M Ronaghi

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Analysis of read length limiting factors in Pyrosequencing chemistry
    Foad Mashayekhi
    Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
    Anal Biochem 363:275-87. 2007
  2. pmc High throughput automated allele frequency estimation by pyrosequencing
    Julie Doostzadeh
    The Parkinson s Institute, Sunnyvale, California, United States of America
    PLoS ONE 3:e2693. 2008
  3. pmc Bacterial flora-typing with targeted, chip-based Pyrosequencing
    Andreas Sundquist
    Department of Computer Science, Stanford University, Stanford, CA 94305, USA
    BMC Microbiol 7:108. 2007
  4. ncbi request reprint Improved performance of pyrosequencing using single-stranded DNA-binding protein
    M Ronaghi
    Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, California 94304, USA
    Anal Biochem 286:282-8. 2000
  5. ncbi request reprint Pyrosequencing for discovery and analysis of DNA sequence variations
    Mostafa Ronaghi
    Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
    Pharmacogenomics 8:1437-41. 2007
  6. ncbi request reprint Pyrosequencing for microbial typing
    Mostafa Ronaghi
    Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto 94304, USA
    J Chromatogr B Analyt Technol Biomed Life Sci 782:67-72. 2002
  7. ncbi request reprint Pyrosequencing sheds light on DNA sequencing
    M Ronaghi
    Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
    Genome Res 11:3-11. 2001
  8. ncbi request reprint Modeling of the bioactivated nanopore devices
    AmirAli H Talasaz
    Dept of Electr Eng, Stanford Univ, CA 94305, USA
    Conf Proc IEEE Eng Med Biol Soc 1:1830-3. 2006
  9. ncbi request reprint Cell trapping in activated micropores for functional analysis
    AmirAli H Talasaz
    Electr Eng Dept, Stanford Univ, CA 94305, USA
    Conf Proc IEEE Eng Med Biol Soc 1:1838-41. 2006
  10. ncbi request reprint Unusual selection on the KIR3DL1/S1 natural killer cell receptor in Africans
    Paul J Norman
    Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Nat Genet 39:1092-9. 2007

Research Grants

  1. High-throughput Sequencing by Pyrosequencing
    Mostafa Ronaghi; Fiscal Year: 2006
  2. Pyrosequencing Array for Genome Sequencing
    Ronald Davis; Fiscal Year: 2007
  3. Pyrosequencing Array for Genome Sequencing
    Ronald Davis; Fiscal Year: 2007

