Original Research Articles: 152
2024
152. Tariq A, Meng M, Jiang X, Bolger A, Beier S, Buchmann JP, Fernie AR, Wen W, Usadel B (2024) In-depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of Camellia sinensis. Plant J. 2024 Jun 14. doi: 10.1111/tpj.16874. #
151. Nemati Z, Kazemi-Shahandashti SS, Garibay-Hernández A, Mock HP, Schmidt MH, Usadel B, Blattner FR. Metabolomic and transcriptomic analyses of yellow-flowered crocuses to infer alternative sources of saffron metabolites. BMC Plant Biol. 2024 May 7;24(1):369. doi: 10.1186/s12870-024-05036-1.
150. Serra Mari R, Schrinner S, Finkers R, Ziegler FMR, Arens P, Schmidt MH, Usadel B, Klau GW, Marschall T. Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data. Genome Biol. 2024 Jan 19;25(1):26. doi: 10.1186/s13059-023-03160-z.
2023.
149. Tiozon RJN, Sreenivasulu N, Alseekh S, Sartagoda KJD, Usadel B, Fernie AR. Metabolomics and machine learning technique revealed that germination enhances the multi-nutritional properties of pigmented rice. Commun Biol. 2023 Oct 2;6(1):1000. doi: 10.1038/s42003-023-05379-9.
148. Weil HL, Schneider K, Tschöpe M, Bauer J, Maus O, Frey K, Brilhaus D, Martins Rodrigues C, Doniparthi G, Wetzels F, Lukasczyk J, Kranz A, Grüning B, Zimmer D, Deßloch S, von Suchodoletz D, Usadel B, Garth C, Mühlhaus T. PLANTdataHUB: a collaborative platform for continuous FAIR data sharing in plant research. Plant J. 2023 Nov;116(4):974-988. doi: 10.1111/tpj.16474.
147 Qiu H, Zhang X, Zhang Y, Jiang X, Ren Y, Gao D, Zhu X, Usadel B, Fernie AR, Wen W. Depicting the genetic and metabolic panorama of chemical diversity in the tea plant. Plant Biotechnol J. 2023 Dec 4. doi: 10.1111/pbi.14241.
146. A Pandya, B Thiele, S Köppchen, A Zurita-Silva, B Usadel, F Fiorani (2023) Characterization of Bioactive Phenolic Compounds in Seeds of Chilean Quinoa (Chenopodium quinoa Willd.) Germplasm Agronomy 13 (8), 2170
145. Jayakodi M, Golicz AA, Kreplak J, Fechete LI, Angra D, Bednář P, Bornhofen E, Zhang H, Boussageon R, Kaur S, Cheung K, Čížková J, Gundlach H, Hallab A, Imbert B, Keeble-Gagnère G, Koblížková A, Kobrlová L, Krejčí P, Mouritzen TW, Neumann P, Nadzieja M, Nielsen LK, Novák P, Orabi J, Padmarasu S, Robertson-Shersby-Harvie T, Robledillo LÁ, Schiemann A, Tanskanen J, Törönen P, Warsame AO, Wittenberg AHJ, Himmelbach A, Aubert G, Courty PE, Doležel J, Holm LU, Janss LL, Khazaei H, Macas J, Mascher M, Smýkal P, Snowdon RJ, Stein N, Stoddard FL, Stougaard J, Tayeh N, Torres AM, Usadel B, Schubert I, O'Sullivan DM, Schulman AH, Andersen SU. The giant diploid faba genome unlocks variation in a global protein crop. Nature. 2023 Mar;615(7953):652-659. doi: 10.1038/s41586-023-05791-5.
144. Julca I, Mutwil-Anderwald D, Manoj V, Khan Z, Lai SK, Yang LK, Beh IT, Dziekan J, Lim YP, Lim SK, Low YW, Lam YI, Tjia S, Mu Y, Tan QW, Nuc P, Choo LM, Khew G, Shining L, Kam A, Tam JP, Bozdech Z, Schmidt M, Usadel B, Kanagasundaram YS, Alseekh S, Fernie A, Li HY, Mutwil M (2023) Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites. J Integr Plant Biol. 65(6):1442-1466 doi: 10.1111/jipb.13469
143. Muñoz P, Castillejo C, Gómez JA, Miranda L, Lesemann S, Olbricht K, Petit A, Chartier P, Haugeneder A, Trinkl J, Mazzoni L, Masny A, Zurawicz E, Ziegler FMR, Usadel B, Schwab W, Denoyes B, Mezzetti B, Osorio S, Sánchez-Sevilla JF, Amaya I (2023) QTL analysis for ascorbic acid content in strawberry fruit reveals a complex genetic architecture and association with GDP-L-galactose phosphorylase. Hortic Res. 10(3):uhad006. doi: 10.1093/hr/uhad006.
142. Lippi N, Senger E, Karhu S, Mezzetti B, Cianciabella M, Denoyes B, Sönmez DA, Fidelis M, Gatti E, Höfer M, Kafkas NE, Mazzoni L, McCallum S, Olbricht K, Orsucci S, Osorio S, Pinczinger D, Predieri S, Rokka S, Sánchez-Sevilla JF, Savini G, Soria C, Usadel B, Zucchi P, Chiara M. Development and Validation of a Multilingual Lexicon as a Key Tool for the Sensory Analyses and Consumer Tests of Blueberry and Raspberry Fruit. Agriculture. 2023; 13(2):314.
141. Pott DM, Durán-Soria S, Allwood JW, Pont S, Gordon SL, Jennings N, Austin C, Stewart D, Brennan RM, Masny A, Sønsteby A, Krüger E, Jarret D, Vallarino JG, Usadel B, Osorio S (2023) Dissecting the impact of environment, season and genotype on blackcurrant fruit quality traits. Food Chem. 2023 Feb 15;402:134360. doi: 10.1016/j.foodchem.2022.134360
2022
140 Hajheidari M, Gerlach N, Dorau K, Omidbakhshfard MA, Pesch L, Hofmann J, Hallab A, Ponce-Soto GY, Kuhalskaya A, Medeiros DB, Bourceret A; the RECONSTRUCT Consortium; Usadel B, Mayer J, Fernie A, Mansfeldt T, Sonnewald U, Bucher M (2022) Crop genetic diversity uncovers metabolites, elements, and gene networks predicted to be associated with high plant biomass yields in maize. PNAS Nexus. 1(3):pgac068. doi: 10.1093/pnasnexus/pgac068.
139. Liu J, Willick IR, Hiraki H, Forand AD, Lawrence JR, Swerhone GDW, Wei Y, Ghosh S, Lee YK, Olsen JE, Usadel B, Wormit A, Günl M, Karunakaran C, Dynes JJ, Tanino KK. Cold and exogenous calcium alter Allium fistulosum cell wall pectin to depress intracellular freezing temperatures. J Exp Bot. 2022 Jun 2;73(11):3807-3822.
