Publications & Patents
Publications
TRANSFAC
6 PUBLICATIONS
1.
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.
2.
Kolpakov F., Akberdin I., Kiselev I., Kolmykov S., Kondrakhin Y., Kulyashov M., Kutumova E., Pintus S., Ryabova A., Sharipov R., Yevshin I., Zhatchenko S., Kel A. (2022).
BioUML — towards a universal research platform
Nucleic Acids Research, 50(W1), W124–W131.
3.
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?
International Journal of Molecular Sciences, 21(8), 2716.
4.
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., Wingender E. (2019).
Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer
BMC Bioinformatics, 20(Suppl 4), 119.
5.
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 Medical Genomics, 11(Suppl 1), 12.
6.
Kel A. E., Stegmaier P., Valeev T., Koschmann J., Poroikov V., Kel-Margoulis O. V., 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.
TRANSFAC applications
39 PUBLICATIONS
1.
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
International Journal of Molecular Sciences, 25(9), 4618.
2.
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.
3.
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, 40(1), 395.
4.
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.
5.
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
Computational and Structural Biotechnology Journal, 19, 2447–2459.
6.
Li X., Shi J., Li L. M. (2025).
The human intelligence evolved from proximal cis-regulatory saltations
Quantitative Biology, 13(2).
7.
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., et al. (2025).
Contribution of hypoxia-inducible factor 1alpha to pathogenesis of sarcomeric hypertrophic cardiomyopathy
Scientific Reports, 15(1), 2132.
8.
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.
9.
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.
10.
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.
11.
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.
12.
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.
13.
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.
14.
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 (MDPI), 15(1), 19.
15.
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.
16.
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.
17.
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.
18.
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, Advance online publication.
19.
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 (MDPI), 14(23), 3514.
20.
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.
21.
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.
22.
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
Briefings in Bioinformatics, 25(5), bbae368.
23.
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.
24.
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
Nature Communications, 15(1), 9245.
25.
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
Journal of Experimental & Clinical Cancer Research, 43, 295.
26.
Mahat D. B., Tippens N. D., Martin-Rufino J. D., Waterton S. K., Fu J., Blatt S. E., Sharp P. A. (2024).
Single-cell nascent RNA sequencing unveils coordinated global transcription
Nature, 631, 216–223.
27.
Park S.-J., Nakai K. (2024).
A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response
NAR Genomics & Bioinformatics, 6(2).
28.
Farrim M. I., Gomes A., Milenkovic D., Menezes R. (2024).
Gene expression analysis reveals diabetes-related gene signatures
Human Genomics, 18, 16.
29.
Eni-Aganga I., Lanaghan Z. M., Ismail F., Korolkova O., Goodwin J. S., Balasubramaniam M., Dash C., Pandhare J. (2024).
KLF6 activates Sp1-mediated prolidase transcription during TGF-β1 signaling
Journal of Biological Chemistry, 300(2), 105605.
30.
Hasegawa K., Tamaki M., Sakamaki Y., Wakino S. (2024).
Nmnat1 deficiency causes mitoribosome excess in diabetic nephropathy mediated by transcriptional repressor HIC1
International Journal of Molecular Sciences, 25(12), 6384.
31.
Abrar M., Ali S., Hussain I., Khatoon H., Batool F., Ghazanfar S., Corcoran D., Kawakami Y., Abbasi A. A. (2024).
Cis-regulatory control of mammalian Trps1 gene expression
Journal of Experimental Zoology B: Molecular and Developmental Evolution, 342(2), 85–100.
32.
Scaramuzzo R. T., 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.
33.
Skubic C., Trček H., Nassib P., Kreft T., Walakira A., Pohar K., Petek S., Režen T., Ihan A., Rozman D. (2024).
Knockouts of CYP51A1, DHCR24, or SC5D from cholesterol synthesis reveal pathways modulated by sterol intermediates
iScience, 27(9), 110651.
34.
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
Frontiers in Genetics, 15, 1302685.
35.
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
Biochimica et Biophysica Acta — Gene Regulatory Mechanisms, 1867(2), 195031.
36.
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.
37.
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.
38.
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 (Edinburgh), 131, 102139.
39.
Thompson 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
Ocular Surface, 22, 190–203.
geneXplain Platform applications
40 PUBLICATIONS
1.
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.
2.
