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).

 

Reviews

  1. Yeast chemical genomics and drug discovery: an update.
    Hoon S, St Onge RP, Giaever G, Nislow C. Trends Pharmacol Sci. 2008 Aug 26. [Epub ahead of print]. [PubMed]
  2. Genetic variation analyses by Pyrosequencing.
    Langaee, T., Ronaghi, M. Mutat Res 573, 96-102 (2005). [PubMed], [Publisher Full Text]
  3. Maximizing the potential of functional genomics.
    Steimetz, L.M., Davis, R.W. (2004). Nature Reviews Genetics 5, 190 -201 (2004); doi:10.1038/nrg1293. [PubMed], [Publisher Full Text]
  4. Progress in maize gene discovery: a project update.
    Lunde, C. F., Morrow, D. J., Roy, L. M., Walbot, V. Funct Integr Genomics. 2003 Mar;3(1-2):25-32. Epub 2002 Oct 01. [PubMed]
  5. Denaturing high performance liquid chromatography in the molecular diagnosis of genetic disorders.
    Sivakumaran T.A., Kucheria, K., Oefner, P.J. Current Science, 2003, 84, 101-106
  6. Gene mutation analysis by denaturing high performance liquid chromatography.
    Premstaller, A., Oefner, P.J. PharmaGenomics 2003, 3(2):20-37.
  7. Denaturing high performance liquid chromatography of nucleic acids.
    Premstaller, A., Oefner, P.J. (2002) LC&GC, 15(7),410-422.
  8. Technologische Neuentwicklungen in der Genomwissenschaft - Von Mutation zu Funktion mittels DHPLC und DNS Chips; 2. Teil
    Steinmetz L., Oefner P.J. (2002). Lebensmittel- und Biotechnologie 19(3):93-96.
  9. Technologische Neuentwicklungen in der Genomwissenschaft - Von Mutation zu Funktion mittels DHPLC und DNS Chips; 1. Teil
    Steinmetz L., Oefner P.J. (2002). Lebensmittel- und Biotechnologie 19(2):60-64.
  10. Gene function on a genomic scale.
    Steinmetz L.M., Deutschbauer A.M. (2002) J Chromatogr B Analyt Technol Biomed Life Sci Dec 25;782(1-2):151-63. [PubMed Abstract], [Publisher Full Text]
  11. New trends in DHPLC.
    Premstaller, A., Oefner, P.J., (2002). American Genomic/Proteomic Technology, 2(1):27-29.
  12. A decade of high-resolution liquid chromatography of nucleic acids on styrene-divinylbenzene copolymers.
    Oefner, P.J., Huber, C.G., (2002). J. Chromatogr. B Analyt Technol Biomed Life Sci Dec 25;782(1-2):3-25
  13. Progress in Maize Gene Discovery: a project update.
    Lunde, C.F., Morrow, D. R., Roy L.M., Walbot V., (2002). Funct Integr Genomics. 2003 Mar;3(1-2):25-32. Epub 2002 Oct 01. [PubMed]
  14. Pyrosequencing™: an accurate detection platform for single nucleotide polymorphisms.
    Fakhrai-Rad, H., Pourmand, N., Ronaghi, M., (2002). May, Hum Mutat, 19(5):479-485. [Publisher Abstract].
  15. Comparative genomics of Arabidopsis and maize: prospects and limitations.
    Brendel, V., Kurtz, S., Walbot, V., (2002). Genome Biol, 3(3):REVIEWS1005. [PubMed Abstract].
  16. Denaturing high-performance liquid chromatography: A review.
    Xiao, W., Oefner, P.J., (2001). Jun, Hum Mutat, 17(6):439-474. [PubMed Abstract].
  17. 3rd International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis: SNPs: 'some notable progress'.
    White, P.S., Kwok, P.Y., Oefner, P., Brookes, A.J., (2001). Apr, Eur J Hum Genet, 9(4):316-318. [Publisher Abstract].
  18. Pyrosequencing sheds light on DNA sequencing.
    Ronaghi, M., (2001). Jan, Genome Res, 11(1):3-11. [Publisher Full Text].
