Philipp Kapranov

Summary

Affiliation: Affymetrix Inc
Country: USA

Publications

  1. ncbi request reprint Large-scale transcriptional activity in chromosomes 21 and 22
    Philipp Kapranov
    Affymetrix, Santa Clara, CA 95051, USA, National Cancer Institute, Bethesda, MD 20892, USA
    Science 296:916-9. 2002
  2. pmc Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
    Philipp Kapranov
    Affymetrix Inc, Santa Clara, California 95051, USA
    Genome Res 15:987-97. 2005
  3. ncbi request reprint Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    Jill Cheng
    Affymetrix Inc, Santa Clara, CA 95051, USA
    Science 308:1149-54. 2005
  4. pmc Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
    Dione Kampa
    Affymetrix, Santa Clara, California 95051, USA
    Genome Res 14:331-42. 2004
  5. ncbi request reprint RNA maps reveal new RNA classes and a possible function for pervasive transcription
    Philipp Kapranov
    Affymetrix Laboratory, Affymetrix, Inc, 3420 Central Expressway, Santa Clara, CA, 95051, USA
    Science 316:1484-8. 2007
  6. pmc Differential analysis for high density tiling microarray data
    Srinka Ghosh
    Affymetrix Inc, Santa Clara, CA 95051, USA
    BMC Bioinformatics 8:359. 2007
  7. ncbi request reprint Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    Simon Cawley
    Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA
    Cell 116:499-509. 2004
  8. ncbi request reprint Biological function of unannotated transcription during the early development of Drosophila melanogaster
    J Robert Manak
    Affymetrix, Inc, Santa Clara, California, 95051, USA
    Nat Genet 38:1151-8. 2006
  9. ncbi request reprint Beyond expression profiling: next generation uses of high density oligonucleotide arrays
    Philipp Kapranov
    Affymetrix, Inc, Santa Clara, CA 95051, USA
    Brief Funct Genomic Proteomic 2:47-56. 2003
  10. ncbi request reprint Genome-wide transcription and the implications for genomic organization
    Philipp Kapranov
    Affymetrix, Inc, 3420 Central Expressway, Santa Clara, California 95051, USA
    Nat Rev Genet 8:413-23. 2007

Detail Information

Publications20

  1. ncbi request reprint Large-scale transcriptional activity in chromosomes 21 and 22
    Philipp Kapranov
    Affymetrix, Santa Clara, CA 95051, USA, National Cancer Institute, Bethesda, MD 20892, USA
    Science 296:916-9. 2002
    ..When compared with the sequence annotations available for these chromosomes, it is noted that as much as an order of magnitude more of the genomic sequence is transcribed than accounted for by the predicted and characterized exons...
  2. pmc Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
    Philipp Kapranov
    Affymetrix Inc, Santa Clara, California 95051, USA
    Genome Res 15:987-97. 2005
    ..These results have important implications concerning the correlation of genotypes to phenotypes, the regulation of complex interlaced transcriptional patterns, and the definition of a gene...
  3. ncbi request reprint Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    Jill Cheng
    Affymetrix Inc, Santa Clara, CA 95051, USA
    Science 308:1149-54. 2005
    ..This organization has important implications for interpreting genotype-phenotype associations, regulation of gene expression, and the definition of a gene...
  4. pmc Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
    Dione Kampa
    Affymetrix, Santa Clara, California 95051, USA
    Genome Res 14:331-42. 2004
    ..These observations strongly support the argument for a re-evaluation of the total number of human genes and an alternative term for "gene" to encompass these growing, novel classes of RNA transcripts in the human genome...
  5. ncbi request reprint RNA maps reveal new RNA classes and a possible function for pervasive transcription
    Philipp Kapranov
    Affymetrix Laboratory, Affymetrix, Inc, 3420 Central Expressway, Santa Clara, CA, 95051, USA
    Science 316:1484-8. 2007
    ..These data support a highly interleaved organization of the human transcriptome...
  6. pmc Differential analysis for high density tiling microarray data
    Srinka Ghosh
    Affymetrix Inc, Santa Clara, CA 95051, USA
    BMC Bioinformatics 8:359. 2007
    ....
  7. ncbi request reprint Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    Simon Cawley
    Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA
    Cell 116:499-509. 2004
    ..Thus, the human genome contains roughly comparable numbers of protein-coding and noncoding genes that are bound by common transcription factors and regulated by common environmental signals...
  8. ncbi request reprint Biological function of unannotated transcription during the early development of Drosophila melanogaster
    J Robert Manak
    Affymetrix, Inc, Santa Clara, California, 95051, USA
    Nat Genet 38:1151-8. 2006
    ..Collectively, these data indicate that at least 85% of the fly genome is transcribed and processed into mature transcripts representing at least 30% of the fly genome...
  9. ncbi request reprint Beyond expression profiling: next generation uses of high density oligonucleotide arrays
    Philipp Kapranov
    Affymetrix, Inc, Santa Clara, CA 95051, USA
    Brief Funct Genomic Proteomic 2:47-56. 2003
    ..Integrating all this information will provide novel global views of the locations of RNA transcription, DNA replication and the protein nucleic acid interactions that regulate these processes...
  10. ncbi request reprint Genome-wide transcription and the implications for genomic organization
    Philipp Kapranov
    Affymetrix, Inc, 3420 Central Expressway, Santa Clara, California 95051, USA
    Nat Rev Genet 8:413-23. 2007
    ..What are the implications and consequences of such an interleaved genomic architecture in terms of increased information content, transcriptional complexity, evolution and disease states?..
  11. pmc Efficient targeted transcript discovery via array-based normalization of RACE libraries
    Sarah Djebali
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
    Nat Methods 5:629-35. 2008
    ....
  12. pmc Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    David S Johnson
    Department of Genetics, Stanford University Medical Center, Stanford, California 94305, USA
    Genome Res 18:393-403. 2008
    ..The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated...
  13. pmc Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders
    Alvaro Rada-Iglesias
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Genome Res 18:380-92. 2008
    ..This expands our understanding about the transcriptional control of metabolic processes and its alteration in metabolic disorders...
  14. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  15. pmc Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions
    France Denoeud
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
    Genome Res 17:746-59. 2007
    ....
  16. pmc Microarray-based DNA methylation profiling: technology and applications
    Axel Schumacher
    The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON, Canada M5T 1R8
    Nucleic Acids Res 34:528-42. 2006
    ..The principles developed in this work will help to make epigenetic profiling of the entire human genome a routine procedure...
  17. pmc Structured RNAs in the ENCODE selected regions of the human genome
    Stefan Washietl
    Institute for Theoretical Chemistry, University of Vienna, A 1090 Wien, Austria
    Genome Res 17:852-64. 2007
    ..One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%)...
  18. pmc Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution
    Deyou Zheng
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 17:839-51. 2007
    ..These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues...
  19. pmc Temporal profile of replication of human chromosomes
    Yesu Jeon
    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
    Proc Natl Acad Sci U S A 102:6419-24. 2005
    ..Thus, at least for aneuploid cancer cells, a typical discrete time of replication in S phase is not seen for large segments of the chromosomes...
  20. ncbi request reprint Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells
    Annie Yang
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Mol Cell 24:593-602. 2006
    ..Many p63 binding regions are evolutionarily conserved and/or associated with sequence motifs for other transcription factors, suggesting that a substantial portion of p63 sites is biologically relevant...