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Last Update: February, 28th 2007 |
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Papers
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This is a collection of publications that emerged during or in context with the INTERGENOMICS project. They are sorted by year of publication and additionally alphabetically by first author's name. |
2007PathoPlant: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses. Bülow L, Schindler M and Hehl R. (2007) Nucleic Acids Res. 35 (Database issue), D841-D845. Pubmed abstract here , Pubmed Identifier: 17099232 SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas. 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 and Jahn D. (2007) Nucleic Acids Res. 35 (Database issue), D553-D556 Pubmed abstract here , Pubmed Identifier: 17202169 AthaMap web tools for the analysis and identification of co-regulated genes. Galuschka C, Schindler M, Bülow L and Hehl R (2007) Nucleic Acids Res. 35 (Database issue), D857-D862 Pubmed abstract here , Pubmed Identifier: 17148485 2006Beyond microarrays: Finding key transcription factors controlling signal transduction pathways. Kel A, Voss N, Jauregui R, Kel-Margoulis O and Wingender E (2006) BMC Bioinformatics 7 (Suppl 2), S13 Pubmed abstract here , Pubmed Identifier: 17118134 AthaMap: from in silico data to real transcription factor binding sites. Bülow L, Steffens NO, Galuschka C, Schindler M and Hehl R (2006) In Silico Biology 6 , 0023 Pubmed abstract here , Pubmed Identifier: 16922688 MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data. Bunk B, Kucklick M, Jonas R, Münch R, Schobert M, Jahn D and Hiller K (2006) Bioinformatics 22 (23), 2962-2965 Pubmed abstract here , Pubmed Identifier: 17046977 TiProD: the Tissue-specific Promoter Database. Chen X, Wu JM, Hornischer K, Kel A and Wingender E (2006) Nucleic Acids Res. 34 (Database issue), D104-D107 Pubmed abstract here , Pubmed Identifier: 16381824 LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species. Dieterich G, Kärst U, Fischer E, Wehland J and Jänsch L (2006) Nucleic Acids Res. 34 (Database issue), D402-D406 Pubmed abstract here , Pubmed Identifier: 16381897 TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Krull M, Pistor S, Voss N, Kel A, Reuter I, Kronenberg D, Michael H, Schwarzer K, Potapov A, Choi C, Kel-Margoulis O and Wingender E (2006) Nucleic Acids Res. 34 (Database issue), D546-D551 Pubmed abstract here , Pubmed Identifier: 16381929 TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE and Wingender E (2006) Nucleic Acids Res. 34 (Database issue), D108-110 Pubmed abstract here , Pubmed Identifier: 16381825 EndoNet: an information resource about endocrine networks. Potapov A, Liebich I, Dönitz J, Schwarzer K, Sasse N, Schöps T, Crass T and Wingender E (2006) Nucleic Acids Res. 34 (Database issue), D540-D545 Pubmed abstract here , Pubmed Identifier: 16381928 The Fnr regulon of Bacillus subtilis. Reents H, Münch R, Dammeyer T, Jahn D and Härtig E (2006) J. Bacteriol. 188 (3), 1103-1112 Pubmed abstract here , Pubmed Identifier: 16428414 JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Scheer M, Klawonn F, Münch R, Grote A, Hiller K, Choi C, Koch I, Schobert M, Hätig E, Klages U and Jahn D (2006) Nucleic Acids Res. 34 (Web Server issue), W510-W515 Pubmed abstract here , Pubmed Identifier: 16845060 Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm. Waleev T, Shtokalo D, Konovalova T, Voss N, Cheremushkin E, Stegmaier P, Kel-Margoulis O, Wingender E and Kel A. (2006) Nucleic Acids Res. 34 (Web Server issue), W541-W545 Pubmed abstract here , Pubmed Identifier: 16845066 2005VIS-O-BAC: exploratory visualization of functional genome studies from bacteria. Dieterich G, Kärst U, Wehland J and Jänsch L (2005) Bioinformatics 22 (5), 630-631 Pubmed abstract here , Pubmed Identifier: 16339284 MineBlast: a literature presentation service supporting protein annotation by data mining of BLAST results. Dieterich G, Kärst U, Wehland J and Jänsch L (2005) Bioinformatics 21 (16), 3450-3451 Pubmed abstract here , Pubmed Identifier: 15941742 JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Grote