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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.

Vicente R, Bolger AM, Martínez-Carrasco R, Pérez P, Gutiérrez E, Usadel B, Morcuende R.

Front Plant Sci. 2019 Dec 6;10:1605. doi: 10.3389/fpls.2019.01605. eCollection 2019.


Transcriptomic and proteomic data in developing tomato fruit.

Belouah I, Bénard C, Denton A, Blein-Nicolas M, Balliau T, Teyssier E, Gallusci P, Bouchez O, Usadel B, Zivy M, Gibon Y, Colombié S.

Data Brief. 2019 Dec 17;28:105015. doi: 10.1016/j.dib.2019.105015. eCollection 2020 Feb.


Tomato's Green Gold: Bioeconomy Potential of Residual Tomato Leaf Biomass as a Novel Source for the Secondary Metabolite Rutin.

Junker-Frohn LV, Lück M, Schmittgen S, Wensing J, Carraresi L, Thiele B, Groher T, Reimer JJ, Bröring S, Noga G, Jupke A, Schurr U, Usadel B, Wiese-Klinkenberg A, Wormit A.

ACS Omega. 2019 Nov 6;4(21):19071-19080. doi: 10.1021/acsomega.9b01462. eCollection 2019 Nov 19.


Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance.

Baum S, Reimer-Michalski EM, Bolger A, Mantai AJ, Benes V, Usadel B, Conrath U.

Plant Physiol. 2019 Oct;181(2):817-833. doi: 10.1104/pp.19.00673. Epub 2019 Jul 23.


Cell type specific transcriptional reprogramming of maize leaves during Ustilago maydis induced tumor formation.

Villajuana-Bonequi M, Matei A, Ernst C, Hallab A, Usadel B, Doehlemann G.

Sci Rep. 2019 Jul 15;9(1):10227. doi: 10.1038/s41598-019-46734-3.


Modeling Protein Destiny in Developing Fruit.

Belouah I, Nazaret C, Pétriacq P, Prigent S, Bénard C, Mengin V, Blein-Nicolas M, Denton AK, Balliau T, Augé S, Bouchez O, Mazat JP, Stitt M, Usadel B, Zivy M, Beauvoit B, Gibon Y, Colombié S.

Plant Physiol. 2019 Jul;180(3):1709-1724. doi: 10.1104/pp.19.00086. Epub 2019 Apr 23.


Fluctuating Light Interacts with Time of Day and Leaf Development Stage to Reprogram Gene Expression.

Schneider T, Bolger A, Zeier J, Preiskowski S, Benes V, Trenkamp S, Usadel B, Farré EM, Matsubara S.

Plant Physiol. 2019 Apr;179(4):1632-1657. doi: 10.1104/pp.18.01443. Epub 2019 Feb 4.


Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer.

Dong S, Lau V, Song R, Ierullo M, Esteban E, Wu Y, Sivieng T, Nahal H, Gaudinier A, Pasha A, Oughtred R, Dolinski K, Tyers M, Brady SM, Grene R, Usadel B, Provart NJ.

Plant Physiol. 2019 Apr;179(4):1893-1907. doi: 10.1104/pp.18.01216. Epub 2019 Jan 24.


Smut infection of perennial hosts: the genome and the transcriptome of the Brassicaceae smut fungus Thecaphora thlaspeos reveal functionally conserved and novel effectors.

Courville KJ, Frantzeskakis L, Gul S, Haeger N, Kellner R, Heßler N, Day B, Usadel B, Gupta YK, van Esse HP, Brachmann A, Kemen E, Feldbrügge M, Göhre V.

New Phytol. 2019 May;222(3):1474-1492. doi: 10.1111/nph.15692. Epub 2019 Feb 17.


MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis.

Schwacke R, Ponce-Soto GY, Krause K, Bolger AM, Arsova B, Hallab A, Gruden K, Stitt M, Bolger ME, Usadel B.

