Prospective trial of the Oncobox platform RNA sequencing bioinformatic analysis for personalized prescription of targeted drugs

Authors: Sorokin, Maksim ^{a, b, c, 1}, Garazha, Andrew ^{a, b}, Suntsova, Maria ^{c, 1}, Tkachev, Victor ^a, Poddubskaya, Elena ^{d, e}, Gaifullin, Nurshat ^f, Sushinskaya, Tatiana ^g, Lantsov, Dmitriy ^h, Borisov, Vasiliy ⁱ, Naskhletashvili, David ^j, Ilyin, Kirill ^k, Seryakov, Alexander ^k, Glusker, Alex ^c, Moisseev, Alexey ^c, Buzdin, Anton ^{b, e, l, m, ⁎}

Source: In Computers in Biology and Medicine March 2025 187

Pan-cancer antagonistic inhibition pattern of ATM-driven G2/M checkpoint pathway vs other DNA repair pathways

Authors: Zolotovskaia, Marianna A., Modestov, Alexander A., Suntsova, Maria V., Rachkova, Anastasia A., Koroleva, Elena V., Poddubskaya, Elena V., Sekacheva, Marina I., Tkachev, Victor S., Garazha, Andrew V., Glusker, Alexander A., Seryakov, Aleksander P., Vladimirova, Uliana S., Rumiantsev, Pavel O., Moisseev, Aleksey A., Zharkov, Dmitry O., Kuzmin, Denis V., Zhao, Xiaowen, Prassolov, Vladimir S., Shegay, Petr V., Li, Xinmin, Steinbichler, Teresa B., Kim, Ella, Sorokin, Maxim I., Wang, Ye, Buzdin, Anton A.

Source: In DNA Repair March 2023 123

Large-scale assessment of pros and cons of autopsy-derived or tumor-matched tissues as the norms for gene expression analysis in cancers

Authors: Sorokin, Maksim, Buzdin, Anton A., Guryanova, Anastasia, Efimov, Victor, Suntsova, Maria V., Zolotovskaia, Marianna A., Koroleva, Elena V., Sekacheva, Marina I., Tkachev, Victor S., Garazha, Andrew, Kremenchutckaya, Kristina, Drobyshev, Aleksey, Seryakov, Aleksander, Gudkov, Alexander, Alekseenko, Irina V., Rakitina, Olga, Kostina, Maria B., Vladimirova, Uliana, Moisseev, Aleksey, Bulgin, Dmitry, Radomskaya, Elena, Shestakov, Viktor, Baklaushev, Vladimir P., Prassolov, Vladimir, Shegay, Petr V., Li, Xinmin, Poddubskaya, Elena V., Gaifullin, Nurshat

Source: In Computational and Structural Biotechnology Journal 2023 21:3964-3986

OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization

Authors: Zolotovskaia, Marianna A., Tkachev, Victor S., Guryanova, Anastasia A., Simonov, Alexander M., Raevskiy, Mikhail M., Efimov, Victor V., Wang, Ye, Sekacheva, Marina I., Garazha, Andrew V., Borisov, Nicolas M., Kuzmin, Denis V., Sorokin, Maxim I., Buzdin, Anton A.

Source: Computational and Structural Biotechnology Journal. 20:2280-2291

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190063274.0x000001&indx=1&recIds=ETOCvdc_100190063274.0x000001

COVID-19–associated inhibition of energy accumulation pathways in human semen samples

Authors: Adamyan, Leila, Elagin, Vladimir, Vechorko, Valeriy, Stepanian, Assia, Dashko, Anton, Doroshenko, Dmitriy, Aznaurova, Yana, Sorokin, Maxim, Suntsova, Maria, Drobyshev, Alexei, Garazha, Andrew, Buzdin, Anton

Source: In F&S Science November 2021 2(4):355-364

Gene Expression Signature of Endometrial Samples from Women with and without Endometriosis

Authors: Adamyan, Leila, Aznaurova, Yana, Stepanian, Assia, Nikitin, Daniil, Garazha, Andrew, Suntsova, Maria, Sorokin, Maxim, Buzdin, Anton

