Hamid Bolouri

Summary

Affiliation: Fred Hutchinson Cancer Research Center
Country: USA

Publications

  1. ncbi request reprint Modeling genomic regulatory networks with big data
    Hamid Bolouri
    Division of Human Biology, Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, PO Box 19024, Seattle, WA 98109, USA Electronic address
    Trends Genet 30:182-91. 2014
  2. doi request reprint Integration of 198 ChIP-seq datasets reveals human cis-regulatory regions
    Hamid Bolouri
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    J Comput Biol 19:989-97. 2012
  3. pmc Menu-driven cloud computing and resource sharing for R and Bioconductor
    Hamid Bolouri
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 27:2309-10. 2011
  4. pmc A data integration methodology for systems biology
    Daehee Hwang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 102:17296-301. 2005
  5. pmc The Innate Immune Database (IIDB)
    Martin Korb
    Institute for Systems Biology, 1441 North 34thStreet, Seattle, Washington 98103 8904, USA
    BMC Immunol 9:7. 2008
  6. pmc Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism
    Jennifer J Smith
    Institute for Systems Biology, Yeast Group, Seattle, WA 98103 8904, USA
    Mol Syst Biol 2:2006.0009. 2006
  7. ncbi request reprint Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast
    Stephen A Ramsey
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    Nat Genet 38:1082-7. 2006
  8. ncbi request reprint Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4
    Mark Gilchrist
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Nature 441:173-8. 2006
  9. pmc A gene regulatory network armature for T lymphocyte specification
    Constantin Georgescu
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 105:20100-5. 2008
  10. pmc A data integration methodology for systems biology: experimental verification
    Daehee Hwang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 102:17302-7. 2005

Collaborators

Detail Information

Publications13

  1. ncbi request reprint Modeling genomic regulatory networks with big data
    Hamid Bolouri
    Division of Human Biology, Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, PO Box 19024, Seattle, WA 98109, USA Electronic address
    Trends Genet 30:182-91. 2014
    ..iii) Integrative computational analysis of large-scale datasets is becoming a fundamental component of molecular biology. I discuss current and near-term opportunities and challenges related to these three points. ..
  2. doi request reprint Integration of 198 ChIP-seq datasets reveals human cis-regulatory regions
    Hamid Bolouri
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    J Comput Biol 19:989-97. 2012
    ..broadinstitute.org/genome_bio/human_lincrnas/). Our investigation used approximately half of all currently available ENCODE ChIP-seq datasets, suggesting further gains are likely from analysis of all datasets currently available...
  3. pmc Menu-driven cloud computing and resource sharing for R and Bioconductor
    Hamid Bolouri
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Bioinformatics 27:2309-10. 2011
    ..All CRdata services are provided via point-and-click menus...
  4. pmc A data integration methodology for systems biology
    Daehee Hwang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 102:17296-301. 2005
    ..In an accompanying companion paper, we demonstrate the applicability of our approach to biological data. We have integrated our methodology into a free open source software package named POINTILLIST...
  5. pmc The Innate Immune Database (IIDB)
    Martin Korb
    Institute for Systems Biology, 1441 North 34thStreet, Seattle, Washington 98103 8904, USA
    BMC Immunol 9:7. 2008
    ..It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens...
  6. pmc Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism
    Jennifer J Smith
    Institute for Systems Biology, Yeast Group, Seattle, WA 98103 8904, USA
    Mol Syst Biol 2:2006.0009. 2006
    ..Statistical analyses of these and other global data sets suggest that the utilization of distinct control mechanisms for the execution of morphological versus metabolic responses is widespread...
  7. ncbi request reprint Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast
    Stephen A Ramsey
    Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA
    Nat Genet 38:1082-7. 2006
    ....
  8. ncbi request reprint Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4
    Mark Gilchrist
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Nature 441:173-8. 2006
    ..Because ATF3 is itself induced by lipopolysaccharide, it seems to regulate TLR-stimulated inflammatory responses as part of a negative-feedback loop...
  9. pmc A gene regulatory network armature for T lymphocyte specification
    Constantin Georgescu
    Division of Biology 156 29, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 105:20100-5. 2008
    ..1 activity based on Notch activity, the lack of direct opposition between PU.1 and GATA-3, and the need for a distinct, late-acting repressive function or functions to extinguish stem and progenitor-derived regulatory gene expression...
  10. pmc A data integration methodology for systems biology: experimental verification
    Daehee Hwang
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 102:17302-7. 2005
    ..The methodology described here, addresses a critical need across all domains of molecular and cell biology, to effectively integrate large and disparate data sets...
  11. pmc The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example
    Hamid Bolouri
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Dev Biol 340:170-8. 2010
    ....
  12. pmc Visualization, documentation, analysis, and communication of large-scale gene regulatory networks
    William J R Longabaugh
    Institute for Systems Biology, Seattle, WA 98103 8904, USA
    Biochim Biophys Acta 1789:363-74. 2009
    ..We also outline our future development plans, and give some examples of current applications of BioTapestry...
  13. doi request reprint Embryonic pattern formation without morphogens
    Hamid Bolouri
    Institute for Systems Biology, Seattle, 1441 N 34th St, Seattle WA 98103, USA
    Bioessays 30:412-7. 2008
    ..Remarkably, this moving ring of gene expression has now been shown to be controlled entirely by transcriptional cis-regulatory logic.1...