Mol Plant. 2019 Jun 3;12(6):879-892. doi: 10.1016/j.molp.2019.01.003. Epub 2019 Jan 9.


Computational aspects underlying genome to phenome analysis in plants.

Bolger AM, Poorter H, Dumschott K, Bolger ME, Arend D, Osorio S, Gundlach H, Mayer KFX, Lange M, Scholz U, Usadel B.

Plant J. 2019 Jan;97(1):182-198. doi: 10.1111/tpj.14179. Review.


TRM4 is essential for cellulose deposition in Arabidopsis seed mucilage by maintaining cortical microtubule organization and interacting with CESA3.

Yang B, Voiniciuc C, Fu L, Dieluweit S, Klose H, Usadel B.

New Phytol. 2019 Jan;221(2):881-895. doi: 10.1111/nph.15442. Epub 2018 Sep 13.


The Multifaceted Role of Pectin Methylesterase Inhibitors (PMEIs).

Wormit A, Usadel B.

Int J Mol Sci. 2018 Sep 21;19(10). pii: E2878. doi: 10.3390/ijms19102878. Review.


Identification of Key Enzymes for Pectin Synthesis in Seed Mucilage.

Voiniciuc C, Engle KA, Günl M, Dieluweit S, Schmidt MH, Yang JY, Moremen KW, Mohnen D, Usadel B.

Plant Physiol. 2018 Nov;178(3):1045-1064. doi: 10.1104/pp.18.00584. Epub 2018 Sep 18.


Monitoring of Plant Protein Post-translational Modifications Using Targeted Proteomics.

Arsova B, Watt M, Usadel B.

Front Plant Sci. 2018 Aug 17;9:1168. doi: 10.3389/fpls.2018.01168. eCollection 2018. Review.


Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris.

Vogel A, Schwacke R, Denton AK, Usadel B, Hollmann J, Fischer K, Bolger A, Schmidt MH, Bolger ME, Gundlach H, Mayer KFX, Weiss-Schneeweiss H, Temsch EM, Krause K.

Nat Commun. 2018 Jun 28;9(1):2515. doi: 10.1038/s41467-018-04344-z.


One-Step Lignocellulose Fractionation by using 2,5-Furandicarboxylic Acid as a Biogenic and Recyclable Catalyst.

Weidener D, Klose H, Leitner W, Schurr U, Usadel B, Domínguez de María P, Grande PM.

ChemSusChem. 2018 Jul 11;11(13):2051-2056. doi: 10.1002/cssc.201800653. Epub 2018 Jun 19.


Monitoring Polysaccharide Dynamics in the Plant Cell Wall.

Voiniciuc C, Pauly M, Usadel B.

Plant Physiol. 2018 Apr;176(4):2590-2600. doi: 10.1104/pp.17.01776. Epub 2018 Feb 27. Review. No abstract available.


Corrigendum: Towards recommendations for metadata and data handling in plant phenotyping.

Krajewski P, Chen D, Cwiek H, van Dijk ADJ, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap JP, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S.

J Exp Bot. 2018 Mar 24;69(7):1819. doi: 10.1093/jxb/ery006. No abstract available.


The role of COBRA-LIKE 2 function, as part of the complex network of interacting pathways regulating Arabidopsis seed mucilage polysaccharide matrix organization.

Ben-Tov D, Idan-Molakandov A, Hugger A, Ben-Shlush I, Günl M, Yang B, Usadel B, Harpaz-Saad S.

Plant J. 2018 May;94(3):497-512. doi: 10.1111/tpj.13871. Epub 2018 Mar 23.


How to make a tumour: cell type specific dissection of Ustilago maydis-induced tumour development in maize leaves.

Matei A, Ernst C, Günl M, Thiele B, Altmüller J, Walbot V, Usadel B, Doehlemann G.

New Phytol. 2018 Mar;217(4):1681-1695. doi: 10.1111/nph.14960. Epub 2018 Jan 4.


RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H.

Kranz A, Busche T, Vogel A, Usadel B, Kalinowski J, Bott M, Polen T.

