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
  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
  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.
    Mashayekhi, F. Ronaghi, M. Anal Biochem 363(2):275-87 (2007). [PubMed], [Publisher Full Text]
  125. Whole-genome sequencing and assembly with high-throughput, short-read technologies.
    Sundquist, A. Ronaghi, M. Tang, H. Pevzner, P. Batzoglou, S. PLoS ONE 2(5):e484 (2007). [PubMed], [Publisher Full Text]
  126. Patterns of known and novel small RNAs in human cervical cancer.
    Lui, W.O., Pourmand, N., Patterson, B.K., Fire, A. Cancer Res 67(13):6031-43 (2007). [PubMed], [Publisher Full Text]
  127. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance.
    Wang, C., Mitsuya, Y., Gharizadeh, B., Ronaghi, M., Shafer, R.W. Genome Res 17(8):1195-201 (2007). [PubMed], [Publisher Full Text]
  128. Pyrosequencing for discovery and analysis of DNA sequence variations.
    Ronaghi, M., Shokralla, S., Gharizadeh, B. Pharmacogenomics 8(10):1437-41 (2007). [PubMed], [Full Text]
  129. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing.
    Parameswaran, P., Jalili, R., Tao, L., Shokralla, S., Gharizadeh, B., Ronaghi, M., Fire, A.Z. Nucleic Acids Res 35(19):e130 (2007). [PubMed], [Full Text]
  130. Bacterial flora-typing with targeted, chip-based Pyrosequencing.
    Sundquist, A., Bigdeli, S., Jalili, R., Druzin, M.L., Waller, S., Pullen, K.M., El-Sayed, Y.Y., Taslimi, M.M., Batzoglou, S., Ronaghi, M. BMC Microbiol 7:108 (2007). [PubMed], [Full Text]
  131. Human papillomavirus (HPV), DNA aberrations and cell cycle progression in anal squamous cell carcinoma patients.
    Laytragoon-Lewin, N. Nilsson, P.J., Castro, J., Gharizadeh, B., Nyren, P., Glimelius, B., Elmberger, G., Turesson, I., Svensson, C. Anticancer Res27(6C):4473-9. [PubMed]
  132. Combination of high-resolution magic angle spinning proton magnetic resonance spectroscopy and microscale genomics to type brain tumor biopsies.
    Tzika AA, Astrakas L, Cao H, Mintzopoulos D, Andronesi OC, Mindrinos M, Zhang J, Rahme LG, Blekas KD, Likas AC, Galatsanos NP, Carroll RS, Black PM. Int J Mol Med. 2007 Aug;20(2):199-208. [PubMed]
  133. Does HPV-status 6-12 months after treatment of high grade dysplasia in the uterine cervix predict long term recurrence?
    Strander B, Ryd W, Wallin KL, Warleby B, Zheng B, Milsom I, Gharizadeh B, Pourmand N, Andersson-Ellstrom A. Eur J Cancer. 2007 Aug;43(12):1849-55. Epub 2007 Jul 5. [PubMed], [Publisher Full Text]
  134. Patterns of known and novel small RNAs in human cervical cancer
    Lui WO, Pourmand N, Patterson BK, Fire A. Cancer Res. 2007 Jul 1;67(13):6031-43. [PubMed]
  135. Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789.
    Wei, W. McCusker, J. H. Hyman, R. W. 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. Proc Natl Acad Sci U S A 104(31):12825-30. [PubMed], [Publisher Full Text]
  136. INCREASED SIZE EXCLUSION LIMIT2 Encodes a Putative DEVH Box RNA Helicase Involved in Plasmodesmata Function during Arabidopsis Embryogenesis.
    Kobayashi K, Otegui MS, Krishnakumar S, Mindrinos M, Zambryski P. Plant Cell. 2007 Jun;19(6):1885-97. Epub 2007 Jun 29. [PubMed], [Publisher Full Text]
  137. Label-Free Impedance Biosensors: Opportunities and Challenges.
    Daniels, J. S. Pourmand, N. Electroanalysis 19(12):1239-1257 (2007). [PubMed], [Full Text]
  138. Multiplexed protein detection by proximity ligation for cancer biomarker validation.
    Fredriksson S, Dixon W, Ji H, Koong AC, Mindrinos M, Davis RW. Nat Methods. 2007 Apr;4(4):327-9. Epub 2007 Mar 18. [PubMed]
  139. Accelerating the discovery of biologically active small molecules using a high-throughput yeast halo assay.
    Gassner N.C., Tamble C.M., Bock J.E., Cotton N., White K.N., Tenney K., St Onge R.P., Proctor M.J., Giaever G., Nislow C., Davis R.W., Crews P., Holman T.R., Lokey R.S.
    J Nat Prod 70(3):383-90 (2007). [PubMed], [Publisher Full Text]
  140. Inhibition of amyloid fibrillation of lysozyme by indole derivatives--possible mechanism of action.
    Morshedi, D. Rezaei-Ghaleh, N. Ebrahim-Habibi, A. Ahmadian, S. Nemat-Gorgani, M. (2007). Febs J 274(24):6415-25. [PubMed]
  141. Effect of polyamines on the structure, thermal stability and 2,2,2-trifluoroethanol-induced aggregation of alpha-chymotrypsin.
    Rezaei-Ghaleh, N. Ebrahim-Habibi, A. Moosavi-Movahedi, A. A. Nemat-Gorgani, M. (2007). Int J Biol Macromol 41(5):597-604. [PubMed]
  142. Examining protein protein interactions using endogenously tagged yeast arrays: the cross-and-capture system.
    Suter B, Fetchko MJ, Imhof R, Graham CI, Stoffel-Studer I, Zbinden C, Raghavan M, Lopez L, Beneti L, Hort J, Fillingham J, Greenblatt JF, Giaever G, Nislow C, Stagljar I. Genome Res. 2007 Dec;17(12):1774-82. Epub 2007 Nov 7. [PubMed]
  143. Role of electrostatic interactions in 2,2,2-trifluoroethanol-induced structural changes and aggregation of alpha-chymotrypsin.
    Rezaei-Ghaleh, N. Ebrahim-Habibi, A. Moosavi-Movahedi, A. A. Nemat-Gorgani, M. (2007). Arch Biochem Biophys 457(2):160-9. [PubMed]
  144. Thermostabilization of Bacillus amyloliquefaciens alpha-amylase by chemical cross-linking.
    Habibi, A. E. Khajeh, K. Naderi-Manesh, H. Ranjbar, B. Nemat-Gorgani, M. (2006). J Biotechnol 123(4):434-42. [PubMed]
  145. Shot Noise Models for Sequential Processes and the Role of Lateral Mixing.
    Neureuther, A, Pease, R.F.W., Pope, W., Parizi, K.B., Esfandyarpour, H., Liddle A., Anderson, E., et al., J. Vac Sci. and Technol. B, 24 (4), pp. 1902-1908 (2006).
  146. Chemical genomic profiling for identifying intracellular targets of toxicants producing Parkinson's disease.
    Doostzadeh J, Davis RW, Giaever GN, Nislow C, Langston JW. Toxicol Sci. 2007 Jan;95(1):182-7. Epub 2006 Oct 16. [PubMed]
  147. Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions.
    St.Onge, R.P., Mani, R., Oh, J., Proctor, M, Fung, E., Davis, R.W., Nislow, C., Roth, F.P., Giaever, G. Nat Genet 39(2): 199-206 (2007) (Subject of Highlight in Nat Rev Genet 8: 87 (2007). [PubMed Abstract], [Publisher Full Text]
  148. Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae strain YJM789.
    Wu Wei, John H. McCusker, Richard W. Hyman, Ted Jones, Ye Ning, Zhiwei Cao, Zhenglong Gu, Dan Bruno, Molly Miranda, Michelle Nguyen, Julie Wilhelmy, Caridad Komp, Raquel Tamse, Xiaojing Wang, Peilin Jia, Philippe Luedi, Peter J. Oefner, Lior David, Fred S. Dietrich, Yixue Li, Ronald W. Davis, and Lars M. Steinmetz. Proc. Natl. Acad. Sci. U.S.A. 104: 12,825-12,830. 2007. [PubMed]
  149. Uncoupling protein 3 expression and intramyocellular lipid accumulation by NMR following local burn trauma.
    Zhang Q, Cao H, Astrakas LG, Mintzopoulos D, Mindrinos MN, Schulz J 3rd, Tompkins RG, Rahme LG, Tzika AA. Int J Mol Med. 2006 Dec;18(6):1223-9. [PubMed]
  150. Rapid and highly informative diagnostic assay for H5N1 influenza viruses.
    Pourmand N., Diamond L., Garten R., Erickson J.P., Kumm J., Donis R.O., Davis R.W. PLoS ONE. 2006 Dec 20;1:e95. [Publisher Full Text]
  151. Interaction of native and apo-carbonic anhydrase with hydrophobic adsorbents: A comparative structure-function study.
