Yuri Nikolsky

Summary

Affiliation: St. Joseph
Country: USA

Publications

  1. ncbi request reprint Biological networks and analysis of experimental data in drug discovery
    Yuri Nikolsky
    GeneGo, 500 Renaissance Drive, 106, St Joseph, MI 49085, USA
    Drug Discov Today 10:653-62. 2005
  2. pmc Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes
    W Shi
    GeneGo Inc, St Joseph, MI, USA
    Pharmacogenomics J 10:310-23. 2010
  3. doi request reprint Manual annotation of protein interactions
    Svetlana Bureeva
    Metalogic OOO, Moscow, Russia
    Methods Mol Biol 563:75-95. 2009
  4. pmc Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis
    Robert Kleemann
    Department of Vascular and Metabolic Diseases, TNO Quality of Life, Biosciences, Gaubius Laboratory, Zernikedreef 9, 2333 CK Leiden, The Netherlands
    Genome Biol 8:R200. 2007
  5. pmc Effect of training-sample size and classification difficulty on the accuracy of genomic predictors
    Vlad Popovici
    Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Genopode Building, Quartier Sorge, Lausanne CH 1015, Switzerland
    Breast Cancer Res 12:R5. 2010
  6. pmc Integrated network analysis of transcriptomic and proteomic data in psoriasis
    Eleonora Piruzian
    Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina St, 3 GSP 1, 119991 Moscow, Russia
    BMC Syst Biol 4:41. 2010
  7. pmc Network analysis of human glaucomatous optic nerve head astrocytes
    Tatiana Nikolskaya
    Current address Bascom Palmer Eye Institute Department of Ophthalmology, University of Miami Miller School of Medicine 1638 NW 10th Avenue, Miami, FL 33136, USA
    BMC Med Genomics 2:24. 2009
  8. pmc Transcriptional networks in plasmacytoid dendritic cells stimulated with synthetic TLR 7 agonists
    Woubalem Birmachu
    Pharmacology, 3M Pharmaceuticals, St Paul, Minnesota, USA
    BMC Immunol 8:26. 2007
  9. pmc The transcriptomic signature of fasting murine liver
    Milka Sokolovic
    AMC Liver Center, Academic Medical Center, University of Amsterdam, The Netherlands
    BMC Genomics 9:528. 2008
  10. pmc Fasting induces a biphasic adaptive metabolic response in murine small intestine
    Milka Sokolovic
    AMC Liver Centre, Academic Medical Centre, Amsterdam, The Netherlands
    BMC Genomics 8:361. 2007

Collaborators

  • Sean Ekins
  • David J Monsma
  • Raymond R Samaha
  • L Shi
  • Marina Bessarabova
  • W Tong
  • C Furlanello
  • Zoltan Dezso
  • Laura E MacConaill
  • Robert Kleemann
  • Noel R Monks
  • Jun Yao
  • Konstantin V Balakin
  • J C Corton
  • ANDREJ E BUGRIM
  • Tatiana Nikolskaya
  • Svetlana Bureeva
  • Milka Sokolovic
  • Weiwei Shi
  • Vlad Popovici
  • Eleonora Piruzian
  • Alex Ishkin
  • W Shi
  • Svetlana Zvereva
  • Tatiana Serebryiskaya
  • Richard J Brennan
  • Antoine H C van Kampen
  • Diederik Wehkamp
  • Wouter H Lamers
  • Lisa A Gilhuijs-Pederson
  • Aleksandar Sokolovic
  • Theodorus B M Hakvoort
  • Woubalem Birmachu
  • Jim Kaput
  • Dmitry Korolev
  • R J Brennan
  • Daniel Booser
  • M Chen
  • A Guryanov
  • Weijie Chen
  • J Dopazo
  • Marina Tsyganova
  • R Shah
  • Sergey Bruskin
  • Christos Hatzis
  • T Nikolskaya
  • T Serebryiskaya
  • M Dudoladova
  • T Shi
  • W Fraser Symmans
  • G Jurman
  • Y Deng
  • Frank W Samuelson
  • Rustam Abdeev
  • R S Thomas
  • D Dosymbekov
  • Brandon G Gallas
  • Stanislav Melnik
  • Gabriel N Hortobagyi
  • Lajos Pusztai
  • Sergey Moshkovskii
  • Vicente Valero
  • Kenneth R Hess
  • Mauro Delorenzi
  • Nick Yankovsky
  • Olga Agapova
  • Valentin Romanov
  • Sanjoy K Bhattacharya
  • Eugene Sviridov
  • Eugene Rahkmatulin
  • Valery I Shestopalov
  • M Rosario Hernandez
  • Emiel Ver Loren van Themaat
  • Tatiana Nikolskya
  • Dirk R de Waart
  • Raymond M Gleason
  • Kenneth E Lipson
  • Betul Hatipoglu
  • Rachel I M van Haaften
  • Alla Perlina
  • Chris T A Evelo
  • Jacqueline Vermeulen
  • John P Vasilakos
  • Amelia Bartholomew
  • Christie L Riter
  • Barbara J Bulbulian
  • Nikolay P Savchuk
  • Andrey A Ivashchenko
  • Eugene Kirillov
  • Yan A Ivanenkov

