126.
Goemann, B., Wingender, E. and Potapov, A. P.
An approach to evaluate the topological significance of motifs and other patterns in regulatory networks
BMC Syst Biol. 3, 53 (2009). [Epub ahead of print]. PMID: 19454001
125.
Grinkevich, V. V., Nikulenkov, F., Shi, Y., Enge, M., Bao, W., Maljukova, A., Gluch, A., Kel, A., Sangfelt, O. and Selivanova, G.
Ablation of key oncogenic pathways by RITA-reactivated p53 is required for efficient apoptosis
Cancer Cell. 15, 441-53 (2008). PMID: 19411072
124.
Kel, A., Voss, N., Valeev, T., Stegmaier, P., Kel-Margoulis, O. and Wingender E.
ExPlain: finding upstream drug targets in disease gene regulatory networks
SAR QSAR Environ Res., 19, 481-94 (2008). PMID: 18853298
123.
Michael, H., Hogan, J., Kel, A., Kel-Margoulis, O., Schacherer, F., Voss, N. and Wingender, E.
Building a knowledge base for systems pathology
Brief. Bioinformatics 9, 518-31 (2008). PMID: 19073714
122.
Paragh, G., Schling, P., Ugocsai, P., Kel, A. E., Liebisch, G., Heimerl, S.,Moehle, C., Schiemann, Y., Wegmann, M., Farwick, M., Wikonkál, N. M., Mandl, J., Langmann, T. and Schmitz, G.
Novel sphingolipid derivatives promote keratinocyte differentiation
Exp Dermatol. 17, 1004-1016. PMID: 18631249
121.
Potapov, A. P., Goemann, B. and Wingender, E.
The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks
BMC Bioinformatics 9, 227 (2008). PMID: 18454847
120.
Wingender, E.
TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
Brief. Bioinformatics 9, 326-332 (2008). PMID: 18436575
119.
Zubarev, R. A., Nielsen, M. L., Fung, E. M., Savitski, M. M., Kel-Margoulis, O., Wingender, E. and Kel, A.
Identification of dominant signaling pathways from proteomics expression data
J. Proteom. 71, 89-96 (2008). PMID: 18541477
118.
Kel, A. E., Niehof, M., Matys, V., Zemlin, R. and Borlak, J.
Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context
Genome Biol. 9, R36 (2008). PMID: 18291023
117.
Dönitz, J., Goemann, B., Lizé, M., Michael, H., Sasse, N., Wingender, E. and Potapov, A. P.
EndoNet: An information resource about regulatory networks of cell-to-cell communication
Nucleic Acids Res. 36, in press (2008). PMID: 18045786
116.
Minovitsky, S., Stegmaier, P., Kel, A., Kondrashov, A. S. and Dubchak, I.
Short sequence motifs, overrepresented in mammalian conserved non-coding sequences
BMC Genomics 8, 378 (2007). PMID: 17945028
115.
Wingender, E., Hogan, J., Schacherer, F., Potapov, A. P. and Kel-Margoulis, O.
Integrating pathway data for systems pathology
In Silico Biol. 7(2 Suppl), S17-S25 (2007). PMID: 17822386
114.
Posch, S., Grau, J., Gohr, A., Ben-Gal, I., Kel, A. E. and Grosse, I.
Recognition of cis-regulatory elements with vombat
J. Bioinform. Comput. Biol. 5, 561-577 (2007). PMID: 17636862
113.
Wingender, E., Crass, T., Hogan, J. D, Kel, A. E., Kel-Margoulis, O. V. and Potapov, A. P.
Integrative content-driven concepts for bioinformatics "beyond the cell"
J. Biosci. 32, 169-180 (2007). [more]
112.
Shankar, R., Chaurasia, A., Ghosh, B., Chekmenev, D., Cheremushkin, E., Kel, A. and Mukerji, M.
Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories
Mol. Genet. Genomics. 277, 441-455 (2007). PMID: 17375324
111.
Nagel, S., Scherr, M., Kel, A., Hornischer, K., Crawford, G. E., Kaufmann, M., Meyer, C., Drexler, H. G. and MacLeod, R. A.
Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1
Cancer Res. 67, 1461-1471 (2007). PMID: 17308084
110.
Kolpakov, F., Poroikov, V., Sharipov, R., Kondrakhin, Y., Zakharov, A., Lagunin, A., Milanesi, L. and Kel, A.
CYCLONET--an integrated database on cell cycle regulation and carcinogenesis
Nucleic Acids Res. 35(Database issue), D550-D556 (2007). PMID: 17201170
109.