138. Schrinner S, Serra Mari R, Finkers R, Arens P, Usadel B, Marschall T, Klau GW. Genetic polyploid phasing from low-depth progeny samples (2022) iScience. 25(6):104461. doi: 10.1016/j.isci.2022.104461
137. Reimer JJ, Shaaban B, Drummen N, Sanjeev Ambady S, Genzel F, Poschet G, Wiese-Klinkenberg A, Usadel B, Wormit A (2022). Capsicum Leaves under Stress: Using Multi-Omics Analysis to Detect Abiotic Stress Network of Secondary Metabolism in Two Species. Antioxidants (Basel). 11(4):671. doi: 10.3390/antiox11040671.
136. Powell AF, Feder A, Li J, Schmidt MH, Courtney L, Alseekh S, Jobson EM, Vogel A, Xu Y, Lyon D, Dumschott K, McHale M, Sulpice R, Bao K, Lal R, Duhan A, Hallab A, Denton AK, Bolger ME, Fernie AR, Hind SR, Mueller LA, Martin GB, Fei Z, Martin C, Giovannoni JJ, Strickler SR, Usadel B (2022) A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. Plant J. 110(6):1791-1810. doi: 10.1111/tpj.15770 #
135. Eiteneuer C, Velasco D, Atemia J, Wang D, Schwacke R, Wahl V, Schrader A, Reimer JJ, Fahrner S, Pieruschka R, Schurr U, Usadel B, Hallab A (2022). GXP: Analyze and Plot Plant Omics Data in Web Browsers. Plants (Basel). 11(6):745. doi: 10.3390/plants11060745
134. Liu J, Willick IR, Hiraki H, Forand AD, Lawrence JR, Swerhone GDW, Wei Y, Ghosh S, Lee YK, Olsen JE, Usadel B, Wormit A, Günl M, Karunakaran C, Dynes JJ, Tanino KK (2022) Cold and exogenous calcium alter Allium fistulosum cell wall pectin to depress intracellular freezing temperatures. J Exp Bot. 73(11):3807-3822. doi: 10.1093/jxb/erac108.
133. van Rengs WMJ, Schmidt MH, Effgen S, Le DB, Wang Y, Zaidan MWAM, Huettel B, Schouten HJ, Usadel B, Underwood CJ (2022) A chromosome scale tomato genome built from complementary PacBio and Nanopore sequences alone reveals extensive linkage drag during breeding. Plant J. 110(2):572-588. doi: 10.1111/tpj.15690.
132.Hoopes G, Meng X, Hamilton JP, Achakkagari SR, de Alves Freitas Guesdes F, Bolger ME, Coombs JJ, Esselink D, Kaiser NR, Kodde L, Kyriakidou M, Lavrijssen B, van Lieshout N, Shereda R, Tuttle HK, Vaillancourt B, Wood JC, de Boer JM, Bornowski N, Bourke P, Douches D, van Eck HJ, Ellis D, Feldman MJ, Gardner KM, Hopman JCP, Jiang J, De Jong WS, Kuhl JC, Novy RG, Oome S, Sathuvalli V, Tan EH, Ursum RA, Vales MI, Vining K, Visser RGF, Vossen J, Yencho GC, Anglin NL, Bachem CWB, Endelman JB, Shannon LM, Strömvik MV, Tai HH, Usadel B, Buell CR, Finkers R (2022) Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol Plant. 15(3):520-536.
2021
131. Hadizadeh Esfahani A, Maß J, Hallab A, Schuldt BM, Nevarez D, Usadel B, Ott MC, Buer B, Schuppert A (2021) Plant PhysioSpace: a robust tool to compare stress response across plant species. Plant Physiol. 187(3):1795-1811
130. Reimer JJ, Thiele B, Biermann RT, Junker-Frohn LV, Wiese-Klinkenberg A, Usadel B, Wormit A (2021). Tomato leaves under stress: a comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species. Plant Mol Biol. 107(3):177-206
129. Genzel F, Dicke MD, Junker-Frohn LV, Neuwohner A, Thiele B, Putz A, Usadel B, Wormit A, Wiese-Klinkenberg A (2021) Impact of Moderate Cold and Salt Stress on the Accumulation of Antioxidant Flavonoids in the Leaves of Two Capsicum Cultivars J Agric Food Chem. 69(23):6431-6443.
128. De-la-Cruz IM, Hallab A, Olivares-Pinto U, Tapia-López R, Velázquez-Márquez S, Piñero D, Oyama K, Usadel B, Núñez-Farfán J (2021) Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae). Sci Rep. 11(1):882. doi:
2020
127. Schrinner SD, Mari RS, Ebler J, Rautiainen M, Seillier L, Reimer JJ, Usadel B, Marschall T, Klau GW (2020) Haplotype threading: accurate polyploid phasing from long reads. Genome Biol. 21(1):252. doi: 10.1186/s13059-020-02158-1.
126. Fort A, McHale M, Cascella K, Potin P, Usadel B, Guiry MD, Sulpice R (2020) Foliose Ulva Species Show Considerable Inter-Specific Genetic Diversity, Low Intra-Specific Genetic Variation, and the Rare Occurrence of Inter-Specific Hybrids in the Wild. J Phycol. 57(1):219-233 doi: 10.1111/jpy.13079.
125. Vittori VD, Bitocchi E, Rodriguez M, Alseekh S, Bellucci E, Nanni L, Gioia T, Marzario S, Logozzo G, Rossato M, De Quattro C, Murgia ML, Ferreira JJ, Campa A, Xu C, Fiorani F, Sampathkumar A, Fröhlich A, Attene G, Delledonne M, Usadel B, Fernie AR, Rau D, Papa R (2020) Pod indehiscence in common bean is associated to the fine regulation of PvMYB26. J Exp Bot. 72(5):1617-1633 doi: 10.1093/jxb/eraa553.
124. Yang B, Hofmann F, Usadel B, Voiniciuc C (2020) Seed hemicelluloses tailor mucilage properties and salt tolerance New Phytol.229(4):1946-1954 doi: 10.1111/nph.17056.
123. Zhang W, Luo C, Scossa F, Zhang Q, Usadel B, Fernie AR, Mei H, Wen W (2021) A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants. Plant Journal doi: https://doi.org/10.1111/tpj.15051
122 Alonso D, Gramazio P, Plazas M, Ferrante P, Schmidt M, Diez-Niclós MJ, Usadel B, Giuliano G, Prohens J (2020) SILEX: A fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species.
Plant Methods 16: 110
121.Zhang W, Zhang Y, Qiu H, Guo Y, Wan H, Zhang X, Scossa F, Alseekh S, Zhang Q, Wang P, Xu L, Schmidt MH, Jia X, Li D, Zhu A, Guo F, Chen W, Ni D, Usadel B, Fernie AR, Wen W (2020). Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties. Nat Commun. 2020;11(1):3719. doi:10.1038/s41467-020-17498-6
120. Pfaff J, Denton AK, Usadel B, Pfaff C (2020) Phosphate starvation causes different stress responses in the lipid metabolism of tomato leaves and roots. Biochim Biophys Acta Mol Cell Biol Lipids. 1865(9):158763. doi: 10.1016/j.bbalip.2020.158763.
