We provide a comprehensive platform for bioinformatic, cheminformatic and systems biological tools

Publications

  1. Mandić, A. D., Bennek, E., Verdier, J., Zhang, K., Roubrocks, S., Davis, R. J., Denecke, B., Gassler, N., Streetz, K., Kel, A., Hornef, M., Cubero, F. J., Trautwein, C. and Sellge, G. (2017) c-Jun N-terminal kinase 2 promotes enterocyte survival and goblet cell differentiation in the inflamed intestine. Mucosal Immunol., in press. doi: 10.1038/mi.2016.125. Link
  2. Kural, K. C., Tandon, N., Skoblov, M., Kel-Margoulis, O. V. and Baranova, A. V. (2016) Pathways of aging: comparative analysis of gene signatures in replicative senescence and stress induced premature senescence. BMC Genomics 17(Suppl 14), 1030. doi: 10.1186/s12864-016-3352-4. Link
  3. Kel, A. E. (2016) Data on master regulators and transcription factor binding sites found by upstream analysis of multi-omics data on methotrexate resistance of colon cancer. Data Brief. 10, 499-504. doi: 10.1016/j.dib.2016.11.096. Link
  4. Kondrakhin, Y., Valeev, T., Sharipov, R., Yevshin, I., Kolpakov, F. and Kel, A. E. (2016) Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data. EuPA Open Proteomics 13, 14-23. doi: 10.1016/j.euprot.2016.09.001. Link
  5. Kel, A. E., Stegmaier, P., Valeev, T., Koschmann, J., Poroikov, V., Kel-Margoulis, O. V. and Wingender, E. (2016) Multi-omics “upstream analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer. EuPA Open Proteomics 13, 1-13. doi: 10.1016/j.euprot.2016.09.002. Link
  6. Srivastava, A., Mazzocco, G., Kel, A., Wyrwicz, L.S. and Plewczynski, D. (2016) Detecting reliable non interacting proteins (NIPs) significantly enhancing the computational prediction of protein-protein interactions using machine learning methods. Mol. Biosyst. 12, 778-785. doi: 10.1039/c5mb00672d. Link
  7. Koschmann, J., Bhar, A., Stegmaier,P., Kel, A. E. and Wingender, E. (2015) “Upstream Analysis”: An integrated promoter-pathway analysis approach to causal interpretation of microarray data. Microarrays 4, 270-286. doi:10.3390/microarrays4020270. Link
  8. Wingender, E., Schoeps, T., Haubrock, M. and Dönitz, J. (2015) TFClass: a classification of human transcription factors and their rodent orthologs. Nucleic Acids Res. 43, D97-D102. doi: 10.1093/nar/gku1064. Link
  9. Sycheva, A.M., Kel, A., Nikolaev, E.N., and Moshkovskii, S.A. (2014) Equal Impact of Diffusion and DNA Binding Rates on the Potential Spatial Distribution of Nuclear Factor κB Transcription Factor inside the Nucleus. Biochemistry (Moscow) 79, 577-580. Link
  10. Shi, Y., Nikulenkov, F., Zawacka-Pankau, J., Li, H., Gabdoulline, R., Xu, J., Eriksson, S., Hedström, E., Issaeva, N., Kel, A., Arnér, E.S., Selivanova, G. (2014) ROS-dependent activation of JNK converts p53 into an efficient inhibitor of oncogenes leading to robust apoptosis. Cell Death Differ. 21, 612-623. doi:10.1038/cdd.2013.186. Link
  11. Kolker, E., Ozdemir, V., Martens, L., Hancock, W., Anderson, G., Anderson, N., Aynacioglu, S., Baranova, A., Campagna, S.R., Chen, R., Choiniere, J., Dearth, S.P., Feng, W.C., Ferguson, L., Fox, G., Frishman, D., Grossman, R., Heath, A., Higdon, R., Hutz, MH., Janko, I., Jiang, L., Joshi, S., Kel, A., Kemnitz, J.W., Kohane, I.S., Kolker, N., Lancet, D., Lee, E., Li, W., Lisitsa, A., Llerena, A., Macnealy-Koch, C., Marshall, J.C., Masuzzo, P., May, A., Mias, G., Monroe, M., Montague, E., Mooney, S., Nesvizhskii, A., Noronha, S., Omenn, G., Rajasimha, H., Ramamoorthy, P., Sheehan, J., Smarr, L., Smith, C.V., Smith, T., Snyder, M., Rapole, S., Srivastava, S., Stanberry, L., Stewart, E., Toppo, S., Uetz, P., Verheggen, K., Voy, B.H., Warnich, L., Wilhelm, S.W. and Yandl, G. (2014) Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS 18, 10-14. doi:10.1089/omi.2013.0149. Link
