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).

 

Patents & Technology Transfer

Issued Patents

  1. Fetal cell analysis using sample splitting.
    Shoemaker D, Kapur R, Toner M, Stoughton R, Davis RW. (2012). US Patent 8,168,389. [USPTO]
  2. Charge perturbation detection system for DNA and other molecules.
    Pourmand N, Karhanek M, Davis RW. (2012). US Ppatent 8,313,907 [USPTO]
  3. Methods for the diagnosis of fetal abnormalities.
    Kapur, R., Toner, M., Stoughton, R., Shoemaker, D., Davis, RW. (2012). US Patent 8,137,912 [USPTO]
  4. Methods and apparatus for magnetic separation of cells.
    Davis, RW., Jeffrey, SS., Mindrinos, MN., Pease, RF., Powell, AA., Hajhossein,Talasaz, A. (2011). US Patent 8,071,395 [USPTO]
  5. Precircle probe nucleic acid amplification methods.
    Willis, TD. Hardenbol, P. Jain, M. Stolc, V. Ronaghi, M. Davis, RW . (2011). US Patent 7,993,880 [USPTO]
  6. Charge perturbation detection system for DNA and other molecules.
    Pourmand, N. Karhanek, M. Davis, RW. (2011). US Patent 8,012,75 [USPTO]
  7. Rapid, informative diagnostic assay for influenza viruses including H5N1.
    Pourmand, N., Diamond, L., Kumm, J., Davis, RW. (2011). US Patent 7,989,185 [USPTO]
  8. Heat and pH measurement for sequencing of DNA.
    Esfandyarpour, H. Ronaghi, M. (2011). US Patent 7,932,034. [USPTO]
  9. Methods and compositions for use in analyte detection using proximity probes.
    Fredriksson, S., Davis, RW. (2011). US Patent 7,914,987. [USPTO]
  10. Method to produce single stranded DNA of defined length and sequence and DNA probes produced thereby.
    Mindrinos, M., Krishnakumar, S., Davis, RW. (2011). US Patent 7,897,747. [USPTO]
  11. Multiplexed assay and probes for identification of HPV types.
    Pourmand, N., Gharizadeh, B., Davis, RW. (2011). US Patent 7,875,428. [USPTO]
  12. Charge perturbation detection system for DNA and other molecules.
    Pourmand, N., Davis, RW., Karhanek, M. (2010). US Patent 7,785,785. [USPTO]
  13. Semiconductor sensor circuit arrangement.
    Ronaghi, M., Agah, A. (2010). US Patent 7,782,237. [USPTO]
  14. Devices and methods to form a randomly ordered array of magnetic beads and uses thereof.
    Jain, M., White, RL., Roberts, LA. (2010). US Patent 7,682,837. [USPTO]
  15. Method for detecting and amplifying target DNA.
    Willis, TD., Hardenbol, P., Jain, M., Stolc, V., Davis, RW. (2010). US Patent 7,700,323. [USPTO]
  16. Apparatus and methods for parallel processing of micro-volume liquid reactions.
    O'Keefe, M., Foreman, PK. (2010). US Patent 7,833,719. [USPTO]
  17. Methods and compositions for clonal amplification of nucleic acid.
    Ronaghi, M., Mashayekhi, F. (2009). US Patent 7,622,281. [USPTO]
  18. Magnetic sifter.
    Wang, SX., Pourmand, N., White, RL. (2009). US Patent 7,615,382. [USPTO]
  19. Apparatus and methods for parallel processing of micro-volume liquid reactions.
    O'Keefe, M., Foreman, PK. (2009). US Patent 7,604,983. [USPTO]
  20. Renaturation, reassociation, association and hybridization of nucleic acid molecules.
    Namsaraev, E., Davis, RW., Karlin-Neumann, G. (2009). US Patent 7,482,125. [USPTO]
  21. DNA fingerprinting using a branch migration assay.
    Pourmand, N., Davis, RW., Wang, SX. (2009). US Patent 7,501,253. [USPTO]
  22. Apparatus and methods for parallel processing of micro-volume liquid reactions.
    O'Keefe, M., Foreman, PK. (2008). US Patent 7,332,271. [USPTO]
  23. DNA fingerprinting using a branch migration assay.
    Pourmand, N., Davis, RW., Wang, SX. (2007). US Patent 7,238,486. [USPTO]
  24. Charge Sequencing: A New Technique for DNA Sequencing and SNP Detection (Transient electrical signal based methods and devices for characterizing molecular interaction and/or motion in a sample).
    Pourmand, N. Hassibi, A. (2007). US Patent 7,223,540. [USPTO]
  25. Mismatch repair detection.
    Cox, DR, Faham, M., Baharloo, S. (2006). US Patent 7,153,652. [USPTO]
  26. Renaturation, reassociation, association and hybridization of nucleic acid molecules.
    Namsaraev, E., Davis,R.W., Karlin-Neumann, G. (2006). US Patent 7,129,044. [USPTO]
  27. Bioluminescence regenerative cycle (BRC) for nucleic acid quantification.
    Pourmand, N. Hassibi, A. (2006). US Patent 7,141,370. [USPTO]
  28. Direct multiplex characterization of genomic DNA.
    Willis, T.D., Hardenbol, P., Jain, M., Stolc, V., Ronaghi, M., Davis, R.W. (2005). United States Patent 6,858,412. [USPTO]
  29. Method for determining genetic affiliation, substructure and gene flow within human populations.
    Oefner, P.J., Underhill, P.A. (2005). U.S. Patent 6,929,911. [USPTO]
  30. Dimeric fluorescent polypeptides.
    Davis, R.W. Vaillancourt, P. (2005). US Patent US Patent 6,936,428. [USPTO]
  31. Mismatch repair detection.
    Cox D., Faham, M. Bharloo, S. (2004). US Patent 6,709,827. [USPTO]
  32. Identification of drugs and drug targets by detection of the stress response.
    Davis, R.W., Giaever, G. (2004). United States Patent 6,743,583. [USPTO]
  33. Polypeptides from Chlamydia pneumoniae and their use in the diagnosis, prevention and treatment of disease.
    Stephens, R.S., Mitchell, W., Kalman, S.S., Davis, R.W. (2004). US Patent 6,822,071. [USPTO]
  34. Detection of polymorphisms by denaturing high-performance liquid chromatography.
    Oefner, P.J. (2002). United States Patent 6,453,244. [USPTO]
  35. Selecting tag nucleic acids.
    Morris, M.S., Shoemaker, D.D., Davis, R.W. Mittmann, M.P. (2002). US Patent 6,458,530. [USPTO]
  36. Recombinant mycobacteria.
    Bloom, B.R., Davis, R.W., Jacobs, Jr., R., Young, R.A., Husson, R.N. (2002). US Patent 6,372,478. [USPTO]
  37. Mismatch repair detection.
    Cox, D., Faham, M., Bahrloo, S. (2001). US Patent 6,406,847. [USPTO]
  38. Method for simultaneous centrifugation of samples.
    Marziali, A., (2001). United States Patent 6,273,848. [USPTO]
  39. Microcentrifuge.
    Marziali A., (2001), United States Patent 6,238,330. [USPTO]
  40. Recombinant mycobacterial vaccine.
    Bloom, B.R., Davis, R.W. Jacobs, Jr., W.R. Young, R.A. Husson, R.N. (2001). US Patent 6,270,776. [USPTO]
  41. Highly parallel and sensitive method for identifying drugs and drug targets.
    Davis, R.W., Giaever, G.N., Shoemaker D., (2000). United States Patent 6,046,002. [USPTO]
  42. Thermocycling apparatus and method.
    Hunicke-Smith S.P., (2000). United States Patent 6,132,996. [USPTO]
  43. Thermocycling apparatus and method.
    Hunicke-Smith S.P., (1999). United States Patent 5,985,651. [USPTO]
  44. Mycobacteriophages and uses thereof.
    Bloom, B.R., Davis; R.W., Jacobs, Jr., W.R., Young, R.A., Husson, R.N. (1999). US Patent 5,968,733. [USPTO]
  45. Cleaved amplified RFLP detection methods.
    Ausubel, F., Davis, R.W., Preuss, D. (1999). US Patent, 6,004,783. [USPTO]
  46. Apparatus and method for shear breakage of polynucleotides.
    Oefner, P.J., Hunicke-Smith S.P. (1998). United States Patent 5,846,832. [USPTO]
  47. Detection of nucleic acid heteroduplex molecules by denaturing high-performance liquid chromatography and methods for comparative sequencing.
    Oefner, P.J., Underhill, P.A., (1998). US Patent 5,795,976. Licensed to Transgenomic Inc., Omaha, NE, USA, Hewlett-Packard, Palo Alto, CA, USA, Qiagen Inc., Bothell, WA, USA, and Varian, Walnut Creek, CA, USA. [USPTO]
  48. Recombinant mycobacteria.
    Bloom, B.R. Jacobs, Jr., W.R. Davis, R.W. Young, R.A. Husson, R.N. (1998). US Patent 5,854,055. [USPTO]
  49. Software to determine optimum temperature for DHPLC given DNA sequence.
    Hansen, N.F., Oefner, P.J. (1997). Stanford University Invention Disclosure S97-175 (Tangible Research Property in conjunction with U.S. Patent 5,795,976).
  50. Nucleic Acid Separation on Alkylated Nonporous Polymer Beads. US Patent 5,585,236. (Licensed to Transgenomic Inc., Omaha, NE, USA).
