Alexander Kel

Genexplan GMBH (GP)

Biosketch

Alexander Kel, PhD, is Chief Scientific Officer of the leading bioinformatics company geneXplain GmbH situated in Wolfenbuettel, Germany

 

Alexander Kel received his Ph.D. in Bioinformatics, Molecular Biology and Genetics in 1990. He studied biology and mathematics at Novosibirsk State University and obtained his M.S. in biology with special focus on mathematical biology in 1985. The research experience of Dr. Kel in Bioinformatics totals in more than 20 years. During his career, he worked in almost all branches of current bioinformatics including: theoretical models of molecular genetic information systems, sequence analysis, gene recognition, promoter analysis and prediction, analysis of protein secondary structure, prediction of RNA secondary structure, theory of mutation and recombination process, molecular evolution, databases and gene expression studies. Currently, his interests are in the study of complex structure of promoters/enhancers, analysis of signal transduction pathways and identification of drug targets and systems biology and systems medicine. 

Alexander Kel is the author of more than 100 scientific publications. He is also an author of several chapters in books on bioinformatics. Alexander Kel has participated in 20 national and international projects and was a coordinator of three EU projects, Net2Drug (on anti-cancer drug development), SysCo (on study mechanisms of infection) and GlobCell (on systems biology of immune response).   

1. Positions and Honors

Positions and Employment

2022: – CEO, geneXplain GmbH, Wolfenbüttel, Germany 

2010: – CSO, geneXplain GmbH, Wolfenbüttel, Germany 

2008: – Senior Scientist, Institute of Chemical Biology and Fundamental Medicine, SBRAS, Novosibirsk, Russia.

2005 – 2010: Senior Vice President R&D, BIOBASE GmbH, Wolfenbuettel, Germany.

2000 – 2005: Vice President R&D, BIOBASE GmbH, Wolfenbuettel, Germany.

1988 – 2004: Scientist, ICG, Siberian Branch of RAS, Novosibirsk.

1985 – 1988: Programmer, ICG, Siberian Branch of RAS, Novosibirsk.

 

Other Experience and Professional Memberships

The scientific career of Dr. Alexander Kel includes research stays in USA:

1993: Supercomputer Center, Tallahassee (Dr. Hwa Lim); 

1993: Argon National Lab (Dr. Radoje Drmanac)

1997: University of Pennsylvania, Philadelphia (Dr. Chriss Overton), 

1999: Cold Spring Harbor, NY, Visiting scientist (Dr. Michael Zhang), 

Italy (1991,1992: ITBA, Milan, Visiting professor) (Dr. Luciano Milanesi), 

and Germany (1994, 1995, 1996, 1997-1998: GBF (Dr. Edgar Wingender); 

1997: Max Plank Institute of Molecular Biology, Berlin, visiting scientist and Post. Doc.) (Prof. Hans Lehrach).

