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Results: 17

1.

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.

PMID:
24320546
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
23525075
[PubMed - indexed for MEDLINE]
3.

Reference genome sequence of the model plant Setaria.

Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye CY, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM.

Nat Biotechnol. 2012 May 13;30(6):555-61. doi: 10.1038/nbt.2196.

PMID:
22580951
[PubMed - indexed for MEDLINE]
4.

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.

PMID:
22524439
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
22110026
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.

Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV.

Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810. Epub 2011 May 5.

PMID:
21551031
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
20686567
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
20616280
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
20431018
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
20228792
[PubMed - indexed for MEDLINE]
11.

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, Jackson SA.

Nature. 2010 Jan 14;463(7278):178-83. doi: 10.1038/nature08670. Erratum in: Nature. 2010 May 6;465(7294):120.

PMID:
20075913
[PubMed - indexed for MEDLINE]
12.

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-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS.

Nature. 2009 Jan 29;457(7229):551-6. doi: 10.1038/nature07723.

PMID:
19189423
[PubMed - indexed for MEDLINE]
13.

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, Windham E.

Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14802-7. doi: 10.1073/pnas.0805946105. Epub 2008 Sep 22.

PMID:
18809916
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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, Rokhsar DS.

Nature. 2008 Aug 21;454(7207):955-60. doi: 10.1038/nature07191.

PMID:
18719581
[PubMed - indexed for MEDLINE]
15.

Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling.

Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, Schlessinger A, Koh IY, Alexov E, Honig B.

Proteins. 2003;53 Suppl 6:430-5.

PMID:
14579332
[PubMed - indexed for MEDLINE]
16.

Domains 2 and 3 interact to form critical elements of the group II intron active site.

Fedorova O, Mitros T, Pyle AM.

J Mol Biol. 2003 Jul 4;330(2):197-209.

PMID:
12823961
[PubMed - indexed for MEDLINE]
17.

Management of neonatal narcotic abstinence utilizing a phenobarbital loading dose method.

Finnegan LP, Mitros TF, Hopkins LE.

NIDA Res Monogr. 1979;27:247-53.

PMID:
121340
[PubMed - indexed for MEDLINE]

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