    Bonn, G., Huber, C., Oefner, P.J. (1996). [USPTO]
  51. Recombinant mycobacterial vaccine.
    Bloom, BR., Davis, RW., Jacobs, Jr., WR., Young, RA., Husson, RN. (1996). US Patent 5,504,005. [USPTO]
  52. Electrophoresis using contour-clamped electric fields.
    Chu, G., Vollrath, D., Davis, R., (1996). US Patent 5,549,796. [USPTO]
  53. Method for detecting a nucleotide at a specific location within a nucleic acid using exonuclease activity.
    Davis, R.W., Myles, A. (1995). US Patent 5,391,480. [USPTO]
  54. Electrophoresis using contour-clamped electric fields.
    Chu, G., Vollrath, D., Davis, RW. (1992). US Patent 5,165,898. [USPTO]
  55. Use of the GAL1 yeast promoter.
    Botstein, D., Davis, RW., Fink, GR., Taunton-Rigby, A., Knowlton, RG., Mao, J., Moir, DT., Goff, CG. (1992). US Patent 5,139,936. [USPTO]
  56. Encoding antigens of M. Leprae.
    Young, RA., Bloom, BR., Davis, RW. (1990). US Patent 4,906,742. [USPTO]
  57. System for efficient isolation of genes using probes.
    Davis, RW., Young, RA. (1988). US Patent 4,788,135. [USPTO]
  58. Rennin-containing disrupted yeast cells used in cheese manufacture.
    Botstein, D., Fink, GR., Davis, RW. (1987). US Patent 4,695,470. [USPTO]
  59. GAL1 yeast promoter linked to non galactokinase gene.
    Botstein, D., Davis, RW., Fink, DR., Taunton-Rigby, A., Knowlton, RG., Mao, J.,Moir, DT., Goff, CG. (1987). US Patent 4,661,454. [USPTO]

Original Articles

  1. Diversity of the Vaginal Microbiome Correlates With Preterm Birth.
    Hyman, RW., Fukushima, M., Jiang, H., Fung, E., Rand, L., Johnson, B., Vo, KC., Caughey, AB., Hilton, JF., Davis, RW, Guidice, LC. Reproductive Sciences 2014, 21:32, published online 28 May 2013. DOI: 10.1177/1933719113488838. [PubMed]
  2. Multiplex target capture with double-stranded DNA probes.
    Shen, P., Wang, W., Chi, AK., Fan, Y., Davis, RW., Scharfe, C. Genome Medicine 2013, 5:50 doi:10.1186/gm454. [PubMed]
  3. Multiplex target capture with double-stranded DNA probesBenchmarking outcomes in the critically injured trauma patient and the effect of implementing standard operating procedures.
    Cuschieri, J., Johnson, J. L., Sperry, J., West, M. A., Moore, E. E., Minei, J. P., Bankey, P. E., Nathens, A. B., Cuenca, A. G., Efron, P. A., Hennessy, L., Xiao, W., Mindrinos, M. N., McDonald-Smith, G. P., Mason, P. H., Billiar, T. R., Schoenfeld, D. A., Warren, H. S., Cobb, J. P., Moldawer, L. L., Davis, R. W., Maier, R. V., Tompkins, R. G., Ann Surg. 2012;255(5):993-9. PMCID: 3327791. [PubMed]
  4. Microfluidic diagnostic tool for the developing world: contactless impedance flow cytometry.
    Emaminejad S, Javanmard M, Dutton RW, Davis RW. Lab on a chip. 2012. [PubMed]
  5. Control of DNA capture by nanofluidic transistors.
    Paik, K. H., Liu, Y., Tabard-Cossa, V., Waugh, M. J., Huber, D. E., Provine, J., Howe, R. T., Dutton, R.W., Davis, R.W. ACS Nano. 2012;6(8):6767-75. PMCID: 3429714. [PubMed]
  6. Cationic amphiphilic drugs are potent inhibitors of yeast sporulation.
    Schlecht, U., St Onge, RP,. Walther, T., Francois, J. M., Davis, RW. PLoS ONE. 2012;7(8):e42853. PMCID: 3414501. [PubMed]
  7. Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies.
    Xu, W., Gao, H., Seok, J., Wilhelmy, J., Mindrinos, M. N., Davis, R. W., Xiao, W. BioTechniques. 2012;52(6):386-8. [PubMed]
  8. High-throughput, high-fidelity HLA genotyping with deep sequencing.
    Wang, C., Krishnakumar, S., Wilhelmy, J., Babrzadeh, F., Stepanyan, L., Su, L. F. Levinson, D. Fernandez-Vina, M. A. Davis, R. W. Davis, M. M. Mindrinos, M. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(22):8676-81. PMCID: 3365218. [PubMed]
  9. Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research.
    Seok J, Xu W, Jiang H, Davis RW, Xiao W. PLoS ONE. 2012;7(2):e31440. PMCID: 3270033. [PubMed]
  10. JETTA: junction and exon toolkits for transcriptome analysis.
    Seok J, Xu W, Gao H, Davis RW, Xiao W. Bioinformatics. 2012;28(9):1274-5. PMCID: 3338022. [PubMed]. JETTA and its demonstrations are freely available at http://igenomed.stanford.edu/~junhee/JETTA/index.html
  11. Multiplex assay for condition-dependent changes in protein-protein interactions.
    Schlecht U, Miranda M, Suresh S, Davis RW, St Onge RP. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(23):9213-8. [PubMed]
  12. Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines.
    Powell, A. A. Talasaz, A. H. Zhang, H. Coram, M. A. Reddy, A. Deng, G. Telli, M. L. Advani, R. H. Carlson, R. W. Mollick, J. A. Sheth, S. Kurian, A. W. Ford, J. M. Stockdale, F. E. Quake, S. R. Pease, R. F. Mindrinos, M. N. Bhanot, G. Dairkee, S. H. Davis, R. W. Jeffrey, S. S. PLoS ONE. 2012;7(5):e33788. PMCID: 3346739. [PubMed]
  13. Molecular probe technology detects bacteria without culture.
    Hyman, R. W. St Onge, R. P. Kim, H. Tamaresis, J. S. Miranda, M. Aparicio, A. M. Fukushima, M. Pourmand, N. Giudice, L. C. Davis, R. W. BMC microbiology. 2012;12:29. PMCID: 3316761. [PubMed]
  14. The dynamics of the vaginal microbiome during infertility therapy with in vitro fertilization-embryo transfer.
    Richard W. Hyman, Christopher N. Herndon, Hui Jiang, Curtis Palm, Marilyn Fukushima, Denise Bernstein, Kim Chi Vo, Zara Zelenko, Ronald W. Davis and Linda C. Giudice. J Assist Reprod Genet. 2012;29(2):105-15. PMCID: 3270134. [Epub ahead of print] DOI: 10.1007/s10815-011-9694-6. [Publisher], [PubMed]
  15. A rapid, cost-effective method of assembly and purification of synthetic DNA probes >100 bp.
    Jensen MA, Jauregui L, Davis RW. PLoS ONE. 2012;7(4):e34373. PMCID: 3321010. [PubMed]
  16. Competitive Genomic Screens of Barcoded Yeast Libraries.
    Smith, A. M., Durbic, T., Oh, J., Urbanus, M., Proctor, M., Heisler, L. E., et al. J. Vis. Exp. (54), e2864, DOI: 10.3791/2864 (2011).
  17. Bacteria on Human Skin.
    Hyman, RW., Babrzadeh, F., Palm, C., Wang, C., Fukushima, M., Davis, RW. American Journal of Microbiology 2 (2): 25-34, 2011. DOI: 10.3844/ajmsp.2011.25.34 [Publisher]
  18. The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome.
    Newburger DE, Natsoulis G, Grimes S, Bell JM, Davis RW, Batzoglou S, Ji HP. Nucleic Acids Res. 2012 Jan;40(Database issue):D1137-43. Epub 2011 Nov 18. [PubMed], Human OligoGenome Resource at http://oligogenome.stanford.edu/
  19. High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment.
    Logan AC, Gao H, Wang C, Sahaf B, Jones CD, Marshall EL, Buño I, Armstrong R, Fire AZ, Weinberg KI, Mindrinos M, Zehnder JL, Boyd SD, Xiao W, Davis RW, Miklos DB. Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21194-9. Epub 2011 Dec 12. [PubMed]
  20. A genomic storm in critically injured humans.
    Xiao W, Mindrinos MN, Seok J, Cuschieri J, Cuenca AG, Gao H, Hayden DL, Hennessy L, Moore EE, Minei JP, Bankey PE, Johnson JL, Sperry J, Nathens AB, Billiar TR, West MA, Brownstein BH, Mason PH, Baker HV, Finnerty CC, Jeschke MG, López MC, Klein MB, Gamelli RL, Gibran NS, Arnoldo B, Xu W, Zhang Y, Calvano SE, McDonald-Smith GP, Schoenfeld DA, Storey JD, Cobb JP, Warren HS, Moldawer LL, Herndon DN, Lowry SF, Maier RV, Davis RW, Tompkins RG; and the Inflammation and Host Response to Injury Large-Scale Collaborative Research Program. J Exp Med. 2011 Dec 19;208(13):2581-90. Epub 2011 Nov 21. [PubMed], [Publisher]
  21. Performance comparison of whole-genome sequencing platforms.
    Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Nat Biotechnol. 2011 Dec 18;30(1):78-82. doi: 10.1038/nbt.2065. [PubMed]
  22. Use of Negative Dielectrophoresis for Selective Elution of Protein-bound Particles.
    Javanmard M, Emaminejad S, Dutton RW, Davis RW. Analytical chemistry. 2012;84(3):1432-8. PMCID: 3278233. [Epub ahead of print], [PubMed]
  23. Improvement in cell capture throughput using parallel bioactivated microfluidic channels.
    Javanmard M, Babrzadeh F, Nyren P, Davis RW. Biomed Microdevices. 2012;14(4):625-9. PMCID: 3414683. [PubMed]
  24. Targeted sequencing library preparation by genomic DNA circularization.
    Myllykanagas S, Natsoulis G, Bell JM, Ji HP. BMC Biotechnol. 2011 Dec 14;11(1):122. [Epub ahead of print] [PubMed]
  25. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions.
    Deutschbauer A, Price MN, Wetmore KM, Shao W, Baumohl JK, Xu Z, Nguyen M, Tamse R, Davis RW, Arkin AP. PLoS Genet. 2011 Nov;7(11):e1002385. Epub 2011 Nov 17. [PubMed]
  26. Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms.
    Wallace IM, Urbanus ML, Luciani GM, Burns AR, Han MKL, Wang H, Arora K, Heisler LE, Proctor M, St Onge RP, Roemer T, Roy PJ, Cummins CL, Bader GD, Nislow C, Giaever G. Chemistry & Biology, Volume 18, Issue 10, 1273-1283, 28 October 2011. [Article]
  27. Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing.
