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Journal Article (24)

1.
Journal Article
Tohge, T., Scossa, F., Wendenburg, R., Frasse, P., Balbo, I., Watanabe, M., Alseekh, S., Jadha, S. S., Delfin, J. C., Lohse, M., Giavalisco, P., Usadel, B., Zhang, Y. J., Luo, J., Bouzayen, M. & Fernie, A. R. Exploiting natural variation in tomato to define pathway structure and metabolic regulation of fruit polyphenolics in the lycopersicum complex. Molecular Plant 13, 1027–1046 (2020).
2.
Journal Article
Zhang, Y., Zhang, Y. J., McFarlane, H. E., Obata, T., Richter, A. S., Lohse, M., Grimm, B., Persson, S., Fernie, A. R. & Giavalisco, P. Inhibition of TOR Represses Nutrient Consumption, Which Improves Greening after Extended Periods of Etiolation. Plant Physiology 178, 101–117 (2018).
3.
Journal Article
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
4.
Journal Article
Lohse, M., Nagel, A., Herter, T., May, P., Schroda, M., Zrenner, R., Tohge, T., Fernie, A. R., Stitt, M. & Usadel, B. Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environment 37, 1250–1258 (2014).
5.
Journal Article
Mettler, T., Mühlhaus, T., Hemme, D., Schöttler, M. A., Rupprecht, J., Idoine, A., Veyel, D., Pal, S. K., Yaneva-Roder, L., Winck, F. V., Sommer, F., Vosloh, D., Seiwert, B., Erban, A., Burgos, A., Arvidsson, S., Schönfelder, S., Arnold, A., Günther, M., Krause, U., Lohse, M., Kopka, J., Nikoloski, Z., Mueller-Roeber, B., Willmitzer, L., Bock, R., Schroda, M. & Stitt, M. Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii. The Plant Cell 26, 2310–2350 (2014).
6.
Journal Article
Lee, Y. P., Giorgi, F. M., Lohse, M., Kvederaviciute, K., Klages, S., Usadel, B., Meskiene, I., Reinhardt, R. & Hincha, D. K. Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum). BMC Genomics 14, 793–793 (2013).
7.
Journal Article
Lohse, M., Drechsel, O., Kahlau, S. & Bock, R. OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 41, W575–W581 (2013).
8.
Journal Article
Araujo, W. L., Tohge, T., Osorio, S., Lohse, M., Balbo, I., Krahnert, I., Sienkiewicz-Porzucek, A., Usadel, B., Nunes-Nesi, A. & Fernie, A. R. Antisense Inhibition of the 2-Oxoglutarate Dehydrogenase Complex in Tomato Demonstrates Its Importance for Plant Respiration and during Leaf Senescence and Fruit Maturation. The Plant Cell 24, 2328–2351 (2012).
9.
Journal Article
Gaude, N., Bortfeld, S., Duensing, N., Lohse, M. & Krajinski, F. Arbuscule-containing and non-colonized cortical cells of mycorrhizal roots undergo extensive and specific reprogramming during arbuscular mycorrhizal development. Plant Journal 69, 510–528 (2012).
10.
Journal Article
Lohse, M., Bolger, A. M., Nagel, A., Fernie, A. R., Lunn, J. E., Stitt, M. & Usadel, B. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research 40, W622–W627 (2012).
11.
Journal Article
Nagel, A., Lohse, M., Bolger, A., Bolger, A. M., Stitt, M. & Usadel, B. Visualizing large, high-throughput datasets based on the cognitive representation of biological pathways. Human Vision and Electronic Imaging Xvi 7865, 78650h (2011).
12.
Journal Article
Osorio, S., Alba, R., Damasceno, C. M. B., Lopez-Casado, G., Lohse, M., Zanor, M. I., Tohge, T., Usadel, B., Rose, J. K. C., Fei, Z. J., Giovannoni, J. J. & Fernie, A. R. Systems Biology of Tomato Fruit Development: Combined Transcript, Protein, and Metabolite Analysis of Tomato Transcription Factor (nor, rin) and Ethylene Receptor (Nr) Mutants Reveals Novel Regulatory Interactions. Plant Physiology 157, 405–425 (2011).
13.
Journal Article
Ryngajllo, M., Childs, L., Lohse, M., Giorgi, F. M., Lude, A., Selbig, J. & Usadel, B. SLocX: predicting subcellular localization of Arabidopsis proteins leveraging gene expression data. Frontiers in Plant Science 2, 43 (2011).
14.
Journal Article
Giorgi, F. M., Bolger, A. M., Lohse, M. & Usadel, B. Algorithm-driven Artifacts in median polish summarization of Microarray data. BMC Bioinformatics 11, 553 (2010).
15.
Journal Article
Lohse, M., Nunes-Nesi, A., Krueger, P., Nagel, A., Hannemann, J., Giorgi, F. M., Childs, L., Osorio, S., Walther, D., Selbig, J., Sreenivasulu, N., Stitt, M., Fernie, A. R. & Usadel, B. Robin: An Intuitive Wizard Application for R-Based Expression Microarray Quality Assessment and Analysis. Plant Physiology 153, 642–651 (2010).
16.
Journal Article
Howell, K. A., Narsai, R., Carroll, A., Ivanova, A., Lohse, M., Usadel, B., Millar, A. H. & Whelan, J. Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process. Plant Physiology 149, 961–980 (2009).
17.
Journal Article
Oey, M., Lohse, M., Kreikemeyer, B. & Bock, R. Exhaustion of the chloroplast protein synthesis capacity by massive expression of a highly stable protein antibiotic. Plant Journal 57, 436–445 (2009).
18.
Journal Article
Oey, M., Lohse, M., Scharff, L. B., Kreikemeyer, B. & Bock, R. Plastid production of protein antibiotics against pneumonia via a new strategy for high-level expression of antimicrobial proteins. Proceedings of the National Academy of Sciences of the United States of America 106, 6579–6584 (2009).
19.
Journal Article
Rotter, A., Camps, C., Lohse, M., Kappel, C., Pilati, S., Hren, M., Stitt, M., Coutos-Thevenot, P., Moser, C., Usadel, B., Delrot, S. & Gruden, K. Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: Extending MapMan ontology for grapevine. BMC Plant Biology 9, 104 (2009).
20.
Journal Article
Usadel, B., Poree, F., Nagel, A., Lohse, M., Czedik-Eysenberg, A. & Stitt, M. A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell and Environment 32, 1211–1229 (2009).
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