A, Hiller K, Scheer M, Münch R, Nörtemann B, Hempel DC and Jahn D (2005) Nucleic Acids Res. 33 (Web Server issue), W526-W531 Pubmed abstract here , Pubmed Identifier: 15980527 Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures. Khachane AN, Timmis KN and dos Santos VA (2005) Nucleic Acids Res. 33 (13), 4016-4022 Pubmed abstract here , Pubmed Identifier: 16030352 Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M and Jahn D (2005) Bioinformatics 21 (22), 4187-4189 Pubmed abstract here , Pubmed Identifier: 16109747 Deriving an ontology for human gene expression sources from the CYTOMER database on human organs and cell types. Michael H, Chen X, Fricke E, Haubrock M, Ricanek R and Wingender E (2005) In Silico Biology 5 (1), 61-66 Pubmed abstract here , Pubmed Identifier: 15972006 Topology of mammalian transcription networks.. Potapov AP, Voss N, Sasse N and Wingender E (2005) Genome Inform. 16 (2), 270-278 Pubmed abstract here , Pubmed Identifier: 16901109 Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves. Randau L, Münch R, Hohn MJ, Jahn D and Söll D (2005) Nature 433 (7025), 537-541 Pubmed abstract here , Pubmed Identifier: 15690044 BRAGI: linking and visualization of database information in a 3D viewer and modeling tool. Reichelt J, Dieterich G, Kvesic M, Schomburg D and Heinz DW (2005) Bioinformatics 21 (7), 1291-1293 Pubmed abstract here , Pubmed Identifier: 15546941 VBASE2, an integrative V gene database. Retter I, Althaus HH, Münch R and Müller W (2005) Nucleic Acids Res. 33 (Database issue), D671-D674 Pubmed abstract here , Pubmed Identifier: 15608286 Evaluating phylogenetic footprinting for human-rodent comparisons. Sauer T, Shelest E and Wingender E (2005) Bioinformatics 22 (4), 430-437 Pubmed abstract here , Pubmed Identifier: 16332706 Construction of predictive promoter models on the example of antibacterial response of human epithelial cells. Shelest E and Wingender E (2005) Theor. Biol. Med. Model. 2 (1), 2 Pubmed abstract here , Pubmed Identifier: 15647113 AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. Steffens NO, Galuschka C, Schindler M, Bülow L and Hehl R (2005) Nucleic Acids Res. 33 (Web Server issue), W397-W402 Pubmed abstract here , Pubmed Identifier: 15980498 Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data. Sun J, Gunzer F, Westendorf AM, Buer J, Scharfe M, Jarek M, Gössling F, Blöcker H and Zeng AP. (2005) J Biotechnol. 117 (2), 47-61 Pubmed abstract here , Pubmed Identifier: 15823404 Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species. Trost M, Wehmhöner D, Karst U, Dieterich G, Wehland J and Jänsch L (2005) Proteomics 5 (6), 1544-1557 Pubmed abstract here , Pubmed Identifier: 15838904 "LaneSpector", a tool for membrane proteome profiling based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis/liquid chromatography-tandem mass spectrometry analysis: application to Listeria monocytogenes membrane proteins. Wehmhöner D, Dieterich G, Fischer E, Baumgärtner M, Wehland J and Jänsch L (2005) Electrophoresis 26 (12), 2450-2460 Pubmed abstract here , Pubmed Identifier: 15966022 2004PathoPlant®: A Database on Plant-Pathogen Interactions. Bülow L, Schindler M, Choi C, and Hehl R (2004) In Silico Biology 4 , 529-536 Pubmed abstract here , Pubmed Identifier: 15752070 Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database. Choi C, Crass T, Kel A, Kel-Margoulis O, Krull M, Pistor S, Potapov A, Voss N and Wingender E (2004) Genome Inform. Ser. Workshop Genome Inform. 15 (2), 244-254 Pubmed abstract here , Pubmed Identifier: 15706510 A method to determine the elementary flux modes in genome-based large scale metabolic network. He F, Ma H, Yuan YJ, Deckwer WD and Zeng AP (2004) Bioinformatics submitted Isolation and analysis of gene regulatory sequences. Hehl R, Steffens NO and Wingender E (2004) In: Handbook of Plant Biotechnology, Klee H, and Christou P, eds., (Wiley and Sons Ltd.) , 81-102 PrediSi: prediction of signal peptides and their cleavage positions. Hiller K, Grote G, Scheer M, Münch R and Jahn D (2004) Nucleic Acids Res. 32 (Web Server issue), W375-W379 Pubmed abstract here , Pubmed Identifier: 15215414 