    Salemi, Z. Hosseinkhani, S. Ranjbar, B. Nemat-Gorgani, M. (2006). J Biochem Mol Biol 39(5):636-41. [PubMed]
  152. Prediction of protein orientation upon immobilization on biological and nonbiological surfaces.
    Talasaz, A. H. Nemat-Gorgani, M. Liu, Y. Stahl, P. Dutton, R. W. Ronaghi, M. Davis, R. W. (2006). Proc Natl Acad Sci U S A 103(40):14773-8. [PubMed]
  153. Pyrosequencing of the DNA gyrase gene in Neisseria species: effective indicator of ciprofloxacin resistance in Neisseria gonorrhoeae.
    Lindbäck E, Unemo M, Akhras M, Gharizadeh B, Fredlund H, Pourmand N, Wretlind B. APMIS. 2006 Dec;114(12):837-41. [PubMed]
  154. Commonality and differences in leukocyte gene expression patterns among three models of inflammation and injury.
    Brownstein BH, Logvinenko T, Lederer JA, Cobb JP, Hubbard WJ, Chaudry IH, Remick DG, Baker HV, Xiao W, Mannick JA. Physiol Genomics. 2006 Feb 14;24(3):298-309. Epub 2005 Dec 20. [PubMed]
  155. PathogenMIPer: A tool for the design of molecular inversion probes to detect multiple pathogens.
    Thiyagarajan S, Karhanek M, Akhras M, Davis RW, Pourmand N. BMC Bioinformatics. 2006 Nov 14;7(1):500 [Epub ahead of print] [PubMed]
  156. Current Rectification with Poly-l-Lysine-Coated Quartz Nanopipettes.
    Umehara S, Pourmand N, Webb CD, Davis RW, Yasuda K, Karhanek M. Nano Lett. 2006 Nov 8;6(11):2486-2492. [PubMed]
  157. Linking Hydrophilic Macromolecules to Monodisperse Magnetite (Fe3O4) Nanoparticles via Trichloro-s-triazine.
    Jin Xie, Chenjie Xu, Zhichuan Xu, Yanglong Hou, Kaylie L. Young, S. X. Wang, N. Pourmand, and Shouheng Sun. Chem. Mater., 18 (23), 5401 -5403, 2006. [Publisher Full Text]
  158. Cell-specific expression and pathway analyses reveal alterations in trauma-related human T cell and monocyte pathways.
    Laudanski K, Miller-Graziano C, Xiao W, Mindrinos MN, Richards DR, De A, Moldawer LL, Maier RV, Bankey P, Baker HV, Brownstein BH, Cobb JP, Calvano SE, Davis RW, Tompkins RG. Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15564-9. Epub 2006 Oct 10. [PubMed], [Publisher Full Text]
  159. Large-scale pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing.
    Gharizadeh, B., Herman Z.S., Eason R.G., Jejelowo, O., Pourmand, N. Electrophoresis. 2006 Aug;27(15):3042-7. [PubMed]
  160. Spin valve sensors for ultra sensitive detection of super paramagnetic nanoparticles for biological applications.
    Guanxiong Li, Shouheng Sun, Robert J. Wilson, Robert L. White, Nader Pourmand, Shan X. Wang. Sensors and Actuators A 126 (2006)98-106. [PubMed]
  161. One-Pot Synthesis of Mono-disperse Iron Oxide Nanoparticles for Potential Biomedical Applications.
    Jin Xie, Sheng Peng, Nathan Brower, Nader Pourmand, Shan X. Wang, Shouheng Sun. Pure Appl. Chem. Vol 78, No. 5 1003-1014, 2006
  162. Introns regulate RNA and protein abundance in yeast.
    Juneau K, Miranda M, Hillenmeyer ME, Nislow C, Davis RW. Genetics. 2006 Sep;174(1):511-8. Epub 2006 Jul 2. [PubMed]
  163. Local and distant burn injury alter immuno-inflammatory gene expression in skeletal muscle.
    Padfield, KE., Zhang, Q., Gopalan, S., Tzika, AA., Mindrinos, MN., Tompkins, RG., Rahme, LG. J Trauma. 2006 Aug;61(2):280-92. [PubMed]
  164. Analysis of hybridization on the molecular barcode GeneChip microarray.
    Walton, SP., Mindrinos MN., Davis RW. Biochem Biophys Res Commun. 2006 Sep 22;348(2):689-96. Epub 2006 Jul 28. [PubMed], [Publisher Full Text]
  165. Microfluidic isolation of leukocytes from whole blood for phenotype and gene expression analysis.
    Sethu, P., Moldawer, LL., Mindrinos, MN., Scumpia, PO., Tannahill, CL., Wilhelmy, J., Efron, PA., Brownstein, BH., Tompkins, RG., Toner, M. Anal Chem. 2006 Aug 1;78(15):5453-61. [PubMed], [Publisher Full Text]
  166. Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma.
    Ji, H., Kumm, J., Zhang, M., Farnam, K., Salari, K., Faham, M., Ford, J.M., Davis, R.W. Cancer Res. 2006 Aug 15;66(16):7910-9. [PubMed], [Publisher Full Text]
  167. Large-scale pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing.
    Gharizadeh, B., Herman Z.S., Eason R.G., Jejelowo, O., Pourmand, N. Electrophoresis. 2006 Aug;27(15):3042-7. [PubMed]
  168. A unique and universal molecular barcode array.
    Pierce, SE, Fung, EL, Jaramillo, DF, Chu AM, Davis, RW, Nislow, C., Giaever, G. Nat Methods, 2006 Aug;3(8):601-3. [PubMed]
  169. The role of selection in the evolution of human mitochondrial genomes.
    Kivisild, T., Shen, P., Wall, D.P., Do, B., Sung, R., Davis, K., Passarino, G., Underhill, P.A., Scharfe, C., Torroni, A., Scozzari, R., Modiano, D., Coppa, A., de Knijff, P., Feldman, M., Cavalli-Sforza, L.L. & Oefner, P.J. Genetics 172, 373-87 (2006). [PubMed], [Publisher Full Text]
  170. Proteome analysis of mitochondrial outer membrane from Neurospora crassa.
    Schmitt, S., Prokisch, H., Schlunck, T., Camp, D.G., Ahting, U., Waizenegger, T., Scharfe, C., Meitinger, T., Imhof, A., Neupert, W., Oefner, P.J. & Rapaport, D. Proteomics 6(1), 72-80 (2006). [PubMed]
  171. MitoP2: the mitochondrial proteome database--now including mouse data.
    Prokisch, H., Andreoli, C., Ahting, U., Heiss, K., Ruepp, A., Scharfe, C. & Meitinger, T. Nucleic Acids Res 34, D705-11 (2006). [PubMed], [Publisher Full Text]
  172. A haplotype framework for cystic fibrosis mutations in Iran.
    Elahi, E., Khodadad, A., Kupershmidt, I., Ghasemi, F., Alinasab, B., Naghizadeh, R., Eason, R.G., Amini, M., Esmaili, M., Esmaeili Dooki, M.R., Sanati, M.H., Davis, R.W., Ronaghi, M. & Thorstenson, Y.R. J Mol Diagn 8, 119-27 (2006). [PubMed]
  173. A high-resolution map of transcription in the yeast genome.
    David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C.J., Bofkin, L., Jones, T., Davis, R.W. & Steinmetz, L.M. Proc Natl Acad Sci U S A 103, 5320-5 (2006). [PubMed], [Publisher Full Text]
  174. High dynamic range characterization of the trauma patient plasma proteome.
    Liu, T., Qian, W.J., Gritsenko, M.A., Xiao, W., Moldawer, L.L., Kaushal, A., Monroe, M.E., Vamum, S.M., Moore, R.J., Purvine, S.O., Maier, R.V., Davis, R.W., Tompkins, R.G., Camp, D.G., 2nd & Smith, R.D. Mol Cell Proteomics (2006). [PubMed]
  175. The role of selection in the evolution of human mitochondrial genomes.
    Kivisild, T., Shen, P., Wall, D.P., Do, B., Sung, R., Davis, K., Passarino, G., Underhill, P.A., Scharfe, C., Torroni, A., Scozzari, R., Modiano, D., Coppa, A., de Knijff, P., Feldman, M., Cavalli-Sforza, L.L. & Oefner, P.J. Genetics 172, 373-87 (2006). [PubMed], [Publisher Full Text]
  176. Sentinel-base DNA genotyping using multiple sequencing primers for high-risk human papillomaviruses.
    Gharizadeh, B., Zheng, B., Akhras, M., Ghaderi, M., Jejelowo, O., Strander, B., Nyren, P., Wallin, K.L. & Pourmand, N. Mol Cell Probes. 2006 Jun-Aug;20(3-4):230-8. Epub 2006 Mar 3. [PubMed]
  177. Methodological improvements of pyrosequencing technology.
    Gharizadeh, B., Akhras, M., Nourizad, N., Ghaderi, M., Yasuda, K., Nyren, P. & Pourmand, J Biotechnol. 2006 Jul 25;124(3):504-11. Epub 2006 Mar 10. [PubMed]
  178. Direct electrical detection of DNA synthesis.
    Pourmand, N., Karhanek, M., Persson, H.H., Webb, C.D., Lee, T.H., Zahradnikova, A. & Davis, R.W. Proc Natl Acad Sci U S A 103, 6466-70 (2006). [PubMed]
  179. Experimental approaches to identify genetic networks.
    Costanzo M, Giaever G, Nislow C, Andrews B. Curr Opin Biotechnol. 2006 Oct;17(5):472-80. Epub 2006 Sep 8. Review.PMID: 16962766
  180. Microbes on the Human Vaginal Epithelium.
    Hyman, Richard W., Marilyn Fukushima, Lisa Diamond, Jochen Kumm, Linda C. Giudice, and Ronald W. Davis (2005). Proc. Natl. Acad. Sci. U.S.A. 102: 7952-7.
