Research Topics
Species | M RonaghiSummaryAffiliation: Stanford University Country: USA Publications
Research Grants
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Detail Information
Publications
Analysis of read length limiting factors in Pyrosequencing chemistryFoad 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...- High throughput automated allele frequency estimation by pyrosequencingJulie 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... - Bacterial flora-typing with targeted, chip-based PyrosequencingAndreas 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... 
Improved performance of pyrosequencing using single-stranded DNA-binding proteinM 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...- Pyrosequencing for discovery and analysis of DNA sequence variationsMostafa 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... - Pyrosequencing for microbial typingMostafa 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... - Pyrosequencing sheds light on DNA sequencingM 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... - Modeling of the bioactivated nanopore devicesAmirAli 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... - Cell trapping in activated micropores for functional analysisAmirAli 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... - Unusual selection on the KIR3DL1/S1 natural killer cell receptor in AfricansPaul 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... - Whole-genome sequencing and assembly with high-throughput, short-read technologiesAndreas 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... - Multiplex PyrosequencingNader 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... - A multi-enzyme model for PyrosequencingAli 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... - Conformational flexibility of a model protein upon immobilization on self-assembled monolayersSaharnaz 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... - Whole genome survey of coding SNPs reveals a reproducible pathway determinant of Parkinson diseaseBalaji 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... - Pyrosequencing: an accurate detection platform for single nucleotide polymorphismsHossein 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... - Pyrosequencing: a tool for DNA sequencing analysisElahe Elahi
Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
Methods Mol Biol 255:211-9. 2004 - Multiplexed genotyping with sequence-tagged molecular inversion probesPaul 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... - Pyrosequencing for SNP genotypingMostafa Ronaghi
Stanford Genome Technology Center, Palo Alto, CA, USA
Methods Mol Biol 212:189-95. 2003 - A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexingPoornima 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%... - Determination of hepatitis C virus genotype by PyrosequencingElahe 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... - Prediction of protein orientation upon immobilization on biological and nonbiological surfacesAmirAli 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... - Global genetic analysisElahe 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... - Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutationsYumi Mitsuya
Department of Medicine, Division of Infectious Diseases, Stanford University Medical Center, Stanford, California 94305, USA
J Virol 82:10747-55. 2008.... - Genome-wide linkage analysis of a Parkinsonian-pyramidal syndrome pedigree by 500 K SNP arraysSeyedmehdi 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... - Viral population estimation using pyrosequencingNicholas 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... - Long-read pyrosequencing using pure 2'-deoxyadenosine-5'-O'-(1-thiotriphosphate) Sp-isomerBaback 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... - Molecular inversion probe assayFarnaz 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... - Genetic variation analyses by PyrosequencingTaimour 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... - A haplotype framework for cystic fibrosis mutations in IranElahe 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 Grants
- High-throughput Sequencing by PyrosequencingMostafa 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. ..
- Pyrosequencing Array for Genome SequencingRonald Davis; Fiscal Year: 2007....
- Pyrosequencing Array for Genome SequencingRonald Davis; Fiscal Year: 2007..abstract_text> ..