BMC Genomics. 2018 Jan 6;19(1):24. doi: 10.1186/s12864-017-4415-x.


A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley.

Delventhal R, Rajaraman J, Stefanato FL, Rehman S, Aghnoum R, McGrann GRD, Bolger M, Usadel B, Hedley PE, Boyd L, Niks RE, Schweizer P, Schaffrath U.

BMC Plant Biol. 2017 Dec 4;17(1):232. doi: 10.1186/s12870-017-1178-0.


Life cycle assessment and sustainable engineering in the context of near net shape grown components: striving towards a sustainable way of future production.

Kämpfer C, Seiler TB, Beger AL, Jacobs G, Löwer M, Moser F, Reimer J, Trautz M, Usadel B, Wormit A, Hollert H.

Environ Sci Eur. 2017;29(1):27. doi: 10.1186/s12302-017-0125-x. Epub 2017 Oct 20.


The genetic architecture of photosynthesis and plant growth-related traits in tomato.

de Oliveira Silva FM, Lichtenstein G, Alseekh S, Rosado-Souza L, Conte M, Suguiyama VF, Lira BS, Fanourakis D, Usadel B, Bhering LL, DaMatta FM, Sulpice R, Araújo WL, Rossi M, de Setta N, Fernie AR, Carrari F, Nunes-Nesi A.

Plant Cell Environ. 2018 Feb;41(2):327-341. doi: 10.1111/pce.13084. Epub 2017 Nov 29.


De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.

Schmidt MH, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B.

Plant Cell. 2017 Oct;29(10):2336-2348. doi: 10.1105/tpc.17.00521. Epub 2017 Oct 12.


OrganoCat pretreatment of perennial plants: Synergies between a biogenic fractionation and valuable feedstocks.

Damm T, Grande PM, Jablonowski ND, Thiele B, Disko U, Mann U, Schurr U, Leitner W, Usadel B, Domínguez de María P, Klose H.

Bioresour Technol. 2017 Nov;244(Pt 1):889-896. doi: 10.1016/j.biortech.2017.08.027. Epub 2017 Aug 9.


Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives.

Schmutzer T, Bolger ME, Rudd S, Chen J, Gundlach H, Arend D, Oppermann M, Weise S, Lange M, Spannagl M, Usadel B, Mayer KFX, Scholz U.

J Biotechnol. 2017 Nov 10;261:37-45. doi: 10.1016/j.jbiotec.2017.07.006. Epub 2017 Jul 8. Review.


From plant genomes to phenotypes.

Bolger M, Schwacke R, Gundlach H, Schmutzer T, Chen J, Arend D, Oppermann M, Weise S, Lange M, Fiorani F, Spannagl M, Scholz U, Mayer K, Usadel B.

J Biotechnol. 2017 Nov 10;261:46-52. doi: 10.1016/j.jbiotec.2017.06.003. Epub 2017 Jun 9. Review.


Insights into cell wall structure of Sida hermaphrodita and its influence on recalcitrance.

Damm T, Pattathil S, Günl M, Jablonowski ND, O'Neill M, Grün KS, Grande PM, Leitner W, Schurr U, Usadel B, Klose H.

Carbohydr Polym. 2017 Jul 15;168:94-102. doi: 10.1016/j.carbpol.2017.03.062. Epub 2017 Mar 20.


High precision genome sequencing of engineered Gluconobacter oxydans 621H by combining long nanopore and short accurate Illumina reads.

Kranz A, Vogel A, Degner U, Kiefler I, Bott M, Usadel B, Polen T.

J Biotechnol. 2017 Sep 20;258:197-205. doi: 10.1016/j.jbiotec.2017.04.016. Epub 2017 Apr 19.


Metabolic Adaptation, a Specialized Leaf Organ Structure and Vascular Responses to Diurnal N2 Fixation by Nostoc azollae Sustain the Astonishing Productivity of Azolla Ferns without Nitrogen Fertilizer.