Kel, A., Voss, N., Jauregui, R., Kel-Margoulis, O. and Wingender, E.
Beyond microarrays: Finding key transcription factors controlling signal transduction pathways
BMC Bioinformatics, 7(Suppl. 2), S13 (2006). [more]
108.
Moehle, C., Ackermann, N., Langmann, T., Aslanidis, C., Kel, A., Kel-Margoulis, O., Schmitz-Madry, A., Zahn, A., Stremmel, W. and Schmitz, G.
Aberrant intestinal expression and allelic variants of mucin genes associated with inflammatory bowel disease
J. Mol. Med. 84, 1055-10566 (2006).
107.
Deyneko, I. V., Bredohl, B., Wesely, D., Kalybaeva, Y. M., Kel, A. E., Blöcker,
H. and Kauer, G.
FeatureScan: revealing property-dependent similarity of nucleotide sequences
Nucleic Acids Res. 34, W591-595 (2006). [more]
106.
Waleev, T., Shtokalo, D., Konovalova, T., Voss, N., Cheremushkin, E., Stegmaier, P., Kel-Margoulis, O., Wingender, E. and Kel, A.
Composite Module Analyst: Identification of transcription factor binding site combinations using genetic algorithm
Nucleic Acids Res. 34, W541-W545 (2006). [more]
105.
Kel, A., Konovalova, T., Waleev, T., Cheremushkin, E., Kel-Margoulis, O. and Wingender, E.
Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations
Bioinformatics 22, 1190-1197 (2006). [more]
104.
Sauer, T., Shelest, E. and Wingender, E.
Evaluating phylogenetic footprinting for human-rodent comparisons
Bioinformatics 22, 430-437 (2006). [more]
103.
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.
TRANSPATH®: An Information Resource for Storing and Visualizing Signaling Pathways and their Pathological Aberrations
Nucleic Acids Res. 34, D546-D551 (2006). [more]
102.
Potapov, A., Liebich, I., Dönitz, J., Schwarzer, K., Sasse, N., Schoeps, T., Crass, T. and Wingender, E.
EndoNet: An information resource about endocrine networks
Nucleic Acids Res. 34, D540-D545 (2006). [more]
101.
Matys, V., Kel-Margoulis, O., 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, A. and Wingender, E.
TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes
Nucleic Acids Res. 34, D108-D110 (2006). [more]
100.
Chen, X., Wu, J.-m., Hornischer, K., Kel, A. and Wingender, E.
TiProD: The Tissue-specific Promoter Database
Nucleic Acids Res. 34, D104-D107 (2006). [more]
99.
Potapov, A. P., Voss, N., Sasse, N. and Wingender, E.
Topology of mammalian transcription networks
Genome Inf. Ser. 16, 270-279 (2005). [more] (PDF 185KB)
98.
Krull, M., Wingender, E.
Eukaryotic regulatory sequences
In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics; Dunn, M. J., Jorde, L. B., Little, P. F., Subramaniam, S. (eds.), John Wiley & Sons, Ltd., UK, 2895-2899 (2005). [more]
97.
Kel, A., Konovalova, T., Valeev, T., Cheremushkin, E., Kel-Margoulis, O. and Wingender, E.
Composite Module Analyst: A Fitness-Based Tool for Prediction of Transcription Regulation
Lecture Notes in Informatics, Proceedings of the German Conference on Bioinformatics 2005 (GCB 2005), Torda, A., Kurtz, S. and Rarey, M. (eds.), Gesellschaft für Informatik, Bonn, 63-75 (2005).
96.
Chekmenev, D.S., Haid, C., Kel, A.E.
P-Match: transcription factor binding site search by combining patterns and weight matrices
Nucleic Acids Res. 33, W432-W437 (2005). PMID: 15980505
95.
Kel-Margoulis, O., Matys, V., Choi, C., Reuter, I., Krull, M., Potapov, A.P., Voss, N., Liebich, I., Kel, A., Wingender, E.
Databases on Gene Regulation
In: Information Processing and Living Systems, Bajic, V.B. and Wee, T.T. (eds.), Imperial College Press, London, 709-727 (2005). [more]
94.
Kersey, P., Bower, L., Morris, L., Horne, A., Petryszak, R., Kanz, C., Kanapin, A., Das, U., Michoud, K., Phan, I., Gattiker, A., Kulikova, T., Faruque, N., Duggan, K., Mclaren, P., Reimholz, B., Duret, L., Penel, S., Reuter, I., Apweiler, R.