Detail Information

Publications26

  1. ncbi request reprint Biological networks and analysis of experimental data in drug discovery
    Yuri Nikolsky
    GeneGo, 500 Renaissance Drive, 106, St Joseph, MI 49085, USA
    Drug Discov Today 10:653-62. 2005
    ..Here we outline recent advances in the field, available tools and applications of network analysis in drug discovery...
  2. pmc Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes
    W Shi
    GeneGo Inc, St Joseph, MI, USA
    Pharmacogenomics J 10:310-23. 2010
    ..These findings will aid the understanding, and application of predictive genomic signatures, and support their broader application in predictive medicine...
  3. doi request reprint Manual annotation of protein interactions
    Svetlana Bureeva
    Metalogic OOO, Moscow, Russia
    Methods Mol Biol 563:75-95. 2009
    ..Here we describe our ever-evolving annotation approach, the important annotation issues and our solutions, and the mammalian protein interactions database MetaBase which we have been working on for over 8 years...
  4. pmc Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis
    Robert Kleemann
    Department of Vascular and Metabolic Diseases, TNO Quality of Life, Biosciences, Gaubius Laboratory, Zernikedreef 9, 2333 CK Leiden, The Netherlands
    Genome Biol 8:R200. 2007
    ..25%) and high (HC; 1%) cholesterol diets, scored early atherosclerosis and profiled the (patho)physiological state of the liver using novel whole-genome and metabolome technologies...
  5. pmc Effect of training-sample size and classification difficulty on the accuracy of genomic predictors
    Vlad Popovici
    Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Genopode Building, Quartier Sorge, Lausanne CH 1015, Switzerland
    Breast Cancer Res 12:R5. 2010
    ....
  6. pmc Integrated network analysis of transcriptomic and proteomic data in psoriasis
    Eleonora Piruzian
    Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina St, 3 GSP 1, 119991 Moscow, Russia
    BMC Syst Biol 4:41. 2010
    ..Psoriasis is complex inflammatory skin pathology of autoimmune origin. Several cell types are perturbed in this pathology, and underlying signaling events are complex and still poorly understood...
  7. pmc Network analysis of human glaucomatous optic nerve head astrocytes
    Tatiana Nikolskaya
    Current address Bascom Palmer Eye Institute Department of Ophthalmology, University of Miami Miller School of Medicine 1638 NW 10th Avenue, Miami, FL 33136, USA
    BMC Med Genomics 2:24. 2009
    ..CONCLUSION: Our results suggest several key biological network modules that are involved in regulating neurotoxicity of reactive astrocytes in glaucoma, and comprise potential targets for cell-based therapy...
  8. pmc Transcriptional networks in plasmacytoid dendritic cells stimulated with synthetic TLR 7 agonists
    Woubalem Birmachu
    Pharmacology, 3M Pharmaceuticals, St Paul, Minnesota, USA
    BMC Immunol 8:26. 2007
    ..To this end, we evaluated changes in global gene expression upon stimulation of 99.9% pure human pDC with the TLR7 selective agonists 3M-852A, and the TLR7/8 agonist 3M-011...
  9. pmc The transcriptomic signature of fasting murine liver
    Milka Sokolovic
    AMC Liver Center, Academic Medical Center, University of Amsterdam, The Netherlands
    BMC Genomics 9:528. 2008
    ..Hence, gene-expression profiling, pathway, network and gene-set enrichment analysis and immunohistochemistry were carried out on mouse liver after 0, 12, 24 and 72 hours of fasting...
  10. pmc Fasting induces a biphasic adaptive metabolic response in murine small intestine
    Milka Sokolovic
    AMC Liver Centre, Academic Medical Centre, Amsterdam, The Netherlands