119. Roch L, Prigent S, Klose H, Cakpo CB, Beauvoit B, Deborde C, Fouillen L, van Delft P, Jacob D, Usadel B, Dai Z, Génard M, Vercambre G, Colombié S, Moing A, Gibon Y (2020) Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species. J Exp Bot. 71 (19), 5823-5836. doi: 10.1093/jxb/eraa302.
118 Widzgowski J, Vogel A, Altrogge L, Pfaff J, Schoof H, Usadel B, Nedbal L, Schurr U, Pfaff C (2020) High light induces species specific changes in the membrane lipid composition of Chlorella. Biochem J. 2020;477(13):2543-2559. doi:10.1042/BCJ20200160
117. Tohge T, Scossa F, Wendenburg R, Frasse P, Balbo I, Watanabe M, Alseekh S, Jadhav SS, Delfin JC, Lohse M, Giavalisco P, Usadel B, Zhang Y, Luo J, Bouzayen M, Fernie AR.(2020) Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex. Mol Plant. ;13:1027-1046. doi:10.1016/j.molp.2020.04.004
116. Borlinghaus J, Bolger A, Schier C, Vogel A, Usadel B, Gruhlke MC, Slusarenko AJ (2020) Genetic and molecular characterization of multicomponent resistance of Pseudomonas against allicin. Life Sci Alliance. Mar 31;3(5).
2019
115. Vicente R, Bolger AM, Martínez-Carrasco R, Pérez P, Gutiérrez E, Usadel B, Morcuende R. De Novo Transcriptome Analysis of Durum Wheat Flag Leaves Provides New Insights Into the Regulatory Response to Elevated CO(2) and High Temperature (2019). Front Plant Sci. 2019 Dec 6;10:1605. doi: 10.3389/fpls.2019.01605.
114. 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 (2019). Transcriptomic and proteomic data in developing tomato fruit. Data Brief. Dec 17;28:105015. doi: 10.1016/j.dib.2019.105015.
113. 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 (2019) Tomato's Green Gold: Bioeconomy Potential of Residual Tomato Leaf Biomass as a Novel Source for the Secondary Metabolite Rutin. ACS Omega 4(21):19071-19080.
112. Baum S, Reimer-Michalski EM, Bolger A, Mantai AJ, Benes V, Usadel B, Conrath U (2019) Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance. Plant Physiol. 181:817-833.
111. Villajuana-Bonequi M, Matei A, Ernst C, Hallab A, Usadel B, Doehlemann G. Cell type specific transcriptional reprogramming of maize leaves during Ustilago maydis induced tumor formation. Sci Rep. 2019 Jul 15;9(1):10227.
110. Belouah I, Nazaret C, Pétriacq P, Prigent S, Bénard C, Mengin V, Blein-Nicolas M, Denton AK, Balliau T, Augé S, Bouchez O, Mazat J-P, Stitt M, Usadel B, Zivy M, Beauvoit B, Gibon Y, Colombié S (2019) Modeling protein destiny in developing tomato fruit. Plant Physiology 180(3):1709-1724 https://doi.org/10.1104/pp.19.00086
109.Schneider T, Bolger A, Zeier J, Preiskowski S, Benes V, Trenkamp S, Usadel B, Farre EM, Matsubara S (2019) Fluctuating Light Interacts with Time of Day and Leaf Development Stage to Reprogram Gene Expression. Plant Physiol. 179(4):1632-1657 doi: 10.1104/pp.18.01443.
108. Dong S, Lau V, Song R, Ierullo M, Esteban E, Wu Y, Sivieng T, Nahal-Bose H, Gaudinier A, Pasha A, Rose Oughtred R, Dolinski K, Tyers M, Brady S, Grene R, Usadel B, Provart N (2019) Structure-based Protein-Protein Interaction Prediction and New Tools for Exploring these Interactions, Plant Physiology, 179(4):1893-1907
107. Courville K, Frantzeskakis L, Gul S, Haeger N; Kellner R, Hessler N; Day B, Usadel B, Gupta Y, van Esse P, Brachmann A, Kemen E., Feldbrugge M, Göhre V. (2019) Smut infection of perennial hosts: the genome and the transcriptome of the Brassicaceae smut fungus Thecaphora thlaspeos reveal functionally conserved and novel effectors New Phytologist, 222(3):1474-1492
106. Schwacke R, Ponce-Soto GY, Krause K, Bolger AM, Arsova B, Hallab A, Gruden K, Stitt M, Bolger ME, Usadel B (2019) MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis. Molecular Plant 12(6):879-892 #
2018
105. Voiniciuc C, Engle KA, Günl M, Dieluweit S, Schmidt MH, Yang JY, Moremen KW, Mohnen D, Usadel B (2018) Identification of Key Enzymes for Pectin Synthesis in Seed Mucilage Plant Physiology 178(3):1045-1064 https://doi.org/10.1104/pp.18.00584
104 Yang B, Voiniciuic C, Fu L, Dieluweit S, Klose H, Usadel B (2018) TRM4 is essential for cellulose deposition in Arabidopsis seed mucilage by maintaining cortical microtubule organization and interacting with CESA3. New Phytologist 221: 881–895 https://doi.org/10.1111/nph.15442
103 Vogel A, Schwacke R, Denton AK, Usadel B, Hollmann J, Fischer K, Bolger A, Schmidt HMW, Bolger ME, Gundlach H, Mayer KFX, Weiss-Schneeweiss H, Temsch EM, Krause K (2018) Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris Nature Communicationsvolume 9: 2515 +&
102. Weidener D, Klose H, Leitner W, Schurr U, Usadel B, Domínguez de María P, Grande PM (2018) One-step lignocellulose fractionation using 2,5-furandicarboxylic acid as biogenic and recyclable catalyst. ChemSusChem. 11:2051-2056 doi: 10.1002/cssc.201800653.
101. Matei A, Ernst C, Thiele B, Günl M, Altmüller J, Valbot V, Usadel B, Doehlemann G (2018) How to make a tumour: cell type specific dissection of Ustilago maydis-induced tumour development in maize leaves. New Phytologist 217:1681-1695
100. Kranz A, Busche T, Vogel A, Usadel B, Kalinowski J, Bott M, Polen T (2018) RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H. BMC Genomics. 19(1):24. doi: 10.1186/s12864-017-4415-x.
2017
99. 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. A (2017) Comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley. BMC Plant Biol. 17:232. doi: 10.1186/s12870-017-1178-0.