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes
Nucleic Acids Res. 33, 297-302 (2005). PMID: 15608201
93.
Shelest, E., Wingender, E.
Construction of predictive promoter models on the example of antibacterial response of human epithelial cells
Theor. Biol. Med. Model. 2, 2 (2005). [more]
92.
Kel, A., Kel-Margoulis, O., Borlak J., Tchekmenev, D., Wingender, E.
Databases and tools for in silico analysis of regulation of gene expression
Handbook of Toxicogenomics, Borlak, J. (ed.), Wiley-VCH, Weinheim, 253-290 (2005).
[more] (PDF 234KB)
91.
Kel, A., Tikunov, Y., Voss, N., Borlak, J., Wingender, E.
Application of Kernel Method to Reveal Subtypes of TF Binding Motifs
Lecture Notes in Computer Science 3318, 42 (2005). [more] (PDF 125KB)
90.
Johnson, R. J., Williams, J. M., Schreiber, B. M., Elfe, C. D., Lennon-Hopkins, K. L., Skrzypek, M. S., White, R. D.
Analysis of Gene Ontology features in microarray data using the Proteome BioKnowledge Library
In Silico Biol. 5, 0035 (2005). [more]
89.
Michael, H., Chen, X., Fricke, E., Haubrock, M., Ricanek, R., Wingender, E.
Deriving an ontology for human gene expression sources from the CYTOMER® database on human organs and cell types
In Silico Biol. 5, 0007 (2004). [more]
88.
Bülow, L., Schindler, M., Choi, C., Hehl, R.
PathoPlant®: A Database on Plant-Pathogen Interactions
In Silico Biol. 4, 0044 (2004). [more]
87.
Choi, C., Crass, T., Kel, A., Kel-Margoulis, O., Krull, M., Pistor, S., Potapov, A., Voss, N., Wingender, E.
Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database
Genome Inf. Ser. 15, 244-254 (2004). [more]
86.
Stegmaier, P., Kel, A. E., Wingender, E.
Systematic DNA-binding domain classification of transcription factors
Genome Inf. Ser. 15, 276-286 (2004). [more]
85.
Kel, A., Reymann, S., Matys, V., Nettesheim, P., Wingender, E., Borlak, J.
A novel computational approach for the prediction of networked transcription factors of aryl hydrocarbon-receptor-regulated genes
Mol. Pharmacol. 66, 1557-1572 (2004). PMID: 15342792
84.
Kel, A., Tikunov, Y., Voss, N., Wingender, E.
Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods
Bioinformatics 20, 1512-1516 (2004). PMID: 15231544
83.
Choi, C., Krull, M., Kel, A., Kel-Margoulis, O., Pistor, S., Potapov, A., Voss, N., Wingender, E.
TRANSPATH®- a high quality database focused on signal transduction
Comp. Funct. Genom. 5, 163-168 (2004). [more]
82.
Hehl, R., Steffens, N. O., Wingender, E.
Isolation and analysis of gene regulatory sequences
Handbook of Plant Biotechnology, Christou, P., Klee, H. (eds.), Wiley and Sons Ltd., 81-102 (2004).
81.
Kel, A., Tikunov, Y., Voss, N., Borlak, J., Wingender, E.
Application of kernel method to reveal subtypes of TF binding motifs. Causal analysis of gene expression data
Proceedings of the First Annual RECOMB Satellite Workshop on Regulatory Genomics, University of California, San Diego. (2004).
80.
Wingender, E.
TRANSFAC®, TRANSPATH® and CYTOMER® as starting points for an ontology of regulatory networks
In Silico Biol. 4, 0006 (2003). [more]
79.
D'Souza, U.M., Kel, A., Sluyter, F.
From transcriptional regulation to aggressive behavior
Behav. Genet. 33, 549-62 (2003). PMID: 14574132
78.
Kel, A., Tikunov, Y., Voss, N., Wingender, E.
Recognition of multiple patterns in unaligned sets of sequences. Comparison of kernel clustering method with other methods
Proceedings of the German Conference on Bioinformatics (GCB '03), Garching,
H.-W. Mewes, D. Frishman, V. Heun, S. Kramer (eds.), v.I: oral presentations, 63-68 (2003). [more]
77.
Swat, M., Kel, A., Kielbasa, S. M., Herzel, H.