Collaborators

Detail Information

Publications30

  1. pmc Analysis of read length limiting factors in Pyrosequencing chemistry
    Foad Mashayekhi
    Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
    Anal Biochem 363:275-87. 2007
    ..The main limiting factor of the three-enzyme system is shown to be loss of DNA fragments during the washing step. If this loss is minimized to 0.1% per washing cycle, the read length of Pyrosequencing would be well beyond 300 bases...
  2. pmc High throughput automated allele frequency estimation by pyrosequencing
    Julie Doostzadeh
    The Parkinson s Institute, Sunnyvale, California, United States of America
    PLoS ONE 3:e2693. 2008
    ..We also discuss potential improvements of the software for more accurate allele frequency analysis...
  3. pmc Bacterial flora-typing with targeted, chip-based Pyrosequencing
    Andreas Sundquist
    Department of Computer Science, Stanford University, Stanford, CA 94305, USA
    BMC Microbiol 7:108. 2007
    ..In particular, classifying the microbial content of samples by sequencing the < 1,600 bp 16S rRNA gene will be affected by such limitations...
  4. ncbi request reprint Improved performance of pyrosequencing using single-stranded DNA-binding protein
    M Ronaghi
    Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, California 94304, USA
    Anal Biochem 286:282-8. 2000
    ..The usefulness of these results for future Pyrosequencing applications is discussed...
  5. ncbi request reprint Pyrosequencing for discovery and analysis of DNA sequence variations
    Mostafa Ronaghi
    Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
    Pharmacogenomics 8:1437-41. 2007
    ..This review intends to cover recent advances in this technology and discuss its application for low and high-throughput DNA variation studies...
  6. ncbi request reprint Pyrosequencing for microbial typing
    Mostafa Ronaghi
    Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto 94304, USA
    J Chromatogr B Analyt Technol Biomed Life Sci 782:67-72. 2002
    ..Here, we review the methodology and the use of this technique for viral typing, bacterial typing, and fungal typing. In addition, we describe how to use multiplexing for accurate and rapid typing...
  7. ncbi request reprint Pyrosequencing sheds light on DNA sequencing
    M Ronaghi
    Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
    Genome Res 11:3-11. 2001
    ..This article considers key features regarding different aspects of pyrosequencing technology, including the general principles, enzyme properties, sequencing modes, instrumentation, and potential applications...
  8. ncbi request reprint Modeling of the bioactivated nanopore devices
    AmirAli H Talasaz
    Dept of Electr Eng, Stanford Univ, CA 94305, USA
    Conf Proc IEEE Eng Med Biol Soc 1:1830-3. 2006
    ..These devices are capable of detecting and analyzing interactions between the attached biomolecule and the molecules in the analyte at a single molecule level...
  9. ncbi request reprint Cell trapping in activated micropores for functional analysis
    AmirAli H Talasaz
    Electr Eng Dept, Stanford Univ, CA 94305, USA
    Conf Proc IEEE Eng Med Biol Soc 1:1838-41. 2006
    ..In the process, single cells are precisely positioned and captured in activated micropores. To show the performance of the proposed device, cultured yeast cells and human epithelial circulating tumor cells are successfully captured...
  10. ncbi request reprint Unusual selection on the KIR3DL1/S1 natural killer cell receptor in Africans
    Paul J Norman
    Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Nat Genet 39:1092-9. 2007
    ..Natural killer cells express the dominant KIR3DL1 at a high frequency and with high surface density, providing strong responses to cells perturbed in Bw4 expression...
  11. pmc Whole-genome sequencing and assembly with high-throughput, short-read technologies
    Andreas Sundquist
    Department of Computer Science, Stanford University, Stanford, California, United States of America
    PLoS ONE 2:e484. 2007
    ..Thus, we have demonstrated that truly inexpensive de novo sequencing of mammalian genomes will soon be possible with high-throughput, short-read technologies using our methodology...
  12. pmc Multiplex Pyrosequencing
    Nader Pourmand
    Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
    Nucleic Acids Res 30:e31. 2002
    ..Here, we demonstrate the use of this multiplex Pyrosequencing for single nucleotide polymorphisms genotyping and microbial typing...
  13. pmc A multi-enzyme model for Pyrosequencing
    Ali Agah
    Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
    Nucleic Acids Res 32:e166. 2004
    ..Simulation results are shown to be compatible with experimental data. Based on these simulations, the rate-limiting steps in the chain can be determined, and K(M) and kcat of all four enzymes in Pyrosequencing can be calculated...
  14. ncbi request reprint Conformational flexibility of a model protein upon immobilization on self-assembled monolayers
    Saharnaz Bigdeli
    Stanford Genome Technology Center, 855 California Ave, Palo Alto, California 94304, USA
    Biotechnol Bioeng 100:19-27. 2008
    ..The general significance of these observations in connection with retention of native properties of protein structures upon immobilization on SAMs is discussed...
  15. pmc Whole genome survey of coding SNPs reveals a reproducible pathway determinant of Parkinson disease
    Balaji S Srinivasan
    Department of Statistics, Stanford University, Stanford, California, USA
    Hum Mutat 30:228-38. 2009
    ..We conclude by relating this seeming inconsistency to the molecular heterogeneity of PD, and suggest future analyses that may resolve such discrepancies...
