mips plant group

Selected publications

Publications > 2011

Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA.
The Medicago genome provides insight into the evolution of rhizobial symbioses.
Nature. 2011 Nov 16. doi: 10.1038/nature10625. Read more ..

Hernandez P, Martis M, Dorado G, Pfeifer M, Gálvez S, Schaaf S, Jouve N, Simková H, Valárik M, Doležel J, Mayer KF.
Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content
Plant J. 2011 Oct. doi: 10.1111/j.1365-313X.2011.04808.x. Read more ..

Dario Leister, Xi Wang, Georg Haberer, Klaus F.X. Mayer and Tatjana Kleine
Intra- and intercompartmental transcriptional networks coordinate the expression of genes for organellar functions
Plant Physiol. 2011 Sep;157(1):386-404. Epub 2011 Jul 20. Read more ..

Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
Nat Genet, 2011, 43(5):476-81. PMID: 21478890 Read more ..

Mayer KF, Martis M, Hedley PE, Simková H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Dolezel J, Waugh R, Stein N
Unlocking the Barley Genome by Chromosomal and Comparative Genomics
Plant Cell 2011, epub.PMID: 21467582 Read more ..

Mewes HW, Ruepp A, Theis F, Rattei T, Walter M, Frishman D, Suhre K, Spannagl M, Mayer KF, Stümpflen V, Antonov A
MIPS: curated databases and comprehensive secondary data resources in 2010
Nucleic Acids Res, 2011 Jan;39(Database issue):D220-4. Epub 2010 Nov 24.PMID: 21109531 Read more ..

Spannagl M, Mayer K, Durner J, Haberer G, Fröhlich A
Exploring the genomes: from Arabidopsis to crops
J Plant Physiol, 2011 Jan 1;168(1):3-8.PMID: 20817312 Read more ..

Wicker T, Mayer KFX, Gundlach H, Martis M, Steuernagel B, Scholz U, Šimková H, Kubaláková M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Doležel J, Keller B, Stein N
Frequent Gene Movement and Pseudogene Evolution Is Common to the Large and Complex Genomes of Wheat, Barley, and Their Relatives
The Plant Cell, 2011, epub.PMID: 21622801 Read more ..

Publications > 2010

Yu Z, Haberer G, Matthes M, Rattei T, Mayer KF, Gierl A, Torres-Ruiz RA
Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana
Proc Natl Acad Sci U S A, 2010 Oct 12;107(41):17809-14. Epub 2010 Sep 27.PMID: 20876110 Read more ..

International Brachypodium Initiative
Genome sequencing and analysis of the model grass Brachypodium distachyon
Nature, 2010 Feb 11;463(7282):763-8.PMID: 20148030 Read more ..

Schallau A, Arzenton F, Johnston AJ, Hähnel U, Koszegi D, Blattner FR, Altschmied L, Haberer G, Barcaccia G, Bäumlein H
Identification and genetic analysis of the APOSPORY locus in Hypericum perforatum L
Plant J, 2010 Jun 1;62(5):773-84. Epub 2010 Feb 26 Read more ..

Das M, Reichman JR, Haberer G, Welzl G, Aceituno FF, Mader MT, Watrud LS, Pfleeger TG, Gutiérrez RA, Schäffner AR, Olszyk DM
A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus
Plant Mol Biol, 2010 Mar;72(4-5):545-56. Epub 2009 Dec 31 Read more ..

Publications > 2009

Xi Wang, Georg Haberer, and Klaus F.X. Mayer
Analysis of correlative expression modules, cis element detection and sequence conservation between Oryza sativa and Sorghum bicolor
BMC Genomics , 10:284 (2009)