Modeling the G1/S transition in mammals - bifurcation analysis of elementary modules
Proceedings of the German Conference on Bioinformatics (GCB '03), Garching,
H.-W. Mewes, D. Frishman, V. Heun, S. Kramer (eds.), v.I: oral presentations, 147-152 (2003). [more]
76.
Stegmaier, P., Kel, A., Matys, V., Kel-Margoulis, O., Wingender, E.
Hierarchical classification of transcription factor domains and corresponding Hidden Markov Models
Proceedings of the German Conference on Bioinformatics (GCB '03), Garching,
H.-W. Mewes, D. Frishman, V. Heun, S. Kramer (eds.), v.II: posters, 95 (2003).
75.
Voss, N., Potapov, A. P., Kel, A., Wingender, E.
Array Analysis and visualization of signaling networks: introducing indirect edges and chains
Proceedings of the German Conference on Bioinformatics (GCB '03), Garching,
H.-W. Mewes, D. Frishman, V. Heun, S. Kramer (eds.), v.II: posters, 199-201 (2003).
74.
Cheremushkin, E., Kel, A.
Whole genome human/mouse phylogenetic footprinting of potential transcription regulatory signals
Proceedings of the Pacific Symposia on Biocomputing, 2003; 291-302 (2003). PMID: 12603036
73.
Cheremushkin, E., Kel, A.
Whole genome human/mouse phylogenetic footprinting of potential transcription regulatory signals
Proceedings of the Pacific Symposia on Biocomputing, 2003; 291-302 (2003). PMID: 12603036
72.
Shelest, E., Kel, A., Wingender, E.
Constructing a promoter model for antibacterial response of lung epithelial cells
Proceedings of the European Conference on Computational Biology, (ECCB’2003), Paris, France, Sept. 27-30, 451-452 (2003). [more]
71.
Konovalova (Ivanova), T., Cheremushkin, E., Beschastnov, E., Kel, A.
Applicating of the metropolis algorithm to reveal composite modules in promoters of eukaryotic genes
Proceedings of the European Conference on Computational Biology, (ECCB’2003), Paris, France, Sept. 27-30, 447-448 (2003).
70.
Kel-Margoulis, O., Matys, V., Choi, C., Reuter, I., Goessling, E., Voss, N., Krull, M., Pistor, S., Thiele, S., Fricke, E., Land, S., Potapov, A., Tchekmenev, D., Lewicki-Potapov, B., Kel, A., Wingender, E.
Databases on eukaryotic gene regulation: TRANSFAC®, TRANSCompel®, and TRANSPATH®. Annotation, information processing, and application for analysis of gene expression data
Proceedings of the European Conference on Computational Biology, (ECCB’2003), Paris, France, Sept. 27-30, 131-132 (2003).
69.
Kel, A.E., Goessling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O.V., Wingender, E.
MATCH™: a tool for searching transcription factor binding sites in DNA sequences
Nucleic Acids Res. 31, 3576-3579 (2003). PMID: 12824369
68.
Kel-Margoulis, O.V., Tchekmenev D., Kel, A.E., Goessling, E., Hornischer, K., Lewicki-Potapov, B., Wingender, E.
Composition-sensitive analysis of the human genome for regulatory signals
In Silico Biol. 3, 0013 (2003) [more]
67.
Shelest, E., Kel, A., Gößling, E., Wingender, E.
Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods
In Silico Biol. 3, 0007 (2003). [more]
66.
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.
TRANSFAC®: transcriptional regulation, from patterns to profiles
Nucleic Acids Res. 31, 374-378 (2003). PMID: 12520026
65.
Münch, R., Hiller, K., Barg, H., Heldt, D., Linz, S., Wingender, E., Jahn, D.
PRODORIC: prokaryotic database of gene regulation
Nucleic Acids Res. 31, 266-269 (2003) PMID: 12519998
64.
Krull, M., Voss, N., Choi, V., Pistor, S., Potapov, A., Wingender, E.
TRANSPATH®: an integrated database on signal transduction and a tool for array analysis
Nucleic Acids Res. 31, 97-100 (2003). PMID: 12519957
63.
Csank, C, Costanzo, MC, Hirschman, J, Hodges, P, Kranz, JE, Mangan, M, O'Neill, K, Robertson, LS, Skrzypek, MS, Brooks, J, Garrels, JI.
Three yeast proteome databases: YPD, PombePD, and CalPD (MycoPathPD).
Methods Enzymol. 2002;350:347-73. No abstract available. PMID: 12073323 [PubMed - indexed for MEDLINE]
62.