Kisakol, B., Matveeva, A., Salvucci, M., Kel, A., McDonough, E., Ginty, F., Longley, D., Prehn, J. (2024).
Identification of unique rectal cancer-specific subtypes
Br J Cancer, 130, 1809–1818.
3.
Xinxin Liu., Zhihua Huang., Qiuzheng Chen., Kai Chen., Weikang Liu., Guangnian Liu., Xiangyu Chu., Dongqi Li., Yongsu Ma., Xiaodong Tian., Yinmo Yang. (2024).
Hypoxia-induced epigenetic regulation of miR-485-3p promotes stemness and chemoresistance in pancreatic ductal adenocarcinoma via SLC7A11-mediated ferroptosis
Cell Death Discovery, 10, 262.
4.
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, 5.
5.
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.
6.
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.
7.
Myer P.A., Kim H., Blümel A.M., Finngan 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.
8.
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.
9.
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.
10.
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.
11.
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
J Exp Clin Cancer Res, 40, 395.
12.
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.
13.
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, 42.
14.
Heinrich F., Ramzan F., Rajavel A., Schmitt A.O., Gültas M. (2021).
MIDESP: Mutual Information-Based Detection of Epistatic SNP Pairs for Qualitative and Quantitative Phenotypes
Biology (Basel), 10(9), 921.
15.
Tenesaca S., Vasquez M., Alvarez M., Otano I., Fernandez-Sendin M., Di Trani C.A., Ardaiz N., Gomar C., Bella A., Aranda F., Medina-Echeverz J., Melero I., Berraondo P. (2021).
Statins act as transient type I interferon inhibitors to enable the antitumor activity of modified vaccinia Ankara viral vectors
J Immunother Cancer, 9(7), e001587.
16.
Vanvanhossou S.F.U., Giambra I.J., Yin T., Brügemann K., Dossa L.H., König S. (2021).
First DNA Sequencing in Beninese Indigenous Cattle Breeds Captures New Milk Protein Variants
Genes (Basel), 12(11), 1702.
17.
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(11), dmm044040.
18.
Odagiu L., Boulet S., Maurice De Sousa D., Daudelin J.F., Nicolas S., Labrecque N. (2020).
Early programming of CD8+ T cell response by the orphan nuclear receptor NR4A3
Proc Natl Acad Sci U S A, 117(39), 24392–24402.
19.
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.
20.
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.
21.
Leiherer A., Muendlein A., Saely C.H., Fraunberger P., Drexel H. (2019).
Serotonin is elevated in risk-genotype carriers of TCF7L2 – rs7903146
Sci Rep, 9, 12863.
22.
Wang B., Ran Z., Liu M., Ou Y. (2019).
Prognostic Significance of Potential Immune Checkpoint Member HHLA2 in Human Tumors: A Comprehensive Analysis
Front Immunol, 10, 1573.
23.
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.
24.
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.
25.
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.
26.
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.
27.
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.
28.
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.
29.
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.
30.
Triska, M., Solovyev, V., Baranova, A., Kel, A., Tatarinova, T.V. (2017).
Nucleotide patterns aiding in prediction of eukaryotic promoters
PLoS One, 12, e0187243.
31.
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.
32.
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.
33.
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.
34.
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.
35.
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.
36.
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.
37.
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.
38.
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.
39.
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.
40.
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.
PASS
1 PUBLICATION
1.
Lagunin A., Stepanchikova A., Filimonov D., Poroikov V. (2000).
PASS: prediction of activity spectra for biologically active substances
Bioinformatics, 16(8), 747–748.
PharmaExpert
1 PUBLICATION
1.
Lagunin A. A., Goel R. K., Gawande D. Y., Pahwa P., Gloriozova T. A., Dmitriev A. V., Ivanov S. M., Rudik A. V., Konova V. I., Pogodin P. V., Druzhilovsky D. S., Poroikov V. V. (2014).
Chemo- and bioinformatics resources for in silico drug discovery from medicinal plants beyond their traditional use: a critical review
Natural Product Reports, 31(11), 1585–1611.
PASS & PharmaExpert applications
1 PUBLICATION
1.
Bocharova O. A., Ionov N. S., Kazeev I. V., Shevchenko V. E., Bocharov E. V., Karpova R. V., Sheychenko O. P., Aksyonov A. A., Chulkova S. V., Kucheryanu V. G., Revishchin A. V., Pavlova G. V., Kosorukov V. S., Filimonov D. A., Lagunin A. A., Matveev V. B., Pyatigorskaya N. V., Stilidi I. S., Poroikov V. V. (2023).