    BMC Genomics 8:361. 2007
    ..Gene-expression profiling, pathway analysis, and immunohistochemistry were therefore carried out on mouse small intestine after 0, 12, 24, and 72 hours of fasting...
  11. pmc Bimodal gene expression patterns in breast cancer
    Marina Bessarabova
    Russian Academy of Sciences, Vavilov Institute for General Genetics, ul Gubkina, 3, Moscow, Russia
    BMC Genomics 11:S8. 2010
    ..The groups tend to form concise network modules underlying their function in cancerogenesis of breast neoplasms...
  12. pmc Identifying disease-specific genes based on their topological significance in protein networks
    Zoltan Dezso
    GeneGo Inc, Renaissance Drive, Saint Joseph, Michigan 49085, USA
    BMC Syst Biol 3:36. 2009
    ..To be useful in a research or clinical laboratory, the results need to be translated to the level of testable hypotheses about individual genes and proteins within the condition of interest...
  13. doi request reprint Functional analysis of OMICs data and small molecule compounds in an integrated "knowledge-based" platform
    Yuri Nikolsky
    GeneGo, Inc, Saint Joseph, MI, USA
    Methods Mol Biol 563:177-96. 2009
    ....
  14. doi request reprint Genome-wide functional synergy between amplified and mutated genes in human breast cancer
    Yuri Nikolsky
    GeneGo, Inc, St Joseph, Michigan, USA
    Cancer Res 68:9532-40. 2008
    ..Our results support the hypothesis that multiple genetic events, including copy number gains and somatic mutations, are necessary for establishing the malignant cell phenotype...
  15. ncbi request reprint Pathway mapping tools for analysis of high content data
    Sean Ekins
    GeneGo, Jerkintown, PA, USA
    Methods Mol Biol 356:319-50. 2007
    ..We describe in detail the integrated data-mining tools applicable to building biological networks developed by GeneGo, namely, MetaCore and MetaDrug...
  16. doi request reprint Functional synergies yet distinct modulators affected by genetic alterations in common human cancers
    Marina Bessarabova
    Thomson Reuters, Healthcare and Life Science, St Joseph, Michigan 49085, USA
    Cancer Res 71:3471-81. 2011
    ..Our findings provide a novel integrated perspective on the complex signaling and regulatory networks that underlie common human cancers...
  17. doi request reprint Quantitative knowledge-based analysis in compound safety assessment
    Svetlana Bureeva
    Thomson Reuters, 169 Saxony Road, Encinitas, CA 92024, USA
    Expert Opin Drug Metab Toxicol 7:287-98. 2011
    ..Another reason is the poor mechanistic understanding of drug side effects as currently just a few compound targets are linked to specific adverse reactions...
  18. pmc A comprehensive functional analysis of tissue specificity of human gene expression
    Zoltan Dezso
    GeneGo, Inc, Renaissance Drive, St, Joseph, MI 49085, USA
    BMC Biol 6:49. 2008
    ..We have performed a functional and topological analysis of housekeeping and tissue-specific networks to identify universally necessary biological processes, and those unique to or characteristic of particular tissues...
  19. ncbi request reprint A novel method for generation of signature networks as biomarkers from complex high throughput data
    Yuri Nikolsky
    Computational Biology Genego Inc, 500 Renaissance Drive, Suite 106, St Joseph, MI 49085, USA
    Toxicol Lett 158:20-9. 2005
    ..These signature networks represent an approach to identify biomarkers and a general approach for discovering new relationships in complex high throughput toxicology data...
  20. ncbi request reprint Early prediction of drug metabolism and toxicity: systems biology approach and modeling
    Andrej Bugrim