Csank C, Costanzo MC, Hirschman J, Hodges P, Kranz JE, Mangan M, O'Neill K, Robertson LS, Skrzypek MS, Brooks J, Garrels JI.
Three yeast proteome databases: YPD, PombePD, and CalPD (MycoPathPD).
Methods Enzymol. 2002;350:347-73. No abstract available.
PMID: 12073323
61.
Liebich, I., Bode, J., Reuter, I., Wingender, E.
Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs)
Nucleic Acids Res. 30, 3433-3442 (2002). PMID: 12140328
60.
Wingender, E.
Modeling regulatory pathways with the use of the TRANSFAC system
Gene Function & Disease 3, 3-11 (2002). [more]
59.
Kel-Margoulis, O.V., Ivanova, T.G., Wingender, E., Kel, A.E.
Automatic annotation of genomic regulatory sequences by searching for composite clusters
Pac. Symp. Biocomput. 7, 187-198 (2002). PMID: 11928475
58.
Kloos, D.U., Choi, C., Wingender, E.
The TGF-beta-Smad network: introducing bioinformatic tools
Trends Genet. 18, 96-103. (2002). PMID: 11818142
57.
Kel-Margoulis, O.V., Kel, A.E., Reuter, I., Deineko, I.V., Wingender, E.
TRANSCompel: a database on composite regulatory elements in eukaryotic genes
Nucleic Acids Res. 30, 332-334 (2002). PMID: 11752329
56.
Liebich, I., Bode, J., Frisch, M., Wingender, E.
S/MARt DB: a database on scaffold/matrix attached regions
Nucleic Acids Res. 30, 372-374 (2002). PMID: 11752340
55.
Schacherer, F., Choi, C., Götze, U., Krull, M., Pistor, S., Wingender, E.
The TRANSPATH signal transduction database: a knowledge base on signal transduction networks
Bioinformatics 17, 1053-1057 (2001). PMID: 11724734
54.
Kel, A. E., Kel-Margoulis, O. V. Farnham, P. J., Bartley, S. M., Wingender, E., Zhang, M. Q.
Computer-assisted Identification of Cell Cycle-related Genes: New Targets for E2F Transcription Factors
J. Mol. Biol. 309, 99-120 (2001). PMID: 11491305
53.
Potapov, A., Seidl, K. Christensen, M., Drewes, V., Schacherer, F., Wingender, E.
The integrated TRANSFAC system as a basis for modeling the architecture of gene regulatory networks
Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig
E. Wingender, R. Hofestaedt, I. Liebich (eds.), 218-219 (2001). [more]
52.
Michael, H., Thiele, S., Wingender, E.
TRANSFAC_YEAST
Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig
E. Wingender, R. Hofestaedt, I. Liebich (eds.), 208-209 (2001). [more]
51.
Kloos, U.D., Choi, C., Wingender, E.
The SMAD-TGF-Beta signalling network: TRANSFAC meets TRANSPATH
Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig [more]
50.
Kel-Margoulis, O.V., Deineko, I.V., Reuter, I., Wingender, E., Kel, A.E.
TRANSCompel a professional database on composite regulary elements in eukaryotic genes
Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig
E. Wingender, R. Hofestaedt, I. Liebich (eds.), 185-187 (2001). [more]
49.
Götze, U., Pistor, S., Choi, C., Krull, M., Schacherer, F., Voss, N., Wingender, E.
TRANSPATH - a database on signal transduction networks
Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig
E. Wingender, R. Hofestaedt, I. Liebich (eds.), 162-163 (2001). [more]
48.
Goessling, E., Kel-Margoulis, O.V., Kel, A.E., Wingender, E.
MATCH™ - a tool for searching transcription factor binding sites in DNA sequences. Application for the analysis of human chromosomes
Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig
E. Wingender, R. Hofestaedt, I. Liebich (eds.), 158-161 (2001). [more]
47.
Fricke, E., Land, S., Rotert, S., Karas, D., Wingender, E.
Cytomer: A database on gene expression sources
Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig
E. Wingender, R. Hofestaedt, I. Liebich (eds.), 149-151 (2001). [more]
46.
Kel, A.E., Kel-Margoulis, O.V, Ivanova, T., Wingender, E.
ClusterScan: a tool for automatic annotation of genomic regulatory sequences by searching for composite clusters
Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig
E. Wingender, R. Hofestaedt, I. Liebich (eds.), 96-101 (2001). [more]
45.
Potapov, A. and Wingender, E.
