TY - JOUR AU - Bowers, J. E. AU - Chapman, B. A. AU - Rong, J. AU - Paterson, A. H. PY - 2003 DA - 2003// TI - Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events JO - Nature VL - 422 UR - https://doi.org/10.1038/nature01521 DO - 10.1038/nature01521 ID - Bowers2003 ER - TY - JOUR AU - Blanc, G. AU - Hokamp, K. AU - Wolfe, K. H. PY - 2003 DA - 2003// TI - A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.751803 DO - 10.1101/gr.751803 ID - Blanc2003 ER - TY - JOUR AU - Paterson, A. H. AU - Bowers, J. E. AU - Chapman, B. A. PY - 2004 DA - 2004// TI - Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0307901101 DO - 10.1073/pnas.0307901101 ID - Paterson2004 ER - TY - JOUR AU - Wang, X. AU - Shi, X. AU - Hao, B. AU - Ge, S. AU - Luo, J. PY - 2005 DA - 2005// TI - Duplication and DNA segmental loss in the rice genome: implications for diploidization JO - New Phytol VL - 165 UR - https://doi.org/10.1111/j.1469-8137.2004.01293.x DO - 10.1111/j.1469-8137.2004.01293.x ID - Wang2005 ER - TY - JOUR AU - Tuskan, G. A. AU - Difazio, S. AU - Jansson, S. AU - Bohlmann, J. AU - Grigoriev, I. AU - Hellsten, U. AU - Putnam, N. AU - Ralph, S. AU - Rombauts, S. AU - Salamov, A. PY - 2006 DA - 2006// TI - The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) JO - Science VL - 313 UR - https://doi.org/10.1126/science.1128691 DO - 10.1126/science.1128691 ID - Tuskan2006 ER - TY - JOUR AU - Blanc, G. AU - Wolfe, K. H. PY - 2004 DA - 2004// TI - Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution JO - Plant Cell VL - 16 UR - https://doi.org/10.1105/tpc.021410 DO - 10.1105/tpc.021410 ID - Blanc2004 ER - TY - JOUR AU - Subramanian, S. AU - Kumar, S. PY - 2004 DA - 2004// TI - Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome JO - Genetics VL - 168 UR - https://doi.org/10.1534/genetics.104.028944 DO - 10.1534/genetics.104.028944 ID - Subramanian2004 ER - TY - JOUR AU - Pal, C. AU - Papp, B. AU - Hurst, L. D. PY - 2001 DA - 2001// TI - Highly expressed genes in yeast evolve slowly JO - Genetics VL - 158 ID - Pal2001 ER - TY - JOUR AU - Fraser, H. B. AU - Wall, D. P. AU - Hirsh, A. E. PY - 2003 DA - 2003// TI - A simple dependence between protein evolution rate and the number of protein-protein interactions JO - BMC Evol Biol VL - 3 UR - https://doi.org/10.1186/1471-2148-3-11 DO - 10.1186/1471-2148-3-11 ID - Fraser2003 ER - TY - JOUR AU - Blomme, T. AU - Vandepoele, K. AU - De Bodt, S. AU - Simillion, C. AU - Maere, S. AU - Peer, Y. V. a. n. d. e. PY - 2006 DA - 2006// TI - The gain and loss of genes during 600 million years of vertebrate evolution JO - Genome Biol VL - 7 UR - https://doi.org/10.1186/gb-2006-7-5-r43 DO - 10.1186/gb-2006-7-5-r43 ID - Blomme2006 ER - TY - JOUR AU - Thomas, B. C. AU - Pedersen, B. AU - Freeling, M. PY - 2006 DA - 2006// TI - Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.4708406 DO - 10.1101/gr.4708406 ID - Thomas2006 ER - TY - JOUR AU - Gout, J. F. AU - Duret, L. AU - Kahn, D. PY - 2009 DA - 2009// TI - Differential retention of metabolic genes following whole-genome duplication JO - Mol Biol Evol VL - 26 UR - https://doi.org/10.1093/molbev/msp026 