Helmholtz Zentrum München - German Research Center for Environmental Health

2015

Unterholzner SJ, Rozhon W, Papacek M, Ciomas J, Lange T, Kugler KG, Mayer KF, Sieberer T, Poppenberger B
Brassinosteroids Are Master Regulators of Gibberellin Biosynthesis in Arabidopsis
Plant Cell, 2015 Aug, PMID 26243314, DOI 10.1105/tpc.15.00433

Haberer G, Mayer KF
Barley: From Brittle to Stable Harvest
Cell, 2015 Jul, 162(3):469-71 PMID 26232216, DOI 10.1016/j.cell.2015.07.023

Poursarebani N, Seidensticker T, Koppolu R, Trautewig C, Gawroński P, Bini F, Govind G, Rutten T, Sakuma S, Tagiri A, Wolde GM, Youssef HM, Battal A, Ciannamea S, Fusca T, Youssef HM, Nussbaumer T, Pozzi C, Börner A, Lundqvist U, Komatsuda T, Salvi S, Tuberosa R, Uauy C, Sreenivasulu N, Rossini L, Schnurbusch T
The Genetic Basis of Composite Spike Form in Barley and "Miracle-Wheat"
Genetics, 2015 Jul, PMID 26156223, DOI 10.1534/genetics.115.176628

Alter S, Bader KC, Spannagl M, Wang Y, Bauer E, Schön CC, Mayer KF
DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species.
Database (Oxford), 2015 May, PMID 25979979, DOI 10.1093/database/bav046

Schimek MG, Budinská E, Kugler KG, Švendová V, Ding J, Lin S
TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists
Stat Appl Genet Mol Biol, 2015 May, PMID 25968440, DOI 10.1515/sagmb-2014-0093

Mathew LS, Seidel MA, George B, Mathew S, Spannagl M, Haberer G, Torres MF, Al-Dous EK, Al-Azwani EK, Diboun I, Krueger RR, Mayer KF, Mohamoud YA, Suhre K, Malek JA
A Genome-Wide Survey of Date Palm Cultivars Supports Two Major Subpopulations in Phoenix dactylifera
G3 (Bethesda), 2015 May, PMID 25957276, DOI 10.1534/g3.115.018341

Helguera M, Rivarola M, Clavijo B, Martis MM, Vanzetti LS, González S, Garbus I, Leroy P, Šimková H, Valárik M, Caccamo M, Doležel J, Mayer KF, Feuillet C, Tranquilli G, Paniego N, Echenique V
New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing
Plant Sci, 2015 Apr, 233:200-12 PMID 25711827, DOI 10.1016/j.plantsci.2014.12.004

Czaban A, Sharma S, Byrne SL, Spannagl M, Mayer KF, Asp T
Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation
BMC Genomics, 2015 Mar, 16:249 PMID 25886302, DOI 10.1186/s12864-015-1447-y

Dietzel L, Gläßer C, Liebers M, Hiekel S, Courtois F, Czarnecki O, Schlicke H, Zubo Y, Börner T, Mayer K, Grimm B, Pfannschmidt T
Identification of Early Nuclear Target Genes of Plastidial Redox Signals that Trigger the Long-Term Response of Arabidopsis to Light Quality Shifts
Mol Plant, 2015 Mar, PMID 25778986, DOI 10.1016/j.molp.2015.03.004

Cviková K, Cattonaro F, Alaux M, Stein N, Mayer KF, Doležel J, Bartoš J
High-throughput physical map anchoring via BAC-pool sequencing
BMC Plant Biol, 2015 Jan, 15(1):99 PMID 25887276, DOI 10.1186/s12870-015-0429-1

Banaei-Moghaddam AM, Martis MM, Macas J, Gundlach H, Himmelbach A, Altschmied L, Mayer KF, Houben A
Genes on B chromosomes: old questions revisited with new tools
Biochim Biophys Acta, 2015 Jan, 1849(1):64-70 PMID 25481283, DOI 10.1016/j.bbagrm.2014.11.007

2014

Dey S, Wenig M, Langen G, Sharma S, Kugler KG, Knappe C, Hause B, Bichlmeier M, Babaeizad V, Imani J, Janzik I, Stempfl T, Hückelhoven R, Kogel KH, Mayer KF, Vlot AC
Bacteria-triggered systemic immunity in barley is associated with WRKY and ETHYLENE RESPONSIVE FACTORs but not with salicylic acid
Plant Physiol, 2014 Dec, 166(4):2133-51 PMID 25332505, DOI 10.1104/pp.114.249276

Nussbaumer T, Kugler KG, Schweiger W, Bader KC, Gundlach H, Spannagl M, Poursarebani N, Pfeifer M, Mayer KF
chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes
BMC Plant Biol, 2014 Nov, 14:348 PMID 25491094, DOI 10.1186/s12870-014-0348-6

Demko V, Perroud PF, Johansen W, Delwiche CF, Cooper ED, Remme P, Ako AE, Kugler KG, Mayer KF, Quatrano R, Olsen OA
Genetic analysis of DEFECTIVE KERNEL1 loop function in three-dimensional body patterning in Physcomitrella patens
Plant Physiol, 2014 Oct, 166(2):903-19 PMID 25185121, DOI 10.1104/pp.114.243758

Chaki M, Kovacs I, Spannagl M, Lindermayr C
Computational prediction of candidate proteins for S-nitrosylation in Arabidopsis thaliana
PLoS One, 2014 Sep, 9(10):e110232 PMID 25333472, DOI 10.1371/journal.pone.0110232

Unterseer S, Bauer E, Haberer G, Seidel M, Knaak C, Ouzunova M, Meitinger T, Strom TM, Fries R, Pausch H, Bertani C, Davassi A, Mayer KF, Schön CC
A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array
BMC Genomics, 2014 Sep, 15:823 PMID 25266061, DOI 10.1186/1471-2164-15-823

