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

Publications

  1. Wingender, E., Schoeps, T., Haubrock, M., Krull, M. and Dönitz, J. (2018) TFClass: expanding the classification of human transcription factors to their mammalian orthologs. Nucleic Acids Res. 46, D343-D347. doi: 10.1093/nar/gkx987  Link
  2. Boyarskikh, U., Pintus, S., Mandrik, N., Stelmashenko, D., Kiselev, I., Evshin, I., Sharipov, R., Stegmaier, P., Kolpakov, F., Filipenko, M. and Kel A. (2018) Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3. BMC Med. Genomics 11(Suppl 1), 12. doi: 10.1186/s12920-018-0330-5
    Link
  3. Stegmaier, P., Kel, A and Wingender, E. (2017) geneXplainR: An R interface for the geneXplain platform. J. Open Source Softw. 2, 412. doi: 10.21105/joss.00412. Link
  4. Triska, M., Solovyev, V., Baranova, A., Kel, A. and Tatarinova, T. V. (2017) Nucleotide patterns aiding in prediction of eukaryotic promoters. PLoS One 12, e0187243. doi: 10.1371/journal.pone.0187243. Link
  5. Kel, A.E. (2017). Search for Master Regulators in Walking Cancer Pathways. Methods Mol. Biol. 1613, 161-191. doi: 10.1007/978-1-4939-7027-8_8. Link
  6. Kechin, A., Boyarskikh, U., Kel, A. and Filipenko, M. (2017) cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing. J. Comput. Biol. 24, 1138-1143. doi: 10.1089/cmb.2017.0096. Link
  7. Yevshin, I., Sharipov, R., Valeev, T., Kel, A. and Kolpakov, F. (2017) GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. Nucleic Acids Res. 45(D1), D61-D67. doi: 10.1093/nar/gkw951. Link
  8. Niehof, M., Hildebrandt, T., Danov, O., Arndt, K., Koschmann, J., Dahlmann, F., Hansen, T. and Sewald, K. (2017) RNA isolation from precision-cut lung slices (PCLS) from different species. BMC Res. Notes 10, 121. doi: 10.1186/s13104-017-2447-6. Link
  9. 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., 2017;10(5):1211-1223. doi: 10.1038/mi.2016.125. Link
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. Wingender, E., Kel, A. (2012) geneXplain – eine integrierte Bioinformatik-Plattform. BIOspektrum 18, 554-556 (German). Link
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. Find here the complete list of publications of E. Wingender and A. Kel as indexed by PubMed.
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