Philipp Kapranov

Summary

Publications

  1. doi request reprint Error tolerant indexing and alignment of short reads with covering template families
    Eldar Giladi
    Helicos BioSciences Corporation, Cambridge, Massachusetts 02139, USA
    J Comput Biol 17:1397-1411. 2010
  2. pmc Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations
    John F Thompson
    Helicos BioSciences Corporation, Cambridge, Massachusetts 02139, USA
    Genome Res 22:340-5. 2012
  3. pmc Native molecular state of adeno-associated viral vectors revealed by single-molecule sequencing
    Philipp Kapranov
    Helicos BioSciences, Cambridge, MA 02139, USA
    Hum Gene Ther 23:46-55. 2012
  4. pmc Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells
    Georges St Laurent
    Immunovirology Biogenisis Group, University of Antioquia, Medellin A A 1226, Colombia
    BMC Genomics 13:504. 2012
  5. pmc Studying chromosome-wide transcriptional networks: new insights into disease?
    Philipp Kapranov
    Helicos BioSciences Corporation, One Kendall Square Bldg 700, Cambridge, MA 02139, USA
    Genome Med 1:50. 2009
  6. pmc High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans
    Arun K Ramani
    Donnelly CCBR, College Street, University of Toronto, Toronto, M5S 3E1, Canada
    Genome Biol 10:R101. 2009
  7. pmc The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA
    Philipp Kapranov
    Helicos BioSciences Corporation, One Kendall Square, Building 700, Cambridge, MA 02139, USA
    BMC Biol 8:149. 2010
  8. pmc Profiling of short RNAs using Helicos single-molecule sequencing
    Philipp Kapranov
    Helicos BioSciences Corporation, Cambridge, MA, USA
    Methods Mol Biol 822:219-32. 2012
  9. pmc New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism
    Philipp Kapranov
    Helicos BioSciences Corporation, 1 Kendall Sq Ste B7301 Cambridge, Massachusetts 02139 1671, USA
    Nature 466:642-6. 2010
  10. pmc From transcription start site to cell biology
    Philipp Kapranov
    Helicos BioSciences Corporation, One Kendall Square Building 700, Cambridge, MA 02139, USA
    Genome Biol 10:217. 2009