DO - 10.1093/molbev/msp026 ID - Gout2009 ER - TY - JOUR AU - Dixon, R. A. PY - 2001 DA - 2001// TI - Natural products and plant disease resistance JO - Nature VL - 411 UR - https://doi.org/10.1038/35081178 DO - 10.1038/35081178 ID - Dixon2001 ER - TY - JOUR AU - Qi, X. AU - Bakht, S. AU - Leggett, M. AU - Maxwell, C. AU - Melton, R. AU - Osbourn, A. PY - 2004 DA - 2004// TI - A gene cluster for secondary metabolism in oat: implications for the evolution of metabolic diversity in plants JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0401301101 DO - 10.1073/pnas.0401301101 ID - Qi2004 ER - TY - JOUR AU - Qi, X. AU - Bakht, S. AU - Qin, B. AU - Leggett, M. AU - Hemmings, A. AU - Mellon, F. AU - Eagles, J. AU - Werck-Reichhart, D. AU - Schaller, H. AU - Lesot, A. PY - 2006 DA - 2006// TI - A different function for a member of an ancient and highly conserved cytochrome P450 family: from essential sterols to plant defense JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0607849103 DO - 10.1073/pnas.0607849103 ID - Qi2006 ER - TY - JOUR AU - Barabasi, A. L. AU - Oltvai, Z. N. PY - 2004 DA - 2004// TI - Network biology: understanding the cell's functional organization JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1272 DO - 10.1038/nrg1272 ID - Barabasi2004 ER - TY - JOUR AU - Sweetlove, L. J. AU - Fell, D. AU - Fernie, A. R. PY - 2008 DA - 2008// TI - Getting to grips with the plant metabolic network JO - Biochem J VL - 409 UR - https://doi.org/10.1042/BJ20071115 DO - 10.1042/BJ20071115 ID - Sweetlove2008 ER - TY - JOUR AU - Yu, H. AU - Kim, P. M. AU - Sprecher, E. AU - Trifonov, V. AU - Gerstein, M. PY - 2007 DA - 2007// TI - The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics JO - PLoS Comput Biol VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030059 DO - 10.1371/journal.pcbi.0030059 ID - Yu2007 ER - TY - JOUR AU - Mueller, L. A. AU - Zhang, P. AU - Rhee, S. Y. PY - 2003 DA - 2003// TI - AraCyc: a biochemical pathway database for Arabidopsis JO - Plant Physiol VL - 132 UR - https://doi.org/10.1104/pp.102.017236 DO - 10.1104/pp.102.017236 ID - Mueller2003 ER - TY - JOUR AU - Wei, H. AU - Persson, S. AU - Mehta, T. AU - Srinivasasainagendra, V. AU - Chen, L. AU - Page, G. P. AU - Somerville, C. AU - Loraine, A. PY - 2006 DA - 2006// TI - Transcriptional coordination of the metabolic network in Arabidopsis JO - Plant Physiol VL - 142 UR - https://doi.org/10.1104/pp.106.080358 DO - 10.1104/pp.106.080358 ID - Wei2006 ER - TY - JOUR AU - Papp, B. AU - Pal, C. AU - Hurst, L. D. PY - 2004 DA - 2004// TI - Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast JO - Nature VL - 429 UR - https://doi.org/10.1038/nature02636 DO - 10.1038/nature02636 ID - Papp2004 ER - TY - JOUR AU - Light, S. AU - Kraulis, P. AU - Elofsson, A. PY - 2005 DA - 2005// TI - Preferential attachment in the evolution of metabolic networks JO - BMC Genomics VL - 6 UR - https://doi.org/10.1186/1471-2164-6-159 DO - 10.1186/1471-2164-6-159 ID - Light2005 ER - TY - JOUR AU - Tang, H. AU - Bowers, J. E. AU - Wang, X. AU - Ming, R. AU - Alam, M. AU - Paterson, A. H. PY - 2008 DA - 2008// TI - Synteny