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Items: 1 to 50 of 161

1.

Integrated transcriptomic and epigenomic analysis of ovarian cancer reveals epigenetically silenced GULP1.

Maldonado L, Brait M, Izumchenko E, Begum S, Chatterjee A, Sen T, Loyo M, Barbosa A, Poeta ML, Makarev E, Zhavoronkov A, Fazio VM, Angioli R, Rabitti C, Ongenaert M, Van Criekinge W, Noordhuis MG, de Graeff P, Wisman GBA, van der Zee AGJ, Hoque MO.

Cancer Lett. 2018 Jun 28;433:242-251. doi: 10.1016/j.canlet.2018.06.030. [Epub ahead of print]

PMID:
29964205
2.

Reinforced Adversarial Neural Computer for de Novo Molecular Design.

Putin E, Asadulaev A, Ivanenkov Y, Aladinskiy V, Sanchez-Lengeling B, Aspuru-Guzik A, Zhavoronkov A.

J Chem Inf Model. 2018 Jun 25;58(6):1194-1204. doi: 10.1021/acs.jcim.7b00690. Epub 2018 Jun 12.

PMID:
29762023
3.

Vive la radiorésistance!: converging research in radiobiology and biogerontology to enhance human radioresistance for deep space exploration and colonization.

Cortese F, Klokov D, Osipov A, Stefaniak J, Moskalev A, Schastnaya J, Cantor C, Aliper A, Mamoshina P, Ushakov I, Sapetsky A, Vanhaelen Q, Alchinova I, Karganov M, Kovalchuk O, Wilkins R, Shtemberg A, Moreels M, Baatout S, Izumchenko E, de Magalhães JP, Artemov AV, Costes SV, Beheshti A, Mao XW, Pecaut MJ, Kaminskiy D, Ozerov IV, Scheibye-Knudsen M, Zhavoronkov A.

Oncotarget. 2018 Feb 12;9(18):14692-14722. doi: 10.18632/oncotarget.24461. eCollection 2018 Mar 6. Review.

4.

Adversarial Threshold Neural Computer for Molecular de Novo Design.

Putin E, Asadulaev A, Vanhaelen Q, Ivanenkov Y, Aladinskaya AV, Aliper A, Zhavoronkov A.

Mol Pharm. 2018 Mar 30. doi: 10.1021/acs.molpharmaceut.7b01137. [Epub ahead of print]

PMID:
29569445
5.

Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor.

Solanki HS, Raja R, Zhavoronkov A, Ozerov IV, Artemov AV, Advani J, Radhakrishnan A, Babu N, Puttamallesh VN, Syed N, Nanjappa V, Subbannayya T, Sahasrabuddhe NA, Patil AH, Prasad TSK, Gaykalova D, Chang X, Sathyendran R, Mathur PP, Rangarajan A, Sidransky D, Pandey A, Izumchenko E, Gowda H, Chatterjee A.

Oncoscience. 2018 Feb 23;5(1-2):21-38. doi: 10.18632/oncoscience.395. eCollection 2018 Jan.

6.

Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression of COX7A1 in embryonic and cancer cells.

West MD, Labat I, Sternberg H, Larocca D, Nasonkin I, Chapman KB, Singh R, Makarev E, Aliper A, Kazennov A, Alekseenko A, Shuvalov N, Cheskidova E, Alekseev A, Artemov A, Putin E, Mamoshina P, Pryanichnikov N, Larocca J, Copeland K, Izumchenko E, Korzinkin M, Zhavoronkov A.

Oncotarget. 2017 Dec 28;9(8):7796-7811. doi: 10.18632/oncotarget.23748. eCollection 2018 Jan 30.

7.

3D Molecular Representations Based on the Wave Transform for Convolutional Neural Networks.

Kuzminykh D, Polykovskiy D, Kadurin A, Zhebrak A, Baskov I, Nikolenko S, Shayakhmetov R, Zhavoronkov A.

Mol Pharm. 2018 Mar 5. doi: 10.1021/acs.molpharmaceut.7b01134. [Epub ahead of print]

PMID:
29473756
8.

Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy.

Ravi R, Noonan KA, Pham V, Bedi R, Zhavoronkov A, Ozerov IV, Makarev E, V Artemov A, Wysocki PT, Mehra R, Nimmagadda S, Marchionni L, Sidransky D, Borrello IM, Izumchenko E, Bedi A.

Nat Commun. 2018 Feb 21;9(1):741. doi: 10.1038/s41467-017-02696-6.

