Recent applications

Selection of articles reporting about TRANSPATH applications:
  • 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
  • Kechin A.A., Ivanov A.A., Kel A.E., Kalmykov A.S., Oskorbin I.P., Boyarskikh U.A., Kharpov E.A., Bakharev S.Y., Oskina N.A., Samuilenkova O.V., Vikhlyanov I.V., Kushlinskii N.E., Filipenko M.L. (2022) Prediction of EVT6-NTRK3-Dependent Papillary Thyroid Cancer Using Minor Expression Profile. Bull Exp Biol Med. 173(2),252-256. 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
  • 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),42. Link
  • Kalya M., Kel A., Wlochowitz D., Wingender E., Beißbarth T. (2021) IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme. Front Genet. 12, 670240. 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
  • Ivanov, S., Filimonov, D., & Tarasova, O. (2021) A computational analysis of transcriptional profiles from CD8(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression. Comput Struct Biotechnol J. 19, 2447–2459. 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
  • 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. Using systems medicine to identify a therapeutic agent with potential for repurposing in inflammatory bowel disease. Dis Model Mech. 13(11), dmm044040. Link
  • Ramzan, F., Klees, S., Schmitt, A. O., Cavero, D., & Gültas, M. (2020) Identification of Age-Specific and Common Key Regulatory Mechanisms Governing Eggshell Strength in Chicken Using Random Forests. Genes (Basel). 11(4), 464. Link
  • Ayyildiz D., Antoniali G., D’Ambrosio C., Mangiapane G., Dalla E., Scaloni A., Tell G., Piazza S. (2020) Architecture of The Human Ape1 Interactome Defines Novel Cancers Signatures. Sci Rep. 10, 28. 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
  • Nobis, C. C., Dubeau Laramée, G., Kervezee, L., Maurice De Sousa, D., Labrecque, N., & Cermakian, N. (2019) The circadian clock of CD8 T cells modulates their early response to vaccination and the rhythmicity of related signaling pathways. Proc Natl Acad Sci U S A. 116(40), 20077–20086. 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(26),3143-3151. 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
  • 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
  • Malusa, F., Taranta, M., Zaki, N., Cinti, C., & Capobianco, E. (2015) Time-course gene profiling and networks in demethylated retinoblastoma cell line. Oncotarget. 6(27), 23688–23707. Link
  • Kutumova E.O., Kiselev I.N., Sharipov R.N., Lavrik I.N., Kolpakov F.A. (2012) A modular model of the apoptosis machinery. Adv Exp Med Biol. 736, 235-45. Link
  • Schuler, M., Keller, A., Backes, C., Philippar, K., Lenhof, H. P., & Bauer, P. (2011) Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana. BMC Plant Biol. 11, 87. Link
  • Ante M., Wingender E., Fuchs M. (2011) Integration of gene expression data with prior knowledge for network analysis and validation. BMC Res Notes. 4,520. Link
  • Chiu SC, Tsao SW, Hwang PI, Vanisree S, Chen YA, Yang NS. (2010) Differential functional genomic effects of anti-inflammatory phytocompounds on immune signaling. BMC Genomics. 11, 513. Link