Alla Karnovsky

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. pmc Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data
    Alla Karnovsky
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 2218, USA
    Bioinformatics 28:373-80. 2012
  2. pmc Epithelial-mesenchymal transition-associated secretory phenotype predicts survival in lung cancer patients
    Ajaya Kumar Reka
    Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine and Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA, MS Bioworks, LLC, Ann Arbor, MI 48108, USA, Department of Biostatistics, Rutgers School of Public Health, Piscataway, NJ 08854, USA and Center for Computational Medicine and Bioinformatics and Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, MI 48109, USA
    Carcinogenesis 35:1292-300. 2014
  3. pmc Molecular characterization of the endoplasmic reticulum: insights from proteomic studies
    Xuequn Chen
    Department of Molecular and Integrative Physiology, The University of Michigan, Ann Arbor, MI, USA
    Proteomics 10:4040-52. 2010
  4. ncbi request reprint MetDisease-connecting metabolites to diseases via literature
    William Duren
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Departments of Medicine and Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA and Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 30:2239-41. 2014
  5. pmc LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types
    Jung H Kim
    Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
    BMC Genomics 13:526. 2012
  6. pmc ConceptGen: a gene set enrichment and gene set relation mapping tool
    Maureen A Sartor
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 26:456-63. 2010
  7. pmc Convergence of genetic influences in comorbidity
    Richard C McEachin
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48105, USA
    BMC Bioinformatics 13:S8. 2012
  8. pmc Metabolic consequences of sepsis-induced acute lung injury revealed by plasma ¹H-nuclear magnetic resonance quantitative metabolomics and computational analysis
    Kathleen A Stringer
    Dept of Clinical, Social, and Administrative Sciences, Univ of Michigan, Ann Arbor, 48109 1065, USA
    Am J Physiol Lung Cell Mol Physiol 300:L4-L11. 2011
  9. pmc Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks
    Jing Gao
    National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 26:971-3. 2010
  10. pmc Metab2MeSH: annotating compounds with medical subject headings
    Maureen A Sartor
    National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 28:1408-10. 2012

Collaborators

Detail Information

Publications11

  1. pmc Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data
    Alla Karnovsky
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 2218, USA
    Bioinformatics 28:373-80. 2012
    ..g. transcriptomics, proteomics), and incorporate prior knowledge of pathways and molecular interactions...
  2. pmc Epithelial-mesenchymal transition-associated secretory phenotype predicts survival in lung cancer patients
    Ajaya Kumar Reka
    Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine and Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA, MS Bioworks, LLC, Ann Arbor, MI 48108, USA, Department of Biostatistics, Rutgers School of Public Health, Piscataway, NJ 08854, USA and Center for Computational Medicine and Bioinformatics and Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, MI 48109, USA
    Carcinogenesis 35:1292-300. 2014
    ..These results demonstrate that integrative analysis of the critical biological process of EMT provides mechanism-based and clinically relevant biomarkers with significant prognostic value...
  3. pmc Molecular characterization of the endoplasmic reticulum: insights from proteomic studies
    Xuequn Chen
    Department of Molecular and Integrative Physiology, The University of Michigan, Ann Arbor, MI, USA
    Proteomics 10:4040-52. 2010
    ....
  4. ncbi request reprint MetDisease-connecting metabolites to diseases via literature
    William Duren
    Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Departments of Medicine and Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA and Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 30:2239-41. 2014
    ..Availability and implementation: MetDisease can be downloaded from http://apps.cytoscape.org/apps/metdisease or installed via the Cytoscape app manager. Further information about MetDisease can be found at http://metdisease.ncibi.org..
  5. pmc LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types
    Jung H Kim
    Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
    BMC Genomics 13:526. 2012
    ..The ability of our logistic regression-based gene set enrichment method to implicate important biological pathways in high-throughput data is well established...
  6. pmc ConceptGen: a gene set enrichment and gene set relation mapping tool
    Maureen A Sartor
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 26:456-63. 2010
    ..Accomplishing these tasks requires a unified framework for agglomeration of data from various genomic resources, novel visualizations, and user functionality...
  7. pmc Convergence of genetic influences in comorbidity
    Richard C McEachin
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48105, USA
    BMC Bioinformatics 13:S8. 2012
    ..The Rank Product (RP) method overcomes limitations posed by Fisher assumptions, though RP was not designed for GWA data...
  8. pmc Metabolic consequences of sepsis-induced acute lung injury revealed by plasma ¹H-nuclear magnetic resonance quantitative metabolomics and computational analysis
    Kathleen A Stringer
    Dept of Clinical, Social, and Administrative Sciences, Univ of Michigan, Ann Arbor, 48109 1065, USA
    Am J Physiol Lung Cell Mol Physiol 300:L4-L11. 2011
    ..In addition, it justifies the continued study of this approach to determine whether sepsis-induced ALI has a distinct metabolic phenotype and whether there are predictive biomarkers of severity and outcome in these patients...
  9. pmc Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks
    Jing Gao
    National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 26:971-3. 2010
    ..Color and size of the nodes are used to visualize these dynamic changes. Metscape can display the entire metabolic network or any of the pathway-specific networks that exist in the database...
  10. pmc Metab2MeSH: annotating compounds with medical subject headings
    Maureen A Sartor
    National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 28:1408-10. 2012
    ..These annotations provide links from compounds to biomedical literature and complement existing resources such as PubChem and the Human Metabolome Database...
  11. pmc Quantitative organellar proteomics analysis of rough endoplasmic reticulum from normal and acute pancreatitis rat pancreas
    Xuequn Chen
    Departments of Molecular and Integrative Physiology, The University of Michigan, Ann Arbor, Michigan 48109, USA
    J Proteome Res 9:885-96. 2010
    ..These results suggest that the early stages of AP involve changes of multiple RER proteins that may affect the synthesis and processing of digestive enzymes...