Plant Genomics Program at JGI Home

Announcements

  • Jan 16, 2012
    Phytozome v8.0 has been released!
  • Oct 07, 2011
     Release of Thellungiella halophila genome and Biomart sequence issue fixed.

Releases

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Plants Publications of Genomes

2010

  1. 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, Bottger 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 and Steele RE. Nature. 2010 Mar 25; 464 (7288): 592-6
  2. 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 and Dawson SC. Cell. 2010 Mar 5; 140 (5): 631-42
  3. Parallel evolution of nacre building gene sets in molluscs. Jackson DJ, McDougall C, Woodcroft B, Moase P, Rose RA, Kube M, Reinhardt R, Rokhsar DS, Montagnani C, Joubert C, Piquemal D and Degnan BM. Mol Biol Evol. 2010 Mar; 27 (3): 591-608
  4. Genome sequencing and analysis of the model grass Brachypodium distachyon.International Brachypodium Initiative: Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M, Lail K, Tice H, Schmutz J, Grimwood J, McKenzie N, Bevan MW, Huo N, Gu YQ, Lazo GR, Anderson OD, Vogel JP, You FM, Luo MC, Dvorak J, Wright J, Febrer M, Bevan MW, Idziak D, Hasterok R, Garvin DF, Lindquist E, Wang M, Fox SE, Priest HD, Filichkin SA, Givan SA, Bryant DW, Chang JH, Mockler TC, Wu H, Wu W, Hsia AP, Schnable PS, Kalyanaraman A, Barbazuk B, Michael TP, Hazen SP, Bragg JN, Laudencia-Chingcuanco D, Vogel JP, Garvin DF, Weng Y, McKenzie N, Bevan MW, Haberer G, Spannagl M, Mayer K, Rattei T, Mitros T, Rokhsar D, Lee SJ, Rose JK, Mueller LA, York TL, Wicker T, Buchmann JP, Tanskanen J, Schulman AH, Gundlach H, Wright J, Bevan M, de Oliveira AC, Maia Lda C, Belknap W, Gu YQ, Jiang N, Lai J, Zhu L, Ma J, Sun C, Pritham E, Salse J, Murat F, Abrouk M, Haberer G, Spannagl M, Mayer K, Bruggmann R, Messing J, You FM, Luo MC, Dvorak J, Fahlgren N, Fox SE, Sullivan CM, Mockler TC, Carrington JC, Chapman EJ, May GD, Zhai J, Ganssmann M, Gurazada SG, German M, Meyers BC, Green PJ, Bragg JN, Tyler L, Wu J, Gu YQ, Lazo GR, Laudencia-Chingcuanco D, Thomson J, Vogel JP, Hazen SP, Chen S, Scheller HV, Harholt J, Ulvskov P, Fox SE, Filichkin SA, Fahlgren N, Kimbrel JA, Chang JH, Sullivan CM, Chapman EJ, Carrington JC, Mockler TC, Bartley LE, Cao P, Jung KH, Sharma MK, Vega-Sanchez M, Ronald P, Dardick CD, De Bodt S, Verelst W, Inzé D, Heese M, Schnittger A, Yang X, Kalluri UC, Tuskan GA, Hua Z, Vierstra RD, Garvin DF, Cui Y, Ouyang S, Sun Q, Liu Z, Yilmaz A, Grotewold E, Sibout R, Hematy K, Mouille G, Höfte H, Michael T, Pelloux J, O'Connor D, Schnable J, Rowe S, Harmon F, Cass CL, Sedbrook JC, Byrne ME, Walsh S, Higgins J, Bevan M, Li P, Brutnell T, Unver T, Budak H, Belcram H, Charles M, Chalhoub B, Baxter I. Nature. 2010 Feb 11; 463 (7282): 763-8
  5. Early evolution of the LIM homeobox gene family. Srivastava M, Larroux C, Lu DR, Mohanty K, Chapman J, Degnan BM and Rokhsar DS. BMC Biol. 2010 Jan 18; 8:4.
  6. Genome sequence of the palaeopolyploid soybean. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC and Jackson SA. Nature. 2010 Jan 14; 463 (7278): 178-83