Weßling R, Epple P, Altmann S, He Y, Yang L, Henz SR, McDonald N, Wiley K, Bader KC, Gläßer C, Mukhtar MS, Haigis S, Ghamsari L, Stephens AE, Ecker JR, Vidal M, Jones JD, Mayer KF, Ver Loren van Themaat E, Weigel D, Schulze-Lefert P, Dangl JL, Panstruga R, Braun P
Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life
Cell Host Microbe, 2014 Sep, 16(3):364-75 PMID 25211078, DOI 10.1016/j.chom.2014.08.004

Behringer C, Bastakis E, Ranftl QL, Mayer KF, Schwechheimer C
Functional diversification within the family of B-GATA transcription factors through the leucine-leucine-methionine domain
Plant Physiol, 2014 Sep, 166(1):293-305 PMID 25077795, DOI 10.1104/pp.114.246660

Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KF, Rounsley S, Wing RA
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication
Nat Genet, 2014 Sep, 46(9):982-8 PMID 25064006, DOI 10.1038/ng.3044

Nussbaumer T, Kugler KG, Bader KC, Sharma S, Seidel M, Mayer KF
RNASeqExpressionBrowser-a web interface to browse and visualize high-throughput expression data
Bioinformatics, 2014 Sep, 30(17):2519-20 PMID 24833805, DOI 10.1093/bioinformatics/btu334

Guo H, Wang X, Gundlach H, Mayer KF, Peterson DG, Scheffler BE, Chee PW, Paterson AH
Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton)
Genetics, 2014 Aug, 197(4):1153-63 PMID 24907262, DOI 10.1534/genetics.114.166124

International Wheat Genome Sequencing Consortium (IWGSC)
A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
Science, 2014 Jul, 345(6194):1251788 PMID 25035500, DOI 10.1126/science.1251788

Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M, International Wheat Genome Sequencing Consortium,, Jakobsen KS, Wulff BB, Steuernagel B, Mayer KF, Olsen OA
Ancient hybridizations among the ancestral genomes of bread wheat
Science, 2014 Jul, 345(6194):1250092 PMID 25035499, DOI 10.1126/science.1250092

Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR, International Wheat Genome Sequencing Consortium, Mayer KF, Olsen OA
Genome interplay in the grain transcriptome of hexaploid bread wheat
Science, 2014 Jul, 345(6194):1250091 PMID 25035498, DOI 10.1126/science.1250091

Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C
Structural and functional partitioning of bread wheat chromosome 3B
Science, 2014 Jul, 345(6194):1249721 PMID 25035497, DOI 10.1126/science.1249721

Eversole K, Feuillet C, Mayer KF, Rogers J
Slicing the wheat genome. Introduction
Science, 2014 Jul, 345(6194):285-7 PMID 25035484, DOI 10.1126/science.1257983

Poursarebani N, Nussbaumer T, Simková H, Safář J, Witsenboer H, van Oeveren J, Doležel J, Mayer KF, Stein N, Schnurbusch T
Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A
Plant J, 2014 Jul, 79(2):334-47 PMID 24813060, DOI 10.1111/tpj.12550

Gläßer C, Haberer G, Finkemeier I, Pfannschmidt T, Kleine T, Leister D, Dietz KJ, Häusler RE, Grimm B, Mayer KF
Meta-analysis of retrograde signaling in Arabidopsis thaliana reveals a core module of genes embedded in complex cellular signaling networks
Mol Plant, 2014 Jul, 7(7):1167-90 PMID 24719466, DOI 10.1093/mp/ssu042

Schlicke H, Hartwig AS, Firtzlaff V, Richter AS, Glässer C, Maier K, Finkemeier I, Grimm B
Induced deactivation of genes encoding chlorophyll biosynthesis enzymes disentangles tetrapyrrole-mediated retrograde signaling
Mol Plant, 2014 Jul, 7(7):1211-27 PMID 24658417, DOI 10.1093/mp/ssu034

El Kelish A, Zhao F, Heller W, Durner J, Winkler JB, Behrendt H, Traidl-Hoffmann C, Horres R, Pfeifer M, Frank U, Ernst D
Ragweed (Ambrosia artemisiifolia) pollen allergenicity: SuperSAGE transcriptomic analysis upon elevated CO2 and drought stress
BMC Plant Biol, 2014 Jun, 14:176 PMID 24972689, DOI 10.1186/1471-2229-14-176

Keilwagen J, Kilian B, Özkan H, Babben S, Perovic D, Mayer KF, Walther A, Poskar CH, Ordon F, Eversole K, Börner A, Ganal M, Knüpffer H, Graner A, Friedel S
Separating the wheat from the chaff - a strategy to utilize plant genetic resources from ex situ genebanks
Sci Rep, 2014 May, 4:5231 PMID 24912875, DOI 10.1038/srep05231

Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, Gentzbittel L, Childs KL, Yandell M, Gundlach H, Mayer KF, Schwartz DC, Town CD
An improved genome release (version Mt4.0) for the model legume Medicago truncatula
BMC Genomics, 2014 Apr, 15:312 PMID 24767513, DOI 10.1186/1471-2164-15-312

Mathew LS, Spannagl M, Al-Malki A, George B, Torres MF, Al-Dous EK, Al-Azwani EK, Hussein E, Mathew S, Mayer KF, Mohamoud YA, Suhre K, Malek JA
A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms
BMC Genomics, 2014 Apr, 15:285 PMID 24735434, DOI 10.1186/1471-2164-15-285

Bolger ME, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer KF
Plant genome sequencing - applications for crop improvement
Curr Opin Biotechnol, 2014 Apr, 26:31-7 PMID 24679255, DOI 10.1016/j.copbio.2013.08.019

Jacquemin J, Ammiraju JS, Haberer G, Billheimer DD, Yu Y, Liu LC, Rivera LF, Mayer K, Chen M, Wing RA
Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion
Mol Plant, 2014 Apr, 7(4):642-56 PMID 24214894, DOI 10.1093/mp/sst149

Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, Lomsadze A, Borodovsky M, Kerstetter RA, Shanklin J, Byrant DW, Mockler TC, Appenroth KJ, Grimwood J, Jenkins J, Chow J, Choi C, Adam C, Cao XH, Fuchs J, Schubert I, Rokhsar D, Schmutz J, Michael TP, Mayer KF, Messing J
The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle
Nat Commun, 2014 Jan, 5:3311 PMID 24548928, DOI 10.1038/ncomms4311

Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S, Felder M, Platzer M, Himmelbach A, Schmutzer T, Hedley PE, Muehlbauer GJ, Scholz U, Korol A, Mayer KF, Waugh R, Langridge P, Graner A, Stein N
A sequence-ready physical map of barley anchored genetically by two million single-nucleotide polymorphisms
Plant Physiol, 2014 Jan, 164(1):412-23 PMID 24243933, DOI 10.1104/pp.113.228213

2013

Kopecký D, Martis M, Číhalíková J, Hřibová E, Vrána J, Bartoš J, Kopecká J, Cattonaro F, Stočes Š, Novák P, Neumann P, Macas J, Šimková H, Studer B, Asp T, Baird JH, Navrátil P, Karafiátová M, Kubaláková M, Šafář J, Mayer K, Doležel J
Flow sorting and sequencing meadow fescue chromosome 4F
Plant Physiol, 2013 Nov, 163(3):1323-37 PMID 24096412, DOI 10.1104/pp.113.224105

Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-Amatriaín M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KF, Scholz U, Poland JA, Stein N, Waugh R
Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)
Plant J, 2013 Nov, 76(4):718-27 PMID 23998490, DOI 10.1111/tpj.12319

Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KF, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N
Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond
Plant J, 2013 Nov, 76(3):494-505 PMID 23889683, DOI 10.1111/tpj.12294

Kugler KG, Siegwart G, Nussbaumer T, Ametz C, Spannagl M, Steiner B, Lemmens M, Mayer KF, Buerstmayr H, Schweiger W
Quantitative trait loci-dependent analysis of a gene co-expression network associated with Fusarium head blight resistance in bread wheat (Triticum aestivum L.)
BMC Genomics, 2013 Oct, 14:728 PMID 24152241, DOI 10.1186/1471-2164-14-728

Lüpken T, Stein N, Perovic D, Habekuß A, Serfling A, Krämer I, Hähnel U, Steuernagel B, Scholz U, Ariyadasa R, Martis M, Mayer K, Niks RE, Collins NC, Friedt W, Ordon F
High-resolution mapping of the barley Ryd3 locus controlling tolerance to BYDV
Molecular Breeding, 2013 Oct, 1-12 DOI 10.1007/s11032-013-9966-1

Martis MM, Zhou R, Haseneyer G, Schmutzer T, Vrána J, Kubaláková M, König S, Kugler KG, Scholz U, Hackauf B, Korzun V, Schön CC, Dolezel J, Bauer E, Mayer KF, Stein N
Reticulate evolution of the rye genome
Plant Cell, 2013 Oct, 25(10):3685-98 PMID 24104565, DOI 10.1105/tpc.113.114553

Livaja M, Wang Y, Wieckhorst S, Haseneyer G, Seidel M, Hahn V, Knapp SJ, Taudien S, Schön CC, Bauer E
BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower
BMC Genomics, 2013 Sep, 14:628 PMID 24330545, DOI 10.1186/1471-2164-14-628

Ma J, Stiller J, Berkman PJ, Wei Y, Rogers J, Feuillet C, Dolezel J, Mayer KF, Eversole K, Zheng YL, Liu C
Sequence-based analysis of translocations and inversions in bread wheat (Triticum aestivum L.)
PLoS One, 2013 Sep, 8(11):e79329 PMID 24260197, DOI 10.1371/journal.pone.0079329

Vigeland MD, Spannagl M, Asp T, Paina C, Rudi H, Rognli OA, Fjellheim S, Sandve SR
Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor
New Phytol, 2013 Sep, 199(4):1060-8 PMID 23701123, DOI 10.1111/nph.12337

Poursarebani N, Ariyadasa R, Zhou R, Schulte D, Steuernagel B, Martis MM, Graner A, Schweizer P, Scholz U, Mayer K, Stein N
Conserved synteny-based anchoring of the barley genome physical map
Funct Integr Genomics, 2013 Aug, 13(3):339-50 PMID 23812960, DOI 10.1007/s10142-013-0327-2

Spannagl M, Martis MM, Pfeifer M, Nussbaumer T, Mayer KF
Analysing complex Triticeae genomes - concepts and strategies
Plant Methods, 2013 Jul, 9(1):35 PMID 24011260, DOI 10.1186/1746-4811-9-35

Bolle C, Huep G, Kleinbölting N, Haberer G, Mayer K, Leister D, Weisshaar B
GABI-DUPLO: a collection of double mutants to overcome genetic redundancy in Arabidopsis thaliana
Plant J, 2013 Jul, 75(1):157-71 PMID 23573814, DOI 10.1111/tpj.12197

Schweiger W, Pasquet JC, Nussbaumer T, Paris MP, Wiesenberger G, Macadré C, Ametz C, Berthiller F, Lemmens M, Saindrenan P, Mewes HW, Mayer KF, Dufresne M, Adam G
Functional characterization of two clusters of Brachypodium distachyon UDP-glycosyltransferases encoding putative deoxynivalenol detoxification genes
Mol Plant Microbe Interact, 2013 Jul, 26(7):781-92 PMID 23550529, DOI 10.1094/MPMI-08-12-0205-R

Philippe R, Paux E, Bertin I, Sourdille P, Choulet F, Laugier C, Simková H, Safář J, Bellec A, Vautrin S, Frenkel Z, Cattonaro F, Magni F, Scalabrin S, Martis MM, Mayer KF, Korol A, Bergès H, Doležel J, Feuillet C
A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat
Genome Biol, 2013 Jun, 14(6):R64 PMID 23800011, DOI 10.1186/gb-2013-14-6-r64