Computer-aided evaluation of polyvalent medications’ pharmacological potential. Multiphytoadaptogen as a case study
Molecular Informatics, 42(1), e2200176.
BRENDA
10 PUBLICATIONS
1.
Schomburg I., Jeske L., Ulbrich M., Placzek S., Chang A., Schomburg D. (2017).
The BRENDA enzyme information system — From a database to an expert system
Journal of Biotechnology, 261, 194–206.
2.
Placzek S., Schomburg I., Chang A., Jeske L., Ulbrich M., Tillack J., Schomburg D. (2017).
BRENDA in 2017: new perspectives and new tools in BRENDA
Nucleic Acids Research, 45, D380–D388.
3.
Chang A., Schomburg I., Placzek S., Jeske L., Ulbrich M., Xiao M., Sensen C. W., Schomburg D. (2015).
BRENDA in 2015: exciting developments in its 25th year of existence
Nucleic Acids Research, 43, D439–D446.
4.
Schomburg I., Chang A., Placzek S., Söhngen C., Rother M., Lang M., Munaretto C., Ulas S., Stelzer M., Grote A., Scheer M., Schomburg D. (2013).
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA
Nucleic Acids Research, 41, 764–772.
5.
Gremse M., Chang A., Schomburg I., Grote A., Scheer M., Ebeling C., Schomburg D. (2011).
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
Nucleic Acids Research, 39, D507–D513.
6.
Barthelmes J., Ebeling C., Chang A., Schomburg I., Schomburg D. (2007).
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007
Nucleic Acids Research, 35, D511–D514.
7.
Schomburg I., Chang A., Hofmann O., Ebeling C., Ehrentreich F., Schomburg D. (2002).
BRENDA: a resource for enzyme data and metabolic information
Trends in Biochemical Sciences, 27, 54–56.
8.
Schomburg I., Chang A., Schomburg D. (2002).
BRENDA, enzyme data and metabolic information
Nucleic Acids Research, 30, 47–49.
10.
Schomburg I., Hofmann O., Baensch C., Chang A., Schomburg D. (2000).
Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine
Gene Function & Disease, 3–4, 109–118.
BRENDA applications
8 PUBLICATIONS
1.
Singh P. K., et al. (2020).
Exploring RdRp–remdesivir interactions to screen RdRp inhibitors for the management of novel coronavirus 2019-nCoV
SAR and QSAR in Environmental Research, 31, 857–867.
2.
Khurshid G., et al. (2020).
A cyanobacterial photorespiratory bypass model to enhance photosynthesis by rerouting photorespiratory pathway in C3 plants
Scientific Reports, 10, 20879.
3.
Bartman C., et al. (2017).
Factors influencing the development of visceral metastasis of breast cancer: a retrospective multi-center study
The Breast, 31, 66–75.
5.
Wei Y., et al. (2015).
Insight into dominant cellulolytic bacteria from two biogas digesters and their glycoside hydrolase genes
PLoS ONE, 10, e0129921.
6.
Tagore S., et al. (2014).
Analyzing methods for path mining with applications in metabolomics
Gene, 534, 125–138.
7.
Mayer G., et al. (2014).
Controlled vocabularies and ontologies in proteomics: overview, principles and practice
Biochimica et Biophysica Acta, 1844, 98–107.
8.
Ranjan S., et al. (2013).
Computational approach for enzymes present in Capsicum annuum: a review
International Journal of Drug Development & Research, 5, 88–97.
Patents
Translating computational discovery into protected, clinically-relevant intellectual property.
LCTA — a novel class of anticancer compounds targeting thioredoxin reductase 1
Filed as: Quinoxaline thioredoxin reductase inhibitors
Identified through geneXplain’s upstream analysis methodology, the LCTA family exploits a rarely-used mechanism of action: selective inhibition of thioredoxin reductase 1 (TrxR1), triggering fatal oxidative stress in tumour cells while sparing normal tissue.
INVENTORS
Kel A., Selivanova G., Shchekotikhin A., Buravchenko G., Koutcherov V., Poroikov V., Zoubarev R., Arnér E. (2021).
DETAILS
geneXplain GmbH · Filed Dec 2021 · Granted Aug 2024 · European Patent Office