  19. Expression monitoring using cDNA microarrays. A general protocol.
    Lou, X.J., Schena, M., Horrigan, F.T., Lawn, R.M., Davis, R.W., (2001). Methods Mol Biol, 175:323-340.
  20. Computational methods for gene annotation: the Arabidopsis genome.
    Cho, Y., Walbot, V., (2001). Apr, Curr Opin Biotechnol, 12(2):126-130. [PubMed Abstract].
  21. SNiPpets from the Third International Meeting on Single Nucleotide Polymorphism and Complex Genome Analysis.
    Brookes, A.J., Kwok, P.Y., White, P.S., Oefner, J.P., (2001). September 8-11, 2000, Taos, New Mexico, USA, Hum. Mutat, 17:241-242.
  22. Combining genome sequences and new technologies for dissecting the genetics of complex phenotypes.
    Steinmetz, L.M., Mindrinos, M., Oefner, P.J., (2000). Sep, Trends Plant Sci, 5(9):397-401.
  23. High-density arrays and insights into genome function.
    Steinmetz, L.M., Davis, R.W., (2000). Biotechnol Genet Eng Rev, 17:109-146.
  24. Fluorescence-based expression monitoring using microarrays.
    Winzeler, E.A., Schena, M., Davis, R.W., (1999). Methods Enzymol, 306:3-18.
  25. Microarrays: biotechnology's discovery platform for functional genomics.
    Schena, M., Heller, R.A., Theriault, T.P., Konrad, K., Lachenmeier, E., Davis, R.W., (1998). Jul, Trends Biotechnol, 16(7):301-306. [PubMed Abstract].
  26. Quantitative analysis of gene expression by ion-pair high-performance liquid chromatography.
    Doris, P.A., Oefner, P.J., Chilton, B.S., Hayward-Lester, A., (1998). May 8, J Chromatogr A, 806(1):47-60. [PubMed Abstract].
  27. Functional analysis of the yeast genome.
    Winzeler, E.A., Davis, R.W., (1997). Dec, Curr Opin Genet Dev, 7(6):771-776. [PubMed Abstract].
  28. Life with 6000 genes.
    Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M., Louis, E.J., Mewes, H.W., Murakami, Y., Philippsen, P., Tettelin, H., Oliver, S.G., (1996). Oct 25, Science, 274(5287):546, 563-547. [Publisher Full Text].

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Short Communications

  1. Analysis of eight exons of the CFTR gene in 65 Iranian cystic fibrosis patients by DHPLC and sequencing.
    Elahi, E., Alinasab, B., Esson, G., Ghassemi, F., Houshmand, M., Khodadad, A., Oefner, P., Reihani-Sabet, F., Ronaghi, M., Shahabi, M., Thorstenson, Y. (2002) Am. J. Hum. Genet. 71 [Suppl], 546.
  2. Interspecies comparisons of the ATM gene.
    Wayne, T.L., Thorstenson, Y.R., Oefner, P.J. (2001) Am. J. Hum. Genet. 69 [Suppl.], 542.
  3. Parallels and contrasts in female and male human evolutionary history.
    Shen, P., Tang, H., Passarino, P., Do, B., Sung, R., Davis, K., Scharfe, C., Cavalli-Sforza, L.L., Feldman, M.W., Oefner, P.J. (2001) Am. J. Hum. Genet. 69 [Suppl.], 423.
  4. BRCA1 and BRCA2 analysis in 523 Austrian HPOC and HBC families.
    Kroiss, R., Wagner, T., Muhr, D., Fleischmann, E., Korn, V., Helbich, T., Zielinski, C., Kubista, E., Oefner, P. (2001) Am. J. Hum. Genet. 69 [Suppl.], 252.