Muñoz-Amatriaín M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KF, Taudien S, Platzer M, Jeddeloh JA, Springer NM, Muehlbauer GJ, Stein N
Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome
Genome Biol, 2013 Jun, 14(6):R58 PMID 23758725, DOI 10.1186/gb-2013-14-6-r58

Silvar C, Perovic D, Nussbaumer T, Spannagl M, Usadel B, Casas A, Igartua E, Ordon F
Towards positional isolation of three quantitative trait loci conferring resistance to powdery mildew in two Spanish barley landraces
PLoS One, 2013 May, 8(6):e67336 PMID 23826271, DOI 10.1371/journal.pone.0067336

Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, Jorgensen CM, Zhang Y, McGuire PE, Pasternak S, Stein JC, Ware D, Kramer M, McCombie WR, Kianian SF, Martis MM, Mayer KF, Sehgal SK, Li W, Gill BS, Bevan MW, Simková H, Dolezel J, Weining S, Lazo GR, Anderson OD, Dvorak J
A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor
Proc Natl Acad Sci U S A, 2013 May, 110(19):7940-5 PMID 23610408, DOI 10.1073/pnas.1219082110

Lüpken T, Stein N, Perovic D, Habekuss A, Krämer I, Hähnel U, Steuernagel B, Scholz U, Zhou R, Ariyadasa R, Taudien S, Platzer M, Martis M, Mayer K, Friedt W, Ordon F
Genomics-based high-resolution mapping of the BaMMV/BaYMV resistance gene rym11 in barley (Hordeum vulgare L.)
Theor Appl Genet, 2013 May, 126(5):1201-12 PMID 23456135, DOI 10.1007/s00122-013-2047-3

Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, Appels R, Pfeifer M, Tao Y, Zhang X, Jing R, Zhang C, Ma Y, Gao L, Gao C, Spannagl M, Mayer KF, Li D, Pan S, Zheng F, Hu Q, Xia X, Li J, Liang Q, Chen J, Wicker T, Gou C, Kuang H, He G, Luo Y, Keller B, Xia Q, Lu P, Wang J, Zou H, Zhang R, Xu J, Gao J, Middleton C, Quan Z, Liu G, Wang J, International Wheat Genome Sequencing Consortium, Yang H, Liu X, He Z, Mao L, Wang J
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation
Nature, 2013 Apr, 496(7443):91-5 PMID 23535592, DOI 10.1038/nature12028

Kanter U, Heller W, Durner J, Winkler JB, Engel M, Behrendt H, Holzinger A, Braun P, Hauser M, Ferreira F, Mayer K, Pfeifer M, Ernst D
Molecular and immunological characterization of ragweed (Ambrosia artemisiifolia L.) pollen after exposure of the plants to elevated ozone over a whole growing season
PLoS One, 2013 Mar, 8(4):e61518 PMID 23637846, DOI 10.1371/journal.pone.0061518

Pfeifer M, Martis M, Asp T, Mayer KF, Lübberstedt T, Byrne S, Frei U, Studer B
The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics
Plant Physiol, 2013 Feb, 161(2):571-82 PMID 23184232, DOI 10.1104/pp.112.207282

Nussbaumer T, Martis MM, Roessner SK, Pfeifer M, Bader KC, Sharma S, Gundlach H, Spannagl M
MIPS PlantsDB: a database framework for comparative plant genome research
Nucleic Acids Res, 2013 Jan, 41(Database issue):D1144-51 PMID 23203886, DOI 10.1093/nar/gks1153

2012

Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, Yoo MJ, Byers R, Chen W, Doron-Faigenboim A, Duke MV, Gong L, Grimwood J, Grover C, Grupp K, Hu G, Lee TH, Li J, Lin L, Liu T, Marler BS, Page JT, Roberts AW, Romanel E, Sanders WS, Szadkowski E, Tan X, Tang H, Xu C, Wang J, Wang Z, Zhang D, Zhang L, Ashrafi H, Bedon F, Bowers JE, Brubaker CL, Chee PW, Das S, Gingle AR, Haigler CH, Harker D, Hoffmann LV, Hovav R, Jones DC, Lemke C, Mansoor S, ur Rahman M, Rainville LN, Rambani A, Reddy UK, Rong JK, Saranga Y, Scheffler BE, Scheffler JA, Stelly DM, Triplett BA, Van Deynze A, Vaslin MF, Waghmare VN, Walford SA, Wright RJ, Zaki EA, Zhang T, Dennis ES, Mayer KF, Peterson DG, Rokhsar DS, Wang X, Schmutz J
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
Nature, 2012 Dec, 492(7429):423-7 PMID 23257886, DOI 10.1038/nature11798

Gaupels F, Sarioglu H, Beckmann M, Hause B, Spannagl M, Draper J, Lindermayr C, Durner J
Deciphering systemic wound responses of the pumpkin extrafascicular phloem by metabolomics and stable isotope-coded protein labeling
Plant Physiol, 2012 Dec, 160(4):2285-99 PMID 23085839, DOI 10.1104/pp.112.205336

Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N
Analysis of the bread wheat genome using whole-genome shotgun sequencing
Nature, 2012 Nov, 491(7426):705-10 PMID 23192148, DOI 10.1038/nature11650

Feuillet C, Stein N, Rossini L, Praud S, Mayer K, Schulman A, Eversole K, Appels R
Integrating cereal genomics to support innovation in the Triticeae
Funct Integr Genomics, 2012 Nov, 12(4):573-83 PMID 23161406, DOI 10.1007/s10142-012-0300-5

