Publikationen

Autoren Titel
2015
Aliyeva-Schnorr L, Beier S, Karafiátová M, Schmutzer T, Scholz U, Doležel J, Stein N, Houben A Cytogenetic mapping with centromeric BAC contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. Plant J. 84 (2015) 385–394. dx.doi.org/10.1111/tpj.13006
Cao H X, Schmutzer T, Scholz U, Pecinka A, Schubert I, Vu G T H Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species. Front. Microbiol. 6 (2015) 526. dx.doi.org/10.3389/fmicb.2015.00526
Chapman J A, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Seghal S, Oliker L, Schmutz J, Yelick K A, Scholz U, Waugh R, Poland J A, Muehlbauer G J, Stein N, Rokhsar D S A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol. 16 (2015) 26. dx.doi.org/10.1186/s13059-015-0582-8
Colmsee C, Beier S, Himmelbach A, Schmutzer T, Stein N, Scholz U, Mascher M BARLEX – the barley draft genome explorer. Mol. Plant 8 (2015) 964-966. dx.doi.org/10.1016/j.molp.2015.03.009
Esch M, Chen J, Colmsee C, Klapperstück M, Grafahrend-Belau E, Scholz U, Lange M LAILAPS – the plant science search engine. Plant Cell Physiol. 56 (2015) e8. dx.doi.org/10.1093/pcp/pcu185
Gerlach N, Schmitz J, Polatajko A, Schlüter U, Fahnenstich H, Witt S, Fernie A R, Uroic K, Scholz U, Sonnewald U, Bucher M An integrated functional approach to dissect systemic responses in maize to arbuscular mycorrhizal symbiosis. Plant Cell Environ. 38 (2015) 1591-1612. dx.doi.org/10.1111/pce.12508
Krajewski P, Chen D, Ćwiek H, van Dijk A D J, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap J P, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S Towards recommendations for metadata and data handling in plant phenotyping. J. Exp. Bot. 66 (2015) 5417-5427. dx.doi.org/10.1093/jxb/erv271
Muraya M M, Schmutzer T, Ulpinnis C, Scholz U, Altmann T Targeted sequencing reveals large-scale sequence polymorphism in maize candidate genes for biomass production and composition. PLoS One 10 (2015) e0132120. dx.doi.org/10.1371/journal.pone.0132120
Schilling F Analyse von Genstrukturen in der Kulturpflanze Gerste. (Bachelor Thesis) Köthen, Hochschule Anhalt (FH) (2015) 91 pp.
Schmutzer T, Samans B, Dyrszka E, Ulpinnis C, Weise S, Stengel D, Colmsee C, Lespinasse D, Micic Z, Abel S, Duchscherer P, Breuer F, Abbadi A, Leckband G, Snowdon R, Scholz U Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus. Sci. Data 2 (2015) 150072. dx.doi.org/10.1038/sdata.2015.72
Snowdon R J, Abbadi A, Kox T, Schmutzer T, Leckband G Heterotic Haplotype Capture: precision breeding for hybrid performance. Trends Plant Sci. 20 (2015) 410-413. dx.doi.org/10.1016/j.tplants.2015.04.013
Spannagl M, Alaux M, Lange M, Bolser D M, Bader K C, Letellier T, Kimmel E, Flores R, Pommier C, Kerhornou A, Walts B, Nussbaumer T, Grabmuller C, Chen J, Colmsee C, Beier S, Mascher M, Schmutzer T, Arend D, Thanki A, Ramirez-Gonzalez R, Ayling M, Ayling S, Caccamo M, Mayer K F X, Scholz U, Steinbach D, Quesneville H, Kersey P J transPLANT resources for Triticeae genomic data. Plant Genome 9 (2015) 1-13. dx.doi.org/10.3835/plantgenome2015.06.0038
Sretenovic Rajicic T, Lübberstedt T, Bach Jensen L, Scholz U, Weber E, Graner A, Dehmer K J Single nucleotide polymorphism (SNP) markers for allele quantification in Lolium (Poaceae): development and first applications. In: Budak H, Spangenberg G (Eds.): The Proceedings of the 8th International Symposium on the Molecular Breeding of Forage and Turf. Cham: Springer (2015) 143-163.
Tavakol E, Okagaki R, Verderio G, Shariati V, Hussien A, Bilgic H, Scanlon M J, Todt N R, Close T J, Druka A, Waugh R, Steuernagel B, Ariyadasa R, Himmelbach A, Stein N, Muehlbauer G J, Rossini L The barley Uniculme4 gene encodes a BLADE-ON-PETIOLE-like protein that controls tillering and leaf patterning. Plant Physiol. 168 (2015) 164-174. dx.doi.org/10.1104/pp.114.252882
Vu G T H, Schmutzer T, Bull F, Cao H X, Fuchs J, Tran D T, Jovtchev G, Pistrick K, Stein N, Pecinka A, Neumann P, Novák P, Macas J, Dear P H, Blattner F R, Scholz U, Schubert I Comparative genome analysis reveals divergent genome size evolution in a carnivorous plant genus. Plant Genome 8 (2015) 1-14. dx.doi.org/10.3835/plantgenome2015.04.0021
Zang W, Eckstein P E, Colin M, Voth D, Himmelbach A, Beier S, Stein N, Scoles G J, Beattie A D Fine mapping and identification of a candidate gene for the barley Un8 true loose smut resistance gene. Theor. Appl. Genet. 128 (2015) 1343-1357. dx.doi.org/10.1007/s00122-015-2510-4
2014
Ahkami A, Scholz U, Steuernagel B, Strickert M, Haensch K T, Druege U, Reinhardt D, Nouri E, von Wirén N, Franken P, Hajirezaei M-R Comprehensive transcriptome analysis unravels the existence of crucial genes regulating primary metabolism during adventitious root formation in Petunia hybrida. PLoS One 9 (2014) e100997. dx.doi.org/10.1371/journal.pone.0100997
Arend D, Colmsee C, Knüpffer H, Oppermann M, Scholz U, Schüler D, Weise S, Lange M Data management experiences and best practices from the perspective of a plant research institute. In: Galhardas H, Rahm E (Eds.): Data integration in the life sciences: 10th international conference, DILS 2014, Lisbon, Portugal, July 17-18, 2014; proceedings (Series: Lecture Notes in Computer Science, Vol. 8574) Berlin [u.a.]: Springer (2014) 41-49. dx.doi.org/10.1007/978-3-319-08590-6_4 ISBN 978-3-319-08589-0
Arend D, Lange M, Chen J, Colmsee C, Flemming S, Hecht D, Scholz U e!DAL - a framework to store, share and publish research data. BMC Bioinformatics 15 (2014) 214. dx.doi.org/10.1186/1471-2105-15-214
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 P E, Muehlbauer G J, Scholz U, Korol A, Mayer K F X, 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. 164 (2014) 412-423. dx.doi.org/10.1104/pp.113.228213
Bolger M E, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer K F Plant genome sequencing - applications for crop improvement. Curr. Opin. Biotechnol. 26 (2014) 31-37. dx.doi.org/10.1016/j.copbio.2013.08.019
Colmsee C Datenmanagement und Visualisierung von BAC-Netzwerken zur Unterstützung der Sequenzierung des Gerstengenoms. (Master Thesis) Wernigerode, Hochschule Harz, Fachbereich Automatisierung und Informatik (2014) 72 pp.
