Drake, C., Zobl W., Wehr M., Koschmann J., De Luca D., Kühne B. A., Vrieling H. , Boei J. , Hansen T. , Escher S. E. (2023) Substantiate a read-across hypothesis by using transcriptome data—A case study on volatile diketones. Front. Toxicol. 5Link

Rajavel A., Klees S., Hui Y., Schmitt A.O., Gültas M. (2022) Deciphering the Molecular Mechanism Underlying African Animal Trypanosomiasis by Means of the 1000 Bull Genomes Project Genomic Dataset. Biology (Basel). 11(5), 742. Link

Menck K., Wlochowitz D., Wachter A., Conradi L.C., Wolff A., Scheel A.H., Korf U., Wiemann S., Schildhaus H.U., Bohnenberger H., Wingender E., Pukrop T., Homayounfar K., Beißbarth T., Bleckmann A. (2022) High-Throughput Profiling of Colorectal Cancer Liver Metastases Reveals Intra- and Inter-Patient Heterogeneity in the EGFR and WNT Pathways Associated with Clinical Outcome. Cancers 14(9), 2084. Link

Myer P.A., Kim H., Blümel A.M., Finnegan E., Kel A., Thompson T.V., Greally J.M., Prehn J.H., 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(3), 328–341. Link

Kawashima Y., Nagai H., Konno R., Ishikawa M., Nakajima D., Sato H., Nakamura R., Furuyashiki T., Ohara O. (2022) Single-Shot 10K Proteome Approach: Over 10,000 Protein Identifications by Data-Independent Acquisition-Based Single-Shot Proteomics with Ion Mobility Spectrometry. J Proteome Res. 21(6), 1418–1427. Link

Klees S., Schlüter J.S., Schellhorn J., Bertram H., Kurzweg A.C., Ramzan F., Schmitt A.O., Gültas M. (2022) Comparative Investigation of Gene Regulatory Processes Underlying Avian Influenza Viruses in Chicken and Duck. Biology (Basel). 11(2), 219. Link

Benjamin, S.J., Hawley, K.L., Vera-Licona, P., La Vake, C.J., Cervantes, J.L., Ruan, Y., Radolf, J.D., Salazar, J.C. (2021) Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation. BMC Immunol. 22, 32 Link

Meier, T., Timm, M., Montani, M., Wilkens, L. (2021) Gene networks and transcriptional regulators associated with liver cancer development and progression. BMC Med. Genomics 14, 41. Link

Ural, B.B., Yeung, S.T., Damani-Yokota, P., Devlin, J.C., de Vries, M., Vera-Licona, P., Samji, T., Sawai, C.M., Jang, G., Perez, O.A., Pham, Q., Maher, L., Loke, P., Dittmann, M., Reizis, B., Khanna, K.M. (2020) Identification of a nerve-associated, lung-resident interstitial macrophage subset with distinct localization and immunoregulatory properties. Sci. Immunol. 5, eaax8756. Link

Mekonnen, Y.A., Gültas, M., Effa, K., Hanotte, O., Schmitt, A.O. (2019) Identification of Candidate Signature Genes and Key Regulators Associated With Trypanotolerance in the Sheko Breed. Front. Genet. 10, 1095. Link

Blazquez, R., Wlochowitz, D., Wolff, A., Seitz, S., Wachter, A., Perera-Bel, J., Bleckmann, A., Beißbarth, T., Salinas, G., Riemenschneider, M.J., Proescholdt, M., Evert, M., Utpatel, K., Siam, L., Schatlo, B., Balkenhol, M., Stadelmann, C., Schildhaus, H.U., Korf, U., Reinz, E., Wiemann, S., Vollmer, E., Schulz, M., Ritter, U., Hanisch, U.K., Pukrop, T. (2018) PI3K: A master regulator of brain metastasis-promoting macrophages/microglia. Glia 66, 2438-2455. Link

Orekhov, A.N., Oishi, Y., Nikiforov, N.G., Zhelankin, A.V., Dubrovsky, L., Sobenin, I.A., Kel, A., Stelmashenko, D., Makeev, V.J., Foxx, K., Jin, X., Kruth, H.S. Bukrinsky, M. (2018) Modified LDL Particles Activate Inflammatory Pathways in Monocyte-derived Macrophages: Transcriptome Analysis. Curr. Pharm. Des. 24, 3143-3151. Link

Kalozoumi, G., Kel-Margoulis, O., Vafiadaki, E., Greenberg, D., Bernard, H., Soreq, H., Depaulis, A., Sanoudou, D. (2018) Glial responses during epileptogenesis in Mus musculus point to potential therapeutic targets. PLoS One 13, e0201742. Link

Smetanina, M.A., Kel, A.E., Sevost’ianova, K.S., Maiborodin, I.V., Shevela, A.I., Zolotukhin, I.A., Stegmaier, P., 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. Link

Boyarskikh, U., Pintus, S., Mandrik, N., Stelmashenko, D., Kiselev, I., Evshin, I., Sharipov, R., Stegmaier, P., Kolpakov, F., Filipenko, M., 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. Link

Triska, M., Solovyev, V., Baranova, A., Kel, A., Tatarinova, T.V. (2017) Nucleotide patterns aiding in prediction of eukaryotic promoters. PLoS One 12, e0187243. Link

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. Link

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. 10, 1211-1223. Link

Pietrzyńska, M., Zembrzuska, J., Tomczak, R., Mikołajczyk, J., Rusińska-Roszak, D., Voelkel, A., Buchwald, T., Jampílek, J., Lukáč, M., Devínsky, F. (2016) Experimental and in silico investigations of organic phosphates and phosphonates sorption on polymer-ceramic monolithic materials and hydroxyapatite. Eur. J. Pharm. Sci. 93, 295-303. Link

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. Link

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. Link

Ciribilli, Y., Singh, P., Inga, A., Borlak, J. (2016) c-Myc targeted regulators of cell metabolism in a transgenic mouse model of papillary lung adenocarcinoma. Oncotarget 7, 65514-65539. Link

Wlochowitz, D., Haubrock, M., Arackal, J., Bleckmann, A., Wolff, A., Beißbarth, T., Wingender, E., Gültas, M. (2016) Computational Identification of Key Regulators in Two Different Colorectal Cancer Cell Lines. Front. Genet. 7, 42. Link

Lee, E.H., Oh, J.H., Selvaraj, S., Park, S.M., Choi, M.S., Spanel, R., Yoon, S. and Borlak, J. (2016) Immunogenomics reveal molecular circuits of diclofenac induced liver injury in mice. Oncotarget 7, 14983-15017. Link

Borlak, J., Singh, P. and Gazzana, G. (2015) Proteome mapping of epidermal growth factor induced hepatocellular carcinomas identifies novel cell metabolism targets and mitogen activated protein kinase signalling events. BMC Genomics 16, 124. Link

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. Link

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. Link

Schlereth, K., Heyl, C., Krampitz, A.M., Mernberger, M., Finkernagel, F., Scharfe, M., Jarek, M., Leich, E., Rosenwald, A., Stiewe, T. (2013) Characterization of the p53 Cistrome – DNA Binding Cooperativity Dissects p53’s Tumor Suppressor Functions. PLoS Genet. 9, e1003726. PubMed

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, 1992-2002. PubMed

Zawacka-Pankau, J., Grinkevich, V.V., Hunten, 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

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