Stefan Wuchty

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Important miRs of pathways in different tumor types
    Stefan Wuchty
    National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Comput Biol 9:e1002883. 2013
  2. pmc Genome-wide associations of signaling pathways in glioblastoma multiforme
    Stefan Wuchty
    National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Med Genomics 6:11. 2013
  3. pmc Involvement of microRNA families in cancer
    Stefan Wuchty
    National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:8219-26. 2012
  4. pmc Shared molecular strategies of the malaria parasite P. falciparum and the human virus HIV-1
    Stefan Wuchty
    National Center of Biotechnology Information, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell Proteomics 10:M111.009035. 2011
  5. pmc Viral organization of human proteins
    Stefan Wuchty
    National Center of Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
    PLoS ONE 5:e11796. 2010
  6. pmc Computational prediction of host-parasite protein interactions between P. falciparum and H. sapiens
    Stefan Wuchty
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 6:e26960. 2011
  7. pmc Prediction of Associations between microRNAs and Gene Expression in Glioma Biology
    Stefan Wuchty
    Neuro Oncology Branch, National Cancer Institute, National Institutes of Neurological Disorder and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 6:e14681. 2011
  8. pmc Cancer missense mutations alter binding properties of proteins and their interaction networks
    Hafumi Nishi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 8:e66273. 2013
  9. pmc Identifying causal genes and dysregulated pathways in complex diseases
    Yoo Ah Kim
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Comput Biol 7:e1001095. 2011
  10. pmc Symmetric Epistasis Estimation (SEE) and its application to dissecting interaction map of Plasmodium falciparum
    Yang Huang
    National Center for Biotechnology Information, NLM, NIH, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
    Mol Biosyst 8:1544-52. 2012

