TY - JOUR AU - Taylor, J. S. AU - Raes, J. PY - 2004 DA - 2004// TI - Duplication and divergence: the evolution of new genes and old ideas JO - Annu Rev Genet VL - 38 UR - https://doi.org/10.1146/annurev.genet.38.072902.092831 DO - 10.1146/annurev.genet.38.072902.092831 ID - Taylor2004 ER - TY - JOUR AU - Tekaia, F. AU - Dujon, B. PY - 1999 DA - 1999// TI - Pervasiveness of gene conservation and persistence of duplicates in cellular genomes JO - J Mol Evol VL - 49 UR - https://doi.org/10.1007/PL00006580 DO - 10.1007/PL00006580 ID - Tekaia1999 ER - TY - JOUR AU - Wapinski, I. AU - Pfeffer, A. AU - Friedman, N. AU - Regev, A. PY - 2007 DA - 2007// TI - Natural history and evolutionary principles of gene duplication in fungi JO - Nature VL - 449 UR - https://doi.org/10.1038/nature06107 DO - 10.1038/nature06107 ID - Wapinski2007 ER - TY - JOUR PY - 2000 DA - 2000// TI - Analysis of the genome sequence of the flowering plant Arabidopsis thaliana JO - Nature VL - 408 UR - https://doi.org/10.1038/35048692 DO - 10.1038/35048692 ID - ref4 ER - TY - JOUR AU - Yu, J. AU - Hu, S. AU - Wang, J. AU - Wong, G. K. AU - Li, S. AU - Liu, B. AU - Deng, Y. AU - Dai, L. AU - Zhou, Y. AU - Zhang, X. PY - 2002 DA - 2002// TI - A draft sequence of the rice genome (Oryza sativa L. ssp. indica) JO - Science VL - 296 UR - https://doi.org/10.1126/science.1068037 DO - 10.1126/science.1068037 ID - Yu2002 ER - TY - JOUR AU - Lynch, M. AU - Conery, J. S. PY - 2000 DA - 2000// TI - The evolutionary fate and consequences of duplicate genes JO - Science VL - 290 UR - https://doi.org/10.1126/science.290.5494.1151 DO - 10.1126/science.290.5494.1151 ID - Lynch2000 ER - TY - JOUR AU - Koszul, R. AU - Caburet, S. AU - Dujon, B. AU - Fischer, G. PY - 2004 DA - 2004// TI - Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments JO - Embo J VL - 23 UR - https://doi.org/10.1038/sj.emboj.7600024 DO - 10.1038/sj.emboj.7600024 ID - Koszul2004 ER - TY - JOUR AU - Holland, P. W. PY - 1997 DA - 1997// TI - Vertebrate evolution: something fishy about Hox genes JO - Curr Biol VL - 7 UR - https://doi.org/10.1016/S0960-9822(06)00284-3 DO - 10.1016/S0960-9822(06)00284-3 ID - Holland1997 ER - TY - JOUR AU - Pebusque, M. J. AU - Coulier, F. AU - Birnbaum, D. AU - Pontarotti, P. PY - 1998 DA - 1998// TI - Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution JO - Mol Biol Evol VL - 15 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026022 DO - 10.1093/oxfordjournals.molbev.a026022 ID - Pebusque1998 ER - TY - JOUR AU - Spring, J. PY - 1997 DA - 1997// TI - Vertebrate evolution by interspecific hybridisation – are we polyploid? JO - FEBS Lett VL - 400 UR - https://doi.org/10.1016/S0014-5793(96)01351-8 DO - 10.1016/S0014-5793(96)01351-8 ID - Spring1997 ER - TY - JOUR AU - Simillion, C. AU - Vandepoele, K. AU - Van Montagu, M. C. AU - Zabeau, M. AU - Peer, Y. V. a. n. d. e. PY - 2002 DA - 2002// TI - The hidden duplication past of Arabidopsis thaliana JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.212522399 DO - 10.1073/pnas.212522399 ID - Simillion2002 ER - TY - JOUR AU - Blanc, G. AU - Wolfe, K. H. PY - 2004 DA - 2004// TI - Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes JO - Plant Cell VL - 16 UR - https://doi.org/10.1105/tpc.021345 DO - 10.1105/tpc.021345 