Müller LA, Lankhorst RK, Tanksley SD, Giovannoni JJ, White R, Vrebalov J, Fei Z, van Eck J, Buels R, Mills AA, Menda N, Tecle IY, Bombarely A, Stack S, Royer SM, Chang S, Shearer LA, Kim BD, Jo S, Hur C, Choi D, Li C, Zhao J, Jiang H, Geng Y, Dai Y, Fan H, Chen J, Lu F, Shi J, Sun S, Chen J, Yang X, Lu C, Chen M, Cheng Z, Li C, Ling H, Xue Y, Wang Y, Seymour GB, Bishop GJ, Bryan G, Rogers J, Sims S, Butcher S, Buchan D, Abbott J, Beasley H, Nicholson C, Riddle C, Humphray S, McLaren K, Mathur S, Vyas S, Solanke AU, Kumar R, Gupta V, Sharma AK, Khurana P, Khurana JP, Tyagi A, Sarita , Chowdhury P, Shridhar S, Chattopadhyay D, Pandit A, Singh P, Kumar A, Dixit R, Singh A, Praveen S, Dalal V, Yadav M, Ghazi IA, Gaikwad K, Sharma TR, Mohapatra T, Singh NK, Szinay D, Jong HD, Peters S, Staverenvan Staveren M, Datema E, Fiers MW, Hamvan Ham RC, Lindhout P, Philippot M, Frasse P, Regad F, Zouine M, Bouzayen M, Asamizu E, Sato S, Fukuoka H, Tabata S, Shibata D, Botella MA, Perez-Alonso M, Fernandez-Pedrosa V, Osorio S, Mico A, Granell A, Zhang Z, He J, Huang S, Du Y, Qu D, Liu L, Liu D, Wang J, Ye Z, Yang W, Wang G, Vezzi A, Todesco S, Valle G, Falcone G, Pietrella M, Giulianovan Giuliano , Grandillovan Grandillo , Traini A, D'Agostino N, Chiusano ML, Ercolano M, Barone A, Frusciante L, Schoof H, Jöcker A, Bruggmann R, Spannagl M, Mayer KFX, Guigó R, Camara F, Rombauts S, Fawcett JA, Peer YVD, Knapp S, and DZ, Stiekema W
A Snapshot of the Emerging Tomato Genome Sequence
The Plant Genome,2009, 2(1):78-92.

Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KFX, Messing J, Rokhsar DS.
The Sorghum bicolor genome and the diversification of grasses
Nature, 2009. 457:551-556.PMID: 19189423 Read more ..

Mayer KF, Taudien S, Martis M, Simková H, Suchánková P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B, Scholz U, Graner A, Platzer M, Dolezel J, Stein N
Gene content and virtual gene order of barley chromosome 1H
Plant Physiol, 2009 Oct;151(2):496-505. Epub 2009 Aug 19.PMID: 19692534 Read more ..

Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS
The Sorghum bicolor genome and the diversification of grasses
Nature, 2009 Jan 29;457(7229):551-6.PMID: 19189423 Read more ..

Steuernagel B, Taudien S, Gundlach H, Seidel M, Ariyadasa R, Schulte D, Petzold A, Felder M, Graner A, Scholz U, Mayer KF, Platzer M, Stein N
De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley
BMC Genomics, 2009 Nov 20;10:547.PMID: 19930547 Read more ..

Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer KF, Aranda MA, Llave C
Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes
Virology, 2009 Sep 30;392(2):203-14. Epub 2009 Aug 7.PMID: 19665162 Read more ..

Wang X, Haberer G, Mayer KF
Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation
BMC Genomics, 2009 Jun 26;10:284.PMID: 19558665 Read more ..

Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KF, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas
Science, 2009 Apr 10;324(5924):268-72 Read more ..

Publications > 2008

Moes D, Himmelbach A, Korte A, Haberer G, Grill E
Nuclear localization of the mutant protein phosphatase abi1 is required for insensitivity towards ABA responses in Arabidopsis
Plant J. 2008 Jun;54(5):806-19. Epub 2008 Feb 22 Read more ..

Greiner S, Wang X, Rauwolf U, Silber MV, Mayer K, Meurer J, Haberer G, Herrmann RG.
The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. sequence evaluation and plastome evolution
Nucleic Acids Res, 2008. 36(7):2366-78.PMID: 18299283 Read more ..

Greiner S, Wang X, Herrmann RG, Rauwolf U, Mayer K, Haberer G, Meurer J.
The complete nucleotide sequences of the 5 genetically distinct plastid genomes of Oenothera, subsection Oenothera: II. A microevolutionary view using bioinformatics and formal genetic data.
Mol Biol Evol, 2008 Sep;25(9):2019-30. Epub 2008 Jul 8. Read more ..

Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL.
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
Science, 2008 Jan 4;319(5859):64-9. Epub 2007 Dec 13. Read more ..

Mewes HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, Mayer KF, Münsterkötter M, Ruepp A, Spannagl M, Stümpflen V, Rattei T.:
MIPS: analysis and annotation of genome information in 2007.
Nucleic Acids Res, 2008 Jan;36(Database issue):D196-201. Epub 2007 Dec 23. Read more ..

Rice Annotation Project, Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M.:
The Rice Annotation Project Database (RAP-DB): 2008 update.
Nucleic Acids Res, 2008 Jan;36(Database issue):D1028-33. Epub 2007 Dec 17. Read more ..

Greiner S, Wang X, Herrmann RG, Rauwolf U, Mayer K, Haberer G, Meurer J
The complete nucleotide sequences of the 5 genetically distinct plastid genomes of Oenothera, subsection Oenothera: II. A microevolutionary view using bioinformatics and formal genetic data
Mol Biol Evol, 2008 Sep;25(9):2019-30. Epub 2008 Jul 8 Read more ..

Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
Science, 2008 Jan 4;319(5859):64-9. Epub 2007 Dec 13 Read more ..

Publications > 2007

Manuel Spannagl, Octave Noubibou, Dirk Haase, Li Yang, Heidrun Gundlach, Tobias Hindemitt, Kathrin Klee, Georg Haberer, Heiko Schoof and Klaus F. X. Mayer:
MIPSPlantsDB plant database resource for integrative and comparative plant genome research
Nucleic Acids Research 2007, Vol. 35, Database issue D834-D840, PMID: 17202173. Read more ..

Klee K, Ernst R, Spannagl M, Mayer KF.:
Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation.
BMC Bioinformatics, 2007 Aug 30;8:320 Read more ..

Eyüboglu B, Pfister K, Haberer G, Chevalier D, Fuchs A, Mayer KF, Schneitz K.:
Molecular characterisation of the STRUBBELIG-RECEPTOR FAMILY of genes encoding putative leucine-rich repeat receptor-like kinases in Arabidopsis thaliana.
BMC Plant Biol, 2007 Mar 30;7:16 Read more ..

Rice Annotation Project, Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T.:
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
Genome Res, 2007 Feb;17(2):175-83. Epub 2007 Jan 8. Read more ..

Publications > 2006

Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer KFX, Messing J.:
Uneven chromosome contraction and expansion in the maize genome
Genome Res, 16(10):1241-51, 2006, PMID: 16902087. Read more ..

Domoney C, Duc G, Ellis TH, Ferrandiz C, Firnhaber C, Gallardo K, Hofer J, Kopka J, Kuster H, Madueno F, Munier-Jolain NG, Mayer K, Thompson R, Udvardi M, Salon C.:
Genetic and genomic analysis of legume flowers and seeds
Curr Opin Plant Biol, 9(2):133-41, 2006, PMID: 16480914. Read more ..

Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Scheix T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KF, Rogers J, Quetier F, Oldroyd GE, Debelle F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND.:
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
Proc Natl Acad Sci USA, 103(40):14959-64, 2006, PMID: 17003129. Read more ..

Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KFX.:
Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana
PloS Comput Biol, 2(3):e21, 2006, PMID: 16604187. Read more ..

Haberer G, Mader MT, Kosarev P, Spannagl M, Yang L, Mayer KF.:
Large-scale Cis-element Detection by Analysis of Correlated Expression and Sequence Conservation between Arabidopsis and Brassica oleracea
Plant Physiol, epub, 2006, PMID: 17028152. Read more ..

Publications > 2005

Hindemitt T, Mayer KFX:
CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences
Bioinformatics, 21(23):4304-6, 2005, PMID: 16204349. Read more ..

Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Birren B, Nusbaum C, Mayer KFX, Messing J.:
Structure and Architecture of the Maize Genome
Plant Physiology, 139: 1612-1624, 2005, PMID: 16339807. Read more ..

Wilkinson, M., Schoof, H., Ernst, R., Haase, D.:
BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case.
Plant Physiol, 138(1):5-17, 2005, PMID: 15888673. Read more ..