9.

Converging blockchain and next-generation artificial intelligence technologies to decentralize and accelerate biomedical research and healthcare.

Mamoshina P, Ojomoko L, Yanovich Y, Ostrovski A, Botezatu A, Prikhodko P, Izumchenko E, Aliper A, Romantsov K, Zhebrak A, Ogu IO, Zhavoronkov A.

Oncotarget. 2017 Nov 9;9(5):5665-5690. doi: 10.18632/oncotarget.22345. eCollection 2018 Jan 19.

10.

The Evaluation of Geroprotective Effects of Selected Flavonoids in Drosophila melanogaster and Caenorhabditis elegans.

Lashmanova E, Zemskaya N, Proshkina E, Kudryavtseva A, Volosnikova M, Marusich E, Leonov S, Zhavoronkov A, Moskalev A.

Front Pharmacol. 2017 Dec 7;8:884. doi: 10.3389/fphar.2017.00884. eCollection 2017.

11.

Population specific biomarkers of human aging: a big data study using South Korean, Canadian and Eastern European patient populations.

Mamoshina P, Kochetov K, Putin E, Cortese F, Aliper A, Lee WS, Ahn SM, Uhn L, Skjodt N, Kovalchuk O, Scheibye-Knudsen M, Zhavoronkov A.

J Gerontol A Biol Sci Med Sci. 2018 Jan 11. doi: 10.1093/gerona/gly005. [Epub ahead of print]

PMID:
29340580
12.

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;17(4):486-491. doi: 10.1080/15384101.2017.1417706. Epub 2018 Jan 17.

PMID:
29251172
13.

Residual γH2AX foci induced by low dose x-ray radiation in bone marrow mesenchymal stem cells do not cause accelerated senescence in the progeny of irradiated cells.

Pustovalova M, Astrelina ТA, Grekhova A, Vorobyeva N, Tsvetkova A, Blokhina T, Nikitina V, Suchkova Y, Usupzhanova D, Brunchukov V, Kobzeva I, Karaseva Т, Ozerov IV, Samoylov A, Bushmanov A, Leonov S, Izumchenko E, Zhavoronkov A, Klokov D, Osipov AN.

Aging (Albany NY). 2017 Nov 21;9(11):2397-2410. doi: 10.18632/aging.101327.

14.

Towards natural mimetics of metformin and rapamycin.

Aliper A, Jellen L, Cortese F, Artemov A, Karpinsky-Semper D, Moskalev A, Swick AG, Zhavoronkov A.

Aging (Albany NY). 2017 Nov 15;9(11):2245-2268. doi: 10.18632/aging.101319.

15.

Potentialities of MicroRNA Diagnosis in Patients with Bladder Cancer.

Shegay PV, Zhavoronkov AA, Gaifullin NM, Vorob'ev NV, Alekseev BY, Popov SV, Garazha AV, Buzdin AA, Kaprin AD.

Bull Exp Biol Med. 2017 Nov;164(1):106-108. doi: 10.1007/s10517-017-3935-3. Epub 2017 Nov 9.

PMID:
29119388
16.

γH2AX, 53BP1 and Rad51 protein foci changes in mesenchymal stem cells during prolonged X-ray irradiation.

Tsvetkova A, Ozerov IV, Pustovalova M, Grekhova A, Eremin P, Vorobyeva N, Eremin I, Pulin A, Zorin V, Kopnin P, Leonov S, Zhavoronkov A, Klokov D, Osipov AN.

Oncotarget. 2017 Jul 12;8(38):64317-64329. doi: 10.18632/oncotarget.19203. eCollection 2017 Sep 8.

17.

Bioinformatics Meets Biomedicine: OncoFinder, a Quantitative Approach for Interrogating Molecular Pathways Using Gene Expression Data.

Buzdin AA, Prassolov V, Zhavoronkov AA, Borisov NM.

Methods Mol Biol. 2017;1613:53-83. doi: 10.1007/978-1-4939-7027-8_4.

PMID:
28849558
18.

Mathematical Justification of Expression-Based Pathway Activation Scoring (PAS).

Aliper AM, Korzinkin MB, Kuzmina NB, Zenin AA, Venkova LS, Smirnov PY, Zhavoronkov AA, Buzdin AA, Borisov NM.

Methods Mol Biol. 2017;1613:31-51. doi: 10.1007/978-1-4939-7027-8_3.

PMID:
28849557
19.

