PUB - Publikationen an der Universität Bielefeld

A combined proteome and transcriptome analysis of developing Medicago truncatula seeds: evidence for metabolic specialization of maternal and filial tissues.
Gallardo K, Firnhaber C, Zuber H, Hericher D, Belghazi M, Henry C, Kuster H, Thompson R., Mol. Cell Proteomics 6(12), 2007
PMID: 17848586

Transcriptional snapshots provide insights into the molecular basis of arbuscular mycorrhiza in the model legume Medicago truncatula
Hohnjec N, Henckel K, Bekel T, Gouzy J, Dondrup M, Goesmann A, Küster H., 2006

Metabolite profiles of nodulated alfalfa plants indicate that distinct stages of nodule organogenesis are accompanied by global physiological adaptations.
Barsch A, Tellstrom V, Patschkowski T, Kuster H, Niehaus K., Mol. Plant Microbe Interact. 19(9), 2006
PMID: 16941904

Overlaps in the transcriptional profiles of Medicago truncatula roots inoculated with two different Glomus fungi provide insights into the genetic program activated during arbuscular mycorrhiza.
Hohnjec N, Vieweg MF, Puhler A, Becker A, Kuster H., Plant Physiol. 137(4), 2005
PMID: 15778460

ArrayExpress--a public database of microarray experiments and gene expression profiles.
Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A., Nucleic Acids Res. 35(Database issue), 2006
PMID: 17132828

The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface.
Chen J, Zhao P, Massaro D, Clerch LB, Almon RR, DuBois DC, Jusko WJ, Hoffman EP., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681485

The Stanford Microarray Database.
Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM., Nucleic Acids Res. 29(1), 2001
PMID: 11125075

BarleyBase/PLEXdb.
Wise RP, Caldo RA, Hong L, Shen L, Cannon E, Dickerson JA., Methods Mol. Biol. 406(), 2007
PMID: 18287702

dbEST--database for "expressed sequence tags".
Boguski MS, Lowe TM, Tolstoshev CM., Nat. Genet. 4(4), 1993
PMID: 8401577

GenMapDB: a database of mapped human BAC clones.
Morley M, Arcaro M, Burdick J, Yonescu R, Reid T, Kirsch IR, Cheung VG., Nucleic Acids Res. 29(1), 2001
PMID: 11125073

Short Read Archive
AUTHOR UNKNOWN, 0

The GeWare data warehouse platform for the analysis of molecular-biological and clinical data
Rahm E, Kirsten T, Lange J., 2007

Biomedical informatics: development of a comprehensive data warehouse for clinical and genomic breast cancer research.
Hu H, Brzeski H, Hutchins J, Ramaraj M, Qu L, Xiong R, Kalathil S, Kato R, Tenkillaya S, Carney J, Redd R, Arkalgudvenkata S, Shahzad K, Scott R, Cheng H, Meadow S, McMichael J, Sheu SL, Rosendale D, Kvecher L, Ahern S, Yang S, Zhang Y, Jordan R, Somiari SB, Hooke J, Shriver CD, Somiari RI, Liebman MN., Pharmacogenomics 5(7), 2004
PMID: 15469411

IGetDB
AUTHOR UNKNOWN, 0

Java
AUTHOR UNKNOWN, 0

MySQL
AUTHOR UNKNOWN, 0

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.
Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W., Bioinformatics 21(16), 2005
PMID: 16082012

Gene-expression analysis and network discovery using Genevestigator.
Zimmermann P, Hennig L, Gruissem W., Trends Plant Sci. 10(9), 2005
PMID: 16081312

Kimball R, Caserta J., 2004

TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.
Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J., Bioinformatics 19(5), 2003
PMID: 12651724

The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.
Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J., Nucleic Acids Res. 29(1), 2001
PMID: 11125077

The Sequence Analysis and Management System-SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies
Bekel T, Henckel K, Dondrup M, Küster H, Meyer F, Mittard-Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A., 0

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712

InterPro and InterProScan: tools for protein sequence classification and comparison.
Mulder N, Apweiler R., Methods Mol. Biol. 396(), 2007
PMID: 18025686

A hidden Markov model for predicting transmembrane helices in protein sequences.
Sonnhammer EL, von Heijne G, Krogh A., Proc Int Conf Intell Syst Mol Biol 6(), 1998
PMID: 9783223

KEGG: kyoto encyclopedia of genes and genomes.
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651

The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510

The qcGene Database
AUTHOR UNKNOWN, 0

Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes.
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, Quetier F, Oldroyd GE, Debelle F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND., Proc. Natl. Acad. Sci. U.S.A. 103(40), 2006
PMID: 17003129