Rudd S, Schoof H, Mayer K.:
PlantMarkers--a database of predicted molecular markers from plants
Nucleic Acids Res, 33(Database issue):D628-32., 2005, PMID: 15608276. Read more ..

Publications > 2004

Englbrecht CC, Schoof H and Bohm S.:
Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome
BMC Genomics, 5(1):39, 2004, PMID: 15236668. Read more ..

Haberer G, Hindemitt T, Meyers BC and Mayer KF.:
Transcriptional Similarities, Dissimilarities, and Conservation of cis-Elements in Duplicated Genes of Arabidopsis
Plant Physiol, Oct, 136(2):3009-22, 2004, PMID: 15489284. Read more ..

Lai J, Dey N, Kim CS, Bharti AK, Rudd S, Mayer KF, Larkins BA, Becraft P and Messing J.:
Characterization of the maize endosperm transcriptome and its comparison to the rice genome
Genome Res, 14(10A):1932-7, 2004, PMID: 15466291. Read more ..

Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei F, Fuks G, Soderlund CA, Mayer KF and Wing RA.:
Sequence composition and genome organization of maize
Proc Natl Acad Sci USA, 101(40):14349-54. Epub 2004 Sep 23, 2004, PMID: 15388850. Read more ..

Mayer K, Rudd S, Schoof H.:
Arabidopsis and its use in cereal genomics. Cereal Genomics
Cereal Genomics, Kluwer Academic Publishers, Dordrecht, Netherlands, 2004.

Rudd S, Frisch M, Grote K, Meyers BC, Mayer K and Werner T.:
Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression
Plant Physiol, 135:715-22, 2004, PMID: 15208419. Read more ..

Schoof H, Ernst R, Nazarov V, Pfeifer L, Mewes HW and Mayer KF.:
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics
Nucleic Acids Res, 32 Database issue:D373-6, 2004, PMID: 14681437. Read more ..

Schoof H, Ernst R and Mayer KF.:
The PlaNet consortium: A network of European plant databases connecting plant genome data in an integrated biological knowledge resource
Comparative and Functional Genomics, 5, 184-189 (2004).

Schrick K, Nguyen D, Karlowski WM and Mayer KF.:
START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors
Genome Biol, 5(6):R41. Epub 2004 May 27, 2004, PMID: 15186492. Read more ..

Shiu SH, Karlowski WM, Pan R, Tzeng YH, Mayer KF and Li WH.:
Comparative analysis of the receptor-like kinase family in Arabidopsis and rice
Plant Cell, 16(5):1220-34. Epub 2004 Apr 22, 2004, PMID: 15105442. Read more ..

Publications > 2003

Rudd, S., H. W. Mewes, and K. F. X. Mayer:
SPUTNIK: A database platform for comparative plant genomics
Nucleic Acids Research, 31: 128-132, 2003.

Karlowski, W. M., H. Schoof, V. Janakiraman, V. Stümpflen, and K. F. X. Mayer:
MOsDB: an integrated information resource for rice genomics
Nucleic Acids Research, 31: 190-192, 2003.

Schoof, H., and W. M. Karlowski:
Comparison of rice and Arabidopsis annotation.
Curr.Opin.Plant Biol, 6: 1-7, 2003.

Publications > 2002

Kosarev, P., K. F. Mayer, and C. S. Hardtke:
Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome
Genome Biol, 3: RESEARCH0016, 2002.

Mayer, K. and H. W. Mewes:
How can we deliver the large plant genomes? Strategies and perspectives
Curr.Opin.Plant Biol, 5: 173-177, 2002.

Schoof, H., P. Zaccaria, H. Gundlach, K. Lemcke, S. Rudd, G. Kolesov, R. Arnold, H. W. Mewes, and K. F. Mayer:
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome
Nucleic Acids Res, 30: 91-93, 2002.

Mewes, H. W., D. Frishman, U. Guldener, G. Mannhaupt, K. Mayer, M. Mokrejs, B. Morgenstern, M. Munsterkotter, S. Rudd, and B. Weil:
MIPS: a database for genomes and protein sequences
Nucleic Acids Res, 30: 31-34, 2002.

