Affiliation: St. Joseph
- Biological networks and analysis of experimental data in drug discoveryYuri 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...
- Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genesW 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...
- Manual annotation of protein interactionsSvetlana 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...
- Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysisRobert 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...
- Effect of training-sample size and classification difficulty on the accuracy of genomic predictorsVlad Popovici
Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Genopode Building, Quartier Sorge, Lausanne CH 1015, Switzerland
Breast Cancer Res 12:R5. 2010....
- Integrated network analysis of transcriptomic and proteomic data in psoriasisEleonora 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...
- Network analysis of human glaucomatous optic nerve head astrocytesTatiana 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...
- Transcriptional networks in plasmacytoid dendritic cells stimulated with synthetic TLR 7 agonistsWoubalem 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...
- The transcriptomic signature of fasting murine liverMilka 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...
- Fasting induces a biphasic adaptive metabolic response in murine small intestineMilka 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...
- Bimodal gene expression patterns in breast cancerMarina 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...
- Identifying disease-specific genes based on their topological significance in protein networksZoltan 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...
- Functional analysis of OMICs data and small molecule compounds in an integrated "knowledge-based" platformYuri Nikolsky
GeneGo, Inc, Saint Joseph, MI, USA
Methods Mol Biol 563:177-96. 2009....
- Genome-wide functional synergy between amplified and mutated genes in human breast cancerYuri 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...
- Pathway mapping tools for analysis of high content dataSean 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...
- Functional synergies yet distinct modulators affected by genetic alterations in common human cancersMarina 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...
- Quantitative knowledge-based analysis in compound safety assessmentSvetlana 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...
- A comprehensive functional analysis of tissue specificity of human gene expressionZoltan 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...
- A novel method for generation of signature networks as biomarkers from complex high throughput dataYuri 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...
- Early prediction of drug metabolism and toxicity: systems biology approach and modelingAndrej 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...
- Characteristics of genomic signatures derived using univariate methods and mechanistically anchored functional descriptors for predicting drug- and xenobiotic-induced nephrotoxicityWeiwei 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...
- Techniques: application of systems biology to absorption, distribution, metabolism, excretion and toxicitySean 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...
- Systems biology approaches to the study of cardiovascular drugsYuri 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...
- Modeling of human cytochrome p450-mediated drug metabolism using unsupervised machine learning approachDmitry 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...
- Genomic characterization of explant tumorgraft models derived from fresh patient tumor tissueDavid 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...
- Nutrigenomics: concepts and applications to pharmacogenomics and clinical medicineJim 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...
- In Silico Assesment of Drug Metabolism and ToxicityYuri Nikolsky; Fiscal Year: 2006..These new features and database content will then be marketed to pharmaceutical companies and academia. ..
- Systems Biology Platform for Integrative Cancer Biology ResearchYuri 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]..
- Systems Biology Platform to Study the Influence of Nutrient Compounds on Cancer DYuri Nikolsky; Fiscal Year: 2008..unreadable] [unreadable] [unreadable]..