Source: In The Journal of Minimally Invasive Gynecology October 2021 28(10):1774-1785

DNA repair pathway activation features in follicular and papillary thyroid tumors, interrogated using 95 experimental RNA sequencing profiles

Authors: Vladimirova, Uliana ^{a, e}, Rumiantsev, Pavel ^{b, e}, Zolotovskaia, Marianna ^e, Albert, Eugene ^c, Abrosimov, Aleksander ^b, Slashchuk, Konstantin ^b, Nikiforovich, Petr ^b, Chukhacheva, Olga ^b, Gaifullin, Nurshat ^f, Suntsova, Maria ^a, Zakharova, Galina ^b, Glusker, Alexander ^a, Nikitin, Daniil ^{c, g}, Garazha, Andrew ^c, Li, Xinmin ^h, Kamashev, Dmitriy ^a, Drobyshev, Alexei ^a, Kochergina-Nikitskaya, Irina ^g, Sorokin, Maxim ^{a, c, d}, Buzdin, Anton ^{a, c, d, g, ∗}

Source: In Heliyon March 2021 7(3)

Using proteomic and transcriptomic data to assess activation of intracellular molecular pathways

Authors: Buzdin, Anton, Tkachev, Victor, Zolotovskaia, Marianna, Garazha, Andrew, Moshkovskii, Sergey, Borisov, Nicolas, Gaifullin, Nurshat, Sorokin, Maksim, Suntsova, Maria

Source: Advances in protein chemistry and structural biology. 127:1-54

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN627000065&indx=1&recIds=ETOCRN627000065

Biomarkers of success of anti-PD-(L)1 immunotherapy for non-small cell lung cancer derived from RNA- and whole-exome sequencing: results of a prospective observational study on a cohort of 85 patients.

Authors: Poddubskaya, Elena, Suntsova, Maria, Lyadova, Marina, Luppov, Daniil, Guryanova, Anastasia, Lyadov, Vladimir, Garazha, Andrew, Sorokin, Maksim, Semenova, Anna, Shatalov, Vitaly, Biakhova, Maria, Simonov, Alexander, Moisseev, Aleksey, Buzdin, Anton

Source: Frontiers in Immunology; 2024, p1-21, 21p

Subject Terms: NON-small-cell lung carcinoma, GENE expression, TREATMENT effectiveness, IMMUNE checkpoint inhibitors, IMMUNE checkpoint proteins

RNA sequencing for research and diagnostics in clinical oncology

Authors: Buzdin, Anton, Sorokin, Maxim, Garazha, Andrew, Glusker, Alexander, Aleshin, Alex, Poddubskaya, Elena, Sekacheva, Marina, Kim, Ella, Gaifullin, Nurshat, Giese, Alf, Seryakov, Alexander, Rumiantsev, Pavel, Moshkovskii, Sergey, Moiseev, Alexey

Source: In Seminars in Cancer Biology February 2020 60:311-323

Quantitation of Molecular Pathway Activation Using RNA Sequencing Data

Authors: Borisov, Nicolas, Sorokin, Maxim, Garazha, Andrew, Buzdin, Anton

Source: Methods in molecular biology. 2063:189-206

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN622251277&indx=1&recIds=ETOCRN622251277

Oncobox Method for Scoring Efficiencies of Anticancer Drugs Based on Gene Expression Data

Authors: Tkachev, Victor, Sorokin, Maxim, Garazha, Andrew, Borisov, Nicolas, Buzdin, Anton

Source: Methods in molecular biology. 2063:235-256

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN622251290&indx=1&recIds=ETOCRN622251290

Molecular Pathway Analysis of Mutation Data for Biomarkers Discovery and Scoring of Target Cancer Drugs

Authors: Zolotovskaia, Marianna, Sorokin, Maxim, Garazha, Andrew, Borisov, Nikolay, Buzdin, Anton

Source: Methods in molecular biology. 2063:207-234

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN622251289&indx=1&recIds=ETOCRN622251289

Molecular pathway activation – New type of biomarkers for tumor morphology and personalized selection of target drugs

