Publications of D. M. Riano-Pachon

Winck, F. V.; Riano-Pachon, D. M.; Sommer, F.; Rupprecht, J.; Mueller-Roeber, B.: The nuclear proteome of the green alga Chlamydomonas reinhardtii. Proteomics 12 (1), pp. 95 - 100 (2012)

Banks, J. A.; Nishiyama, T.; Hasebe, M.; Bowman, J. L.; Gribskov, M.; dePamphilis, C.; Albert, V. A.; Aono, N.; Aoyama, T.; Ambrose, B. A. et al.; Ashton, N. W.; Axtell, M. J.; Barker, E.; Barker, M. S.; Bennetzen, J. L.; Bonawitz, N. D.; Chapple, C.; Cheng, C. Y.; Correa, L. G. G.; Dacre, M.; DeBarry, J.; Dreyer, I.; Elias, M.; Engstrom, E. M.; Estelle, M.; Feng, L.; Finet, C.; Floyd, S. K.; Frommer, W. B.; Fujita, T.; Gramzow, L.; Gutensohn, M.; Harholt, J.; Hattori, M.; Heyl, A.; Hirai, T.; Hiwatashi, Y.; Ishikawa, M.; Iwata, M.; Karol, K. G.; Koehler, B.; Kolukisaoglu, U.; Kubo, M.; Kurata, T.; Lalonde, S.; Li, K. J.; Li, Y.; Litt, A.; Lyons, E.; Manning, G.; Maruyama, T.; Michael, T. P.; Mikami, K.; Miyazaki, S.; Morinaga, S.; Murata, T.; Mueller-Roeber, B.; Nelson, D. R.; Obara, M.; Oguri, Y.; Olmstead, R. G.; Onodera, N.; Petersen, B. L.; Pils, B.; Prigge, M.; Rensing, S. A.; Riano-Pachon, D. M.; Roberts, A. W.; Sato, Y.; Scheller, H. V.; Schulz, B.; Schulz, C.; Shakirov, E. V.; Shibagaki, N.; Shinohara, N.; Shippen, D. E.; Sorensen, I.; Sotooka, R.; Sugimoto, N.; Sugita, M.; Sumikawa, N.; Tanurdzic, M.; Theissen, G.; Ulvskov, P.; Wakazuki, S.; Weng, J. K.; Willats, W. W. G. T.; Wipf, D.; Wolf, P. G.; Yang, L. X.; Zimmer, A. D.; Zhu, Q. H.; Mitros, T.; Hellsten, U.; Loque, D.; Otillar, R.; Salamov, A.; Schmutz, J.; Shapiro, H.; Lindquist, E.,. e. a.: The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. Science 332 (6032), pp. 960 - 963 (2011)

Rohrmann, J.; Tohge, T.; Alba, R.; Osorio, S.; Caldana, C.; McQuinn, R.; Arvidsson, S.; van der Merwe, M. J.; Riano-Pachon, D. M.; Mueller-Roeber, B. et al.; Fei, Z.; Nunes-Nesi, A.; Giovannoni, J. J.; Fernie, A. R.: Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development. The Plant Journal 68 (6), pp. 999 - 1013 (2011)

Lang, D.; Weiche, B.; Timmerhaus, G.; Richardt, S.; Riano-Pachon, D. M.; Correa, L. G. G.; Reski, R.; Mueller-Roeber, B.; Rensing, S. A.: Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity. Genome Biology and Evolution 2, pp. 488 - 503 (2010)

Perez-Rodriguez, P.; Riano-Pachon, D. M.; Correa, L. G. G.; Rensing, S. A.; Kersten, B.; Mueller-Roeber, B.: PInTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Research 38, pp. D822 - D827 (2010)

Riano-Pachon, D. M.; Kleessen, S.; Neigenfind; Durek, P.; Weber, E.; Engelsberger, W. R.; Walther, D.; Selbig, J.; Schulze, W. X.; Kersten, B.: Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. BMC Genomics 11, p. 411 (2010)