  181. Significance analysis of time course microarray experiments.
    Storey JD, Xiao W, Leek JT, Tompkins RG, Davis RW. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12837-42. Epub 2005 Sep 2.
  182. Deglycosylation of glucoamylase from Aspergillus niger: effects on structure, activity and stability.
    Jafari-Aghdam, J. Khajeh, K. Ranjbar, B. Nemat-Gorgani, M. (2005). Biochim Biophys Acta 1750(1):61-8. [PubMed]
  183. Positive Selection of a Pre-Expansion CAG Repeat of the Human SCA2 Gene.
    Yu, F., Sabeti, P.C., Hardenbol, P., Fu, Q., Fry, B., Lu, X., Ghose, S., Vega, R., Perez, A., Pasternak, S., Leal, S.M., Willis, T.D., Nelson, D.L., Belmont, J. & Gibbs, R.A. PLoS Genet 1, e41 (2005). [PubMed], [Publisher Full Text]
  184. Fisher's theorems for multivariable, time-and space-dependent systems, with applications in population genetics and chemical kinetics.
    Vlad, M.O., Szedlacsek, S.E., Pourmand, N., Cavalli-Sforza, L.L., Oefner, P. & Ross, J. Proc Natl Acad Sci U S A 102, 9848-53 (2005). [PubMed], [Publisher Full Text]
  185. Identifying new candidate genes for hereditary facial paresis on chromosome 3q21-q22 by RNA in situ hybridization in mouse.
    van der Zwaag, B., Burbach, J.P., Scharfe, C., Oefner, P.J., Brunner, H.G., Padberg, G.W. & van Bokhoven, H.Genomics 86, 55-67 (2005). [PubMed]
  186. Optimal genotype determination in highly multiplexed SNP data.
    Moorhead, M., Hardenbol, P., Siddiqui, F., Falkowski, M., Bruckner, C., Ireland, J., Jones, H.B., Jain, M., Willis, T.D. & Faham, M. Eur J Hum Genet (2005). [PubMed]
  187. Younger birth cohort correlates with higher breast and ovarian cancer risk in European BRCA1 mutation carriers.
    Kroiss, R., Winkler, V., Bikas, D., Fleischmann, E., Mainau, C., Frommlet, F., Muhr, D., Fuerhauser, C., Tea, M., Bittner, B., Kubista, E., Oefner, P.J., Bauer, P. & Wagner, T.M. Hum Mutat 26, 583-9 (2005). [PubMed]
  188. The role of selection in the evolution of human mitochondrial genomes.
    Kivisild, T., Shen, P., Wall, D.P., Do, B., Sung, R., Davis, K.K., Passarino, G., Underhill, P.A., Scharfe, C., Torroni, A., Scozzari, R., Modiano, D., Coppa, A., de Knjiff, P., Feldman, M.W., Cavalli-Sforza, L.L. & Oefner, P.J. Genetics (2005). [PubMed]
  189. Detection of gyrA mutations associated with ciprofloxacin resistance in Neisseria gonorrhoeae by rapid and reliable pre-programmed short DNA sequencing.
    Gharizadeh, B., Akhras, M., Unemo, M., Wretlind, B., Nyren, P. & Pourmand, N.Int J Antimicrob Agents 26, 486-90 (2005). [PubMed]
  190. Population structure, differential bias and genomic control in a large-scale, case-control association study.
    Clayton, D.G., Walker, N.M., Smyth, D.J., Pask, R., Cooper, J.D., Maier, L.M., Smink, L.J., Lam, A.C., Ovington, N.R., Stevens, H.E., Nutland, S., Howson, J.M., Faham, M., Moorhead, M., Jones, H.B., Falkowski, M., Hardenbol, P., Willis, T.D. & Todd, J.A. Nat Genet 37, 1243-6 (2005). [PubMed], [Publisher Full Text]
  191. Proton NMR spectroscopy shows lipids accumulate in skeletal muscle in response to burn trauma-induced apoptosis.
    Astrakas, L.G., Goljer, I., Yasuhara, S., Padfield, K.E., Zhang, Q., Gopalan, S., Mindrinos, M.N., Dai, G., Yu, Y.M., Martyn, J.A., Tompkins, R.G., Rahme, L.G. & Tzika, A.A. Faseb J 19, 1431-40 (2005). [PubMed], [Publisher Full Text]
  192. Genome-wide requirements for resistance to functionally distinct DNA damaging agents.
    Lee, W., St.Onge R.P., Proctor, M., Flaherty, P., Arkin A.P. , Davis, R.W., Nislow, C., Giaever, G. PLoS Genet 1, e24 (2005). [PubMed], [Publisher Full Text]
  193. Functional genomic analysis of the rates of protein evolution.
    Wall, D.P., Hirsh, A.E., Fraser, H.B., Kumm, J., Giaever, G., Eisen, M.B., Feldman, M.W. Proc Natl Acad Sci U S A 102, 5483-8 (2005). Epub 2005 Mar 30. Erratum in: Proc Natl Acad Sci U S A. 2006 May 16;103(20):7935. [PubMed], [Publisher Full Text]
  194. Two ATM variants and breast cancer risk.
    Thompson, D., Antoniou, A.C., Jenkins, M., Marsh, A., Chen, X., Wayne, T., Tesoriero, A., Milne, R., Spurdle, A., Thorstenson, Y., Southey, M., Giles, G.G., Khanna, K.K., Sambrook, J., Oefner, P., Goldgar, D., Hopper, J.L., Easton, D., Chenevix-Trench, G. Hum Mutat 25, 594-5 (2005). [PubMed], [Publisher]
  195. Conservation of the RB1 gene in human and primates.
    Sivakumaran, T.A., Shen, P., Wall, D.P., Do, B.H., Kucheria, K., Oefner, P.J. Hum Mutat Apr 25(4):396-409 (2005). [PubMed], [Publisher]
  196. DNA-functionalized MFe2O4 (M = Fe, Co, or Mn) nanoparticles and their hybridization to DNA-functionalized surfaces.
    Robinson, D.B., Persson, H.H., Zeng, H., Li, G., Pourmand, N., Sun, S., Wang, S.X. Langmuir 21, 3096-103 (2005). [PubMed], [Publisher Full Text]
  197. Quantitative Proteome Analysis of Human Plasma following in Vivo Lipopolysaccharide Administration Using 16O/18O Labeling and the Accurate Mass and Time Tag Approach.
    Qian, W.J., Monroe, M.E., Liu, T., Jacobs, J.M., Anderson, G.A., Shen, Y., Moore, R.J., Anderson, D.J., Zhang, R., Calvano, S.E., Lowry, S.F., Xiao, W., Moldawer, L.L., Davis, R.W., Tompkins, R.G., Camp, D.G., 2nd, Smith, R.D. Mol Cell Proteomics 4, 700-709 (2005). [PubMed]
  198. Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry.
    Qian, W.J., Jacobs, J.M., Camp, D.G., 2nd, Monroe, M.E., Moore, R.J., Gritsenko, M.A., Calvano, S.E., Lowry, S.F., Xiao, W., Moldawer, L.L., Davis, R.W., Tompkins, R.G., Smith, R.D. Proteomics 5, 572-84 (2005). [PubMed]
  199. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.
    Loftus, B.J., Fung, E., Roncaglia, P., Rowley, D., Amedeo, P., Bruno, D., Vamathevan, J., Miranda, M., Anderson, I.J., Fraser, J.A., Allen, J.E., Bosdet, I.E., Brent, M.R., Chiu, R., Doering, T.L., Donlin, M.J., D'Souza, C.A., Fox, D.S., Grinberg, V., Fu, J., Fukushima, M., Haas, B.J., Huang, J.C., Janbon, G., Jones, S.J., Koo, H.L., Krzywinski, M.I., Kwon-Chung, J.K., Lengeler, K.B., Maiti, R., Marra, M.A., Marra, R.E., Mathewson, C.A., Mitchell, T.G., Pertea, M., Riggs, F.R., Salzberg, S.L., Schein, J.E., Shvartsbeyn, A., Shin, H., Shumway, M., Specht, C.A., Suh, B.B., Tenney, A., Utterback, T.R., Wickes, B.L., Wortman, J.R., Wye, N.H., Kronstad, J.W., Lodge, J.K., Heitman, J., Davis, R.W., Fraser, C.M., Hyman, R.W. Science 307, 1321-4 (2005). [PubMed], [Publisher Full Text]
  200. Single DNA molecule detection using nanopipettes and nanoparticles.
    Karhanek, M., Kemp, J.T., Pourmand, N., Davis, R.W., Webb, C.D. Nano Lett 5, 403-7 (2005). [PubMed], [Publisher Full Text]
  201. Task-specific expression of the foraging gene in harvester ants.
    Ingram, K.K., Oefner, P, Gordon, D.M. Mol Ecol 14, 813-8 (2005). [PubMed], [Publisher Full Text]
  202. Bioluminescence regenerative cycle (BRC) system: Theoretical considerations for nucleic acid quantification assays.
    Hassibi, A., Contag, C., Vlad, M.O., Hafezi, M., Lee, T.H., Davis, R.W., Pourmand, N. Biophys Chem 116, 175-85 (2005). [PubMed], [Publisher Full Text]
  203. Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay.