Authors: Buzdin, Anton, Sorokin, Maxim, Garazha, Andrew, Sekacheva, Marina, Kim, Ella, Zhukov, Nikolay, Wang, Ye, Li, Xinmin, Kar, Souvik, Hartmann, Christian, Samii, Amir, Giese, Alf, Borisov, Nicolas

Source: In Seminars in Cancer Biology December 2018 53:110-124

Shambhala: a platform-agnostic data harmonizer for gene expression data

Authors: Borisov, Nicolas, Shabalina, Irina, Tkachev, Victor, Sorokin, Maxim, Garazha, Andrew, Pulin, Andrey, Eremin, Ilya, Buzdin, Anton

Source: BMC bioinformatics. 20(1):1-10

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185577342.0x000001&indx=1&recIds=ETOCvdc_100185577342.0x000001

Atlas of RNA sequencing profiles for normal human tissues

Authors: Suntsova, Maria, Gaifullin, Nurshat, Allina, Daria, Reshetun, Alexey, Li, Xinmin, Mendeleeva, Larisa, Surin, Vadim, Sergeeva, Anna, Spirin, Pavel, Prassolov, Vladimir, Morgan, Alexander, Garazha, Andrew, Sorokin, Maxim, Buzdin, Anton

Source: Scientific data. 6(1):1-9

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100133343924.0x000001&indx=1&recIds=ETOCvdc_100133343924.0x000001

Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data

Authors: Borisov, Nicolas, Suntsova, Maria, Sorokin, Maxim, Garazha, Andrew, Kovalchuk, Olga, Aliper, Alexander, Ilnitskaya, Elena, Lezhnina, Ksenia, Korzinkin, Mikhail, Tkachev, Victor, Saenko, Vyacheslav, Saenko, Yury, Sokov, Dmitry G., Gaifullin, Nurshat M., Kashintsev, Kirill, Shirokorad, Valery, Shabalina, Irina, Zhavoronkov, Alex, Mishra, Bhubaneswar, Cantor, Charles R., Buzdin, Anton

Source: Cell cycle. 16(19):1810-1823

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100049296343.0x000001&indx=1&recIds=ETOCvdc_100049296343.0x000001

New bioinformatic tool for quick identification of functionally relevant endogenous retroviral inserts in human genome

Authors: Garazha, Andrew, Ivanova, Alena, Suntsova, Maria, Malakhova, Galina, Roumiantsev, Sergey, Zhavoronkov, Alex, Buzdin, Anton

Source: Cell cycle. 14(9):1476-1484

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCETOCvdc_100029002646.0x000001&indx=1&recIds=ETOCETOCvdc_100029002646.0x000001

Early stage of cytomegalovirus infection suppresses host microRNA expression regulation in human fibroblasts

Authors: Buzdin, Anton A., Artcibasova, Alina V., Fedorova, Natalya F., Suntsova, Maria V., Garazha, Andrew V., Sorokin, Maxim I., Allina, Daria, Shalatonin, Mikhail, Borisov, Nikolay M., Zhavoronkov, Alex A., Kovalchuk, Igor, Kovalchuk, Olga, Kushch, Alla A.

Source: Cell cycle. 15(24):3378-3389

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100052046063.0x000001&indx=1&recIds=ETOCvdc_100052046063.0x000001

Human-specific endogenous retroviral insert serves as an enhancer for the schizophrenia-linked gene PRODH

Authors: Suntsova, Maria, Gogvadze, Elena V., Salozhin, Sergey, Gaifullin, Nurshat, Eroshkin, Fedor, Dmitriev, Sergey E., Martynova, Natalia, Kulikov, Kirill, Malakhova, Galina, Tukhbatova, Gulnur, Bolshakov, Alexey P., Ghilarov, Dmitry, Garazha, Andrew, Aliper, Alexander, Cantor, Charles R., Solokhine, Yuri, Roumiantsev, Sergey, Balaban, Pavel, Zhavoronkov, Alex, Buzdin, Anton

Source: Proceedings of the National Academy of Sciences of the United States of America, 2013 Nov . 110(48), 19472-19477.

Access URL: https://www.jstor.org/stable/23757283