MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis von Schwacke, Rainer, Ponce-Soto, Gabriel Y., Krause, Kirsten, Bolger, Anthony M., Arsova, Borjana, Hallab, Asis, Gruden, Kristina, Stitt, Mark, Bolger, Marie E., Usadel, Björn

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Trimmomatic: a flexible trimmer for Illumina sequence data von Bolger, Anthony M, Lohse, Marc, Usadel, Bjoern

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De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing von Schmidt, Maximilian H.-W., Vogel, Alexander, Denton, Alisandra K., Istace, Benjamin, Wormit, Alexandra, van de Geest, Henri, Bolger, Marie E., Alseekh, Saleh, Maß, Janina, Pfaff, Christian, Schurr, Ulrich, Chetelat, Roger, Maumus, Florian, Aury, Jean-Marc, Koren, Sergey, Fernie, Alisdair R., Zamir, Dani, Bolger, Anthony M., Usadel, Björn

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Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris von Vogel, Alexander, Schwacke, Rainer, Denton, Alisandra K., Usadel, Björn, Hollmann, Julien, Fischer, Karsten, Bolger, Anthony, Schmidt, Maximilian H.-W., Bolger, Marie E., Gundlach, Heidrun, Mayer, Klaus F. X., Weiss-Schneeweiss, Hanna, Temsch, Eva M., Krause, Kirsten

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Tomato facultative parthenocarpy results from SlAGAMOUS‐LIKE 6 loss of function von Klap, Chen, Yeshayahou, Ester, Bolger, Anthony M., Arazi, Tzahi, Gupta, Suresh K., Shabtai, Sara, Usadel, Björn, Salts, Yehiam, Barg, Rivka

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RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics von Lohse, Marc, Bolger, Anthony M, Nagel, Axel, Fernie, Alisdair R, Lunn, John E, Stitt, Mark, Usadel, Björn

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Computational aspects underlying genome to phenome analysis in plants von Bolger, Anthony M., Poorter, Hendrik, Dumschott, Kathryn, Bolger, Marie E., Arend, Daniel, Osorio, Sonia, Gundlach, Heidrun, Mayer, Klaus F. X., Lange, Matthias, Scholz, Uwe, Usadel, Björn

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Algorithm-driven artifacts in median polish summarization of microarray data von Giorgi, Federico M, Bolger, Anthony M, Lohse, Marc, Usadel, Bjoern

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Evolution of a Complex Locus for Terpene Biosynthesis in Solanum von Matsuba, Yuki, Nguyen, Thuong T.H., Wiegert, Krystle, Falara, Vasiliki, Gonzales-Vigil, Eliana, Leong, Bryan, Schäfer, Petra, Kudma, David, Wing, Rod A., Bolger, Anthony M., Usadel, Bjöm, Tissier, Alain, Fernie, Alisdair R., Barry, Cornelius S., Picherskya, Eran

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Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato von Koenig, Daniel, Jiménez-Gómez, José M, Kimura, Seisuke, Fulop, Daniel, Chitwood, Daniel H, Headland, Lauren R, Kumar, Ravi, Covington, Michael F, Devisetty, Upendra Kumar, Tat, An V, Tohge, Takayuki, Bolger, Anthony, Schneeberger, Korbinian, Ossowski, Stephan, Lanz, Christa, Xiong, Guangyan, Taylor-Teeples, Mallorie, Brady, Siobhan M, Pauly, Markus, Weigel, Detlef, Usadel, Björn, Fernie, Alisdair R, Peng, Jie, Sinha, Neelima R, Maloof, Julin N

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De Novo Transcriptome Analysis of Durum Wheat Flag Leaves Provides New Insights Into the Regulatory Response to Elevated CO2 and High Temperature von Vicente, Rubén, Bolger, Anthony M., Martínez-Carrasco, Rafael, Pérez, Pilar, Gutiérrez, Elena, Usadel, Björn, Morcuende, Rosa