ID - Blanc2004 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 - Rubin, G. M. AU - Yandell, M. D. AU - Wortman, J. R. AU - Gabor Miklos, G. L. AU - Nelson, C. R. AU - Hariharan, I. K. AU - Fortini, M. E. AU - Li, P. W. AU - Apweiler, R. AU - Fleischmann, W. PY - 2000 DA - 2000// TI - Comparative genomics of the eukaryotes JO - Science VL - 287 UR - https://doi.org/10.1126/science.287.5461.2204 DO - 10.1126/science.287.5461.2204 ID - Rubin2000 ER - TY - JOUR AU - Llorente, B. AU - Durrens, P. AU - Malpertuy, A. AU - Aigle, M. AU - Artiguenave, F. AU - Blandin, G. AU - Bolotin-Fukuhara, M. AU - Bon, E. AU - Brottier, P. AU - Casaregola, S. PY - 2000 DA - 2000// TI - Genomic exploration of the hemiascomycetous yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae JO - FEBS Lett VL - 487 UR - https://doi.org/10.1016/S0014-5793(00)02291-2 DO - 10.1016/S0014-5793(00)02291-2 ID - Llorente2000 ER - TY - JOUR AU - Lynch, M. AU - Conery, J. S. PY - 2003 DA - 2003// TI - The evolutionary demography of duplicate genes JO - J Struct Funct Genomics VL - 3 UR - https://doi.org/10.1023/A:1022696612931 DO - 10.1023/A:1022696612931 ID - Lynch2003 ER - TY - JOUR AU - Scannell, D. R. AU - Frank, A. C. AU - Conant, G. C. AU - Byrne, K. P. AU - Woolfit, M. AU - Wolfe, K. H. PY - 2007 DA - 2007// TI - Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0608218104 DO - 10.1073/pnas.0608218104 ID - Scannell2007 ER - TY - JOUR AU - Kondrashov, F. A. AU - Rogozin, I. B. AU - Wolf, Y. I. AU - Koonin, E. V. PY - 2002 DA - 2002// TI - Selection in the evolution of gene duplications JO - Genome Biol VL - 3 UR - https://doi.org/10.1186/gb-2002-3-2-research0008 DO - 10.1186/gb-2002-3-2-research0008 ID - Kondrashov2002 ER - TY - JOUR AU - Maere, S. AU - De Bodt, S. AU - Raes, J. AU - Casneuf, T. AU - Van Montagu, M. AU - Kuiper, M. AU - Peer, Y. V. a. n. d. e. PY - 2005 DA - 2005// TI - Modeling gene and genome duplications in eukaryotes JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0501102102 DO - 10.1073/pnas.0501102102 ID - Maere2005 ER - TY - JOUR AU - Seoighe, C. AU - Wolfe, K. H. PY - 1999 DA - 1999// TI - Updated map of duplicated regions in the yeast genome JO - Gene VL - 238 UR - https://doi.org/10.1016/S0378-1119(99)00319-4 DO - 10.1016/S0378-1119(99)00319-4 ID - Seoighe1999 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 - Gaillardin, C. AU - Duchateau-Nguyen, G. AU - Tekaia, F. AU - Llorente, B. AU - Casaregola, S. AU - Toffano-Nioche, C. AU - Aigle, M. AU - Artiguenave, F. AU - Blandin, G. AU - Bolotin-Fukuhara, M. PY - 2000 DA - 2000// TI - Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes JO - FEBS Lett VL - 487 UR - https://doi.org/10.1016/S0014-5793(00)02292-4 DO - 10.1016/S0014-5793(00)02292-4 ID - Gaillardin2000 ER - TY - JOUR AU - Clauss, M. J. AU - Mitchell-Olds, T. PY - 2004 DA - 2004// TI - Functional divergence in tandemly duplicated Arabidopsis thaliana trypsin inhibitor genes JO - Genetics VL - 166 UR - https://doi.org/10.1534/genetics.166.3.1419 DO - 10.1534/genetics.166.3.1419 ID - Clauss2004 ER - TY - JOUR AU - Lawton-Rauh, A. PY - 2003 DA - 2003// TI - Evolutionary dynamics of duplicated genes in plants JO - Mol Phylogenet Evol VL - 29 UR - https://doi.org/10.1016/j.ympev.2003.07.004 DO - 