Esch M, Chen J, Weise S, Hassani-Pak K, Scholz U, Lange M A query suggestion workflow for life science IR-systems. J. Integr. Bioinform. 11 (2014) 237. dx.doi.org/doi:10.2390/biecoll-jib-2014-237
Gawroński P, Ariyadasa R, Himmelbach A, Poursarebani N, Kilian B, Stein N, Steuernagel B, Hensel G, Kumlehn J, Sehgal S K, Gill B S, Gould P, Hall A, Schnurbusch T A distorted circadian clock causes early flowering and temperature-dependent variation in spike development in the Eps-3Am mutant of einkorn wheat. Genetics 196 (2014) 1253-1261. dx.doi.org/10.1534/genetics.113.158444
Kuhlmann M, Finke A, Mascher M, Mette M F DNA methylation maintenance consolidates RNA-directed DNA methylation and transcriptional gene silencing over generations in Arabidopsis thaliana. Plant J. 80 (2014) 269-281. dx.doi.org/10.1111/tpj.12630
Kunze G, Gaillardin C, Czernicka M, Durrens P, Martin T, Böer E, Gabaldón T, Cruz J A, Talla E, Marck C, Goffeau A, Barbe V, Baret P, Baronian K, Beier S, Bleykasten C, Bode R, Casaregola S, Despons L, Fairhead C, Giersberg M, Gierski P P, Hähnel U, Hartmann A, Jankowska D, Jubin C, Jung P, Lafontaine I, Leh-Louis V, Lemaire M, Marcet-Houben M, Mascher M, Morel G, Richard G-F, Riechen J, Sacerdot C, Sarkar A, Savel G, Schacherer J, Sherman D J, Stein N, Straub M-L, Thierry A, Trautwein-Schult A, Vacherie B, Westhof E, Worch S, Dujon B, Souciet J-L, Wincker P, Scholz U, Neuvéglise C The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest. Biotechnol. Biofuels 7 (2014) 66. dx.doi.org/10.1186/1754-6834-7-66
Lange M, Henkel R, Müller W, Waltemath D, Weise S Information retrieval in life sciences: a programmatic survey. In: Chen M, Hofestädt R (Eds.): Approaches in integrative bioinformatics: towards the virtual cell. Berlin [u.a.]: Springer (2014) 73-109. dx.doi.org/10.1007/978-3-642-41281-3_3 ISBN 978-3-642-41280-6
Lüpken T, Stein N, Perovic D, Habekuß A, Serfling A, Krämer I, Hähnel U, Steuernagel B, Scholz U, Ariyadasa R, Martis M M, Mayer K F X, Niks R E, Collins N C, Friedt W, Ordon F High resolution mapping of the barley Ryd3 locus controlling tolerance to BYDV. Mol. Breed. 33 (2014) 477-488. dx.doi.org/10.1007/s11032-013-9966-1
Mascher M POPSEQ Anchoring and ordering contig assemblies from next generation sequencing data by population sequencing. (PhD Thesis) Bielefeld, Universität Bielefeld, Technische Fakultät (2014) 133 pp.
Mascher M, Gerlach N, Gahrtz M, Bucher M, Scholz U, Dresselhaus T Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype. PLoS One 9 (2014) e96782. dx.doi.org/10.1371/journal.pone.0096782
Mascher M, Jost M, Kuon J E, Himmelbach A, Assfalg A, Beier S, Scholz U, Graner A, Stein N Mapping-by-sequencing accelerates forward genetics in barley. Genome Biol. 15 (2014) R78. dx.doi.org/10.1186/gb-2014-15-6-r78
Mascher M, Stein N Genetic anchoring of whole-genome shotgun assemblies. Front. Genet. 5 (2014) 208. dx.doi.org/10.3389/fgene.2014.00208
Pasquariello M, Barabaschi D, Himmelbach A, Steuernagel B, Ariyadasa R, Stein N, Gandolfi F, Tenedini E, Bernardis I, Tagliafico E, Pecchioni N, Francia E The barley Frost resistance-H2 locus. Funct. Integr. Genomics 14 (2014) 85-100. dx.doi.org/10.1007/s10142-014-0360-9
Poursarebani N, Ma L, Schmutzer T, Houben A, Stein N FISH mapping for physical map improvement in the large genome of barley: a case study on chromosome 2H. Cytogenet. Genome Res. 143 (2014) 275-279. dx.doi.org/10.1159/000366028
Schmutzer T, Ma L, Pousarebani N, Bull F, Stein N, Houben A, Scholz U Kmasker – a tool for in silico prediction of single-copy FISH probes for the large-genome species Hordeum vulgare. Cytogenet. Genome Res. 142 (2014) 66-78. dx.doi.org/10.1159/000356460
Schwender J, König C, Klapperstück M, Heinzel N, Munz E, Hebbelmann I, Hay J O, Denolf P, de Bodt S, Redestig H, Caestecker E, Jakob P M, Borisjuk L, Rolletschek H Transcript abundance on its own cannot be used to infer fluxes in central metabolism. Front. Plant Sci. 5 (2014) 668. dx.doi.org/10.3389/fpls.2014.00668
Stein N, Steuernagel B Advances in sequencing the barley genome. In: Tuberosa R, Graner A, Frison E (Eds.): Genomics of plant genetic resources. Vol. 1. Managing, sequencing and mining genetic resources. Dordrecht [u.a.]: Springer (2014) 391-403. dx.doi.org/10.1007/978-94-007-7572-5_16 ISBN 978-94-007-7571-8
The International Wheat Genome Sequencing Consortium (IWGSC; IPK Authors: Mascher M, Scholz, U. & Stein, N.) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345 (2014) 1251788. dx.doi.org/10.1126/science.1251788
Wendler N, Mascher M, Nöh C, Himmelbach A, Scholz U, Ruge-Wehling B, Stein N Unlocking the secondary gene-pool of barley with next-generation sequencing. Plant Biotechnol. J. 12 (2014) 1122-1131. dx.doi.org/10.1111/pbi.12219
Yang P, Lüpken T, Habekuss A, Hensel G, Steuernagel B, Kilian B, Ariyadasa R, Himmelbach A, Kumlehn J, Scholz U, Ordon F, Stein N PROTEIN DISULFIDE ISOMERASE LIKE 5-1 is a susceptibility factor to plant viruses. Proc. Natl. Acad. Sci. U.S.A. 111 (2014) 2104-2109. dx.doi.org/10.1073/pnas.1320362111
Zanke C, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, Argillier O, Stiewe G, Hinze M, Beier S, Ganal M W, Röder M S Genetic architecture of main effect QTL for heading date in European winter wheat. Front. Plant Sci. 5 (2014) 217. dx.doi.org/10.3389/fpls.2014.00217
2013
Arend D, Lange M, Chen J, Colmsee C, Flemming S, Scholz U The e!DAL JAVA-API: Store, share and cite primary data in life sciences. In: Schreiber F, Hofestädt R, Lange M, Scholz U, Czauderna T, Schnee R, Weise S (Eds.): Proceedings of the 9th International Symposium on Integrative Bioinformatics 2013, March 18 - 20, 2013, Gatersleben, Germany. Gatersleben: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) (2013) 143-154.
Behrens A-K Modellierung und Simulation des Purin-Abbaus in der Hefe Arxula adeninivorans. (Bachelor Thesis) Köthen, Hochschule Anhalt (FH), Fachbereich Angewandte Biowissenschaften und Prozesstechnik (2013) 69 pp.
