Publications

20 Major Scientific Publications of Oncobox Team.

  1. Personalized prescription of imatinib in recurrent granulosa cell tumor of the ovary: case report. Poddubskaya EV, Baranova MP, Allina DO, Sekacheva MI, Makovskaia LA, Kamashev DE, Suntsova MV, Barbara VS, Kochergina-Nikitskaya IN, Aleshin AA. Cold Spring Harb Mol Case Stud. 2019 Apr 1;5(2). pii: a003434. doi: 10.1101/mcs.a003434 Details

  1. Personalized prescription of tyrosine kinase inhibitors in unresectable metastatic cholangiocarcinoma. Poddubskaya EV, Baranova MP, Allina DO, Smirnov PY, Albert EA, Kirilchev AP, Aleshin AA, Sekacheva MI, Suntsova MV. Exp Hematol Oncol. 2018 Sep 6;7:21. doi: 10.1186/s40164-018-0113-x Details

  1. Molecular pathway activation – new type of biomarkers for tumor morphology and personalized selection of target drugs. A.Buzdin, M.Sorokin, A.Garazha, E.Sekacheva, E.Kim, N.Zhukov, Y.Wang, X.Li, S.Kar, C.Hartmann, A.Samii, A.Giese, N.Borisov. Seminars in Cancer Biology. 2018; Jun 20. pii: S1044-579X(18)30043-9. doi: 10.1016/j.semcancer.2018.06.003 Details

  1. Shambhala: a platform-agnostic data harmonizer for gene expression data. N.Borisov, I.Shabalina, V.Tkachev, M.Sorokin, A.Aliper, A.Anisenko, A.Pulin, I.I. Eremin, A.Garazha, A.Buzdin. BMC Bioinformatics. 2019 Feb 6;20(1):66. doi: 10.1186/s12859-019-2641-8 Details

  1. FLOating-Window Projective Separator (FloWPS): a data trimming tool for support vector machines (SVM) to improve robustness of the classifier V.Tkachev, M.Sorokin, A.Mescheryakov, A.Simonov, A.Garazha, A.Buzdin, I.Muchnik, N.Borisov. Frontiers in Genetics. 2019 Jan 15;9:717. doi: 10.3389/fgene.2018.00717 Details

  1. A method of gene expression data transfer from cell lines to cancer patients for machine-learning prediction of drug efficiency. Borisov N, Tkachev V, Suntsova M, Kovalchuk O, Zhavoronkov A, Muchnik I, Buzdin A. Cell Cycle. 2018 Jan 17:1-6. doi: 10.1080/15384101.2017.1417706 Details

  1. Pathway based analysis of mutation data is efficient for scoring target cancer drugs. M.A. Zolotovskaia, M. Sorokin, A.A. Emelianova, N.Borisov, D.V.Kuzmin, A. Buzdin. Frontiers in Pharmacology. 2019 Jan 23;10:1. doi: 10.3389/fphar.2019.00001 Details

  1. Atlas of RNA sequencing profiles for normal human tissues. M. Suntsova, N. Gaifullin, D. Allina, A. Reshetun, X. Li, L. Mendeleeva, V. Surin, A. Sergeeva, P. Spirin, V. Prasolov, A.A. Morgan, A.Garazha, M.Sorokin, A.Buzdin. Scientific Data. 2019; in press

  1. A method for predicting target drug efficiency in cancer based on the analysis of signaling pathway activation. Artem Artemov, Alexander Aliper, Michael Korzinkin, Ksenia Lezhnina, Leslie Jellen, Nicolay Zhukov, Sergey Roumiantsev, Nurshat Gaifullin, Alex Zhavoronkov, Nicolas Borisov, Anton Buzdin. Oncotarget. 2015 Details

  1. Oncobox bioinformatical platform for selecting potentially effective combinations of target drugs using high-throughput gene expression data. M.Sorokin, R.Kholodenko, M.Suntsova, G.Malakhova, A.Garazha, R.Vasilov, E.Poddubskaya, I.S. Stilidi, P.Arhirii and A.Buzdin. Cancers. 2018; 2018 Sep 29;10(10), pii: E365. doi: 10.3390/cancers10100365 Details

  1. Synergistic suppression of t(8;21)-positive leukemia cell growth by combining oridonin and MAPK1/ERK2 inhibitors. PSpirin P, Lebedev T, Orlova N, Morozov A, Poymenova N, Dmitriev SE, Buzdin A, Stocking C, Olga K, Vladimir P. Oncotarget. 2017 Jun 16. doi: 10.18632/oncotarget.18503. Details