10.1016/j.ympev.2003.07.004 ID - Lawton-Rauh2003 ER - TY - JOUR AU - Gutierrez, R. A. AU - Green, P. J. AU - Keegstra, K. AU - Ohlrogge, J. B. PY - 2004 DA - 2004// TI - Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms? JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-8-r53 DO - 10.1186/gb-2004-5-8-r53 ID - Gutierrez2004 ER - TY - JOUR AU - Gollery, M. AU - Harper, J. AU - Cushman, J. AU - Mittler, T. AU - Girke, T. AU - Zhu, J. K. AU - Bailey-Serres, J. AU - Mittler, R. PY - 2006 DA - 2006// TI - What makes species unique? The contribution of proteins with obscure features JO - Genome Biol VL - 7 UR - https://doi.org/10.1186/gb-2006-7-7-r57 DO - 10.1186/gb-2006-7-7-r57 ID - Gollery2006 ER - TY - JOUR AU - Chothia, C. AU - Gough, J. AU - Vogel, C. AU - Teichmann, S. A. PY - 2003 DA - 2003// TI - Evolution of the protein repertoire JO - Science VL - 300 UR - https://doi.org/10.1126/science.1085371 DO - 10.1126/science.1085371 ID - Chothia2003 ER - TY - JOUR AU - Wolfe, K. H. AU - Gouy, M. AU - Yang, Y. W. AU - Sharp, P. M. AU - Li, W. H. PY - 1989 DA - 1989// TI - Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data JO - Proc Natl Acad Sci USA VL - 86 UR - https://doi.org/10.1073/pnas.86.16.6201 DO - 10.1073/pnas.86.16.6201 ID - Wolfe1989 ER - TY - JOUR AU - Chaw, S. M. AU - Chang, C. C. AU - Chen, H. L. AU - Li, W. H. PY - 2004 DA - 2004// TI - Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes JO - J Mol Evol VL - 58 UR - https://doi.org/10.1007/s00239-003-2564-9 DO - 10.1007/s00239-003-2564-9 ID - Chaw2004 ER - TY - JOUR AU - Blair, J. E. AU - Shah, P. AU - Hedges, S. B. PY - 2005 DA - 2005// TI - Evolutionary sequence analysis of complete eukaryote genomes JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-53 DO - 10.1186/1471-2105-6-53 ID - Blair2005 ER - TY - JOUR AU - Bateman, A. AU - Coin, L. AU - Durbin, R. AU - Finn, R. D. AU - Hollich, V. AU - Griffiths-Jones, S. AU - Khanna, A. AU - Marshall, M. AU - Moxon, S. AU - Sonnhammer, E. L. PY - 2004 DA - 2004// TI - The Pfam protein families database JO - Nucleic Acids Research VL - 32 UR - https://doi.org/10.1093/nar/gkh121 DO - 10.1093/nar/gkh121 ID - Bateman2004 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Sterck, L. AU - Rombauts, S. AU - Vandepoele, K. AU - Rouzé, P. AU - Peer, Y. V. a. n. d. e. PY - 2007 DA - 2007// TI - How many genes are there in plants (and why are they there)? JO - Current Opinion in Plant Biology VL - 10 UR - https://doi.org/10.1016/j.pbi.2007.01.004 DO - 10.1016/j.pbi.2007.01.004 ID - Sterck2007 ER - TY - STD TI - Mohseni-Zadeh S, Louis A, Brezellec P, Risler JL: PHYTOPROT: a database of clusters of plant proteins. Nucleic Acids Research. 2004, D351-D353. 10.1093/nar/gkh040. 32 Database ID - ref34 ER - TY - JOUR AU - Wu, F. AU - Mueller, L. A. AU - Crouzillat, D. AU - Petiard, V. AU - Tanksley, S. D. PY - 2006 DA - 2006// TI - Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade JO - Genetics VL - 174 UR - https://doi.org/10.1534/genetics.106.062455 DO - 10.1534/genetics.106.062455 ID - Wu2006 ER - TY - JOUR AU - Glemet, E. AU - Codani, J. J. PY - 1997 DA - 1997// TI - LASSAP, a LArge Scale Sequence compArison Package JO - Comput Appl Biosci VL - 13 ID - Glemet1997 ER - TY - STD TI - Gagnot S, Tamby JP, Martin-Magniette ML, Bitton F, Taconnat L, Balzergue S, Aubourg S, Renou JP, Lecharny A, Brunaud V: CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. Nucleic Acids Res. 2008, D986-990. 