International Barley Genome Sequencing Consortium, Mayer KF, Waugh R, Brown JW, Schulman A, Langridge P, Platzer M, Fincher GB, Muehlbauer GJ, Sato K, Close TJ, Wise RP, Stein N
A physical, genetic and functional sequence assembly of the barley genome
Nature, 2012 Nov, 491(7426):711-6 PMID 23075845, DOI 10.1038/nature11543

Piednoël M, Aberer AJ, Schneeweiss GM, Macas J, Novak P, Gundlach H, Temsch EM, Renner SS
Next-generation sequencing reveals the impact of repetitive DNA across phylogenetically closely related genomes of Orobanchaceae
Mol Biol Evol, 2012 Nov, 29(11):3601-11 PMID 22723303, DOI 10.1093/molbev/mss168

Netzer M, Kugler KG, Müller LA, Weinberger KM, Graber A, Baumgartner C, Dehmer M
A network-based feature selection approach to identify metabolic signatures in disease
J Theor Biol, 2012 Oct, 310:216-22 PMID 22771628, DOI 10.1016/j.jtbi.2012.06.003

Martis MM, Klemme S, Banaei-Moghaddam AM, Blattner FR, Macas J, Schmutzer T, Scholz U, Gundlach H, Wicker T, Šimková H, Novák P, Neumann P, Kubaláková M, Bauer E, Haseneyer G, Fuchs J, Doležel J, Stein N, Mayer KF, Houben A
Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences
Proc Natl Acad Sci U S A, 2012 Aug, 109(33):13343-6 PMID 22847450, DOI 10.1073/pnas.1204237109

Fröhlich A, Gaupels F, Sarioglu H, Holzmeister C, Spannagl M, Durner J, Lindermayr C
Looking deep inside: detection of low-abundance proteins in leaf extracts of Arabidopsis and phloem exudates of pumpkin
Plant Physiol, 2012 Jul, 159(3):902-14 PMID 22555880, DOI 10.1104/pp.112.198077

International Arabidopsis Informatics Consortium
Taking the next step: building an Arabidopsis information portal
Plant Cell, 2012 Jun, 24(6):2248-56 PMID 22751211, DOI 10.1105/tpc.112.100669

Tomato Genome Consortium
The tomato genome sequence provides insights into fleshy fruit evolution
Nature, 2012 May, 485(7400):635-41 PMID 22660326, DOI 10.1038/nature11119

Studer B, Byrne S, Nielsen RO, Panitz F, Bendixen C, Islam MS, Pfeifer M, Lübberstedt T, Asp T
A transcriptome map of perennial ryegrass (Lolium perenne L.)
BMC Genomics, 2012 Apr, 13:140 PMID 22513206, DOI 10.1186/1471-2164-13-140

Hernandez P, Martis M, Dorado G, Pfeifer M, Gálvez S, Schaaf S, Jouve N, Šimková 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, 2012 Feb, 69(3):377-86 PMID 21974774, DOI 10.1111/j.1365-313X.2011.04808.x

Leroy P, Guilhot N, Sakai H, Bernard A, Choulet F, Theil S, Reboux S, Amano N, Flutre T, Pelegrin C, Ohyanagi H, Seidel M, Giacomoni F, Reichstadt M, Alaux M, Gicquello E, Legeai F, Cerutti L, Numa H, Tanaka T, Mayer K, Itoh T, Quesneville H, Feuillet C
TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes
Front Plant Sci, 2012 Jan, 3:5 PMID 22645565, DOI 10.3389/fpls.2012.00005

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 Dec, 480(7378):520-4 PMID 22089132, DOI 10.1038/nature10625

Asp T, Byrne S, Gundlach H, Bruggmann R, Mayer KF, Andersen JR, Xu M, Greve M, Lenk I, Lübberstedt T
Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice
Mol Genet Genomics, 2011 Dec, 286(5-6):433-47 PMID 22081040, DOI 10.1007/s00438-011-0654-8

Haseneyer G, Schmutzer T, Seidel M, Zhou R, Mascher M, Schön CC, Taudien S, Scholz U, Stein N, Mayer KF, Bauer E
From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.)
BMC Plant Biol, 2011 Sep, 11:131 PMID 21951788, DOI 10.1186/1471-2229-11-131

Leister D, Wang X, Haberer G, Mayer KF, Kleine T
Intracompartmental and intercompartmental transcriptional networks coordinate the expression of genes for organellar functions
Plant Physiol, 2011 Sep, 157(1):386-404 PMID 21775496, DOI 10.1104/pp.111.177691

Gehrmann E, Glässer C, Jin Y, Sendhoff B, Drossel B, Hamacher K
Robustness of glycolysis in yeast to internal and external noise
Phys Rev E Stat Nonlin Soft Matter Phys, 2011 Aug, 84(2 Pt 1):021913 PMID 21929026

Wicker T, Mayer KF, Gundlach H, Martis M, Steuernagel B, Scholz U, Simková H, Kubaláková M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Dolezel 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
Plant Cell, 2011 May, 23(5):1706-18 PMID 21622801, DOI 10.1105/tpc.111.086629

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 May, 43(5):476-81 PMID 21478890, DOI 10.1038/ng.807

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 Apr, 23(4):1249-63 PMID 21467582, DOI 10.1105/tpc.110.082537

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 PMID 21109531, DOI 10.1093/nar/gkq1157

Spannagl M, Mayer K, Durner J, Haberer G, Fröhlich A
Exploring the genomes: from Arabidopsis to crops
J Plant Physiol, 2011 Jan, 168(1):3-8 PMID 20817312, DOI 10.1016/j.jplph.2010.07.008

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, 107(41):17809-14 PMID 20876110, DOI 10.1073/pnas.1000852107

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, 62(5):773-84 PMID 20202173, DOI 10.1111/j.1365-313X.2010.04188.x

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 PMID 20043233, DOI 10.1007/s11103-009-9590-y

International Brachypodium Initiative
Genome sequencing and analysis of the model grass Brachypodium distachyon
Nature, 2010 Feb, 463(7282):763-8 PMID 20148030, DOI 10.1038/nature08747