    Myllykangas S, Buenrostro J, Natsoulis G, Bell JM, Ji HP. Nature Biotechnology (2011) doi:10.1038/nbt.1996. [Publisher]
  28. Ultrasensitive detection of rare mutations using next-generation targeted resequencing.
    Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, Bell J, Brown S, Holodniy M, Zhang N, Ji HP. Nucleic Acids Res. 2012;40(1):e2. PMCID: 3245950. [Epub ahead of print], [PubMed]
  29. Benchmarking outcomes in the critically injured trauma patient and the effect of implementing standard operating procedures.
    Cuschieri, J. Johnson, J. L. Sperry, J. West, M. A. Moore, E. E. Minei, J. P. Bankey, P. E. Nathens, A. B. Cuenca, A. G. Efron, P. A. Hennessy, L. Xiao, W. Mindrinos, M. N. McDonald-Smith, G. P. Mason, P. H. Billiar, T. R. Schoenfeld, D. A. Warren, H. S. Cobb, J. P. Moldawer, L. L. Davis, R. W. Maier, R. V. Tompkins, R. G. Ann Surg. 2012;255(5):993-9. PMCID: 3327791. [PubMed]
  30. Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1.
    Babrzadeh, F. Jalili, R. Wang, C. Shokralla, S. Pierce, S. Robinson-Mosher, A. Nyren, P. Shafer, R. W. Basso, L. C. de Amorim, H. V. de Oliveira, A. J. Davis, R. W. Ronaghi, M. Gharizadeh, B. Stambuk, B. U. Mol Genet Genomics. 2012;287(6):485-94. [PubMed]
  31. Competitive Genomic Screens of Barcoded Yeast Libraries.
    Smith AM, Durbic T, Oh J, Urbanus M, Proctor M, Heisler LE, Giaever G, Nislow C. J Vis Exp. 2011 Aug 11;(54). pii: 2864. doi: 10.3791/2864. [PubMed], [Video]
  32. The Automated Cell: Compound and Environment Screening System (ACCESS) for Chemogenomic Screening.
    Proctor M, Urbanus ML, Fung EL, Jaramillo DF, Davis RW, Nislow C, Giaever G. Methods Mol Biol. 2011;759:239-69. [PubMed]
  33. A flexible approach for highly multiplexed candidate gene targeted resequencing.
    Natsoulis G, Bell JM, Xu H, Buenrostro JD, Ordonez H, Grimes S, Newburger D, Jensen M, Zahn JM, Zhang N, Ji HP. PLoS One. 2011;6(6):e21088. Epub 2011 Jun 30. [PubMed]
  34. Combining magnetic resonance spectroscopy and molecular genomics offers better accuracy in brain tumor typing and prediction of survival than either methodology alone.
    Astrakas L, Blekas KD, Constantinou C, Andronesi OC, Mindrinos MN, Likas AC, et al. Int J Oncol. 2011;38(4):1113-27. PMID: 21274507. [PubMed]
  35. Human transcriptome array for high-throughput clinical studies.
    Xu, W., Seok, J., Mindrinos, M.N., Schweitzer, A.C., Jiang, H., Wilhelmy, J., Clark, T.A., Kapur, K., Xing, Y., Faham, M., Storey, J.D., Moldawer, L.L., Maier, R.V., Tompkins, R.G., Wong, W.H., Davis, R.W. and Xiao, W. PNAS. (2011) 108 (9):I3707-3712. PMCID: 3048146. [PubMed]
  36. Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing.
    Wang W, Shen P, Thiyagarajan S, Lin S, Palm C, Horvath R, Klopstock T, Cutler D, Pique L, Schrijver I, Davis RW, Mindrinos M, Speed TP, Scharfe C. Nucleic Acids Res. 39: 44-58. 2011. PMCID: 3017602. [Epub ahead of print] [PubMed]
  37. Distinctive responsiveness to stromal signaling accompanies histologic grade programming of cancer cells.
    Luciani MG, Seok J, Sayeed A, Champion S, Goodson WH, Jeffrey SS, Xiao W, Mindrinos M, Davis RW, Dairkee SH. PLoS One. 2011;6(5):e20016. Epub 2011 May 19. [PubMed]
  38. High-quality DNA sequence capture of 524 disease candidate genes.
    Shen, P., Wang, W., Krishnakumar, S., Palm, C., Chi, A.K., Enns, G., Davis, RW., Speed, T.P., Mindrinos, MN., Scharfe, C. (2011). Published online ahead of print April 5, 2011, doi: 10.1073/pnas.1018981108. PMCID: 3080966. [PubMed]
  39. Targeted deep resequencing of the human cancer genome using next-generation technologies.
    Myllykangas S, Ji HP. Biotechnol Genet Eng Rev. 2010;27:135-58. Review. [PubMed]
  40. Predicting patient survival from longitudinal gene expression.
    Zhang Y, Tibshirani RJ, Davis RW. Stat Appl Genet Mol Biol. 2010;9(1):Article41. PMCID: 3004784. [PubMed]
  41. Analysis of factorial time-course microarrays with application to a clinical study of burn injury.
    Zhou, B., Xu, W., Herndon, D., Tompkins, R., Davis, R., Xiao, W., Wong, W.H., Toner, M., Warren, H.S., Schoenfeld, D.A., Rahme, L., McDonald-Smith, G.P., Hayden, D., Mason, P., Fagan, S., Yu, Y.M., Cobb, J.P., Remick, D.G., Mannick, J.A., Lederer, J.A., Gamelli, R.L., Silver, G.M., West, M.A., Shapiro, M.B., Smith, R., Camp, D.G., 2nd, Qian, W., Storey, J., Mindrinos, M., Tibshirani, R., Lowry, S., Calvano, S., Chaudry, I., Cohen, M., Moore, E.E., Johnson, J., Moldawer, L.L., Baker, H.V., Efron, P.A., Balis, U.G., Billiar, T.R., Ochoa, J.B., Sperry, J.L., Miller-Graziano, C.L., De, A.K., Bankey, P.E., Finnerty, C.C., Jeschke, M.G., Minei, J.P., Arnoldo, B.D., Hunt, J.L., Horton, J., Brownstein, B., Freeman, B., Maier, R.V., Nathens, A.B., Cuschieri, J., Gibran, N., Klein, M. and O'Keefe, G. PNAS. (2010) 107 (22):I9923-8. PMCID: 2890487. [PubMed]
  42. Gas-phase cleavage and dephosphorylation of universal linker-bound oligodeoxynucleotides.
    Jensen MA, Anderson KM, Davis RW. (2010). Nucleosides, nucleotides & nucleic acids. (2010) 29 (11):I867-78. PMID: 21128173. [PubMed]
  43. DMSO and Betaine Greatly Improve Amplification of GC-Rich Constructs in De Novo Synthesis.
    Jensen, MA, Fukushima, M, Davis RW. (2010). PLoS ONE 5(6): e11024. doi:10.1371/journal.pone.0011024. PMCID: 2883997. [Full Text]
  44. A molecular inversion probe assay for detecting alternative splicing.
    Lin, S., Wang, W., Palm, C,Davis, RW., Juneau, K.BMC Genomics 2010, 11:712, doi:10.1186/1471-2164-11-712. PMCID: 3022918. [PubMed]
  45. Semi-automated library preparation for high-throughput DNA sequencing platforms.
    Farias-Hesson E, Erikson J, Atkins A, Shen P, Davis RW, Scharfe C, Pourmand N. J Biomed Biotechnol. 2010;2010:617469. Epub 2010 Jun 8. PMCID: 2896710.. [PubMed]
  46. Multiplex Identification of Microbes.
    Hyman, RW., St.Onge, RP., Allen, EA., Miranda, M., Aparicio, AM., Fukushima, M. and Davis, RW. Applied and environmental biology, June 2010, p. 3904–3910 Vol. 76, No. 12, doi:10.1128/AEM.02785-09. PMCID: 2893500. [PubMed]
  47. A direct comparison of the KB Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry.
    Hyman, R.W., Jiang, H., Fukushima, M. and Davis, RW. BMC research notes. (2010) 3 257. PMCID: 3020662. [PubMed]
  48. Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation.
    Wadia, P.P., Coram, M., Armstrong, R.J., Mindrinos, M., Butte, A.J. and Miklos, D.B. Blood. (2010) 115 2077-87. PMCID:2837325. [PubMed]
  49. Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples.
    Smith, A.M., Heisler, L.E., St Onge, R.P., Farias-Hesson, E., Wallace, I.M., Bodeau, J., Harris, A.N., Perry, K.M., Giaever, G., Pourmand, N. and Nislow, C. Nucleic Acids Res. (2010) 38 (13):Ie142. PMCID: 2910071. [PubMed]
  50. Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships.
    Seok, J., Kaushal, A., Davis, R.W. and Xiao, W. BMC Bioinformatics. (2010) 11 Suppl 1 S8. PMCID: 3009543. [PubMed]
  51. Gene annotation and drug target discovery in Candida albicans with a tagged transposon mutant collection.
    Oh, J., Fung, E., Schlecht, U., Davis, R.W., Giaever, G., St Onge, R.P., Deutschbauer, A. and Nislow, C. PLoS pathogens. (2010) 6 (10):I. PMCID: 2951378. [PubMed]
  52. A universal TagModule collection for parallel genetic analysis of microorganisms.
    Oh, J., Fung, E., Price, M.N., Dehal, P.S., Davis, R.W., Giaever, G., Nislow, C., Arkin, A.P. and Deutschbauer, A. Nucleic acids research. (2010) 38 (14):Ie146. [PubMed]
  53. Sensitive giant magnetoresistive-based immunoassay for multiplex mycotoxin detection.
    Mak, A.C., Osterfeld, S.J., Yu, H., Wang, S.X., Davis, R.W., Jejelowo, O.A. and Pourmand, N. Biosens Bioelectron. (2010) 25 1635-9. [PubMed]
  54. Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action.