Sequencing the genespaces of Medicago truncatula and Lotus japonicus.
Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S., Plant Physiol. 137(4), 2005
PMID: 15824279

Affymetrix
AUTHOR UNKNOWN, 0

Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology.
Cheung F, Haas BJ, Goldberg SM, May GD, Xiao Y, Town CD., BMC Genomics 7(), 2006
PMID: 17062153

Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.
Kuster H, Becker A, Firnhaber C, Hohnjec N, Manthey K, Perlick AM, Bekel T, Dondrup M, Henckel K, Goesmann A, Meyer F, Wipf D, Requena N, Hildebrandt U, Hampp R, Nehls U, Krajinski F, Franken P, Puhler A., Phytochemistry 68(1), 2006
PMID: 17081576

Identification of gene functions by applying TILLING and insertional mutagenesis strategies on microarray-based expression data
Thompson R, Ratet P, Küster H., 2005

EMMA: a platform for consistent storage and efficient analysis of microarray data.
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651856

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Dondrup M, Albaum SP, Griebel T, Henckel K, Junemann S, Kahlke T, Kleindt CK, Kuster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Puhler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M., Nat. Genet. 29(4), 2001
PMID: 11726920

Design and implementation of microarray gene expression markup language (MAGE-ML).
Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, Shojatalab M, Pizarro A, White J, Hubley R, Deutsch E, Senger M, Aronow BJ, Robinson A, Bassett D, Stoeckert CJ Jr, Brazma A., Genome Biol. 3(9), 2002
PMID: 12225585

Biodiscovery
AUTHOR UNKNOWN, 0

MDS Analytical Technologies
AUTHOR UNKNOWN, 0

Evidence for the involvement in nodulation of the two small putative regulatory peptide-encoding genes MtRALFL1 and MtDVL1.
Combier JP, Kuster H, Journet EP, Hohnjec N, Gamas P, Niebel A., Mol. Plant Microbe Interact. 21(8), 2008
PMID: 18616408

A combined proteome and transcriptome analysis of developing Medicago truncatula seeds: evidence for metabolic specialization of maternal and filial tissues.
Gallardo K, Firnhaber C, Zuber H, Hericher D, Belghazi M, Henry C, Kuster H, Thompson R., Mol. Cell Proteomics 6(12), 2007
PMID: 17848586

Identification of transcription factors involved in root apex responses to salt stress in Medicago truncatula.
Gruber V, Blanchet S, Diet A, Zahaf O, Boualem A, Kakar K, Alunni B, Udvardi M, Frugier F, Crespi M., Mol. Genet. Genomics 281(1), 2008
PMID: 18987888

A gene expression atlas of the model legume Medicago truncatula.
Benedito VA, Torres-Jerez I, Murray JD, Andriankaja A, Allen S, Kakar K, Wandrey M, Verdier J, Zuber H, Ott T, Moreau S, Niebel A, Frickey T, Weiller G, He J, Dai X, Zhao PX, Tang Y, Udvardi MK., Plant J. 55(3), 2008
PMID: 18410479

Echo Web Framework
AUTHOR UNKNOWN, 0

Nodulation signaling in legumes requires NSP2, a member of the GRAS family of transcriptional regulators.
Kalo P, Gleason C, Edwards A, Marsh J, Mitra RM, Hirsch S, Jakab J, Sims S, Long SR, Rogers J, Kiss GB, Downie JA, Oldroyd GE., Science 308(5729), 2005
PMID: 15961668

NSP1 of the GRAS protein family is essential for rhizobial Nod factor-induced transcription.
Smit P, Raedts J, Portyanko V, Debelle F, Gough C, Bisseling T, Geurts R., Science 308(5729), 2005
PMID: 15961669

Lotus japonicus nodulation requires two GRAS domain regulators, one of which is functionally conserved in a non-legume.
Heckmann AB, Lombardo F, Miwa H, Perry JA, Bunnewell S, Parniske M, Wang TL, Downie JA., Plant Physiol. 142(4), 2006
PMID: 17071642

Signaling in symbiosis.
Limpens E, Bisseling T., Curr. Opin. Plant Biol. 6(4), 2003
PMID: 12873529

Kimball R, Margy R., 2002

NetAffx: Affymetrix probesets and annotations.
Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA., Nucleic Acids Res. 31(1), 2003
PMID: 12519953

An overview of Ensembl.
Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark KC, Cameron G, Durbin R, Cox A, Hubbard T, Clamp M., Genome Res. 14(5), 2004
PMID: 15078858

RefSeq and LocusLink: NCBI gene-centered resources.
Pruitt KD, Maglott DR., Nucleic Acids Res. 29(1), 2001
PMID: 11125071