Genome Technology Center

SGTC Publications

Following is a list of publications starting in 1993, when the Stanford Genome Technology Center was founded.

The references below are hyper-linked to their abstract in PubMed or, whenever possible, directly to the journal. (Access to journals may require membership or subscription).

For some papers supplemental web sites provide additional information.

Detailed information about patents can be found under Stanford References (Office of Technology Licensing at Stanford University) or at the United States Patent and Trademark Office (USPTO).

 

Books & Book Chapters

  1. High-Throughput Creation of a Whole-Genome Collection of Yeast Knockout Strains.
    Chu, A.M., Davis, R.W. (2008) In: Osterman, A., Gerdes, S.(Eds.), Microbial Gene Essentiality: Protocols and Bioinformatics, Methods in Molecular Biology, Volume 416, Humana Press, Inc., Totowa, New Jersey, pp.205-220. [PubMed], [Publisher]
  2. Denaturing high-performance liquid chromatography.
    Premstaller, A., Oefner, P.J. (2003). In: P.-Y. Kwok (Ed), Single Nucleotide Polymorphisms: Methods and Protocols, Methods in Molecular Biology, Volume 212, Humana Press Inc., Totowa, New Jersey, pp. 15-35.
  3. Pyrosequencing: A tool for DNA sequence analysis.
    Elahi, E., Ronaghi, M., (2002). Humana Press.
  4. Pyrosequencing for SNP genotyping.
    Ronaghi, M., (2002), in Methods in molecular Biology Volume 212 Single Nucleotide Polymorphisms: Methods and Protocols. Humana press. pp 189-196.
  5. Pyrosequencing a bioluminometric method of DNA sequencing.
    Ronaghi, M., Pourmand, N., Stolc. V., (2001), in Advances in luminescence biotechnology. CRS press. p. 247-253.
  6. Parallel analysis with Biological Chips.
    Schena, M., Davis, R.W., (1999); in PCR Applications. Academic Press. p. 445-456.
  7. Genes, Genomes and Chips.
    Schena, M., Davis, R.W., (1999); in DNA Microarrays: A Practical Approach; Schena, M., Editor. Oxford University Press: Oxford, United Kingdom. p. 1-16.
  8. Kinetics of competitive RT PCR.
    Hayward, A.L., Oefner, P.J., Kainer, D., Hinojos, C.A., Doris, P.A., (1999); in PCR Methods Manual, Academic Press, San Diego, M. Innis, D. Gelfand, J. Sninsky, Editor. Academic Press: San Diego. p. 231-261.
  9. DNA mutation detection using denaturing high-performance liquid chromatography (DHPLC).
    Oefner, P.J., Underhill, P.A., (1998); in Current Protocols in Human Genetics. Wiley & Sons: New York. p. 7.10.11-17.10.12.
  10. Y Chromosome Variation and Human Evolution.
    Underhill, P.A., Jin, L., Oefner, P.J., Cavalli-Sforza, L.L., (1997); in Advances in Research on DNA Polymorphisms, Proceedings of ISFH Hakone Symposium on DNA Polymorphisms 1996, Katsumata, Y., et al., Editor: Toyoshoten, Tokyo, Japan. p. 24-32.
  11. Rapid quantification of gene expression by competitive RT-PCR and ion-pair reversed-phase HPLC.
    Hayward-Lester, A., Oefner, P.J., Doris, P.A., (1997);in The PCR Technique: Quantitative PCR, Larrick, J.W., Editor. Eaton Publishing: Natick, MA. p. 125-139.
  12. Quantification of specific nucleic acids, regulated RNA processing and genomic polymorphisms using reversed-phase HPLC.
    Hayward-Lester, A., Chilton, B.S., Underhill, P.A., Oefner, P.J., Doris, P.A., (1997); in Gene Quantification, Ferré, F., Editor. Birkhäuser Verlag. p. 44-77.
  13. Yeast Artificial Chromosome (YAC) construction and applications.
    Loehrlein, C., Davis, Ronald W., (1996); in Encyclopedia of Molecular Biology and Molecular Medicine, Meyers, Robert A., Editor. VCH Publishers: Weinheim. p. 291-302.
  14. Analysis of carbohydrates and oligo-saccharides.
    Chiesa, C., O`Neill, R., Horváth, Cs., Oefner, P.J. (1995); in: Capillary Electrophoresis: An Analytical Tool in Biotechnology. Righetti, P.G., Editor. CRC Press, Boca Raton, p. 277-430.
  15. Capillary electrophoresis of carbohydrates.
    Oefner, P., Bonn, G., Chiesa, C., (1995); in: Encyclopedia of Analytical Science. Academic Press, London. p. 1135-1152.