2009

  1. Domain shuffling and the evolution of vertebrates. Kawashima T, Kawashima S, Tanaka C, Murai M, Yoneda M, Putnam NH, Rokhsar DS, Kanehisa M, Satoh N and Wada H. Genome Res. 2009 Aug; 19 (8): 1393-403
  2. Anatomy and development of the nervous system of Nematostella vectensis, an anthozoan cnidarian. Marlow HQ, Srivastava M, Matus DQ, Rokhsar D and Martindale MQ. Dev Neurobiol. 2009 Mar; 69 (4): 235-54
  3. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT, Kersten P, Hammel KE, Vanden Wymelenberg A, Gaskell J, Lindquist E, Sabat G, Bondurant SS, Larrondo LF, Canessa P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro AG, Lavin JL, Oguiza JA, Master E, Henrissat B, Coutinho PM, Harris P, Magnuson JK, Baker SE, Bruno K, Kenealy W, Hoegger PJ, Kues U, Ramaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee CL, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev IV, Brettin T, Rokhsar D, Berka R and Cullen D. Proc Natl Acad Sci U S A. 2009 Feb 10; 106 (6): 1954-9
  4. The Sorghum bicolor genome and the diversification of grasses. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob ur R, Ware D, Westhoff P, Mayer KF, Messing J and Rokhsar DS. Nature. 2009 Jan 29; 457 (7229): 551-6
  5. Old can be new again: HAPPY whole genome sequencing, mapping and assembly. Jiang Z, Rokhsar DS and Harland RM. Int J Biol Sci. 2009 5 (4): 298-303

2008

  1. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, Lapidus A, Rokhsar DS, Lebrilla CB, German JB, Price NP, Richardson PM and Mills DA. Proc Natl Acad Sci U S A. 2008 Dec 2; 105 (48): 18964-9
  2. Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs. Horton AC, Mahadevan NR, Minguillon C, Osoegawa K, Rokhsar DS, Ruvinsky I, de Jong PJ, Logan MP and Gibson-Brown JJ. Dev Genes Evol. 2008 Dec; 218 (11-12): 613-28
  3. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJ, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kroger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin-Jezequel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Oudot-Le Secq MP, Napoli C, Obornik M, Parker MS, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y and Grigoriev IV. Nature. 2008 Nov 13; 456 (7219): 239-44
  4. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS and Bartel DP. Nature. 2008 Oct 30; 455 (7217): 1193-7
  5. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Chen F, Rokhsar DS, McKernan KJ, Jeffries TW, Marth GT and Richardson PM. Genome Res. 2008 Oct; 18 (10): 1638-42
  6. Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Opperman CH, Bird DM, Williamson VM, Rokhsar DS, Burke M, Cohn J, Cromer J, Diener S, Gajan J, Graham S, Houfek TD, Liu Q, Mitros T, Schaff J, Schaffer R, Scholl E, Sosinski BR, Thomas VP and Windham E. Proc Natl Acad Sci U S A. 2008 Sep 30; 105 (39): 14802-7
  7. The Trichoplax genome and the nature of placozoans. Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, Signorovitch AY, Moreno MA, Kamm K, Grimwood J, Schmutz J, Shapiro H, Grigoriev IV, Buss LW, Schierwater B, Dellaporta SL and Rokhsar DS. Nature. 2008 Aug 21; 454 (7207): 955-60
  8. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Holland LZ, Albalat R, Azumi K, Benito-Gutierrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernandez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallbook F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N and Holland PW. Genome Res. 2008 Jul; 18 (7): 1100-11
  9. The amphioxus genome and the evolution of the chordate karyotype. Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutierrez EL, Dubchak I, Garcia-Fernandez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin IT, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N and Rokhsar DS. Nature. 2008 Jun 19; 453 (7198): 1064-71
  10. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS and Levine MS. Proc Natl Acad Sci U S A. 2008 Jun 3; 105 (22): 7762-7
  11. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M and Brettin TS. Nat Biotechnol. 2008 May; 26 (5): 553-60
  12. Genesis and expansion of metazoan transcription factor gene classes. Larroux C, Luke GN, Koopman P, Rokhsar DS, Shimeld SM and Degnan BM. Mol Biol Evol. 2008 May; 25 (5): 980-96
  13. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, Zuzow R, Dirks W, Good M, Goodstein D, Lemons D, Li W, Lyons JB, Morris A, Nichols S, Richter DJ, Salamov A, Sequencing JG, Bork P, Lim WA, Manning G, Miller WT, McGinnis W, Shapiro H, Tjian R, Grigoriev IV and Rokhsar D. Nature. 2008 Feb 14; 451 (7180): 783-8