    GeneGo, 500 Renaissance Drive, Suite 106, St Joseph, MI 49085, USA
    Drug Discov Today 9:127-35. 2004
    ..systems biology' databases of metabolic pathways, genes and regulatory networks. In this review, we outline the advantages and drawbacks of each of these systems and suggest directions for their integration...
  21. ncbi request reprint Characteristics of genomic signatures derived using univariate methods and mechanistically anchored functional descriptors for predicting drug- and xenobiotic-induced nephrotoxicity
    Weiwei Shi
    GeneGo, Inc 500 Renaissance Drive, 106, St Joseph, MI, 49085
    Toxicol Mech Methods 18:267-76. 2008
    ..Such functional descriptors of toxicity promise to better integrate predictive toxicogenomics with mechanistic analysis, facilitating the interpretation and risk assessment of predictive genomic investigations...
  22. ncbi request reprint Techniques: application of systems biology to absorption, distribution, metabolism, excretion and toxicity
    Sean Ekins
    GeneGo, 500 Renaissance Drive, Suite 106, St Joseph, MI 49085, USA
    Trends Pharmacol Sci 26:202-9. 2005
    ..In this review, we focus on the most recent advances and applications in this area...
  23. doi request reprint Systems biology approaches to the study of cardiovascular drugs
    Yuri Nikolsky
    GeneGo, Inc, St Joseph, MI, USA
    Methods Mol Biol 662:221-43. 2010
    ..All relevant steps, for example, experimental design, tissue collection and high quality RNA preparation, bioinformatical analysis of functional processes, and pathways (targeted and untargeted) are addressed...
  24. ncbi request reprint Modeling of human cytochrome p450-mediated drug metabolism using unsupervised machine learning approach
    Dmitry Korolev
    GeneGo, Inc, 227 South Berrien Street, New Buffalo, MI 49117, USA
    J Med Chem 46:3631-43. 2003
    ..The developed algorithm can be used in early stages of drug discovery as an efficient tool for the assessment of human metabolism and toxicity of novel compounds in designing discovery libraries and in lead optimization...
  25. pmc Genomic characterization of explant tumorgraft models derived from fresh patient tumor tissue
    David J Monsma
    Laboratory for Translational Medicine, Van Andel Research Institute, Grand Rapids, MI, USA
    J Transl Med 10:125. 2012
    ..This report directly compares the genomic characteristics of patient tumors and the derived tumorgraft models, including gene expression, and oncogenic mutation status...
  26. ncbi request reprint Nutrigenomics: concepts and applications to pharmacogenomics and clinical medicine
    Jim Kaput
    Department of Surgery, University of Illinois Chicago, 909 South Wolcott Street MC 958, Chicago, IL 60612, USA
    Pharmacogenomics 8:369-90. 2007
    ..Nutrigenomic concepts, research strategies and clinical implementation are similar to and overlap those of pharmacogenomics, and both are fundamental to the treatment of disease and maintenance of optimal health...

Research Grants3

  1. In Silico Assesment of Drug Metabolism and Toxicity
    Yuri Nikolsky; Fiscal Year: 2006
    ..These new features and database content will then be marketed to pharmaceutical companies and academia. ..
  2. Systems Biology Platform for Integrative Cancer Biology Research
    Yuri Nikolsky; Fiscal Year: 2008
    ..The system will include novel tools for clustering of cancer patients based on functional descriptors and integration of data of different types based on network topology. [unreadable] [unreadable] [unreadable] [unreadable]..
  3. Systems Biology Platform to Study the Influence of Nutrient Compounds on Cancer D
    Yuri Nikolsky; Fiscal Year: 2008
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