Search Results - "Victor Tkachev"

Current Concepts and Advances in Graft-Versus-Host Disease Immunology by Hill, Geoffrey R, Betts, Brian C, Tkachev, Victor, Kean, Leslie S, Blazar, Bruce R

“…Worldwide, each year over 30,000 patients undergo an allogeneic hema-topoietic stem cell transplantation with the intent to cure high-risk hematologic…”
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Cancer gene expression profiles associated with clinical outcomes to chemotherapy treatments by Borisov, Nicolas, Sorokin, Maxim, Tkachev, Victor, Garazha, Andrew, Buzdin, Anton

“…Machine learning (ML) methods still have limited applicability in personalized oncology due to low numbers of available clinically annotated molecular…”
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Shambhala: a platform-agnostic data harmonizer for gene expression data by Borisov, Nicolas, Shabalina, Irina, Tkachev, Victor, Sorokin, Maxim, Garazha, Andrew, Pulin, Andrey, Eremin, Ilya I, Buzdin, Anton

“…Harmonization techniques make different gene expression profiles and their sets compatible and ready for comparisons. Here we present a new bioinformatic tool…”
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Flexible Data Trimming Improves Performance of Global Machine Learning Methods in Omics-Based Personalized Oncology by Tkachev, Victor, Sorokin, Maxim, Borisov, Constantin, Garazha, Andrew, Buzdin, Anton, Borisov, Nicolas

“…(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…”
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Next-Generation Grade and Survival Expression Biomarkers of Human Gliomas Based on Algorithmically Reconstructed Molecular Pathways by Zolotovskaia, Marianna A, Kovalenko, Max A, Tkachev, Victor S, Simonov, Alexander M, Sorokin, Maxim I, Kim, Ella, Kuzmin, Denis V, Karademir-Yilmaz, Betul, Buzdin, Anton A

“…In gliomas, expression of certain marker genes is strongly associated with survival and tumor type and often exceeds histological assessments. Using a human…”
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Better Agreement of Human Transcriptomic and Proteomic Cancer Expression Data at the Molecular Pathway Activation Level by Raevskiy, Mikhail, Sorokin, Maxim, Zakharova, Galina, Tkachev, Victor, Borisov, Nicolas, Kuzmin, Denis, Kremenchutckaya, Kristina, Gudkov, Alexander, Kamashev, Dmitry, Buzdin, Anton

“…Previously, we have shown that the aggregation of RNA-level gene expression profiles into quantitative molecular pathway activation metrics results in lesser…”
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Pan-cancer antagonistic inhibition pattern of ATM-driven G2/M checkpoint pathway vs other DNA repair pathways by 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.

“…DNA repair mechanisms keep genome integrity and limit tumor-associated alterations and heterogeneity, but on the other hand they promote tumor survival after…”
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Disparity between Inter-Patient Molecular Heterogeneity and Repertoires of Target Drugs Used for Different Types of Cancer in Clinical Oncology by Zolotovskaia, Marianna A, Sorokin, Maxim I, Petrov, Ivan V, Poddubskaya, Elena V, Moiseev, Alexey A, Sekacheva, Marina I, Borisov, Nicolas M, Tkachev, Victor S, Garazha, Andrew V, Kaprin, Andrey D, Shegay, Peter V, Giese, Alf, Kim, Ella, Roumiantsev, Sergey A, Buzdin, Anton A

“…Inter-patient molecular heterogeneity is the major declared driver of an expanding variety of anticancer drugs and personalizing their prescriptions. Here, we…”
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Number of human protein interactions correlates with structural, but not regulatory conservation of the respective genes by Mekic, Rijalda, Zolotovskaia, Marianna A., Sorokin, Maksim, Mohammad, Tharaa, Shaban, Nina, Musatov, Ivan, Tkachev, Victor, Modestov, Alexander, Simonov, Alexander, Kuzmin, Denis, Buzdin, Anton

“…Introduction The differential ratio of nonsynonymous to synonymous nucleotide substitutions (dN/dS) is a common measure of the rate of structural evolution in…”
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OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization by 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.

