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, 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., 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).

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).

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).

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).

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).

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).

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).

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).

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).

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).

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).

Riano-Pachon, D. M., Ruzicic, S., Dreyer, I. & Mueller-Roeber, B. PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics 8, 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, 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, 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, 63–75 (2008).