  16. ncbi request reprint Pyrosequencing: an accurate detection platform for single nucleotide polymorphisms
    Hossein Fakhrai-Rad
    Stanford Genome Technology Center, Stanford University, Palo Alto, California, USA
    Hum Mutat 19:479-85. 2002
    ..In addition, we describe new schemes for template preparation and multiplexing as an effort for cost reduction in large-scale studies...
  17. ncbi request reprint Pyrosequencing: a tool for DNA sequencing analysis
    Elahe Elahi
    Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
    Methods Mol Biol 255:211-9. 2004
  18. ncbi request reprint Multiplexed genotyping with sequence-tagged molecular inversion probes
    Paul Hardenbol
    Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, California 94304, USA
    Nat Biotechnol 21:673-8. 2003
    ..Genotypes are generated with a high call rate (95%) and high accuracy (>99%) as determined by independent sequencing...
  19. ncbi request reprint Pyrosequencing for SNP genotyping
    Mostafa Ronaghi
    Stanford Genome Technology Center, Palo Alto, CA, USA
    Methods Mol Biol 212:189-95. 2003
  20. pmc A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing
    Poornima Parameswaran
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 35:e130. 2007
    ..The false-discovery rate, as measured by the percentage of sequences with unexpected perfect pairings of unmatched forward and reverse barcodes, was estimated to be <0.005%...
  21. ncbi request reprint Determination of hepatitis C virus genotype by Pyrosequencing
    Elahe Elahi
    Stanford Genome Technology Center, Stanford University, 855 California Avenue, Palo Alto, CA 94304, USA
    J Virol Methods 109:171-6. 2003
    ..For rapid population-specific HCV subtyping, a multiplex assay was developed. This study demonstrates the suitability of this technology for low-cost, high throughput and accurate microbial genotyping...
  22. pmc Prediction of protein orientation upon immobilization on biological and nonbiological surfaces
    AmirAli H Talasaz
    Department of Electrical Engineering, Stanford University, Palo Alto, CA 94305, USA
    Proc Natl Acad Sci U S A 103:14773-8. 2006
    ..Finally, we also propose an orientation of membrane-bound cytochrome c, a protein for which the membrane orientation has not been unequivocally determined...
  23. ncbi request reprint Global genetic analysis
    Elahe Elahi
    Faculty of Science, Tehran University, Tehran, Iran
    J Biochem Mol Biol 37:11-27. 2004
    ..This review discusses approaches for genetic analysis, use of different markers, and emerging technologies for large-scale genetic analysis where millions of genotyping need to be performed...
  24. pmc Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations
    Yumi Mitsuya
    Department of Medicine, Division of Infectious Diseases, Stanford University Medical Center, Stanford, California 94305, USA
    J Virol 82:10747-55. 2008
    ....
  25. pmc Genome-wide linkage analysis of a Parkinsonian-pyramidal syndrome pedigree by 500 K SNP arrays
    Seyedmehdi Shojaee
    Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
    Am J Hum Genet 82:1375-84. 2008
    ..Our results suggest that linkage in our pedigree may have been missed had we used chips containing less than 100,000 SNPs across the genome...
  26. pmc Viral population estimation using pyrosequencing
    Nicholas Eriksson
    Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Comput Biol 4:e1000074. 2008
    ..Thus, pyrosequencing can be used for cost-effective estimation of the structure of virus populations, promising new insights into viral evolutionary dynamics and disease control strategies...
  27. ncbi request reprint Long-read pyrosequencing using pure 2'-deoxyadenosine-5'-O'-(1-thiotriphosphate) Sp-isomer
    Baback Gharizadeh
    Department of Biotechnology, Royal Institute of Technology, Roslagstullsbacken 21, Stockholm, SE 10691, Sweden
    Anal Biochem 301:82-90. 2002
    ..The longer read will enable numerous new applications, such as identification and typing of medically important microorganisms as well as resequencing of DNA fragments for mutation screening and clone checking...
  28. ncbi request reprint Molecular inversion probe assay
    Farnaz Absalan
    Methods Mol Biol 396:315-30. 2007
    ..This enables more informative, genome-wide studies with either the functional (direct detection) approach or the indirect detection approach...
  29. ncbi request reprint Genetic variation analyses by Pyrosequencing
    Taimour Langaee
    Department of Pharmacy Practice, University of Florida, Center for Pharmacogenomics, Gainesville, FL, USA
    Mutat Res 573:96-102. 2005
    ..Here, we review recent advances and discuss new applications of this technique. Cost reduction efforts and future potentials of this technique for large-scale genotyping applications will also be discussed...
  30. pmc A haplotype framework for cystic fibrosis mutations in Iran
    Elahe Elahi
    Department of Biological Sciences, Tehran University, Tehran, Iran
    J Mol Diagn 8:119-27. 2006
    ..3661A>T (p.K1177X) at 2.5%. Three of the five most frequent Iranian mutations are not included in a commonly used panel of CF mutations, underscoring the importance of identifying geographic-specific mutations in this population...

Research Grants3

  1. High-throughput Sequencing by Pyrosequencing
    Mostafa Ronaghi; Fiscal Year: 2006
    ..The diverse array of research projects supported by the HTS facility will spark the development of new applications, accelerating the Center's technology development program and opening a new horizon in biomedical research at Stanford. ..
  2. Pyrosequencing Array for Genome Sequencing
    Ronald Davis; Fiscal Year: 2007
    ....
  3. Pyrosequencing Array for Genome Sequencing
    Ronald Davis; Fiscal Year: 2007
    ..abstract_text> ..