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

Publications

  1. Kisakol, B., Matveeva, A., Salvucci, M., Kel, A., McDonough, E., Ginty, F., Longley, D., Prehn, J. (2024) Identification of unique rectal cancer-specific subtypes. Br J Cancer. 130, 1809–1818. DOI https://doi.org/10.1038/s41416-024-02656-0. Link
  2. Kechin, A., Borobova, V., Kel, A., Ivanov, A., & Filipenko, M. (2022) ErbB4 Is a Potential Key Regulator of the Pathways Activated by NTRK-Fusions in Thyroid Cancer. Appl. Sci. 12, 2506. Link
  3. Klopot, A., Baida, G., Kel, A., Tsoi, L. C., White, B. E. P., Budunova, I. (2022) Transcriptome Analysis Reveals Intrinsic Proinflammatory Signaling in Healthy African American Skin. J. Invest. Dermatol. 142, 1360-1371. Link
  4. Myer, P. A., Kim, H., Blümel, A. M., Finnegan, E., Kel, A., Thompson, T. V., Greally, J.M., Prehn, J.HM., O’Connor, D.P., Friedman, R.A., Floratos, A., Das, S. (2022) Master Transcription Regulators and Transcription Factors Regulate Immune-Associated Differences Between Patients of African and European Ancestry With Colorectal Cancer. Gastro Hep Adv. 1, 328-341. Link
  5. Wang, K., Stevens, R., Alachram, H., Li, Y., Soldatova, L., King, R., Ananiadou, S., Schoene, A.M., Li, M., Christopoulou, F., Ambite, J.L., Matthew, J., Garg, S., Hermjakob, U., Marcu, D., Sheng, E., Beißbarth, T., Wingender, E., Galstyan, A., Gao, X., Chambers, B., Pan, W., Khomtchouk, B.B., Evans, J.A., Rzhetsky, A. (2021) NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding. NPJ Syst. Biol. Appl. 7, 38. Link
  6. Alachram, H., Chereda, H., Beißbarth, T., Wingender, E., Stegmaier. P. (2021) Text mining-based word representations for biomedical data analysis and protein-protein interaction networks in machine learning tasks. PLoS One 16, e0258623. Link
  7. Chereda, H., Bleckmann, A., Menck, K., Perera-Bel, J., Stegmaier, P., Auer, F., Kramer, F., Leha, A., Beißbarth, T. (2021) Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer. Genome Med. 13, 1-16. Link
  8. Kolmykov, S., Yevshin, I., Kulyashov, M., Sharipov, R., Kondrakhin, Y., Makeev, V.J., Kulakovskiy, I.V., Kel, A., Kolpakov, F. (2020) GTRD: an integrated view of transcription regulation. Nucleic Acids Res. 49, D104–D111. Link
  9. Lloyd, K., Papoutsopoulou, S., Smith, E., Stegmaier, P., Bergey, F., Morris, L., Kittner, M., England, H., Spiller, D., White, M.H.R., Duckworth, C.A., Campbell, B.J., Poroikov, V., Martins Dos Santos, V.A.P., Kel, A., Muller, W., Pritchard, D.M., Probert, C., Burkitt, M.D., SysmedIBD consortium. (2020) Using systems medicine to identify a therapeutic agent with potential for repurposing in inflammatory bowel disease. Dis. Model. Mech. 13, dmm044040. Link
  10. Lasri, A., Juric, V., Verreault, M., Bielle, F., Idbaih, A., Kel, A., Murphy, B., Sturrock, M. (2020) Phenotypic selection through cell death: stochastic modelling of O-6-methylguanine-DNA methyltransferase dynamics. R. Soc. Open Sci. 7, 191243. Link
