CRP-DNA Complex
PRODORIC logo Release 8.9
Publications about PRODORIC, Tools and Applications
PUBMED: 17202169, PDF
Klein, J., Leupold, S., Münch, R., Pommerenke, C., Johl, T., Kärst, U., Jänsch, L., Jahn, D. & Retter, I. (2008)
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks.. Nucleic Acids Res. 36, W460-W464.
Reference: Link
Pommerenke, C., Gabriel, I., Bunk, B., Münch, R., Haddad, I., Tielen, P., Wagner-Döbler, I. & Jahn, D. (2008)
ROSY – A flexible and universal database and bioinformatics tool platform for Roseobacter related species. In Silico Biol. 8, 177-186.
PUBMED: 17202169, PDF
Choi C, Münch R, Leupold S, Klein J, Siegel I, Thielen B, Benkert B, Kucklick M, Schobert M, Barthelmes J, Ebeling C, Haddad I, Scheer M, Grote A, Hiller K, Bunk B, Schreiber K, Retter I, Schomburg D & Jahn D. (2007)
SYSTOMONAS - an integrated database for systems biology analysis of Pseudomonas. Nucleic Acids Res. 35, 533-537.
Reference: Link, PDF
Choi, C., Münch, R., Bunk, B., Barthelmes, J., Ebeling, C., Schomburg, D., Schobert, M. & Jahn, D. (2007)
Combination of a data warehouse concept with web services for the establishment of the Pseudomonas systems biology database SYSTOMONAS. Journal of Integrative Bioinformatics 4, 48.
Reference: Link, PDF
Klawonn, F., Choi, C., Benkert, B., Thielen, B., Münch, R., Schobert, M., Schomburg, D. & Jahn, D. (2007)
A Likelihood Ratio Test for Differential Metabolic Profiles in Multiple Intensity Measurements. KES 2007, 485-492.
PUBMED: 17046977, PDF
Bunk, B., Kucklick, M., Jonas, R., Münch, R., Schobert, M., Jahn, D. & Hiller, K. (2006)
MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data. Bioinformatics 22, 2962-2965.
PUBMED: 17028277, PDF
Jensen, V., Löns, D., Zaoui, C., Bredenbruch, F., Meissner, A., Dieterich, G., Münch, R. & Häussler, S. (2006)
RhlR expression in Pseudomonas aeruginosa is modulated by the Pseudomonas quinolone signal via PhoB-dependent and -independent pathways. J. Bacteriol. 188, 8601-8606.
PUBMED: 16870933, PDF
Hiller, K., Grote, A., Maneck, M., Münch, R. & Jahn D. (2006)
JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins. Bioinformatics 22, 2441-2443.
PUBMED: 16845060, PDF
Scheer, M., Klawonn, F., Münch, R., Grote, A., Hiller, K., Choi, C., Koch, I., Schobert, M., Härtig, E., Klages, U. & Jahn D. (2006)
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Nucleic Acids Res. 34, 510-515.
Reference: SpringerLink, PDF
Mathiak, B., Kupfer, A., Münch, R., Täubner, C. & Eckstein, S. (2006)
Improving literature preselection by searching for images. Lecture Notes in Computer Science (LNCS) 3886, 18-28.
PUBMED: 16428414, PDF
Reents, H., Münch, R., Dammeyer, T., Jahn, D. & Härtig, E. (2006)
The Fnr regulon of Bacillus subtilis. J. Bacteriol. 188, 1103-1112.
PUBMED: 16109747, PDF
Münch, R., Hiller, K., Grote, A., Scheer, M., Klein, J., Schobert, M. & Jahn D. (2005)
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Bioinformatics 21, 4187-4189.
PUBMED: 15980527, PDF
Grote, A., Hiller, K., Scheer, M., Münch, R., Nörtemann, B., Hempel, D.C. & Jahn, D. (2005)
JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 33, 526-531.
PUBMED: 15690044, PDF
Randau, L., Münch, R., Hohn, M.J., Jahn, D. & Söll, D. (2005)
Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves. Nature 433, 537-541.
PUBMED: 15608286, PDF
Retter, I., Althaus, H.H., Münch, R. & Müller W. (2005)
VBASE2, an integrative V gene database. Nucleic Acids Res. 33,671-674.
PUBMED: 15375128, PDF
Härtig, E., Geng, H., Hartmann, A., Hubacek, A., Münch, R., Ye, R.W., Jahn, D & Nakano M.M. (2004)
Bacillus subtilis ResD induces expression of the potential regulatory genes yclJK upon oxygen limitation. J Bacteriol. 186, 6477-6484.
PUBMED: 15215414, PDF
Hiller, K., Grote, A., Scheer, M., Münch, R. & Jahn D. (2004)
PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res. 32, 375-375.
PUBMED: 12824438, PDF
Hiller, K., Schobert, M., Hundertmark, C., Jahn, D. & Münch, R. (2003)
JVirGel: Calculation of virtual two-dimensional protein gels. Nucleic Acids Res. 31, 3862-3865.
PUBMED: 12520026, PDF
Matys, V., Fricke, E., Geffers, R., Gössling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A.E., Kel-Margoulis, O.V., Kloos, D.U., Land, S., Lewicki-Potapov, B., Michael, H., Münch, R., Reuter, I., Rotert, S., Saxel, H., Scheer, M., Thiele, S. & Wingender, E. (2003)
TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378.
PUBMED: 12519998, PDF
Münch,R., Hiller,K., Barg,H., Heldt,D., Linz,S., Wingender,E. & Jahn,D. (2003)
PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res. 31, 266-269.
PRODORIC Database, Tools and Supplementary Data
DOWNLOAD PRODORIC database structure as PostgreSQL DDL (Database Definition Language)
Miscellaneous Downloads
Adobe Acrobat Reader to read PDF files
Java 2 PLatform Standard Edition (J2SE)
PostgreSQL Database Management System
PHP Hypertext Preprocessor
Apache Webserver