2009

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, 10:547 PMID 19930547, DOI 10.1186/1471-2164-10-547

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 PMID 19692534, DOI 10.1104/pp.109.142612

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, 392(2):203-14 PMID 19665162, DOI 10.1016/j.virol.2009.07.005

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, de Jong H, Peters S, van Staveren M, Datema E, Fiers MW, van 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, Giuliano G, Grandillo S, Traini A, D'Agostino N, Chiusano ML, Ercolano M, Barone A, Frusciante L, Schoof H, Jöcker A, Bruggmann R, Spannagl M, Mayer KXF, Guigó R, Camara F, Rombauts S, Fawcett JA, Van de Peer Y, Knapp S, Zamir D, Stiekema W
A Snapshot of the Emerging Tomato Genome Sequence
Plant Gen., 2009 Aug, 2: 78-92 doi:10.3835/plantgenome2008.08.0005

Wang X, Haberer G, Mayer KF
Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation
BMC Genomics, 2009 Jun, 10:284 PMID 19558665, DOI 10.1186/1471-2164-10-284

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, 324(5924):268-72 PMID 19359590, DOI 10.1126/science.1167222

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, 457(7229):551-6 PMID 19189423, DOI 10.1038/nature07723

2008

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 PMID 18614526, DOI 10.1093/molbev/msn149

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 PMID 18298671, DOI 10.1111/j.1365-313X.2008.03454.x

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 Apr, 36(7):2366-78 PMID 18299283, DOI 10.1093/nar/gkn081

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 PMID 18158298, DOI 10.1093/nar/gkm980

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 PMID 18089549, DOI 10.1093/nar/gkm978

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, 319(5859):64-9 PMID 18079367, DOI 10.1126/science.1150646

2007

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, 8:320 PMID 17760972, DOI 10.1186/1471-2105-8-320

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, 7:16 PMID 17397538, DOI 10.1186/1471-2229-7-16

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 PMID 17210932, DOI 10.1101/gr.5509507

Spannagl M, Noubibou O, Haase D, Yang L, Gundlach H, Hindemitt T, Klee K, Haberer G, Schoof H, Mayer KF
MIPSPlantsDB-plant database resource for integrative and comparative plant genome research
Nucleic Acids Res, 2007 Jan, 35(Database issue):D834-40 PMID 17202173, DOI 10.1093/nar/gkl945

2006

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, 2006 Dec, 142(4):1589-602 PMID 17028152, DOI 10.1104/pp.106.085639

Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, Scheix T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KF, Rogers J, Quétier F, Oldroyd GE, Debellé 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 U S A, 2006 Oct, 103(40):14959-64 PMID 17003129, DOI 10.1073/pnas.0603228103

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 KF, Messing J
Uneven chromosome contraction and expansion in the maize genome
Genome Res, 2006 Oct, 16(10):1241-51 PMID 16902087, DOI 10.1101/gr.5338906

Domoney C, Duc G, Ellis TH, Ferrándiz C, Firnhaber C, Gallardo K, Hofer J, Kopka J, Küster H, Madueño 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, 2006 Apr, 9(2):133-41 PMID 16480914, DOI 10.1016/j.pbi.2006.01.014

Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KF
Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana
PLoS Comput Biol, 2006 Mar, 2(3):e21 PMID 16604187, DOI 10.1371/journal.pcbi.0020021

2005

Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Birren B, Nusbaum C, Mayer KF, Messing J
Structure and architecture of the maize genome
Plant Physiol, 2005 Dec, 139(4):1612-24 PMID 16339807, DOI 10.1104/pp.105.068718

Hindemitt T, Mayer KF
CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences
Bioinformatics, 2005 Dec, 21(23):4304-6 PMID 16204349, DOI 10.1093/bioinformatics/bti691

Wilkinson M, Schoof H, Ernst R, Haase D
BioMOBY successfully integrates distributed heterogeneous bioinformatics Web Services. The PlaNet exemplar case
Plant Physiol, 2005 May, 138(1):5-17 PMID 15888673, DOI 10.1104/pp.104.059170

Rudd S, Schoof H, Mayer K
PlantMarkers-a database of predicted molecular markers from plants
Nucleic Acids Res, 2005 Jan, 33(Database issue):D628-32 PMID 15608276, DOI 10.1093/nar/gki074

2004

Haberer G, Hindemitt T, Meyers BC, Mayer KF
Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis
Plant Physiol, 2004 Oct, 136(2):3009-22 PMID 15489284, DOI 10.1104/pp.104.046466

Lai J, Dey N, Kim CS, Bharti AK, Rudd S, Mayer KF, Larkins BA, Becraft P, Messing J
Characterization of the maize endosperm transcriptome and its comparison to the rice genome
Genome Res, 2004 Oct, 14(10A):1932-7 PMID 15466291, DOI 10.1101/gr.2780504

Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei F, Fuks G, Soderlund CA, Mayer KF, Wing RA
Sequence composition and genome organization of maize
Proc Natl Acad Sci U S A, 2004 Oct, 101(40):14349-54 PMID 15388850, DOI 10.1073/pnas.0406163101

Englbrecht CC, Schoof H, Böhm S
Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome
BMC Genomics, 2004 Jul, 5(1):39 PMID 15236668, DOI 10.1186/1471-2164-5-39

Rudd S, Frisch M, Grote K, Meyers BC, Mayer K, 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, 2004 Jun, 135(2):715-22 PMID 15208419, DOI 10.1104/pp.103.037861

Shiu SH, Karlowski WM, Pan R, Tzeng YH, Mayer KF, Li WH
Comparative analysis of the receptor-like kinase family in Arabidopsis and rice
Plant Cell, 2004 May, 16(5):1220-34 PMID 15105442, DOI 10.1105/tpc.020834