and collinearity in plant genomes JO - Science VL - 320 UR - https://doi.org/10.1126/science.1153917 DO - 10.1126/science.1153917 ID - Tang2008 ER - TY - JOUR AU - Krylov, D. M. AU - Wolf, Y. I. AU - Rogozin, I. B. AU - Koonin, E. V. PY - 2003 DA - 2003// TI - Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1589103 DO - 10.1101/gr.1589103 ID - Krylov2003 ER - TY - JOUR AU - Papp, B. AU - Pal, C. AU - Hurst, L. D. PY - 2003 DA - 2003// TI - Dosage sensitivity and the evolution of gene families in yeast JO - Nature VL - 424 UR - https://doi.org/10.1038/nature01771 DO - 10.1038/nature01771 ID - Papp2003 ER - TY - JOUR AU - Birchler, J. A. AU - Bhadra, U. AU - Bhadra, M. P. AU - Auger, D. L. PY - 2001 DA - 2001// TI - Dosage-dependent gene regulation in multicellular eukaryotes: implications for dosage compensation, aneuploid syndromes, and quantitative traits JO - Dev Biol VL - 234 UR - https://doi.org/10.1006/dbio.2001.0262 DO - 10.1006/dbio.2001.0262 ID - Birchler2001 ER - TY - BOOK AU - Veitia, R. A. PY - 2002 DA - 2002// TI - Rosetta Stone proteins: "chance and necessity"? ID - Veitia2002 ER - TY - JOUR AU - Birchler, J. A. AU - Veitia, R. A. PY - 2007 DA - 2007// TI - The gene balance hypothesis: from classical genetics to modern genomics JO - Plant Cell VL - 19 UR - https://doi.org/10.1105/tpc.106.049338 DO - 10.1105/tpc.106.049338 ID - Birchler2007 ER - TY - JOUR AU - Freeling, M. AU - Thomas, B. C. PY - 2006 DA - 2006// TI - Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.3681406 DO - 10.1101/gr.3681406 ID - Freeling2006 ER - TY - JOUR AU - Freeling, M. PY - 2009 DA - 2009// TI - Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition JO - Annu Rev Plant Biol VL - 60 UR - https://doi.org/10.1146/annurev.arplant.043008.092122 DO - 10.1146/annurev.arplant.043008.092122 ID - Freeling2009 ER - TY - JOUR AU - Field, B. AU - Osbourn, A. E. PY - 2008 DA - 2008// TI - Metabolic diversification--independent assembly of operon-like gene clusters in different plants JO - Science VL - 320 UR - https://doi.org/10.1126/science.1154990 DO - 10.1126/science.1154990 ID - Field2008 ER - TY - JOUR AU - Mylona, P. AU - Owatworakit, A. AU - Papadopoulou, K. AU - Jenner, H. AU - Qin, B. AU - Findlay, K. AU - Hill, L. AU - Qi, X. AU - Bakht, S. AU - Melton, R. AU - Osbourn, A. PY - 2008 DA - 2008// TI - Sad3 and sad4 are required for saponin biosynthesis and root development in oat JO - Plant Cell VL - 20 UR - https://doi.org/10.1105/tpc.107.056531 DO - 10.1105/tpc.107.056531 ID - Mylona2008 ER - TY - JOUR AU - Schnable, P. S. AU - Ware, D. AU - Fulton, R. S. AU - Stein, J. C. AU - Wei, F. AU - Pasternak, S. AU - Liang, C. AU - Zhang, J. AU - Fulton, L. AU - Graves, T. A. PY - 2009 DA - 2009// TI - The B73 maize genome: complexity, diversity, and dynamics JO - Science VL - 326 UR - https://doi.org/10.1126/science.1178534 DO - 10.1126/science.1178534 ID - Schnable2009 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. PY - 2000 DA - 2000// TI - KEGG: kyoto encyclopedia of genes and genomes JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.27 DO - 10.1093/nar/28.1.27 ID - Kanehisa2000 