Detail Information

Publications18

  1. doi request reprint Error tolerant indexing and alignment of short reads with covering template families
    Eldar Giladi
    Helicos BioSciences Corporation, Cambridge, Massachusetts 02139, USA
    J Comput Biol 17:1397-1411. 2010
    ..A general algorithm for finding those families is presented, and a recursive construction that creates families with higher error tolerance from ones with a lower error tolerance is developed...
  2. pmc Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations
    John F Thompson
    Helicos BioSciences Corporation, Cambridge, Massachusetts 02139, USA
    Genome Res 22:340-5. 2012
    ..Additionally, this approach has applications for sequencing integration sites for gene therapy vectors, transposons, retroviruses, and other mobile DNA elements in a more facile manner than possible with other methods...
  3. pmc Native molecular state of adeno-associated viral vectors revealed by single-molecule sequencing
    Philipp Kapranov
    Helicos BioSciences, Cambridge, MA 02139, USA
    Hum Gene Ther 23:46-55. 2012
    ..SMS may become a valuable tool during the development phase of vectors that are candidates for clinical use and for facilitating/accelerating studies on vector biology...
  4. pmc Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells
    Georges St Laurent
    Immunovirology Biogenisis Group, University of Antioquia, Medellin A A 1226, Colombia
    BMC Genomics 13:504. 2012
    ..This would suggest that RNAs produced from the vast expanse of intronic space are just pieces of pre-mRNAs or excised introns en route to degradation...
  5. pmc Studying chromosome-wide transcriptional networks: new insights into disease?
    Philipp Kapranov
    Helicos BioSciences Corporation, One Kendall Square Bldg 700, Cambridge, MA 02139, USA
    Genome Med 1:50. 2009
    ..Any given base-pair in a genome could be traversed by many protein-coding and non-coding RNAs. We discuss the implications of these effects for our understanding of disease...
  6. pmc High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans
    Arun K Ramani
    Donnelly CCBR, College Street, University of Toronto, Toronto, M5S 3E1, Canada
    Genome Biol 10:R101. 2009
    ..We utilized this framework to identify transcriptome changes in animals lacking the nonsense-mediated decay (NMD) pathway...
  7. pmc The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA
    Philipp Kapranov
    Helicos BioSciences Corporation, One Kendall Square, Building 700, Cambridge, MA 02139, USA
    BMC Biol 8:149. 2010
    ..For example, efforts to elucidate how non-coding RNAs (ncRNAs) regulate genome function will be compromised if that class of RNAs is dismissed as simply 'transcriptional noise'...
  8. pmc Profiling of short RNAs using Helicos single-molecule sequencing
    Philipp Kapranov
    Helicos BioSciences Corporation, Cambridge, MA, USA
    Methods Mol Biol 822:219-32. 2012
    ..Here, we describe the strategies and procedures we developed to profile short RNA species using single-molecule sequencing (SMS) and the advantages SMS offers...
  9. pmc New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism
    Philipp Kapranov
    Helicos BioSciences Corporation, 1 Kendall Sq Ste B7301 Cambridge, Massachusetts 02139 1671, USA
    Nature 466:642-6. 2010
    ..Finally, we show that genes are also flanked by sense, 3' polyadenylated sRNAs that are likely to be capped...
  10. pmc From transcription start site to cell biology
    Philipp Kapranov
    Helicos BioSciences Corporation, One Kendall Square Building 700, Cambridge, MA 02139, USA
    Genome Biol 10:217. 2009
    ..The regulation of transcription is a complex process. Recent novel insights concerning the in vivo regulation and expression of protein-coding and non-coding RNAs have added previously unimagined levels of complexity to these processes...
  11. pmc Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, MA 02139, USA
    Cell 143:1018-29. 2010
    ..Our data provide a comprehensive view of the polyadenylation state and overlapping transcription...
  12. doi request reprint Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila
    Georges St Laurent
    1 Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA 2 St Laurent Institute, Cambridge, Massachusetts, USA
    Nat Struct Mol Biol 20:1333-9. 2013
    ..Finally, editing regulates expression levels of target mRNAs and strongly correlates with alternative splicing. ..
  13. pmc A concept of eliminating nonhomologous recombination for scalable and safe AAV vector generation for human gene therapy
    Biao Dong
    Department of Microbiology and Immunology, Sol Sherry Thrombosis Research Center, Temple University, Philadelphia, PA 19140, USA
    Nucleic Acids Res 41:6609-17. 2013
    ..The rcAAV contamination was undetectable at the limit of our assay. Furthermore, this new concept can be used not only for production of rAAV, but also for other DNA vectors. ..
  14. doi request reprint On the importance of small changes in RNA expression
    Georges St Laurent
    Immunovirology Biogenisis Group, University of Antioquia, A A 1226, Medellin, Colombia St Laurent Institute, One Kendall Square, Cambridge, MA, USA Electronic address
    Methods 63:18-24. 2013
    ..In conclusion, given the prevalence of expression profiling in current research, the loss of data in half of all expression studies results in a significant, yet needless drain on the discovery process...
  15. pmc Dark Matter RNA: Existence, Function, and Controversy
    Philipp Kapranov
    St Laurent Institute Cambridge, MA, USA
    Front Genet 3:60. 2012
    ..Thus, this question could be referred to without much exaggeration as the most important issue in genetics today...
  16. pmc Identification of functional elements and regulatory circuits by Drosophila modENCODE
    Sushmita Roy
    Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology MIT, Cambridge, MA 02139, USA
    Science 330:1787-97. 2010
    ..Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation...
  17. 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...