    Hardenbol, P., Yu, F., Belmont, J., Mackenzie, J., Bruckner, C., Brundage, T., Boudreau, A., Chow, S., Eberle, J., Erbilgin, A., Falkowski, M., Fitzgerald, R., Ghose, S., Iartchouk, O., Jain, M., Karlin-Neumann, G., Lu, X., Miao, X., Moore, B., Moorhead, M., Namsaraev, E., Pasternak, S., Prakash, E., Tran, K., Wang, Z., Jones, H.B., Davis, R.W., Willis, T.D., Gibbs, R.A. Genome Res 15, 269-75 (2005). [PubMed], [Publisher Full Text]
  204. Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae.
    Gu, Z., David, L., Petrov, D., Jones, T., Davis, R.W., Steinmetz, L.M. Proc Natl Acad Sci U S A 102, 1092-7 (2005). [PubMed], [Publisher Full Text]
  205. Type-specific multiple sequencing primers: a novel strategy for reliable and rapid genotyping of human papillomaviruses by pyrosequencing technology.
    Gharizadeh, B., Oggionni, M., Zheng, B., Akom, E., Pourmand, N., Ahmadian, A., Wallin, K.L., Nyren, P. J Mol Diagn 7, 198-205 (2005). [PubMed]
  206. A latent variable model for chemogenomic profiling.
    Flaherty, P., Giaever, G., Kumm, J., Jordan, M.I., Arkin, A.P. Bioinformatics 21, 3286-9, Epub 2005 May 26. (2005). [PubMed]
  207. Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast.
    Deutschbauer, A.M., Jaramillo, D.F., Proctor, M., Kumm, J., Hillenmeyer, M.E., Davis, R.W., Nislow, C., Giaever, G. Genetics 169, 1915-25 (2005). [PubMed], [Publisher Full Text]
  208. Burn injury causes mitochondrial dysfunction in skeletal muscle.
    Padfield KE, Astrakas LG, Zhang Q, Gopalan S, Dai G, Mindrinos MN, Tompkins RG, Rahme LG, Tzika AA. Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5368-73. Epub 2005 Apr 4. [PubMed], [Publisher]
  209. Application of genome-wide expression analysis to human health and disease.
    Cobb, J.P., Mindrinos, M.N., Miller-Graziano, C., Calvano, S.E., Baker, H.V., Xiao, W., Laudanski, K., Brownstein, B.H., Elson, C.M., Hayden, D.L., Herndon, D.N., Lowry, S.F., Maier, R.V., Schoenfeld, D.A., Moldawer, L.L., Davis, R.W., Tompkins, R.G., Baker, H.V., Bankey, P., Billiar, T., Brownstein, B.H., Calvano, S.E., Camp, D., Chaudry, I., Cobb, J.P., Davis, R.W., Elson, C.M., Freeman, B., Gamelli, R., Gibran, N., Harbrecht, B., Hayden, D.L., Heagy, W., Heimbach, D., Herndon, D.N., Horton, J., Hunt, J., Laudanski, K., Lederer, J., Lowry, S.F., Maier, R.V., Mannick, J., McKinley, B., Miller-Graziano, C., Mindrinos, M.N., Minei, J., Moldawer, L.L., Moore, E., Moore, F., Munford, R., Nathens, A., O'Keefe, G., Purdue, G., Rahme, L., Remick, D., Sailors, M., Schoenfeld, D.A., Shapiro, M., Silver, G., Smith, R., Stephanopoulos, G., Stormo, G., Tompkins, R.G., Toner, M., Warren, S., West, M., Wolfe, S., Xiao, W, Young, V. Proc Natl Acad Sci U S A 102, 4801-6 (2005). [PubMed], [Publisher]
  210. Profiling early infection responses: Pseudomonas aeruginosa eludes host defenses by suppressing antimicrobial peptide gene expression.
    Apidianakis, Y., Mindrinos, M.N., Xiao, W., Lau, G.W., Baldini, R.L., Davis, R.W., Rahme, L.G. Proc Natl Acad Sci U S A 102, 2573-8 (2005). [PubMed], [Publisher]
  211. Microbes on the human vaginal epithelium.
    Hyman R.W., Fukushima M., Diamond L., Kumm J., Giudice L.C., Davis R.W. (2005). PNAS May 31, 2005;102(22):7952-57. [PubMed]
  212. Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast.Genetics.
    Deutschbauer AM, Jaramillo DF, Proctor M, Kumm J, Hillenmeyer ME, Davis RW, Nislow C, Giaever G. 2005 Apr;169(4):1915-25. Epub 2005 Feb 16.
  213. A transcriptional profile of aging in the human kidney.
    Rodwell GEJ., Sonu R., Zahn JM., Lund J., Wilhelmy J., Wang L., Xiao W, Mindrinos MN., Crane E., Segal E., Myers BD., Brooks JD., Davis RW., Higgins J, Owen AB., Kim SK. PLoS Biol. 2004 Dec;2(12):e427. Epub 2004 Nov 30. [PubMed], [Publisher Full Text]
  214. Whole blood and leukocyte RNA isolation for gene expression analyses.
    Feezor RJ., Baker HV., Mindrinos MN., Hayden D., Tannahill CL., Brownstein BH., Fay A., MacMillan S., Laramie J., Xiao W., Moldawer LL., Cobb JP., Laudanski K., Miller-Graziano CL., Maier RV., Schoenfeld D, Davis RW., Tompkins RG.; and the Inflammation and Host Response to Injury, Large-Scale Collaborative Research ProgramPhysiol Genomics. 2004 Nov 17;19(3):247-54. [PubMed], [Publisher Full Text]
  215. Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-chromosome and mitochondrial DNA sequence variation.
    Shen P, Lavi T, Kivisild T, Chou V, Sengun D, Gefel D, Shpirer I, Woolf E, Hillel J, Feldman MW, Oefner PJ. (2004). Hum Mutat. 2004 Sep;24(3):248-60. [PubMed], [Publisher]
  216. Reduced genetic structure of the Iberian peninsula revealed by Y-chromosome analysis: implications for population demography.
    Flores C, Maca-Meyer N, Gonzalez AM, Oefner PJ, Shen P, Perez JA, Rojas A, Larruga JM, Underhill PA. (2004). Eur J Hum Genet. 2004 Oct;12(10):855-63. [PubMed]
  217. Genomic and proteomic determinants of outcome in patients undergoing thoracoabdominal aortic aneurysm repair.
    Feezor RJ, Baker HV, Xiao W, Lee WA, Huber TS, Mindrinos M, Kim RA, Ruiz-Taylor L, Moldawer LL, Davis RW, Seeger JM. (2004). J Immunol. 2004 Jun 1;172(11):7103-9. [PubMed], [Publisher Full Text]
  218. Sister-chromatid cohesion mediated by the alternative RF-CCtf18/Dcc1/Ctf8, the helicase Chl1 and the polymerase-alpha-associated protein Ctf4 is essential for chromatid disjunction during meiosis II.
    Petronczki M, Chwalla B, Siomos MF, Yokobayashi S, Helmhart W, Deutschbauer AM, Davis RW, Watanabe Y, Nasmyth K. (2004). J Cell Sci. 2004 Jul 15;117(Pt 16):3547-59. Epub 2004 Jun 29. [PubMed], [Publisher Full Text]
  219. SNP discovery in pooled samples with mismatch repair detection.
    Fakhrai-Rad H, Zheng J, Willis TD, Wong K, Suyenaga K, Moorhead M, Eberle J, Thorstenson YR, Jones T, Davis RW, Namsaraev E, Faham M. (2004). Genome Res. 2004 Jul;14(7):1404-12. [PubMed], [Publisher Full Text]
  220. Global analysis of the membrane subproteome of Pseudomonas aeruginosa using liquid chromatography-tandem mass spectrometry.
    Blonder J, Goshe MB, Xiao W, Camp DG 2nd, Wingerd M, Davis RW, Smith RD. (2004). J Proteome Res. 2004 May-Jun;3(3):434-44. [PubMed]
  221. Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains.