36 Database ID - ref37 ER - TY - JOUR AU - Zimmermann, P. AU - Hennig, L. AU - Gruissem, W. PY - 2005 DA - 2005// TI - Gene-expression analysis and network discovery using Genevestigator JO - Trends Plant Sci VL - 10 UR - https://doi.org/10.1016/j.tplants.2005.07.003 DO - 10.1016/j.tplants.2005.07.003 ID - Zimmermann2005 ER - TY - JOUR AU - Zimmermann, P. AU - Hirsch-Hoffmann, M. AU - Hennig, L. AU - Gruissem, W. PY - 2004 DA - 2004// TI - GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox JO - Plant Physiol VL - 136 UR - https://doi.org/10.1104/pp.104.046367 DO - 10.1104/pp.104.046367 ID - Zimmermann2004 ER - TY - JOUR AU - Guyot, R. AU - Keller, B. PY - 2004 DA - 2004// TI - Ancestral genome duplication in rice JO - Genome VL - 47 UR - https://doi.org/10.1139/g04-016 DO - 10.1139/g04-016 ID - Guyot2004 ER - TY - JOUR PY - 2005 DA - 2005// TI - The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications JO - BMC Biology VL - 3 UR - https://doi.org/10.1186/1741-7007-3-20 DO - 10.1186/1741-7007-3-20 ID - ref41 ER - TY - JOUR AU - Yu, J. AU - Wang, J. AU - Lin, W. AU - Li, S. AU - Li, H. AU - Zhou, J. AU - Ni, P. AU - Dong, W. AU - Hu, S. AU - Zeng, C. PY - 2005 DA - 2005// TI - The Genomes of Oryza sativa: a history of duplications JO - PLoS Biol VL - 3 UR - https://doi.org/10.1371/journal.pbio.0030038 DO - 10.1371/journal.pbio.0030038 ID - Yu2005 ER - TY - JOUR AU - Carmel, L. AU - Rogozin, I. B. AU - Wolf, Y. I. AU - Koonin, E. V. PY - 2007 DA - 2007// TI - Evolutionarily conserved genes preferentially accumulate introns JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.5978207 DO - 10.1101/gr.5978207 ID - Carmel2007 ER - TY - JOUR AU - Brooks, A. R. AU - Nagy, B. P. AU - Taylor, S. AU - Simonet, W. S. AU - Taylor, J. M. AU - Levy-Wilson, B. PY - 1994 DA - 1994// TI - Sequences containing the second-intron enhancer are essential for transcription of the human apolipoprotein B gene in the livers of transgenic mice JO - Mol Cell Biol VL - 14 UR - https://doi.org/10.1128/MCB.14.4.2243 DO - 10.1128/MCB.14.4.2243 ID - Brooks1994 ER - TY - JOUR AU - Carmel, L. AU - Wolf, Y. I. AU - Rogozin, I. B. AU - Koonin, E. V. PY - 2007 DA - 2007// TI - Three distinct modes of intron dynamics in the evolution of eukaryotes JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.6438607 DO - 10.1101/gr.6438607 ID - Carmel2007 ER - TY - JOUR AU - Benabdellah, K. AU - Gonzalez-Rey, E. AU - Gonzalez, A. PY - 2007 DA - 2007// TI - Alternative trans-splicing of the Trypanosoma cruzi LYT1 gene transcript results in compartmental and functional switch for the encoded protein JO - Mol Microbiol VL - 65 UR - https://doi.org/10.1111/j.1365-2958.2007.05892.x DO - 10.1111/j.1365-2958.2007.05892.x ID - Benabdellah2007 ER - TY - JOUR AU - Tremousaygue, D. AU - Garnier, L. AU - Bardet, C. AU - Dabos, P. AU - Herve, C. AU - Lescure, B. PY - 2003 DA - 2003// TI - Internal telomeric repeats and 'TCP domain' protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells JO - Plant J VL - 33 UR - https://doi.org/10.1046/j.1365-313X.2003.01682.x DO - 