    Hillenmeyer, M.E., Ericson, E., Davis, R.W., Nislow, C., Koller, D. and Giaever, G. Genome Biol. (2010) 11 R30. [PubMed]
  55. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets.
    Wang, C., Sanders, C.M., Yang, Q., Schroeder, H.W., Jr., Wang, E., Babrzadeh, F., Gharizadeh, B., Myers, R.M., Hudson, J.R., Jr., Davis, R.W. and Han, J. Proc Natl Acad Sci U S A. (2010) 107 1518-23. PMCID:2824416. [PubMed]
  56. The genetic landscape of a cell.
    Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E.D., Sevier, C.S., Ding, H., Koh, J.L., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R.P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F.J., Alizadeh, S., Bahr, S., Brost, R.L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z.Y., Liang, W., Marback, M., Paw, J., San Luis, B.J., Shuteriqi, E., Tong, A.H., van Dyk, N., Wallace, I.M., Whitney, J.A., Weirauch, M.T., Zhong, G., Zhu, H., Houry, W.A., Brudno, M., Ragibizadeh, S., Papp, B., Pal, C., Roth, F.P., Giaever, G., Nislow, C., Troyanskaya, O.G., Bussey, H., Bader, G.D., Gingras, A.C., Morris, Q.D., Kim, P.M., Kaiser, C.A., Myers, C.L., Andrews, B.J. and Boone, C. Science. (2010) 327 425-31. [PubMed]
  57. Molecular inversion probes reveal patterns of 9p21 deletion and copy number aberrations in childhood leukemia.
    Schiffman JD, Wang Y, McPherson LA, Welch K, Zhang N, Davis R, Lacayo NJ, Dahl GV, Faham M, Ford JM, Ji HP. Cancer Genet Cytogenet. 2009 Aug;193(1):9-18. [PubMed]
  58. Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample.
    Qian, W.J., Liu, T., Petyuk, V.A., Gritsenko, M.A., Petritis, B.O., Polpitiya, A.D., Kaushal, A., Xiao, W., Finnerty, C.C., Jeschke, M.G., Jaitly, N., Monroe, M.E., Moore, R.J., Moldawer, L.L., Davis, R.W., Tompkins, R.G., Herndon, D.N., Camp, D.G. and Smith, R.D. J Proteome Res. (2009) 8 290-9. PMCID:2752204. [PubMed]
  59. Whole genome survey of coding SNPs reveals a reproducible pathway determinant of Parkinson disease.
    Srinivasan, B.S., Doostzadeh, J., Absalan, F., Mohandessi, S., Jalili, R., Bigdeli, S., Wang, J., Mahadevan, J., Lee, C.L., Davis, R.W., William Langston, J. and Ronaghi, M. Hum Mutat. (2009) 30 228-38. PMCID:2793088. [PubMed]
  60. Chemogenomic approaches to elucidation of gene function and genetic pathways.
    Pierce, S.E., Davis, R.W., Nislow, C. and Giaever, G. Methods Mol Biol. (2009) 548 115-43. [PubMed]
  61. Label-free biosensing with functionalized nanopipette probes.
    Umehara, S., Karhanek, M., Davis, R.W. and Pourmand, N. Proc Natl Acad Sci U S A. (2009) 106 4611-6. PMCID:2651834. [PubMed]
  62. Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device.
    Talasaz, A.H., Powell, A.A., Huber, D.E., Berbee, J.G., Roh, K.H., Yu, W., Xiao, W., Davis, M.M., Pease, R.F., Mindrinos, M.N., Jeffrey, S.S. and Davis, R.W. Proc Natl Acad Sci U S A. (2009) 106 3970-5. PMCID:2645911. [PubMed]
  63. High-throughput, high-accuracy array-based resequencing.
    Zheng, J., Moorhead, M., Weng, L., Siddiqui, F., Carlton, V.E., Ireland, J.S., Lee, L., Peterson, J., Wilkins, J., Lin, S., Kan, Z., Seshagiri, S., Davis, R.W. and Faham, M. Proc Natl Acad Sci U S A. (2009) 106 6712-7. PMCID:2672536. [PubMed]
  64. Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes.
    Norman, P.J., Abi-Rached, L., Gendzekhadze, K., Hammond, J.A., Moesta, A.K., Sharma, D., Graef, T., McQueen, K.L., Guethlein, L.A., Carrington, C.V., Chandanayingyong, D., Chang, Y.H., Crespi, C., Saruhan-Direskeneli, G., Hameed, K., Kamkamidze, G., Koram, K.A., Layrisse, Z., Matamoros, N., Mila, J., Park, M.H., Pitchappan, R.M., Ramdath, D.D., Shiau, M.Y., Stephens, H.A., Struik, S., Tyan, D., Verity, D.H., Vaughan, R.W., Davis, R.W., Fraser, P.A., Riley, E.M., Ronaghi, M. and Parham, P. Genome Res. (2009) 19 757-69. PMCID:2675964. [PubMed]
  65. Electrical detection of protein biomarkers using bioactivated microfluidic channels.
    Javanmard, M., Talasaz, A.H., Nemat-Gorgani, M., Pease, F., Ronaghi, M. and Davis, R.W. Lab Chip. (2009) 9 1429-34. PMCID:2778468. [PubMed]
  66. A genome-wide screen for regulators of TORC1 in response to amino acid starvation reveals a conserved Npr2/3 complex.
    Neklesa, T.K. and Davis, R.W. PLoS Genet. (2009) 5 e1000515. PMCID:2686269. [PubMed]
  67. Alternative splicing of PTC7 in Saccharomyces cerevisiae determines protein localization.
    Juneau, K., Nislow, C. and Davis, R.W. Genetics. (2009) 183 185-94. PMCID:2746143. [PubMed]
  68. A dynamic network of transcription in LPS-treated human subjects.
    Seok, J. Xiao, W. Moldawer, L. L. Davis, R. W. Covert, M. W. BMC Syst Biol. (2009) 3 78. PMCID:2729748. [PubMed]
  69. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging.
    Wheeler, H. E. Metter, E. J. Tanaka, T. Absher, D. Higgins, J. Zahn, J. M. Wilhelmy, J. Davis, R. W. Singleton, A. Myers, R. M. Ferrucci, L. Kim, S. K. [PubMed]
  70. Genome-wide transcriptome analysis of 150 cell samples.
    Irimia, D. Mindrinos, M. Russom, A., Xiao, W., Wilhelmy, J., Wang, S., Heath, J. D., Kurn, N., Tompkins, R. G., Davis, R. W., Toner, M. Integr Biol (Camb). (2009) 1 99-107. [PubMed]
  71. Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes.
    Scharfe, C., Horng-Shing Lu, H., Neuenburg, JK., Allen, EA., Li4, G-C., Klopstock, T., Cowan, TM., Enns, GM., Davis, RW. PLoS Comput Biol. (2009) 5 e1000374. PMCID:2668170. [Publisher Full Text]
  72. Minority HIV-1 Variants in Antiretroviral Naive Persons with Reverse Transcriptase Codon 215 Revertant Mutations.
    Mitsuya Y, Varghese V, Wang C, Liu TF, Holmes SP, Jayakumar R, Gharizadeh B, Ronaghi M, Klein D, Fessel WJ, Shafer RW. J Virol. 2008 Aug 20. [Epub ahead of print]. [PubMed]
  73. An integrated platform of genomic assays reveals small-molecule bioactivities.
    Hoon, S. Smith, A. M. Wallace, I. M. Suresh, S. Miranda, M. Fung, E. Proctor, M. Shokat, K. M. Zhang, C. Davis, R. W. Giaever, G. StOnge, R. P. Nislow, C. Nat Chem Biol. 2008 Aug;4(8):498-506. Epub 2008 Jul 11. [PubMed], [Publisher Full Text]
  74. A comprehensive assay for targeted multiplex amplification of human DNA sequences.
    Krishnakumar S, Zheng J, Wilhelmy J, Faham M, Mindrinos M, Davis R. Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9296-301. Epub 2008 Jul 2. [PubMed], [Publisher Full Text]
  75. The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes.
    Hillenmeyer, M.E. Fung, E. Wildenhain, J. Pierce, S.E. Hoon, S. Lee, W. Proctor, M. St.Onge, R.P. Tyers, M. Koller, D. Altman, R.B. Davis, R.W. Nislow, C. Giaever, G. (2008). Science 320(5874): 362 - 365. [PubMed], [Publisher Full Text]
  76. High-resolution, in vivo magnetic resonance imaging of Drosophila at 18.8 Tesla.
    Null, B. Liu, C. W. Hedehus, M. Conolly, S. Davis, R. W. PLoS ONE. 2008 Jul 30;3(7):e2817. [PubMed], [Publisher Full Text]
  77. Pervasive and persistent redundancy among duplicated genes in yeast.
    Dean, E. J. Davis, J. C. Davis, R. W. Petrov, D. A. PLoS Genet. 2008 Jul 4;4(7):e1000113. [PubMed], [Publisher Full Text]
  78. High throughput automated allele frequency estimation by pyrosequencing.
    Doostzadeh, J. Shokralla, S. Absalan, F. Jalili, R. Mohandessi, S. Langston, J. W. Davis, R. W. Ronaghi, M. Gharizadeh, B. PLoS ONE. 2008 Jul 16;3(7):e2693. [PubMed], [Publisher Full Text]
  79. Magnetic Bar Array with Linker Technology for Detection and Investigation of Non-magnetic Molecules.
    Lee, D.W. Roberts, L.A. Peroziello, E. Fontana, R. Maat, S. Boone, T. Nemat-Gorgani, M. Hoon, S. Huber, D. White, R.L. EEE Transactions on Magnetics, vol. 44, issue 11, pp. 4468-4471.DOI: 10.1109/TMAG.2008.2001517
  80. Defining genetic interaction.
    Mani R, St Onge RP, Hartman JL 4th, Giaever G, Roth FP. Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3461-6. [PubMed], [Publisher Full Text]
  81. Identification of Small Molecule Inhibitors of Pseudomonas aeruginosa Exoenzyme S Using a Yeast Phenotypic Screen.
    Arnoldo, A. Curak, J. Kittanakom, S. Chevelev, I. Lee, V. T. Sahebol-Amri, M. Koscik, B. Ljuma, L. Roy, P. J. Bedalov, A. Giaever, G. Nislow, C. Merrill, A. R. Lory, S. Stagljar, I. (2008). PLoS Genet 4(2): e1000005. [PubMed]
  82. Microfluidic Leukocyte Isolation for Gene Expression Analysis in Critically Ill Hospitalized Patients.
    Russom A, Sethu P, Irimia D, Mindrinos MN, Calvano SE, Garcia I, Finnerty C, Tannahill C, Abouhamze A, Wilhelmy J, López MC, Baker HV, Herndon DN, Lowry SF, Maier RV, Davis RW, Moldawer LL, Tompkins RG, Toner M; The Inflammation and Host Response to Injury Large Scale Collaborative Research Program. Clin Chem. 2008 May;54(5):891-900. Epub 2008 Mar 28. [PubMed], [Publisher Full Text]
  83. Simultaneous genotyping of all hemagglutinin and neuraminidase subtypes of avian influenza viruses using padlock probes.
