Paul Bertone

Summary

Affiliation: Yale University
Country: USA

Publications

  1. ncbi request reprint Advances in functional protein microarray technology
    Paul Bertone
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    FEBS J 272:5400-11. 2005
  2. ncbi request reprint Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery
    Paul Bertone
    Department of Molecular, Cellular, and Developmental Biology Yale University, New Haven, CT 06520 8103, USA
    Chromosome Res 13:259-74. 2005
  3. pmc CREB binds to multiple loci on human chromosome 22
    Ghia Euskirchen
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8005, USA gt
    Mol Cell Biol 24:3804-14. 2004
  4. pmc Distribution of NF-kappaB-binding sites across human chromosome 22
    Rebecca Martone
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 8005, USA
    Proc Natl Acad Sci U S A 100:12247-52. 2003
  5. pmc Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
    Thomas E Royce
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Trends Genet 21:466-75. 2005
  6. ncbi request reprint Global identification of human transcribed sequences with genome tiling arrays
    Paul Bertone
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 8103, USA
    Science 306:2242-6. 2004
  7. pmc Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes
    Nathaniel Echols
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Box 208114, New Haven, CT 06520 8114, USA
    Nucleic Acids Res 30:2515-23. 2002
  8. pmc ExpressYourself: A modular platform for processing and visualizing microarray data
    Nicholas M Luscombe
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, PO Box 208114, New Haven CT 06520 8114, USA
    Nucleic Acids Res 31:3477-82. 2003
  9. pmc Global changes in STAT target selection and transcription regulation upon interferon treatments
    Stephen E Hartman
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Genes Dev 19:2953-68. 2005
  10. pmc Target hub proteins serve as master regulators of development in yeast
    Anthony R Borneman
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
    Genes Dev 20:435-48. 2006

