John Stamatoyannopoulos

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. pmc Identification of higher-order functional domains in the human ENCODE regions
    Robert E Thurman
    Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
    Genome Res 17:917-27. 2007
  2. pmc Human mutation rate associated with DNA replication timing
    John A Stamatoyannopoulos
    Department of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
    Nat Genet 41:393-5. 2009
  3. pmc Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors
    Qian Xiong
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P, R, China
    BMC Genomics 14:587. 2013
  4. pmc Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding
    Ximiao He
    Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Genomics 14:428. 2013
  5. pmc What does our genome encode?
    John A Stamatoyannopoulos
    Departments of Genome Sciences and Medicine, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Genome Res 22:1602-11. 2012
  6. ncbi request reprint Predicting the in vivo signature of human gene regulatory sequences
    William Stafford Noble
    Department of Genome Sciences, University of Washington Seattle, WA, USA
    Bioinformatics 21:i338-43. 2005
  7. pmc Quantifying similarity between motifs
    Shobhit Gupta
    Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA
    Genome Biol 8:R24. 2007
  8. pmc Transcriptional environment and chromatin architecture interplay dictates globin expression patterns of heterospecific hybrids derived from undifferentiated human embryonic stem cells or from their erythroid progeny
    Kai Hsin Chang
    Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA
    Exp Hematol 41:967-979.e6. 2013
  9. pmc Sequencing newly replicated DNA reveals widespread plasticity in human replication timing
    R Scott Hansen
    Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 107:139-44. 2010
  10. ncbi request reprint Unsupervised segmentation of continuous genomic data
    Nathan Day
    Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
    Bioinformatics 23:1424-6. 2007

Research Grants

  1. Site-Specific Recovery of Regulatory Proteins
    John Stamatoyannopoulos; Fiscal Year: 2004
  2. A Comprehensive catalog of human DNasel hypersensitive sites
    John Stamatoyannopoulos; Fiscal Year: 2007
  3. Computational discovery of cis-regulatory sequences
    John Stamatoyannopoulos; Fiscal Year: 2007
  4. Regulatory Genomics of Inflammatory Response Genes
    John Stamatoyannopoulos; Fiscal Year: 2007
  5. Engineered Cell Lines for Regulatory Protein Analysis
    John Stamatoyannopoulos; Fiscal Year: 2004

