Selection of articles reporting about TRANSFAC 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 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 

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 

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

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

Li, X., Shi, J., & Li, L. M. (2025) The human intelligence evolved from proximal cis-regulatory saltations. Quantitative Biology 13(2) Link

Raj Murthi, S., Petry, A., Shashikadze, B., Stöckl, J. B., Schmid, M., Santamaria, G., Klingel, K., Kračun, D., Chen, X., Bauer, S., Schmitt, J. P., Flenkenthaler, F., Gorham, J., Toepfer, C. N., Potěšil, D., Hruška, P., Zdráhal, Z., Mayer, Z., Klop, M., Lehmann, L., … Wolf, C. M. (2025). Contribution of hypoxia-inducible factor 1alpha to pathogenesis of sarcomeric hypertrophic cardiomyopathy. Scientific reports, 15(1), 2132. Link

Cihan, M., Schmauck, G., Sprang, M., & Andrade-Navarro, M. A. (2025). Unveiling cell-type-specific microRNA networks through alternative polyadenylation in glioblastoma. BMC biology, 23(1), 15. Link

Jian, Y., Xu, H., Wang, Z., Zhang, Z., & Zhang, X. (2025). Histone modification-based functional characterization and genetic association of polymorphisms in LRRC6 and MTMR10 within CRC susceptibility regions 8q24 and 15q13.3. Gene, 943, 149286. Link

Ferreira Dos Santos, T. C., Silva, E. N., Frezarim, G. B., Salatta, B. M., Baldi, F., Simielli Fonseca, L. F., De Albuquerque, L. G., Magalhães Muniz, M. M., & Dos Santos Silva, D. B. (2025). Cis-eQTL analysis reveals genes involved in biological processes of the immune system in Nelore cattle. Gene, 937, 149138. Link

Hosseinpouri, A., Sadegh, K., Zarei-Behjani, Z., Dehghan, Z., & Karbalaei, R. (2025). Identification of critical genes and drug repurposing targets in entorhinal cortex of Alzheimer’s disease. Neurogenetics, 26(1), 27. Link

Woelk, J., Hornsteiner, F., Aschauer-Wallner, S., Stoitzner, P., Baier, G., & Hermann-Kleiter, N. (2025). Regulation of NK cell development, maturation, and antitumor responses by the nuclear receptor NR2F6. Cell death & disease, 16(1), 77.  Link

Batool, F., Shireen, H., Malik, M. F., Abrar, M., & Abbasi, A. A. (2025). The combinatorial binding syntax of transcription factors in forebrain-specific enhancers. Biology open, 14(2), BIO061751. Link

Liang, Y., Yao, X., Han, J., Wang, J., Zhang, X., Zhao, D., Jiang, C., Geng, L., Lv, S., Liu, Z., & Mu, Y. (2024). Establishment of a CRISPR-Based Lentiviral Activation Library for Transcription Factor Screening in Porcine Cells. Animals : an open access journal from MDPI, 15(1), 19. Link

Dong, J. P., Xu, Y. C., Jiang, Y. N., Jiang, R. Z., Ma, L., Li, X. Z., Zeng, W. H., & Lin, Y. (2024). Identification of transcriptional signature change and critical transcription factors involved during the differentiation of mouse trophoblast stem cell into maternal blood vessel associated trophoblast giant cell. Cellular signalling, 123, 111359. Link

Mandić, K., Milutin Gašperov, N., Božinović, K., Dediol, E., Krasić, J., Sinčić, N., Grce, M., Sabol, I., & Barešić, A. (2024). Integrative analysis in head and neck cancer reveals distinct role of miRNome and methylome as tumour epigenetic drivers. Scientific reports, 14(1), 9062. Link

Syed, R., Rengasamy, P., Rajagopalan, S., Deiuliis, J. A., & Maiseyeu, A. (2024). MicroRNA 223 Enhances ABCA1 Protein Stability and Supports Efflux in Cholesterol-Burdened Macrophages. Cell  Link

Nadeem, H., Jamal, S. B., Basheer, A., Bakhtiar, S. M., Faheem, M., Aziz, T., Nabi, G., Al-Harbi, M., & Raza, R. Z. (2024). Genetic Insights into Facial Variation and Craniofacial Development: Unraveling the Interplay of Genes, Expression Patterns, and Evolutionary Significance. Molecular biotechnology, 10.1007/s12033-024-01349-6. Advance online publication. Link

Zhou, Z., Lv, Y., Li, L., Yuan, X., Zhou, X., & Li, J. (2024). FoxO1 Mediated by H3K27me3 Inhibits Porcine Follicular Development by Regulating the Transcription of CYP1A1. Animals : an open access journal from MDPI, 14(23), 3514. Link

Zhou, L., Yang, Y., Qiao, Q., Mi, Y., Gan, Y., Zheng, Y., Wang, Y., Liu, M., & Zhou, Y. (2024). AKT1-Mediated NOTCH1 phosphorylation promotes gastric cancer progression via targeted regulation of IRS-1 transcription. Journal of cancer research and clinical oncology, 151(1), 15. Link

Zhou L., Yang Y., Ye Y., Qiao Q., Mi Y., Liu H., Zheng Y., Wang Y., Liu M., Zhou Y. (2024). Notch1 signaling pathway promotes growth and metastasis of gastric cancer via modulating CDH5. Aging (Albany NY). 16(16):11893–11903. Link

Li F., Wang J., Li M., Zhang X., Tang Y., Song X., Zhang Y., Pei L., Liu J., Zhang C., Li X., Xu Y., Zhang Y. (2024). Identifying cell type-specific transcription factor-mediated activity immune modules reveal implications for immunotherapy and molecular classification of pan-cancer. Brief Bioinform. 25(5):bbae368. Link