98. de Oliveira Silva FM, Lichtenstein G, Alseekh S, Rosado-Souza L, Conte M, Fuentes Suguiyama V, Silvestre Lira B, Fanourakis D, Usadel B, Lopes Bhering L, DaMatta FM, Sulpice R, Auraújo WL, Rossi M, de Setta Nathalia, Fernie AR, Carrari F, Nunes-Nesi A (2017) The Genetic Architecture of Photosynthesis and Plant Growth Related Traits in Tomato. Plant Cell Environ. 41(2):327-341 https://doi.org/10.1111/pce.13084
97. Schmidt MHW, 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 (2017) De novo assembly of a new Solanum pennellii accession using Nanopore sequencing. Plant Cell Oct;29(10):2336-2348 https://doi.org/10.1105/tpc.17.00521 #~
96. Damm T, Grande PM, Jablonowski ND, Thiele B, Disko U, Mann U, Schurr U, Leitner W, Usadel B, Dominguez de Maria P, Klose H (2017) OrganoCat pretreatment of perennial plants: Synergies between a biogenic fractionation and valuable feedstocks. Bioresource Technology 244,889-896 doi: 10.1016/j.biortech.2017.08.027
95. Kranz A, Vogel A, Degner U, Kiefler I, Bott M, Usadel B, Polen T (2017) High precision genome sequencing of engineered G. oxydans 621H by combining long nanopore and short accurate Illumina reads. J Biotechnol. 258:197-205 doi: 10.1016/j.jbiotec.2017.04.016.
94. Damm T, Pattathil S, Günl M, Jablonowski ND, O'Neill M, Grün KS, Grande PM, Leitner W, Schurr U, Usadel B, Klose H (2017) Insights into cell wall structure of Sida hermaphrodita and its influence on recalcitrance. Carbohydrate Polymers 168: 94–102
93. Brouwer P,Bräutigam A,Buijs VA, Tazelaar AOE,van der Werf A,Schlüter U,Reichart G-J, Bolger A,Usadel B,Weber APM,Schluepmann H (2017) 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. Frontiers in Plant Science 8:442. doi: 10.3389/fpls.2017.00442
92. Härtl K, Denton A, Franz-Oberdorf K, Hoffmann T, Spornraft M, Usadel B, Schwab W (2017) Early metabolic and transcriptional variations in fruit of natural white-fruited Fragaria vesca genotypes. Scientific reports 7:45113 doi: 10.1038/srep45113
91. Klap C, Yeshayahou C, Bolger AM, Arazi T, Gupta SK, Shabtai S, Usadel B, Salts Y, Barg R (2017) Tomato facultative parthenocarpy results from SlAGAMOUS-LIKE 6 loss of function Plant Biotechnology Journal 15:634-647
2016
90. 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 S-A, Scholz U, van Schriek M, Seren Ü, Usadel B, Weise S, Kersey P, Krajewski P (2016) Measures for interoperability of phenotypic data: minimum information requirements and formatting Plant Methods 12:44
89. 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 (2017) Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping. New Phytol. 213:1346-1362. doi: 10.1111/nph.14220.
88. Li Z, Omranian N, Neumetzler L, Wang T, Herter T, Usadel B, Demura T, Giavalisco P, Nikoloski Z, Persson S (2016) A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis Plant Physiol. 172:1334-1351 doi:10.1104/pp.16.01100
87. Millet E, Welcker C, Kruijer W, Negro S, Nicolas S, Praud S, Ranc N, Presterl T, Tuberosa R, Bedo Z, Draye X, Usadel B, Charcosset A, van Eeuwijk F, Tardieu F, Coupel-Ledru A, Bauland C (2016) Genome-wide analysis of yield in Europe: allelic effects as functions of drought and heat scenarios Plant Physiol. 172:749-764; doi:10.1104/pp.16.00621
86. Ghaffari MR, Shahinnia F, Usadel B, Junker B, Schreiber F, Sreenivasulu N, Hajirezaei MR (2016) The metabolic signature of biomass formation in barley. Plant & Cell Physiology 57:1943-60. doi: 10.1093/pcp/pcw117
85. Liepelt A, Naarmann-de Vries IS, Simons N, Eichelbaum K, Foehr S, Archer SK, Castello A, Usadel B, Krijgsveld J, Preiss T, Marx G, Hentze MW, Ostareck DH, Ostareck-Lederer A (2016) Identification of RNA-binding proteins in macrophages by interactome capture Mol Cell Proteomics 15:2699-714 doi: mcp.M115.056564.
84. Voiniciuc C, Zimmermann E, Schmidt MHW, Günl M, Fu L, North H, Usadel B (2016) Extensive Natural Variation in Arabidopsis Seed Mucilage Structure. Frontiers in Plant Sciences 7:803 #
83. MacKellar D, Lieber L, Norman JS, Bolger A, Tobin C, Murray JW, Oksaksin M, Chang RL, Ford TJ, Nguyen PQ, Woodward J, Permingeat H, Joshi N, Silver P, Usadel B, Rutherford WA, Friesen ML (2016) Streptomyces Thermoautotrophicus Does Not Fix Nitrogen. Scientific Reports. 10, 1055-1060
2015
82. Voiniciuc C, Guenl M, Schmidt MH, Usadel B (2015) Highly Branched Xylan Made by IRX14 and MUCI21 Links Mucilage to Arabidopsis Seeds. Plant Physiol. 169:2481-95 doi pp.01441.2015. #
81. Cookson SJ, Yadav UP, Klie S, Morcuende R, Usadel B, Lunn JE, Stitt M (2016) Temporal kinetics of the transcriptional response to carbon depletion and sucrose readdition in Arabidopsis seedlings. Plant Cell Environ. 39:768-86
80. Wang H, Paulo J, Kruijer W, Boer M, Jansen H, Tikunov Y, Usadel B, van Heusden S, Bovy A, van Eeuwijk F. (2015) Genotype-phenotype modeling considering intermediate level of biological variation: a case study involving sensory traits, metabolites and QTLs in ripe tomatoes. Mol Biosyst. 11:3101-10
79. Voiniciuc C, Schmidt MH, Berger A, Yang B, Ebert B, Scheller HV, North HM, Usadel B, Guenl M (2015) MUCI10 Produces Galactoglucomannan That Maintains Pectin and Cellulose Architecture in Arabidopsis Seed Mucilage. Plant Physiol.169:403-20
78. Vicente R, Pérez P, Martínez-Carrasco R, Usadel B, Kostadinova S, Morcuende R (2015) 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 N Supplies Plant Cell Physiol 56:1556-73
77. Krajewski P, Chen D, Ćwiek 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 (2015) Towards recommendations for metadata and data handling in plant phenotyping J. Exp. Bot. 66: 5417-5427.
76. Klose H, Günl M, Usadel B, Fischer R, Commandeur U (2015) Cell wall modification in tobacco by differential targeting of recombinant endoglucanase from Trichoderm reesei. BMC Plant Biol. 15:54.
75. Lang V, Usadel B, Obermeyer G (2015) De novo sequencing and analysis of the lily pollen transcriptome - an open access data source for an orphan plant species. Plant Molecular Biology 87:69-80.