Biselli C, Urso S, Tacconi G, Steuernagel B, Schulte D, Gianinetti A, Bagnaresi P, Stein N, Cattivelli L, Valè G Haplotype variability and identification of new functional alleles at the Rdg2a leaf stripe resistance gene locus. Theor. Appl. Genet. 126 (2013) 1575-1586. dx.doi.org/10.1007/s00122-013-2075-z
Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Lange M, Mascher M, Weise S, Scholz U, Schreiber F OPTIMAS-DW, MetaCrop and VANTED: a case study for data integration, curation and visualisation in life sciences. In: Horbach M (Ed.): GI-Jahrestagung. (Series: LNI, Vol. 220) (2013) 1834-1840. ISBN 978-3-88579-614-5
Colmsee C, Keller E R J, Oppermann M, Senula A, Zanke C, Funke T, Weise S, Scholz U The Garlic and Shallot Core Collection (GSCC). www.ipk-gatersleben.de/databases/genetic_resources/gscc (2013).
Esch M Effizienzsteigerung des Life-Science-IR-Systems LAILAPS mittels Suchanfragenerweiterung. (Master Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 94 pp.
Gellner M Evaluating the impact of genome quality on RNA-seq analysis. (Master Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 48 pp.
Hecht D Konzeption und Implementierung eines Freigabeservices zur Registrierung von DOI-Nummern für IPK-Primärdaten. (Bachelor Thesis) Wernigerode, Hochschule Harz (FH), Fachbereich Automatisierung und Informatik (2013) 49 pp.
Hofestädt R, Kormeier B, Lange M, Schreiber F, Sommer B, Weise S Editorial. J. Integr. Bioinform. 10 (2013) e226. dx.doi.org/10.2390/biecoll-jib-2013-226
Keller E R J, Zanke C, Scholz U EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound. euralliveg.ipk-gatersleben.de (2013).
Lüpken T, Stein N, Perovic D, Habekuss A, Kramer 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. 126 (2013) 1201-1212. dx.doi.org/10.1007/s00122-013-2047-3
Martis M M, Zhou R, Haseneyer G, Schmutzer T, Vrána J, Kubaláková M, König S, Kugler K G, Scholz U, Hackauf B, Korzun V, Schön C-C, Doležel J, Bauer E, Mayer K F X, Stein N Reticulate evolution of the rye genome. Plant Cell 25 (2013) 3685-3698. dx.doi.org/10.1105/tpc.113.114553
Mascher M, Muehlbauer G J, Rokhsar D S, Chapman J, Schmutz J, Barry K, Munoz-Amatriain M, Close T J, Wise R P, Schulman A H, Himmelbach A, Mayer K F, Scholz U, Poland J A, Stein N, Waugh R Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J. 76 (2013) 718-727. dx.doi.org/10.1111/tpj.12319
Mascher M, Richmond T A, Gerhardt D J, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov E D, Hedley P E, Gonzales A M, Morrell P L, Kilian B, Blattner F R, Scholz U, Mayer K F, Flavell A J, Muehlbauer G J, Waugh R, Jeddeloh J A, Stein N Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J. 76 (2013) 494-505. dx.doi.org/10.1111/tpj.12294
Mascher M, Schubert I, Scholz U, Friedel S Patterns of nucleotide asymmetries in plant and animal genomes. Biosystems 111 (2013) 181-189. dx.doi.org/10.1016/j.biosystems.2013.02.001
Mascher M, Wu S, Amand P S, Stein N, Poland J Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 8 (2013) e76925. dx.doi.org/10.1371/journal.pone.0076925
Matthies I E, Weise S, Förster J, Korzun V, Stein N, Röder M S Nitrogen-metabolism related genes in barley - haplotype diversity, linkage mapping and associations with malting and kernel quality parameters. BMC Genet 14 (2013) e77. dx.doi.org/10.1186/1471-2156-14-77
Mehlhorn H, Lange M, Scholz U, Schreiber F Extraction and prediction of biomedical database identifier using neural networks towards data network construction. In: Ordóñez de Pablos P, Lytras M D, Tennyson R, Labra Gayo J E (Eds.): Cases on open-linked data and semantic web applications. Hershey: Information Science Reference (2013) 58-83. ISBN 978-1-4666-2827-4
Muñoz-Amatriaín M, Eichten S R, Wicker T, Richmond T A, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer K F X, Taudien S, Platzer M, Jeddeloh J A, Springer N M, Muehlbauer G J, Stein N Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol. 14 (2013) R58. dx.doi.org/10.1186/gb-2013-14-6-r58
Pellino M, Hojsgaard D, Schmutzer T, Scholz U, Hörandl E, Vogel H, Sharbel T F Asexual genome evolution in the apomictic Ranunculus auricomus complex: examining the effects of hybridization and mutation accumulation. Mol. Ecol. 22 (2013) 5908-5921. dx.doi.org/10.1111/mec.12533
Peukert M, Weise S, Röder M S, Matthies I E Development of SNP markers for genes of the phenylpropanoid pathway and their association to kernel and malting traits in barley. BMC Genet. 14 (2013) e97. dx.doi.org/10.1186/1471-2156-14-97
Poursarebani N, Ariyadasa R, Zhou R, Schulte D, Steuernagel B, Martis M M, Graner A, Schweizer P, Scholz U, Mayer K, Stein N Conserved synteny-based anchoring of the barley genome physical map. Funct. Integr. Genomics 13 (2013) 339-350. dx.doi.org/10.1007/s10142-013-0327-2
Pratzka V In silico analysis of genes involved in the initiation of barley pollen embryogenesis. (Bachelor Thesis) Mittweida, Hochschule Mittweida (FH) (2013) 54 pp.
Schlüter U, Colmsee C, Scholz U, Bräutigam A, Weber A P M, Zellerhoff N, Bucher M, Fahnenstich H, Sonnewald U Adaptation of maize source leaf metabolism to stress related disturbances in carbon, nitrogen and phosphorus balance. BMC Genomics 14 (2013) e442. dx.doi.org/10.1186/1471-2164-14-442
Schreiber F, Hofestädt R, Lange M, Scholz U, Czauderna T, Schnee R, Weise S (Eds.) Proceedings of the 9th International Symposium on Integrative Bioinformatics 2013: 18 - 20 March 2013, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben. Gatersleben (2013) 214 pp.
Ulpinnis C Evaluation von Fehlerkorrektur-Algorithmen für Sequenzdaten in komplexen Pflanzengenomen. (Bachelor Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 119 pp.
2012
Arend D Konzeption und Implementierung einer Datenhaltungsinfrastruktur zur digitalen Langzeitarchivierung und dauerhaften Zitierbarkeit biologischer Primärdaten am Beispiel von ”Next-Generation-Sequencing“-Daten. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2012) 121 pp.