    Eason RG, Pourmand N, Tongprasit W, Herman ZS, Anthony K, Jejelowo O, Davis RW, Stolc V. (2004). Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11046-51. Epub 2004 Jul 16. [PubMed], [Publisher Full Text]
  222. Regulatory networks affected by iron availability in Candida albicans.
    Lan C.Y., Rodarte G., Murilla L.A., Jones T., Davis R.W., Dungan J., Newport G., Agabia N. (2004). Mol Microbiol. 2004 Sep;53(5):1451-69. [PubMed], [Publisher Full Text]
  223. The diploid genome sequence of Candida albicans.
    Jones T., Federspiel N.A., Chibana H., Dungan J., Kalman S. Magee B.B., Newport G., Thorstenson YR., Agabian N., Magee P.T., Davis R.W., Scherer S. (2004). Proc Natl Acad Sci U S A. 2004 May 11;101(19):7329-34. Epub 2004 May 03. [PubMed], [Publisher Full Text]
  224. To give or not to give? That is the question.
    Theologis A., Davis R.W. (2004) Plant Physiology, May 2004, 135:4-9. [PubMed], [Publisher Full Text]
  225. Integrative Analysis of the Mitochondrial Proteome in Yeast
    Prokisch H., Scharfe C., Camp D.G., Xiao W., David L., Andreoli C., Monroe M.E., Moore R.J., Gritsenko M.A. Kozany C., Hixson K.K., Mottaz H.M., Zischka H., Ueffing M., Herman Z.S., Davis R.W., Meitinger T., Oefner P.J., Smith R.D., Steinmetz L.M. (2004). PLoS Biology 2004; 2(6). [Publisher Full Text]
  226. Noise Minimization in Eukaryotic Gene Expression.
    Fraser H.B., Hirsh A.E., Giaver G., Eisen M.B. (2004) PLOS biology June 2004; 2(6). [Publisher Full Text]
  227. Demographic estimates from Y chromosome microsatellite polymorphisms: Analysis of a worldwide sample.
    Macpherson M., Ramachandran S., Diamond L., Feldman M.W. (2004) Human Genomics Aug. 2004, 1(5):345-354. [PubMed]
  228. Phylogeography of y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in Europe.
    Rootsi S, Magri C, Kivisild T, Benuzzi G, Help H, Bermisheva M, Kutuev I, Barac L, Pericic M, Balanovsky O, Pshenichnov A, Dion D, Grobei M, Zhivotovsky LA, Battaglia V, Achilli A, Al-Zahery N, Parik J, King R, Cinnioglu C, Khusnutdinova E, Rudan P, Balanovska E, Scheffrahn W, Simonescu M, Brehm A, Goncalves R, Rosa A, Moisan JP, Chaventre A, Ferak V, Furedi S, Oefner PJ, Shen P, Beckman L, Mikerezi I, Terzic R, Primorac D, Cambon-Thomsen A, Krumina A, Torroni A, Underhill PA, Santachiara-Benerecetti AS, Villems R, Semino O. (2004). Am J Hum Genet. 2004 Jul;75(1):128-37. Epub 2004 May 25. [PubMed], [Publisher Full Text]
  229. Patterned Magnetic Bar Array for High-Throughput DNA Detection.
    Roberts L.A; Crawford A.M., Zappe S., Jain M. White R.L. IEEE Transaction on Magnetics.
  230. Analysis of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs) reveals a role for 4-hydroxy-2-heptylquinoline in cell-to-cell communication.
    Deziel E, Lepine F, Milot S, He J, Mindrinos MN, Tompkins RG, Rahme LG. (2004). Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1339-44. Epub 2004 Jan 22. [PubMed], [Publisher Full Text]
  231. Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome.
    Shen Y, Jacobs JM, Camp DG 2nd, Fang R, Moore RJ, Smith RD, Xiao W, Davis RW, Tompkins RG. (2004). Anal Chem. 2004 Feb 15;76(4):1134-44. [PubMed], [Publisher Full Text]
  232. Pyrosequencing: a tool for DNA sequencing analysis.
    Elahi E., Ronaghi, M. (2004). Methods Mol Biol. 2004;255:211-20. [PubMed]
  233. Global Genetic Analysis.
    Elahi E., Kumm, J., Ronaghi, M. (2004). J Biochem Mol Biol. 2004 Jan 31;37(1):11-27. [PubMed]
  234. Origin, diffusion and differentiation of Y-chromosome haplogroups E and J: inferences on the Neolithization of Europe and later migratory events in the Mediterranean area.
    Am J Hum Genet. 2004 May;74(5):1023-34. Epub 2004 Apr 06. [PubMed], [Publisher Full Text]
  235. Expression of foraging gene differs in ants and bees.
    Ingram, K., Gordon, D., Oefner, P. (2004). Science, submitted.
  236. Comparison of HPLC, LC/MS, and CZE in the mapping of an LOH interval on 11p in ovarian cancer.
    Hauenstein, E., Arnold, N., Hoelzl, G., Jacobsen, A., Ramser, J., Meindl, A., Kiechle, M., Oefner, P., Gross, E. (2004). Hum. Mutat., submitted.
  237. A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo.
    Wang QT, Piotrowska K, Ciemerych MA, Milenkovic L, Scott MP, Davis RW, Zernicka-Goetz M. (2004). Dev Cell. 2004 Jan;6(1):133-44. [PubMed], [Publisher Full Text]
  238. Chemogenomic profiling: identifying the functional interactions of small molecules in yeast.
    Giaever, G., Flaherty, P., Kumm, J., Proctor, M., Nislow, C., Jaramillo, D. F., Chu, A. M., Jordan, M. I., Arkin, A. P., Davis, R. W. (2004). Proc Natl Acad Sci U S A. 2004 Jan 20;101(3):793-8. Epub 2004 Jan 12 [PubMed], [Publisher Full Text]
  239. Bioluminescence Regenerative Cycle (BRC) System for Nucleic Acid Quantification Assays.
    Arjang Hassibi, Thomas H. Lee, Ronald W. Davis and Nader Pourmand. Proc. of SPIE, Vol. 4966, pp. 65-75 2003.
  240. Excavating Y-chromosome haplotype strata in Anatolia.
    Cinnioglu, C., King, R., Kivisild, T., Kalfoglu, E., Atasoy, S., Cavalleri, G. L., Lillie, A. S., Roseman, C. C., Lin, A. A., Prince, K., Oefner, P. J., Shen, P., Semino, O., Cavalli-Sforza, L. L., Underhill, P. A. (2004). Hum Genet. 2004 Jan;114(2):127-48. Epub 2003 Oct 29. [PubMed], [Publisher]
  241. MitoP2, an integrated database on mitochondrial proteins in yeast and man.
    Andreoli, C., Prokisch, H., Hortnagel, K., Mueller, J. C., Munsterkotter, M. Scharfe, C., Meitinger, T. (2004). Nucleic Acids Res. 2004 Jan 1;32 Database issue:D459-62. [PubMed]
  242. Noise minimization in eukaryotic gene expression.
    Fraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB. PLoS Biol. 2004 Jun;2(6):e137. Epub 2004 Apr 27.
  243. A novel Y-chromosome variant puts an upper limit on the timing of first entry into the Americas.
    Seielstad, M., Yuldasheva, N., Singh, N., Underhill, P., Oefner, P., Shen, P., Wells, R. S. Am J Hum Genet. 2003 Sep;73(3):700-5. [Publisher]
  244. Applicability of tandem mass spectrometry to the automated comparative sequencing of 38- to 80-mer oligonucleotides.
    Oberacher, H., Mayr, B.M., Parson, W., Oefner, P.J., Huber, C.G. (2003). J Am Soc Mass Spectrom. 2004 Apr;15(4):510-22. [PubMed]
  245. First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome.
    Rickert, A.M., Kim, J.H., Meyer, S., Nagel, A., Ballvora, A., Oefner, P.J., Gebhardt, C. (2003) Plant Biotechnology J. 1, 399-410.
  246. A tRNA(Ala) mutation causing mitochondrial myopathy clinically resembling myotonic dystrophy.
    Horvath, R., Lochmuller, H., Scharfe, C., Do, B.H., Oefner, P.J., Muller-Hocker,s J., Schoser, B.G., Pongratz, D., Auer, D.P., Jaksch, M. (2003). J. Med. Genet. 40, 752-757. [PubMed]
  247. Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Yamada, K., Lim, J., Dale, J. M., Chen, H., Shinn, P., Palm, C. J., Southwick, A. M., Wu, H. C., Kim, C., Nguyen, M., Pham, P., Cheuk, R., Karlin-Newmann, G., Liu, S. X., Lam, B., Sakano, H., Wu, T., Yu, G., Miranda, M., Quach, H. L., Tripp, M., Chang, C. H., Lee, J. M., Toriumi, M., Chan, M. M., Tang, C. C., Onodera, C. S., Deng, J. M., Akiyama, K., Ansari, Y., Arakawa, T., Banh, J., Banno, F., Bowser, L., Brooks, S., Carninci, P., Chao, Q., Choy, N., Enju, A., Goldsmith, A. D., Gurjal, M., Hansen, N. F., Hayashizaki, Y., Johnson-Hopson, C., Hsuan, V. W., Iida, K., Karnes, M., Khan, S., Koesema, E., Ishida, J., Jiang, P. X., Jones, T., Kawai, J., Kamiya, A., Meyers, C., Nakajima, M., Narusaka, M., Seki, M., Sakurai, T., Satou, M., Tamse, R., Vaysberg, M., Wallender, E. K., Wong, C., Yamamura, Y., Yuan, S., Shinozaki, K., Davis, R. W., Theologis, A., Ecker, J. R. (2003). Science. 2003 Oct 31;302(5646):842-6. [PubMed], [Publisher Full Text]