Analysis of disturbed images. Kauer G and Blöcker H (2004) Bioinformatics 20 , 1381-1387 Pubmed abstract here , Pubmed Identifier: 14962927 Phylogenetic comparison of metabolic capacities of organisms at genome level. Ma H and Zeng AP (2004) Molecular Phylogenetics and Evolution 31 (1), 204-213 Pubmed abstract here , Pubmed Identifier: 15019620 Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. Ma HW, Buer J and Zeng AP (2004) BMC Bioinformatics 5 , 199 Pubmed abstract here , Pubmed Identifier: 15603590 Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Ma HW, Zhao XM, Yuan YJ and Zeng AP (2004) Bioinformatics 20 (12), 1870-1876 Pubmed abstract here , Pubmed Identifier: 15037506 Insights into the genomic basis of niche specificity of Pseudomonas putida strain KT2440. Martins dos Santos VAP, Heim S, Nelson KE and Timmis KN (2004) Environm. Microbiol. 6 (12), 1264-1286 Pubmed abstract here , Pubmed Identifier: 15560824 AthaMap, an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. Steffens NO, Galuschka C, Schindler M, Bülow L and Hehl R (2004) Nucleic Acids Res. 32 (Database issue), D368-D372 Pubmed abstract here , Pubmed Identifier: 14681436 Systematic DNA-binding domain classification of transcription factors. Stegmaier P, Kel AE and Wingender E (2004) Genome Inform. Ser. Workshop Genome Inform. 15 (2), 276-286 Pubmed abstract here , Pubmed Identifier: 15706513 IdentiCS - Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. Sun J and Zeng AP (2004) BMC Bioinformatics 5 , 112 Pubmed abstract here , Pubmed Identifier: 15312235 Iron availability, oxygen limitation, Pseudomonas aeruginosa and cystic fibrosis. Zeng AP and Kim EJ (2004) Microbiology 150 (3), 516-518 Pubmed abstract here , Pubmed Identifier: 14993296 2003Genome sequence completed of Alcanivorax borkumensis, a hydrocarbon-degrading bacterium that plays a global role in oil removal from marine systems. Golyshin PN, Martins Dos Santos VA, Kaiser O, Ferrer M, Sabirova YS, Lunsdorf H, Chernikova TN, Golyshina OV, Yakimov MM, Pühler A and Timmis KN (2003) J. Biotechnol. 106 , 215-220 Pubmed abstract here , Pubmed Identifier: 14651863 JVirGel: calculation of virtual two-dimensional protein gels. Hiller K, Schobert M, Hundertmark C, Jahn D and Münch R (2003) Nucleic Acids Res. 31 (13), 3862-3865 Pubmed abstract here , Pubmed Identifier: 12824438 Applying signal theory to the analysis of biomolecules. Kauer G and Blöcker H (2003) Bioinformatics 19 (16), 2016-2021 Pubmed abstract here , Pubmed Identifier: 14594705 Iron deficiency leads to inhibition of oxygen transfer and enhanced formation of virulence factors in cultures of Pseudomonas aeruginosa PAO1. Kim EJ, Sabra W and Zeng AP (2003) Microbiology 149 , 2627-2634 Pubmed abstract here , Pubmed Identifier: 12949186 TRANSPATH®: an integrated database on signal transduction and a tool for array analysis. Krull M, Voss N, Choi C, Pistor S, Potapov A and Wingender E (2003) Nucleic Acids Res. 31 (1), 97-100 Pubmed abstract here , Pubmed Identifier: 12519957 PRODORIC: prokaryotic database of gene regulation. Münch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E and Jahn D (2003) Nucleic Acids Res. 31 (1), 266-269 Pubmed abstract here , Pubmed Identifier: 12519998 Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Ma H and Zeng AP (2003) Bioinformatics 19 , 270-277 Pubmed abstract here , Pubmed Identifier: 12538249 The connectivity structure, giant strong component and centrality of metabolic networks. Ma H and Zeng AP (2003) Bioinformatics 19 (11), 1423-1430 Pubmed abstract here , Pubmed Identifier: 12874056 Genomic features of Pseudomonas putida strain KT2440. Martins dos Santos VAP, Timmis KN, Tümmler B and Weinel C (2003) In: The Pseudomonads Vol I. Genomics, life style and molecular architecture, Chapter 3, Ramos J. (Ed.), 2003, Kluyver Academic Publishers, The Hague, The Netherlands 6 (12), 1264-1286 Pubmed abstract here , Pubmed Identifier: 15560824 TRANSFAC: transcriptional regulation, from patterns to profiles. Matys V, Fricke E, Geffers R, Gössling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Münch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S and Wingender