Publications > 2001

Mayer, K., G. Murphy, R. Tarchini, R. Wambutt, G. Volckaert, T. Pohl, A. Duesterhoeft, W. Stiekema, K. D. Entian, N. Terryn, K. Lemcke, D. Haase, C. R. Hall, A. M. van Dodeweerd, S. V. Tingey, H. W. Mewes, M. W. Bevan, and I. Bancroft:
Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana
Genome Res, 11: 1167-1174, 2001.

Heidenreich, B., K. Mayer, H. Sandermann, and D. Ernst:
Mercury induced genes in Arabidopsis thaliana: identification of induced genes upon long term mercuric ion exposure
Plant, Cell and Environment 24: 1227-1234, 2001.

Bevan, M., K. Mayer, O. White, J. A. Eisen, D. Preuss, T. Bureau, S. L. Salzberg, and H. W. Mewes:
Sequence and Analysis of the Arabidopsis Genome
Curr.Opin.Plant Biol, 4: 105-110, 2001.

Publications > 2000

Salanoubat, M., K. Lemcke, M. Rieger, W. Ansorge, M. Unseld, B. Fartmann, G. Valle, H. Blocker, M. Perez-Alonso, B. Obermaier, M. Delseny, M. Boutry, L. A. Grivell, R. Mache, P. Puigdomenech, S. de, V, N. Choisne, F. Artiguenave, C. Robert, P. Brottier, P. Wincker, L. Cattolico, J. Weissenbach, W. Saurin, F. Quetier, M. Schafer, S. Muller-Auer, C. Gabel, M. Fuchs, V. Benes, E. Wurmbach, H. Drzonek, H. Erfle, N. Jordan, S. Bangert, R. Wiedelmann, H. Kranz, H. Voss, R. Holland, P. Brandt, G. Nyakatura, A. Vezzi, M. D'Angelo, A. Pallavicini, S. Toppo, B. Simionati, A. Conrad, K. Hornischer, G. Kauer, T. H. Lohnert, G. Nordsiek, J. Reichelt, M. Scharfe, O. Schon, M. Bargues, J. Terol, J. Climent, P. Navarro, C. Collado, A. Perez-Perez, B. Ottenwalder, D. Duchemin, R. Cooke, M. Laudie, C. Berger-Llauro, B. Purnelle, D. Masuy, M. de Haan, A. C. Maarse, J. P. Alcaraz, A. Cottet, E. Casacuberta, A. Monfort, A. Argiriou, M. flores, R. Liguori, D. Vitale, G. Mannhaupt, D. Haase, H. Schoof, S. Rudd, P. Zaccaria, H. W. Mewes, and K. F. Mayer:
Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. European Union Chromosome 3 Arabidopsis Sequencing Consortium, The Institute for Genomic Research & Kazusa DNA Research Institute.
Nature, 408: 820-822, 2000.

Wambutt, R. and et al.:
Progress in Arabidopsis genome sequencing and functional genomics.
J Biotechnol, 78: 281-292, 2000.

The Arabidopsis Genome Initiative:
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Nature, 408: 796-815, 2000.

Tabata, S., T. Kaneko, Y. Nakamura, H. Kotani, T. Kato, E. Asamizu, N. Miyajima, S. Sasamoto, T. Kimura, T. Hosouchi, K. Kawashima, M. Kohara, M. Matsumoto, A. Matsuno, A. Muraki, S. Nakayama, N. Nakazaki, K. Naruo, S. Okumura, S. Shinpo, C. Takeuchi, T. Wada, A. Watanabe, M. Yamada, M. Yasuda, S. Sato, B. M. de la, E. Huang, L. Spiegel, L. Gnoj, A. O'Shaughnessy, R. Preston, K. Habermann, J. Murray, D. Johnson, T. Rohlfing, J. Nelson, T. Stoneking, K. Pepin, J. Spieth, M. Sekhon, J. Armstrong, M. Becker, E. Belter, H. Cordum, M. Cordes, L. Courtney, W. Courtney, M. Dante, H. Du, J. Edwards, J. Fryman, B. Haakensen, E. Lamar, P. Latreille, S. Leonard, R. Meyer, E. Mulvaney, P. Ozersky, A. Riley, C. Strowmatt, C. Wagner-McPherson, A. Wollam, M. Yoakum, M. Bell, N. Dedhia, L. Parnell, R. Shah, M. Rodriguez, L. H. See, D. Vil, J. Baker, K. Kirchoff, K. Toth, L. King, A. Bahret, B. Miller, M. Marra, R. Martienssen, W. R. McCombie, R. K. Wilson, G. Murphy, I. Bancroft, G. Volckaert, R. Wambutt, and A. Dusterhoft:
Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. The Kazusa DNA Research Institute, The Cold Spring Harbor and Washington University in St Louis Sequencing Consortium & The European Union Arabidopsis Genome Sequencing Consortium.
Nature, 408: 823-826, 2000.

