Selection of articles reporting about TRANSPATH applications:

Novikova S., Tolstova T., Kurbatov L., Farafonova T., Tikhonova O., Soloveva N., Rusanov A., Zgoda V. (2024) Systems Biology for Drug Target Discovery in Acute Myeloid Leukemia. Int. J. Mol. Sci.  25(9), 4618 (2024) Link

Kisakol, B., Matveeva, A., Salvucci, M., Kel, A., McDonough, E., Ginty, F., Longley, D. B., & Prehn, J. H. M. (2024). Identification of unique rectal cancer-specific subtypes. British journal of cancer, 130(11), 1809–1818. Link

Ivanov, S. M., Tarasova, O. A., & Poroikov, V. V. (2023). Transcriptome-based analysis of human peripheral blood reveals regulators of immune response in different viral infections. Frontiers in immunology, 14, 1199482. Link 

Bertram, H., Wilhelmi, S., Rajavel, A., Boelhauve, M., Wittmann, M., Ramzan, F., Schmitt, A. O., & Gültas, M. (2023). Comparative Investigation of Coincident Single Nucleotide Polymorphisms Underlying Avian Influenza Viruses in Chickens and Ducks. Biology, 12(7), 969. Link

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

Menck, K., Heinrichs, S., Wlochowitz, D., Sitte, M., Noeding, H., Janshoff, A., Treiber, H., Ruhwedel, T., Schatlo, B., von der Brelie, C., Wiemann, S., Pukrop, T., Beißbarth, T., Binder, C., & Bleckmann, A. (2021). WNT11/ROR2 signaling is associated with tumor invasion and poor survival in breast cancer. Journal of experimental & clinical cancer research : CR, 40(1), 395. 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

Andreev-Andrievskiy, A. A., Zinovkin, R. A., Mashkin, M. A., Frolova, O. Y., Kazaishvili, Y. G., Scherbakova, V. S., Rudoy, B. A., & Nesterenko, V. G. (2021). Gene Expression Pattern of Peyer’s Patch Lymphocytes Exposed to Kagocel Suggests Pattern-Recognition Receptors Mediate Its Action. Frontiers in pharmacology, 12, 679511. 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