Brouwer P, Bräutigam A, Buijs VA, Tazelaar AO, van der Werf A, Schlüter U, Reichart GJ, Bolger A, Usadel B, Weber AP, Schluepmann H.

Front Plant Sci. 2017 Mar 31;8:442. doi: 10.3389/fpls.2017.00442. eCollection 2017.


Early metabolic and transcriptional variations in fruit of natural white-fruited Fragaria vesca genotypes.

Härtl K, Denton A, Franz-Oberdorf K, Hoffmann T, Spornraft M, Usadel B, Schwab W.

Sci Rep. 2017 Mar 22;7:45113. doi: 10.1038/srep45113.


Plant genome and transcriptome annotations: from misconceptions to simple solutions.

Bolger ME, Arsova B, Usadel B.

Brief Bioinform. 2018 May 1;19(3):437-449. doi: 10.1093/bib/bbw135.


Tomato facultative parthenocarpy results from SlAGAMOUS-LIKE 6 loss of function.

Klap C, Yeshayahou E, Bolger AM, Arazi T, Gupta SK, Shabtai S, Usadel B, Salts Y, Barg R.

Plant Biotechnol J. 2017 May;15(5):634-647. doi: 10.1111/pbi.12662. Epub 2016 Dec 27.


Measures for interoperability of phenotypic data: minimum information requirements and formatting.

Ćwiek-Kupczyńska H, Altmann T, Arend D, Arnaud E, Chen D, Cornut G, Fiorani F, Frohmberg W, Junker A, Klukas C, Lange M, Mazurek C, Nafissi A, Neveu P, van Oeveren J, Pommier C, Poorter H, Rocca-Serra P, Sansone SA, Scholz U, van Schriek M, Seren Ü, Usadel B, Weise S, Kersey P, Krajewski P.

Plant Methods. 2016 Nov 9;12:44. eCollection 2016.


Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping.

Thoen MP, Davila Olivas NH, Kloth KJ, Coolen S, Huang PP, Aarts MG, Bac-Molenaar JA, Bakker J, Bouwmeester HJ, Broekgaarden C, Bucher J, Busscher-Lange J, Cheng X, Fradin EF, Jongsma MA, Julkowska MM, Keurentjes JJ, Ligterink W, Pieterse CM, Ruyter-Spira C, Smant G, Testerink C, Usadel B, van Loon JJ, van Pelt JA, van Schaik CC, van Wees SC, Visser RG, Voorrips R, Vosman B, Vreugdenhil D, Warmerdam S, Wiegers GL, van Heerwaarden J, Kruijer W, van Eeuwijk FA, Dicke M.

New Phytol. 2017 Feb;213(3):1346-1362. doi: 10.1111/nph.14220. Epub 2016 Oct 4.


A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis.

Li Z, Omranian N, Neumetzler L, Wang T, Herter T, Usadel B, Demura T, Giavalisco P, Nikoloski Z, Persson S.

Plant Physiol. 2016 Oct;172(2):1334-1351. Epub 2016 Aug 26.


Genome-Wide Analysis of Yield in Europe: Allelic Effects Vary with Drought and Heat Scenarios.

Millet EJ, Welcker C, Kruijer W, Negro S, Coupel-Ledru A, Nicolas SD, Laborde J, Bauland C, Praud S, Ranc N, Presterl T, Tuberosa R, Bedo Z, Draye X, Usadel B, Charcosset A, Van Eeuwijk F, Tardieu F.

Plant Physiol. 2016 Oct;172(2):749-764. Epub 2016 Jul 19.


The Metabolic Signature of Biomass Formation in Barley.

Ghaffari MR, Shahinnia F, Usadel B, Junker B, Schreiber F, Sreenivasulu N, Hajirezaei MR.

Plant Cell Physiol. 2016 Sep;57(9):1943-60. doi: 10.1093/pcp/pcw117. Epub 2016 Jul 7.