    Gyarmati P, Conze T, Zohari S, Leblanc N, Nilsson M, Landegren U, Banér J, Belák S. J Clin Microbiol. 2008 Mar 19; [Epub ahead of print] PMID: 18353937. [PubMed], [Publisher Full Text]
  84. Comparison of longitudinal leukocyte gene expression after burn injury or trauma-hemorrhage in mice.
    Lederer JA, Brownstein BH, Lopez MC, Macmillan S, Delisle AJ, Macconmara MP, Choudhry MA, Xiao W, Lekousi S, Cobb JP, Baker HV, Mannick JA, Chaudry IH; Inflammation and the Host Response to Injury Collaborative Research Program Participants. Physiol Genomics. 2008 Feb 19;32(3):299-310. Epub 2007 Nov 6. [PubMed], [Publisher Full Text]
  85. Bisphenol A Induces a Profile of Tumor Aggressiveness in High-Risk Cells from Breast Cancer Patients.
    Dairkee SH, Seok J, Champion S, Sayeed A, Mindrinos MN, Xiao W, Davis RW, Goodson WH. Cancer Res 2008 68: 2076-2080. [PubMed], [Publisher Full Text]
  86. SNP discovery and molecular evolution in Anopheles gambiae, with special emphasis on innate immune system.
    Cohuet, A. Krishnakumar, S. Simard, F. Morlais, I. Koutsos, A. Fontenille, D. Mindrinos, M. Kafatos, F. C. BMC Genomics. 2008 May 19;9:227. [PubMed], [Publisher Full Text]
  87. Murine intramyocellular lipids quantified by NMR act as metabolic biomarkers in burn trauma.
    Tzika, A. A. Astrakas, L. G. Cao, H. Mintzopoulos, D. Zhang, Q. Padfield, K. Yu, H. Mindrinos, M. N. Rahme, L. G. Tompkins, R. G. Int J Mol Med. 2008 Jun;21(6):825-32. [PubMed], [Publisher]
  88. Genome-wide linkage analysis of a Parkinsonian-pyramidal syndrome pedigree by 500 K SNP arrays.
    Shojaee S, Sina F, Banihosseini SS, Kazemi MH, Kalhor R, Shahidi GA, Fakhrai-Rad H, Ronaghi M, Elahi E. Am J Hum Genet. 2008 Jun;82(6):1375-84. [PubMed], [Publisher Full Text]
  89. Viral population estimation using pyrosequencing.
    Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, Beerenwinkel N. PLoS Comput Biol. 2008 May 9;4(4):e1000074. [PubMed], [Publisher Full Text]
  90. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function.
    Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, Christopherson KS, Xing Y, Lubischer JL, Krieg PA, Krupenko SA, Thompson WJ, Barres BA (2008). J Neurosci. 2008 Jan 2;28(1):264-78. [PubMed Abstract]
  91. A system for multiplexed direct electrical detection of DNA synthesis.
    Anderson, E. P. Daniels, J. S. Yu, H. Karhanek, M. Lee, T. H. Davis, R. W. Pourmand, N. (2008). Sensors & Actuators: B. Chemical, 129(1):79. [PubMed]
  92. Thermal aggregation of alpha-chymotrypsin: role of hydrophobic and electrostatic interactions.
    Rezaei-Ghaleh, N. Ramshini, H. Ebrahim-Habibi, A. Moosavi-Movahedi, A. A. Nemat-Gorgani, M. (2008). Biophys Chem 132(1):23-32. [PubMed]
  93. Magnetic Bar Array with Linker Technology for Detection and Investigation of Non-magnetic Molecules.
    Lee, D.W. Roberts, L.A. Peroziello, E. Fontana, R. Maat, S. Boone, T. Nemat-Gorgani, M. Hoon, S. Huber, D. White, R.L (2008). I.E.E.E. Transactions on Magnetics, Vol. 44, No. 11, November 2008. [Publisher Full Text, PDF]
  94. Interference of globin genes with biomarker discovery for allograft rejection in peripheral blood samples.
    Li, L. Ying, L. Naesens, M. Xiao, W. Sigdel, T. Hsieh, S. Martin, J. Chen, R. Liu, K. Mindrinos, M. Davis, R. Sarwal, M. Physiol Genomics 32(2):190-7. (2008). [PubMed], [Publisher Full Text]
  95. Reduced rate of adenosine triphosphate synthesis by in vivo 31P nuclear magnetic resonance spectroscopy and downregulation of PGC-1beta in distal skeletal muscle following burn.
    Tzika, A. A. Mintzopoulos, D. Padfield, K. Wilhelmy, J. Mindrinos, M. N. Yu, H. Cao, H. Zhang, Q. Astrakas, L. G. Zhang, J. Yu, Y. M. Rahme, L. G. Tompkins, R. G. Int J Mol Med. 2008 Feb;21(2):201-8. [PubMed], [Publisher]
  96. A pico-calorimetric method for DNA sequencing.
    Esfandyarpour, H., Pease, R.F.W., Davis, R.W., J. Vac Sci. and Technol. B, 26 (2)2008.
  97. Real Time Simulation of Pyrophosphate Concentration and Heat Detection in Thermosequencing.
    Esfandyarpour, H. Zheng, B., Pease, RFW, Davis, R.W., J Biomicrofluidics, 2 (1), 2008.
  98. Gate-Controlled Microfluidic with Magnetic Bead in DNA Sequencing.
    Esfandyarpour, H., Davis R.W., invited and to appear in International Journal of Microfluidics and Nanofluidics, (2008).
  99. Challenges and Opportunities Challenges and Potentials in Industrialization of Future Nanobiosensors.
    Esfandyarpour, H., to appear at Journal of Dispersion Science and Technology, JDST 29 4 (2008).
  100. Label-free impedance biosensors: Opportunities and challenges.
    Daniels, J. S. Pourmand, N. (2008). Electroanalysis 19(12):1239. [PubMed]
  101. Involvement of skeletal muscle gene regulatory network in susceptibility to wound infection following trauma.
    Apidianakis Y, Mindrinos MN, Xiao W, Tegos GP, Papisov MI, Hamblin MR, Davis RW, Tompkins RG, Rahme LG. PLoS ONE. 2007 Dec 26;2(12):e1356. [PubMed]
  102. Conformational flexibility of a model protein upon immobilization on self-assembled monolayers.
    Bigdeli, S. Talasaz, A. H. Stahl, P. Persson, H. H. Ronaghi, M. Davis, R. W. Nemat-Gorgani, M. (2007). Biotechnol Bioeng 100(1):19-27. [PubMed]
  103. A study on the two binding sites of hexokinase on brain mitochondria.
    Golestani, A. Ramshini, H. Nemat-Gorgani, M. (2007). BMC Biochem 8:p20. [PubMed]
  104. The Role of NanoBiotechnology in the Detection of Infectious Diseases.
    Esfandyarpour, H., submitted to the Journal of Nanotechnology, Sep. 2007.
  105. A Novel Receptacle for Gene Sequencing.
    Esfandyarpour, H., Davis, R.W., NSTI-Nanotech 2007, Vol.3, pp. 422-425.
  106. Geometrical Optimization of Pyrophosphate Concentration in Thermosequencing Platform for DNA Sequencing.
    Esfandyarpour, H. Zheng, B., Pease, RFW, Davis, R.W., Proceeding of Int’l COMSOL Conference, 2007, pp-141-147.
  107. Gate-Controlled Microfluidic Chamber with magnetic bead for DNA Sequencing-by-synthesis Technology.
    Esfandyarpour, H. and Davis R.W., ICNMM2007, ref- 3119.
  108. 3D Modeling of Impedance Spectroscopy for Protein Detection in Nanoneedle Biosensors.
    Esfandyarpour, Mayguin, A., Pease, R.F.W., Davis, R.W., International COMSOL Conference 2007, 4-6 Oct. 2007, Boston, MA, USA, pp- 169-173.
  109. Nano-Biotechnology toward Diagnostic Industry: Obstacles and Opportunities.
    Esfandyarpour, H., ”NSTI-Nanotech 2007, Vol. 4, pp 421-423.
  110. Multiplexed proximity ligation assays to profile putative plasma biomarkers relevant to pancreatic and ovarian cancer.
    Fredriksson, S. Horecka, J. Terje Brustugun, O. Schlingemann, J. Koong, A. C. Tibshirani, R. Davis, R. W. Clin Chem 54(3):582-9. (2008). [PubMed], [Publisher Full Text]
  111. Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures.
    Pierce, S. E. Davis, R. W. Nislow, C. Giaever, G. Nat Protoc 2(11):2958-74 (2007). [PubMed], [Publisher Full Text]
  112. Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches.