Riano-Pachon, D. M.; Nagel, A.; Neigenfind, J.; Wagner, R.; Basekow, R.; Weber, E.; Mueller-Roeber, B.; Diehl, S.; Kersten, B.: GabiPD: the GABI primary database-a plant integrative 'omics' database. Nucleic Acids Research 37 (Database issue), pp. 954 - 959 (2009)

Arvidsson, S.; Kwasniewski, M.; Riano-Pachon, D. M.; Mueller-Roeber, B.: QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinformatics 9, p. 465 (2008)

Correa, L. G.; Riano-Pachon, D. M.; Schrago, C. G.; dos Santos, R. V.; Mueller-Roeber, B.; Vincentz, M.: The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes. PLoS One 3 (8), p. e2944 (2008)

Riano-Pachon, D. M.; Correa, L. G. G.; Trejos-Espinosa, R.; Mueller-Roeber, B.: Green transcription factors: A Chlamydomonas overview. Genetics 179 (1), pp. 31 - 39 (2008)

Gomez-Porras, J. L.; Riano-Pachon, D. M.; Dreyer, I.; Mayer, J. E.; Mueller-Roeber, B.: Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC Genomics 8, p. 260 (2007)

Merchant, S. S.; Prochnik, S. E.; Vallon, O.; Harris, E. H.; Karpowicz, S. J.; Witman, G. B.; Terry, A.; Salamov, A.; Fritz-Laylin, L. K.; Marechal-Drouard, L. et al.; Marshall, W. F.; Qu, L. H.; Nelson, D. R.; Sanderfoot, A. A.; Spalding, M. H.; Kapitonov, V. V.; Ren, Q.; Ferris, P.; Lindquist, E.; Shapiro, H.; Lucas, S. M.; Grimwood, J.; Schmutz, J.; Cardol, P.; Cerutti, H.; Chanfreau, G.; Chen, C. L.; Cognat, V.; Croft, M. T.; 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, P. A.; Lemaire, S. D.; Lobanov, A. V.; Lohr, M.; Manuell, A.; Meier, I.; Mets, L.; Mittag, M.; Mittelmeier, T.; Moroney, J. V.; Moseley, J.; Napoli, C.; Nedelcu, A. M.; Niyogi, K.; Novoselov, S. V.; Paulsen, I. T.; Pazour, G.; Purton, S.; Ral, J. P.; Riano-Pachon, D. M.; Riekhof, W.; Rymarquis, L.; Schroda, M.; Stern, D.; Umen, J.; Willows, R.; Wilson, N.; Zimmer, S. L.; Allmer, J.; Balk, J.; Bisova, K.; Chen, C. J.; Elias, M.; Gendler, K.; Hauser, C.; Lamb, M. R.; Ledford, H.; Long, J. C.; Minagawa, J.; Page, M. D.; Pan, J.; Pootakham, W.; Roje, S.; Rose, A.; Stahlberg, E.; Terauchi, A. M.; Yang, P.; Ball, S.; Bowler, C.; Dieckmann, C. L.; Gladyshev, V. N.; Green, P.; Jorgensen, R.; Mayfield, S.; Mueller-Roeber, B.; Rajamani, S.; Sayre, R. T.; Brokstein, P.,. e. a.: The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318 (5848), pp. 245 - 250 (2007)

Riano-Pachon, D. M.; Ruzicic, S.; Dreyer, I.; Mueller-Roeber, B.: PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics 8, p. 42 (2007)

Riano-Pachon, D. M.; Dreyer, I.; Mueller-Roeber, B.: Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognized genes. Plant Journal 43 (2), pp. 205 - 212 (2005)

Mueller-Roeber, B.; Arvidsson, S.; Balazadeh, S.; Correa, L. G. G.; Perez-Rodriguez, P.; Riano-Pachon, D. M.: Gene regulatory networks and transcription factor transcriptomics. In New Biotechnology, 25, p. S318 - S318. (2009)

Balazadeh, S.; Riano-Pachon, D. M.; Mueller-Roeber, B.: Transcription factors regulating leaf senescence in Arabidopsis thaliana. Plant Biology 10 Suppl 1, pp. 63 - 75 (2008)