Schrick K, Nguyen D, Karlowski WM, Mayer KF
START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors
Genome Biol, 2004 Apr, 5(6):R41 PMID 15186492, DOI 10.1186/gb-2004-5-6-r41

Schoof H, Ernst R, Nazarov V, Pfeifer L, Mewes HW, Mayer KF
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics
Nucleic Acids Res, 2004 Jan, 32(Database issue):D373-6 PMID 14681437, DOI 10.1093/nar/gkh068

2003

Schoof H, Ernst R, Mayer KF
The PlaNet Consortium: a network of European plant databases connecting plant genome data in an integrated biological knowledge resource
Comp Funct Genomics, 2003 Nov, 5(2):184-9 PMID 18629059, DOI 10.1002/cfg.374

Schoof H, Karlowski WM
Comparison of rice and Arabidopsis annotation
Curr Opin Plant Biol, 2003 Apr, 6(2):106-12 PMID 12667865

Karlowski WM, Schoof H, Janakiraman V, Stuempflen V, Mayer KF
MOsDB: an integrated information resource for rice genomics
Nucleic Acids Res, 2003 Jan, 31(1):190-2 PMID 12519979

Rudd S, Mewes HW, Mayer KF
Sputnik: a database platform for comparative plant genomics
Nucleic Acids Res, 2003 Jan, 31(1):128-32 PMID 12519965

2002

Mayer K, Mewes HW
How can we deliver the large plant genomes? Strategies and perspectives
Curr Opin Plant Biol, 2002 Apr, 5(2):173-7 PMID 11856615

Heidenreich B, Mayer K, Sandermann H, Ernst D
Mercury-induced genes in Arabidopsis thaliana: identification of induced genes upon long-term mercuric ion exposure
Plant, Cell & Env, 2002 Mar, 24(11):1227-7 DOI 10.1046/j.0016-8025.2001.00775.x

Kosarev P, Mayer KF, Hardtke CS
Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome
Genome Biol, 2002 Feb, 3(4):RESEARCH0016 PMID 11983057

Schoof H, Zaccaria P, Gundlach H, Lemcke K, Rudd S, Kolesov G, Arnold R, Mewes HW, Mayer KF
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome
Nucleic Acids Res, 2002 Jan, 30(1):91-3 PMID 11752263

Mewes HW, Frishman D, Güldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Münsterkötter M, Rudd S, Weil B
MIPS: a database for genomes and protein sequences
Nucleic Acids Res, 2002 Jan, 30(1):31-4 PMID 11752246

2001

Mayer K, Murphy G, Tarchini R, Wambutt R, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian KD, Terryn N, Lemcke K, Haase D, Hall CR, van Dodeweerd AM, Tingey SV, Mewes HW, Bevan MW, Bancroft I
Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana
Genome Res, 2001 Jul, 11(7):1167-74 PMID 11435398, DOI 10.1101/gr.161701

Bevan M, Mayer K, White O, Eisen JA, Preuss D, Bureau T, Salzberg SL, Mewes HW
Sequence and analysis of the Arabidopsis genome
Curr Opin Plant Biol, 2001 Apr, 4(2):105-10 PMID 11228431

2000

Tabata S, Kaneko T, Nakamura Y, Kotani H, Kato T, Asamizu E, Miyajima N, Sasamoto S, Kimura T, Hosouchi T, Kawashima K, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Naruo K, Okumura S, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Sato S, de la Bastide M, Huang E, Spiegel L, Gnoj L, O'Shaughnessy A, Preston R, Habermann K, Murray J, Johnson D, Rohlfing T, Nelson J, Stoneking T, Pepin K, Spieth J, Sekhon M, Armstrong J, Becker M, Belter E, Cordum H, Cordes M, Courtney L, Courtney W, Dante M, Du H, Edwards J, Fryman J, Haakensen B, Lamar E, Latreille P, Leonard S, Meyer R, Mulvaney E, Ozersky P, Riley A, Strowmatt C, Wagner-McPherson C, Wollam A, Yoakum M, Bell M, Dedhia N, Parnell L, Shah R, Rodriguez M, See LH, Vil D, Baker J, Kirchoff K, Toth K, King L, Bahret A, Miller B, Marra M, Martienssen R, McCombie WR, Wilson RK, Murphy G, Bancroft I, Volckaert G, Wambutt R, Düsterhöft A, Stiekema W, Pohl T, Entian KD, Terryn N, Hartley N, Bent E, Johnson S, Langham SA, McCullagh B, Robben J, Grymonprez B, Zimmermann W, Ramsperger U, Wedler H, Balke K, Wedler E, Peters S, van Staveren M, Dirkse W, Mooijman P, Lankhorst RK, Weitzenegger T, Bothe G, Rose M, Hauf J, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Villarroel R, Gielen J, Ardiles W, Bents O, Lemcke K, Kolesov G, Mayer K, Rudd S, Schoof H, Schueller C, Zaccaria P, Mewes HW, Bevan M, Fransz P, Kazusa DNA Research Institute, Cold Spring Harbor and Washington University in St Louis Sequencing Consortium
Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana
Nature, 2000 Dec, 408(6814):823-6 PMID 11130714, DOI 10.1038/35048507

Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blöcker H, Perez-Alonso M, Obermaier B, Delseny M, Boutry M, Grivell LA, Mache R, Puigdomènech P, De Simone V, Choisne N, Artiguenave F, Robert C, Brottier P, Wincker P, Cattolico L, Weissenbach J, Saurin W, Quétier F, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Benes V, Wurmbach E, Drzonek H, Erfle H, Jordan N, Bangert S, Wiedelmann R, Kranz H, Voss H, Holland R, Brandt P, Nyakatura G, Vezzi A, D'Angelo M, Pallavicini A, Toppo S, Simionati B, Conrad A, Hornischer K, Kauer G, Löhnert TH, Nordsiek G, Reichelt J, Scharfe M, Schön O, Bargues M, Terol J, Climent J, Navarro P, Collado C, Perez-Perez A, Ottenwälder B, Duchemin D, Cooke R, Laudie M, Berger-Llauro C, Purnelle B, Masuy D, de Haan M, Maarse AC, Alcaraz JP, Cottet A, Casacuberta E, Monfort A, Argiriou A, flores M, Liguori R, Vitale D, Mannhaupt G, Haase D, Schoof H, Rudd S, Zaccaria P, Mewes HW, Mayer KF, Kaul S, Town CD, Koo HL, Tallon LJ, Jenkins J, Rooney T, Rizzo M, Walts A, Utterback T, Fujii CY, Shea TP, Creasy TH, Haas B, Maiti R, Wu D, Peterson J, Van Aken S, Pai G, Militscher J, Sellers P, Gill JE, Feldblyum TV, Preuss D, Lin X, Nierman WC, Salzberg SL, White O, Venter JC, Fraser CM, Kaneko T, Nakamura Y, Sato S, Kato T, Asamizu E, Sasamoto S, Kimura T, Idesawa K, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S, European Union Chromosome 3 Arabidopsis Sequencing Consortium, Institute for Genomic Research
Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana
Nature, 2000 Dec, 408(6814):820-2 PMID 11130713, DOI 10.1038/35048706

Arabidopsis Genome Initiative
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Nature, 2000 Dec, 408(6814):796-815 PMID 11130711, DOI 10.1038/35048692

Wambutt R, Murphy G, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian KD, Terryn N, Harris B, Ansroge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, Müller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Bountry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham SA, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang YJ, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Rose M
Progress in Arabidopsis genome sequencing and functional genomics
J Biotechnol, 2000 Mar, 78(3):281-92 PMID 10751689

1999

Mayer K, Schüller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian KD, Terryn N, Harris B, Ansorge W, Brandt P, Grivell L, Rieger M, Weichselgartner M, de Simone V, Obermaier B, Mache R, Müller M, Kreis M, Delseny M, Puigdomenech P, Watson M, Schmidtheini T, Reichert B, Portatelle D, Perez-Alonso M, Boutry M, Bancroft I, Vos P, Hoheisel J, Zimmermann W, Wedler H, Ridley P, Langham SA, McCullagh B, Bilham L, Robben J, Van der Schueren J, Grymonprez B, Chuang YJ, Vandenbussche F, Braeken M, Weltjens I, Voet M, Bastiaens I, Aert R, Defoor E, Weitzenegger T, Bothe G, Ramsperger U, Hilbert H, Braun M, Holzer E, Brandt A, Peters S, van Staveren M, Dirske W, Mooijman P, Klein Lankhorst R, Rose M, Hauf J, Kötter P, Berneiser S, Hempel S, Feldpausch M, Lamberth S, Van den Daele H, De Keyser A, Buysshaert C, Gielen J, Villarroel R, De Clercq R, Van Montagu M, Rogers J, Cronin A, Quail M, Bray-Allen S, Clark L, Doggett J, Hall S, Kay M, Lennard N, McLay K, Mayes R, Pettett A, Rajandream MA, Lyne M, Benes V, Rechmann S, Borkova D, Blöcker H, Scharfe M, Grimm M, Löhnert TH, Dose S, de Haan M, Maarse A, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Fartmann B, Granderath K, Dauner D, Herzl A, Neumann S, Argiriou A, Vitale D, Liguori R, Piravandi E, Massenet O, Quigley F, Clabauld G, Mündlein A, Felber R, Schnabl S, Hiller R, Schmidt W, Lecharny A, Aubourg S, Chefdor F, Cooke R, Berger C, Montfort A, Casacuberta E, Gibbons T, Weber N, Vandenbol M, Bargues M, Terol J, Torres A, Perez-Perez A, Purnelle B, Bent E, Johnson S, Tacon D, Jesse T, Heijnen L, Schwarz S, Scholler P, Heber S, Francs P, Bielke C, Frishman D, Haase D, Lemcke K, Mewes HW, Stocker S, Zaccaria P, Bevan M, Wilson RK, de la Bastide M, Habermann K, Parnell L, Dedhia N, Gnoj L, Schutz K, Huang E, Spiegel L, Sehkon M, Murray J, Sheet P, Cordes M, Abu-Threideh J, Stoneking T, Kalicki J, Graves T, Harmon G, Edwards J, Latreille P, Courtney L, Cloud J, Abbott A, Scott K, Johnson D, Minx P, Bentley D, Fulton B, Miller N, Greco T, Kemp K, Kramer J, Fulton L, Mardis E, Dante M, Pepin K, Hillier L, Nelson J, Spieth J, Ryan E, Andrews S, Geisel C, Layman D, Du H, Ali J, Berghoff A, Jones K, Drone K, Cotton M, Joshu C, Antonoiu B, Zidanic M, Strong C, Sun H, Lamar B, Yordan C, Ma P, Zhong J, Preston R, Vil D, Shekher M, Matero A, Shah R, Swaby IK, O'Shaughnessy A, Rodriguez M, Hoffmann J, Till S, Granat S, Shohdy N, Hasegawa A, Hameed A, Lodhi M, Johnson A, Chen E, Marra M, Martienssen R, McCombie WR
Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana
Nature, 1999 Dec, 402(6763):769-77 PMID 10617198, DOI 10.1038/47134

Bevan M, Bancroft I, Mewes HW, Martienssen R, McCombie R
Clearing a path through the jungle: progress in Arabidopsis genomics
Bioessays, 1999 Feb, 21(2):110-20 PMID 10193185, DOI 10.1002/(SICI)1521-1878(199902)21:2<110::AID-BIES5>3.0.CO;2-V

Mewes HW, Heumann K, Kaps A, Mayer K, Pfeiffer F, Stocker S, Frishman D
MIPS: a database for genomes and protein sequences
Nucleic Acids Res, 1999 Jan, 27(1):44-8 PMID 9847138