Lleshi E., Milne-Clark T., Yu H.L., Martin H.W., Hanson R., Lach R., Rossi S.H., Riediger A.L., Görtz M., Sültmann H., Flewitt A., Lynch A.G., Gnanapragasam V.J., Massie C.E., Dev H.S. (2024). Prostate cancer detection through unbiased capture of methylated cell-free DNA. iScience. 27(7):110330. Link

Ceroni F., Cicekdal M.B., Holt R., Sorokina E., Chassaing N., Clokie S., Naert T., Talbot L.V., Muheisen S., Bax D.A., Kesim Y., Kivuva E.C., Vincent-Delorme C., Lienkamp S.S., Plaisancié J., De Baere E., Calvas P., Vleminckx K., Semina E.V., Ragge N.K. (2024). Deletion upstream of MAB21L2 highlights the importance of evolutionarily conserved non-coding sequences for eye development. Nat Commun. 15(1):9245. Link

De Freitas J.T., Thakur V., LaPorte K.M., Thakur V.S., Flores B., Caicedo V., Ajaegbu C.G.E., Ingrasci G., Lipman Z.M., Zhang K., Qiu H., Malek T.R., Bedogni B. (2024). Notch1 blockade by a novel, selective anti-Notch1 neutralizing antibody improves immunotherapy efficacy in melanoma by promoting an inflamed TME. J Exp Clin Cancer Res. 43:295. Link

Dig B. Mahat., Nathaniel D. Tippens., Jorge D. Martin-Rufino., Sean K. Waterton., Jiayu Fu., Sarah E. Blatt & Phillip A. Sharp. (2024) Single-cell nascent RNA sequencing unveils coordinated global transcription. Nature. 631, 216–223. Link

Sung-Joon Park., Kenta Nakai. (2024) A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response. NAR Genomics & Bioiformatics. Volume 6, issue 2. Link

Farrim M.I., Gomes A., Milenkovic D., Menezes R. (2024) Gene expression analysis reveals diabetes-related gene signatures. Hum Genomics 18, 16. Link

Eni-Aganga I., Lanaghan ZM., Ismail F., Korolkova O., Goodwin JS., Balasubramaniam M., Dash C., Pandhare J. (2024). KLF6 activates Sp1-mediated prolidase transcription during TGF-β1 signaling. J Biol Chem. 2024 300(2):105605. Link

Hasegawa K., Tamaki M., Sakamaki Y., Wakino S. (2024) Nmnat1  Deficiency Causes Mitoribosome Excess in Diabetic Nephropathy Mediated by Transcriptional Repressor HIC1. Int J Mol Sci. 25(12):6384. Link

Abrar M., Ali S., Hussain I., Khatoon H., Batool F., Ghazanfar S., Corcoran D., Kawakami Y., Abbasi AA. (2024). Cis-regulatory control of mammalian Trps1 gene expression. J Exp Zool B Mol Dev Evol. 342(2):85-100. Link

Scaramuzzo RT., Crucitta S., Del Re M., Cammalleri M., Bagnoli P., Dal Monte M., Pini A., Filippi L.. (2024) β3-adREnoceptor Analysis in CORD Blood of Neonates (β3 RECORD): Study Protocol of a Pilot Clinical Investigation. Life (Basel). 14(6):776. Link

Cene Skubic., Hana Trček., Petra Nassib., Tinkara Kreft., Andrew Walakira., Katka Pohar., Sara Petek., zadeja Režen., Alojz Ihan., Damjana Rozman. (2024) Knockouts of CYP51A1, DHCR24, or SC5D from cholesterol synthesis reveal pathways modulated by sterol intermediates. iScience, Volume 27, Issue 9, 110651. Link

Jamil M.A., Al-Rifai R., Nuesgen N., Altmüller J., Oldenburg J., El-Maarri O. (2024) The role of microRNAs in defining LSECs cellular identity and in regulating F8 gene expression. Front Genet. 15: 1302685 Link

Coatti G.C., Vaghela N., Gillurkar P., Leir S., Harris A. (2024) A promoter-dependent upstream activator augments CFTR expression in diverse epithelial cell types. Biochim Biophys Acta Gene Regul Mech. 1867(2):195031 Link

Satsu H., Gondo Y., Shimanaka H., Imae M., Murakami S., Watari K., Wakabayashi S., Park S.J., Nakai K., Shimizu M. (2022) Signaling Pathway of Taurine-Induced Upregulation of TXNIP. Metabolites. 12(7),636. Link

Deepti P., Pasha A., Kumbhakar D.V., Doneti R., Heena S.K., Bhanoth S., Poleboyina P.K., Yadala R., Anapurna S.D., Pawar S.C. (2022) Overexpression of Secreted Phosphoprotein 1 (SPP1) predicts poor survival in HPV positive cervical cancer. Gene. 824,146381. Link

Song Q., Bian Q., Liang T., Zhang Y., Zhang K. (2021) Identification of immune-related genes and susceptible population of pulmonary tuberculosis by constructing TF-miRNA-mRNA regulatory network. Tuberculosis (Edinb). 131,102139. LinkThompson B., Chen Y., Davidson E.A., Garcia-Milian R., Golla J.P., Apostolopoulos N., Orlicky D.J., Schey K., Thompson D.C., Vasiliou V. (2021) Impaired GSH biosynthesis disrupts eye development, lens morphogenesis and PAX6 function. Ocul Surf. 22,190-203. Link