Fatih Ozsolak

Summary

Publications

  1. ncbi request reprint Direct RNA sequencing
    Fatih Ozsolak
    Helicos BioSciences Corporation, One Kendall Square, Cambridge, Massachusetts 02139, USA
    Nature 461:814-8. 2009
  2. 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
  3. doi request reprint Quantitative polyadenylation site mapping with single-molecule direct RNA sequencing
    Fatih Ozsolak
    Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA, 02139, USA
    Methods Mol Biol 1125:145-55. 2014
  4. pmc Third-generation sequencing techniques and applications to drug discovery
    Fatih Ozsolak
    Helicos BioSciences Corp, Cambridge, MA 02139, USA
    Expert Opin Drug Discov 7:231-43. 2012
  5. pmc Digital transcriptome profiling from attomole-level RNA samples
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, MA 02139, USA
    Genome Res 20:519-25. 2010
  6. pmc Amplification-free digital gene expression profiling from minute cell quantities
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, Massachusetts, USA
    Nat Methods 7:619-21. 2010
  7. 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
  8. doi request reprint Single-molecule sequencing: sequence methods to enable accurate quantitation
    Christopher Hart
    Helicos BioSciences Corporation, Cambridge, Massachusetts, USA
    Methods Enzymol 472:407-30. 2010
  9. 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
  10. pmc Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA
    Alon Goren
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Methods 7:47-9. 2010

Collaborators

Detail Information

Publications16

  1. ncbi request reprint Direct RNA sequencing
    Fatih Ozsolak
    Helicos BioSciences Corporation, One Kendall Square, Cambridge, Massachusetts 02139, USA
    Nature 461:814-8. 2009
    ..This study provides a path to high-throughput and low-cost direct RNA sequencing and achieving the ultimate goal of a comprehensive and bias-free understanding of transcriptomes...
  2. 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...
  3. doi request reprint Quantitative polyadenylation site mapping with single-molecule direct RNA sequencing
    Fatih Ozsolak
    Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA, 02139, USA
    Methods Mol Biol 1125:145-55. 2014
    ..This chapter outlines the quantitative polyadenylation site mapping and analysis strategies developed with the single-molecule direct RNA sequencing technology...
  4. pmc Third-generation sequencing techniques and applications to drug discovery
    Fatih Ozsolak
    Helicos BioSciences Corp, Cambridge, MA 02139, USA
    Expert Opin Drug Discov 7:231-43. 2012
    ..By expanding the power of genetics and pharmacogenetics studies, next-generation nucleic acid sequencing technologies have started to play an important role in all stages of drug discovery...
  5. pmc Digital transcriptome profiling from attomole-level RNA samples
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, MA 02139, USA
    Genome Res 20:519-25. 2010
    ....
  6. pmc Amplification-free digital gene expression profiling from minute cell quantities
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, Massachusetts, USA
    Nat Methods 7:619-21. 2010
    ..We applied LQ-DGE to profile malignant and nonmalignant mouse and human cells, demonstrating its quantitative power and potential applicability to archival specimens...
  7. 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...
  8. doi request reprint Single-molecule sequencing: sequence methods to enable accurate quantitation
    Christopher Hart
    Helicos BioSciences Corporation, Cambridge, Massachusetts, USA
    Methods Enzymol 472:407-30. 2010
    ..This chapter will describe the various methods available to researchers...
  9. 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'...
  10. pmc Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA
    Alon Goren
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Methods 7:47-9. 2010
    ..This method is compatible with just 50 pg of DNA and should thus facilitate charting chromatin maps from limited cell populations...
  11. 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...
  12. pmc Transcriptome profiling using single-molecule direct RNA sequencing
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, MA, USA
    Methods Mol Biol 733:51-61. 2011
    ..Here, we describe the strategies and procedures we employ to prepare various RNA species for analysis with DRS...
  13. pmc Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains
    Elizabeth E Slawson
    Biology Department, Washington University, St Louis, MO 63130, USA
    Genome Biol 7:R15. 2006
    ..In contrast, the absence of HP1 and H3K9me from the dot chromosome in D. virilis suggests that this region is euchromatic. D. virilis diverged from D. melanogaster 40 to 60 million years ago...
  14. pmc An in-depth map of polyadenylation sites in cancer
    Yuefeng Lin
    Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
    Nucleic Acids Res 40:8460-71. 2012
    ..In summary, these results highlight the need to go beyond monitoring only the cumulative transcript levels for a gene, to separately analysing the expression of its RNA isoforms...
  15. pmc Single-molecule direct RNA sequencing without cDNA synthesis
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, MA, USA
    Wiley Interdiscip Rev RNA 2:565-70. 2011
    ..This review focuses on the underlying principles behind the DRS, sample preparation steps, and the current and novel avenues of research and applications DRS offers...
  16. pmc RNA sequencing: advances, challenges and opportunities
    Fatih Ozsolak
    Helicos BioSciences Corporation, One Kendall Square, Cambridge, Massachusetts 02139, USA
    Nat Rev Genet 12:87-98. 2011
    ..Ongoing developments promise further advances in the application of RNA-seq, particularly direct RNA sequencing and approaches that allow RNA quantification from very small amounts of cellular materials...