing RA, San Miguel P, Jackson SA.

BMC Genomics. 2006 Aug 8;7:199.

14.

The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza.

Ammiraju JS, Luo M, Goicoechea JL, Wang W, Kudrna D, Mueller C, Talag J, Kim H, Sisneros NB, Blackmon B, Fang E, Tomkins JB, Brar D, MacKill D, McCouch S, Kurata N, Lambert G, Galbraith DW, Arumuganathan K, Rao K, Walling JG, Gill N, Yu Y, SanMiguel P, Soderlund C, Jackson S, Wing RA.

Genome Res. 2006 Jan;16(1):140-7. Epub 2005 Dec 12.

15.

Utilization of a zebra finch BAC library to determine the structure of an avian androgen receptor genomic region.

Luo M, Yu Y, Kim H, Kudrna D, Itoh Y, Agate RJ, Melamed E, Goicoechea JL, Talag J, Mueller C, Wang W, Currie J, Sisneros NB, Wing RA, Arnold AP.

Genomics. 2006 Jan;87(1):181-90. Erratum in: Genomics. 2006 May;87(5):678-9.

16.

The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species.

Wing RA, Ammiraju JS, Luo M, Kim H, Yu Y, Kudrna D, Goicoechea JL, Wang W, Nelson W, Rao K, Brar D, Mackill DJ, Han B, Soderlund C, Stein L, SanMiguel P, Jackson S.

Plant Mol Biol. 2005 Sep;59(1):53-62.

PMID:
16217601
17.

Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome.

Ammiraju JS, Yu Y, Luo M, Kudrna D, Kim H, Goicoechea JL, Katayose Y, Matsumoto T, Wu J, Sasaki T, Wing RA.

Theor Appl Genet. 2005 Nov;111(8):1596-607. Epub 2005 Nov 10.

PMID:
16200416
18.

Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.

Buell CR, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A, Maiti R, Haas B, Wortman J, Pertea M, Jones KM, Kim M, Overton L, Tsitrin T, Fadrosh D, Bera J, Weaver B, Jin S, Johri S, Reardon M, Webb K, Hill J, Moffat K, Tallon L, Van Aken S, Lewis M, Utterback T, Feldblyum T, Zismann V, Iobst S, Hsiao J, de Vazeille AR, Salzberg SL, White O, Fraser C, Yu Y, Kim H, Rambo T, Currie J, Collura K, Kernodle-Thompson S, Wei F, Kudrna K, Ammiraju JS, Luo M, Goicoechea JL, Wing RA, Henry D, Oates R, Palmer M, Pries G, Saski C, Simmons J, Soderlund C, Nelson W, de la Bastide M, Spiegel L, Nascimento L, Huang E, Preston R, Zutavern T, Palmer L, O'Shaughnessy A, Dike S, McCombie WR, Minx P, Cordum H, Wilson R, Jin W, Lee HR, Jiang J, Jackson S; Rice Chromosome 3 Sequencing Consortium.

Genome Res. 2005 Sep;15(9):1284-91. Epub 2005 Aug 18.

19.

New genomic resources for the honey bee(Apis mellifera L.): development of a deep-coverage BAC library and a preliminary STC database.

Tomkins JP, Luo M, Fang GC, Main D, Goicoechea JL, Atkins M, Frisch DA, Page RE, Guzmán-Novoa E, Yu Y, Hunt G, Wing RA.

Genet Mol Res. 2002 Dec 31;1(4):306-16.

20.

An integrated physical and genetic map of the rice genome.

Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Budiman MA, Tomkins JP, Luo M, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, Wing RA.

Plant Cell. 2002 Mar;14(3):537-45.

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