Publications > 1999

Mewes, H. W., K. Heumann, A. Kaps, K. Mayer, F. Pfeiffer, S. Stocker, and D. Frishman:
MIPS: a database for genomes and protein sequences.
Nucleic Acid Research, 27: 44-48, 1999.

Mayer, K., C. Schuller, R. Wambutt, G. Murphy, G. Volckaert, T. Pohl, A. Dusterhoft, W. Stiekema, K. D. Entian, N. Terryn, B. Harris, W. Ansorge, P. Brandt, L. Grivell, M. Rieger, M. Weichselgartner, S. de, V, B. Obermaier, R. Mache, M. Muller, M. Kreis, M. Delseny, P. Puigdomenech, M. Watson, W. R. McCombie, T. Schmidtheini, B. Reichert, D. Portatelle, M. Perez-Alonso, M. Boutry, I. Bancroft, P. Vos, Hoheisel J.D., W. Zimmermann, H. Wedler, P. Ridley, S. A. Langham, B. McCullagh, L. Bilham, J. Robben, J. Van der Schueren, B. Grymonprez, Y.-J. Chuang, Vandenbussche F., M. Braeken, I. Weltjens, M. Voet, I. Bastiaens, R. Aert, E. Defoor, T. Weitzenegger, G. Bothe, U. Ramsperger, H. Hilbert, M. Braun, E. Holzer, A. Brandt, S. Peters, M. van Staveren, W. Dirkse, P. Mooijman, R. Klein-Lankhorst, M. Rose, J. Hauf, P. Kütter, S. Berneiser, S. Hempel, M. Feldpausch, S. Lamberth, H. Van den Daele, A. De Keyser, C. Buysshaert, J. Gielen, R. Villarroel, R. De Clerck, M. Van Montagu, J. Rogers, A. Cronin, M. Quail, S. Bray-Allen, L. Clark, J. Doggett, S. Hall, M. Kay, N. Lennard, K. McLay, R. Mayes, A. Pettett, M. A. Rajandream, M. Lyne, V. Benes, S. Rechmann, D. Borkova, H. Blöcker, M. Scharfe, M. Grimm, T. H. Löhnert, S. Dose, M. de Haan, A. Maarse, M. Schäfer, S. Müller-Auer, C. Gabel, M. Fuchs, B. Fartmann, K. Granderath, D. Dauner, A. Herzl, S. Neumann, A. Argiriou, D. Vitale, R. Liguori, E. Piravandi, O. Massenet, F. Quigley, G. Clabauld, A. Mündlein, R. Felber, S. Schnabl, R. Hiller, W. Schmidt, A. Lechamy, S. Aubourg, F. Chefdor, R. Cooke, C. Berger, A. Montfort, E. Casacuberta, T. Gibbons, N. Weber, M. Vandenbol, M. Bargues, J. Terol, A. Torres, A. Perez-Perez, B. Pumelle, E. Bent, S. Johnson, D. Tacon, T. Jesse, L. Heijnen, S. Schwarz, P. Scholler, S. Heber, P. Francs, C. Bielke, D. Frishman, D. Haase, K. Lemcke, H. W. Mewes, S. Stocker, P. Zaccaria, M. Bevan, and The Cold Spring Harbour Sequencing Consortium:
Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana
Nature, 402: 769-777, 1999.

Bevan, M., I. Bancroft, H. W. Mewes, R. Martienssen, and R. McCombie:
Clearing a path through the jungle: progress in Arabidopsis genomics
Bioessays, 21: 110-120, 1999.