Selected publications

1. Kel-Margoulis, O V, A G Romashchenko, N A Kolchanov, E Wingender, and A E Kel. 2000. “COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation.” Nucleic acids research 28 (1) (January 1): 311-5.
2. 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, Wingender E. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2006 Jan 1;34 (Database issue):D108-10. doi: 10.1093/nar/gkj143.PMID: 16381825.
3. Stegmaier P, Voss N, Meier T, Kel A, Wingender E, Borlak J. Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer. PLoS One. 2011 Mar 28;6(3):e17738. PubMed PMID:  21464922; PubMed Central PMCID: PMC3065454.
4. 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 
5. Stegmaier, P., Kel, A., Wingender, E., Borlak, J. (2013) A discriminative approach for unsupervised clustering of DNA sequence motifs. PLoS Comput. Biol. 9, e1002958.
6. 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.
7. Kel A, Boyarskikh U, Stegmaier P, Leskov LS, Sokolov AV, Yevshin I, Mandrik N, Stelmashenko D, Koschmann J, Kel-Margoulis O, Krull M, Martínez-Cardús A, Moran S, Esteller M, Kolpakov F, Filipenko M, Wingender E. Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer. BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):119. doi: 10.1186/s12859-019-2687-7.
8. Aarestrup FM, Albeyatti A, Armitage WJ, Auffray C, Augello L, Balling R, Benhabiles N, Bertolini G, Bjaalie JG, 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 AE, Gut I, Gyllenberg A, Hemmrich-Stanisak G, Hjorth L, Ioannidis Y, Jarmalaite S, Kel A, Kherif F, Korbel JO, Larue C, Laszlo M, Maas A, Magalhaes L, Manneh-Vangramberen I, Morley-Fletcher E, Ohmann C, Oksvold P, Oxtoby NP, 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. Towards a European health research and innovation cloud (HRIC). Genome Med. 2020 Feb 19;12(1):18. doi: 10.1186/s13073-020-0713-z, PMID: 32075696 
9. Orekhov AN, Sukhorukov VN, Nikiforov NG, Kubekina MV, Sobenin IA, Foxx KK, Pintus S, Stegmaier P, Stelmashenko D, Kel A, Poznyak AV, Wu WK, Kasianov AS, Makeev VY, Manabe I, Oishi Y. Signaling Pathways Potentially Responsible for Foam Cell Formation: Cholesterol Accumulation or Inflammatory Response-What is First? Int J Mol Sci. 2020 Apr 14;21(8):2716. doi: 10.3390/ijms21082716. PMID: 32295185
10. Kolmykov S, Yevshin I, Kulyashov M, Sharipov R, Kondrakhin Y, Makeev VJ, Kulakovskiy IV, Kel A, Kolpakov F. GTRD: an integrated view of transcription regulation. Nucleic Acids Res. 2020 Nov 24:gkaa1057. doi: 10.1093/nar/gkaa1057. Epub ahead of print. PMID: 33231677
11. Lloyd K, Papoutsopoulou S, Smith E, Stegmaier P, Bergey F, Morris L, Kittner M, England H, Spiller D, White MHR, Duckworth CA, Campbell BJ, Poroikov V, Martins Dos Santos VAP, Kel A, Muller W, Pritchard DM, Probert C, Burkitt MD; SysmedIBD consortium. Using systems medicine to identify a therapeutic agent with potential for repurposing in inflammatory bowel disease. Dis Model Mech. 2020 Sep 21;13(11):dmm044040. doi: 10.1242/dmm.044040. Epub ahead of print. PMID: 32958515; PMCID: PMC7710021
12. 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  
13. Kolpakov F, Akberdin I, Kashapov T, Kiselev L, Kolmykov S, Kondrakhin Y, Kutumova E, Mandrik N, Pintus S, Ryabova A, Sharipov R, Yevshin I, Kel A.  BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. Nucleic Acids Res. 2019 Jul 2;47(W1):W225-W233. doi: 10.1093/nar/gkz440.
14. 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. 
15. 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. 
16. 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. 
17. 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.
18. 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. 
19. 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. 
20. 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.

Institution description

GeneXplain GmbH (GEX) was founded in 2010 by Edgar Wingender, the creator of the TRANSFAC® database, & Alexander Kel, a renowned expert in bioinformatic algorithms, with an international team of experts in software development & chemoinformatics. The company has developed a comprehensive platform for statistical, bioinformatic & systems biological tools. The geneXplain platform integrates statistical, bioinformatics, & systems biological modules with access to the manually curated knowledge base on transcription factors & their binding sites (TRANSFAC® – gold standard in the field) & the most detailed database on signal transduction (TRANSPATH™), both of which are maintained & distributed exclusively by GEX. The goal of the geneXplain platform is to integrate software tools & databases to assist translational research in life sciences, in the context of systems biology modelling, drug development, personalized medicine & pharmacogenomics. Using the geneXplain platform a global workflow Genome Enhancer https://genexplain.com/genome-enhancer/ was created, which is a fully automatized pipeline for patient omics data analysis that identifies prospective drug targets and corresponding treatments by reconstructing the molecular mechanism of the studied pathology and finding master-regulators of the network.

The platform & concept have proven value in several studies of such disorders as diabetes, autoimmune diseases, Parkinson disease, obesity and metabolic syndrome, cancer, including a big study of multi-omics data of colon cancer. GeneXplain is participating in many national and international EU funded project:  COPreDict, OxidoResist, E-REDALERT, FindingMS, COLOSSUS. And previously we were project partners (or coordinators) in such projects as  GlioTrain, PD-MitoQUANT, ExITox-II, OxidoCurin, miRCol, MyPathSem, miRNA-DisEASY, Optogenerapy, SysmedIBD, MIMOmics, Mediomics, ExITox, SYSCOL, EPIMETAB, RESOLVE, GERONTOSHIELD, TEMPUS.

The geneXplain approach can help reveal causal biomarkers that can be used for classifying diseases, & thus provide a powerful tool for developing system-based patient stratification solutions. The business activity of GENEXPLAIN is mainly in offering access to the geneXplain platform as “software as a service (SaaS)” to academic research organisations, core facilities, biotech & pharmaceutical companies. GENEXPLAIN also offers data analysis & interpretation services & complex research project consulting that are performed by a dedicated multidisciplinary team. It is geneXplain’s mission to provide the computational methodology required to achieve the goal of “system-based patient stratification”.

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www.genexplain.com