Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 126

1.

Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.

Wang B, Mojica JP, Perera N, Lee CR, Lovell JT, Sharma A, Adam C, Lipzen A, Barry K, Rokhsar DS, Schmutz J, Mitchell-Olds T.

Genome Biol. 2019 Aug 9;20(1):161. doi: 10.1186/s13059-019-1781-5.

2.

Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.

Wang B, Mojica JP, Perera N, Lee CR, Lovell JT, Sharma A, Adam C, Lipzen A, Barry K, Rokhsar DS, Schmutz J, Mitchell-Olds T.

Genome Biol. 2019 Jun 21;20(1):126. doi: 10.1186/s13059-019-1729-9. Erratum in: Genome Biol. 2019 Aug 9;20(1):161.

3.

A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.

Mitros T, Lyons JB, Session AM, Jenkins J, Shu S, Kwon T, Lane M, Ng C, Grammer TC, Khokha MK, Grimwood J, Schmutz J, Harland RM, Rokhsar DS.

Dev Biol. 2019 Aug 1;452(1):8-20. doi: 10.1016/j.ydbio.2019.03.015. Epub 2019 Apr 10.

4.

Acoel genome reveals the regulatory landscape of whole-body regeneration.

Gehrke AR, Neverett E, Luo YJ, Brandt A, Ricci L, Hulett RE, Gompers A, Ruby JG, Rokhsar DS, Reddien PW, Srivastava M.

Science. 2019 Mar 15;363(6432). pii: eaau6173. doi: 10.1126/science.aau6173.

PMID:
30872491
5.

A large CRISPR-induced bystander mutation causes immune dysregulation.

Simeonov DR, Brandt AJ, Chan AY, Cortez JT, Li Z, Woo JM, Lee Y, Carvalho CMB, Indart AC, Roth TL, Zou J, May AP, Lupski JR, Anderson MS, Buaas FW, Rokhsar DS, Marson A.

Commun Biol. 2019 Feb 18;2:70. doi: 10.1038/s42003-019-0321-x. eCollection 2019.

6.

A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans.

Marlétaz F, Peijnenburg KTCA, Goto T, Satoh N, Rokhsar DS.

Curr Biol. 2019 Jan 21;29(2):312-318.e3. doi: 10.1016/j.cub.2018.11.042. Epub 2019 Jan 10.

PMID:
30639106
7.

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.

Belcaid M, Casaburi G, McAnulty SJ, Schmidbaur H, Suria AM, Moriano-Gutierrez S, Pankey MS, Oakley TH, Kremer N, Koch EJ, Collins AJ, Nguyen H, Lek S, Goncharenko-Foster I, Minx P, Sodergren E, Weinstock G, Rokhsar DS, McFall-Ngai M, Simakov O, Foster JS, Nyholm SV.

Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):3030-3035. doi: 10.1073/pnas.1817322116. Epub 2019 Jan 11.

8.

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.

Kliver S, Rayko M, Komissarov A, Bakin E, Zhernakova D, Prasad K, Rushworth C, Baskar R, Smetanin D, Schmutz J, Rokhsar DS, Mitchell-Olds T, Grossniklaus U, Brukhin V.

Genes (Basel). 2018 Mar 28;9(4). pii: E185. doi: 10.3390/genes9040185.

9.

Genomics of the origin and evolution of Citrus.

Wu GA, Terol J, Ibanez V, López-García A, Pérez-Román E, Borredá C, Domingo C, Tadeo FR, Carbonell-Caballero J, Alonso R, Curk F, Du D, Ollitrault P, Roose ML, Dopazo J, Gmitter FG, Rokhsar DS, Talon M.

Nature. 2018 Feb 15;554(7692):311-316. doi: 10.1038/nature25447. Epub 2018 Feb 7.

PMID:
29414943
10.

Publisher correction: Young inversion with multiple linked QTLs under selection in a hybrid zone.