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The Arabidopsis thaliana onset of leaf death 12 mutation in the lectin receptor kinase P2K2 results in an autoimmune phenotype von Zhao, Liming, Wang, Hao-Jie, Martins, Patricia Dalcin, van Dongen, Joost T, Bolger, Anthony M, Schmidt, Romy R, Jing, Hai-Chun, Mueller-Roeber, Bernd, Schippers, Jos H M

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Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify von Dijkhuizen, Laura W., Brouwer, Paul, Bolhuis, Henk, Reichart, Gert‐Jan, Koppers, Nils, Huettel, Bruno, Bolger, Anthony M., Li, Fay‐Wei, Cheng, Shifeng, Liu, Xin, Wong, Gane Ka‐Shu, Pryer, Kathleen, Weber, Andreas, Bräutigam, Andrea, Schluepmann, Henriette

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Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance von Baum, Stephani, Reimer-Michalski, Eva-Maria, Bolger, Anthony, Mantai, Andrea J, Benes, Vladimir, Usadel, Björn, Conrath, Uwe

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Dual Resistance of Melon to Fusarium oxysporum Races 0 and 2 and to Papaya ring-spot virus is Controlled by a Pair of Head-to-Head-Oriented NB-LRR Genes of Unusual Architecture von Brotman, Yariv, Normantovich, Michael, Goldenberg, Zachi, Zvirin, Zvi, Kovalski, Irina, Stovbun, Nastacia, Doniger, Tirza, Bolger, Anthony M., Troadec, Christelle, Bendahmane, Abdelhafid, Cohen, Roni, Katzir, Nurit, Pitrat, Michel, Dogimont, Catherine, Perl-Treves, Rafael

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Identification of candidate genes for phenolics accumulation in tomato fruit von Di Matteo, Antonio, Ruggieri, Valentino, Sacco, Adriana, Rigano, Maria Manuela, Carriero, Filomena, Bolger, Anthony, Fernie, Alisdair R, Frusciante, Luigi, Barone, Amalia

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Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N 2 but may denitrify von Dijkhuizen, Laura W, Brouwer, Paul, Bolhuis, Henk, Reichart, Gert-Jan, Koppers, Nils, Huettel, Bruno, Bolger, Anthony M, Li, Fay-Wei, Cheng, Shifeng, Liu, Xin, Wong, Gane Ka-Shu, Pryer, Kathleen, Weber, Andreas, Bräutigam, Andrea, Schluepmann, Henriette

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The genome of the stress-tolerant wild tomato species Solanum pennellii von Bolger, Anthony, Scossa, Federico, Bolger, Marie E, Lanz, Christa, Maumus, Florian, Tohge, Takayuki, Quesneville, Hadi, Alseekh, Saleh, Sørensen, Iben, Lichtenstein, Gabriel, Fich, Eric A, Conte, Mariana, Keller, Heike, Schneeberger, Korbinian, Schwacke, Rainer, Ofner, Itai, Vrebalov, Julia, Xu, Yimin, Osorio, Sonia, Aflitos, Saulo Alves, Schijlen, Elio, Jiménez-Goméz, José M, Ryngajllo, Malgorzata, Kimura, Seisuke, Kumar, Ravi, Koenig, Daniel, Headland, Lauren R, Maloof, Julin N, Sinha, Neelima, van Ham, Roeland C H J, Lankhorst, René Klein, Mao, Linyong, Vogel, Alexander, Arsova, Borjana, Panstruga, Ralph, Fei, Zhangjun, Rose, Jocelyn K C, Zamir, Dani, Carrari, Fernando, Giovannoni, James J, Weigel, Detlef, Usadel, Björn, Fernie, Alisdair R

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Fluctuating Light Interacts with Time of Day and Leaf Development Stage to Reprogram Gene Expression von Schneider, Trang, Bolger, Anthony, Zeier, Jürgen, Preiskowski, Sabine, Benes, Vladimir, Trenkamp, Sandra, Usadel, Björn, Farré, Eva M, Matsubara, Shizue

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In‐depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of Camellia sinensis von Tariq, Arslan, Meng, Minghui, Jiang, Xiaohui, Bolger, Anthony, Beier, Sebastian, Buchmann, Jan P., Fernie, Alisdair R., Wen, Weiwei, Usadel, Björn

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