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IPK Gatersleben > Research > Dept. Cytogenetics and Genome Analysis > Bioinformatics and Information Technology
 

 
Bioinformatics and Information Technology
Head: Dr Uwe Scholz
Tel: +49 (0)39482 5513
Fax: +49 (0)39482 5595
Email: scholz@ipk-gatersleben.de

Research Interest

The research group Bioinformatics and Information Technology focuses on the development, installation and provision of bioinformatic tools and the implementation of biological databases to support in silico analysis of various IPK research groups.
Primary tasks are the effective support to store genomic data within specific databases (e.g. CR-EST), to offer selected tools for data analysis with information retrieval as the final goal, the evaluation of currently available bioinformatic tools and consulting concerning topics like data storage and use of the analysis tools.
An additional interest is the data integration. Goal of these activities is the consolidation of the worldwide distributed data including the minimisation of redundancy and the provision of user-specific views onto the integrated data set.

The tasks of the group also include the operation of the central IT services, like network, central file server, archiving and backup. In this context, the group provides a file server cluster for the central storage of user files. Furthermore, the group operates an Active Directory service for the homogeneous management of user data. Parts of the PCs of the institute have been successfully integrated into the provided Windows domain. Thus, a homogeneous, central and resource saving management of files and printers can be established.
The technical basis for the external presentation of information, resources and scientific results of the IPK using an Internet portal is also managed by the IT group. To support internal communication, management and information exchange, a collaboration suite has been integrated into the Intranet portal.
Beside these central services, the individual desktop support of scientific and non-scientific IT users is an
important and challenging task for the IT resource planning.

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Recent References
2010200920082007200620052004
[ ^ ] 2010
2010 M. LANGE, K. SPIES, J. BARGSTEN, G. HABERHAUER, M. KLAPPERSTÜCK, M. LEPS, C. WEINEL, R. WÜNSCHIERS, M. WEIßBACH, J. STEIN & U. SCHOLZ The LAILAPS Search Engine: Relevance Ranking in Life Science Databases. Journal of Integrative Bioinformatics, 7(2):e110, 2010.
2010 I.E. MATTHIES, S. WEISE & M.S. RÖDER Assoziationskartierung in Gerste – Ein genomweiter und Kandidatengenansatz. In Bericht der 60. Tagung der Vereinigung der Pflanzenzüchter und Saatgutkaufleute Österreichs, 24.–26. November 2009, Gumpenstein, pp. 91-96, 2010.
[ ^ ] 2009
2009 M. KLAPPERSTÜCK, T. SCHMUTZER, M. LANGE & U. SCHOLZ LIMS lite: a system for management and search of primary lab data. In International Workshop on Computational and Integrative Biology, Hangzhou, China, September 18–20, page 63, 2009.
2009 M. LANGE, K. SPIES, J. BARGSTEN, M. WEIßBACH, M. KLAPPERSTÜCK & SCHOLZ The LAILAPS Search Engine: Relevance Ranking in Life Science Databases. In International Workshop on Computational and Integrative Biology, Hangzhou, China, September 18–20, pages 62–63, 2009.
2009 I.E. MATTHIES, S. WEISE, J. FÖRSTER & M.S. RÖDER 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(1-2):109-122, 2009.
2009 I.E. MATTHIES, S. WEISE & M.S. RÖDER Association of haplotype diversity in the α-amylase gene amy1 with malting quality parameters in barley. Molecular Breeding, 23(1):139-152, January 2009.
2009 K.F.X. MAYER, S. TAUDIEN, M. MARTIS, H. SIMKOVA, P. SUCHANKOVA, H. GUNDLACH, T. WICKER, A. PETZOLD, M. FELDER, B. STEUERNAGEL, U. SCHOLZ, A. GRANER, M. PLATZER, J. DOLEZEL, AND N. STEIN Gene content and virtual gene order of barley chromosome 1H. Plant Physiology, 151(2):496-505, 2009
2009 M. NAGEL, H. VOGEL, S. LANDJEVA, G. BUCK-SORLIN, U. LOHWASSER, U. SCHOLZ AND A. BÖRNER Seed conservation in ex situ genebanks - genetic studies on longevity in barley. Euphytica, 170(1-2):5-14, 2009.