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Proceedings

  1. High-throughput Pyrosequencing for analysis Single Nucleotide Polymorphisms Genomics, Proteomics and Related Technologies for Biomedical Applications.
    Ronaghi, M., (2001), in Proceedings of SPIE's International Symposium on Biomedical Optics. pp 4626-4660.
  2. A novel bioluminometric approach for DNA sequencing.
    Nyrén, P., Ronaghi, M., Karamohammed, S., Nordström, T., Nourizad, K., (1998), in Proceedings of 10th International Symposium on Bioluminescence & Chemiluminescence.
  3. Automation of a novel DNA sequencing method.
    Nordström, T., Ronaghi, M., Nyrén, P., (1998), in Proceedings of 10th International Symposium on Bioluminescence & Chemiluminescence.
  4. A method for real-time detection of the effect of different inhibitors on reverse transciptase activity.
    Karamohammed, S., Ronaghi, M., Nyrén, P., (1996), in Proceedings of 9th International Symposium on Bioluminescence & Chemiluminescence.
  5. Real-time sequence-based DNA analyses using bioluminscence.
    Nyrén, P., Karamohammed, S., Ronaghi, M., (1996), in Proceedings of 9th International Symposium on Bioluminescence & Chemiluminescence.

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Letters

  1. Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae.
    Kastenmayer, JP, Ni, L Chu, A, Kitchen, LE, Au, W-C, Yang, H, Carter, CD, Wheeler, D, Davis, RW, Boeke, JD, Snyder, MA and Basrai MA (2006). Genome Res 16(3):365-373.
  2. A network-based analysis of systemic inflammation in humans.
    Calvano, S.E., Xiao, W., Richards, D.R., Felciano, R.M., Baker, H.V., Cho, R.J., Chen, R.O., Brownstein, B.H., Cobb, J.P., Tschoeke, S.K., Miller-Graziano, C., Moldawer, L.L., Mindrinos, M.N., Davis, R.W., Tompkins, R.G. & Lowry, S.F. and Inflamm and Host Response to Injury Large Scale Collab. Res. Program. Nature 437, 1032-7 (2005). [PubMed], [Publisher]
  3. Re: genetic analysis of the beta-tubulin gene, TUBB, in non-small-cell lung cancer.
    Sale, S., Oefner, P.J., Sikic, B.I., (2002). May 15, J Natl Cancer Inst, 94(10):776-777; discussion 777.
  4. Childhood onset mitochondrial myopathy and lactic acidosis caused by a stop mutation in the mitochondrial cytochrome c oxidase III gene. Horvath, R., Scharfe, C., Hoeltzenbein, M., Do, B.H., Schroder, C., Warzok, R., Vogelgesang, S., Lochmuller, Genet 2002 Nov;39(11):812-6.
  5. Sequence data: posted vs. published.
    Hyman, R.W., (2001). Feb 2, Science, 291(5505):827
  6. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography.
    Underhill, P.A., Jin, L., Lin, A.A., Mehdi, S.Q., Jenkins, T., Vollrath, D., Davis, R.W., Cavalli-Sforza, L.L., Oefner, P.J., (1997). Oct, Genome Res, 7(10):996-1005. [Publisher Full Text].