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

Borisov N, Suntsova M, Sorokin M, Garazha A, Kovalchuk O, Aliper A, Ilnitskaya E, Lezhnina K, Korzinkin M, Tkachev V, Saenko V, Saenko Y, Sokov DG, Gaifullin NM, Kashintsev K, Shirokorad V, Shabalina I, Zhavoronkov A, Mishra B, Cantor CR, Buzdin A.

Cell Cycle. 2017 Oct 2;16(19):1810-1823. doi: 10.1080/15384101.2017.1361068. Epub 2017 Aug 21.

PMID:
28825872
20.

A comparative review of computational methods for pathway perturbation analysis: dynamical and topological perspectives.

Vanhaelen Q, Aliper AM, Zhavoronkov A.

Mol Biosyst. 2017 Aug 22;13(9):1692-1704. doi: 10.1039/c7mb00170c. Review.

PMID:
28714509
21.

druGAN: An Advanced Generative Adversarial Autoencoder Model for de Novo Generation of New Molecules with Desired Molecular Properties in Silico.

Kadurin A, Nikolenko S, Khrabrov K, Aliper A, Zhavoronkov A.

Mol Pharm. 2017 Sep 5;14(9):3098-3104. doi: 10.1021/acs.molpharmaceut.7b00346. Epub 2017 Aug 4.

PMID:
28703000
22.

An analysis of gene expression data involving examination of signaling pathways activation reveals new insights into the mechanism of action of minoxidil topical foam in men with androgenetic alopecia.

Stamatas GN, Wu J, Pappas A, Mirmirani P, McCormick TS, Cooper KD, Consolo M, Schastnaya J, Ozerov IV, Aliper A, Zhavoronkov A.

Cell Cycle. 2017;16(17):1578-1584. doi: 10.1080/15384101.2017.1327492. Epub 2017 Jun 8.

23.

In silico analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia.

Makarev E, Schubert AD, Kanherkar RR, London N, Teka M, Ozerov I, Lezhnina K, Bedi A, Ravi R, Mehra R, Hoque MO, Sloma I, Gaykalova DA, Csoka AB, Sidransky D, Zhavoronkov A, Izumchenko E.

Cell Death Discov. 2017 May 22;3:17022. doi: 10.1038/cddiscovery.2017.22. eCollection 2017.

24.

SMAD4 Loss Is Associated with Cetuximab Resistance and Induction of MAPK/JNK Activation in Head and Neck Cancer Cells.

Ozawa H, Ranaweera RS, Izumchenko E, Makarev E, Zhavoronkov A, Fertig EJ, Howard JD, Markovic A, Bedi A, Ravi R, Perez J, Le QT, Kong CS, Jordan RC, Wang H, Kang H, Quon H, Sidransky D, Chung CH.

Clin Cancer Res. 2017 Sep 1;23(17):5162-5175. doi: 10.1158/1078-0432.CCR-16-1686. Epub 2017 May 18.

PMID:
28522603
25.

The DrugAge database of aging-related drugs.

Barardo D, Thornton D, Thoppil H, Walsh M, Sharifi S, Ferreira S, Anžič A, Fernandes M, Monteiro P, Grum T, Cordeiro R, De-Souza EA, Budovsky A, Araujo N, Gruber J, Petrascheck M, Fraifeld VE, Zhavoronkov A, Moskalev A, de Magalhães JP.

Aging Cell. 2017 Jun;16(3):594-597. doi: 10.1111/acel.12585. Epub 2017 Mar 16.

26.

Effect of lentivirus-mediated shRNA inactivation of HK1, HK2, and HK3 genes in colorectal cancer and melanoma cells.

Kudryavtseva AV, Fedorova MS, Zhavoronkov A, Moskalev AA, Zasedatelev AS, Dmitriev AA, Sadritdinova AF, Karpova IY, Nyushko KM, Kalinin DV, Volchenko NN, Melnikova NV, Klimina KM, Sidorov DV, Popov AY, Nasedkina TV, Kaprin AD, Alekseev BY, Krasnov GS, Snezhkina AV.

BMC Genet. 2016 Dec 22;17(Suppl 3):156. doi: 10.1186/s12863-016-0459-1.

27.

Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer.

Snezhkina AV, Krasnov GS, Zaretsky AR, Zhavoronkov A, Nyushko KM, Moskalev AA, Karpova IY, Afremova AI, Lipatova AV, Kochetkov DV, Fedorova MS, Volchenko NN, Sadritdinova AF, Melnikova NV, Sidorov DV, Popov AY, Kalinin DV, Kaprin AD, Alekseev BY, Dmitriev AA, Kudryavtseva AV.

