Publications of D. M. Riano-Pachon

Journal Article (15)

1.
Journal Article
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, 95–100 (2012).
2.
Journal Article
Banks, J. A., Nishiyama, T., Hasebe, M., Bowman, J. L., Gribskov, M., dePamphilis, C., Albert, V. A., Aono, N., Aoyama, T., Ambrose, B. A., 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. et al. The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. Science 332, 960–963 (2011).
3.
Journal Article
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., 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, 999–1013 (2011).
4.
Journal Article
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, 488–503 (2010).
5.
Journal Article
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, D822–D827 (2010).
6.
Journal Article
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, 411 (2010).
7.
Journal Article
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, 954–959 (2009).
8.
Journal Article
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, 465 (2008).
9.
Journal Article
Balazadeh, S., Riano-Pachon, D. M. & Mueller-Roeber, B. Transcription factors regulating leaf senescence in Arabidopsis thaliana. Plant Biology 10 Suppl 1, 63–75 (2008).
10.
Journal Article
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, e2944 (2008).
11.
Journal Article
Riano-Pachon, D. M., Correa, L. G. G., Trejos-Espinosa, R. & Mueller-Roeber, B. Green transcription factors: A Chlamydomonas overview. Genetics 179, 31–39 (2008).
12.
Journal Article
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, 260 (2007).
13.
Journal Article
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., 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. et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318, 245–250 (2007).
14.
Journal Article
Riano-Pachon, D. M., Ruzicic, S., Dreyer, I. & Mueller-Roeber, B. PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics 8, 42 (2007).
15.
Journal Article
Riano-Pachon, D. M., Dreyer, I. & Mueller-Roeber, B. Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognized genes. Plant Journal 43, 205–212 (2005).

Meeting Abstract (1)

16.
Meeting Abstract
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, S318–S318 (2009).
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