Reference genome sequence of the model plant Setaria

[1]  J. Grimwood,et al.  A Genome-Wide Survey of Switchgrass Genome Structure and Organization , 2012, PloS one.

[2]  David M. Goodstein,et al.  Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..

[3]  Jeremy D. DeBarry,et al.  De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera) , 2011, Nature Biotechnology.

[4]  K. Naito,et al.  Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet. , 2011, Genome.

[5]  Ana Kozomara,et al.  miRBase: integrating microRNA annotation and deep-sequencing data , 2010, Nucleic Acids Res..

[6]  Wei Li,et al.  Population genetics of foxtail millet and its wild ancestor , 2010, BMC Genetics.

[7]  Susan R. Wessler,et al.  MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences , 2010, Nucleic acids research.

[8]  Xin-Guang Zhu,et al.  Setaria viridis: A Model for C4 Photosynthesis[C][W] , 2010, Plant Cell.

[9]  R. Wu,et al.  Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions , 2010, Genetics.

[10]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[11]  J. Higgins,et al.  Comparative Genomics of Flowering Time Pathways Using Brachypodium distachyon as a Model for the Temperate Grasses , 2010, PloS one.

[12]  C. Lata,et al.  Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress. , 2010, Biochemical and biophysical research communications.

[13]  R. Bettinger,et al.  The origins of food production in north China: A different kind of agricultural revolution , 2010 .

[14]  M. VanGessel,et al.  Herbicide-Resistant Weeds in the United States and Their Impact on Extension , 2009, Weed Technology.

[15]  Lixing Yang,et al.  Distribution, diversity, evolution, and survival of Helitrons in the maize genome , 2009, Proceedings of the National Academy of Sciences.

[16]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[17]  Cristian Chaparro,et al.  Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome , 2009, PLoS genetics.

[18]  J. Bennetzen,et al.  Structure-based discovery and description of plant and animal Helitrons , 2009, Proceedings of the National Academy of Sciences.

[19]  J. Hibberd The evolution of C4 photosynthesis , 2009 .

[20]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[21]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[22]  J. Bennetzen,et al.  Gene Content and Distribution in the Nuclear Genome of Fragaria vesca , 2009 .

[23]  Mihaela M. Martis,et al.  The Sorghum bicolor genome and the diversification of grasses , 2009, Nature.

[24]  E. Kellogg,et al.  A Phylogeny of Setaria (Poaceae, Panicoideae, Paniceae) and Related Genera Based on the Chloroplast Gene ndhF , 2009, International Journal of Plant Sciences.

[25]  E. Kellogg,et al.  Integrating Phylogeny into Studies of C4 Variation in the Grasses , 2009, Plant Physiology.

[26]  T. Sang Genes and Mutations Underlying Domestication Transitions in Grasses , 2009, Plant Physiology.

[27]  J. Bennetzen,et al.  Foxtail Millet: A Sequence-Driven Grass Model System[W] , 2009, Plant Physiology.

[28]  E. Kellogg,et al.  The age of the grasses and clusters of origins of C4 photosynthesis , 2008 .

[29]  Haibao Tang,et al.  Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. , 2008, Genome research.

[30]  Xinyi Liu,et al.  Millets across Eurasia: chronology and context of early records of the genera Panicum and Setaria from archaeological sites in the Old World , 2008, Vegetation history and archaeobotany.

[31]  Andrew H. Paterson,et al.  Synteny and Collinearity in Plant Genomes , 2008, Science.

[32]  David Haussler,et al.  Using native and syntenically mapped cDNA alignments to improve de novo gene finding , 2008, Bioinform..

[33]  Yoshihiro Kawahara,et al.  The Rice Annotation Project Database (RAP-DB): 2008 update , 2007, Nucleic Acids Res..

[34]  V. Savolainen,et al.  C4 Photosynthesis Evolved in Grasses via Parallel Adaptive Genetic Changes , 2007, Current Biology.

[35]  J. Bennetzen,et al.  A GeneTrek analysis of the maize genome , 2007, Proceedings of the National Academy of Sciences.

[36]  Jun Zheng,et al.  Construction and application of EST library from Setaria italica in response to dehydration stress. , 2007, Genomics.

[37]  Fabio Fornara,et al.  FT Protein Movement Contributes to Long-Distance Signaling in Floral Induction of Arabidopsis , 2007, Science.

[38]  Zhao Xu,et al.  LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons , 2007, Nucleic Acids Res..