    McClellan, A. J. Xia, Y. Deutschbauer, A. M. Davis, R. W. Gerstein, M. Frydman, J. Cell 131(1):121-35 (2007). [PubMed], [Publisher Full Text]
  113. Conformational flexibility of a model protein upon immobilization on selfassembled monolayers.
    Bigdeli, S. Talasaz, A. H. Stahl, P. Persson, H. H. Ronaghi, M. Davis, R. W. Nemat-Gorgani, M. Biotechnol Bioeng (2007). [PubMed]
  114. A novel catechol-based universal support for oligonucleotide synthesis.
    Anderson, K.M. Jaquinod, L. Jensen, M.A. Ngo, N. Davis, R.W. J Org Chem 72(26):9875-80 (2007). [PubMed], [Publisher Full Text]
  115. Connector inversion probe technology: a powerful one-primer multiplex DNA amplification system for numerous scientific applications.
    Akhras, M. S. Unemo, M. Thiyagarajan, S. Nyren, P. Davis, R. W. Fire, A. Z. Pourmand, N. PLoS ONE 2(9):e915 (2007). [PubMed], [Publisher Full Text]
  116. A high-resolution atlas of nucleosome occupancy in yeast.
    Lee, W. Tillo, D. Bray, N. Morse, R.H. Davis, R.W. Hughes, T. R. Nislow, C. Nat Genet 39(10):1235-44 (2007). [PubMed], [Publisher Full Text]
  117. Unusual selection on the KIR3DL1/S1 natural killer cell receptor in Africans.
    Norman, P. J. Abi-Rached, L. Gendzekhadze, K. Korbel, D. Gleimer, M. Rowley, D. Bruno, D. Carrington, C. V. Chandanayingyong, D. Chang, Y. H. Crespi, C. Saruhan-Direskeneli, G. Fraser, P. A. Hameed, K. Kamkamidze, G. Koram, K. A. Layrisse, Z. Matamoros, N. Mila, J. Park, M. H. Pitchappan, R. M. Ramdath, D. D. Shiau, M. Y. Stephens, H. A. Struik, S. Verity, D. H. Vaughan, R. W. Tyan, D. Davis, R. W. Riley, E. M. Ronaghi, M. Parham, P. Nat Genet 39(9):1092-9 (2007). [PubMed], [Publisher Full Text]
  118. Multigene amplification and massively parallel sequencing for cancer mutation discovery.
    Dahl, F. Stenberg, J. Fredriksson, S. Welch, K. Zhang, M. Nilsson, M. Bicknell, D. Bodmer, W. F. Davis, R. W. Ji, H. Proc Natl Acad Sci U S A 104(22):9387-92 (2007). [PubMed], [Publisher Full Text]
  119. Branch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays.
    Pourmand, N. Caramuta, S. Villablanca, A. Mori, S. Karhanek, M. Wang, S. X. Davis, R.W. Proc Natl Acad Sci U S A 104(15):6146-51 (2007). [PubMed], [Publisher Full Text]
  120. Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector.
    Fredriksson, S. Baner, J. Dahl, F. Chu, A. Ji, H. Welch, K. Davis, R.W. Nucleic Acids Res35(7):e47 (2007). [PubMed], [Publisher Full Text]
  121. PathogenMip assay: a multiplex pathogen detection assay.
    Akhras, M. S. Thiyagarajan, S. Villablanca, A. C. Davis, R. W. Nyren, P. Pourmand, N. PLoS ONE 2(2):e223 (2007). [PubMed], [Publisher Full Text]
  122. High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing.
    Juneau, K. Palm, C. Miranda, M. Davis, R.W. Proc Natl Acad Sci U S A 104(5):1522-7. [PubMed], [Publisher Full Text].
  123. Molecular characterization of Neisseria gonorrhoeae identifies transmission and resistance of one ciprofloxacin-resistant strain.
    Unemo, M. Sjostrand, A. Akhras, M. Gharizadeh, B. Lindback, E. Pourmand, N. Wretlind, B. Fredlund, H. Apmis 115(3):231-41 (2007). [PubMed], [Publisher Full Text]
  124. Analysis of read length limiting factors in Pyrosequencing chemistry.
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    Winzeler, E.A., Shoemaker, D.D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J.D., Bussey, H., Chu, A.M., Connelly, C., Davis, K., Dietrich, F., Dow, S.W., El Bakkoury, M., Foury, F., Friend, S.H., Gentalen, E., Giaever, G., Hegemann, J.H., Jones, T., Laub, M., Liao, H., Davis, R.W., et al., (1999). Aug 6, Science, 285(5429):901-906. [PubMed Abstract].
  356. Whole genome genetic-typing in yeast using high-density oligonucleotide arrays.
    Winzeler, E.A., Lee, B., McCusker, J.H., Davis, R.W., (1999). Parasitology, 118 Suppl:S73-80. [PubMed Abstract].
  357. Global sequence diversity of BRCA2: analysis of 71 breast cancer families and 95 control individuals of worldwide populations.
    Wagner, T.M., 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., Langbauer, G., Kubista, E., Scheiner, O., Underhill, P., Mountain, J., Stierer, M., Zielinski, C., Oefner, P., (1999). Mar, Hum Mol Genet, 8(3):413-423. [Publisher Full Text].
  358. Denaturing high-performance liquid chromatography detects reliably BRCA1 and BRCA2 mutations.
    Wagner, T., Stoppa-Lyonnet, D., Fleischmann, E., Muhr, D., Pages, S., Sandberg, T., Caux, V., Moeslinger, R., Langbauer, G., Borg, A., Oefner, P., (1999). Dec 15, Genomics, 62(3):369-376. [PubMed Abstract].
  359. Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae.
    ter Linde, J.J., Liang, H., Davis, R.W., Steensma, H.Y., van Dijken, J.P., Pronk, J.T., (1999). Dec, J Bacteriol, 181(24):7409-7413. [Publisher Full Text].
  360. Y-Chromosome evidence for a northward migration of modern humans into Eastern Asia during the last Ice Age.
    Su, B., Xiao, J., Underhill, P., Deka, R., Zhang, W., Akey, J., Huang, W., Shen, D., Lu, D., Luo, J., Chu, J., Tan, J., Shen, P., Davis, R., Cavalli-Sforza, L., Chakraborty, R., Xiong, M., Du, R., Oefner, P., Chen, Z., Jin, L., (1999). Dec, Am J Hum Genet, 65(6):1718-1724. [Publisher].
  361. Analyses of secondary structures in DNA by pyrosequencing.
    Ronaghi, M., Nygren, M., Lundeberg, J., Nyren, P., (1999). Feb 1, Anal Biochem, 267(1):65-71. [Publisher] DOI: 10.1006/abio.1998.2978.
  362. An arrayable flow-through microcentrifuge for high-throughput instrumentation.
    Marziali, A., Willis, T.D., Davis, R.W., (1999). Jan 5, Proc Natl Acad Sci U S A, 96(1):61-66. [Publisher Full Text].
  363. An automated sample preparation system for large-scale DNA sequencing.
    Marziali, A., Willis, T.D., Federspiel, N.A., Davis, R.W., (1999). May,Genome Res, 9(5):457-462. [Publisher Full Text].
  364. Production, purification, and luminometric analysis of recombinant Saccharomyces cerevisiae MET3 adenosine triphosphate sulfurylase expressed in Escherichia coli.
    Karamohamed, S., Nilsson, J., Nourizad, K., Ronaghi, M., Pettersson, B., Nyren, P., (1999). Apr, Protein Expr Purif, 15(3):381-388. [Publisher] DOI: 10.1006/prep.1999.1032.
  365. Comparative genomes of Chlamydia pneumoniae and C. trachomatis.
    Kalman, S., Mitchell, W., Marathe, R., Lammel, C., Fan, J., Hyman, R.W., Olinger, L., Grimwood, J., Davis, R.W., Stephens, R.S., (1999). Apr, Nat Genet, 21(4):385-389. [Publisher Full Text].
  366. Optimal temperature selection for mutation detection by denaturing HPLC and comparison to single-stranded conformation polymorphism and heteroduplex analysis.
    Jones, A.C., Austin, J., Hansen, N., Hoogendoorn, B., Oefner, P.J., Cheadle, J.P., O'Donovan, M.C., (1999). Aug, Clin Chem, 45(8 Pt 1):1133-1140. [Publisher Full Text].
  367. Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations.
    Jin, L., Underhill, P.A., Doctor, V., Davis, R.W., Shen, P., Cavalli-Sforza, L.L., Oefner, P.J., (1999). Mar 30, Proc Natl Acad Sci U S A, 96(7):3796-3800. [Publisher Full Text].
  368. 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., (1999). Jan, Hum Genet, 104(1):89-93. [Publisher].
  369. Altered sodium pump alpha and gamma subunit gene expression in nephron segments from hypertensive rats.
    Hayward, A.L., Hinojos, C.A., Nurowska, B., Hewetson, A., Sabatini, S., Oefner, P.J., Doris, P.A., (1999). Aug, J Hypertens, 17(8):1081-1087. [PubMed Abstract].
  370. The mouse mahogany locus encodes a transmembrane form of human attractin.
    Gunn, T.M., Miller, K.A., He, L., Hyman, R.W., Davis, R.W., Azarani, A., Schlossman, S.F., Duke-Cohan, J.S., Barsh, G.S., (1999). Mar 11, Nature, 398(6723):152-156. [Publisher Full Text].
  371. Identification by denaturing high-performance liquid chromatography of numerous polymorphisms in a candidate region for multiple sclerosis susceptibility.
    Giordano, M., Oefner, P.J., Underhill, P.A., Cavalli Sforza, L.L., Tosi, R., Richiardi, P.M., (1999). Mar 15, Genomics, 56(3):247-253. [PubMed Abstract].
  372. Genomic profiling of drug sensitivities via induced haploinsufficiency.
    Giaever, G., Shoemaker, D.D., Jones, T.W., Liang, H., Winzeler, E.A., Astromoff, A., Davis, R.W., (1999). Mar, Nat Genet, 21(3):278-283. [Publisher Full Text].
  373. Genome-wide mapping with biallelic markers in Arabidopsis thaliana.
    Cho, R.J., Mindrinos, M., Richards, D.R., Sapolsky, R.J., Anderson, M., Drenkard, E., Dewdney, J., Reuber, T.L., Stammers, M., Federspiel, N., Theologis, A., Yang, W.H., Hubbell, E., Au, M., Chung, E.Y., Lashkari, D., Lemieux, B., Dean, C., Lipshutz, R.J., Ausubel, F.M., Davis, R.W., Oefner, P.J., (1999). Oct, Nat Genet, 23(2):203-207. [Publisher Full Text].