  1. VEGF blockade enhances the antitumor effect of BRAFV600E inhibition. Corà D, Orso F, Consonni FM, Middonti E, Di Nicolantonio F, Buzdin A, Sica A, Medico E, Sangiolo D, Taverna D, Bussolino F. EMBO Molecular Medicine. 2016 Dec 14. pii: e201505774. Details

  1. Combinatorial high-throughput experimental and bioinformatic approach identifies molecular pathways linked with the sensitivity to anticancer target drugs. Larisa Venkova, Alexander Aliper, Maria Suntsova, Roman Kholodenko, Denis Shepelin, Nicolas Borisov, Galina Malakhova, Raif Vasilov, Sergey Roumiantsev, Alex Zhavoronkov, Anton Buzdin. Oncotarget. 2015 Details

  1. Pathway instability is an effective new mutation-based type of cancer biomarkers. Zolotovskaia, M.Sorokin, S.Roumiantsev, N.Borisov, A.Buzdin. Frontiers in Oncology. 2019 Jan 4;8:658. doi: 10.3389/fonc.2018.00658 Details

  1. In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development. Ozerov IV, Lezhnina KV, Izumchenko E, Artemov AV, Medintsev S, Vanhaelen Q, Aliper A, Vijg J, Osipov AN, Labat I, West MD, Buzdin A, Cantor CR, Nikolsky Y, Borisov N, Irincheeva I, Khokhlovich E, Sidransky D, Camargo ML, Zhavoronkov A. Nature Communications. 2016 Nov 16;7:13427. doi: 10.1038/ncomms13427 Details

  1. Pathway Activation Strength (PAS) is a Novel Independent Prognostic Biomarker for Cetuximab Sensitivity in Colorectal Cancer Patients. Qingsong Zhu, Evgeny Izumchenko, Alexander Aliper, Evgeny Makarev, Keren Paz, Anton Buzdin, Alex Zhavoronkov, and David Sidransky. Human Genome Variation. 2015. Details

  1. Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways. K. Lezhnina, O. Kovalchuk, A.A. Zhavoronkov, M.B. Korzinkin, A.A. Zabolotneva, P.V. Shegay, D.G. Sokov, N.M. Gaifullin, I.G. Rusakov, A.M. Aliper, S.A., Roumiantsev, B.Y. Alekseev, N.M. Borisov, and A.A. Buzdin. Oncotarget, 2014, Oct 15;5(19):9022-32 Details

  1. Signaling pathway activation profiles make better markers of cancer than expression of individual genes. N.M. Borisov, N.V. Terekhanova, A.M. Aliper, L.S. Venkova, P.Yu. Smirnov, S.Roumiantsev, M.B. Korzinkin, A.A. Zhavoronkov, A.A. Buzdin. Oncotarget, 2014 Oct 30;5(20):10198-205 Details

  1. OncoFinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data. Buzdin AA, Zhavoronkov AA, Korzinkin MB, Venkova LS, Zenin AA, Smirnov PY, Borisov NM. Frontiers in Genetics. 2014 Mar 25;5:55. doi: 10.3389/fgene.2014.00055. Details

  1. Acquired resistance to tyrosine kinase inhibitors may be linked with the decreased sensitivity to X-ray irradiation. Sorokin M, Kholodenko R, Grekhova A, Suntsova M, Pustovalova M, Vorobyeva N, Kholodenko I, Malakhova G, Garazha A, Nedoluzhko A, Vasilov R, Poddubskaya E, Kovalchuk O, Adamyan L, Prassolov V, Allina D, Kuzmin D, Ignatev K, Osipov A, Buzdin A. Oncotarget. 2017 Dec 27;9(4):5111-5124. doi: 10.18632/oncotarget.23700 Details

  1. Silencing AML1-ETO gene expression leads to simultaneous activation of both pro-apoptotic and proliferation signaling. Spirin PV, Lebedev TD, Orlova NN, Gornostaeva AS, Prokofjeva MM, Nikitenko NA, Dmitriev SE,Buzdin AA, Borisov NM, Aliper AM, Garazha AV, Rubtsov PM, Stocking C, Prassolov VS. Leukemia (Nature Publishing Group). 2014 Apr 14. doi: 10.1038/leu.2014.130. Details

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