Boris Adryan

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. pmc BioSAVE: display of scored annotation within a sequence context
    Richard F Pollock
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
    BMC Bioinformatics 9:157. 2008
  2. ncbi request reprint FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster
    Boris Adryan
    MRC Laboratory of Molecular Biology Cambridge CB2 2QH, UK
    Bioinformatics 22:1532-3. 2006
  3. pmc Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila
    Boris Adryan
    Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
    Genome Biol 8:R167. 2007
  4. pmc Stability and dynamics of polycomb target sites in Drosophila development
    Camilla Kwong
    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
    PLoS Genet 4:e1000178. 2008
  5. pmc CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex
    Eimear E Holohan
    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
    PLoS Genet 3:e112. 2007
  6. pmc FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database
    Ulrike Pfreundt
    Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
    Nucleic Acids Res 38:D443-7. 2010
  7. pmc Specificity of Notch pathway activation: twist controls the transcriptional output in adult muscle progenitors
    Fred Bernard
    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
    Development 137:2633-42. 2010
  8. pmc GRiP: a computational tool to simulate transcription factor binding in prokaryotes
    Nicolae Radu Zabet
    Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, UK
    Bioinformatics 28:1287-9. 2012
  9. doi request reprint Computational models for large-scale simulations of facilitated diffusion
    Nicolae Radu Zabet
    Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1QR, UK
    Mol Biosyst 8:2815-27. 2012
  10. pmc Biases in Drosophila melanogaster protein trap screens
    Jelena Aleksic
    Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
    BMC Genomics 10:249. 2009

Detail Information

Publications19

  1. pmc BioSAVE: display of scored annotation within a sequence context
    Richard F Pollock
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK
    BMC Bioinformatics 9:157. 2008
    ..Unfortunately, many visualisation solutions are somewhat static in the way they handle such score cutoffs...
  2. ncbi request reprint FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster
    Boris Adryan
    MRC Laboratory of Molecular Biology Cambridge CB2 2QH, UK
    Bioinformatics 22:1532-3. 2006
    ..We propose a set of 753 TFs in the fruit fly, of which 23 are confident novel predictions of this function for previously uncharacterized proteins...
  3. pmc Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila
    Boris Adryan
    Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
    Genome Biol 8:R167. 2007
    ..Immunolocalization studies suggest that there are several hundred Su(Hw) sites in the genome, but few of these endogenous Su(Hw) binding sites have been identified...
  4. pmc Stability and dynamics of polycomb target sites in Drosophila development
    Camilla Kwong
    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
    PLoS Genet 4:e1000178. 2008
    ..Pc/Pho binding does not preclude transcription, but levels of Pc/Pho binding change during development, and loss of Pc/Pho binding can be associated with both stable gene activity and inactivity...
  5. pmc CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex
    Eimear E Holohan
    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
    PLoS Genet 3:e112. 2007
    ..Comparison of the locations of the CTCF sites with characterised Polycomb target sites and histone modification provides support for the domain model of BX-C regulation...
  6. pmc FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database
    Ulrike Pfreundt
    Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
    Nucleic Acids Res 38:D443-7. 2010
    ....
  7. pmc Specificity of Notch pathway activation: twist controls the transcriptional output in adult muscle progenitors
    Fred Bernard
    Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
    Development 137:2633-42. 2010
    ....
  8. pmc GRiP: a computational tool to simulate transcription factor binding in prokaryotes
    Nicolae Radu Zabet
    Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, UK
    Bioinformatics 28:1287-9. 2012
    ..We developed a comprehensive computational model of this process and estimated the model parameters in (N.R.Zabet and B.Adryan, submitted for publication)...
  9. doi request reprint Computational models for large-scale simulations of facilitated diffusion
    Nicolae Radu Zabet
    Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1QR, UK
    Mol Biosyst 8:2815-27. 2012
    ..Finally, we review which biological parameters need to be included in such computational models in order to obtain a detailed representation of the actual process...
  10. pmc Biases in Drosophila melanogaster protein trap screens
    Jelena Aleksic
    Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
    BMC Genomics 10:249. 2009
    ..Despite recent efforts aimed at achieving comprehensive coverage of the genes encoded in the Drosophila genome, the repertoire of genes that yield protein traps is still small...
  11. pmc Scoring overlapping and adjacent signals from genome-wide ChIP and DamID assays
    Audrey Qiuyan Fu
    Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, UK
    Mol Biosyst 5:1429-38. 2009
    ..We provide a simple guide to some of the statistical tools used by these methods...
  12. pmc The developmental expression dynamics of Drosophila melanogaster transcription factors
    Boris Adryan
    Computational Biology Group, Structural Studies Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Genome Biol 11:R40. 2010
    ..Their binding to cis-regulatory modules of target genes mediates the precise cell- and context-specific activation and repression of genes. The expression of TFs should therefore reflect the core expression program of each cell...
  13. pmc A comprehensive computational model of facilitated diffusion in prokaryotes
    Nicolae Radu Zabet
    Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, UK
    Bioinformatics 28:1517-24. 2012
    ..Gene activity is mediated by site-specific transcription factors (TFs). Their binding to defined regions in the genome determines the rate at which their target genes are transcribed...
  14. pmc New androgen receptor genomic targets show an interaction with the ETS1 transcription factor
    Charles E Massie
    Uro Oncology Research Group, Department of Oncology, University of Cambridge, Cancer Research UK Cambridge, Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    EMBO Rep 8:871-8. 2007
    ..Binding sequences for the avian erythroblastosis virus E26 homologue (ETS) transcription factor family were also highly enriched, and we uncovered an interaction between the AR and ETS1 at a subset of AR promoter targets...
  15. pmc A graphical modelling approach to the dissection of highly correlated transcription factor binding site profiles
    Robert Stojnic
    Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
    PLoS Comput Biol 8:e1002725. 2012
    ....
  16. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew G Clark
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
    Nature 450:203-18. 2007
    ..These may prove to underlie differences in the ecology and behaviour of these diverse species...
  17. ncbi request reprint Identification of FGF-dependent genes in the Drosophila tracheal system
    Markus Stahl
    Department of Molecular Developmental Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
    Gene Expr Patterns 7:202-9. 2007
    ..Thus, we identified and confirmed by quantitative PCR 13 Bnl-dependent genes that are expressed in cells within and outside of the tracheal system...
  18. ncbi request reprint Gene-Ontology-based clustering of gene expression data
    Boris Adryan
    Department of Molecular Developmental Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany
    Bioinformatics 20:2851-2. 2004
    ..GO-Cluster uses the tree structure of the Gene Ontology database as a framework for numerical clustering, and thus allowing a simple visualization of gene expression data at various levels of the ontology tree...
  19. pmc Drosophila awd, the homolog of human nm23, regulates FGF receptor levels and functions synergistically with shi/dynamin during tracheal development
    Vincent Dammai
    Department of Pathology and Laboratory Medicine, and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425, USA
    Genes Dev 17:2812-24. 2003
    ..Thus, we propose that awd regulates tracheal cell motility by modulating the FGFR levels, through a dynamin-mediated pathway...