  374. Toxic mutations in the recA gene of E. coli prevent proper chromosome segregation.
    Campbell, M.J., Davis, R.W., (1999). Feb 19, J Mol Biol, 286(2):417-435. [PubMed Abstract].
  375. On the in vivo function of the RecA ATPase.
    Campbell, M.J., Davis, R.W., (1999). Feb 19, J Mol Biol, 286(2):437-445. [PubMed Abstract].
  376. Direct allelic variation scanning of the yeast genome.
    Kalman, S., McCullough, M.J., McCusker, J.H., Stevens, D.A., Wodicka, L., Lockhart, D.J., Davis, R.W., (1998). Aug 21, Science, 281(5380):1194-1197. [Publisher Full Text].
  377. BRCA1-related breast cancer in Austrian breast and ovarian cancer families: specific BRCA1 mutations and pathological characteristics.
    Wagner, T.M., Moslinger, R.A., Muhr, D., Langbauer, G., Hirtenlehner, K., Concin, H., Doeller, W., Haid, A., Lang, A.H., Mayer, P., Ropp, E., Kubista, E., Amirimani, B., Helbich, T., Becherer, A., Scheiner, O., Breiteneder, H., Borg, A., Devilee, P., Oefner, P., Zielinski, C., (1998). Jul 29, Int J Cancer, 77(3):354-360. [Publisher Abstract]. Multicenter Study
  378. An automated hydrodynamic process for controlled, unbiased DNA shearing.
    Thorstenson, Y.R., Hunicke-Smith, S.P., Oefner, P.J., Davis, R.W., (1998). Aug, Genome Res, 8(8):848-855. [Publisher Full Text].
  379. Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis.
    Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R.L., Zhao, Q., Koonin, E.V., Davis, R.W., (1998). Oct 23, Science, 282(5389):754-759. [Publisher Full Text].
  380. A sequencing method based on real-time pyrophosphate.
    Ronaghi, M., Uhlen, M., Nyren, P., (1998). Jul 17, Science, 281(5375):363, 365. [Publisher Full Text].
  381. PCR-introduced loop structure as primer in DNA sequencing.
    Ronaghi, M., Pettersson, B., Uhlen, M., Nyren, P., (1998). Nov, Biotechniques, 25(5):876-878, 880-872, 884. [PubMed Abstract].
  382. Phylogeny of the family Moraxellaceae by 16S rDNA sequence analysis, with special emphasis on differentiation of Moraxella species.
    Pettersson, B., Kodjo, A., Ronaghi, M., Uhlen, M., Tonjum, T., (1998). Jan, Int J Syst Bacteriol, 48 Pt 1:75-89. [PubMed Abstract].
  383. 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). Aug 15, Genomics, 52(1):44-49. [PubMed Abstract].
  384. Bioluminometric method for real-time detection of reverse transcriptase activity.
    Karamohammed, S., Ronaghi, M., Nyren, P., (1998). Feb, Biotechniques, 24(2):302-306. [PubMed Abstract].
  385. Analyses of the NRAMP1 and IFN-gammaR1 genes in women with Mycobacterium avium-intracellulare pulmonary disease.
    Huang, J.H., Oefner, P.J., Adi, V., Ratnam, K., Ruoss, S.J., Trako, E., Kao, P.N., (1998). Feb, Am J Respir Crit Care Med, 157(2):377-381. [Publisher Full Text].
  386. Modeling and analysis of competitive RT-PCR.
    Hayward, A.L., Oefner, P.J., Sabatini, S., Kainer, D.B., Hinojos, C.A., Doris, P.A., (1998). Jun 1, Nucleic Acids Res, 26(11):2511-2518. [Publisher Full Text].
  387. Parallel analysis of genetic selections using whole genome oligonucleotide arrays.
    Cho, R.J., Fromont-Racine, M., Wodicka, L., Feierbach, B., Stearns, T., Legrain, P., Lockhart, D.J., Davis, R.W., (1998). Mar 31, Proc Natl Acad Sci U S A, 95(7):3752-3757. [Publisher Full Text].
  388. A genome-wide transcriptional analysis of the mitotic cell cycle.
    Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J., Davis, R.W., (1998). Jul, Mol Cell, 2(1):65-73. [PubMed Abstract].
  389. Mapping cloned sequences on YACs.
    Agyare, F.D., Lagos, G., Lashkari, D., Davis, R.W., Lemieux, B., (1998). Methods Mol Biol, 82:199-208.
  390. Hepatitis G virus infection in hemodialysis patients and the effects of interferon treatment.
    Umlauft, F., Wong, D.T., Underhill, P.A., Oefner, P.J., Jin, L., Urbanek, M., Gruenewald, K., Greenberg, H.B., (1997). Nov, Am J Gastroenterol, 92(11):1986-1991. [PubMed Abstract].
  391. Capillary electrophoresis measurement of metabolites in glycolysis.
    Shen, P., Hauri, D., Ross, J., Oefner, P.J., (1997). J. Cap. Elec, 3:155-163.
  392. Quantification of alternatively spliced RUSH mRNA isoforms by QRT-PCR and IP-RP-HPLC analysis: a new approach to measuring regulated splicing efficiency.
    Robinson, C.A., Hayward-Lester, A., Hewetson, A., Oefner, P.J., Doris, P.A., Chilton, B.S., (1997). Oct 1, Gene, 198(1-2):1-4. [PubMed Abstract].
  393. A crtB Homolog Essential for Photochromogenicity in Mycobacterium marinum: Isolation, Characterization, and Gene Disruption via Homologous Recombination.
    Ramakrishnan, L., Tran, H.T., Federspiel, N.A., Falkow, S., (1997). J. Bacteriol, 179:5862-5868.
  394. Detection of single-base changes using a bioluminometric primer extension assay.
    Nyren, P., Karamohamed, S., Ronaghi, M., (1997). Jan 15, Anal Biochem, 244(2):367-373. [PubMed Abstract] DOI: 10.1006/abio.1996.9913.
  395. Automation for the Arabidopsis genome sequencing project.
    Marziali, A., Federspiel, N., and Davis, R.W., (1997). Trends in Plant Science, 2:71-74.
  396. Denaturing HPLC-identified novel FBN1 mutations, polymorphisms, and sequence variants in Marfan syndrome and related connective tissue disorders.
    Liu, W.O., Oefner, P.J., Qian, C., Odom, R.S., Francke, U., (1997). Genet Test, 1(4):237-242. [PubMed Abstract].
  397. Ca(2+)-activated anion channels and membrane depolarizations induced by blue light and cold in Arabidopsis seedlings.
    Lewis, B.D., Karlin-Neumann, G., Davis, R.W., Spalding, E.P., (1997). Aug, Plant Physiol, 114(4):1327-1334. [PubMed Abstract].
  398. Whole genome analysis: experimental access to all genome sequenced segments through larger-scale efficient oligonucleotide synthesis and PCR.
    Lashkari, D.A., McCusker, J.H., Davis, R.W., (1997). Aug 19, Proc Natl Acad Sci U S A, 94(17):8945-8947. [Publisher Full Text].
  399. Yeast microarrays for genome wide parallel genetic and gene expression analysis.
    Lashkari, D.A., DeRisi, J.L., McCusker, J.H., Namath, A.F., Gentile, C., Hwang, S.Y., Brown, P.O., Davis, R.W., (1997). Nov 25, Proc Natl Acad Sci U S A, 94(24):13057-13062. [Publisher Full Text].
  400. The nucleotide sequence of chromosome IV.
    Jacq, C., Davis, R.W., et al. (144 co-authors). (1997). Nature 387 suppl:75-78. [PubMed Abstract]
  401. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays.
    Heller, R.A., Schena, M., Chai, A., Shalon, D., Bedilion, T., Gilmore, J., Woolley, D.E., Davis, R.W., (1997). Mar 18, Proc Natl Acad Sci U S A, 94(6):2150-2155. [Publisher Full Text].
  402. The nucleotide sequence of Saccharomyces cerevisiae chromosome V.
    Dietrich, F.S., Mulligan, J., Hennessy, K., Yelton, M.A., Allen, E., Araujo, R., Aviles, E., Berno, A., Brennan, T., Carpenter, J., Chen, E., Cherry, J.M., Chung, E., Duncan, M., Guzman, E., Hartzell, G., Hunicke-Smith, S., Hyman, R.W., Kayser, A., Komp, C., Lashkari, D., Lew, H., Lin, D., Mosedale, D., Nakahara, K., Namath, A., Norgren, R. Oefner, P., Oh, C., Petel, F.X., Roberts, D., Sehl, P., Schramm, S., Shogren, T., Smith, V., Taylor, P., Wei, Y., Botstein, D., Davis, R.W. (1997). May 29, Nature, 387(6632 Suppl):78-81. [PubMed Abstract].
  403. Application of DNA typing methods and genetic analysis to epidemiology and taxonomy of Saccharomyces isolates.
    Clemons, K.V., Park, P., McCusker, J.H., McCullough, M.J., Davis, R.W., Stevens, D.A., (1997). Jul, J Clin Microbiol, 35(7):1822-1828
  404. Hepatitis C virus detection by single-round PCR specific for the terminal 3' noncoding region.
    Umlauft, F., Wong, D.T., Oefner, P.J., Underhill, P.A., Cheung, R.C., Wright, T.L., Kolykhalov, A.A., Gruenewald, K., Greenberg, H.B., (1996). Oct, J Clin Microbiol, 34(10):2552-2558. [Publisher Abstract].
  405. Mapping expressed sequence tag sites on yeast artificial chromosome clones of Arabidopsis thaliana DNA.
    Agyare, F.D., Lashkari, D.A., Lagos, A., Namath, A.F., Lagos, G., Davis, R.W., Lemieux, B., (1997). Jan, Genome Res, 7(1):1-9. [PubMed Abstract].