2014
74. Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstei G, Fich EA, Conte M, Keller, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N,. van Ham RCHJ, Klein Lankhorst R, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JCK, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B**, Fernie AR (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii Nature Genetics, 4:1034-8 ~
73. Löhrer M, Vogel A, Huettel B, Reinhardt R, Benes V, Duplessis S, Usadel B, Schaffrath U (2014) On the current status of Phakopsora pachyrhizi genome sequencing Front. Plant Sci. 5:377 doi: 10.3389/fpls.2014.00377
72. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: A flexible trimmer for Illumina Sequence Data, Bioinformatics, 30 (15): 2114-2120. #~
71. Ito J, Herter T, Baidoo EE, Lao J, Vega-Sánchez ME, Michelle Smith-Moritz A, Adams PD, Keasling JD, Usadel B, Petzold CJ, Heazlewood JL. Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry (2014). Anal Biochem. 448, 14-22
70. Lohse M, Nagel A, Herter T, May P, Schroda M, Zrenner R, Tohge T, Fernie AR, Stitt M, Usadel B (2014) Mercator: A fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environ. 37(5):1250-8 #
69. Ramsak Z, Baebler S, Rotter A, Korbar M, Mozetic I, Usadel B, Gruden K (2014) GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology. Nucleic Acids Research 42:D1167-75
2013
68. Lee YP, Giorgi FM, Lohse M, Kvederaviciute K, Klages S, Usadel B, Meskiene I, Reinhardt R, Hincha DK (2013) Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum). BMC Genomics. 14:793.
67. Muller K, Levesque-Tremblay G, Fernande A, Wormit A, Bartels S, Usadel B, Kermode A (2013) Overexpression of a pectin methylesterase inhibitor in Arabidopsis thaliana leads to altered growth morphology of the stem and defective organ separation. Plant signaling & behavior 8:e26464
66. Silvar C, Perovic D, Nussbaumer T, Spannagl M, Usadel B, Casas A, Igartua E, Ordon F (2013) Towards positional isolation of three quantitative trait Loci conferring resistance to powdery mildew in two spanish barley landraces. PLoS One. 8:e67336.
65. Koenig D, Jiménez-Gómez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, Tohge T, Bolger A,Schneeberger K,Ossowski S,Lanz V, Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D, Usadel B, Fernie AR, Peng J, Sinha NR, Maloof JN (2013) Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato PNAS 110:E2655-62
64. Matsubaa Y, Nguyena THH, Wiegert K, Falara V, Gonzales-Vigil E, Leong B, Schäfer P, Kudrna D, Wing RA, Bolger AM, Usadel B, Tissier A, Fernie AR, Barry CS, Pichersky E (2013) Evolution of a Complex Locus for Terpene Biosynthesis in Solanum. Plant Cell 25:2022-2036
63. Li J-W, Bolser D, Manske M, Giorgi FM , Vyahhi N, Usadel B, Clavijo BJ, Chan TF, Wong N, Zerbino D, Schneider MV (2013) The NGS WikiBook: a dynamic collaborative online training effort with long term sustainability. Briefings in Bioinformatics 14:548-55.
62. Pal SK, Liput M, Piques M, Ishihara H, Obata T, Martins MCM, Sulpice R,van Dongen JT, Fernie AR, Yadav UP, Lunn JE, Usadel B, Stitt M (2013) Diurnal changes of polysome loading track sucrose content in the rosette of wildtype Arabidopsis and the starchless pgm mutant Plant Physiol 162:1246-1265
61. Klose H, Günl M, Usadel B, Fischer R, Commandeur U (2013) Ethanol inducible expression of a mesophilic cellulase avoids adverse effects on plant development. Biotechnol Biofuels. 6:53
60. Müller K, Levesque-Tremblay G, Bartels S, Weitbrecht K, Wormit A, Usadel B, Haughn G, Kermode AR (2013) Demethylesterification of cell wall pectins in Arabidopsis thaliana plays a role in seed germination Plant Physiology, 161:305-16
2012
59. Friedel S, Usadel B, von Wirén N, Sreenivasulu N (2012) Reverse engineering: a key component of systems biology to unravel global abiotic stress cross-talk. Front Plant Sci. 2012;3:294.
58. Araújo WL, Tohge T, Osorio S, Lohse M, Balbo I, Krahnert I, Sienkiewicz-Porzucek A, Usadel B, Nunes-Nesi A, Fernie AR. (2012) Antisense Inhibition of the 2-Oxoglutarate Dehydrogenase Complex in Tomato Demonstrates Its Importancefor Plant Respiration and during Leaf Senescence and Fruit Maturation. Plant Cell, 24:2328-51.
57. Neumetzler L, Humphrey T, Lumba S, Snyder S, Yeats TH, Usadel B, Vasilevski A, Patel J, Rose JKC, Persson S, Bonetta D (2012) The FRIABLE1 gene product affects cell adhesion in Arabidopsis. PLOS ONE, 7:e42914
56. Gouws L, Botes E, Wiese AJ, Trenkamp S, Torres-Jerez I, Tang Y, Hills PN, Usadel B, Lloyd JR, Fernie A, Kossmann J, Van Der Merwe MJ (2012) The plant growth promoting substance, lumichrome, mimics starch and ethylene-associated symbiotic responses in lotus and tomato roots. Frontiers in Plant Science, 3:120
55. Lohse M, Bolger A, Nagel A, Fernie A, Lunn J, Stitt M, Usadel B (2012) Robina: A user-friendly, integrated software solution for RNA-Seq based transcriptomics. Nucleic Acids Research, 40:W622-7 #
54. Vasilevski A, Giorgi FM, Bertinetti L, Usadel B (2012) LASSO modeling of the Arabidopsis thaliana seed/seedling Transcriptome: a model case for detection of novel mucilage and pectin metabolism genes. Molecular Biosystems, 8:2566-74. #
53. Poorter H, Fiorani F, Stitt M, Schurr U, Finck A, Gibon Y, Usadel B, Munns R, Atkin O, Tardieu F, Pons T (2012) The art of growing plants for experimental purposes; a practical guide for the plant biologist. Functional Plant Biology, 39:821-838.