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Submissions to GenBank

  1. Saccharomyces cerevisiae strain YJM789, full genome. Genbank: accession number AAFW00000000 (for nuclear genome); EU004203 (for mitochondrial genome). Wei, W., McCusker, J.H., Hyman, R.H., Jones, T., Ning, Y., Cao, Z., Gu, Z., Bruno, D., Miranda, M., Nguyen, M., Wilhelmy, J., Komp, C., Tamse, R., Wang, X., Jia, P., Luedi, P., Oefner P.J., David, L., Dietrich, F.S., Li, Y., Davis, R.W., Steinmetz, L.M. (2005)
  2. Escherichia coli chromosome minutes 9-12. Genbank: accession number U82598
    Chung, E., Allen, E., Araujo,R., Aparicio, A., Davis, K., Duncan, M., Federspiel, N., Hyman, R.W., Kalman, S., Komp, C., Kurdi, O., Lew, H., Lin, D., Namath, A., Oefner, P., Schramm, S., Davis, R.W., (1997)
  3. Human chromosome 1 BAC 89N6 genomic sequence.GenBank: accession number AC003118.
    Chung, E., Babb, V., Hyman, R.W., Kurdi, O., Rexan, M., Vollrath, D., Davis, Ronald W., (1997)
  4. Human chromosome 1 BAC 308G1 genomic sequence. GenBank: accession number AC003117.
    Fan, J., Babb, V., Hyman, R.W., Kalman, S., Kurdi, O., Marathe, R., Rexan, M., Vollrath, D., Davis, R.W. (1997)
  5. Human chromosome Y cosmid 16E4 genomic sequence. GenBank: accession number AC003094.
    Hyman, R.W., Chung, E., Kurdi, O., Roberts, D., Schramm, S., Vollrath, D., Davis, R.W., (1997)
  6. Human chromosome Y cosmid 54E8 genomic sequence. GenBank: accession number AC003095.
    Hyman, R.W., Vollrath, D., Davis, R.W., (1997)
  7. Human chromosome 1 BAC 13512 genomic sequence. GenBank: accession number AC003115.
    Hyman, R.W., Babb, V., Chung, E., Kurdi, O., Rexan, M., Vollrath, D., Davis, R.W., (1997)
  8. Human chromosome Y cosmid 56B5 genomic sequence. GenBank: accession number AC003097.
    Lin, D., Chung, E., Hyman, R.W., Schramm, S., Vollrath, D., Davis, R.W., (1997)
  9. Escherichia coli chromosome minutes 9-11. Genbank: accession number U82598. Chung, E., Allen, E., Araujo,R., Aparicio, A., Davis, K., Duncan, M., Federspiel, N., Hyman, R. W., Kalman, S., Komp, C., Kurdi, O., Lew, H., Lin, D., Namath, A., Oefner, P., Schramm, S. and Davis, Ronald W. (1997)
  10. Human chromosome Y cosmid 30H9 genomic sequence. GenBank: accession number AC003031.
    Shen, P., Chung, E., Hyman, R.W., Roberts, D., Schramm, S., Vollrath, D., Davis, R.W., (1997)
  11. Human chromosome Y cosmid 7A1 genomic sequence. GenBank: accession number AC003032.
    Thorstenson, Y., Au, M., Chung, E., Hyman, R., Schramm, S., Vollrath, D., Davis, R.W., (1997)
  12. Plasmodium falciparum 3D7 chromosome 12, complete sequence. GenBank: accession number AE014188.
    Hyman, R.W., Fung, E., Conway, A., Kurdi, O., Mao, J., Miranda, M., Nakao, B., Rowley, D., Tamaki, T., Wang, F. and Davis, R.W.
  13. Saccharomyces cerevisiae chromosome XVI left arm from MMN to PH085. Genbank: accession number U44030.
    Dietrich, F.S., Allen, E., Araujo, R., Aparicio, A., Carpenter, J., Cherry, J.M., Chung, E., E., Davis, K., Duncan, M., Hunicke-Smith, S., Hyman, R.W., Kalman, S., Komp, C., Kurdi, O., Lashkari, D., Lew, H., Lin, A., Lin, D., Marathe, R., Mirtipati, S., Namath, A., Oefner, P., Petel, F., Roberts, D., Schramm, S., Schroeder, M., Botstein, D., Davis, Ronald W., (1996)
  14. Escherichia coli chromosome minutes 6-8. Genbank: accession number U73857
    Duncan, M., Allen, E., Araujo, R., Aparicio, A., Chung, E., Davis, K., Federspiel, N., Hyman, R.W., Kalman, S., Komp, C., Kurdi, O., Lew, H., Lin, D., Namath, A., Oefner, P., Roberts, D., Schramm, S., Davis, Ronald W., (1996)
  15. Escherichia coli chromosome minutes 4-6. Genbank: accession number U70214
    Schramm, S., Duncan, M., Allen, E., Araujo, R., Aparicio, A., Chung, E., Davis, K., Federspiel, N., Hyman, R.W., Kalman, S., Komp, C., Kurdi, O., Lashkari, D., Lew, H., Lin, D., Namath, A., Oefner, P., Roberts, D., Davis, Ronald W., (1996)
updated March 26, 2012

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