2009 S. NAVAKODE, A. WEIDNER, U. LOHWASSER, U. SCHOLZ & A. BÖRNER A QTL analysis of aluminium tolerance in barley, using gene-based markers. Cereal Research Comm. (in press).
2009 P. SCHÄFER, S. PFIFFI, L.M. VOLL, D. ZAJIC, P.M. CHANDLER, F. WALLER, U. SCHOLZ, J. PONS-KÜHNEMANN, S. SONNEWALD, U. SONNEWALD, AND K.-H. KOGEL Manipulation of plant innate immunity and gibberellin as factor of compatibility in the mutualistic association of barley roots with Piriformospora indica. The Plant Journal, 59(3):461-474, 2009.
2009 P. SCHÄFER, S. PFIFFI, L.M. VOLL, D. ZAJIC, P.M. CHANDLER, F. WALLER, U. SCHOLZ, J. PONS-KÜHNEMANN, S. SONNEWALD, U. SONNEWALD & K.-H. KOGEL Phytohormones in plant root-Piriformospora indica mutualism. Plant Signaling & Behavior, 4(7):669-671, 2009.
2009 W. SCHOOR, R. MECKE, U SEIFFERT, F. BOLLENBECK, AND U. SCHOLZ Remote rendering of large biological datasets. In A.K. Ranchordas, J. Pereira, and P. Richard, editors, Proceedings of the Fourth International Conference on Computer Graphics Theory and Applications (GRAPP 2009), 5th - 9th February 2009, Lisboa, Portugal, pages 223–227, 2009.
2009 B. STEUERNAGEL, S. TAUDIEN, H. GUNDLACH, M. SEIDEL, R. ARIYADASA, D. SCHULTE, A. PETZOLD, M. FELDER, A. GRANER, U. SCHOLZ, K. MAYER, M. PLATZER & N. STEIN De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley. BMC Genomics, 10(1):e547, 2009.
2009 S. WEISE, C. COLMSEE, E. GRAFAHREND-BELAU, B. JUNKER, C. KLUKAS, M. LANGE, U. SCHOLZ, F. SCHREIBER An integration and analysis pipeline for systems biology in crop plant metabolism. In N.W. Paton, P. Missier, and C. Hedeler (editors): Data Integration in the Life Sciences; 6th International Workshop, DILS 2009, Manchester, UK, 20–22 July 2009, volume 5647 of Lecture Notes in Bioinformatics, pages 196–203, Berlin et al.: Springer, 2009.
2009 S. WEISE, U. SCHOLZ, M.S. RÖDER & I.E. MATTHIES MetaBrew: A comprehensive database of malting quality traits in brewing barley. Barley Genetics Newsletter, 39:1-4, 2009.
2009 S. WEISE, C. COLMSEE, E. GRAFAHREND-BELAU, B.H. JUNKER, C. KLUKAS, M. LANGE, U. SCHOLZ & F. SCHREIBER Datenaustausch und Datenintegration zur Modellierung und Analyse metabolischer Netzwerke am Beispiel von Kulturpflanzen. In S. Fischer, E. Maehle und R. Reischuk, (Ed.), INFORMATIK 2009 – Im Focus das Leben, Beiträge der 39. Jahrestagung der Gesellschaft für Informatik e.V. (GI), 28.09. – 02.10.2009, Lübeck, volume P-154 of Lecture Notes in Informatics (LNI), pages 693–697, 2009.
2009 S. WEISE Integrierte Analyse pflanzenbiologischer Daten unter besonderer Berücksichtigung der Datenqualität. Dissertation, Universität Bielefeld, Technische Fakultät, 2009.
[ ^ ] 2008
2008 E. GRAFAHREND-BELAU, B.H. JUNKER, D. KOSCHÜTZKI, C. KLUKAS, S. WEISE, U. SCHOLZ, & F. SCHREIBER Towards systems biology of developing barley grains: A framework for modelling metabolism. In M. Ahdesmäki, K. Strimmer, N. Radde, K. Rahnenführer, K. Klemm, H. Lähdesmäki and O. Yli-Harja: Proceedings of the Fifth International Workshop on Computational Systems Biology, WCSB 2008, Leipzig, June 11-13 2008, p. 41-44, 2008.