Detail Information

Publications20

  1. pmc Important miRs of pathways in different tumor types
    Stefan Wuchty
    National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS Comput Biol 9:e1002883. 2013
    ..Such gains/losses of miR and gene expression correlation indicated miR/gene pairs that may play a causal role in the underlying cancers...
  2. pmc Genome-wide associations of signaling pathways in glioblastoma multiforme
    Stefan Wuchty
    National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Med Genomics 6:11. 2013
    ..However, genes mediate their biological roles in groups rather than in isolation, prompting us to extend the concept of eQTLs to whole gene pathways...
  3. pmc Involvement of microRNA families in cancer
    Stefan Wuchty
    National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:8219-26. 2012
    ..Further confirming their relevance, predicted cancer miR families are significantly indicated in increasing, non-random numbers of tumor types...
  4. pmc Shared molecular strategies of the malaria parasite P. falciparum and the human virus HIV-1
    Stefan Wuchty
    National Center of Biotechnology Information, National Institutes of Health, Bethesda, MD 20892, USA
    Mol Cell Proteomics 10:M111.009035. 2011
    ..Such an identification of shared molecular strategies by the virus HIV-1 and the eukaryotic intracellular pathogen P. falciparum may allow us to illuminate new avenues of disease intervention...
  5. pmc Viral organization of human proteins
    Stefan Wuchty
    National Center of Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA
    PLoS ONE 5:e11796. 2010
    ....
  6. pmc Computational prediction of host-parasite protein interactions between P. falciparum and H. sapiens
    Stefan Wuchty
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 6:e26960. 2011
    ....
  7. pmc Prediction of Associations between microRNAs and Gene Expression in Glioma Biology
    Stefan Wuchty
    Neuro Oncology Branch, National Cancer Institute, National Institutes of Neurological Disorder and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 6:e14681. 2011
    ....
  8. pmc Cancer missense mutations alter binding properties of proteins and their interaction networks
    Hafumi Nishi
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 8:e66273. 2013
    ..Such observations suggest that genes with mutations directly affecting protein binding properties are preferably located in central network positions and may influence critical nodes and edges in signal transduction networks. ..
  9. pmc Identifying causal genes and dysregulated pathways in complex diseases
    Yoo Ah Kim
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    PLoS Comput Biol 7:e1001095. 2011
    ..While copy number alterations and gene expression data of glioblastoma patients provided opportunities to test our approach, our method can be applied to any disease system where genetic variations play a fundamental causal role...
  10. pmc Symmetric Epistasis Estimation (SEE) and its application to dissecting interaction map of Plasmodium falciparum
    Yang Huang
    National Center for Biotechnology Information, NLM, NIH, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA
    Mol Biosyst 8:1544-52. 2012
    ..falciparum, potentially reflecting host-pathogen interactions or drug-induced selection...
  11. pmc Modeling information flow in biological networks
    Yoo Ah Kim
    National Center for Biotechnology Information, NLM, NIH, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Phys Biol 8:035012. 2011
    ....
  12. pmc FastMEDUSA: a parallelized tool to infer gene regulatory networks
    Serdar Bozdag
    Neuro Oncology Branch, National Cancer Institute, National Institute of Neurological Diseases and Stroke, Bethesda, MD 20892, USA
    Bioinformatics 26:1792-3. 2010
    ..While the determination of a regulatory network of brain tumor in Homo sapiens takes 12 days with MEDUSA, FastMEDUSA obtained the same results in 6 h by utilizing 100 processors...
  13. pmc Controllability in protein interaction networks
    Stefan Wuchty
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892
    Proc Natl Acad Sci U S A 111:7156-60. 2014
    ....
  14. doi request reprint Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology
    Stefan Wuchty
    Neuro Oncology Branch, National Cancer Institute, National Institutes of Neurological Disorder and Stroke, National Institutes of Health, Bethesda, MD 20894, USA
    J Biomed Inform 43:945-52. 2010
    ..In the absence of enrichment of genes that are genomically altered we assume that genetic changes largely exert an indirect rather than direct regulatory influence on a number of tumor-defining regulatory networks...
  15. pmc Large-scale mapping of human protein interactome using structural complexes
    Manoj Tyagi
    National Center for Biotechnology Information, US National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
    EMBO Rep 13:266-71. 2012
    ..Moreover, structurally inferred and high-confidence HTP networks complement each other well, allowing us to construct a merged network to generate testable hypotheses and provide valuable experimental leads...
  16. pmc A comprehensive Plasmodium falciparum protein interaction map reveals a distinct architecture of a core interactome
    Stefan Wuchty
    Northwestern Institute of Complexity, Northwestern University, Evanston, IL 60201, USA
    Proteomics 9:1841-9. 2009
    ..As such, the inference of potential protein interactions and their analysis contributes to our understanding of the parasite, indicating basic pathways and processes as unique targets for therapeutic intervention...
  17. pmc Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum
    Yang Huang
    National Center for Biotechnology Information, NLM, NIH, Bethesda, MD 20894, USA
    Bioinformatics 25:i15-20. 2009
    ..Methods are limited in their ability to illuminate the full structure of the eQTL data. Most rely on an exhaustive, genome scale search that considers all possible locus-gene pairs and tests the linkage between each locus and gene...
  18. pmc eQTL Epistasis - Challenges and Computational Approaches
    Yang Huang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD, USA
    Front Genet 4:51. 2013
    ..This problem is aggravated, when epistatic effects between eQTLs are analyzed. In this review, we discuss recent algorithmic approaches for the detection of eQTL epistasis and highlight lessons that can be learned from current methods...
  19. pmc Computational large-scale mapping of protein-protein interactions using structural complexes
    Benjamin Shoemaker
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland
    Curr Protoc Protein Sci 73:3.9.1-9. 2013
    ..Curr. Protoc. Protein Sci. 73:3.9.1-3.9.9. © 2013 by John Wiley & Sons, Inc. ..
  20. pmc CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations
    Yuri Kotliarov
    Neuro Oncology Branch, National Cancer Institute, National Institutes of Neurological Disorder and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Med Genomics 3:11. 2010
    ....