52. Riegler H, Herter T, Grishkovskaya I, Lude A, Ryngajllo M, Bolger ME, Essigmann B, Usadel B (2012) Crystal structure and functional characterisation of a glucosamine-6-phosphate N-acetyltransferase from Arabidopsis thaliana. Biochemical Journal, 443:427-437 #
2011
51. Li J-W, Robison K, Martin M, Sjödin A, Usadel B, Young M, Olivares EC, Bolser DM (2011) The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis. Nucleic acid research, 40:D1313-D1317
50. Licausi F, Giorgi FM, Schmälzlin E, Usadel B, Perata P, van Dongen JT, Geigenberger P (2011) HRE-Type Genes Are Regulated By Growth-Related Changes In Internal Oxygen Concentrations During The Normal Development Of Potato (Solanum tuberosum) Tubers. Plant and Cell physiology, 52:1957-72
49. Steinhauser M-C, Steinhauser D, Gibon Y, Bolger M, Arrivault S, Usadel B, Zamir D, Fernie AR, Stitt M (2011) Identification of Enzyme Activity Quantitative Trait Loci in a Solanum lycopersicum x Solanum pennellii introgression line population. Plant Physiology, 157:998-1014
48. Ryngajllo M, Childs L, Lohse M, Giorgi FM, Lude A, Selbig J, Usadel B (2011) SLocX: Predicting subcellular localization of Arabidopsis proteins leveraging gene expression data. Front. Plant Sci., 2:43 #
47. Osorio S, Alba R, Damasceno CMB, López-Casado G, Lohse M, Zanor MI, Tohge T, Usadel B, Rose JKC,Fei Z, Giovannoni JJ, Fernie AR (2011) 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, 157:405-25
46. Rautengarten C, Ebert B, Herter T, Petzold CJ, Ishii T, Mukhopadhyay A, Usadel B, Scheller HV (2011) The Interconversion of UDP-Arabinopyranose and UDP-Arabinofuranose Is Indispensable for Plant Development in Arabidopsis. Plant Cell, 23:1373-90
45. Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S (2011) PlaNet: Combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell, 23:895-910
44. Krueger S, Giavalisco P, Krall L, Steinhauser M-C, Büssis D, Usadel B, Flügge U-I, Fernie AR, Willmitzer L, Steinhauser, D (2011) A topological map of the compartmentalized Arabidopsis thaliana leaf metabolome. Plos One, 6:e17806
43. Araújo WL, Nunes-Nesi A, Osorio S, Usadel B, Fuentes D, Nagy R, Balbo I, Lehmann M, Studart-Witkowski C, Tohge T, Martinoia E, Jordana X, Damatta FM, Fernie AR (2011) Antisense Inhibition of the Iron-Sulphur Subunit of Succinate Dehydrogenase Enhances Photosynthesis and Growth in Tomato via an Organic Acid-Mediated Effect on Stomatal Aperture. Plant Cell, 23:600-27
42. Osorio S, Bombarely A, Giavalisco P, Usadel B, Stephens C, Aragüez I, Medina-Escobar N, Botella MA, Fernie AR, Valpuesta V (2011) Highly coordinated defense signaling triggered by partially demethylated oligogalacturonides. Journal of Experimental Botany, 62:2855-73
2010
41. Giorgi FM, Bolger A, Lohse M, Usadel B (2010) Algorithm-driven Artifacts in median polish summarization of Microarray data. BMC Bioinformatics, 11:553 #~
40. Sulpice R, Trenkamp S, Steinfath M, Usadel B, Gibon Y, Witucka-Wall H, Pyl ET, Tschoep H, Steinhauser MC, Guenther M, Hoehne M, Rohwer JM, Altmann T, Fernie AR, Stitt M (2010) Network Analysis of Enzyme Activities and Metabolite Levels and their Relation to Biomass in a Large Panel of Arabidopsis Accessions. Plant Cell, 22:2872-93
39. Sreenivasulu N, Radchuk V, Alawady A, Borisjuk L, Weier D, Staroske N, Fuchs J, Miersch O, Strickert M, Usadel B, Wobus U, Grimm B, Weber H, Weschke W (2010) Deregulation of abscisic acid contents causes abnormal endosperm development in the barley mutant seg8. Plant Journal, 64:589-603
38. Nashilevitz S, Melamed-Bessudo C, Izckovich Y, Rogachev I, Osorio S, Itkin M, Adato A, Pankartov I, Hirschberg J, Fernie AR, Wolf S, Usadel B, Levy A, Rumeau D, Aharoni A (2010) The ORR Gene Links The Plastid NAD(P)H Dehydrogenase Complex Activity to Central and Specialized Metabolism During Tomato Fruit Maturation. Plant Cell, 22:1977-97
37. Lohse M, Nunes-Nesi A, Krueger P, Nagel A, Hannemann J, Giorgi FM, Childs L, Osorio S, Walther D, Selbig J, Sreenivasulu N, Stitt M, Fernie AR, Usadel B (2010) Robin: An intuitive wizard application for R-based expression microarray quality assessment and analysis. Plant Physiology, 153:642-51 #
36. Dorn KV, Willmund F, Schwarz C, Henselmann C, Pohl T, Heß B, Veyel D, Usadel B, Friedrich T, Nickelsen J, Schroda M. (2010) Chloroplast DnaJ-like proteins 3 and 4 (CDJ3/4) from Chlamydomonas reinhardtii contain redox-active Fe-S clusters and interact with stromal HSP70B. Biochem Journal, 427:205-15
35. Mutwil M, Usadel B, Schutte M, Loraine A, Ebenhoh O, Persson S (2010) Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm. Plant Physiol, 152: 29-43
2009
34. Piques M, Schulze WX, Höhne M, Usadel B, Gibon Y, Rohwer J, Stitt M (2009) Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Molecular Systems Biology, 5:314
33. Garcia V, Stevens R, Gila L,Gilbert L, Gest N, Petit J, Faurobert M, Maucourt M, Deborde C, Moing A, Poessel J-L, Jacob D, Bouchet J-P, Giraudel J-L, Gouble B, Page D, Alhagdow M, Massot C, Gautier H, Lemaire-Chamleya M, de Daruvarg A, Rolin D, Usadel B, Lahayed M, Causse M, Baldet P Rothan C (2009) An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato. Compte Rendu Biologie, 332: 1007-1021
32. Rotter A, Camps C, Lohse M, Kappel C, Pilati S, Hren M, Stitt M, Coutos-Thévenot P, Moser C, Usadel B, Delrot S, Gruden K. (2009) Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending MapMan ontology for grapevine. BMC Plant Biol., 9:104
31. Sulpice R, Pyl ET, Ishihara H, Trenkamp S, Steinfath M, Witucka-Wall H, Gibon Y, Usadel B, Poree F, Piques MC, Von Korff M, Steinhauser MC, Keurentjes JJ, Guenther M, Hoehne M, Selbig J, Fernie AR, Altmann T, Stitt M. (2009) Starch as a major integrator in the regulation of plant growth. PNAS, 106:10348-53
30. Zanor MI, Osorio S, Nunes-Nesi A, Carrari F, Lohse M, Usadel B, Kuhn C, Bleiss W, Giavalisco P, Willmitzer L, Sulpice R, Zhou YH, Fernie AR (2009) RNA interference of LIN5 in Solanum lycopersicum confirms its role in controlling Brix content, uncovers the influence of sugars on the levels of fruit hormones and demonstrates the importance of sucrose cleavage for normal fruit development and fertility. Plant Physiology, 150:1204-18
29. Wang H, Schauer N, Usadel B, Frassea P, Zouinea M, Hernould M, Latché A, Pecha J-C, Fernie AR, Bouzayen M (2009) Regulatory Features Underlying Pollination-dependent and independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling. Plant Cell, 21:1428-52
28. Hannemann J, Poorter H, Usadel B, Bläsing OE, Finck A, Tardieu F, Atkin O, Pons T, Stitt M, Gibon Y (2009) Xeml Lab: a software suite for a standardised description of the growth environment of plants. Plant Cell Environment, 32:1185-200.