Arend D The e!DAL JAVA-API – store, share and cite primary data in life sciences. In: Hofestädt R, Kolchanov N (Eds.): German/Russian Network of Computational Systems Biology: Report 2012. (Series: Berichte aus der Medizinischen Informatik und Bioinformatik) Aachen: Shaker (2012) 46-47. ISBN 978-3-8440-1573-7
Arend D, Lange M, Colmsee C, Flemming S, Chen J, Scholz U The e!DAL JAVA-API: Store, share and cite primary data in life sciences. In: Gao J, Alhaij R, Dubitzky W, Ungar L, Wu C, Christianson A, Liebman M, Hu X (Eds.): IEEE International Conference on Bioinformatics and Biomedicine workshops (BIBMW 2012), 4–7 October 2012, Philadelphia, U.S.A., proceedings. Piscataway, NJ: IEEE (2012) 511-515. dx.doi.org/10.1109/BIBM.2012.6392737 ISBN 978-1-4673-2746-6
Cockram J, Thiel T, Steuernagel B, Stein N, Taudien S, Bailey P C, O'Sullivan D M Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae. PLoS One 7 (2012) e45307. dx.doi.org/10.1371/journal.pone.0045307
Colmsee C, Keller E R J, Zanke C, Senula A, Funke T, Oppermann M, Weise S, Scholz U The Garlic and Shallot Core Collection image database of IPK presenting two vegetatively maintained crops in the Federal ex situ genebank for agricultural and horticultural crops at Gatersleben, Germany. Genet. Resour. Crop Evol. 59 (2012) 1407-1415. dx.doi.org/10.1007/s10722-011-9768-4
Colmsee C, Mascher M, Czauderna T, Hartmann A, Schlüter U, Zellerhoff N, Schmitz J, Bräutigam A, Pick T R, Alter P, Gahrtz M, Witt S, Fernie A R, Börnke F, Fahnenstich H, Bucher M, Dresselhaus T, Weber A P, Schreiber F, Scholz U, Sonnewald U OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. BMC Plant Biol. 12 (2012) 245. dx.doi.org/10.1186/1471-2229-12-245
Colmsee C, Zanke C, Funke T, Weise S, Keller E R J, Scholz U The Garlic and Shallot Core Collection (GSCC). www.ipk-gatersleben.de/databases/genetic_resources/gscc (2012).
Keller E R J, Zanke C, Scholz U EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound. euralliveg.ipk-gatersleben.de (2012).
Kohl S, Hollmann J, Blattner F R, Radchuk V, Andersch F, Steuernagel B, Schmutzer T, Scholz U, Krupinska K, Weber H, Weschke W A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq. BMC Plant Biol. 12 (2012) 154. dx.doi.org/10.1186/1471-2229-12-154
Lange M Management of scientific data at the IPK Gatersleben. In: Hofestädt R, Kolchanov N (Eds.): German/Russian Network of Computational Systems Biology: Report 2012. (Series: Berichte aus der Medizinischen Informatik und Bioinformatik) Aachen: Shaker (2012) 32-33. ISBN 978-3-8440-1573-7
Lange M, Chen J, Scholz U The LAILAPS search engine: new features. Proceedings of the 8th International Symposium on Integrative Bioinformatics (IB2012), Zhejiang University, Hangzhou, China, April 2 - 4, 2012 (2012) 155-157.
Lange M, Chen J, Scholz U LAILAPS– The Life Science Search Engine. lailaps.ipk-gatersleben.de (2012).
Lange M, Chen J, Scholz U The LAILAPS Search Engine. In: U. Goltz, M. Magnor, H.-J. Appelrath, H. K. Matthies, W.-T. Balke, Wolf L (Eds.): Informatik 2012: Was bewegt uns in der/die Zukunft?: 42. Jahrestagung der Gesellschaft für Informatik e.V. (GI), 16. bis 21.9.2012, TU Braunschweig. (Series: GI-Edition, Lecture notes in informatics, Vol. 208) Bonn: Ges. für Informatik (2012) 1552-1558. ISBN 978-3-88579-602-2
Mameaux S, Cockram J, Thiel T, Steuernagel B, Stein N, Taudien S, Jack P, Werner P, Gray J C, Greenland A J, Powell W Molecular, phylogenetic and comparative genomic analysis of the cytokinin oxidase/dehydrogenase gene family in the Poaceae. Plant Biotechnol. J. 10 (2012) 67-82. dx.doi.org/10.1111/j.1467-7652.2011.00645.x
Martis M M, Klemme S, Banaei Moghaddam A M, Blattner F R, 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 K F X, Houben A Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. Proc. Natl. Acad. Sci. U.S.A. 109 (2012) 13343-13346. dx.doi.org/10.1073/pnas.1204237109
Matthies I E, Sharma S, Weise S, Röder M S Sequence variation in the barley genes encoding sucrose synthase I and sucrose phosphate synthase II, and its association with variation in grain traits and malting quality. Euphytica 184 (2012) 73-83. dx.doi.org/10.1007/s10681-011-0563-2
Matthies I E, van Hintum T, Weise S, Röder M S Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars. Mol. Breed. 30 (2012) 951-966. dx.doi.org/10.1007/s11032-011-9678-3
Matthies I E, Weise S, Förster K, Röder M S Association mapping and marker development of the candidate genes (1->3),(1->4)-β-D-Glucan-4-glucanohydrolase and (1->4)-β-Xylan-endohydrolase 1 for malting quality in barley. pgrc.ipk-gatersleben.de/glb, pgrc.ipk-gatersleben.de/X-1 & pgrc.ipk-gatersleben.de/Phendat (2012).
Matthies I E, Weise S, Röder M S Association of haplotype diversity in the α-amylase gene amy1 with malting quality parameters in barley. pgrc.ipk-gatersleben.de/alpha-amylase (2012).
Mayer K F X, Waugh R, Langridge P, Close T J, Wise R P, Graner A, Matsumoto T, Sato K, Schulman A, Ariyadasa R, Schulte D, Poursarebani N, Zhou R, Steuernagel B, Mascher M, Scholz U, Shi B, Madishetty K, Svensson J T, Bhat P, Moscou M, Resnik J, Muehlbauer G J, Hedley P, Liu H, Morris J, Frenkel Z, Korol A, Bergès H, Taudien S, Felder M, Groth M, Platzer M, Himmelbach A, Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Ciardo G, Ma Y, Wanamaker S, Cattonaro F, Vendramin V, Scalabrin S, Radovic S, Wing R, Morgante M, Nussbaumer T, Gundlach H, Martis M, Poland J, Pfeifer M, Moisy C, Tanskanen J, Zuccolo A, Spannagl M, Russell J, Druka A, Marshall D, Bayer M, Swarbreck D, Sampath D, Ayling S, Febrer M, Caccamo M, Tanaka T, Wannamaker S, Schmutzer T, Brown J W S, Fincher G B, Stein N A physical, genetic and functional sequence assembly of the barley genome. Nature 491 (2012) 711-716. dx.doi.org/10.1038/nature11543
Mehlhorn H, Lange M, Scholz U, Schreiber F IDPredictor: predict database links in biomedical database. J. Integr. Bioinform. 9 (2012) e190. dx.doi.org/10.2390/biecoll-jib-2012-190
Röhl B Entwurf und Implementierung einer Software zur Registrierung von DOI-Nummern für IPK-Primärdaten. (Bachelor Thesis) Magdeburg, Otto-von-Guericke-Universität Magdeburg, Fakultät für Informatik (2012) 54 pp.
Schlüter U, Mascher M, Colmsee C, Scholz U, Bräutigam A, Fahnenstich H, Sonnewald U Maize source leaf adaptation to nitrogen deficiency effects not only nitrogen and carbon metabolism but also control of phosphate homeostasis. Plant Physiol. 160 (2012) 1384-1406. dx.doi.org/10.1104/pp.112.204420
Scholz U, Künne C, Lange M, Miehe H, Funke T CR-EST: a resource for crop ESTs. pgrc.ipk-gatersleben.de/cr-est (2012).
Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker B H, Klapperstück M, Scholz U, Weise S MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res. 40 (2012) D1173-D1177. dx.doi.org/10.1093/nar/gkr1004
Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker B H, Koschützki D, Scholz U, Weise S MetaCrop 2.0. metacrop.ipk-gatersleben.de (2012).
Silvar C, Perovic D, Scholz U, Casas A M, Igartua E, Ordon F Fine mapping and comparative genomics integration of two quantitative trait loci controlling resistance to powdery mildew in a Spanish barley landrace. Theor. Appl. Genet. 124 (2012) 49-62. dx.doi.org/10.1007/s00122-011-1686-5
Steuernagel B Next generation sequence analysis of the highly repetitive barley genome. (PhD Thesis) Jena, Friedrich-Schiller-Universität Jena, Biologisch-Pharmazeutische Fakultät (2012) 115 pp.
Thiel J, Hollmann J, Rutten T, Weber H, Scholz U, Weschke W 454 transcriptome sequencing suggests a role for two-component signalling in cellularization and differentiation of barley endosperm transfer cells. PLoS One 7 (2012) e41867. dx.doi.org/10.1371/journal.pone.0041867
Weise S, Harrer S, Grosse I, Knüpffer H, Willner E The European Poa Database (EPDB). poa.ipk-gatersleben.de (2012).
Weise S, Scholz U, Röder M S, Matthies I E MetaBrew: A comprehensive database of malting quality traits in brewing barley. metabrew.ipk-gatersleben.de (2012).
Wolff D Sequenzanalyse und Visualisierung von Triticum aestivum BACs. (Bachelor Thesis) Köthen, Hochschule Anhalt (FH), Fachbereich Angewandte Biowissenschaften und Prozesstechnik (2012) 68 pp.
Zakhrabekova S, Gough S P, Braumann I, Müller A H, Lundqvist J, Ahmann K, Dockter C, Matyszczak I, Kurowska M, Druka A, Waugh R, Graner A, Stein N, Steuernagel B, Lundqvist U, Hansson M Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range extension in cultivated barley. Proc. Natl. Acad. Sci. U.S.A. 109 (2012) 4326-4331. dx.doi.org/10.1073/pnas.1113009109
2011
Bachmann A Anfrageranking in Suchmaschinen der Lebenswissenschaften unter Berücksichtigung der Bewertung von Querverweisen. (Bachelor Thesis) Magdeburg, Otto-von-Guericke Universität Magdeburg, Fakultät für Informatik (2011) 71 pp.
Bachmann A, Schult R, Lange M, Spiliopoulou M Extracting cross references from life science databases for search result ranking. In: Berendt B, de Vries A, Fan W, Macdonald C, Ounis I, Ruthven I (Eds.): Proceedings of the 20th ACM International Conference on Information and Knowledge Management, 24 - 28 October 2011, Glasgow, Scotland/UK. New York, NY, USA: ACM (2011) 1253-1258. dx.doi.org/10.1145/2063576.2063758 ISBN 978-1-4503-0717-8
Colmsee C, Flemming S, Klapperstück M, Lange M, Scholz U A case study for efficient management of high throughput primary lab data. BMC Res. Notes 4 (2011) 413. dx.doi.org/10.1186/1756-0500-4-413
Colmsee C, Zanke C, Funke T, Weise S, Keller E R J, Scholz U The Garlic and Shallot Core Collection (GSCC). www.ipk-gatersleben.de/databases/genetic_resources/gscc (2011).
Friedrich C Entwurf und Implementierung einer JAVA-API zum Zugriff und zur DBMS-unabhängigen Persistierung von Bild- und Metadaten aus einer Pflanzenphänotypisierungsanlage. (Diploma Thesis) Wernigerode, Hochschule Harz, Fachbereich Automatisierung und Informatik (2011) 147 pp.
Haseneyer G, Schmutzer T, Seidel M, Zhou R, Mascher M, Schon C C, Taudien S, Scholz U, Stein N, Mayer K F, Bauer E From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.). BMC Plant Biol. 11 (2011) 131. dx.doi.org/10.1186/1471-2229-11-131
Keller E R J, Zanke C, Scholz U EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound euralliveg.ipk-gatersleben.de (2011).
Lange M, Chen J, Scholz U LAILAPS– The Life Science Search Engine. lailaps.ipk-gatersleben.de (2011).
Matthies I E, Weise S, Förster K, Röder M S Association mapping and marker development of the candidate genes (1->3),(1->4)-β-D-Glucan-4-glucanohydrolase and (1->4)-β-Xylan-endohydrolase 1 for malting quality in barley. pgrc.ipk-gatersleben.de/glb, pgrc.ipk-gatersleben.de/X-1 & pgrc.ipk-gatersleben.de/Phendat (2011).
Matthies I E, Weise S, Röder M S Association of haplotype diversity in the α-amylase gene amy1 with malting quality parameters in barley. pgrc.ipk-gatersleben.de/alpha-amylase (2011).
Mayer K F X, Martis M, Hedley P E, Šimková H, Liu H, Morris J A, 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, Doležel J, Waugh R, Stein N Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23 (2011) 1249-1263. dx.doi.org/10.1105/tpc.110.082537
Pick T R, Bräutigam A, Schluter U, Denton A K, Colmsee C, Scholz U, Fahnenstich H, Pieruschka R, Rascher U, Sonnewald U, Weber A P Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation. Plant Cell 23 (2011) 4208-4220. dx.doi.org/10.1105/tpc.111.090324
Scholz U, Künne C, Lange M, Miehe H, Funke T CR-EST: a resource for crop ESTs. pgrc.ipk-gatersleben.de/cr-est (2011).
Schönherr I S Assemblierung und Analyse des Vitis vinifera Genoms der Rebsorte Riesling. (Bachelor Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik (2011) 40 pp.
Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker B H, Koschützki D, Scholz U, Weise S MetaCrop 2.0. metacrop.ipk-gatersleben.de (2011).
Seiler C, Harshavardhan V T, Kalladan R, Reddy P S, Strickert M, Rolletschek H, Scholz U, Wobus U, Sreenivasulu N ABA biosynthesis and degradation contributing to ABA homeostasis during barley seed development under control and terminal drought-stress conditions. J. Exp. Bot. 62 (2011) 2615-2632. dx.doi.org/10.1093/jxb/erq446
Steuernagel B, Scholz U POCI annotation tool. pgrc.ipkgatersleben.de/poci (2011).
Taudien S, Steuernagel B, Ariyadasa R, Schulte D, Schmutzer T, Groth M, Felder M, Petzold A, Scholz U, Mayer K F, Stein N, Platzer M Sequencing of BAC pools by different next generation sequencing platforms and strategies. BMC Res Notes 4 (2011) 411. dx.doi.org/10.1186/1756-0500-4-411
Weise S, Chen J, Junker B H, Klapperstück M, Lange M, Schreiber F, Scholz U Das Informationssystem MetaCrop zur Unterstützung systembiologischer Forschung an Kulturpflanzen. it - Information Technology 53 (2011) 234-240. dx.doi.org/10.1524/itit.2011.0648
Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H Meta-All: A system for managing metabolic pathway information. meta-all.ipk-gatersleben.de (2011).