  248. Advantages of external periodic events to the evolution of biochemical oscillatory reactions.
    Tsuchiya, M., Ross, J. (2003). Proc. Natl. Acad. Sci. USA Aug 19; 100(17):9691-9695. [Publisher Full Text]
  249. ZmDB, an integrated database for maize genome research.
    Dong, Q., Roy, L., Freeling, M., Walbot, V., Brendel, V. Nucleic Acids Res. 2003 Jan 1;31(1):244-7. [PubMed Abstract], [Publisher Full Text]
  250. Analysis of FAS (CD95) gene mutations in higher-grade transformation of follicle center lymphoma.
    Do, B., Lossos, I. S., Thorstenson, Y., Oefner, P.J., Levy, R. Leuk Lymphoma. 2003 Aug;44(8):1317-23. [PubMed Abstract]
  251. Genotyping African haplotypes in ATM using a co-spotted single-base extension assay.
    Jain, M., Thorstenson, Y. R., Faulkner, D. M., Pourmand, N., Jones, T., Au, M., Oefner, P. J., White, K. P., Davis, R. W. Hum Mutat. 2003 Sep;22(3):214-21. [PubMed Abstract], [Publisher]
  252. 'Chemogenomics: tools for protein families' and 'Chemical genomics: chemical and biological integration'.
    Nislow, C., Giaever, G. Pharmacogenomics. 2003 Jan;4(1):15-8.
  253. A chemical genomics approach to understanding drug action.
    Giaever, G. Trends Pharmacol Sci. 2003 Sep;24(9):444-6. [PubMed Abstract]
  254. Use of a genome-wide approach to identify new genes that control resistance of Saccharomyces cerevisiae to ionizing radiation.
    Game, JC, Birrell, GW, Brown, JA, Shibata, T, Baccari, C, Chu, AM, Williamson, MS and Brown JM (2003). Radiat Res, 160(1): 14-24.
  255. Contributions of ATM Mutations to Familial Breast and Ovarian Cancer.
    Thorstenson, Y. R., Roxas, A., Kroiss, R., Jenkins, M. A., Yu, K. M., Bachrich, T., Muhr, D., Wayne, T. L., Chu, G., Davis, R. W., Wagner, T. M., Oefner, P. J. Cancer Res. 2003 Jun 15;63(12):3325-33. [PubMed Abstract], [Publisher Full Text]
  256. Peopling of three Mediterranean islands (Corsica, Sardinia, and Sicily) inferred by Y-chromosome biallelic variability.
    Francalacci, P., Morelli, L., Underhill, P. A., Lillie, A. S., Passarino, G., Useli, A., Madeddu, R., Paoli, G., Tofanelli, S., Calo, C. M., Ghiani, M. E., Varesi, L., Memmi, M., Vona, G., Lin, A. A., Oefner, P., Cavalli-Sforza, L. L. Am J Phys Anthropol. 2003 Jul;121(3):270-9. [PubMed Abstract], [Publisher Full Text]
  257. Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea.
    Kayser, M., Brauer, S., Weiss, G., Schiefenhövel, W.; Underhill, P., Shen, P., Oefner, P., Tommaseo-Ponzetta, M., Stoneking, M. Am J Hum Genet. 2003 Feb;72(2):281-302. Epub 2002 Jan 16. [PubMed Abstract], [Publisher Full Text]
  258. Pyrosequencing for SNP genotyping.
    Ronaghi, M. (2003) Methods Mol Biol 212, 189-95. [PubMed]
  259. Mutation scanning by ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry (ICEMS).
    Oberacher, H., Huber, C.G. & Oefner, P.J. Hum Mutat 21, 86-95 (2003). [PubMed Abstract], [Publisher Abstract]
  260. Multiplexed genotyping with sequence-tagged molecular inversion probes.
    Hardenbol, P., Baner, J., Jain, M., Nilsson, M., Namsaraev, E. A., Karlin-Neumann, G. A., Fakhrai-Rad, H., Ronaghi, M., Willis, T. D., Landegren, U., Davis, R. W. Nat Biotechnol Jun;21(6):673-8 (2003). [PubMed Abstract], [Publisher Full Text]
  261. Determination of hepatitis C virus genotype by Pyrosequencing.
    Elahi E, Pourmand N, Chaung R, Rofoogaran A, Boisver J, Samimi-Rad K, Davis RW, Ronaghi M..J Virol Methods. 2003 May;109(2):171-6. [PubMed Abstract], [Publisher Full Text]
  262. Denaturing high-performance liquid chromatography.
    Premstaller, A. & Oefner, P.J. (2003) Methods Mol Biol 212, 15-35. [PubMed]
  263. Experimental test of a method for determining causal connectivities of species in reactions.
    Torralba A.S., Yu K., Shen P., Oefner P.J., Ross J.; PNAS, published online before print Februray 7, 2003, Proc. Natl. Acad. Sci. USA, Vol. 100, Issue 4, 1494-1498, February 18, 2003 [Publisher Abstract], [Publisher Full Text]
  264. Role of duplicate genes in genetic robustness against null mutations.
    Gu, Z., Steinmetz, L.M., Gu, X., Scharfe, C., Davis , R.W., Li, W.H. (2003). Nature Jan 2;421(6918):63-66. [PubMed Abstract], [Publisher Full Text]
  265. Denaturing HPLC of Nucleic Acids
    Premstaller A, Oefner P.J.; PharmaGenomics, Feb 1,2003, Cover Story [PDF]
  266. ATM mutations on distinct SNP and STR haplotypes in ataxia-telangiectasia patients of differing ethnicities reveal ancestral founder effects.
    Campbell, C., Mitui, M., Eng, L., Coutinho, G., Thorstenson, Y., Gatti, R.A. Hum Mutat. 2003 Jan;21(1):80-5. [PubMed Abstract], [Publisher]
  267. Pyrosequencing: an accurate detection platform for single nucleotide polymorphisms.
    Hossein Fakhrai-Rad, Nader Pourmand, Mostafa Ronaghi. Hum Mutat. 2002 May ;19:479-85 [PubMed]
  268. Monolithic capillary columns for liquid chromatography-electrospray ionization mass spectrometry in proteomic and genomic research.
    Walcher W, Oberacher H, Troiani S, Holzl G, Oefner P, Zolla L, Huber CG. (2002) J Chromatogr B Analyt Technol Biomed Life Sci. Dec 25;782(1-2):111-25. [PubMed Abstract], [Publisher Full Text]
  269. Sequence variation and the biological function of genes: methodological and biological considerations.
    Oefner PJ.; (2002) J Chromatogr B Analyt Technol Biomed Life Sci. Dec 25;782(1-2):3-25. [PubMed Abstract], [Publisher Full Text]
  270. Polymerase chain reaction fidelity and denaturing high-performance liquid chromatography.
    Muhr D, Wagner T, Oefner PJ., (2002) J Chromatogr B Analyt Technol Biomed Life Sci. Dec 25;782(1-2):105-10. [PubMed Abstract], [Publisher Full Text]
  271. Metabolic specialization associated with phenotypic switching in Candida albicans.
    Lan, C.Y., Newport, G., Murillo, L.A., Jones, T., Scherer, S., Davis, R.W., Agabian, N., (2002). Nov 12, Proc Natl Acad Sci U S A, 99(23):14907-14912. [PubMed Abstract]
  272. Yeast tRNA as carrier in the isolation of microscale RNA for global amplification and expression profiling.
    Wang QT, Xiao W, Mindrinos M, Davis RW.; (2002). Biotechniques 2002 Oct;33(4):788, 790, 792 passim
  273. Parallel phenotypic analysis of sporulation and postgermination growth in Saccharomyces cerevisiae.
    Deutschbauer, A.M., Williams, R.M., Chu, A.M., Davis, R.W., (2002). Nov 26, Proc Natl Acad Sci USA, 99(24):15530-15535. [PubMed Abstract]
  274. The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast.
    Williams, R.M., Primig, M., Washburn, B.K., Winzeler, E.A., Bellis, M., Sarrauste De Menthiere, C., Davis, R.W., Esposito, R.E., (2002). Oct 7, Proc Natl Acad Sci USA. [Publisher Full Text].
  275. Bayesian analysis of systems with random chemical composition: renormalization-group approach to Dirichlet distributions and the statistical theory of dilution.
    Vlad, M.O., Tsuchiya, M., Oefner, P., Ross, J., (2002). Jan, Phys Rev E Stat Nonlin Soft Matter Phys, 65(1 Pt 1):011112. [PubMed Abstract].
  276. Neutrality condition and response law for nonlinear reaction-diffusion equations, with application to population genetics.
    Vlad, M.O., Moran, F., Tsuchiya, M., Cavalli-Sforza, L.L., Oefner, P.J., Ross, J., (2002). Jun, Phys Rev E Stat Nonlin Soft Matter Phys, 65(6 Pt 1):061110. [PubMed Abstract].
  277. Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition.