10.1046/j.1365-313X.2003.01682.x ID - Tremousaygue2003 ER - TY - JOUR AU - Hudson, M. E. AU - Quail, P. H. PY - 2003 DA - 2003// TI - Identification of promoter motifs involved in the network of phytochrome A-regulated gene expression by combined analysis of genomic sequence and microarray data JO - Plant Physiol VL - 133 UR - https://doi.org/10.1104/pp.103.030437 DO - 10.1104/pp.103.030437 ID - Hudson2003 ER - TY - JOUR AU - Bucher, P. AU - Trifonov, E. N. PY - 1988 DA - 1988// TI - CCAAT box revisited: bidirectionality, location and context JO - J Biomol Struct Dyn VL - 5 UR - https://doi.org/10.1080/07391102.1988.10506466 DO - 10.1080/07391102.1988.10506466 ID - Bucher1988 ER - TY - JOUR AU - Skovgaard, M. AU - Jensen, L. J. AU - Brunak, S. AU - Ussery, D. AU - Krogh, A. PY - 2001 DA - 2001// TI - On the total number of genes and their length distribution in complete microbial genomes JO - Trends Genet VL - 17 UR - https://doi.org/10.1016/S0168-9525(01)02372-1 DO - 10.1016/S0168-9525(01)02372-1 ID - Skovgaard2001 ER - TY - JOUR AU - Linial, M. PY - 2003 DA - 2003// TI - How incorrect annotations evolve – the case of short ORFs JO - Trends Biotechnol VL - 21 UR - https://doi.org/10.1016/S0167-7799(03)00139-2 DO - 10.1016/S0167-7799(03)00139-2 ID - Linial2003 ER - TY - JOUR AU - Snyder, M. AU - Gerstein, M. PY - 2003 DA - 2003// TI - Genomics. Defining genes in the genomics era JO - Science VL - 300 UR - https://doi.org/10.1126/science.1084354 DO - 10.1126/science.1084354 ID - Snyder2003 ER - TY - JOUR AU - Lease, K. A. AU - Walker, J. C. PY - 2006 DA - 2006// TI - The Arabidopsis unannotated secreted peptide database, a resource for plant peptidomics JO - Plant Physiol VL - 142 UR - https://doi.org/10.1104/pp.106.086041 DO - 10.1104/pp.106.086041 ID - Lease2006 ER - TY - JOUR AU - Hanada, K. AU - Zhang, X. AU - Borevitz, J. O. AU - Li, W. H. AU - Shiu, S. H. PY - 2007 DA - 2007// TI - A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.5836207 DO - 10.1101/gr.5836207 ID - Hanada2007 ER - TY - JOUR AU - Aubourg, S. AU - Martin-Magniette, M. L. AU - Brunaud, V. AU - Taconnat, L. AU - Bitton, F. AU - Balzergue, S. AU - Jullien, P. E. AU - Ingouff, M. AU - Thareau, V. AU - Schiex, T. PY - 2007 DA - 2007// TI - Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome JO - BMC Genomics VL - 8 UR - https://doi.org/10.1186/1471-2164-8-401 DO - 10.1186/1471-2164-8-401 ID - Aubourg2007 ER - TY - JOUR AU - Moskal, W. A. AU - Wu, H. C. AU - Underwood, B. A. AU - Wang, W. AU - Town, C. D. AU - Xiao, Y. PY - 2007 DA - 2007// TI - Experimental validation of novel genes predicted in the un-annotated regions of the Arabidopsis genome JO - BMC Genomics VL - 8 UR - https://doi.org/10.1186/1471-2164-8-18 DO - 10.1186/1471-2164-8-18 ID - Moskal2007 ER - TY - JOUR AU - Frith, M. C. AU - Forrest, A. R. AU - Nourbakhsh, E. AU - Pang, K. C. AU - Kai, C. AU - Kawai, J. AU - Carninci, P. AU - Hayashizaki, Y. AU - Bailey, T. L. AU - Grimmond, S. M. PY - 2006 DA - 2006// TI - The abundance of short proteins in the mammalian proteome JO - PLoS Genet VL - 2 UR - https://doi.org/10.1371/journal.pgen.0020052 DO - 10.1371/journal.pgen.0020052 ID - Frith2006 ER - TY - JOUR AU - Kastenmayer, J. P. AU - Ni, L. AU - Chu, A. AU - Kitchen, L. E. AU - Au, W. C. AU - Yang, H. AU - Carter, C. D. AU - Wheeler, D. AU - Davis, R. W. AU - Boeke, J. D. PY - 2006 DA - 2006// TI - Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.4355406 DO - 10.1101/gr.4355406 ID - Kastenmayer2006 ER - TY - JOUR AU - Galindo, M. I. AU - Pueyo, J. I. AU - Fouix, S. AU - Bishop, S. A. AU - Couso, J. P. PY - 2007 DA - 2007// TI - Peptides encoded by short ORFs control development and define a new eukaryotic gene family JO - PLoS Biol VL - 5 UR - https://doi.org/10.1371/journal.pbio.0050106 DO - 10.1371/journal.pbio.0050106 ID - Galindo2007 ER - TY - STD TI - Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, et al: The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 2008, D1009-1014. 36 Database ID - ref60 ER - TY - JOUR AU - Farrokhi, N. AU - Whitelegge, J. P. AU - Brusslan, J. A. PY - 2008 DA - 2008// TI - Plant peptides and peptidomics JO - Plant Biotechnol J VL - 6 UR - https://doi.org/10.1111/j.1467-7652.2007.00315.x DO - 10.1111/j.1467-7652.2007.00315.x ID - Farrokhi2008 ER - TY - JOUR AU - Tatusov, R. L. AU - Koonin, E. V. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - A genomic perspective on protein families JO - Science VL - 278 UR - https://doi.org/10.1126/science.278.5338.631 DO - 10.1126/science.278.5338.631 ID - Tatusov1997 ER - TY - JOUR AU - Knowles, D. G. AU - McLysaght, A. PY - 2006 DA - 2006// TI - High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msl017 DO - 10.1093/molbev/msl017 ID - Knowles2006 ER - TY - JOUR AU - Roy, S. W. AU - Penny, D. PY - 2007 DA - 2007// TI - Patterns of intron loss and gain in plants: Intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana JO - Molecular Biology and Evolution VL - 24 UR - https://doi.org/10.1093/molbev/msl159 DO - 10.1093/molbev/msl159 ID - Roy2007 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 - Drummond, D. A. AU - Raval, A. AU - Wilke, C. O. PY - 2006 DA - 2006// TI - A single determinant dominates the rate of yeast protein evolution JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msj038 DO - 10.1093/molbev/msj038 ID - Drummond2006 ER - TY - JOUR AU - Wright, S. I. AU - Yau, C. B. AU - Looseley, M. AU - Meyers, B. C. PY - 2004 DA - 2004// TI - Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh191 DO - 10.1093/molbev/msh191 ID - Wright2004 ER - TY - JOUR AU - Berezikov, E. AU - Guryev, V. AU - Cuppen, E. PY - 2005 DA - 2005// TI - CONREAL web server: identification and visualization of conserved transcription factor binding sites JO - Nucleic Acids Research VL - 33 UR - https://doi.org/10.1093/nar/gki378 DO - 10.1093/nar/gki378 ID - Berezikov2005 ER - TY - JOUR AU - Hindemitt, T. AU - Mayer, K. F. PY - 2005 DA - 2005// TI - CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti691 DO - 10.1093/bioinformatics/bti691 ID - Hindemitt2005 ER - TY - JOUR AU - Thijs, G. AU - Lescot, M. AU - Marchal, K. AU - Rombauts, S. AU - De Moor, B. AU - Rouze, P. AU - Moreau, Y. PY - 2001 DA - 2001// TI - A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.12.1113 DO - 10.1093/bioinformatics/17.12.1113 ID - Thijs2001 ER - TY - JOUR AU - Walther, D. AU - Brunnemann, R. AU - Selbig, J. PY - 2007 DA - 2007// TI - The regulatory code for transcriptional response diversity and its relation to genome structural