ER - TY - JOUR AU - Ma, H. AU - Zeng, A. P. PY - 2003 DA - 2003// TI - Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/19.2.270 DO - 10.1093/bioinformatics/19.2.270 ID - Ma2003 ER - TY - JOUR AU - Huss, M. AU - Holme, P. PY - 2007 DA - 2007// TI - Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks JO - IET Syst Biol VL - 1 UR - https://doi.org/10.1049/iet-syb:20060077 DO - 10.1049/iet-syb:20060077 ID - Huss2007 ER - TY - JOUR AU - Girvan, M. AU - Newman, M. E. PY - 2002 DA - 2002// TI - Community structure in social and biological networks JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.122653799 DO - 10.1073/pnas.122653799 ID - Girvan2002 ER - TY - STD TI - Wu J, Mao X, Cai T, Luo J, Wei L: KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res. 2006, W720-724. 10.1093/nar/gkl167. 34 Web Server ID - ref38 ER - TY - JOUR AU - Schmid, M. AU - Davison, T. S. AU - Henz, S. R. AU - Pape, U. J. AU - Demar, M. AU - Vingron, M. AU - Scholkopf, B. AU - Weigel, D. AU - Lohmann, J. U. PY - 2005 DA - 2005// TI - A gene expression map of Arabidopsis thaliana development JO - Nat Genet VL - 37 UR - https://doi.org/10.1038/ng1543 DO - 10.1038/ng1543 ID - Schmid2005 ER - TY - JOUR AU - Yanai, I. AU - Benjamin, H. AU - Shmoish, M. AU - Chalifa-Caspi, V. AU - Shklar, M. AU - Ophir, R. AU - Bar-Even, A. AU - Horn-Saban, S. AU - Safran, M. AU - Domany, E. PY - 2005 DA - 2005// TI - Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti042 DO - 10.1093/bioinformatics/bti042 ID - Yanai2005 ER - TY - JOUR AU - Shiu, S. H. AU - Shih, M. C. AU - Li, W. H. PY - 2005 DA - 2005// TI - Transcription factor families have much higher expansion rates in plants than in animals JO - Plant Physiol VL - 139 UR - https://doi.org/10.1104/pp.105.065110 DO - 10.1104/pp.105.065110 ID - Shiu2005 ER - TY - CHAP AU - Van Dongen, S. PY - 2000 DA - 2000// TI - Graph clustering by flow simulation BT - PhD thesis PB - University of Utrecht CY - Utrecht, The, Netherlands ID - Van Dongen2000 ER - TY - STD TI - Thompson JD, Gibson TJ, Higgins DG: Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics. 2002, Chapter 2 (3): ID - ref43 ER - TY - JOUR AU - Chen, K. AU - Durand, D. AU - Farach-Colton, M. PY - 2000 DA - 2000// TI - NOTUNG: a program for dating gene duplications and optimizing gene family trees JO - J Comput Biol VL - 7 UR - https://doi.org/10.1089/106652700750050871 DO - 10.1089/106652700750050871 ID - Chen2000 ER - TY - JOUR AU - Yang, Z. PY - 1997 DA - 1997// TI - PAML: a program package for phylogenetic analysis by maximum likelihood JO - Comput Appl Biosci VL - 13 ID - Yang1997 ER - TY - JOUR AU - Rice, P. AU - Longden, I. AU - Bleasby, A. PY - 2000 DA - 2000// TI - EMBOSS: the European Molecular Biology Open Software Suite JO - Trends Genet VL - 16 UR - https://doi.org/10.1016/S0168-9525(00)02024-2 DO - 10.1016/S0168-9525(00)02024-2 ID - Rice2000 ER - TY - JOUR AU - Storey, J. D. AU - Tibshirani, R. PY - 2003 DA - 2003// TI - Statistical significance for genomewide studies JO - Proc Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.1530509100 DO - 10.1073/pnas.1530509100 ID - Storey2003 ER -