Collaborators

Detail Information

Publications25

  1. ncbi request reprint Advances in functional protein microarray technology
    Paul Bertone
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    FEBS J 272:5400-11. 2005
    ..This technology holds great potential for basic molecular biology research, disease marker identification, toxicological response profiling and pharmaceutical target screening...
  2. ncbi request reprint Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery
    Paul Bertone
    Department of Molecular, Cellular, and Developmental Biology Yale University, New Haven, CT 06520 8103, USA
    Chromosome Res 13:259-74. 2005
    ....
  3. pmc CREB binds to multiple loci on human chromosome 22
    Ghia Euskirchen
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8005, USA gt
    Mol Cell Biol 24:3804-14. 2004
    ..Our results provide novel molecular insights into how CREB mediates its functions in humans...
  4. pmc Distribution of NF-kappaB-binding sites across human chromosome 22
    Rebecca Martone
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 8005, USA
    Proc Natl Acad Sci U S A 100:12247-52. 2003
    ....
  5. pmc Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
    Thomas E Royce
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Trends Genet 21:466-75. 2005
    ..We introduce the informatics challenges arising in the analysis of tiling microarray experiments as open problems to the scientific community and present initial approaches for the analysis of this nascent technology...
  6. ncbi request reprint Global identification of human transcribed sequences with genome tiling arrays
    Paul Bertone
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 8103, USA
    Science 306:2242-6. 2004
    ..A large fraction of these are located in intergenic regions distal from previously annotated genes and exhibit significant homology to other mammalian proteins...
  7. pmc Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes
    Nathaniel Echols
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Box 208114, New Haven, CT 06520 8114, USA
    Nucleic Acids Res 30:2515-23. 2002
    ..Our compositional analyses with the interactive viewer are available over the web at http://genecensus.org/pseudogene...
  8. pmc ExpressYourself: A modular platform for processing and visualizing microarray data
    Nicholas M Luscombe
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, PO Box 208114, New Haven CT 06520 8114, USA
    Nucleic Acids Res 31:3477-82. 2003
    ..The program is freely available for use at http://bioinfo.mbb.yale.edu/expressyourself...
  9. pmc Global changes in STAT target selection and transcription regulation upon interferon treatments
    Stephen E Hartman
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Genes Dev 19:2953-68. 2005
    ..Overall, our results reveal a wealth of new information regarding IFN/STAT-binding targets and also fundamental insights into mechanisms of regulation of gene expression in different cell states...
  10. pmc Target hub proteins serve as master regulators of development in yeast
    Anthony R Borneman
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
    Genes Dev 20:435-48. 2006
    ..Our results indicate that target hubs can serve as master regulators whose activity is sufficient for the induction of complex developmental responses and therefore represent important regulatory nodes in biological networks...
  11. ncbi request reprint SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes
    Suganthi Balasubramanian
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520 8114, USA
    Pharmacogenomics 3:393-402. 2002
    ..This could imply that protein structures, in general, can tolerate a wide degree of substitutions. Tables relating to our results are available from http://genecensus.org/pseudogene...
  12. pmc The transcriptional activity of human Chromosome 22
    John L Rinn
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
    Genes Dev 17:529-40. 2003
    ..mbb.yale.edu/chr22...
  13. pmc Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
    Yoav Gilad
    Yale University School of Medicine, Department of Genetics, Yale University, New Haven, CT 06520, USA
    Genome Res 15:674-80. 2005
    ..Our results indicate that naive use of single-species arrays in direct interspecies comparisons can yield spurious results...
  14. pmc Design optimization methods for genomic DNA tiling arrays
    Paul Bertone
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CN 06520, USA P50 HG02357
    Genome Res 16:271-81. 2006
    ..A Web resource has also been developed, accessible at http://tiling.gersteinlab.org, to generate optimal tile paths from user-provided DNA sequences...
  15. pmc Identification of pseudogenes in the Drosophila melanogaster genome
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, PO Box 208114, New Haven, CT 06520 8114, USA
    Nucleic Acids Res 31:1033-7. 2003
    ..The data are useful for molecular evolution study in Drosophila...
  16. pmc SPINE 2: a system for collaborative structural proteomics within a federated database framework
    Chern Sing Goh
    Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
    Nucleic Acids Res 31:2833-8. 2003
    ..g. crystallization LIMS local to particular laboratories) and (iii) international archival resources that SPINE links to and passes on information to (e.g. TargetDB at the PDB)...
  17. pmc Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
    Christine E Horak
    Department of Molecular, Cellular, and Developmental Biology, Connecticut 06520 8103, USA
    Genes Dev 16:3017-33. 2002
    ....
  18. pmc Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22
    Paul M Harrison
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Genome Res 12:272-80. 2002
    ..Finally, we find that chromosome 22 pseudogene population is dominated by immunoglobulin segments, which have a greater rate of disablement per amino acid than the other pseudogene populations and are also substantially more diverged...
  19. pmc Prospects and challenges in proteomics
    Paul Bertone
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
    Plant Physiol 138:560-2. 2005
  20. pmc Structural genomics: a new era for pharmaceutical research
    Yang Liu
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA
    Genome Biol 3:REPORTS4004. 2002
  21. ncbi request reprint An integrated approach for finding overlooked genes in yeast
    Anuj Kumar
    Department of Molecular, Cellular, and Developmental Biology, Yale University, P O Box 208103, New Haven, CT 06520 8103, USA
    Nat Biotechnol 20:58-63. 2002
    ..In total, the genes discovered using this approach constitute 2% of the yeast genome and represent a wealth of overlooked biology...
  22. ncbi request reprint Fast optimal genome tiling with applications to microarray design and homology search
    Piotr Berman
    Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA
    J Comput Biol 11:766-85. 2004
    ..Finally, computational results from applying our tiling algorithms to genomic sequences of five model eukaryotes are reported...
  23. ncbi request reprint Transcriptional regulatory networks in bacteria: from input signals to output responses
    Aswin S N Seshasayee
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
    Curr Opin Microbiol 9:511-9. 2006
    ..Eventually, these components of the regulatory system could be assembled to describe complex bacterial behaviour at the level of whole organisms...
  24. doi request reprint Modeling of C/EBPalpha mutant acute myeloid leukemia reveals a common expression signature of committed myeloid leukemia-initiating cells
    Peggy Kirstetter
    European Molecular Biology Laboratory, Mouse Biology Unit, Monterotondo 00016, Italy
    Cancer Cell 13:299-310. 2008
    ..Expression profiling of this population against normal Mac1+c-Kit+ progenitors revealed a signature shared with MLL-AF9-transformed AML...
  25. doi request reprint Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila
    Jop Kind
    Gene Expression Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Cell 133:813-28. 2008
    ..Therefore, MOF is not only involved in the onset of dosage compensation, but also acts as a regulator of gene expression in the Drosophila genome...