Extensive Natural Variation in Arabidopsis Seed Mucilage Structure.

Voiniciuc C, Zimmermann E, Schmidt MH, Günl M, Fu L, North HM, Usadel B.

Front Plant Sci. 2016 Jun 7;7:803. doi: 10.3389/fpls.2016.00803. eCollection 2016.


Identification of RNA-binding Proteins in Macrophages by Interactome Capture.

Liepelt A, Naarmann-de Vries IS, Simons N, Eichelbaum K, Föhr S, Archer SK, Castello A, Usadel B, Krijgsveld J, Preiss T, Marx G, Hentze MW, Ostareck DH, Ostareck-Lederer A.

Mol Cell Proteomics. 2016 Aug;15(8):2699-714. doi: 10.1074/mcp.M115.056564. Epub 2016 Jun 8.


Streptomyces thermoautotrophicus does not fix nitrogen.

MacKellar D, Lieber L, Norman JS, Bolger A, Tobin C, Murray JW, Oksaksin M, Chang RL, Ford TJ, Nguyen PQ, Woodward J, Permingeat HR, Joshi NS, Silver PA, Usadel B, Rutherford AW, Friesen ML, Prell J.

Sci Rep. 2016 Feb 1;6:20086. doi: 10.1038/srep20086.


Plant Pathway Databases.

Jaiswal P, Usadel B.

Methods Mol Biol. 2016;1374:71-87. doi: 10.1007/978-1-4939-3167-5_4.


Highly Branched Xylan Made by IRREGULAR XYLEM14 and MUCILAGE-RELATED21 Links Mucilage to Arabidopsis Seeds.

Voiniciuc C, Günl M, Schmidt MH, Usadel B.

Plant Physiol. 2015 Dec;169(4):2481-95. doi: 10.1104/pp.15.01441. Epub 2015 Oct 19.


Temporal kinetics of the transcriptional response to carbon depletion and sucrose readdition in Arabidopsis seedlings.

Cookson SJ, Yadav UP, Klie S, Morcuende R, Usadel B, Lunn JE, Stitt M.

Plant Cell Environ. 2016 Apr;39(4):768-86. doi: 10.1111/pce.12642. Epub 2015 Dec 1.


Genotype-phenotype modeling considering intermediate level of biological variation: a case study involving sensory traits, metabolites and QTLs in ripe tomatoes.

Wang H, Paulo J, Kruijer W, Boer M, Jansen H, Tikunov Y, Usadel B, van Heusden S, Bovy A, van Eeuwijk F.

Mol Biosyst. 2015 Nov;11(11):3101-10. doi: 10.1039/c5mb00477b. Epub 2015 Sep 7.


MUCILAGE-RELATED10 Produces Galactoglucomannan That Maintains Pectin and Cellulose Architecture in Arabidopsis Seed Mucilage.

Voiniciuc C, Schmidt MH, Berger A, Yang B, Ebert B, Scheller HV, North HM, Usadel B, Günl M.

Plant Physiol. 2015 Sep;169(1):403-20. doi: 10.1104/pp.15.00851. Epub 2015 Jul 28.


Quantitative RT-PCR Platform to Measure Transcript Levels of C and N Metabolism-Related Genes in Durum Wheat: Transcript Profiles in Elevated [CO2] and High Temperature at Different Levels of N Supply.

Vicente R, Pérez P, Martínez-Carrasco R, Usadel B, Kostadinova S, Morcuende R.

Plant Cell Physiol. 2015 Aug;56(8):1556-73. doi: 10.1093/pcp/pcv079. Epub 2015 Jun 10.


Towards recommendations for metadata and data handling in plant phenotyping.

Krajewski P, Chen D, Ćwiek H, van Dijk AD, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap JP, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S.

J Exp Bot. 2015 Sep;66(18):5417-27. doi: 10.1093/jxb/erv271. Epub 2015 Jun 4. Erratum in: J Exp Bot. 2018 Mar 24;69(7):1819.


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