[39]  Kanako O. Koyanagi,et al.  Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. , 2007, Genome research.

[40]  Yasuyuki Fujii,et al.  The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information , 2005, Nucleic Acids Res..

[41]  Derrick J. Zwickl Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion , 2006 .

[42]  Jianxin Ma,et al.  Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[43]  J. Bennetzen,et al.  Transposable elements, gene creation and genome rearrangement in flowering plants. , 2005, Current opinion in genetics & development.

[44]  David Posada,et al.  ProtTest: selection of best-fit models of protein evolution , 2005, Bioinform..

[45]  P. Klein,et al.  Chromosome Identification and Nomenclature of Sorghum bicolor , 2005, Genetics.

[46]  J. Gressel,et al.  Incestuous relations of foxtail millet (Setaria italica) with its parents and cousins. , 2005 .

[47]  F. Chardon,et al.  Phylogenomic Analysis of the PEBP Gene Family in Cereals , 2005, Journal of Molecular Evolution.

[48]  Jianxin Ma,et al.  Consistent over-estimation of gene number in complex plant genomes. , 2004, Current opinion in plant biology.

[49]  H. Darmency,et al.  Breeding strategy in foxtail millet, Setaria italica (L.P. Beauv.), following interspecific hybridization , 1992, Euphytica.

[50]  J. Pernès,et al.  Genetic variability of foxtail millet (Setaria italica P. Beauv.) , 1985, Theoretical and Applied Genetics.

[51]  X. Perrier,et al.  Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F2 populations , 2004, Theoretical and Applied Genetics.

[52]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[53]  J. Dekker The foxtail (Setaria) species-group , 2003, Weed Science.

[54]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[55]  E. Kellogg,et al.  A molecular phylogeny of Panicum (Poaceae: Paniceae): tests of monophyly and phylogenetic placement within the Panicoideae. , 2003, American journal of botany.

[56]  John F. McDonald,et al.  LTR_STRUC: a novel search and identification program for LTR retrotransposons , 2003, Bioinform..

[57]  D. Maddison,et al.  MacClade 4: analysis of phy-logeny and character evolution , 2003 .

[58]  E. Mauceli,et al.  Whole-genome sequence assembly for mammalian genomes: Arachne 2. , 2003, Genome research.

[59]  A. Doust,et al.  Inflorescence diversification in the panicoid "bristle grass" clade (Paniceae, Poaceae): evidence from molecular phylogenies and developmental morphology. , 2002, American journal of botany.

[60]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[61]  R. Bernardo,et al.  Chromosomal regions associated with segregation distortion in maize , 2002, Theoretical and Applied Genetics.

[62]  Anton J. Enright,et al.  An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.

[63]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[64]  R. Voorrips MapChart: software for the graphical presentation of linkage maps and QTLs. , 2002, The Journal of heredity.

[65]  E. Kellogg,et al.  A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis. , 2001, American journal of botany.

[66]  B. Toupance,et al.  Assessment of genetic relationships between Setaria italica and its wild relative S. viridis using AFLP markers , 2000, Theoretical and Applied Genetics.

[67]  K. Devos,et al.  Genome Relationships: The Grass Model in Current Research , 2000, Plant Cell.

[68]  A. Paterson,et al.  Construction of plant bacterial artificial chromosome (BAC) libraries: an illustrated guide. , 2000 .

[69]  Phillip SanMiguel,et al.  The paleontology of intergene retrotransposons of maize , 1998, Nature Genetics.

[70]  T. Sasaki,et al.  Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa) , 1998, Theoretical and Applied Genetics.

[71]  K. Devos,et al.  Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv. , 1998, Theoretical and Applied Genetics.

[72]  I. Olivieri,et al.  Insight on segregation distortions in two intraspecific crosses between annual species of Medicago (Leguminosae) , 1997, Theoretical and Applied Genetics.

[73]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[74]  P. Stam,et al.  Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP. , 1993 .

[75]  D. Sutherland Genera Graminum. Grasses of the World , 1987 .

[76]  D. Zamir,et al.  Unequal Segregation of Nuclear Genes in Plants , 1986, Botanical Gazette.

[77]  H. Darmency,et al.  Use of wild Setaria viridis (L.) Beauv. to improve triazine resistance in cultivated S. italica (L.) by hybridization , 1985 .

[78]  R. Ornduff,et al.  Crops and Man. , 1977 .

[79]  G. Kimber The addition of the chromosomes of Aegilops umbellulata to Triticum aestivum (var. Chinese Spring) , 1967 .