properties in A. thaliana JO - PLoS Genet VL - 3 UR - https://doi.org/10.1371/journal.pgen.0030011 DO - 10.1371/journal.pgen.0030011 ID - Walther2007 ER - TY - JOUR AU - Moshonov, S. AU - Elfakess, R. AU - Golan-Mashiach, M. AU - Sinvani, H. AU - Dikstein, R. PY - 2008 DA - 2008// TI - Links between core promoter and basic gene features influence gene expression JO - BMC Genomics VL - 9 UR - https://doi.org/10.1186/1471-2164-9-92 DO - 10.1186/1471-2164-9-92 ID - Moshonov2008 ER - TY - JOUR AU - Palenik, B. AU - Grimwood, J. AU - Aerts, A. AU - Rouze, P. AU - Salamov, A. AU - Putnam, N. AU - Dupont, C. AU - Jorgensen, R. AU - Derelle, E. AU - Rombauts, S. PY - 2007 DA - 2007// TI - The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation JO - Proc Natl Acad Sci USA VL - 104 UR - https://doi.org/10.1073/pnas.0611046104 DO - 10.1073/pnas.0611046104 ID - Palenik2007 ER - TY - JOUR AU - Rensing, S. A. AU - Lang, D. AU - Zimmer, A. D. AU - Terry, A. AU - Salamov, A. AU - Shapiro, H. AU - Nishiyama, T. AU - Perroud, P. F. AU - Lindquist, E. A. AU - Kamisugi, Y. PY - 2008 DA - 2008// TI - The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants JO - Science VL - 319 UR - https://doi.org/10.1126/science.1150646 DO - 10.1126/science.1150646 ID - Rensing2008 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 - Jaillon, O. AU - Aury, J. M. AU - Noel, B. AU - Policriti, A. AU - Clepet, C. AU - Casagrande, A. AU - Choisne, N. AU - Aubourg, S. AU - Vitulo, N. AU - Jubin, C. PY - 2007 DA - 2007// TI - The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla JO - Nature VL - 449 UR - https://doi.org/10.1038/nature06148 DO - 10.1038/nature06148 ID - Jaillon2007 ER - TY - JOUR AU - Vandepoele, K. AU - Peer, Y. V. a. n. d. e. PY - 2005 DA - 2005// TI - Exploring the plant transcriptome through phylogenetic profiling JO - Plant Physiol VL - 137 UR - https://doi.org/10.1104/pp.104.054700 DO - 10.1104/pp.104.054700 ID - Vandepoele2005 ER - TY - JOUR AU - Zimmer, A. AU - Lang, D. AU - Richardt, S. AU - Frank, W. AU - Reski, R. AU - Rensing, S. A. PY - 2007 DA - 2007// TI - Dating the early evolution of plants: detection and molecular clock analyses of orthologs JO - Mol Genet Genomics VL - 278 UR - https://doi.org/10.1007/s00438-007-0257-6 DO - 10.1007/s00438-007-0257-6 ID - Zimmer2007 ER - TY - JOUR AU - Hedges, S. B. AU - Blair, J. E. AU - Venturi, M. L. AU - Shoe, J. L. PY - 2004 DA - 2004// TI - A molecular timescale of eukaryote evolution and the rise of complex multicellular life JO - BMC Evol Biol VL - 4 UR - https://doi.org/10.1186/1471-2148-4-2 DO - 10.1186/1471-2148-4-2 ID - Hedges2004 ER - TY - JOUR AU - Nei, M. AU - Gojobori, T. PY - 1986 DA - 1986// TI - Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions JO - Mol Biol Evol VL - 3 ID - Nei1986 ER - TY - JOUR AU - Yang, Z. PY - 2007 DA - 2007// TI - PAML 4: Phylogenetic Analysis by Maximum Likelihood JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm088 DO - 10.1093/molbev/msm088 ID - Yang2007 ER - TY - JOUR AU - Nekrutenko, A. AU - Makova, K. D. AU - Li, W. H. PY - 2002 DA - 2002// TI - The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.200901 DO - 10.1101/gr.200901 ID - Nekrutenko2002 ER - TY - JOUR AU - Anisimova, M. AU - Bielawski, J. P. AU - Yang, Z. PY - 2001 DA - 2001// TI - Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003945 DO - 10.1093/oxfordjournals.molbev.a003945 ID - Anisimova2001 ER - TY - JOUR AU - Basehoar, A. D. AU - Zanton, S. J. AU - Pugh, B. F. PY - 2004 DA - 2004// TI - Identification and distinct regulation of yeast TATA box-containing genes JO - Cell VL - 116 UR - https://doi.org/10.1016/S0092-8674(04)00205-3 DO - 10.1016/S0092-8674(04)00205-3 ID - Basehoar2004 ER - TY - JOUR AU - Seoighe, C. AU - Gehring, C. PY - 2004 DA - 2004// TI - Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome JO - Trends Genet VL - 20 UR - https://doi.org/10.1016/j.tig.2004.07.008 DO - 10.1016/j.tig.2004.07.008 ID - Seoighe2004 ER - TY - JOUR AU - Lindsey, K. AU - Casson, S. AU - Chilley, P. PY - 2002 DA - 2002// TI - Peptides: new signalling molecules in plants JO - Trends Plant Sci VL - 7 UR - https://doi.org/10.1016/S1360-1385(01)02194-X DO - 10.1016/S1360-1385(01)02194-X ID - Lindsey2002 ER - TY - STD TI - TAIR. [http://www.arabidopsis.org/] UR - http://www.arabidopsis.org/ ID - ref87 ER - TY - STD TI - TIGR. [http://www.tigr.org] UR - http://www.tigr.org ID - ref88 ER - TY - STD TI - JGI. [http://genome.jgi-psf.org/] UR - http://genome.jgi-psf.org/ ID - ref89 ER - TY - STD TI - Samson F, Brunaud V, Duchene S, De Oliveira Y, Caboche M, Lecharny A, Aubourg S: FLAGdb++: a database for the functional analysis of the Arabidopsis genome. Nucleic Acids Research. 2004, D347-D350. 10.1093/nar/gkh134. 32 Database ID - ref90 ER - TY - JOUR AU - Chenna, R. AU - Sugawara, H. AU - Koike, T. AU - Lopez, R. AU - Gibson, T. J. AU - Higgins, D. G. AU - Thompson, J. D. PY - 2003 DA - 2003// TI - Multiple sequence alignment with the Clustal series of programs JO - Nucleic Acids Research VL - 31 UR - https://doi.org/10.1093/nar/gkg500 DO - 10.1093/nar/gkg500 ID - Chenna2003 ER - TY - JOUR AU - Boudet, N. AU - Aubourg, S. AU - Toffano-Nioche, C. AU - Kreis, M. AU - Lecharny, A. PY - 2001 DA - 2001// TI - Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabditis, and Drosophila JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.200801 DO - 10.1101/gr.200801 ID - Boudet2001 ER - TY - JOUR AU - Lifton, R. P. AU - Goldberg, M. L. AU - Karp, R. W. AU - Hogness, D. S. PY - 1978 DA - 1978// TI - The organization of the histone genes in Drosophila melanogaster: functional and evolutionary implications JO - Cold Spring Harb Symp Quant Biol VL - 42 UR - https://doi.org/10.1101/SQB.1978.042.01.105 DO - 10.1101/SQB.1978.042.01.105 ID - Lifton1978 ER - TY - CHAP AU - Bernard, V. AU - Brunaud, V. AU - Serizet, C. AU - Martin-Magniette, M. L. AU - Caboche, M. AU - Aubourg, S. AU - Lecharny, A. PY - 2006 DA - 2006// TI - Sélection de motifs candidats pour la régulation des gènes chez Arabidopsis thalianasur des critères topologiques BT - JOBIM: 5–7 July 2006; Bordeaux ID - Bernard2006 ER - TY - JOUR AU - Yamamoto, Y. Y. AU - Ichida, H. AU - Matsui, M. AU - Obokata, J. AU - Sakurai, T. AU - Satou, M. AU - Seki, M. AU - Shinozaki, K. AU - Abe, T. PY - 2007 DA - 2007// TI - Identification of plant promoter constituents by analysis of local distribution of short sequences JO - BMC Genomics VL - 8 UR - https://doi.org/10.1186/1471-2164-8-67 DO - 10.1186/1471-2164-8-67 ID - Yamamoto2007 ER -