MDCK-MRP2 - Dkfz

140
Forschungsschwerpunkt B
Funktionelle und Strukturelle Genomforschung
Kartierung, Sequenzierung und funktionelle Analyse
des 6,1 Mb Genoms von Pseudomonas pudita
(BMBF-finanziert)
Innerhalb eines nationalen Netzwerks bestehend aus der
Medizinischen Hochschule Hannover, der GBF in Braunschweig,
QIAGEN in Hilden und uns sowie in Kollaboration
mit TIGR (USA) wurde das gesamte Genom von P. pudita
kartiert und sequenziert. Zusätzlich werden über DNA-Chip
Analysen transkriptionelle Daten produzieren, die mit biologischen
Informationen der anderen deutschen Teilnehmer
in Korrelation gebracht werden.
Publikationen (* = externer Koautor)
[1] Beier, M. & Hoheisel, J.D. (2002). Use of NPE/NPEOC-protected
5'-phosphoramidites for inverse in situ synthesis of oligonucleotides
on DNA-microarrays. J. Biotechnol. 94, 15-22.
[2] Hoheisel, J.D. & *Cahill, D. (2002). Proteomics and
genomics; catching function in action. Curr Opin. Chem. Biol. 6,
11-12.
[3] *Becerra, M., *Lombardía-Ferreira, L.J., Hauser, N.J.,
Hoheisel, J.D., *Tizon, B. & *Cerdán, M.E. (2002). The yeast
transcriptome in aerobic and hypoxic conditions. Effects of HAP1
ROX1 ROX3 and SRB10 deletions. Mol. Microbiol. 43, 545-555.
[4] *Tauch, A., *Homann, I., *Mormann, S., *Rüberg, S.,
*Billaut, A., *Bathe, B., *Brand, S., *Brockmann-Gretza, O.,
*Rückert, C., *Schischka, N., *Wrenger, C., Hoheisel, J.D.,
*Mockel, B., *Huthmacher, K., *Pfefferle, W., *Pühler, A. &
*Kalinowski, J. (2002). Strategy to sequence the genome of
Corynebacterium glutamicum ATCC 13032: use of a cosmid and a
bacterial artificial chromosome library. J. Biotechnol. 95, 25-38.
[5] Scheideler, M., *Schlaich, N.L., Fellenberg, K., Beißbarth, T.,
Hauser, N., Vingron, M., *Slusarenko, A.J. & Hoheisel, J.D.
(2002). Monitoring the switch from housekeeping to pathogen
defence metabolism in Arabidopsis thaliana. J. Biol. Chem. 277,
10555-10561.
[6] Fellenberg, K., Hauser, N.C., Brors, B., Hoheisel, J.D. &
Vingron, M. (2002). Microarray data warehouse allowing for the
statistical analysis of experiment annotations. Bioinformatics 18,
423-433.
[7] Heber, S., Stoye, J., Frohme, M., Hoheisel, J.D. & Vingron,
M. (2002). Resampling methods in physical mapping. Classification,
Automation, and New Media; Studies in Classification, Data
Analysis, and Knowledge Organization (Gaul, W. & Ritter, G.,
eds.), Springer Verlag, 437-444.
[8] Frohme, M., *Zolk, O., *Maurer, A., *Maurer, A., *Kluxen,
F.-W., *Hentsch, B., Zubakov, D., Hoheisel, J.D., *Zucker, I.H.,
*Pepe, S. & *Eschenhagen, T. (2002). Cardiac ankyrin repeat
protein, a negative regulator of cardiac gene expression, is augmented
in human heart failure. Biochem. Biophys. Res. Commun.
293, 1377-1382.
[9] *Beckers, J., Hoheisel, J.D., *Mewes, W., Vingron, M. &
*Hrabé de Angelis, M. (2002). Molecular phenotyping of mouse
mutant resources by RNA expression profiling. Curr. Genet. 3,
121-129.
[10] *Hayes, A., *Zhang, N., *Wu, J., *Butler, P.R., Hauser,
N.C., Hoheisel, J.D., *Lim, F.L., *Sharrocks, A.D., Oliver, S.G.
(2002) Hybridisation array technology coupled with chemostat
culture: tools to interrogate gene expression in Saccharomyces
cerevisiae. Methods 26, 281-290.
[11] Hoheisel, J.D. (ed.) (2002). DNA-Chip Technology. Adv.
Biochem. Engineering/Biotechnol. 77.
[12] *Brazma, A., *Sarkans, U., *Robinson, A., *Vilo, J., Vingron,
M., Hoheisel, J.D. & Fellenberg, K. (2002). Microarray data
representation, annotation and storage. DNA-Chip Technology;
Adv. Biochem. Engineering/Biotechnol. 77, 113-139.
[13] Hauser, N.C., Fellenberg, K. & *Rupp, S. (2002). How to
Discover Pathogenic Mechanisms - New Evaluation Tools Towards
Drug Discovery. Screening 3/02, 28-31.