Collaborators

Detail Information

Publications16

  1. pmc Identification of higher-order functional domains in the human ENCODE regions
    Robert E Thurman
    Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
    Genome Res 17:917-27. 2007
    ..Taken together, our results suggest that higher-order functional domains represent a fundamental organizing principle of human genome architecture...
  2. pmc Human mutation rate associated with DNA replication timing
    John A Stamatoyannopoulos
    Department of Genome Sciences and Medicine, University of Washington, Seattle, WA, USA
    Nat Genet 41:393-5. 2009
    ..This correlation between mutation rate and regionally stratified replication timing may have substantial evolutionary implications...
  3. pmc Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors
    Qian Xiong
    CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P, R, China
    BMC Genomics 14:587. 2013
    ..Several KLFs have been demonstrated to play important roles in hematopoiesis. However, transcriptional regulation of KLFs via CREs, particularly enhancers, in erythroid cells has been poorly understood...
  4. pmc Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding
    Ximiao He
    Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Genomics 14:428. 2013
    ..Recent studies in vertebrates show that many TFs preferentially bind to genomic regions that are well bound by nucleosomes in vitro. Co-occurring secondary motifs sometimes correlated with functional TFBS...
  5. pmc What does our genome encode?
    John A Stamatoyannopoulos
    Departments of Genome Sciences and Medicine, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Genome Res 22:1602-11. 2012
    ..Finally, I consider prospects for the future, including maximizing the accuracy, completeness, and utility of ENCODE data for the community...
  6. ncbi request reprint Predicting the in vivo signature of human gene regulatory sequences
    William Stafford Noble
    Department of Genome Sciences, University of Washington Seattle, WA, USA
    Bioinformatics 21:i338-43. 2005
    ..The ability to discriminate DNaseI HSs computationally would have a major impact on the annotation and utilization of the human genome...
  7. pmc Quantifying similarity between motifs
    Shobhit Gupta
    Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA
    Genome Biol 8:R24. 2007
    ..Experimental simulations demonstrate the accuracy of Tomtom's E values and its effectiveness in finding similar motifs...
  8. pmc Transcriptional environment and chromatin architecture interplay dictates globin expression patterns of heterospecific hybrids derived from undifferentiated human embryonic stem cells or from their erythroid progeny
    Kai Hsin Chang
    Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA
    Exp Hematol 41:967-979.e6. 2013
    ..Our studies provide important insights into the interplay between the transcription environment and existing chromatin domains, and we offer an experimental system to study the time-dependent human globin switching. ..
  9. pmc Sequencing newly replicated DNA reveals widespread plasticity in human replication timing
    R Scott Hansen
    Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 107:139-44. 2010
    ..The data collectively provide a unique, genome-wide picture of the epigenetic compartmentalization of the human genome and suggest that cell-lineage specification involves extensive reprogramming of replication timing patterns...
  10. ncbi request reprint Unsupervised segmentation of continuous genomic data
    Nathan Day
    Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
    Bioinformatics 23:1424-6. 2007
    ..HMMSeg is capable of handling multiple datasets simultaneously, rendering it ideal for integrative analysis of expression, phylogenetic and functional genomic data. AVAILABILITY: http://noble.gs.washington.edu/proj/hmmseg..
  11. pmc A thermodynamic approach to PCR primer design
    Tobias Mann
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    Nucleic Acids Res 37:e95. 2009
    ..Our software is freely available at http://pythia.sourceforge.net...
  12. pmc Mapping and sequencing of structural variation from eight human genomes
    Jeffrey M Kidd
    Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
    Nature 453:56-64. 2008
    ..These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects...
  13. pmc Predicting human nucleosome occupancy from primary sequence
    Shobhit Gupta
    Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
    PLoS Comput Biol 4:e1000134. 2008
    ..The results suggest that the major mechanism of nucleosome positioning in vivo is boundary-event-driven and affirm the classical statistical positioning theory of nucleosome organization...
  14. ncbi request reprint High-throughput localization of functional elements by quantitative chromatin profiling
    Michael O Dorschner
    Department of Molecular Biology, Regulome, 2211 Elliott Avenue, Suite 600, Seattle, Washington 98121, USA
    Nat Methods 1:219-25. 2004
    ....
  15. pmc Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
    Jay R Hesselberth
    Department of Genome Sciences, University of Washington, Seattle, USA
    Nat Methods 6:283-9. 2009
    ..Digital genomic footprinting should be a powerful approach to delineate the cis-regulatory framework of any organism with an available genome sequence...
  16. pmc Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries
    Peter J Sabo
    Department of Molecular Biology, Regulome, Canal View Building, 551 North 34th Street, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 101:4537-42. 2004
    ..The results permit a quantitative approximation of the distribution of HSs and classical cis-regulatory sequences in the human genome...

Research Grants15

  1. Site-Specific Recovery of Regulatory Proteins
    John Stamatoyannopoulos; Fiscal Year: 2004
    ..In Phase II studies, mass spectrometric analyses will be performed on recovered protein substrates. Analyses will be performed on additional cis-regulatory systems, including those known to be involved in specific diseases. ..
  2. A Comprehensive catalog of human DNasel hypersensitive sites
    John Stamatoyannopoulos; Fiscal Year: 2007
    ..Validation of DHS functional classes will be accomplished using well-tested cell and transgenic assays of biological function (Specific Aim 5). ..
  3. Computational discovery of cis-regulatory sequences
    John Stamatoyannopoulos; Fiscal Year: 2007
    ..The resulting database will be of incalculable value in furthering the study of the regulation of human genes and the computational methodologies employed therein. ..
  4. Regulatory Genomics of Inflammatory Response Genes
    John Stamatoyannopoulos; Fiscal Year: 2007
    ..abstract_text> ..
  5. Engineered Cell Lines for Regulatory Protein Analysis
    John Stamatoyannopoulos; Fiscal Year: 2004
    ..Fractionation over sucrose gradients has the added advantage of providing a clean reagent for downstream mass spectrometric studies. Such studies are envisioned to form the basis of a follow-on Phase II proposal. ..