Lee CR, Wang B, Mojica JP, Mandáková T, Prasad KVSK, Luis Goicoechea J, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, Kudrna D, Zhang J, Talag J, Golser W, Ghattas K, Schranz ME, Wing R, Lysak MA, Schmutz J, Rokhsar DS, Mitchell-Olds T.

Nat Ecol Evol. 2017 Oct;1(10):1585. doi: 10.1038/s41559-017-0310-8.

PMID:
29185503
11.

Young inversion with multiple linked QTLs under selection in a hybrid zone.

Lee CR, Wang B, Mojica JP, Mandáková T, Prasad KVSK, Goicoechea JL, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, Kudrna D, Zhang J, Talag J, Golser W, Ghattas K, Schranz ME, Wing R, Lysak MA, Schmutz J, Rokhsar DS, Mitchell-Olds T.

Nat Ecol Evol. 2017 Apr 3;1(5):119. doi: 10.1038/s41559-017-0119. Erratum in: Nat Ecol Evol. 2017 Oct;1(10 ):1585.

12.

QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii.

Nzuki I, Katari MS, Bredeson JV, Masumba E, Kapinga F, Salum K, Mkamilo GS, Shah T, Lyons JB, Rokhsar DS, Rounsley S, Myburg AA, Ferguson ME.

Front Plant Sci. 2017 Jul 21;8:1168. doi: 10.3389/fpls.2017.01168. eCollection 2017.

13.

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).

Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, Bhattacharya D, Klein AS, Badis Y, Brodie J, Cao Y, Collén J, Dittami SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan JL, Peng Y, Qiu H, Shu S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang ZY, Yan J, Yarish C, Zäuner-Riek S, Zhuang Y, Zou Y, Lindquist EA, Grimwood J, Barry KW, Rokhsar DS, Schmutz J, Stiller JW, Grossman AR, Prochnik SE.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):E6361-E6370. doi: 10.1073/pnas.1703088114. Epub 2017 Jul 17.

14.

QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert.

Masumba EA, Kapinga F, Mkamilo G, Salum K, Kulembeka H, Rounsley S, Bredeson JV, Lyons JB, Rokhsar DS, Kanju E, Katari MS, Myburg AA, van der Merwe NA, Ferguson ME.

Theor Appl Genet. 2017 Oct;130(10):2069-2090. doi: 10.1007/s00122-017-2943-z. Epub 2017 Jul 13.

15.

Genome evolution in the allotetraploid frog Xenopus laevis.

Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS.

Nature. 2016 Oct 20;538(7625):336-343. doi: 10.1038/nature19840.

16.

Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers.

Farley EK, Olson KM, Zhang W, Rokhsar DS, Levine MS.

Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):6508-13. doi: 10.1073/pnas.1605085113. Epub 2016 May 6.

17.

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity.

Bredeson JV, Lyons JB, Prochnik SE, Wu GA, Ha CM, Edsinger-Gonzales E, Grimwood J, Schmutz J, Rabbi IY, Egesi C, Nauluvula P, Lebot V, Ndunguru J, Mkamilo G, Bart RS, Setter TL, Gleadow RM, Kulakow P, Ferguson ME, Rounsley S, Rokhsar DS.

Nat Biotechnol. 2016 May;34(5):562-70. doi: 10.1038/nbt.3535. Epub 2016 Apr 18.

PMID:
27088722
18.

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.

Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE.

Genome Res. 2016 Mar;26(3):342-50. doi: 10.1101/gr.193474.115. Epub 2016 Feb 4.

19.

Hemichordate genomes and deuterostome origins.