Modeling the architecture of regulatory networks
Proceedings of the German Conference on Bioinformatics (GCB '01), GBF Braunschweig
E. Wingender, R. Hofestaedt, I. Liebich (eds.), 6-10 (2001). [more]
44.
Hehl, R. and Wingender, E.
Database - assisted promoter analysis
Trends in Plant Science 6, 251-254 (2001). PMID: 11378466
43.
Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu P, Lengieza C, Lew-Smith JE, Tillberg M, Garrels JI.
YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information.
Nucleic Acids. Res. 29, 75-79. PMID: 11125054
42.
Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., Ohnhäuser, R., Prüß, M., Schacherer, F., Thiele, S. and Urbach, S.
The TRANSFAC system on gene expression regulation
Nucleic Acids Res. 29, 281-283 (2001). PMID: 111251135, UI: 2057481
41.
Constanzo, M. C., Hogan, G. D., Cusick, M. E., Davis, B. P., Fancher, A. M., Hodges, P. E., Kondu, P., Lengieza, C., Lew-Smith, J. E., Lingner, C., Roberg-Perez, K. J., Tillberg, M., Brooks, J. E., Garrels, J. I.
The yeast proteome database(YPD) and Caenorhabditis elegans proteome database (WormPD): a comprehensive resource for protein information
Nucleic Acids Res. 28,73-76 (2000). PMID: 10592185
40.
Wingender, E.
The TRANSFAC System on Gene Regulation
Trends in Glycoscience and Glycotechnology 12, 255-264 (2000).
39.
Kel, A. E., Deineko, I., Kel-Margoulis, O. V., Wingender, E., Ratner, V.
Modelling of gene regulatory network of cell cycle control. Role of E2F feedback loops
Proceedings of the German Conference on Bioinformatics (GCB '00), Heidelberg
E. Bornberg-Bauer, U. Rost, J. Stoye, M. Vingron (eds.), 107-114 (2000).
38.
Roulet, E., Bucher, P., Schneider, R., Wingender, E., Dusserre, Y., Werner, T. and Mermod, N.
Experimental analysis and computer prediction of CTF/NFI Transcription Factor DNA binding sites
J. Mol. Biol. 297, 833-848 (2000). PMID: 10736221, UI: 20202367
37.
Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V., Meinhardt, T., Prüß, M., Reuter, I. and Schacherer, F.
TRANSFAC®: an integrated system for gene expression regulation
Nucleic Acids Res. 28, 316-319 (2000). PMID: 10592259, UI: 20063293
36.
Kel-Margoulis, O. V., Romashchenko, A. G., Kolchanov, N. A., Wingender, E. and Kel, A. E.
COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation
Nucleic Acids Res. 28, 311-315 (2000). PMID: 10592258, UI: 20063292
35.
Hodges, P. E., Mc Kee, A. H., Davis, B. P., Payne, W. E., Garrels, J. I.
The Yeast Proteome Database (YPD): amodel for the organization and presentation of genome-wide functional data
Nucleic Acids Res. 27, 69-73 (1999) [more]
34.
Chen, X., Dress, A., Karas, H., Reuter, I. and Wingender, E.
A database framework for mapping expression patterns Computer Science and Biology. Proceedings of the German Conference on Bioinformatics (GCB 1999)
R. Giegerich, R. Hofestädt, T. Lengauer, W. Mewes, D. Schomburg, M. Vingron and E. Wingender (eds.)
GBF-Braunschweig and University of Bielefeld, pp. 174-178 (1999).
33.
Kel, A., Kel-Margoulis, O., Babenko, V. and Wingender, E.
Recognition of NFATp/AP-1 composite elements within genes induced upon the activision of immune cells
J. Mol. Biol. 288, 353-376 (1999). PMID: 10329147, UI: 99262847
32.
Heinemeyer, T., Chen, X., Karas, H., Kel, A. E., Kel, O. V., Liebich, I., Meinhardt, T., Reuter, I., Schacherer, F., Wingender, E.
Expanding the TRANSFAC® database towards an expert system of regulatory molecular mechanisms
Nucleic Acids Res. 27, 318-322 (1999). PMID: 9847216
31.
Heinemeyer, T., Wingender, E., Reuter, I., Hermjakob, H., Kel, A. E., Kel, O. V., Ignatieva, E. V., Ananko, E. A., Podkolodnaya, O. A., Kolpakov, F. A., Podkolodny N. L. and Kolchanov, N. A.
Databases on Transcriptional Regulation: TRANSFAC®, TRRD, and COMPEL
Nucleic Acids Res. 26, 362-367 (1998). PMID: 9399875, UI: 98062468
30.