2008 E. GRAFAHREND-BELAU, S. WEISE, D. KOSCHÜTZKI, U. SCHOLZ, B.H. JUNKER, & F. SCHREIBER MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Research, 36: D954-D958.
2008 B. KLOOSTERMAN, D. DE KOEYER, R. GRIFFITHS, B. FLINN, B. STEUERNAGEL, U. SCHOLZ, S. SONNEWALD, U. SONNEWALD, G.J. BRYAN, S. PRAT, Z. BANFALVI, J.P. HAMMOND, P. GEIGENBERGER, K.L. NIELSEN, R.G.F. VISSER, & C.W.B. BACHEM. Genes driving potato tuber initiation and growth: Identification based on transcriptional changes using the POCI array. Functional & Integrative Genomics, 8(4):329-340.
2008 C. KUENNE, I. GROSSE, I. MATTHIES, U. SCHOLZ, T. SRETENOVIC-RAJICIC, N. STEIN, A. STEPHANIK, B. STEUERNAGEL & S. WEISE Using Data Warehouse Technology in Crop Plant Bioinformatics. Journal of Integrative Bioinformatics, 4(1):88.
2008 LANGE, M., M. KLAPPERSTÜCK, K. SPIES, AND U. SCHOLZ DALIGRES – A Graph Query Tool to Unravel the Life Science Database Maze. In Proceedings of the Fourth International Bulgarian–Greek Scientific Conference — Computer Science 2008, 18 – 19 September ’08, Kavala, Greece, pages 603 – 614, 2008.
2008 N. SREENIVASULU, B. USADEL, A. WINTER, V. RADCHUK, U. SCHOLZ, N. STEIN, W. WESCHKE, M. STRICKERT, T.J. CLOSE, M. STITT, A. GRANER, & U. WOBUS Barley Grain Maturation and Germination: Metabolic Pathway and Regulatory Network Commonalities and Differences Highlighted by New MapMan/PageMan Profiling Tools. Plant Physiol., 146(4):1738–1758.
[ ^ ] 2007
2007 M. LANGE, A. HIMMELBACH, P. SCHWEIZER, & U. SCHOLZ Data Linkage Graph: computation, querying and knowledge discovery of life science database networks. Journal of Integrative Bioinformatics, 4(3):68.
2007 LANGE, M. & U. SCHOLZ Datenverarbeitung in der Biologie. iX Magazin für professionelle Informationstechnik 3:106–109.
2007 M. SENNING, B. STEUERNAGEL, A. HARTMANN, U. SONNEWALD, U. SCHOLZ, & S. SONNEWALD Regulation der Keimruhe von Kartoffelknollen. GenomXPress, number 3, pages 7–10.
2007 STEIN N., M. PRASAD, U. SCHOLZ, T. THIEL, ZHANG H., M. WOLF, R. KOTA, R. K. VARSHNEY, D. PEROVIC, I. GROSSE & A. GRANER A 1000 loci transcript map reveals insight into barley genome evolution. TAG - Theoretical and Applied Genetics, 114(5):823–839.
2007 S. WEISE, S. HARRER, I. GROSSE, H. KNÜPFFER, & E. WILLNER The European Poa Database (EPDB). FAO/IPGRI Plant Genetic Resources Newsletter, No. 150:64-70.
[ ^ ] 2006
2006 EICHMANN, R., S. BIEMELT, P. SCHÄFER, U. SCHOLZ, C. JANSEN, A. FELK, W. SCHÄFER, G. LANGEN, U. SONNEWALD, K.-H. KOGEL & R. HÜCKELHOVEN Macroarray expression analysis of barley susceptibility and nonhost resistance to Blumeria graminis. Journal of Plant Physiology 163:657670.
2006 WEISE, S., I. GROSSE, C. KLUKAS, D. KOSCHÜTZKI, U. SCHOLZ, F. SCHREIBER & B.H. JUNKER Meta-All: a system for managing metabolic pathway information. BMC Bioinformatics 7:465.