  5. Interspecies comparisons of the ATM gene.
    Wayne, T.L., Thorstenson, Y.R., Oefner, P.J., (2001). Am. J. Hum. Genet, 69 [Suppl.]:542
  6. Germline carriers of ATM mutations are prevalent among Austrian hereditary breast and ovarian cancer (HBOC) patients.
    Thorstenson, Y.R., Roxas, A., Kroiss, R., Wagner, T., Oefner, P.J., (2001). Am. J. Hum. Genet, 69 [Suppl.]:205
  7. Estimation of time to the most recent common ancestor by tree-partition.
    Tang, H., Siegmund, D., Shen, P., Oefner, P., Feldman, M., (2001). Am. J. Hum. Genet, 69 [Suppl.]:394
  8. Mapping genes in Saccharomyces cerevisiae and arabidopsis thaliana using high-density DNA arrays and denaturing high-performance liquid chromatography.
    Steinmetz, L., Mindrinos, M., Spiegelman, J., Richards, D., Xiao, W., Fankhauser, C., McCusker, J., Chory, J., Davis, R., Oefner, P., (2001). Hum. Mutat, 17:323
  9. Parallels and contrasts in female and male human evolutionary history.
    Shen, P., Passarino, G., Sung, R., Song, S., Do, B., Roxas, A., Hurlbut, A., Lin, A., Sherry, S., Feldman, M., Cavalli-Sforza, L., Underhill, P., Oefner, P., (2001). Hum. Mutat, 17:341
  10. Parallels and contrasts in female and male human evolutionary history.
    Shen, P., Tang, H., Passarino, P., Do, B., Sung, R., Davis, K., Scharfe, C., Cavalli-Sforza, L.L., Feldman, M.W., Oefner, P.J., (2001). 423, Am. J. Hum. Genet, 69 [Suppl.]
  11. BRCA1 and BRCA2 analysis in 523 Austrian HPOC and HBC families.
    Kroiss, R., Wagner, T., Muhr, D., Fleischmann, E., Korn, V., Helbich, T., Zielinski, C., Kubista, E., Oefner, P., (2001). Am. J. Hum. Genet, 69 [Suppl.]:252
  12. BRCA1 and BRCA2 analysis of 268 HBOC and HBC families by DHPLC.
    Wagner, T., Moeslinger, R., Muhr, D., Richards, D., Schreiber, M., Fleischmann, E., (2000). Am. J. Hum. Genet, 67 [Suppl.2]:87
  13. Comprehensive mutational analysis of the ATM gene by denaturing HPLC.
    Thorstenson, Y.R., Oefner, P.J., Goss, V., Davis, R.W., Gatti, R.A., Chu, G., (2000). Am. J. Hum. Genet, 67 [Suppl. 2]:100
  14. Mutational analyses of BRCA1 and BRCA2 in Ashkenazi and non-Ashkenazi Jewish women with familial breast and ovarian cancer.
    Shiri-Sverdlov, R., Oefner, P., Gershoni-Baruch, R., Green, L., Hofstra, R.M.W., Wagner, T., Friedman, E., (2000). Am. J. Hum. Genet, 67 [Suppl. 2]:88
  15. Attitude towards prophylactic surgery and effects of genetic counselling in families with BRCA mutations. denaturing HPLC.
    Moeslinger, R., Wagner, T., Langbauer, G., Austrian HBOC Group, Fleischmann, E., Autherith, A., Friedmann, A., Helbich, T., Oefner, P., (2000). Am. J. Hum. Genet, 67 [Suppl. 2]:202
  16. BRCA1 Analysis by DHPLC in 272 Austrian Breast Cancer only and Breast and Ovarian Cancer Families.
    Wagner, T., Moeslinger, R., Fleischmann, E., Muhr, D., Hareter, M., Kofler, P., Austrian HBOC Group, Helbich, T., Zielinski, C., Oefner, P., (1999). Am. J. Hum. Genet, 65 [Suppl.]:A328
  17. Denaturing High Performance Liquid Chromatography (DHPLC) Detects BRCA1 and BRCA2 Mutations with High Sensitivity.
    Oefner, P., Stoppa-Lyonnet, D., Fleischmann, E., Muhr, D., Pages, S., Sandberg, T., Caux, V., Moeslinger, R., Langbauer, G., Borg, A., Wagner, T., (1999). Am. J. Hum. Genet, 65 [Suppl.]:A416