    Tang, H., Siegmund, D.O., Shen, P., Oefner, P.J., Feldman, M.W., (2002). May, Genetics, 161(1):447-459. [Publisher Full Text].
  278. Dissecting the architecture of a quantitative trait locus in yeast.
    Steinmetz, L.M., Sinha, H., Richards, D.R., Spiegelman, J.I., Oefner, P.J., McCusker, J.H., Davis, R.W., (2002). Mar 21, Nature, 416(6878):326-330. [Supporting Web Site].
  279. Systematic screen for human disease genes in yeast.
    Steinmetz, L.M., Scharfe, C., Deutschbauer, A.M., Mokranjac, D., Herman, Z.S., Jones, T., Chu, A.M., Giaever, G., Prokisch, H., Oefner, P.J., Davis, R.W., (2002). Aug, Nat Genet, 31(4):400-404.[Supporting Web Site].
  280. Population genetic implications from DNA polymorphism in random human genomic sequences.
    Shen, P., Buchholz, M., Sung, R., Roxas, A., Franco, C., Yang, W.H., Jagadeesan, R., Davis, K., Oefner, P.J., (2002). Sep, Hum Mutat, 20(3):209-217. [PubMed Abstract].
  281. Premature termination mutations in FBN1: distinct effects on differential allelic expression and on protein and clinical phenotypes.
    Schrijver, I., Liu, W., Odom, R., Brenn, T., Oefner, P., Furthmayr, H., Francke, U., (2002). Aug, Am J Hum Genet, 71(2):223-237. [PubMed Abstract].
  282. Conservation of the class I beta tubulin gene in human populations and lack of mutations in lung cancers and paclitaxel resistant ovarian cancers.
    Sale, S., Sung, R., Shen, P., Yu, K., Wang, Y., Duran, G.E., Kim, J.-H., Fojo, T., Oefner, P.J., Sikic, B.I., (2002). Mol. Cancer Ther., 1:215-225. [PubMed Abstract]
  283. Caution in the search for beta tubulin mutations.
    Sale, S., Oefner, P.J., Sikic, B.I. (2002). J. Natl. Cancer Inst.
  284. Pyrosequencing for microbial typing.
    Ronaghi, M., Elahi, E., (2002). J. Chromatogr B Analyt Technol Biomed Life Sci.; Dec 25;782(1-2):67-72. [PubMed Abstract], [Publisher Full Text]
  285. Discovery of single nucleotide polymorphisms and mutations by Pyrosequencing.
    Ronaghi, M., Elahi, E., (2002). Comparative and functional genomics, 3:51-56.
  286. Genotyping of Snps in a polyploid genome by pyrosequencing.
    Rickert, A.M., Premstaller, A., Gebhardt, C., Oefner, P.J., (2002). Mar, Biotechniques, 32(3):592-593, 596-598, 600 passim. [PubMed Abstract].
  287. Multiplex analysis of single-nucleotide extension products on a 16-capillary, denaturing, high-performance liquid chromatography array.
    Premstaller, A., Oberacher, H., Rickert, A., Huber, C.G., Oefner, P.J., (2002). Jun, Genomics, 79(6):793-798.[PubMed Abstract].
  288. Capillary array high-performance liquid chromatography of nucleic acids and proteins.
    Premstaller, A., Oefner, P.J., Oberacher, H., Huber, C.G., (2002). Sep 15, Anal Chem, 74(18):4688-4693. [PubMed Abstract].
  289. Multiplex Pyrosequencing.
    Pourmand, N., Elahi, E., Davis, R.W., Ronaghi, M., (2002). Apr 1, Nucleic Acids Res, 30(7):e31. [Publisher Full Text].
  290. Re-sequencing of multiple single nucleotide polymorphisms by liquid chromatography-electrospray ionization mass spectrometry.
    Oberacher, H., Oefner, P.J., Holzl, G., Premstaller, A., Davis, K., Huber, C.G., (2002). Jul 15, Nucleic Acids Res, 30(14):e67. [PubMed Abstract].
  291. The extent of linkage disequilibrium in Arabidopsis thaliana.
    Nordborg, M., Borevitz, J.O., Bergelson, J., Berry, C.C., Chory, J., Hagenblad, J., Kreitman, M., Maloof, J.N., Noyes, T., Oefner, P.J., Stahl, E.A., Weigel, D., (2002). Feb, Nat Genet, 30(2):190-193. [Publisher Full Text].
  292. Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.
    Lossos, I.S., Alizadeh, A.A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P.J., Brown, P.O., Botstein, D., Levy, R., (2002). Jun 25, Proc Natl Acad Sci U S A, 99(13):8886-8891. [Publisher Full Text].
  293. Mutation of the ATM gene is not involved in the pathogenesis of either follicle center lymphoma or its transformation to higher-grade lymphoma.
    Lossos, I.S., Thorstenson, Y.R., Wayne, T.L., Oefner, P.J., Levy, R., Chu, G., (2002). May, Leuk Lymphoma, 43(5):1079-1085. [PubMed Abstract].
  294. Sequence of Plasmodium falciparum chromosome 12.
    Hyman, R.W., Fung, E., Conway, A., Kurdi, O., Mao, J., Miranda, M., Nakao, B., Rowley, D., Tamaki, T., Wang, F., Davis, R.W., (2002). Oct 3, Nature, 419(6906):534-537. [PubMed Abstract], [Publisher Full Text]
  295. Identification and preliminary characterization of mouse Adam33.
    Gunn, T.M., Azarani, A., Kim, P.H., Hyman, R.W., Davis, R.W., Barsh, G.S., (2002). BMC Genet, 3(1):2. [Publisher].
  296. Functional profiling of the Saccharomyces cerevisiae genome.
    Giaever, G., Chu, A.M., Ni, L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B., Arkin, A.P., Astromoff, A., El-Bakkoury, M., Bangham, R., Benito, R., Brachat, S., Campanaro, S., Curtiss, M., Davis, K., Deutschbauer, A., Entian, K.D., Flaherty, P., Foury, F., Garfinkel, D.J., Gerstein, M., et al., (2002). Jul 25, Nature, 418(6896):387-391. [Publisher Full Text].
  297. Long-read pyrosequencing using pure 2'-deoxyadenosine-5'-O'-(1-thiotriphosphate) Sp-isomer.
    Gharizadeh, B., Nordstrom, T., Ahmadian, A., Ronaghi, M., Nyren, P., (2002). Feb 1, Anal Biochem, 301(1):82-90.[Publisher] DOI: 10.1006/abio.2001.5494.
  298. Genome sequence of the human malaria parasite Plasmodium falciparum.
    Gardner, M.J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R.W., Carlton, J.M., Pain, A., Nelson, K.E., Bowman, S., Paulsen, I.T., James, K., Eisen, J.A., Rutherford, K., Salzberg, S.L., Craig, A., Kyes, S., Chan, M.S., Nene, V., Shallom, S.J., Suh, B., Peterson, J., Angiuoli, S., Pertea, M., Allen, J., Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B. (2002). Oct 3, Nature, 419(6906):498-511. [PubMed Abstract], [Publisher Full Text]
  299. Evolutionary rate in the protein interaction network.
    Fraser, H.B., Hirsh, A.E., Steinmetz, L.M., Scharfe, C., Feldman, M.W., (2002). Apr 26, Science, 296(5568):750-752. [Publisher Full Text].
  300. Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization.
    Fernandes, J., Brendel, V., Gai, X., Lal, S., Chandler, V.L., Elumalai, R.P., Galbraith, D.W., Pierson, E.A., Walbot, V., (2002). Mar, Plant Physiol, 128(3):896-910. [Publisher Full Text].
  301. A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes.
    Cruciani, F., Santolamazza, P., Shen, P., Macaulay, V., Moral, P., Olckers, A., Modiano, D., Holmes, S., Destro-Bisol, G., Coia, V., Wallace, D.C., Oefner, P.J., Torroni, A., Cavalli-Sforza, L.L., Scozzari, R., Underhill, P.A., (2002). May, Am J Hum Genet, 70(5):1197-1214. [PubMed Abstract].
  302. Gene-expression profile comparisons distinguish seven organs of maize.
    Cho, Y., Fernandes, J., Kim, S.H., Walbot, V., (2002). Aug 29, Genome Biol, 3(9):RESEARCH0045. [Publisher Full Text].
  303. Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents.
    Birrell, G.W., Brown, J.A., Wu, H.I., Giaever, G., Chu, A.M., Davis, R.W., Brown, J.M., (2002). Jun 25, Proc Natl Acad Sci U S A, 99(13):8778-8783. [Publisher Full Text].
  304. Gene expression during the life cycle of Drosophila melanogaster.
    Arbeitman, M.N., Furlong, E.E., Imam, F., Johnson, E., Null, B.H., Baker, B.S., Krasnow, M.A., Scott, M.P., Davis, R.W., White, K.P., (2002). Sep 27, Science, 297(5590):2270-2275. [Publisher Full Text].
  305. Denaturing HPLC of Nucleic Acids
    Premstaller, A., Oefner, P.J., (2002). LCGC Europe, July 2002 [Publisher], [PDF]
  306. Application of Genetic Algorithm to Chemical Kinetics: Systematic Determination of Reaction Mechanism and Rate Coefficients for a Complex Reaction Network.