E (2003) Nucleic Acids Res. 31 (1), 374-378 Pubmed abstract here , Pubmed Identifier: 12520026 Alterations in the formation of lipopolysaccharide and membrane vesicles on the surface of Pseudomonas aeruginosa PAO1 under oxygen stress conditions. Sabra W, Lunsdorf H and Zeng AP (2003) Microbiology 149 , 2789-2795 Pubmed abstract here , Pubmed Identifier: 14523112 Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods. Shelest E, Kel AE, Gössling E and Wingender E (2003) In Silico Biol. 3 (1), 71-79 Pubmed abstract here , Pubmed Identifier: 12762847 Identification of ORF similar regions encoding metabolic enzymes for in silico reconstruction of metabolic networks from unannotated raw genome sequences. Sun J and Zeng AP (2003) submitted A comparative genomic analysis of dha regulon and related genes for anaerobic glycerol metabolism in bacteria. Sun J, van den Heuvel J, Soucaille P, Qu Y and Zeng AP (2003) Biotechnol. Prog. 19 (2), 263-272 Pubmed abstract here , Pubmed Identifier: 12675558 Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae. Wang W, Sun J, Hartlep M, Deckwer WD and Zeng AP (2003) Biotechnol. Bioeng. 83 (5), 525-536 Pubmed abstract here , Pubmed Identifier: 12827694 Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences. Wang W, Sun J, Nimtz M, Deckwer WD and Zeng AP (2003) Proteome Sci. 1 (1), 6 Pubmed abstract here , Pubmed Identifier: 14653859 2002TRANSCompel: a database on composite regulatory elements in eukaryotic genes. Kel-Margoulis OV, Kel AE, Reuter I, Deineko IV and Wingender E (2002) Nucleic Acids Res. 30 (1), 332-334 Pubmed abstract here , Pubmed Identifier: 11752329 S/MARt DB: a database on scaffold/matrix attached regions. Liebich I, Bode J, Frisch M and Wingender E (2002) Nucleic Acids Res. 30 (1), 372-374 Pubmed abstract here , Pubmed Identifier: 11752340 Mathematical models to characterise the physiological behaviour of immobilised cells. Martins dos Santos VAP, Tramper J and Wijffels RH . In: Cell Immobilisation Biotechnology. Nedovic V. , Willaert R. (Eds). Focus on Biotechnology Series, 2002, Elsevier Publishers, The Hague, The Netherlands (2002) In: Cell Immobilisation Biotechnology. Nedovic V. , Willaert R. (Eds). Focus on Biotechnology Series Metabolic control analysis of eucaryotic pyruvate dehydrogenase multienzyme complex. Modak J, Deckwer WD and Zeng AP (2002) Biotechnol. Prog. 18 (6), 1157-1169 Pubmed abstract here , Pubmed Identifier: 12467446 Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VA, Fouts DE, Gill SR, Pop M, Holmes M, Brinkac L, Beanan M, DeBoy RT, 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, Straetz M, Heim S, Kiewitz C, Eisen J, Timmis KN, Dusterhoft A, Tummler B and Fraser CM (2002) Environ Microbiol. 4 , 799-808 Pubmed abstract here , Pubmed Identifier: 12534463 Physiological responses of Pseudomonas aeruginosa PAO1 to oxidative stress in controlled microaerobic and aerobic culture. Sabra W, Kim EJ and Zeng AP (2002) Microbiology 148 (148), 3195-3202 Pubmed abstract here , Pubmed Identifier: 12368453 Rekonstruktion und Simulation des metabolischen Netzwerks von Pseudomonas aeruginosa für die Bildung von Virulenzfaktoren. Sabra W, Ma H, Wang W, Kim EJ and Zeng AP (2002) Chem.-Ing. Tech. 74 , 688 Nonlinear dynamics of eucaryotic pyruvate dehydrogenase multienzyme complex: decarboxylation rate, oscillations, and multiplicity. Zeng AP, Modak J and Deckwer WD (2002) Biotechnol. Prog. 18 (6), 1265-1276 Pubmed abstract here , Pubmed Identifier: 12467461 2001Database-assisted promoter analysis. Hehl R and Wingender E (2001) Trends Plant Sci. 6 , 251-255 Pubmed abstract here , Pubmed Identifier: 11378466 The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. Schacherer F, Choi C, Götze U, Krull M, Pistor S and Wingender E (2001) Bioinformatics 17 (11), 1053-1057 Pubmed abstract here , Pubmed Identifier: 11724734 The TRANSFAC system on gene expression regulation. Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhäuser R, Pr¨ss M, Schacherer F, Thiele S and Urbach S (2001) Nucleic Acids Res. 29 (1), 281-283 Pubmed abstract here , Pubmed Identifier: 11125113 |
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