2007

  1. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS and Grossman AR. Science. 2007 Oct 12; 318 (5848): 245-50
  2. The evolutionary origin of hedgehog proteins. Adamska M, Matus DQ, Adamski M, Green K, Rokhsar DS, Martindale MQ and Degnan BM. Curr Biol. 2007 Oct 9; 17 (19): R836-7
  3. Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis. Hellsten U, Khokha MK, Grammer TC, Harland RM, Richardson P and Rokhsar DS. BMC Biol. 2007 5 31
  4. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ and Rokhsar DS. Science. 2007 Jul 6; 317 (5834): 86-94
  5. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Kelleher CT, Chiu R, Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin T, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O'Connor K, Prabhu AL, Smailus DE, Stott JM, Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJ, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ and Schein JE. Plant J. 2007 Jun; 50 (6): 1063-78
  6. IDENTIFICATION AND COMPARATIVE GENOMIC ANALYSIS OF SIGNALING AND REGULATORY COMPONENTS IN THE DIATOM THALASSIOSIRA PSEUDONANA.Anton Montsant, Andrew E. Allen, Sacha Coesel, Alessandra De Martino, Angela Falciatore, Manuela Mangogna, Magali Siaut, Marc Heijde, Kamel Jabbari, Uma Maheswari, Edda Rayko, Assaf Vardi, Kirk E. Apt, John A. Berges, Anthony Chiovitti, Aubrey K. Davis, Kimberlee Thamatrakoln, Masood Z. Hadi, Todd W. Lane, J. Casey Lippmeier, Diego Martinez, Micaela S. Parker, Gregory J. Pazour, Mak A. Saito, Dan S. Rokhsar, E. Virginia Armbrust, Chris Bowler. Journal of Phycology Volume 43, Issue 3, Date: June 2007, Pages: 585-604.
  7. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Palenik B, Grimwood J, Aerts A, Rouze P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H and Grigoriev IV. Proc Natl Acad Sci U S A. 2007 May 1; 104 (18): 7705-10
  8. The NK homeobox gene cluster predates the origin of Hox genes. Larroux C, Fahey B, Degnan SM, Adamski M, Rokhsar DS and Degnan BM. Curr Biol. 2007 Apr 17; 17 (8): 706-10
  9. Evidence for a microRNA expansion in the bilaterian ancestor. Prochnik SE, Rokhsar DS and Aboobaker AA. Dev Genes Evol. 2007 Jan; 217 (1): 73-7

2006

  1. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y and Rokhsar D. Science. 2006 Sep 15; 313 (5793): 1596-604
  2. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS and Boore JL. Science. 2006 Sep 1; 313 (5791): 1261-6
  3. Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis. Shoguchi E, Kawashima T, Satou Y, Hamaguchi M, Sin IT, Kohara Y, Putnam N, Rokhsar DS and Satoh N. Genome Res. 2006 Feb; 16 (2): 297-303

2005

  1. Transcription factor binding site identification using the self-organizing map. Mahony S, Hendrix D, Golden A, Smith TJ and Rokhsar DS. Bioinformatics. 2005 May 1; 21 (9): 1807-14
  2. A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis. Keys DN, Lee BI, Di Gregorio A, Harafuji N, Detter JC, Wang M, Kahsai O, Ahn S, Zhang C, Doyle SA, Satoh N, Satou Y, Saiga H, Christian AT, Rokhsar DS, Hawkins TL, Levine M and Richardson PM. Proc Natl Acad Sci U S A. 2005 Jan 18; 102 (3): 679-83