Hodges, P. E., Payne W. E., Garrels, J. I.
The Yeast Proteome Database (YPD): a curated proteome database for Saccharomyces cerevisiae
Nucleic Acids Res. 25, 68+72 (1998). PMID: 9399803
29.
Flohe, L., Wingender, E. and Brigelius-Flohe, R.
Regulation of glutathione peroxidases Oxidative stress and signal transduction
H. J. Forman, H. Cadenas (eds.), Chapman & Hall, New York, 415-440 (1997)
28.
Kuhlenbäumer, G., Rothenburg, S., Matthes, M., Hollmann, C., Wingender, E., Thiele, H.-G., Koch-Nolte, F. and Haag, F.
Expression of the RT6 mono (ADP-ribosyl) transferases is regulated by two promoter regions
Adv. Exp. Med. Biol. 419, 265-270 (1997). PMID: 9193664, UI: 97336917
27.
Pickert, L., Klawonn, F. and Wingender, E.
Fuzzy Cluster Analysis For Identification Of Gene Regulating Regions
Proc. 7th International Fuzzy Systems Association World Congress (IFSA'97) Vol. IV, Academia, Prague, 56-61 (1997)
26.
Pickert, L., Reuter, I., Klawonn, F. and Wingender, E.
Transcription regulatory regions revealed by signal detection and fuzzy clustering
Proceedings of the German Conference on Bioinformatics GCB '97, Kloster Irsee, Bavaria
H. W. Mewes, D. Frishman (eds.), 99-101 (1997). PMID: 9614267, UI: 98279154
25.
Wingender, E., Kel, A. E., Kel, O. V., Karas, H., Heinemeyer, T., Dietze, P., Knüppel, R., Romaschenko, A. G., Kolchanov, N. A.
TRANSFAC®, TRRD and COMPEL: Towards a federated database system on transcriptional regulation
Nucleic Acids Res. 25, 265-268 (1997). PMID: 9016550, UI: 97169407
24.
Payne, W. E., Garrels, J. I.
Yeast Protein Database (YPD): a database for the complete proteome of Saccharomyces cerevisiae
Nucleic Acids Res. 25, 57-62 (1997). PMID: 9016505
23.
Frech, K., Dietze, P., Werner, T.
ConsInspector 3.0: new library and enhanced functionality
Comp. Appl. Biosci. 13, 109-110 (1997). PMID: 9088717, UI: 97243876
22.
Wingender, E., Karas, H., Knüppel, R.
TRANSFAC® Database as a Bridge between Sequence Data Libraries and Biological Function
Pacific Symposium on Biocomputing '97 (PSB'97)
R. B. Altman, A. K. Dunker, L. Hunter, T. E. Klein (eds.)
World Scientific, Singapore - New Jersey - London - Hong Kong 1996, pp. 477-485. PMID: 9390316, UI: 98051989
21.
Karas, H., Kel, E., Kel, O.V., Kolchanov, N.A., Wingender, E.
Integrating knowledge on transcriptional regulation of eukaryotic genes based on information from TRANSFAC®, TRRD, and COMPEL databases
Mol. Biol. (Mosk) 31(4), 637-646 (1997). PMID: 9340499, UI: 97453249
20.
Wingender, E.
Classification scheme of eukaryotic transcription factors
Molekularnaya Biologiya 31, 584-600 (1997). Mol. Biol. Engl. Tr. 31, 483-497 (1997). PMID: 9340487
19.
Ponomarkeno M. P., Ponomarenko I. u. V., Kel A. E., Kolchanov N. A., Karas H., Wingender E., Sklenar H.
Computer analysis of conformational features of the eukaryotic TATA-box DNA promotors
Mol. Biol. (Mosk) 31(4), 733-40 (1997). PMID: 9340499, UI: 97453257
18.
Haag, F. A., Kuhlenbaeumer, G., Koch-Nolte, F., Wingender, E.,Thiele, H.-G.
Structure of the gene encoding the rat T cell ecto-ADP-ribosyltransferase RT6
J. Immunol. 157, 2022-2030 (1996). PMID: 8757323, UI: 96355006
17.
Karas, H., Knüppel, R., Schulz, W., Sklenar, H., Wingender, E.
Combining structural analysis of DNA with search routines for detection of transcription regulatory elements
Comput. Appl. Biosci. 12, 441-446 (1996). PMID: 8996793, UI: 97150020
16.
Wingender, E., Karas, H., Dietze, P., Knüppel, R., Sklenar, H.