Abteilung B070
Funktionelle Genomanalyse
[14] *Lombardía, L.J., *Becerra, M., *Rodríguez-Belmonte, E.,
Hauser, N.C. & Cerdán, M.E. (2002) Genome-wide analysis of
yeast transcription upon calcium shortage. Cell Calcium 32, 83-
91.
[15] Diehl, F., Beckmann, B., Kellner, N., Hauser, N.C., Diehl, S. &
Hoheisel, J.D. (2002). Manufacturing DNA-microarrays from
unpurified PCR-products. Nucleic Acids Res. 30, e79.
[16] Scheideler, M. & Hoheisel, J.D. (2002). DNA-Microarray
Analyses; benefits, promises and problems. Screening 5/02, 22-
25.
[17] Diehl, S., Diehl, F., *El-Sayed, N.M., *Clayton, C. &
Hoheisel, J.D. (2002). Analysis of stage-specific gene expression
in the bloodstream and the procyclic form of Trypanosoma brucei
using a genomic DNA-microarray. Mol. Biochem. Parasit. 123,
115-123.
[18] *Nelson, K.E., *Weinel, C., *Paulsen, I.T., *Dodson, R.J.,
*Hilbert, H., *Martins Dos Santos, V., *Fouts, D.E., *Gill, S.R.,
*Pop, M., *Holmes, M., *Brinkac, L., *Beanan, M., *DeBoys, R.,
*Daugherty, S., *Kolonay, J., *Madupu, R., *Nelson, W.,
*White, O., *Peterson, J., *Khouri, H., *Hance, I., *Chris Lee,
P., *Holtzapple, E., *Scanlan, D., *Tran, K., *Moazzez, A.,
*Utterback, T., *Rizzo, M., *Lee, K., *Kosack, D., *Moestl, D.,
*Wedler, H., *Lauber, J., Stjepandic, D., Hoheisel, J.D.,
*Straetz, M., *Heim. S., *Kiewitz, C., *Eisen, J., *Timmis, K.N.,
*Düsterhoft, A., *Tümmler, B., & *Fraser, C.M. (2002). The complete
genome sequence and comparative analysis of the metabolically
versatile Pseudomonas putida KT2440. Environ.
Microbiol. 4, 799-808.
[19] Stjepandic, D., *Weinel, C., *Hilbert, H., *Koo, H.L., Diehl,
F., *Nelson, K.E., *Tümmler, B. & Hoheisel, J.D. (2002). The genome
structure of Pseudomonas putida; high-resolution mapping
and microarray analysis. Environ. Microbiol. 4, 819-823.
[20] Kusnezow, W. & Hoheisel, J.D. (2002). Antibody Microarrays:
Promises and Problems. BioTechniques 33 (suppl.), 14-
23.
[21] Würtz, S., Hanke, J., Solinas-Toldo, S. & Hoheisel, J.D.
(2003). Genomanalyse und Gendiagnostik. Grundlagen der
Molekularen Medizin; 2. Auflage (Ganten, D. & Ruckpaul, K.,
Hrsg.), Springer Verlag, 391-440.
[22] Kusnezow, W., Jacob, A., Walijew, A., Diehl, F. & Hoheisel,
J.D. (2003). Antibody microarrays: an evaluation of production
parameters. Proteomics 3, 254-264.
[23] *Mannhaupt, G., *Montrone, C., *Haase, D., *Mewes, W.,
Aign, V., Hoheisel, J.D., *Fartmann, B., *Nyakatura, G.,
*Kempken, F., *Maier, J. and *Schulte, U. (2003). What‘s in the
genome of a filamentous fungus? Analysis of the Neurospora genome
sequence. Nucleic Acids Res. 31, 1944-1954.
[24] Scheideler, M. & Hoheisel, J.D. (2003). Analyses de
microréseaux d’ADN. Bioforum France 1/03, 24-27.
[25] Lagorce, A., Hauser, N.C., *Labourdette, D., *Rodriguez,
C., *Jasson, S., *Arroyo, J., Hoheisel, J.D. & Francois, J.-M.
(2003). Genome-wide analysis of the response to cell wall damage
in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 278,
20345-20357.
[26] *Yin, Z., *Wilson, S., Hauser, N.C., *Tournu, H., Hoheisel,
J.D. & *Brown, A.J.P. (2003). Differential effects of high and low
glucose signals upon global expression patterns in yeast. Mol.
Microbiol. 48, 713-724.
[27] Löhr, M. & Hoheisel, J.D. (2003). DNA-Chip Technologie beim
Pankreaskarzinom. Z. Gastroenterol. 41, 623-624.
[28] Hoheisel, J.D. (2003). Humangenetik leicht gemacht. Forum
DKG 2/03, 61.
[29] Fellenberg, K., Vingron, M., Hauser, N.C. & Hoheisel, J.D.
(2003). Correspondence analysis with microarray data. Perspectives
in Gene Expression (Appasani, K., ed.), Eaton Publishing,
Westborough, 307-343.
[30] Kusnezow, W. & Hoheisel, J.D. (2003). Solid Support for
Microarray Immunoassays. J. Mol. Recognit. 16, 165-176.
DKFZ 2004: Wissenschaftlicher Ergebnisbericht 2002 - 2003