Weise S, Harrer S, Grosse I, Knüpffer H, Willner E The European Poa Database (EPDB). poa.ipk-gatersleben.de (2011).
Weise S, Scholz U, Röder M S, Matthies I E MetaBrew: A comprehensive database of malting quality traits in brewing barley. metabrew.ipk-gatersleben.de (2011).
Wicker T, Mayer K F X, 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. Plant Cell 23 (2011) 1706-1718. dx.doi.org/10.1105/tpc.111.086629
2010
Breuillin F, Schramm J, Hajirezaei M-R, Ahkami A, Favre P, Druege U, Hause B, Bucher M, Kretzschmar T, Bossolini E, Kuhlemeier C, Martinoia E, Franken P, Scholz U, Reinhardt D Phosphate systemically inhibits development of arbuscular mycorrhiza in Petunia hybrida and represses genes involved in mycorrhizal functioning. Plant J. 64 (2010) 1002-1017. dx.doi.org/10.1111/j.1365-313X.2010.04385.x
Cockram J, White J, Zuluaga D L, Smith D, Comadran J, Macaulay M, Luo Z, Kearsey M J, Werner P, Harrap D, Tapsell C, Liu H, Hedley P E, Stein N, Schulte D, Steuernagel B, Marshall D F, Thomas W T, Ramsay L, Mackay I, Balding D J, Consortium T A, Waugh R, O'Sullivan D M Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc. Natl. Acad. Sci. U. S. A. 107 (2010) 21611-21616. dx.doi.org/10.1073/pnas.1010179107
Colmsee C, Zanke C, Funke T, Weise S, Keller E R J, Scholz U The Garlic and Shallot Core Collection (GSCC). www.ipk-gatersleben.de/databases/genetic_resources/gscc (2010).
Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F MetaCrop – A detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2010).
Hippe K, Colmsee C, Czauderna T, Grafahrend-Belau E, Junker B H, Klukas C, Scholz U, Schreiber F, Weise S Novel developments of the MetaCrop information system for facilitating systems biological approaches. J. Integr. Bioinform. 7 (2010) e125. dx.doi.org/10.2390/biecoll-jib-2010-125
Keller E R J, Zanke C, Scholz U EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound euralliveg.ipk-gatersleben.de (2010).
Lange M, Bargsten J, Weißbach M, Spies K, Scholz U LAILAPS– The Life Science Search Engine. lailaps.ipk-gatersleben.de (2010).
Lange M, Rutkowski T, Stephanik A, Steuernagel B, Scholz U FLAREX – The IPK array experiment database. pgrc.ipk-gatersleben.de/flarex (2010).
Lange M, Spies K, Bargsten J, Haberhauer G, Klapperstück M, Leps M, Weinel C, Wunschiers R, Weissbach M, Stein J, Scholz U The LAILAPS search engine: relevance ranking in life science databases. J. Integr. Bioinform. 7 (2010) 110. dx.doi.org/10.2390/biecoll-jib-2010-110
Lange M, Spies K, Colmsee C, Flemming S, Klapperstück M, Scholz U The LAILAPS search engine: a feature model for relevance ranking in life science databases. J. Integr. Bioinform. 7 (2010) 118. dx.doi.org/10.2390/biecoll-jib-2010-118
Lange M, Weise S, Scholz U, Verrier P, Rawlings C (Eds.) Proceedings of the 6th International Symposium on Integrative Bioinformatics 2010, 22 - 24 March 2010, Cambridge, United Kingdom. (2010) 406 pp.
Matthies I E, Weise S, Förster K, Röder M S Association mapping and marker development of the candidate genes (1->3),(1->4)-β-D-Glucan-4-glucanohydrolase and (1->4)-β-Xylan-endohydrolase 1 for malting quality in barley. pgrc.ipk-gatersleben.de/glb, pgrc.ipk-gatersleben.de/X-1 & pgrc.ipk-gatersleben.de/Phendat (2010).
Matthies I E, Weise S, Röder M S Association of haplotype diversity in the α-amylase gene amy1 with malting quality parameters in barley. pgrc.ipk-gatersleben.de/alpha-amylase (2010).
Matthies I E, Weise S, Röder M S Assoziationskartierung in Gerste – Ein genomweiter und Kandidatengenansatz. In: Vereinigung der Pflanzenzüchter und Saatgutkaufleute Österreichs (Ed.): Züchtung und Genressourcen gegen abiotische Stressfaktoren, markergestützte Selektion in der Praxis: 60. Tagung, 24. - 26. November 2009. (Series: Tagung / Vereinigung der Pflanzenzüchter und Saatgutkaufleute Österreichs, Vol. 60) Irdning: Lehr- und Forschungsanstalt für Landwirtschaft Raumberg-Gumpenstein (2010) 91-96. ISBN 978-3-902559-37-1
Navakode S, Weidner A, Varshney R K, Lohwasser U, Scholz U, Röder M S, Börner A A genetic analysis of aluminium tolerance in cereals. Agriculturae Conspectus Scientificus 75 (2010) 191-196.
Scholz U, Künne C, Lange M, Miehe H, Funke T CR-EST: a resource for crop ESTs. pgrc.ipk-gatersleben.de/cr-est (2010).
Steuernagel B, Scholz U POCI annotation tool. pgrc.ipkgatersleben.de/poci (2010).
Weise S, Biermann N, Flemming S, Vorwald J, van Hintum T, Knüpffer H, Grosse I Proposal for improvement of PGR data exchange through XML. In: Proc. EPGRIS Final Conference, 11-13 September 2003, Prague, Czech Republic. International Plant Genetic Resources Institute (IPGRI). www.ecpgr.cgiar.org/Networks/Info_doc/FinalMeetingPresentations/Papers/Bierman_IPK_v0.14.doc (2010).
Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H Meta-All: A system for managing metabolic pathway information. meta-all.ipk-gatersleben.de (2010).
Weise S, Harrer S, Grosse I, Knüpffer H, Willner E The European Poa Database (EPDB). poa.ipk-gatersleben.de (2010).
Weise S, Scholz U, Röder M S, Matthies I E MetaBrew: A comprehensive database of malting quality traits in brewing barley. metabrew.ipk-gatersleben.de (2010).
2009
Bargsten J Nutzerprofilgestütztes Schätzen von Rankingparametern für Suchmaschinen-Anfragen an integrierte biologische Datenbanken. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2009) 103 pp.
Colmsee C Reengineering des SBML-Exporters für das metabolische Netzwerkinformationssystem MetaCrop. (Diploma Thesis) Wernigerode, Hochschule Harz (FH), Fachbereich Automatisierung und Informatik (2009) 99 pp.
Colmsee C, Zanke C, Funke T, Weise S, Keller E R J, Scholz U The Garlic and Shallot Core Collection (GSCC). www.ipk-gatersleben.de/databases/genetic_resources/gscc (2009).
Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F MetaCrop – A detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2009).
Günther M Konzeption und Implementierung einer Textindexierungsinfrastruktur zur Parallelisierung von Suchmaschinen in den Lebenswissenschaften. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2009) 95 pp.
Keller E R J, Zanke C, Scholz U EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound euralliveg.ipk-gatersleben.de (2009).
Lange M, Bargsten J, Günther M, Spies K, Scholz U Lailaps – The Life Science Search Engine. lailaps.ipk-gatersleben.de (2009).