Simakov O, Kawashima T, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, Bredeson J, Shoguchi E, Gyoja F, Yue JX, Chen YC, Freeman RM Jr, Sasaki A, Hikosaka-Katayama T, Sato A, Fujie M, Baughman KW, Levine J, Gonzalez P, Cameron C, Fritzenwanker JH, Pani AM, Goto H, Kanda M, Arakaki N, Yamasaki S, Qu J, Cree A, Ding Y, Dinh HH, Dugan S, Holder M, Jhangiani SN, Kovar CL, Lee SL, Lewis LR, Morton D, Nazareth LV, Okwuonu G, Santibanez J, Chen R, Richards S, Muzny DM, Gillis A, Peshkin L, Wu M, Humphreys T, Su YH, Putnam NH, Schmutz J, Fujiyama A, Yu JK, Tagawa K, Worley KC, Gibbs RA, Kirschner MW, Lowe CJ, Satoh N, Rokhsar DS, Gerhart J.

Nature. 2015 Nov 26;527(7579):459-65. doi: 10.1038/nature16150. Epub 2015 Nov 18.

20.

Suboptimization of developmental enhancers.

Farley EK, Olson KM, Zhang W, Brandt AJ, Rokhsar DS, Levine MS.

Science. 2015 Oct 16;350(6258):325-8. doi: 10.1126/science.aac6948.

21.

The octopus genome and the evolution of cephalopod neural and morphological novelties.

Albertin CB, Simakov O, Mitros T, Wang ZY, Pungor JR, Edsinger-Gonzales E, Brenner S, Ragsdale CW, Rokhsar DS.

Nature. 2015 Aug 13;524(7564):220-4. doi: 10.1038/nature14668.

22.

Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing.

Glazer AM, Killingbeck EE, Mitros T, Rokhsar DS, Miller CT.

G3 (Bethesda). 2015 Jun 3;5(7):1463-72. doi: 10.1534/g3.115.017905. Erratum in: G3 (Bethesda). 2016 Mar;6(3):769.

23.

The deuterostome context of chordate origins.

Lowe CJ, Clarke DN, Medeiros DM, Rokhsar DS, Gerhart J.

Nature. 2015 Apr 23;520(7548):456-65. doi: 10.1038/nature14434. Review.

PMID:
25903627
24.

A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis.

Matsuda Y, Uno Y, Kondo M, Gilchrist MJ, Zorn AM, Rokhsar DS, Schmid M, Taira M.

Cytogenet Genome Res. 2015;145(3-4):187-91. doi: 10.1159/000381292. Epub 2015 Apr 8.

PMID:
25871511
25.

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.

Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS.

Genome Biol. 2015 Jan 31;16:26. doi: 10.1186/s13059-015-0582-8.

26.

The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii.

Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, Chapman JA, Rokhsar DS, Schmutz J, Juenger TE.

New Phytol. 2015 Jan;205(1):402-14. doi: 10.1111/nph.13027. Epub 2014 Sep 23.

27.

The genome of Eucalyptus grandis.

Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, Hussey SG, Pinard D, van der Merwe K, Singh P, van Jaarsveld I, Silva-Junior OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang X, Ranjan P, Tschaplinski TJ, Ye CY, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Külheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Joubert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar DS, Schmutz J.

Nature. 2014 Jun 19;510(7505):356-62. doi: 10.1038/nature13308. Epub 2014 Jun 11.

PMID:
24919147
28.

A reference genome for common bean and genome-wide analysis of dual domestications.

Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MM, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA.

Nat Genet. 2014 Jul;46(7):707-13. doi: 10.1038/ng.3008. Epub 2014 Jun 8.

29.

A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes.

Barling A, Swaminathan K, Mitros T, James BT, Morris J, Ngamboma O, Hall MC, Kirkpatrick J, Alabady M, Spence AK, Hudson ME, Rokhsar DS, Moose SP.

BMC Genomics. 2013 Dec 9;14:864. doi: 10.1186/1471-2164-14-864.

30.

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing.

Hellsten U, Wright KM, Jenkins J, Shu S, Yuan Y, Wessler SR, Schmutz J, Willis JH, Rokhsar DS.

Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19478-82. doi: 10.1073/pnas.1319032110. Epub 2013 Nov 13.

31.

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).

Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-Amatriaín M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KF, Scholz U, Poland JA, Stein N, Waugh R.

Plant J. 2013 Nov;76(4):718-27. doi: 10.1111/tpj.12319. Epub 2013 Oct 10.

32.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

33.

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.

International Peach Genome Initiative, Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A, Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan P, Del Fabbro C, Aramini V, Copetti D, Gonzalez S, Horner DS, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B, Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P, Arús P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M, Rokhsar DS.

Nat Genet. 2013 May;45(5):487-94. doi: 10.1038/ng.2586. Epub 2013 Mar 24.

34.

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.

Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, Yoo MJ, Byers R, Chen W, Doron-Faigenboim A, Duke MV, Gong L, Grimwood J, Grover C, Grupp K, Hu G, Lee TH, Li J, Lin L, Liu T, Marler BS, Page JT, Roberts AW, Romanel E, Sanders WS, Szadkowski E, Tan X, Tang H, Xu C, Wang J, Wang Z, Zhang D, Zhang L, Ashrafi H, Bedon F, Bowers JE, Brubaker CL, Chee PW, Das S, Gingle AR, Haigler CH, Harker D, Hoffmann LV, Hovav R, Jones DC, Lemke C, Mansoor S, ur Rahman M, Rainville LN, Rambani A, Reddy UK, Rong JK, Saranga Y, Scheffler BE, Scheffler JA, Stelly DM, Triplett BA, Van Deynze A, Vaslin MF, Waghmare VN, Walford SA, Wright RJ, Zaki EA, Zhang T, Dennis ES, Mayer KF, Peterson DG, Rokhsar DS, Wang X, Schmutz J.

Nature. 2012 Dec 20;492(7429):423-7. doi: 10.1038/nature11798.

PMID:
23257886
35.

Insights into bilaterian evolution from three spiralian genomes.

Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, Shapiro H, Aerts A, Otillar RP, Terry AY, Boore JL, Grigoriev IV, Lindberg DR, Seaver EC, Weisblat DA, Putnam NH, Rokhsar DS.

Nature. 2013 Jan 24;493(7433):526-31. doi: 10.1038/nature11696. Epub 2012 Dec 19.

36.

A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy.

Swaminathan K, Chae WB, Mitros T, Varala K, Xie L, Barling A, Glowacka K, Hall M, Jezowski S, Ming R, Hudson M, Juvik JA, Rokhsar DS, Moose SP.

BMC Genomics. 2012 Apr 24;13:142. doi: 10.1186/1471-2164-13-142.

37.

The Cassava Genome: Current Progress, Future Directions.

Prochnik S, Marri PR, Desany B, Rabinowicz PD, Kodira C, Mohiuddin M, Rodriguez F, Fauquet C, Tohme J, Harkins T, Rokhsar DS, Rounsley S.

Trop Plant Biol. 2012 Mar;5(1):88-94. Epub 2012 Jan 5.

38.

Phytozome: a comparative platform for green plant genomics.

Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1178-86. doi: 10.1093/nar/gkr944. Epub 2011 Nov 22.

39.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.

Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.

40.

Development and initial characterization of a HAPPY panel for mapping the X. tropicalis genome.

Jiang Z, Michal JJ, Beckman KB, Lyons JB, Zhang M, Pan Z, Rokhsar DS, Harland RM.

Int J Biol Sci. 2011;7(7):1037-44. Epub 2011 Aug 24.

41.

A segmental genomic duplication generates a functional intron.

Hellsten U, Aspden JL, Rio DC, Rokhsar DS.

Nat Commun. 2011 Aug 30;2:454. doi: 10.1038/ncomms1461.

42.

Meraculous: de novo genome assembly with short paired-end reads.

Chapman JA, Ho I, Sunkara S, Luo S, Schroth GP, Rokhsar DS.