“…OncoboxPD (Oncobox pathway databank) available at https://open.oncobox.com is the collection of 51 672 uniformly processed human molecular pathways…”
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Pan-cancer experimental characteristic of human transcriptional patterns connected with telomerase reverse transcriptase ( TERT ) gene expression status by Drobyshev, Aleksey, Modestov, Alexander, Suntsova, Maria, Poddubskaya, Elena, Seryakov, Alexander, Moisseev, Aleksey, Sorokin, Maksim, Tkachev, Victor, Zakharova, Galina, Simonov, Aleksander, Zolotovskaia, Marianna A, Buzdin, Anton

“…The gene encodes the reverse transcriptase subunit of telomerase and is normally transcriptionally suppressed in differentiated human cells but reactivated in…”
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H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks by Igolkina, Anna A, Zinkevich, Arsenii, Karandasheva, Kristina O, Popov, Aleksey A, Selifanova, Maria V, Nikolaeva, Daria, Tkachev, Victor, Penzar, Dmitry, Nikitin, Daniil M, Buzdin, Anton

“…Transposons are selfish genetic elements that self-reproduce in host DNA. They were active during evolutionary history and now occupy almost half of mammalian…”
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Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform by Gerdemann, Ulrike, Fleming, Ryan A, Kaminski, James, McGuckin, Connor, Rui, Xianliang, Lane, Jennifer F, Keskula, Paula, Cagnin, Lorenzo, Shalek, Alex K, Tkachev, Victor, Kean, Leslie S

“…T cell receptor (TCR) clonotype tracking is a powerful tool for interrogating T cell mediated immune processes. New methods to pair a single cell's…”
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Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins by Nikitin, Daniil, Penzar, Dmitry, Garazha, Andrew, Sorokin, Maxim, Tkachev, Victor, Borisov, Nicolas, Poltorak, Alexander, Prassolov, Vladimir, Buzdin, Anton A

“…Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome…”
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Machine Learning Applicability for Classification of PAD/VCD Chemotherapy Response Using 53 Multiple Myeloma RNA Sequencing Profiles by Borisov, Nicolas, Sergeeva, Anna, Suntsova, Maria, Raevskiy, Mikhail, Gaifullin, Nurshat, Mendeleeva, Larisa, Gudkov, Alexander, Nareiko, Maria, Garazha, Andrew, Tkachev, Victor, Li, Xinmin, Sorokin, Maxim, Surin, Vadim, Buzdin, Anton

“…Multiple myeloma (MM) affects ~500,000 people and results in ~100,000 deaths annually, being currently considered treatable but incurable. There are several MM…”
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FLOating-Window Projective Separator (FloWPS): A Data Trimming Tool for Support Vector Machines (SVM) to Improve Robustness of the Classifier by Tkachev, Victor, Sorokin, Maxim, Mescheryakov, Artem, Simonov, Alexander, Garazha, Andrew, Buzdin, Anton, Muchnik, Ilya, Borisov, Nicolas

“…Here, we propose a heuristic technique of data trimming for SVM termed ( ), tailored for personalized predictions based on molecular data. This procedure can…”
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Transcriptome analysis of GVHD reveals aurora kinase A as a targetable pathway for disease prevention by Furlan, Scott N, Watkins, Benjamin, Tkachev, Victor, Flynn, Ryan, Cooley, Sarah, Ramakrishnan, Swetha, Singh, Karnail, Giver, Cindy, Hamby, Kelly, Stempora, Linda, Garrett, Aneesah, Chen, Jingyang, Betz, Kayla M, Ziegler, Carly G K, Tharp, Gregory K, Bosinger, Steven E, Promislow, Daniel E L, Miller, Jeffrey S, Waller, Edmund K, Blazar, Bruce R, Kean, Leslie S

“…Graft-versus-host disease (GVHD) is the most common complication of hematopoietic stem cell transplant (HCT). However, our understanding of the molecular…”
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Uniformly shaped harmonization combines human transcriptomic data from different platforms while retaining their biological properties and differential gene expression patterns by Borisov, Nicolas, Tkachev, Victor, Simonov, Alexander, Sorokin, Maxim, Kim, Ella, Kuzmin, Denis, Karademir-Yilmaz, Betul, Buzdin, Anton

“…Introduction: Co-normalization of RNA profiles obtained using different experimental platforms and protocols opens avenue for comprehensive comparison of…”
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Mutation Enrichment and Transcriptomic Activation Signatures of 419 Molecular Pathways in Cancer by Zolotovskaia, Marianna A, Tkachev, Victor S, Seryakov, Alexander P, Kuzmin, Denis V, Kamashev, Dmitry E, Sorokin, Maxim I, Roumiantsev, Sergey A, Buzdin, Anton A

“…Carcinogenesis is linked with massive changes in regulation of gene networks. We used high throughput mutation and gene expression data to interrogate…”
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Algorithmically Reconstructed Molecular Pathways as the New Generation of Prognostic Molecular Biomarkers in Human Solid Cancers by Zolotovskaia, Marianna, Kovalenko, Maks, Pugacheva, Polina, Tkachev, Victor, Simonov, Alexander, Sorokin, Maxim, Seryakov, Alexander, Garazha, Andrew, Gaifullin, Nurshat, Sekacheva, Marina, Zakharova, Galina, Buzdin, Anton A

“…Individual gene expression and molecular pathway activation profiles were shown to be effective biomarkers in many cancers. Here, we used the human interactome…”
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