  406. A pre-Columbian Y chromosome-specific transition and its implications for human evolutionary history.
    Underhill, P.A., Jin, L., Zemans, R., Oefner, P.J., Cavalli-Sforza, L.L., (1996). Jan 9, Proc Natl Acad Sci U S A, 93(1):196-200. [Publisher Abstract].
  407. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy.
    Shoemaker, D.D., Lashkari, D.A., Morris, D., Mittmann, M., Davis, R.W., (1996). Dec, Nat Genet, 14(4):450-456. [PubMed Abstract].
  408. Analysis of glycolysis metabolites by capillary zone electrophoresis with indirect UV detection.
    Shen, P., Hauri, D., Ross, J., Oefner, P.J., (1996). May-Jun, J Capillary Electrophor, 3(3):155-163. [PubMed Abstract].
  409. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.
    Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P.O., Davis, R.W., (1996). Oct 1, Proc Natl Acad Sci U S A, 93(20):10614-10619. [Publisher Abstract].
  410. Real-time DNA sequencing using detection of pyrophosphate release.
    Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlen, M., Nyren, P., (1996). Nov 1, Anal Biochem, 242(1):84-89. [PubMed Abstract] DOI: 10.1006/abio.1996.0432.
  411. Phylogeny of the Mycoplasma mycoides cluster as determined by sequence analysis of the 16S rRNA genes from the two rRNA operons.
    Pettersson, B., Leitner, T., Ronaghi, M., Bolske, G., Uhlen, M., Johansson, K.E., (1996). Jul, J Bacteriol, 178(14):4131-4142. [PubMed Abstract].
  412. Familial hemiplegic migraine and episodic ataxia type-2 are caused by mutations in the Ca2+ channel gene CACNL1A4.
    Ophoff, R.A., Terwindt, G.M., Vergouwe, M.N., van Eijk, R., Oefner, P.J., Hoffman, S.M., Lamerdin, J.E., Mohrenweiser, H.W., Bulman, D.E., Ferrari, M., Haan, J., Lindhout, D., van Ommen, G.J., Hofker, M.H., Ferrari, M.D., Frants, R.R., (1996). Nov 1, Cell, 87(3):543-552. [PubMed Abstract].
  413. Efficient random subcloning of DNA sheared in a recirculating point-sink flow system.
    Oefner, P.J., Hunicke-Smith, S.P., Chiang, L., Dietrich, F., Mulligan, J., Davis, R.W., (1996). Oct 15, Nucleic Acids Res, 24(20):3879-3886. [Publisher Full Text].
  414. After period of gestation, DNA chips coming of age.
    O’Connell, J.P., Davis, Ronald W., Chee, M., Lockhart, D.J., Fodor, S.P., Collins, F., (1996). Dec, Chem. & Eng. News.
  415. A comparison of micropellicular anion-exchange and reversed-phase stationary phases for HPLC analysis of oligonucleotides.
    Huber, C.G., Stimpfl, E., Oefner, P.J., Bonn, G.K., (1996). LC-GC, 14(2):114-127
  416. Rapid quantification of gene expression by competitive RT-PCR and ion-pair reversed-phase HPLC.
    Hayward-Lester, A., Oefner, P.J., Doris, P.A., (1996). Feb, Biotechniques, 20(2):250-257. [PubMed Abstract].
  417. Cloning, characterization, and steroid-dependent posttranscriptional processing of RUSH-1 alpha and beta, two uteroglobin promoter-binding proteins.
    Hayward-Lester, A., Hewetson, A., Beale, E.G., Oefner, P.J., Doris, P.A., Chilton, B.S., (1996). Nov, Mol Endocrinol, 10(11):1335-1349. [PubMed Abstract].
  418. CDP1, a novel Saccharomyces cerevisiae gene required for proper nuclear division and chromosome segregation.
    Foreman, P.K., Davis, R.W., (1996). Dec, Genetics, 144(4):1387-1397. [PubMed Abstract]
  419. Application of DNA typing methods and genetic analysis to epidemiology and taxonomy of Saccharomyces.
    Clemons, K.V., Park, P.S., McCusker, J.H., Davis, R.W., Stevens, D.A., (1996). J. Infec. Dis
  420. Quantitative monitoring of gene expression patterns with a complementary DNA microarray.
    Schena, M., Shalon, D., Davis, R. W., Brown, P. O. (1995). Science. 1995 Oct 20;270(5235):467-70. [PubMed Abstract]
  421. Analysis of inorganic and organic anions in seminal plasma using charge reversed capillary electrophoresis and indirect UV detection.
    Oefner, P.J. (1995). Electrophoresis 16:46-56
  422. Surface-charge reversed capillary zone electrophoresis of inorganic and organic anions.
    Oefner, P.J. (1995). Electrophoresis. 1995 Jan;16(1):46-56. [PubMed Abstract]
  423. Sliding-plate gel caster.
    Lashkari, D. A., Norgren, R. M., Davis, R. W. (1995). Biotechniques Apr 18(4):625-6
  424. An automated multiplex oligonucleotide synthesizer: development of high-throughput, low-cost DNA synthesis.
    Lashkari, D. A., Hunicke-Smith, S. P., Norgren, R. M., Davis, R. W., Brennan, T. (1995). Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7912-5. [PubMed Abstract], [Publisher]
  425. Rapid and accurate sizing of DNA fragments by ion-pair chromatography on alkylated nonporous poly(styrene-divinylbenzene) particles.
    Huber, C., Oefner, P., Bonn, G. (1995). Anal. Chem 67:587-585
  426. Accurate and absolute quantitative measurement of gene expression by single-tube RT-PCR and HPLC.
    Hayward-Lester, A., Oefner, P. J., Sabatini, S., Doris, P. A. (1995). Genome Res. 1995 Dec;5(5):494-99. [PubMed Abstract]
  427. Micellar electrokinetic chromatography of monosaccharides derivatized with 1-phenyl-3-methyl-2-pyrazolin-5-one.
    Chiesa, C., Oefner, P. J., Zieske, L. R., O'Neill, R. A. (1995). J Capillary Electrophor. 1995 Jul-Aug;2(4):175-83. [PubMed Abstract]
  428. Pathogenicity of Saccharomyces cerevisiae in complement factor five-deficient mice.
    Byron, J. K., Clemons, K. V., McCusker, J. H., Davis, R. W., Stevens, D. A. (1995). Infect Immun. 1995 Feb;63(2):478-85. [PubMed Abstract]
  429. Structure of homeobox-leucine zipper genes suggests a model for the evolution of gene families.
    Schena, M., Davis, R. W. (1994). Proc Natl Acad Sci U S A. 1994 Aug 30;91(18):8393-7. [PubMed Abstract], [Publisher]
  430. Tetrad analysis possible in Arabidopsis with mutation of the QUARTET (QRT) genes.
    Preuss, D., Rhee, S. Y., Davis, R. W. (1994). Science. 1994 Jun 3;264(5164):1458-60. [PubMed Abstract]
  431. Genetic characterization of pathogenic Saccharomyces cerevisiae isolates.
    McCusker, J. H., Clemons, K. V., Stevens, D. A., Davis, R. W. (1994). Genetics. 1994 Apr;136(4):1261-9. [PubMed Abstract]
  432. Saccharomyces cerevisiae virulence phenotype as determined with CD-1 mice is associated with the ability to grow at 42 degrees C and form pseudohyphae.
    McCusker, J. H., Clemons, K. V., Stevens, D. A., Davis, R. W. (1994). Infect Immun. 1994 Dec;62(12):5447-55. [PubMed Abstract]
  433. Functional expression of the yeast FLP/FRT site-specific recombination system in Nicotiana tabacum.
    Lloyd, A. M., Davis, R. W. (1994). Mol Gen Genet. 1994 Mar;242(6):653-7. [PubMed Abstract]
  434. Epidermal cell fate determination in Arabidopsis: patterns defined by a steroid-inducible regulator.
    Lloyd, A. M., Schena, M., Walbot, V., Davis, R. W. (1994). Science. 1994 Oct 21;266(5184):436-9. [PubMed Abstract]
  435. Quantitative trait locus analysis of susceptibility to diet-induced atherosclerosis in recombinant inbred mice.
    Hyman, R. W., Frank, S., Warden, C. H., Daluiski, A., Heller, R., Lusis, A. J. (1994). Biochem Genet. 1994 Dec;32(11-12):397-407. [PubMed Abstract]
  436. The TTG gene is required to specify epidermal cell fate and cell patterning in the Arabidopsis root.
    Galway, M. E., Masucci, J. D., Lloyd, A. M., Walbot, V., Davis, R. W. Schiefelbein, J. W. (1994). Dev Biol. 1994 Dec;166(2):740-54. [PubMed Abstract]
  437. Cloning vectors for the synthesis of epitope-tagged, truncated and chimeric proteins in Saccharomyces cerevisiae.
    Foreman, P.K., Davis, R.W. (1994). Gene. 1994 Jun 24;144(1):63-8. [PubMed Abstract]
  438. The HAT4 gene of Arabidopsis encodes a developmental regulator.
    Schena, M., Lloyd, A. M., Davis, R. W. (1993). Genes Dev. 1993 Mar;7(3):367-79. [PubMed Abstract]
  439. A dominant truncation allele identifies a gene, STE20, that encodes a putative protein kinase necessary for mating in Saccharomyces cerevisiae.
    Ramer, S. W.; Davis, R. W. (1993). Proc Natl Acad Sci U S A. 1993 Jan 15;90(2):452-6. [PubMed Abstract], [Publisher]
  440. A conditional sterile mutation eliminates surface components from Arabidopsis pollen and disrupts cell signaling during fertilization.
    Preuss, D., Lemieux, B., Yen, G., Davis, R. W. (1993). Genes Dev. 1993 Jun;7(6):974-85. [PubMed Abstract]
  441. Point mutations that separate the role of Saccharomyces cerevisiae centromere binding factor 1 in chromosome segregation from its role in transcriptional activation.
    Foreman, P. K., Davis, R. W. (1993). Genetics. 1993 Oct;135(2):287-96. [PubMed Abstract]

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updated December 12, 2013

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