PLoS One. 2011;6(8):e23501. doi: 10.1371/journal.pone.0023501. Epub 2011 Aug 18.

43.

The Amphimedon queenslandica genome and the evolution of animal complexity.

Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM, Oakley TH, Plachetzki DC, Zhai Y, Adamski M, Calcino A, Cummins SF, Goodstein DM, Harris C, Jackson DJ, Leys SP, Shu S, Woodcroft BJ, Vervoort M, Kosik KS, Manning G, Degnan BM, Rokhsar DS.

Nature. 2010 Aug 5;466(7307):720-6. doi: 10.1038/nature09201.

44.

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans.

Taft RJ, Simons C, Nahkuri S, Oey H, Korbie DJ, Mercer TR, Holst J, Ritchie W, Wong JJ, Rasko JE, Rokhsar DS, Degnan BM, Mattick JS.

Nat Struct Mol Biol. 2010 Aug;17(8):1030-4. doi: 10.1038/nsmb.1841. Epub 2010 Jul 11.

PMID:
20622877
45.

Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri.

Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, Schmutz J, Grimwood J, Lindquist E, Lucas S, Grigoriev IV, Schmitt R, Kirk D, Rokhsar DS.

Science. 2010 Jul 9;329(5988):223-6. doi: 10.1126/science.1188800.

46.

The genome of the Western clawed frog Xenopus tropicalis.

Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS.

Science. 2010 Apr 30;328(5978):633-6. doi: 10.1126/science.1183670.

47.

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes.

Wang J, Roe B, Macmil S, Yu Q, Murray JE, Tang H, Chen C, Najar F, Wiley G, Bowers J, Van Sluys MA, Rokhsar DS, Hudson ME, Moose SP, Paterson AH, Ming R.

BMC Genomics. 2010 Apr 23;11:261. doi: 10.1186/1471-2164-11-261.

48.

The dynamic genome of Hydra.

Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, Walenz B, Goodstein DM, Hellsten U, Kawashima T, Prochnik SE, Putnam NH, Shu S, Blumberg B, Dana CE, Gee L, Kibler DF, Law L, Lindgens D, Martinez DE, Peng J, Wigge PA, Bertulat B, Guder C, Nakamura Y, Ozbek S, Watanabe H, Khalturin K, Hemmrich G, Franke A, Augustin R, Fraune S, Hayakawa E, Hayakawa S, Hirose M, Hwang JS, Ikeo K, Nishimiya-Fujisawa C, Ogura A, Takahashi T, Steinmetz PR, Zhang X, Aufschnaiter R, Eder MK, Gorny AK, Salvenmoser W, Heimberg AM, Wheeler BM, Peterson KJ, Böttger A, Tischler P, Wolf A, Gojobori T, Remington KA, Strausberg RL, Venter JC, Technau U, Hobmayer B, Bosch TC, Holstein TW, Fujisawa T, Bode HR, David CN, Rokhsar DS, Steele RE.

Nature. 2010 Mar 25;464(7288):592-6. doi: 10.1038/nature08830. Epub 2010 Mar 14.

49.

The genome of Naegleria gruberi illuminates early eukaryotic versatility.

Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J, Pham J, Shu S, Neupane R, Cipriano M, Mancuso J, Tu H, Salamov A, Lindquist E, Shapiro H, Lucas S, Grigoriev IV, Cande WZ, Fulton C, Rokhsar DS, Dawson SC.

Cell. 2010 Mar 5;140(5):631-42. doi: 10.1016/j.cell.2010.01.032.

50.

Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses.

Swaminathan K, Alabady MS, Varala K, De Paoli E, Ho I, Rokhsar DS, Arumuganathan AK, Ming R, Green PJ, Meyers BC, Moose SP, Hudson ME.

Genome Biol. 2010;11(2):R12. doi: 10.1186/gb-2010-11-2-r12. Epub 2010 Feb 3.

Supplemental Content

Loading ...
Support Center