  12. Masseroli, M., Mons, B., Bongcam-Rudloff, E., Ceri, S., Kel, A., Rechenmann, F., Lisacek, F. and Romano, P. (2014) Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. BMC Bioinformatics 15 (Suppl. 1), S2. doi:10.1186/1471-2105-15-S1-S2. Link
  13. Deyneko, I. V., Kel, A. E., Kel-Margoulis, O. V., Deineko, E. V., Wingender, E. and Weiss, S. (2013) MatrixCatch – a novel tool for the recognition of composite regulatory elements in promoters. BMC Bioinformatics 14, 241. Link
  14. Stegmaier, P., Kel, A., Wingender, E., Borlak, J. (2013) A discriminative approach for unsupervised clustering of DNA sequence motifs. PLoS Comput. Biol. 9, e1002958. Link
  15. Wingender, E. (2013) Criteria for an updated classification of human transcription factor DNA-binding domains. J. Bioinform. Comput. Biol. 11, 1340007. doi: 10.1142/S0219720013400076. Link
  16. Wingender, E., Schoeps, T., Dönitz, J. (2013) TFClass: An expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 41, D165-D170. doi: 10.1093/nar/gks1123. Link
  17. Wingender, E., Kel, A. (2012) geneXplain – eine integrierte Bioinformatik-Plattform. BIOspektrum 18, 554-556 (German). Link
  18. Nikulenkov, F., Spinnler, C., Li, H., Tonelli, C., Shi, Y., Turunen, M., Kivioja, T., Ignatiev, I., Kel, A., Taipale, J., Selivanova, G. (2012) Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis. Cell Death Differ. 19, 992-2002. PubMed badgef1000
  19. Gabdoulline, R., Eckweiler, D., Kel, A., Stegmaier, P. (2012) 3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. Nucleic Acids Res. 40, W180-W185. PubMed
  20. De Pauw, A., Demine, S., Tejerina, S., Dieu, M., Delaive, E., Kel, A., Renard, P., Raes, M., Arnould, T. (2012) Mitochondrial uncoupling does not affect mitochondrial biogenesis but down-regulates pyruvate carboxylase in adipocytes: role for triglyceride content reduction. Am. J. Physiol. Endocrinol. Metab. 302, E1123-E1141. PubMed
  21. Kel, A., Kolpakov, F., Poroikov, V., Selivanova, G. (2011) GeneXplain — Identification of Causal Biomarkers and Drug Targets in Personalized Cancer Pathways. J. Biomol. Tech. 22(suppl.), S16. PubMed
  22. Zawacka-Pankau, J., Grinkevich, V.V., Hünten, S., Nikulenkov, F., Gluch, A., Li, H., Enge, M., Kel, A., Selivanova, G. (2011) Inhibition of glycolytic enzymes mediated by pharmacologically activated p53: targeting Warburg effect to fight cancer. J. Biol. Chem. 286, 41600-41615. PubMed
  23. Ghedira K., Hornischer K., Konovalova T., Jenhani A.Z., Benkahla A., Kel A. (2011) Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis. Infect. Genet. Evol. 11, 769-777. PubMed
  24. Stegmaier P., Voss N., Meier T., Kel A., Wingender E., Borlak, J. (2011) Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer. PLoS ONE 6, e17738. Article
  25. Find here the complete list of publications of E. Wingender and A. Kel as indexed by PubMed.
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