Combined approaches for the detection of regulatory DNA-regions. Computer Science and Biology. Proceedings of the German Conference on Bioinformatics (GCB'96)
R. Hofestaedt, T. Lengauer, M. Loeffler, D. Schomburg (eds.), University of Leipzig, Leipzig 1996, pp. 58-63.
15.
Kel, A., Kel, O., Ischenko, I., Kolchanov, N., Karas, H., Wingender, E., Sklenar, H.
TRRD and COMPEL databases on transcription linked to TRANSFAC® as tools for analysis and recognition of regulatory sequences. Computer Science and Biology
Proceedings of the German Conference on Bioinformatics (GCB'96)
R. Hofestaedt, T. Lengauer, M. Loeffler, D. Schomburg (eds.)
University of Leipzig, Leipzig 1996, pp. 113-117.
14.
Garrels, J. I.
YPD-A database for the proteins of Saccharmyces cerevisiae
Nucleic Acids Res. 25, 46-49 (1996). PMID: 8594598 [more]
13.
Wingender, E., Dietze, P., Karas, H., Knüppel, R.
TRANSFAC®: A database on transcription factors and their DNA binding sites
Nucleic Acids Res., 24, 238-241 (1996). PMID: 8594589, UI: 96128303
12.
Quandt, K., Frech, K., Karas, H., Wingender, E., and Werner, T.
MatInd and MatInspector - New fast and sensitive tools for detection of consensus matches in nucleotide sequence data
Nucleic Acids Res., 23, 4878-4884 (1995), PMID: 8532532, UI: 96128303
11.
Kel, O. V., Romaschenko, A. G., Kel, A. E., Wingender, E., Kolchanov, N. A.
A compilation of composite regulatory elements affecting gene transcription in vertebrates
Nucleic Acids Res., 23, 4097-4103 (1995) [more]
10.
Wingender, E., Knüppel, R., Dietze, P., Karas, H., Frech, K., Quandt, K., Werner, T.
The TRANSFAC® database and ConsInd program as tools for describing and understanding regulatory functions of the genome
SAMS 18-19 (1995) pp. 823-826; Overseas Publishers Association, Amsterdam
9.
Wingender, E., Knüppel, R., Dietze, P., Karas, H.
TRANSFAC® database as tool for the recognition of regulatory genomic sequences. In: Bioinformatics & Genome Research
H.A. Lim and C.R. Cantor (Eds.)
(World Scientific Publishing Co., Inc., New Jersey, 1995), pp. 275-282
8.
Knüppel, R., Dietze, P., Lehnberg, W., Frech, K., Wingender, E.
TRANSFAC® retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins
J. Comput. Biol. 1 (1994) 191-198, PMID: 8790464, UI: 96382600
7.
Wingender, E.
Recognition of regulatory regions in genomic sequences
J. Biotechnol. 35 (1994) 273-280, PMID: 7765063, UI: 94325103
6.
Moeritz, A., Grzeschik, K.-H., Wingender, E., Fink, E.
Organization and sequence of the gene encoding the human acrosin-trypsin inhibitor (HUSI-II)
Gene 123 (1993) 277-281, PMID: 8428671, UI: 93154598
5.
Scutt, A., Mayer, H., Wingender, E.
New perspectives in the differentiation of bone-forming cells
Biofactors 4 (1992) 1-13, PMID: 1292470
4.
Wingender, E., Heinemeyer, T., Lincoln, D.
Regulatory DNA sequences: predictability of their function. Genome Analysis - From Sequence to Function
J. Collins, A.J. Driesel, eds.
BioTechForum- Advances in Molecular Genetics 4 (1991) 95-108
3.
Rupp, E., Mayer, H., Wingender, E.
The promoter of the human parathyroid hormone gene contains a functional cyclic AMP-response element
Nucleic Acids Res. 18 (1990) 5677-5683, PMID: 1977134, UI: 91016901
2.
Wingender, E.
Transcription regulating proteins and their recognition sequences
CRC Crit. Rev. in Eukaryotic Gene Expression 1 (1990) 11-48, PMID: 1983713, UI: 92199431
1.
Wingender, E.
Compilation of transcription regulating proteins
Nucleic Acids Res. 16 (1988) 1879-1902, PMID: 3282223, UI: 88189791
Book:
Wingender, E.
Gene Regulation in Eukaryotes
VCH Weinheim, New York, Basel, Cambridge, 1993 (ISBN 3-527-28460-5)
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