Joshua M Stuart

Summary

Affiliation: University of California
Country: USA

Publications

  1. doi request reprint Large-scale cytological profiling for functional analysis of bioactive compounds
    Marcos H Woehrmann
    Department of Biomolecular Engineering, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Mol Biosyst 9:2604-17. 2013
  2. pmc A global analysis of genetic interactions in Caenorhabditis elegans
    Alexandra B Byrne
    Department of Medical Genetics and Microbiology, The Terrence Donnelly Centre for Cellular and Biomolecular Research, 160 College St, University of Toronto, Toronto, ON, M5S 3E1, Canada
    J Biol 6:8. 2007
  3. pmc The UCSC Interaction Browser: multidimensional data views in pathway context
    Christopher K Wong
    Biomolecular Engineering Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 41:W218-24. 2013
  4. pmc Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
    Evan O Paull
    Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, Department of Systems Biology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115 and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
    Bioinformatics 29:2757-64. 2013
  5. pmc The UCSC Cancer Genomics Browser: update 2011
    J Zachary Sanborn
    Department of Biomolecular Engineering, Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 39:D951-9. 2011
  6. pmc Information-based methods for predicting gene function from systematic gene knock-downs
    Matthew T Weirauch
    Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
    BMC Bioinformatics 9:463. 2008
  7. pmc PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis
    Sam Ng
    Department of Biomolecular Engineering and CBSE, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Bioinformatics 28:i640-i646. 2012
  8. pmc RADIA: RNA and DNA integrated analysis for somatic mutation detection
    Amie J Radenbaugh
    University of California Santa Cruz Genomics Institute, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
    PLoS ONE 9:e111516. 2014
  9. pmc A factor graph nested effects model to identify networks from genetic perturbations
    Charles J Vaske
    Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California, United States of America
    PLoS Comput Biol 5:e1000274. 2009
  10. pmc The synthetic genetic interaction network reveals small molecules that target specific pathways in Sacchromyces cerevisiae
    Craig M Tamble
    Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA
    Mol Biosyst 7:2019-30. 2011

Collaborators

Detail Information

Publications17

  1. doi request reprint Large-scale cytological profiling for functional analysis of bioactive compounds
    Marcos H Woehrmann
    Department of Biomolecular Engineering, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Mol Biosyst 9:2604-17. 2013
    ..The resulting analysis suggests a strategy for probing the biological functions of specific kinases by compiling cytological data from inhibitors of varying specificities. ..
  2. pmc A global analysis of genetic interactions in Caenorhabditis elegans
    Alexandra B Byrne
    Department of Medical Genetics and Microbiology, The Terrence Donnelly Centre for Cellular and Biomolecular Research, 160 College St, University of Toronto, Toronto, ON, M5S 3E1, Canada
    J Biol 6:8. 2007
    ..Here, we describe a reliable high-throughput approach capable of revealing both weak and strong genetic interactions in the nematode Caenorhabditis elegans...
  3. pmc The UCSC Interaction Browser: multidimensional data views in pathway context
    Christopher K Wong
    Biomolecular Engineering Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 41:W218-24. 2013
    ....
  4. pmc Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
    Evan O Paull
    Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, Department of Systems Biology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115 and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA
    Bioinformatics 29:2757-64. 2013
    ..The method computes a subnetwork of protein-protein interactions, predicted transcription factor-to-target connections and curated interactions from literature that connects genomic and transcriptomic perturbations...
  5. pmc The UCSC Cancer Genomics Browser: update 2011
    J Zachary Sanborn
    Department of Biomolecular Engineering, Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 39:D951-9. 2011
    ..The browser is integrated with the UCSC Genome Browser; thus inheriting and integrating the Genome Browser's rich set of human biology and genetics data that enhances the interpretability of the cancer genomics data...
  6. pmc Information-based methods for predicting gene function from systematic gene knock-downs
    Matthew T Weirauch
    Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
    BMC Bioinformatics 9:463. 2008
    ..An open question is how to optimally make use of phenotypic observations, possibly in combination with other functional genomics datasets, to identify genes that share a common role...
  7. pmc PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis
    Sam Ng
    Department of Biomolecular Engineering and CBSE, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Bioinformatics 28:i640-i646. 2012
    ..The method uses a belief-propagation algorithm to infer gene activity from gene expression and copy number data in the context of a set of pathway interactions...
  8. pmc RADIA: RNA and DNA integrated analysis for somatic mutation detection
    Amie J Radenbaugh
    University of California Santa Cruz Genomics Institute, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
    PLoS ONE 9:e111516. 2014
    ..Finally, we highlight mutations in important cancer genes that were rescued due to the incorporation of the RNA. ..
  9. pmc A factor graph nested effects model to identify networks from genetic perturbations
    Charles J Vaske
    Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California, United States of America
    PLoS Comput Biol 5:e1000274. 2009
    ..Nested effects models may be a powerful tool for inferring regulatory connections and genes that operate in normal and disease-related processes...
  10. pmc The synthetic genetic interaction network reveals small molecules that target specific pathways in Sacchromyces cerevisiae
    Craig M Tamble
    Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA
    Mol Biosyst 7:2019-30. 2011
    ..When assayed in human HCT-116 colorectal cancer cells, 1A08 caused DNA-damage resistant DNA synthesis and blocked the DNA-damage checkpoint selectively in S-phase...
  11. pmc ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES
    Artem Sokolov
    Department of Biomolecular Engineering, University of California Santa Cruz, USA
    Pac Symp Biocomput 21:405-16. 2016
    ..In addition, we use a one-class predictor to quantitatively associate an embryonic stem cell signature with an aggressive breast cancer subtype that reveals shared stemness pathways potentially important for treatment. ..
  12. pmc Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
    Charles J Vaske
    Howard Hughes Medical Institute, UC Santa Cruz, CA, USA
    Bioinformatics 26:i237-45. 2010
    ..It is therefore critical to identify relevant pathways involved in cancer progression and detect how they are altered in different patients...
  13. pmc Molecular signatures of quiescent, mobilized and leukemia-initiating hematopoietic stem cells
    E Camilla Forsberg
    Institute for Biology of Stem Cells, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
    PLoS ONE 5:e8785. 2010
    ..These results identify potential key regulators of HSC and give insights into the clinically important processes of HSC mobilization for transplantation and leukemic development from cancer stem cells...
  14. doi request reprint HALO384: a halo-based potency prediction algorithm for high-throughput detection of antimicrobial agents
    Marcos H Woehrmann
    Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, California, USA
    J Biomol Screen 15:196-205. 2010
    ..These results suggest that the HT halo assay provides a rapid and inexpensive way to screen for bioactivity in multiple microorganisms...
  15. pmc A search engine to identify pathway genes from expression data on multiple organisms
    Chunnuan Chen
    Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
    BMC Syst Biol 1:20. 2007
    ..In many cases, the coregulatation of a set of genes across a set of conditions can be used to infer roles for genes of unknown function...
  16. pmc Molecular pathways: extracting medical knowledge from high-throughput genomic data
    Theodore C Goldstein
    Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
    Clin Cancer Res 19:3114-20. 2013
    ....
  17. pmc Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum
    Aaron E Cozen
    Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
    J Bacteriol 191:782-94. 2009
    ..The complete gene expression data set can be viewed in genomic context with the Archaeal Genome Browser at archaea.ucsc.edu...