BMC Genomics. 2016 Dec 28;17(Suppl 14):1011. doi: 10.1186/s12864-016-3351-5.

28.

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

Buzdin AA, Artcibasova AV, Fedorova NF, Suntsova MV, Garazha AV, Sorokin MI, Allina D, Shalatonin M, Borisov NM, Zhavoronkov AA, Kovalchuk I, Kovalchuk O, Kushch AA.

Cell Cycle. 2016 Dec 16;15(24):3378-3389. doi: 10.1080/15384101.2016.1241928.

29.

The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology.

Kadurin A, Aliper A, Kazennov A, Mamoshina P, Vanhaelen Q, Khrabrov K, Zhavoronkov A.

Oncotarget. 2017 Feb 14;8(7):10883-10890. doi: 10.18632/oncotarget.14073.

30.

Accumulation of spontaneous γH2AX foci in long-term cultured mesenchymal stromal cells.

Pustovalova M, Grekhova A, Astrelina Т, Nikitina V, Dobrovolskaya E, Suchkova Y, Kobzeva I, Usupzhanova D, Vorobyeva N, Samoylov A, Bushmanov A, Ozerov IV, Zhavoronkov A, Leonov S, Klokov D, Osipov AN.

Aging (Albany NY). 2016 Dec 11;8(12):3498-3506. doi: 10.18632/aging.101142.

31.

Molecular pathway activation features of pediatric acute myeloid leukemia (AML) and acute lymphoblast leukemia (ALL) cells.

Petrov I, Suntsova M, Mutorova O, Sorokin M, Garazha A, Ilnitskaya E, Spirin P, Larin S, Kovalchuk O, Prassolov V, Zhavoronkov A, Roumiantsev A, Buzdin A.

Aging (Albany NY). 2016 Nov 19;8(11):2936-2947. doi: 10.18632/aging.101102.

32.

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.

Nat Commun. 2016 Nov 16;7:13427. doi: 10.1038/ncomms13427.

33.

Design of efficient computational workflows for in silico drug repurposing.

Vanhaelen Q, Mamoshina P, Aliper AM, Artemov A, Lezhnina K, Ozerov I, Labat I, Zhavoronkov A.

Drug Discov Today. 2017 Feb;22(2):210-222. doi: 10.1016/j.drudis.2016.09.019. Epub 2016 Sep 28. Review.

PMID:
27693712
34.

In search for geroprotectors: in silico screening and in vitro validation of signalome-level mimetics of young healthy state.

Aliper A, Belikov AV, Garazha A, Jellen L, Artemov A, Suntsova M, Ivanova A, Venkova L, Borisov N, Buzdin A, Mamoshina P, Putin E, Swick AG, Moskalev A, Zhavoronkov A.

Aging (Albany NY). 2016 Sep 24;8(9):2127-2152. doi: 10.18632/aging.101047.

35.

Cancer megafunds with in silico and in vitro validation: accelerating cancer drug discovery via financial engineering without financial crisis.

Yang X, Debonneuil E, Zhavoronkov A, Mishra B.

Oncotarget. 2016 Sep 6;7(36):57671-57678. doi: 10.18632/oncotarget.9808.

36.

Common pathway signature in lung and liver fibrosis.

Makarev E, Izumchenko E, Aihara F, Wysocki PT, Zhu Q, Buzdin A, Sidransky D, Zhavoronkov A, Atala A.

Cell Cycle. 2016 Jul 2;15(13):1667-73. doi: 10.1080/15384101.2016.1152435. Epub 2016 Jun 7.

37.

Pro-fibrotic pathway activation in trabecular meshwork and lamina cribrosa is the main driving force of glaucoma.

Zhavoronkov A, Izumchenko E, Kanherkar RR, Teka M, Cantor C, Manaye K, Sidransky D, West MD, Makarev E, Csoka AB.

Cell Cycle. 2016 Jun 17;15(12):1643-52. doi: 10.1080/15384101.2016.1170261.

38.

Deep Learning Applications for Predicting Pharmacological Properties of Drugs and Drug Repurposing Using Transcriptomic Data.

Aliper A, Plis S, Artemov A, Ulloa A, Mamoshina P, Zhavoronkov A.

Mol Pharm. 2016 Jul 5;13(7):2524-30. doi: 10.1021/acs.molpharmaceut.6b00248. Epub 2016 Jun 8.