  11. Orekhov, A.N., Sukhorukov, V.N., Nikiforov, N.G., Kubekina, M.V., Sobenin, I.A., Foxx, K.K., Pintus, S., Stegmaier, P., Stelmashenko, D., Kel, A., Poznyak, A.V., Wu, W.K., Kasianov, A.S., Makeev, V.Y., Manabe, I., Oishi, Y. (2020) Signaling Pathways Potentially Responsible for Foam Cell Formation: Cholesterol Accumulation or Inflammatory Response-What is First? Int. J. Mol. Sci. 21, 2716. Link
  12. Daou, R., Beißbarth, T., Wingender, E., Gültas, M., Haubrock, M. (2020) Constructing temporal regulatory cascades in the context of development and cell differentiation. PLoS One. 15, e0231326. Link
  13. Aarestrup, F.M., Albeyatti, A., Armitage, W.J., Auffray, C., Augello, L., Balling, R., Benhabiles, N., Bertolini, G., Bjaalie, J.G., Black, M., Blomberg, N., Bogaert, P., Bubak, M., Claerhout, B., Clarke, L., De Meulder, B., D’Errico, G., Di Meglio, A., Forgo, N., Gans-Combe, C., Gray, A.E., Gut, I., Gyllenberg, A., Hemmrich-Stanisak, G., Hjorth, L., Ioannidis, Y., Jarmalaite, S., Kel, A., Kherif, F., Korbel, J.O., Larue, C., Laszlo, M., Maas, A., Magalhaes, L., Manneh-Vangramberen, I., Morley-Fletcher, E., Ohmann, C., Oksvold, P., Oxtoby, N.P., Perseil, I., Pezoulas, V., Riess, O., Riper, H., Roca, J., Rosenstiel, P., Sabatier, P., Sanz, F., Tayeb, M., Thomassen, G., Van Bussel, J., Van den Bulcke, M., Van Oyen, H. (2020) Towards a European health research and innovation cloud (HRIC). Genome Med. 12, 18. Link
  14. Orekhov, A.N., Nikiforov, N.G., Sukhorukov, V.N., Kubekina, M.V., Sobenin, I.A., Wu, W.K., Foxx, K.K., Pintus, S., Stegmaier, P., Stelmashenko, D., Kel, A., Gratchev, A.N., Melnichenko, A.A., Wetzker, R., Summerhill, V.I., Manabe, I., Oishi, Y. (2020) Role of Phagocytosis in the Pro-Inflammatory Response in LDL-Induced Foam Cell Formation; a Transcriptome Analysis. Int. J. Mol. Sci. 21, 817. Link
  15. Kel, A., Boyarskikh, U., Stegmaier, P., Leskov, L. S., Sokolov, A. V., Yevshin, I., Mandrik, N., Stelmashenko, D., Koschmann, J., Kel-Margoulis, O., Krull, M., Martínez-Cardús, A., Moran, S., Esteller, M., Kolpakov, F., Filipenko, M. and Wingender, E. (2019) Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer. BMC Bioinformatics 20 (Suppl 4), 119. doi: 0.1186/s12859-019-2687-7  Link
  16. Orekhov, A., Oishi, Y., Nikiforov, N., Zhelankin, A. V., Sobenin, I., Kel, E., Stelmashenko, D., Makeev, V., Foxx, K., Kruth, H., Jin, X. and Bukrinsky, M. I. (2018) Transcriptome analysis revealed inflammatory genes responsible for foam cell formation. Atherosclerosis 275, e116. doi: 10.1016/j.atherosclerosis.2018.06.329) Link
  17. Smetanina, M. A., Kel, A. E., Sevost’ianova, K. S., Maiborodin, I. V., Shevela, A. I., Zolotukhin, I. A., Stegmaier, P. and Filipenko, M. L. (2018) DNA methylation and gene expression profiling reveal MFAP5 as a regulatory driver of extracellular matrix remodeling in varicose vein disease. Epigenomics 10, 1103-1119. doi: 10.2217/epi-2018-0001 Link
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. Wingender, E., Kel, A. (2012) geneXplain – eine integrierte Bioinformatik-Plattform. BIOspektrum 18, 554-556 (German). Link
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. Find here the complete list of publications of E. Wingender and A. Kel as indexed by PubMed.
×