  18. Attitude towards prophylactic surgery and effects of genetic counselling in families with BRCA mutations.
    Moeslinger, R., Wagner, T., Langbauer, G., Austrian HBOC Group, Autherith, A., Friedmann, A., Zielinski, C., Seifert, M., Oefner, P., (1999). Am. J. Hum. Genet, 65 [Suppl.]:A386
  19. Molecular reconstruction of the genealogy of the isolated population of the Costa Rican Central Valley.
    Freimer, N.B., R. Ophoff, R., Meshi1, D., Poon, W., Oefner, P., Service, S., (1999). Am. J. Hum. Genet, 65 [Suppl.]:A203
  20. Polynesian origins: new insights from the Y-chromosome.
    Deka, R., Su, B., Underhill, P., Saha, N., McGarvey, S.T., Chou, J., Oefner, P., Shriver, M.D., Chakraborty, R., Martinson, J. Jin, L., (1999). Am. J. Hum. Genet, 65 [Suppl.]:A83
  21. High frequency of simple sequence variation in BRCA2: Analysis of 70 breast cancer families and 95 control individuals of world wide populations.
    Wagner, T., Hirtenlehner, K., Shen, P., Moeslinger, R., Muhr, D., Fleischmann, E., Concin, H., Doeller, W., Haid, A., Lang, A.H., Mayer, P., Petru, E., Ropp, E., Kubista, E., Scheiner, O., Underhill, P., Stierer, M., Zielinski, C., Oefner, P., (1998). Am. J. Hum. Genet, 63 [Suppl.]:A90
  22. Panorama of Y chromosome SNP haplotype diversity in Pakistan.
    Underhill, P.A., Mehdi, S.Q., Cavalli-Sforza, L.L., Davis, R.W., Oefner, P.J., (1998). Am. J. Hum. Genet, 63 [Suppl.]:A223
  23. Blind Analysis of denaturing high-performance liquid chromatography as a tool for mutation detection.
    O'Donovan, M.C., Oefner, P.J., Roberts, S.C., Austin, J., Hoogendoorn, B., Guy, C., Speight, G., Upadhyaya, M., Sommer, S.S., McGuffin, P., (1998). Am. J. Hum. Genet, 63 [Suppl.]:A238
  24. Genotyping single nucleotide polymorphisms by primer extension and high performance liquid chromatography.
    Hoogendoorn, B., Owen, M.J., Oefner, P.J., Williams, N., Austin, J., O’Donovan, M.C., (1998). Am. J. Hum. Genet, 63 [Suppl.]:A232
  25. Founding BRCA1 and 2 mutations in Austrian HBOC families and individuals of the 5 continents.
    Wagner, T., Muhr, D., Hirtenlehner, K., Möslinger, R., Underhill, P., Scheiner, O., Kubista, E., Oefner, P.J., (1997). Am. J. Hum. Genet, 61 [Suppl.]:A86
  26. An African origin of human Y chromosomes.
    Underhill, P.A., Jin, L., Lin, A., Chan, C., Shen, P., Kauffman, E., Choi, L., Hurlbut, A., Cavalli-Sforza, L.L., Mehdi, S.Q., Jenkins, T., Seielstad, M.T., Wells, R.S., Ibrahim, M., Vollrath, D., Hyman, R., Davis, R., Oefner, P.J., (1997). Am. J. Hum. Genet, 61 [Suppl.]:A18
  27. Hepatitis G virus infection in hemodialysis patients and the effects of interferon.
    Umlauft, F., Wong, D.T., Underhill, P.A., Oefner, P.J., Jin, L., Urbanek, M., Grünewald, K., Greenberg, H.B., (1997). Gastroenterology, 112 [Suppl.]:A1406
  28. Denaturing HPLC identified novel FBN1 mutations, polymorphisms and sequence variants in Marfan syndrome patients.
    Liu, W., Oefner, P., Qian, C., Odom, R., Francke, U., (1997). Am. J. Hum. Genet, 61 [Suppl.]:A223
  29. Autosomal DNA haplotypes distinguish ancient human migrations.
    Jin, L., Underhill, P.A., Doctor, V., Cavalli-Sforza, L.L., Davis, R., Oefner, P.J., (1997). Am. J. Hum. Genet, 61 [Suppl.]:A201
  30. Amassing a wealth of Y chromosome polymorphisms for evolutionary studies.
    Underhill, P.A., Jin, L., Cavalli-Sforza, L.L., Davis, R., Oefner, P.J., (1996). Am. J. Hum. Genet, 59 [Suppl.]:A30. [Abstract].
