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Victor Tkachev
Deutsche Bank
GeneCancerGene expressionComputational biologyBiology
23Publications
7H-index
126Citations
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Publications 23
Newest
#1Elena PoddubskayaH-Index: 10
#2Maxim SorokinH-Index: 11
Last. Victor TkachevH-Index: 7
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e13676Background: Analysis of mutation profiles in cancer patients does not provide clinical benefits in 80-90% of cases in the US (Marquart et al., 2018). Gene expression analysis potentially comp...
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#1Maxim Sorokin (MSMU: I.M. Sechenov First Moscow State Medical University)H-Index: 11
#2Elena Poddubskaya (MSMU: I.M. Sechenov First Moscow State Medical University)H-Index: 10
Last. Andrew GarazhaH-Index: 12
view all 12 authors...
Gastric cancer (GC) is the fifth cancer type by associated mortality. Proportion of early diagnosis is low, and most patients are diagnosed at the advanced stages. First line therapy standardly includes fluoropyrimidines and platinum compounds with trastuzumab for HER2-positive cases. For the recurrent disease there are several alternative options including ramucirumab, a monoclonal therapeutic antibody that inhibits VEGF-mediated tumor angiogenesis by binding with VEGFR2, alone or in combinatio...
2 CitationsSource
#1Marianna A. Zolotovskaia (MIPT: Moscow Institute of Physics and Technology)H-Index: 1
Last. A. D. KaprinH-Index: 14
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Inter-patient molecular heterogeneity is the major declared driver of an expanding variety of anticancer drugs and personalizing their prescriptions. Here, we compared interpatient molecular heterogeneities of tumors and repertoires of drugs or their molecular targets currently in use in clinical oncology. We estimated molecular heterogeneity using genomic (whole exome sequencing) and transcriptomic (RNA sequencing) data for 4890 tumors taken from The Cancer Genome Atlas database. For thirteen m...
2 CitationsSource
#1Marianna A. Zolotovskaia (MIPT: Moscow Institute of Physics and Technology)H-Index: 1
Last. Anton BuzdinH-Index: 28
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Carcinogenesis is linked with massive changes in regulation of gene networks. We used high throughput mutation and gene expression data to interrogate involvement of 278 signaling, 72 metabolic, 48 DNA repair and 47 cytoskeleton molecular pathways in cancer. Totally, we analyzed 4910 primary tumor samples with individual cancer RNA sequencing and whole exome sequencing profiles including ~1.3 million DNA mutations and representing thirteen cancer types. Gene expression in cancers was compared wi...
3 CitationsSource
#1Victor TkachevH-Index: 7
#2Maxim Sorokin (MSMU: I.M. Sechenov First Moscow State Medical University)H-Index: 11
Last. Nicolas M. Borisov (MSMU: I.M. Sechenov First Moscow State Medical University)
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(1) Background: Machine learning (ML) methods are rarely used for an omics-based prescription of cancer drugs, due to shortage of case histories with clinical outcome supplemented by high-throughput molecular data. This causes overtraining and high vulnerability of most ML methods. Recently, we proposed a hybrid global-local approach to ML termed floating window projective separator (FloWPS) that avoids extrapolation in the feature space. Its core property is data trimming, i.e., sample-specific...
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#1Victor TkachevH-Index: 7
#2Maxim Sorokin (MSMU: I.M. Sechenov First Moscow State Medical University)H-Index: 11
Last. Anton Buzdin (MSMU: I.M. Sechenov First Moscow State Medical University)H-Index: 2
view all 5 authors...
We describe here the Oncobox method for scoring efficiencies of anticancer target drugs (ATDs) using high throughput gene expression data. The method rationale, design, and validation are given along with the examples of its practical applications in biomedicine. The method is based on the analysis of intracellular molecular pathways activation and measuring expressions of molecular target genes for every ATD under consideration. Using Oncobox method requires collection of normal (control) expre...
4 CitationsSource
Oct 14, 2019 in ISMCO (International Symposium Mathematical and Computational Oncology)
#1Victor TkachevH-Index: 7
#2Anton Buzdin (MSMU: I.M. Sechenov First Moscow State Medical University)H-Index: 28
Last. Nicolas Borisov (MSMU: I.M. Sechenov First Moscow State Medical University)H-Index: 10
view all 3 authors...
Machine learning (ML) methods are still rarely used for gene expression/mutation-based prediction of individual tumor responses on anticancer chemotherapy due to relatively rare clinical case histories supplemented with high-throughput molecular data. This leads to high vulnerability of most ML methods are to overtraining. Recently, we proposed a novel hybrid global-local approach to ML termed FLOating Window Projective Separator (FloWPS) that avoids extrapolation in the feature space and may im...
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#1Daniil NikitinH-Index: 4
Last. Anton BuzdinH-Index: 28
view all 9 authors...
Background: Retroelements (REs) are mobile genetic elements comprising ~40% of human DNA. They can reshape expression patterns of nearby genes by providing various regulatory sequences. The proportion of regulatory sequences held by REs can serve a measure of regulatory evolution rate of the respective genes and molecular pathways. Methods: We calculated RE-linked enrichment scores for individual genes and molecular pathways based on ENCODE project epigenome data for enhancer-specific histone mo...
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#1Anna A. Igolkina (Saint Petersburg State Polytechnic University)H-Index: 3
#1Anna A. IgolkinaH-Index: 1
Last. Anton Buzdin (MSMU: I.M. Sechenov First Moscow State Medical University)H-Index: 28
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Background: Transposons are selfish genetic elements that self-reproduce in host DNA. They were active during evolutionary history and now occupy almost half of mammalian genomes. Close insertions of transposons reshaped structure and regulation of many genes considerably. Co-evolution of transposons and host DNA frequently results in the formation of new regulatory regions. Previously we published a concept that the proportion of functional features held by transposons positively correlates wit...
4 CitationsSource
#1Daniil Nikitin (MSMU: I.M. Sechenov First Moscow State Medical University)H-Index: 4
#2Andrew GarazhaH-Index: 12
Last. Anton Buzdin (MSMU: I.M. Sechenov First Moscow State Medical University)H-Index: 28
view all 10 authors...
In the article ‘Retroelement—Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution,’ a number of transcription factor binding sites (TFBS) mapped on all retroelement classes were incorrectly calculated as sum of TFBS numbers separately mapped on LINEs, SINEs and LTR retrotransposons/endogenous retroviruses (LR/ERVs) [...]
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