39.

Deep biomarkers of human aging: Application of deep neural networks to biomarker development.

Putin E, Mamoshina P, Aliper A, Korzinkin M, Moskalev A, Kolosov A, Ostrovskiy A, Cantor C, Vijg J, Zhavoronkov A.

Aging (Albany NY). 2016 May;8(5):1021-33. doi: 10.18632/aging.100968.

40.

MiRImpact, a new bioinformatic method using complete microRNA expression profiles to assess their overall influence on the activity of intracellular molecular pathways.

Artcibasova AV, Korzinkin MB, Sorokin MI, Shegay PV, Zhavoronkov AA, Gaifullin N, Alekseev BY, Vorobyev NV, Kuzmin DV, Kaprin АD, Borisov NM, Buzdin AA.

Cell Cycle. 2016;15(5):689-98. doi: 10.1080/15384101.2016.1147633.

41.

Applications of Deep Learning in Biomedicine.

Mamoshina P, Vieira A, Putin E, Zhavoronkov A.

Mol Pharm. 2016 May 2;13(5):1445-54. doi: 10.1021/acs.molpharmaceut.5b00982. Epub 2016 Mar 29. Review.

PMID:
27007977
42.

Developing criteria for evaluation of geroprotectors as a key stage toward translation to the clinic.

Moskalev A, Chernyagina E, Tsvetkov V, Fedintsev A, Shaposhnikov M, Krut'ko V, Zhavoronkov A, Kennedy BK.

Aging Cell. 2016 Jun;15(3):407-15. doi: 10.1111/acel.12463. Epub 2016 Mar 11. Review.

43.

Inhibitors of mTOR in aging and cancer.

Zhavoronkov A.

Oncotarget. 2015 Dec 29;6(42):45010-1. doi: 10.18632/oncotarget.6878. No abstract available.

44.

Editorial: Should We Treat Aging as a Disease? Academic, Pharmaceutical, Healthcare Policy, and Pension Fund Perspectives.

Zhavoronkov A, Moskalev A.

Front Genet. 2016 Feb 16;7:17. doi: 10.3389/fgene.2016.00017. eCollection 2016. No abstract available.

45.

Large-scale profiling of signalling pathways reveals an asthma specific signature in bronchial smooth muscle cells.

Alexandrova E, Nassa G, Corleone G, Buzdin A, Aliper AM, Terekhanova N, Shepelin D, Zhavoronkov A, Tamm M, Milanesi L, Miglino N, Weisz A, Borger P.

Oncotarget. 2016 May 3;7(18):25150-61. doi: 10.18632/oncotarget.7209.

46.

Models of Innate Neural Attractors and Their Applications for Neural Information Processing.

Solovyeva KP, Karandashev IM, Zhavoronkov A, Dunin-Barkowski WL.

Front Syst Neurosci. 2016 Jan 5;9:178. doi: 10.3389/fnsys.2015.00178. eCollection 2015.

47.

DNA repair in species with extreme lifespan differences.

MacRae SL, Croken MM, Calder RB, Aliper A, Milholland B, White RR, Zhavoronkov A, Gladyshev VN, Seluanov A, Gorbunova V, Zhang ZD, Vijg J.

Aging (Albany NY). 2015 Dec;7(12):1171-84.

48.

Molecular pathway activation features linked with transition from normal skin to primary and metastatic melanomas in human.

Shepelin D, Korzinkin M, Vanyushina A, Aliper A, Borisov N, Vasilov R, Zhukov N, Sokov D, Prassolov V, Gaifullin N, Zhavoronkov A, Bhullar B, Buzdin A.

Oncotarget. 2016 Jan 5;7(1):656-70. doi: 10.18632/oncotarget.6394.

49.

Aging Chart: a community resource for rapid exploratory pathway analysis of age-related processes.

Moskalev A, Zhikrivetskaya S, Shaposhnikov M, Dobrovolskaya E, Gurinovich R, Kuryan O, Pashuk A, Jellen LC, Aliper A, Peregudov A, Zhavoronkov A.

Nucleic Acids Res. 2016 Jan 4;44(D1):D894-9. doi: 10.1093/nar/gkv1287. Epub 2015 Nov 23.

50.

Classifying aging as a disease in the context of ICD-11.

Zhavoronkov A, Bhullar B.

Front Genet. 2015 Nov 4;6:326. doi: 10.3389/fgene.2015.00326. eCollection 2015.

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