Matthies I E, Weise S, Förster J, Röder M S Association mapping and marker development of the candidate genes (1→3),(1→4)-β-D-Glucan-4-glucanohydrolase and (1→4)-β-Xylan-endohydrolase 1 for malting quality in barley. Euphytica 170 (2009) 109-122. dx.doi.org/10.1007/s10681-009-9915-6
Matthies I E, Weise S, Röder M S Association of haplotype diversity in the alpha-amylase gene amy1 with malting quality parameters in barley. Mol. Breed. 23 (2009) 139-152. dx.doi.org/10.1007/s11032-008-9221-3
Mayer K F, Taudien S, Martis M, Simkova H, Suchankova 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. 151 (2009) 496-505. dx.doi.org/10.1104/pp.109.142612
Nagel M, Vogel H, Landjeva S, Buck-Sorlin G, Lohwasser U, Scholz U, Börner A Seed conservation in ex situ genebank - genetic studies on longevity in barley. Euphytica 170 (2009) 5-14. dx.doi.org/10.1007/s10681-009-9975-7
Navakode S, Weidner A, Varshney R K, Lohwasser U, Scholz U, Börner A A QTL analysis of aluminium tolerance in barley, using gene-based markers. Cereal Res. Commun. 37 (2009) 531-540. dx.doi.org/10.1556/CRC.37.2009.4.6
Schäfer P, Pfiffi S, Voll L M, Zajic D, Chandler P M, Waller F, Scholz U, Pons-Kuhnemann J, Sonnewald S, Sonnewald U, Kogel K H Manipulation of plant innate immunity and gibberellin as factor of compatibility in the mutualistic association of barley roots with Piriformospora indica. Plant J. 59 (2009) 461-474. dx.doi.org/10.1111/j.1365-313X.2009.03887.x
Schäfer P, Pfiffi S, Voll L M, Zajic D, Chandler P M, Waller F, Scholz U, Pons-Kühnemann J, Sonnewald S, Sonnewald U, Kogel K H Phytohormones in plant root-Piriformospora indica mutualism. Plant Signal. Behav. 4 (2009) 669-671. dx.doi.org/10.4161/psb.4.7.9038
Schoor W, Mecke R, Seiffert U, Bollenbeck F, Schulz U Remote rendering of large biological datasets. In: Ranchordas A K, Pereira J, Richard P (Eds.): GRAPP 2009 - proceedings of the 4th International Conference on Computer Graphics Theory and Applications, Lisboa, Portugal, February 5-8, 2009. [Setúbal]: INSTICC Press (2009) 223-227. ISBN 978-989-8111-67-8
Steuernagel B, Taudien S, Gundlach H, Seidel M, Ariyadasa R, Schulte D, Petzold A, Felder M, Graner A, Scholz U, Mayer K F, 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 10 (2009) 547. dx.doi.org/10.1186/1471-2164-10-547
Sturm J Visualisierungsstrategien für bioinformatische Anwendungen. (Diploma Thesis) Köthen, Hochschule Anhalt (FH), Fachbereich Informatik (2009) 76 pp.
Weise S Integrierte Analyse pflanzenbiologischer Daten unter besonderer Berücksichtigung der Datenqualität. (PhD Thesis) Bielefeld, Universität Bielefeld, Technische Fakultät (2009) 187 pp.
Weise S, Colmsee C, Grafahrend-Belau E, Junker B, Klukas C, Lange M, Scholz U, Schreiber F An integration and analysis pipeline for systems biology in crop plant metabolism. In: Paton N W, Missier P, Hedeler C (Eds.): Data integration in the life sciences: 6th international workshop, DILS 2009, Manchester, UK, July 20-22, 2009, proceedings. (Series: Lecture Notes in Computer Science, Vol. 5647) Berlin [u.a.]: Springer (2009) 196-203. dx.doi.org/10.1007/978-3-642-02879-3_16 ISBN 978-3-642-02878-6
Weise S, Colmsee C, Grafahrend-Belau E, Junker B, Klukas C, Lange M, Scholz U, Schreiber F Datenaustausch und Datenintegration zur Modellierung und Analyse metabolischer Netzwerke am Beispiel von Kulturpflanzen. In: Fischer S, Maehle E, Reischuk R (Eds.): Informatik 2009: im Focus das Leben, Beiträge der 39. Jahrestagung der Gesellschaft für Informatik e.V. (GI), 28.9. - 2.10.2009 in Lübeck. (Series: GI-Edition, Lecture notes in informatics, Vol. 154) Bonn: Ges. für Informatik (2009) 693-697. ISBN 978-3-88579-248-2
Weise S, Scholz U, Röder M S, Matthies I E MetaBrew: A comprehensive database of malting quality traits in brewing barley. metabrew.ipk-gatersleben.de (2009).
Weise S, Scholz U, Röder M S, Matthies I E Metabrew: A comprehensive database of malting quality traits in brewing barley. Barley Genet. Newsl. 39 (2009) 1-4.
Wittwer C Herleitung und Extraktion von Schematagraphen aus integrierten Datenbanken der Lebenswissenschaften. (Bachelor Thesis) Magdeburg, Otto-von-Guericke-Universität, Fakultät für Informatik, Institut für Technische und Betriebliche Informationssysteme (2009) 73 pp.
2008
Grafahrend-Belau E, Junker B H, Koschützki D, Klukas C, Weise S, Scholz U, Schreiber F Towards systems biology of developing barley grains: a framework for modeling metabolism. In: Ahdesmäki M, Strimmer K, Radde N, Rahnenführer J, Klemm K, Lähdesmäki H, Yli-Harja O (Eds.): 5th International Workshop on Computational Systems Biology, WCSB 2008, June 11–13, 2008, Leipzig, Germany, proceedings. (TICSP series, Vol. 41) Tampere: Tampere International Center for Signal Processing (2008) 41-44. ISBN 978-952-15-1988-8
Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res. 36 (2008) D954-D958. dx.doi.org/10.1093/nar/gkm835
Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F MetaCrop: a detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2008).
Hofestädt R, Köhler J, Lange M, Scholz U, Schreiber F, Verrier P (Eds.) Proceedings of the 5th International Symposium on Integrative Bioinformatics 2008: 20 - 22 August 2008 Leucorea, Lutherstadt Wittenberg, Germany. Wittenberg (2008) 345 pp.
Kloosterman B, De Koeyer D, Griffiths R, Flinn B, Steuernagel B, Scholz U, Sonnewald S, Sonnewald U, Bryan G J, Prat S, Bánfalvi Z, Hammond J P, Geigenberger P, Nielsen K L, Visser R G, Bachem C W Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array. Funct. Integr. Genomics 8 (2008) 329-340. dx.doi.org/10.1007/s10142-008-0083-x
Lange M, Klapperstück M, Spies K, Scholz U DALIGRES: A graph query tool to unravel the life science database maze. (Best Paper Award). In: Borovska P (Ed.): Proceedings of the IV International Bulgarian-Greek Scientific Conference on Computer Science 2008, Kavala, Greece, 18-19 September 2008. Heron Press (2008) 603-613. ISBN 978-954-580-254-6
Lange M, Rutkowski T, Stephanik A, Steuernagel B, Scholz U FLAREX – The IPK array experiment database. pgrc.ipk-gatersleben.de/flarex/ (2008).