27. Howell K, Narsai R, Carroll A, Ivanova A, Lohse M, Usadel B, Millar AH, Whelan J (2009) Mapping metabolic and transcript temporal switches during germination in Oryza sativa highlights specific transcription factors and the role of RNA instability in the germination process. Plant Physiology, 149:961-80
2008
26. Crowhurst RN, Gleave AP, MacRae EA, Ampomah-Dwamena C, Atkinson RG, Beuning LL, Bulley SM, Chagne D, Marsh KB, Matich AJ, Montefiori M, Newcomb RD, Schaffer RJ, Usadel B, Allan AC, Boldingh HL, Bowen JH, Davy MW, Eckloff R, Ferguson AR, Fraser LG, Gera E, Hellens RP, Janssen BJ, Klages K, Lo KR, MacDiarmid RM, Nain B, McNeilage MA, Rassam M, Richardson AC, Rikkerink EH, Ross GS, Schröder R, Snowden KC, Souleyre EJ, Templeton MD, Walton EF, Wang D, Wang MY, Wang YY, Wood M, Wu R, Yauk YK, Laing WA (2008) Analysis of expressed sequence tags from actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics, 9:351
25. Doehlemann G, Wahl R, Horst RJ, Voll LM, Usadel B, Poree F, Stitt M, Pons-Kühnemann J, Sonnewald U, Kahmann R, Kämper J (2008) Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis. Plant Journal, 56:181-95
24. May P, Wienkoop S, Kempa S, Usadel B, Christian N, Rupprecht J, Weiss J, Recuenco-Munoz L, Ebenhöh O, Weckwerth W, Walther D (2008) Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics, 179:157-66 +&
23. Usadel B, Blasing OE, Gibon Y, Retzlaff K, Hohne M, Gunther M, Stitt M (2008) Global Transcript Levels respond to Small Changes of the Carbon Status during a Progressive Exhaustion of Carbohydrates in Arabidopsis Rosettes. Plant Physiolgy, 146:1834-1861 +&
22. Sreenivasulu N, Usadel B, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close TJ, Stitt M, Graner A, Wobus U (2008) Barley grain maturation and germination: Metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. Plant Physiology, 146:1734-1761 +&
21. Rautengarten C, Usadel B, Neumetzler L, Hartmann J, Büssis D, Altmann T (2008) A Subtilisin-like Serine Protease essential for Mucilage Release from Arabidopsis Seed Coats. Plant Journal, 54:466-480 +&
20. Usadel B, Blaesing OE, Gibon Y, Poree F, Höhne, F, Tretheway R, Kamlage B, Poorter H, Stitt M (2008) Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range. Plant Cell Environment, 31:518-547 +&
2007
19. Lein W, Usadel B, Stitt M, Reindl A, Ehrhardt T, Sonnewald U, Boernke F (2007) A large-scale phenome analysis for Nicotiana tabacum using unbiased high-throughput gene-silencing. Plant Biotechnology Journal, 6:246-263
18. Studart-Guimaraes C, Fait A, Nunes-Nesi A, Carrari F, Usadel B, Fernie AR (2007) Reduced Expression of Succinyl CoA Ligase can be Compensated for by an Upregulation of the gamma-amino-butyrate (GABA) Shunt in Illuminated Tomato Leaves. Plant Physiology, 145:626-39
17. Rotter A, Usadel B, Baebler S, Stitt M, Gruden K (2007) Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species. Plant Methods, 3:10
16. Sulpice R, Tschoep H, von Korff M, Büssis D, Usadel B, Höhne M, Wituka-Wall H, Altmann T, Stitt M, Gibon Y (2007) Description and applications of a rapid and sensitive non-radioactive microplate-based assay for maximum and initial activity of ribulose-1,5-bisphosphate carboxylase. Plant Cell Environment, 30:1163-75.
15. Strickert M, Sreenivasulu N, Usadel B, Seiffert U (2007): Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue. BMC Bioinformatics, 8:165
14. Tellstrom V, Usadel B, Thimm O, Stitt M, Kuster H, Niehaus K (2007) The Lipopolysaccharide of Sinorhizobium meliloti Suppresses defense-associated Gene Expression in Cell Cultures of the Host Plant Medicago truncatula. Plant Physiology, 143:825-37
13. Morcuende R, Bari R, Gibon Y, Zheng W, Datt Pant B, Blaesing O, Usadel B, Czechowski T, Udvardi MK, Stitt M, Scheible WR (2007) Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus. Plant Cell Environment, 30:85-112.
2006
12. Usadel B, Nagel A, Steinhauser D, Gibon Y, Blaesing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M (2006) PageMan an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics, 18:7:535 +~
11. Carrai F, Baxter C, Urbanczyk-Wochniak E, Zanor MI, Nunes-Nesi A, Usadel B, Nikiforova V, Centero D, Ratzka A, Pauly M, Sweetlove L, Fernie AR (2006) Integrated analysis of metabolite and transcript levels reveals tight co-ordinate regulation of metabolism underlies tomato fruit development. Plant Physiol, 142:1380-96
10. Osuna D, Usadel B, Morcuende R, Gibon Y, Blasing OE, Hohne M, Gunter M, Kamlage B, Trethewey R, Scheible WR, Stitt M (2006) Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings. Plant Journal, 49:463-91
9. Gibon Y, Usadel B, Blaesing OE, Kamlage B, Hoehne M, Trethewey R, Stitt M (2006) Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biology, 7:R76
8. Urbanczyk-Wochniak E, Usadel B, Thimm O, Nunes-Nesi A, Carrari F, Davy M, Blaesing OE, Kowalczyk M, Weicht D, Polinceusz A, Meyer S, Stitt M, Fernie AR (2006) Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf. Plant Molecular Biology, 60:773-92. +&~
7. Blaesing OE, Gibon Y, Guenther M, Hoehne M, Morcuende R, Thimm O, Usadel B, Scheible W-R, Stitt M (2005) Sugars and Circadian Regulation make Major Contributions to the Global Regulation of Diurnal Gene Expression in Arabidopsis. Plant Cell, 17:3257-3281
2005
6. Kanter U, Usadel B, Guerineau F, Li Y, Pauly M, Tenhaken R (2005) The inositol oxygenase gene family of Arabidopsis is involved in the biosynthesis of nucleotide sugar precursors for cell-wall matrix polysaccharides. Planta, 221:243-254. +&
5. Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmuller E, Dormann P, Weckwerth W, Gibon Y, Stitt M, Willmitzer L, Fernie AR, Steinhauser D (2005) GMD@CSB.DB: the Golm Metabolome Database. Bioinformatics, 21:1635-1638
before 2005
4. Steinhauser D, Usadel B, Lüdemann A, Thimm O, Kopka J (2004) CSB.DB: A comprehensive systems biology database. Bioinformatics, 20:3647-51 +&
3. Usadel B, Schlüter U, Molhoj M, Gipmans M, Kossmann J, Reiter W-D, Pauly M (2004) Identification and Characterisation of a UDP-galacturonate 4-epimerase in Arabidopsis. FEBS Letters, 569:327-331. +&
2. Usadel B, Kuschinsky AM, Rosso M, Eckermann N, Pauly M (2004) RHM2 is involved in mucilage pectin synthesis and is required for the development of the seed coat in Arabidopsis thaliana. Plant Physiology, 134:286-285 +&
1. Choo TS, Lerouxel O, Seveno M, Usadel B, Faye L, Lerouge P, Pauly M (2002) Rapid structural phenotyping of plant cell wall mutants by enzymatic oligosaccharide fingerprinting. Plant Physiology, 130:1754-1763
33. Zhang W, Tariq A, Jia X, Yan J, Fernie AR, Usadel B, Wen W. Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points. Nat Protoc. 2024 Oct 2. doi: 10.1038/s41596-024-01063-2. #
32. García Brizuela J, Scharfenberg C, Scheuner C, Hoedt F, König P, Kranz A, Leidel A, Martini D, Schneider G, Schneider J, Singson LS, von Waldow H, Wehrmeyer N, Usadel B, Lesch S, Specka X, Lange M, Arend D. A roadmap for a middleware as a federation service for integrative data retrieval of agricultural data. J Integr Bioinform. 2024 Nov 7. doi: 10.1515/jib-2024-0027.