  31. The terminal 3' non-coding region of hepatitis C virus: A new target for PCR detection.
    Umlauft, F., Wong, D.T., Oefner, P.J., Cheung, R.C., Wright, T.L., Kolykhalov, A.A., Grünewald, K., Greenberg, H.B., (1996). Hepatology, 24:251A
  32. Rapid quantification of HCV RNA by competitive RT-PCR and ion-pair reversed-phase HPLC.
    Umlauft, F., Oefner, P.J., Wong, D.T., Grill, E., Greenberg, H.B., (1996). Gastroenterology, 110:A1349
  33. High-Throughput Differential Genome Analysis by Denaturing HPLC.
    Oefner, P.J., Underhill, P.A., Grill, E.A., Cho, R.J., Jin, L., Cavalli-Sforza, L.L., Davis, R.W., (1996). Microbial & Comparative Genomics, 1:245
  34. Sequencing the Chlamydia trachomatis Genome.
    Kalman, S.S., Araujo, R., Chung, E., Dietrich, F., Komp, C., Otto, G., Lew, H., Lin, D., Marathe, R., Mirthipati, S., Namath, A., Oefner, P., Davis, R.W., Stephens, R., (1996). Microbial & Comparative Genomics, 1:236
  35. Kidney and nephron calcineurin (CaN) expression in spontaneously hypertensive rats (SHR) by competitive RT-PCR and IP-RP-HPLC.
    Hinojos, C.A., Hayward-Lester, A., Sabatini, S., Oefner, P.J., Doris, P.A., (1996). Mol. Biol. Cell, 7 [Suppl.]
  36. Analysis of multiple sodium pump genes expressed in nephrons from spontaneously hypertensive rats (SHR) by competitive RT-PCR and IP-RP-HPLC.
    Hayward-Lester, A., Lonis, B., Sabatini, S., Lee, A.M., Oefner, P.J., Doris, P.A., (1996). Mol. Biol. Cell, 7 [Suppl.]:470A
  37. Mapping and Sequencing of the Arabidopsis Genome.
    Dewar, K., Dunn, P.J., Li, Y.-P., Kim, C.J., Ecker, J.R., Federspiel, N.A., Dietrich, F., Marziali, A., Oefner, P., Norgren, R., Davis, R.W., Vysotskaia, V., Yu, Q., Theologis, A., (1996). Microbial & Comparative Genomics, 1:204
  38. Identification and characterization of pre-Columbian human Y chromo-some specific allele.
    Zemans, R., Jin, L., Underhill, P.J., Oefner, P.J., Cavalli-Sforza, L.L. (1995). Am. J. Hum. Genet 57 [Suppl.]:A174
  39. Y-chromosomal variation and recent conquests in deciphering human origins
    Underhill, P.A., Jin, L., Oefner, P.J., Cavalli-Sforza, L.L. (1995). Am. J. Hum. Genet 57 [Suppl.]:A43
  40. Comparative DNA sequencing by denaturing high-performance liquid chromatography (DHPLC).
    Oefner, P.J., Underhill, P.A. (1995). Am. J. Hum. Genet 57 [Suppl.]:A266
  41. Accurate and absolute quantification of gene expression by single tube RT-PCR and HPLC.
    Hayward-Lester, A., Oefner, P.J., Doris, P. (1995). Mol. Biol. Cell 6 [Suppl.]:444A
  42. Systematic search for polymorphisms in the human genome using denaturing high-performance liquid chromatography (DHPLC).
    Jin, L., Underhill, P.A., Oefner, P.J., Cavalli-Sforza, L.L. (1995). Am. J. Hum. Genet 57 [Suppl.] A26.

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updated March 23, 2012

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