Scholz U, Künne C, Lange M, Miehe H, Funke T IPK crop EST database: CR-EST (Version 1.5). pgrc.ipk-gatersleben.de/cr-est/ (2008).
Spies K, Klapperstück M, Bargsten J, Lange M, Scholz U LAILAPS – Life science search engine. lailaps.ipk-gatersleben.de (2008).
Sreenivasulu N, Usadel B, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close T J, Stitt M, Graner A, Wobus U Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by New MapMan/PageMan profiling tools. Plant Physiol. 146 (2008) 1738-1758. dx.doi.org/10.1104/pp.107.111781
Steuernagel B, Scholz U POCI annotation tool. pgrc.ipk-gatersleben.de/poci/ (2008).
Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H Meta-All: A system for managing metabolic pathway Information. meta-all.ipk-gatersleben.de (2008).
Weise S, Scholz U, Röder M S, Matthies I MetaBrew: A comprehensive database of malting quality traits in brewing barley. metabrew.ipk-gatersleben.de (2008).
2007
Biemelt S, Senning M, Sonnewald U, Scholz U, Steuernagel B, Theres K, Schmitz G, Prat S, Navarro C, Cubas P, Traas J, Nikovics K, Laufs P GABI-GENOSOME: Ertrag und Lagerfähigkeit von Kartoffeln und Tomaten verbessern. GenomXPress Sonderausgabe März (2007) 21.
Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F MetaCrop – A detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2007).
Heiß S Entwicklung eines Data-Warehouses für pflanzengenetische Diversitätsstudien. (Diploma Thesis) Magdeburg, Otto-von-Guericke-Universität Magdeburg (2007)
Keller E R J, Zanke C, Scholz U EURALLIVEG - Vegetative Allium, Europe’s Core Collection, Safe and Sound euralliveg.ipk-gatersleben.de (2007).
Klapperstück M Konzeption und Umsetzung einer Graphanfragesprache zur nicht-materialisierten Integration biologischer Datenbanken. (Diploma Thesis) Halle, Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik (2007) 98 pp.
Koopmann J H Integrierte plattformübergreifende Normalisierung von Expressionsdaten. (Diploma Thesis) Halle, Martin-Luther-Universität Halle-Wittenberg (2007)
Kuenne C, Grosse I, Matthies I, Scholz U, Sretenovic-Rajicic T, Stein N, Stephanik A, Steuernagel B, Weise S Using data warehouse technology in crop plant bioinformatics. J. Integr. Bioinform. 4 (2007) 88. dx.doi.org/10.2390/biecoll-jib-2007-88
Lange M, Himmelbach A, Schweizer P, Scholz U Data Linkage Graph: computation, querying and knowledge discovery of life science database networks. J. Integr. Bioinform. 4 (2007) 68. dx.doi.org/10.2390/biecoll-jib-2007-68
Lange M, Scholz U Datenverarbeitung in der Biologie. Erbe Information. iX 3 (2007) 106-109.
Scholz U, Künne C, Lange M, Miehe H, Funke T IPK Crop EST Database: CR-EST (Version 1.5). pgrc.ipk-gatersleben.de/cr-est/ (2007).
Senning M, Steuernagel B, Hartmann A, Sonnewald U, Scholz U Regulation der Keimruhe von Kartoffelknollen. GenomXPress 3 (2007) 7-10.
Spies K Integration von Bioinformatikdatenbanken und -anwendungen des IPK Gatersleben mittels Web-Services in die internationale Bioinformatik-Infrastruktur. (Diploma Thesis) Halle, Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik (2007) 110 pp.
Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney R K, Perovic D, Grosse I, Graner A A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor. Appl. Genet. 114 (2007) 823-839. dx.doi.org/10.1007/s00122-006-0480-2
Suray M Methoden und Werkzeuge zur automatischen Indexierung und Schemaextraktion über Deep-Web-Datenquellen. (Diploma Thesis) Bielefeld, Universität Bielefeld, Technische Fakultät (2007) 95 pp.
Totz J Workflow-supported Analysis of Gene Expression Data. (Diploma Thesis) Magdeburg, Otto-von-Guericke-Universität (2007)
Weise S, Harrer S, Grosse I, Knüpffer H, Willner E The European Poa Database (EPDB). Plant Genet. Resour. Newsl. 150 (2007) 64-70.
Xia M Hierarchische Datenbankanfrage auf integrierte Datenbanken zur Funktionsklassifikation von molekularbiologischen Daten. (Diploma Thesis) Bielefeld, Universität Bielefeld, Technische Fakultät (2007) 77 pp.
2006
Eichmann R, Biemelt S, Schäfer P, Scholz U, Jansen C, Felk A, Schafer W, Langen G, Sonnewald U, Kogel K H, Hückelhoven R Macroarray expression analysis of barley susceptibility and nonhost resistance to Blumeria graminis. J. Plant Physiol. 163 (2006) 657-670. dx.doi.org/10.1016/j.jplph.2005.06.019
Funke T, Weise S, Knüpffer H, Grosse I Ein neues Gesicht für die Europäische Gerstendatenbank (EBDB). Vortr. Pflanzenzücht. 70 (2006) 79-80.
Große I, Funke T, Kuenne C, Neumannn S, Stephanik A, Thiel T, Weise S Integrative Datenanalyse mit dem Plant Data Warehouse. Vortr. Pflanzenzücht. 70 (2006) 50-53.
Kaule U Analyse und Strukturierung von Workflows im Anwendungsfeld bioinformatischer Prozesse. (Diploma Thesis) Magdeburg, Otto-von-Guericke-Universität - Fakultät für Informatik Institut für Technische und Betriebliche Informationssysteme (2006)
Lange M Methoden zum homogenen Zugriff und zur Integration heterogener, biologischer Datenquellen mittels beschränkter Zugriffsmuster. (PhD Thesis) Magdeburg, Otto-von-Guericke-Universität - Fakultät für Informatik Institut für Technische und Betriebliche Informationssysteme (2006) 218 pp.
Riedel A Konzept zur Daten- und Anwendungsintegration zur Analyse von Gen-Expressionsdaten. (Diploma Thesis) Magdeburg, Otto-von-Guericke-Universität - Fakultät für Informatik Institut für Technische und Betriebliche Informationssysteme (2006)
Spieß K Integration von Bioinformatikdatenbanken und -anwendungen des IPK Gatersleben mittels Web-Services in die internationale Bioinformatik-Infrastruktur. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle/Wittenberg, Institut für Informatik (2006)
Stephanik A, Bachmann H, Funke T, Kuenne C, Langer E, Thiel T, Weise S, Große I Das Plant Bioinformatics Portal. Vortr. Pflanzenzücht. 70 (2006) 81-83.
Tischler T Entwurf und Implementierung einer Integrationslösung für Anwendungen in der Bioinformatik. (Diploma Thesis) Magdeburg, Otto-von-Guericke-Universität - Fakultät für Informatik, Institut für Technische und Betriebliche Informationssysteme (2006)
Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H Meta-All: a system for managing metabolic pathway information. BMC Bioinformatics 7 (2006) 465. dx.doi.org/10.1186/1471-2105-7-465
Weise S, Knüpffer H, Vorwald J, Scholz U, Grosse I Integration von phänotypischen Daten in das Plant Data Warehouse. Vortr. Pflanzenzücht. 70 (2006) 84-86.