2006 LANGE, M. Methoden zum homogenen Zugriff und zur Integration heterogener, biologischer Datenquellen mittels beschränkter Zugriffsmuster. Dissertation, Otto-von-Guericke-Universität Magdeburg, 2006.
[ ^ ] 2005
2005 GRANER, A., T. THIEL, H. ZHANG, E. POTOKINA, M. PRASAD, D. PEROVIC, R. KOTA, R.K. VARSHNEY, U. SCHOLZ, I. GROSSE & N. STEIN Molecular mapping in barley: shifting from the structural to the functional level. Czech Journal of Genetics and Plant Breeding 41 (3): 81-88.
2005 KÜNNE, C., M. LANGE, T. FUNKE, H. MIEHE, I. GROSSE & U. SCHOLZ CR–EST: a resource for crop ESTs. Nucleic Acids Research 33: D619–D621.
2005 VARSHNEY, R. K., R. SIGMUND, A. BÖRNER, V. KORZUN, N. STEIN, M. E. SORRELLS, P. LANGRIDGE & A. GRANER Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Science 168: 195-202.
2005 ZIEROLD, U., U. SCHOLZ & P. SCHWEIZER Transcriptome analysis of mlo-mediated resistance in the epidermis of barley. Molecular Plant Pathology 6: 139–151.
[ ^ ] 2004
2004 BALKO, S., M. LANGE, R. SCHNEE & U. SCHOLZ BioDataServer: An Applied Molecular Biological Data Integration Service. In: Berlin et al., Vol. 2994 Lecture Notes in Bioinformatics. Springer, pp. 140-155.
2004 FREIER, A., M. LANGE & R. HOFESTAEDT Integrative Analysis of Gene Networks Using Dynamic Process Pattern Modeling. In: Kolchanov, N.A. and R. Hofestaedt (eds.), Bioinformatics of Genome Regulation and Structure. Boston, Dordrecht, London, Kluwer Acad. Publ., pp. 257-264.
2004 VARSHNEY, R.K., M. PRASAD, H. ZHANG, R. KOTA, R. SIGMUND, U. SCHOLZ, N. STEIN & A. GRANER EST-Derived Markers and Transcript Map of Barley: A Resource for Interspecific Transferability and Comparative Mapping in Cereals. In: Spunar, J. and J. Janikova (eds.), 9th Intern. Barley Genetics Symp., Brno, Czech Rep., pp. 332-338.
2004 ZHANG,H., N. SREENIVASULU, W. WESCHKE, N. STEIN, S. RUDD, V. RADCHUK, E. POTOKINA, U. SCHOLZ, P. SCHWEIZER, U. ZIEROLD, P. LANGRIDGE, R.K. VARSHNEY, U. WOBUS & A. GRANER Characterization of the barley transcriptome based on large-scale analysis of expressed sequence TAGs (ESTs) generated from tissues representing the barley life cycle. Plant J. 40: 276-290.
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Staff
scientific staff
Lange, Dr.-Ing. Matthias +49 (0)39482 5693
Schmutzer, Thomas +49 (0)39482 5696
Scholz, Dr. Uwe +49 (0)39482 5513
Steuernagel, Burkhard +49 (0)39482 5659
Weise, Dr. Stephan +49 (0)39482 5744
staff or visitors
Bauernfeind, Jens +49 (0)39482 5561
Chen, Jinbo
Colmsee, Christian +49 (0)39482 5428
Czernicka, Dr. Malgorzata
Flemming, Steffen +49 (0)39482 5157
Friedrich, Christian +49 (0)39482 5378
Hoffmann, Knut +49 (0)39482 5323
Jank, Dr. Hans-Wolfgang +49 (0)39482 5448
Kaiser, Thomas +49 (0)39482 5561
Mahmoody, Zahra
Miehe, Heiko +49 (0)39482 5664
Muench, Thomas +49 (0)39482 5742
Reuner, Torsten +49 (0)39482 5322
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Interesting Links
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Keywords
Bioinformatics, Databases, Data Integration, Molecular Biological Databases, Analysis Tools