Original Research Articles: 91

Reviews: 14

Book Chapters: 6

Proceedings: 1

Editorials: 1


Original Research Articles


91. Klap C, Yeshayahou C, Bolger AM, Arazi T, Gupta SK, Shabtai S, Usadel B, Salts Y, Barg R (201x) Tomato facultative parthenocarpy results from SlAGAMOUS-LIKE 6 loss of function Plant Biotechnology Journal

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. Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping. New Phytol. 2016 Oct 4. 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. 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. pp.00621.2016; 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 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 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

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. Nature Scientific Reports. 10, 1055-1060


82. Voiniciuc C, Guenl M, Schmidt MH, Usadel B. Highly Branched Xylan Made by IRX14 and MUCI21 Links Mucilage to Arabidopsis Seeds. Plant Physiol. 2015 Oct 19. pii: 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(4):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. Genotype-phenotype modeling considering intermediate level of biological variation: a case study involving sensory traits, metabolites and QTLs in ripe tomatoes. Mol Biosyst. 2015 Sep 7.

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.

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(8):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 Jan;87(1-2):69-80.


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, 46(9):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.  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


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(5):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


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


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


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


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 [Faculty of 1000: Must read]

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 [Faculty of 1000: Recommended]

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


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 [Faculty of 1000: Recommended]

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


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. [Faculty of 1000: Recommended]

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.


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 [Faculty of 1000: Must read]


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




14. Bolger M, Arsova B, Usadel B (201x) Plant Genome and Transcriptome Annotations: from misconceptions to simple solutions. Briefings in Bioinformatics accepted.

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(2):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 Environ. 32: 1633 - 1651 [Faculty of 1000: Must read]

4.   Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environment, 32: 1211-1229

3. The Biomoby Consortium (2008) Interoperability with Moby 1.0 Its better than sharing your toothbrush! Briefings in Bioinformatics, 9:220-231

2.   Usadel B, Nagel A, Thimm O, Redestig H, Bläsing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D, Scheible WR, Gibon Y, Morcuende R, Weicht D, Meyer S, Stitt M (2005) Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses. Plant Physiology, 138:1195-1204 [Faculty of 1000: Recommended]

1. Usadel B, Kuschinsky AM, Steinhauser D, Pauly M (2005) Transcriptional co-response analysis as a tool to identify new components of the wall biosynthetic machinery. Plant Biosystems, 139:69-73.



Book Chapters

6. Jaiswal P, Usadel B. (2016) Plant Pathway Databases. Methods Mol Biol. 1374:71-87. doi: 10.1007/978-1-4939-3167-5_4.

5.Usadel B, Berendzen KW, Bolger A (2013)  Identifying Cis Elements In Eukaryotes Using Old Tricks And High Throughput Sequence Data. In  The Analysis of Regulatory DNA: Current Developments, Knowledge and Applications Uncovering Gene Regulation, Bentham science, Berendzen W, Kilian J, Wanke D eds

4. Steinhauser D, Krall L, Müssig C, Büssis D, Usadel B (2008) Correlation Networks In Biological Network Analysis, Wiley VCH, Junker B and Schreiber F eds

3. Steinhauser D, Usadel B (2005) CSB.DB – A Comprehensive Systems-Biology Database: Overview and Transcriptional Co-Response (Correlation) Analyses. In Plant Genomics and Bioinformatics Expression Micro Arrays and Beyond – a course book, Ljubljana Slovenia, August 2005, Editor J. Freitag,  ISBN 3-00-018316-7

2. Usadel B. , Nagel A, Blaesing A (2005) MapMan: Visualizing Large Scale Datasets. In Plant Genomics and Bioinformatics Expression Micro Arrays and Beyond – a course book, Ljubljana Slovenia, August 2005, Editor J. Freitag,  ISBN 3-00-018316-7

1. Thimm O, Blaesing O, Usadel B, Gibon Y (2005) Evaluation of the transcriptome and genome to inform the study of metabolic control. In Control of Primary Metabolism in Plants, M. McManus, ed



1. Usadel B, Fernie AR (2013) The plant transcriptome—from integrating observations to models. Front. Plant Sci., 11 March 2013 | doi: 10.3389/fpls.2013.00048



1. Nagel A, Lohse M, Bolger A, Stitt M, Usadel B (2011) Visualizing large, high-throughput datasets based on the cognitive representation of biological pathways. Proceedings of the SPIE - The International Society for Optical Engineering Volume: 7865  Pages: 78650H (7 pp.)