31. Bueno da Silva M, Wiese-Klinkenberg A, Usadel B, Genzel F. Potato Berries as a Valuable Source of Compounds Potentially Applicable in Crop Protection and Pharmaceutical Sectors: A Review. J Agric Food Chem. 2024 Jul 17;72(28):15449-15462. doi: 10.1021/acs.jafc.4c03071.
30. Großkinsky DK, Faure JD, Gibon Y, Haslam RP, Usadel B, Zanetti F, Jonak C. The potential of integrative phenomics to harness underutilized crops for improving stress resilience. Front Plant Sci. 2023 Jun 20;14:1216337. doi: 10.3389/fpls.2023.1216337
29. Dumschott K, Dörpholz H, Laporte MA, Brilhaus D, Schrader A, Usadel B, Neumann S, Arnaud E, Kranz A. Ontologies for increasing the FAIRness of plant research data. Front Plant Sci. 2023 Nov 30;14:1279694. doi: 10.3389/fpls.2023.1279694.
28. Understanding protein import in diverse non-green plastids (2023) Christian R, Labbancz J, Usadel B, Dhingra A Frontiers in Genetics 14 https://doi.org/10.3389/fgene.2023.969931
27. Gui S, Martinez-Rivas FJ, Wen W, Meng M, Yan J, Usadel B, Fernie AR. Going broad and deep: sequencing-driven insights into plant physiology, evolution, and crop domestication (2022). Plant J.113(3):446-459. doi: 10.1111/tpj.16070. #
26. Kazemi-Shahandashti SS, Mann L, El-Nagish A, Harpke D, Nemati Z, Usadel B, Heitkam T (2022) Ancient Artworks and Crocus Genetics Both Support Saffron's Origin in Early Greece. Front Plant Sci. 13:834416. doi: 10.3389/fpls.2022.834416.
25. Senger E, Osorio S, Olbricht K, Shaw P, Denoyes B, Davik J, Predieri S, Karhu S, Raubach S, Lippi N, Höfer M, Cockerton H, Pradal C, Kafkas E, Litthauer S, Usadel B, Mezzetti B (2022). Towards smart and sustainable development of modern berry cultivars in Europe. Plant J. 111,1238–1251 doi: 10.1111/tpj.15876.
24. Dumschott K, Schmidt MH, Chawla HS, Snowdon R, Usadel B (2020) Oxford Nanopore Sequencing: New opportunities for plant genomics? . J Exp Bot. 71: 5313–5322 #
23. Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek-Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte MA, Michotey C, Oppermann M, Ostler R, Poorter H, Ramı Rez-Gonzalez R, Ramšak Ž, Reif JC, Rocca-Serra P, Sansone SA, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam-Blondon AF, Pommier C (2020) Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytol. 2020 Mar 14. doi: 10.1111/nph.16544.
22. Watt M, Fiorani F, Usadel B, Rascher U, Muller O, Schurr U (2020). Phenotyping: New Windows into the Plant for Breeders. Annu Rev Plant Biol. 2020 Feb 25. doi: 10.1146/annurev-arplant-042916-041124.
21. Wibberg D, Batut B, Belmann P, Blom J, Glöckner FO, Grüning B, Hoffmann N, Kleinbölting N, Rahn R, Rey M, Scholz U, Sharan M, Tauch A, Trojahn U, Usadel B, Kohlbacher O (2019) The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research 2019, 8(ELIXIR):1877
20. Bolger AM, Poorter H, Dumschott K, Bolger ME, Arend D, Osorio S, Gundlach H, Mayer KF, Lange M, Scholz U, Usadel B (2019) Computational aspects underlying genome to phenome analysis in plants. Plant J. 97(1):182-198 #~
19. Wormit A, Usadel B (2018) The Multifaceted Role of Pectin Methylesterase Inhibitors (PMEIs). Int J Mol Sci 21;19(10).
18. Arsova B, Watt M, Usadel B (2018) Monitoring of plant protein post-translational modifications using targeted proteomics. Front. Plant Sci. 17;9:1168 doi: 10.3389/fpls.2018.01168
17. Voiniciuc C, Pauly M, Usadel B (2018) Monitoring Polysaccharide Dynamics in the Plant Cell Wall. Plant Physiol. 176:2590-2600. doi: 10.1104/pp.17.01776. #~
16. 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. Bioinformatics in the Plant Genomic and Phenomic Domain: The German Contribution to Resources, Services and Perspectives. J Biotechnol. 261:37-45. doi: 10.1016/j.jbiotec.2017.07.006.
15. 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. From plant genomes to phenotypes. J Biotechnol. 261:46-52 doi: 10.1016/j.jbiotec.2017.06.003. #
14. Bolger M, Arsova B, Usadel B (2018) Plant Genome and Transcriptome Annotations: from misconceptions to simple solutions. Briefings in Bioinformatics, 19:437-449doi: 10.1093/bib/bbw135 #~
13. Damm T, Commandeur U, Fischer R, Usadel B, Klose H (2016) Improving the utilization of lignocellulosic biomass by polysaccharide modification. Process Biochemistry 51:288-296
12. Voiniciuc C, Yang B, Schmidt MH, Günl M, Usadel B (2015) Starting to Gel: How Arabidopsis Seed Coat Epidermal Cells Produce Specialized Secondary Cell Walls. Int J Mol Sci. 16:3452-3473. #~
11. Bolger M, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer KFX (2013) Plant Genome sequencing - applications for crop improvement. Current opinion in Biotechnology, 26:31-37.
10. Usadel B, Schwacke R, Nagel A, Kersten B (2012) GabiPD – The GABI Primary Database integrates plant proteomic data with gene-centric information. Frontiers in Plant Science, 3:154. &
9. Stitt M, Lunn J, Usadel B (2010) Arabidopsis and primary photosynthetic metabolism – more than the icing on the cake. Plant J, 61: 1067–1091
8. Schulze WX, Usadel B (2010) Quantitation in Mass-Spectrometry-Based Proteomics. Annu Rev Plant Biol., 61:491-516
7. Lisso J, Schroeder F, Usadel B, Muessig C (2010) Structure and putative function of NFX1-like proteins in plants. Plant Biology, 12:381-394
6. Mutwil M, Ruprecht C, Giorgi FM, Bringmann M, Usadel B, Persson S (2009) Transcriptional wiring of cell wall-related genes in Arabidopsis. Mol Plant. 2:1015-24
5. Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ (2009) Coexpression Tools for Plant Biology: Opportunities for Hypothesis Generation and Caveats. Plant Cell