    Tsuchiya, M. Ross, J. (2001). J.Phys.Chem. A, 105(16):4052-4058. [Publisher Full Text]
  307. Multiplex capillary denaturing high-performance liquid chromatography with laser-induced fluorescence detection.
    Xiao, W., Stern, D., Jain, M., Huber, C.G., Oefner, P.J., (2001). Jun, Biotechniques, 30(6):1332-1338. [PubMed Abstract].
  308. Maori origins, Y-chromosome haplotypes and implications for human history in the Pacific.
    Underhill, P.A., Passarino, G., Lin, A.A., Marzuki, S., Oefner, P.J., Cavalli-Sforza, L.L., Chambers, G.K., (2001). Apr, Hum Mutat, 17(4):271-280. [PubMed Abstract].
  309. The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations.
    Underhill, P.A., Passarino, G., Lin, A.A., Shen, P., Mirazon Lahr, M., Foley, R.A., Oefner, P.J., Cavalli-Sforza, L.L., (2001). Jan, Ann Hum Genet, 65(Pt 1):43-62. [Publisher].
  310. Genomic evidence for a complete sexual cycle in Candida albicans.
    Tzung, K.W., Williams, R.M., Scherer, S., Federspiel, N., Jones, T., Hansen, N., Bivolarevic, V., Huizar, L., Komp, C., Surzycki, R., Tamse, R., Davis, R.W., Agabian, N., (2001). Mar 13, Proc Natl Acad Sci U S A, 98(6):3249-3253. [Publisher Full Text].
  311. Global analysis of ATM polymorphism reveals significant functional constraint.
    Thorstenson, Y.R., Shen, P., Tusher, V.G., Wayne, T.L., Davis, R.W., Chu, G., Oefner, P.J., (2001). Aug, Am J Hum Genet, 69(2):396-412. [Publisher].
  312. Replication dynamics of the yeast genome.
    Raghuraman, M.K., Winzeler, E.A., Collingwood, D., Hunt, S., Wodicka, L., Conway, A., Lockhart, D.J., Davis, R.W., Brewer, B.J., Fangman, W.L., (2001). Oct 5, Science, 294(5540):115-121. [Publisher Full Text].
  313. Temperature-modulated array high-performance liquid chromatography.
    Premstaller, A., Xiao, W., Oberacher, H., O'Keefe, M., Stern, D., Willis, T., Huber, C.G., Oefner, P.J., (2001). Nov, Genome Res, 11(11):1944-1951. [Publisher Full Text].
  314. The Werner syndrome gene and global sequence variation.
    Passarino, G., Shen, P., Van Kirk, J.B., Lin, A.A., De Benedictis, G., Cavalli Sforza, L.L., Oefner, P.J., Underhill, P.A., (2001). Jan 1, Genomics, 71(1):118-122. [PubMed Abstract].
  315. On-Line Liquid Chromatography Mass Spectrometry: A Useful Tool for the Detection of DNA Sequence Variation.
    This work was financially supported by the Austrian Science Fund (P-14133-PHY) and the National Institutes of Health (HG01932). The suggestion of Dr. Jeff van Ness from the Keck Graduate Institute of Applied Life Sciences in Claremont, CA, USA, to utilize butyldimethylamine for IP-RP-HPLC separations is gratefully acknowledged. Oberacher, H., Oefner, P.J., Parson, W., Huber, C.G., (2001). Oct 15, Angew Chem Int Ed Engl, 40(20):3828-3830.
  316. Quantification of HIV-1 using multiple quantitative polymerase chain reaction standards and bioluminometric detection.
    Nygren, M., Ronaghi, M., Nyren, P., Albert, J., Lundeberg, J., (2001). Jan 1, Anal Biochem, 288(1):28-38. [Publisher] DOI: 10.1006/abio.2000.4871.
  317. Method enabling fast partial sequencing of cDNA clones.
    Nordström, T., Gharizadeh, B., Pourmand, N., Nyren, P., Ronaghi, M., (2001). May 15, Anal Biochem, 292(2):266-271. [Publisher].
  318. A method for parallel, automated, thermal cycling of submicroliter samples.
    Nakane, J., Broemeling, D., Donaldson, R., Marziali, A., Willis, T.D., O'Keefe, M., Davis, R.W., (2001). Mar, Genome Res, 11(3):441-447. [Publisher Full Text].
  319. Initial sequencing and analysis of the human genome.
    Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., LeVine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, J.P., Miranda, C., Morris, W., Naylor, J., et al., (2001). Feb 15, Nature, 409(6822):860-921. [PubMed Abstract].
  320. African origin of modern humans in East Asia: a tale of 12,000 Y chromosomes.
    Ke, Y., Su, B., Song, X., Lu, D., Chen, L., Li, H., Qi, C., Marzuki, S., Deka, R., Underhill, P., Xiao, C., Shriver, M., Lell, J., Wallace, D., Wells, R.S., Seielstad, M., Oefner, P., Zhu, D., Jin, J., Huang, W., Chakraborty, R., Chen, Z., Jin, L., (2001). May 11, Science, 292(5519):1151-1153. [Publisher Full Text].
  321. Mutation detection by capillary denaturing high-performance liquid chromatography using monolithic columns.
    Huber, C.G., Premstaller, A., Xiao, W., Oberacher, H., Bonn, G.K., Oefner, P.J., (2001). Jan 30, J Biochem Biophys Methods, 47(1-2):5-19. [Publisher]
  322. Origins and divergence of the Roma (gypsies).
    Gresham, D., Morar, B., Underhill, P.A., Passarino, G., Lin, A.A., Wise, C., Angelicheva, D., Calafell, F., Oefner, P.J., Shen, P., Tournev, I., de Pablo, R., Kucinskas, V., Perez-Lezaun, A., Marushiakova, E., Popov, V., Kalaydjieva, L., (2001). Dec, Am J Hum Genet, 69(6):1314-1331. [PubMed Abstract].
  323. The composite genome of the legume symbiont Sinorhizobium meliloti.
    Galibert, F., Finan, T.M., Long, S.R., Puhler, A., Abola, P., Ampe, F., Barloy-Hubler, F., Barnett, M.J., Becker, A., Boistard, P., Bothe, G., Boutry, M., Bowser, L., Buhrmester, J., Cadieu, E., Capela, D., Chain, P., Cowie, A., Davis, R.W., Dreano, S., Federspiel, N.A., Fisher, R.F., Gloux, S., Godrie, T., Goffeau, A., et al., (2001). Jul 27, Science, 293(5530):668-672. [Publisher Full Text].
  324. Interpreting epidemiological research: blinded comparison of methods used to estimate the prevalence of inherited mutations in BRCA1.
    Eng, C., Brody, L.C., Wagner, T.M.U., Devilee, P., Vijg, J., Szabo, C., Tavtigian, S.V., Nathanson, K.L., Ostrander, E., Frank, T.S., Zaucha, R., Suter, N.M., Hoogenboom, M., van Eijk, R., Cornelisse, C.J., van Orsouw, N.J., Torres, L., Vrins, E., McGrath, S., Moeslinger, R., Oefner, P.J., Muhr, D., Deffenbaugh, A.M., Zawacki, R.K., (2001). J. Med. Genet, 38:824-833.
  325. Transcriptional regulation and function during the human cell cycle.
    Cho, R.J., Huang, M., Campbell, M.J., Dong, H., Steinmetz, L., Sapinoso, L., Hampton, G., Elledge, S.J., Davis, R.W., Lockhart, D.J., (2001). Jan, Nat Genet, 27(1):48-54. [Publisher Full Text]
  326. High-resolution analysis of human Y-chromosome variation shows a sharp discontinuity and limited gene flow between northwestern Africa and the Iberian Peninsula.
    Bosch, E., Calafell, F., Comas, D., Oefner, P.J., Underhill, P.A., Bertranpetit, J., (2001). Apr, Am J Hum Genet, 68(4):1019-1029. [PubMed Abstract]
  327. A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity.
    Birrell, G.W., Giaever, G., Chu, A.M., Davis, R.W., Brown, J.M., (2001). Oct 23, Proc Natl Acad Sci U S A, 98(22):12608-12613. [Publisher Full Text]
  328. Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid.
    Barnett, M.J., Fisher, R.F., Jones, T., Komp, C., Abola, A.P., Barloy-Hubler, F., Bowser, L., Capela, D., Galibert, F., Gouzy, J., Gurjal, M., Hong, A., Huizar, L., Hyman, R.W., Kahn, D., Kahn, M.L., Kalman, S., Keating, D.H., Palm, C., Peck, M.C., Surzycki, R., Wells, D.H., Yeh, K.C., Davis, R.W., Federspiel, N.A., et al., (2001). Aug 14, Proc Natl Acad Sci U S A, 98(17):9883-9888. [Publisher Full Text]
  329. Infrequent Genetic Exchange and Recombination in the Mitochondrial Genome of Candida albicans.
    Anderson, J.B., Wickens, C., Khan, M., Cowen, L.E., Federspiel, N., Jones, T., Kohn, L.M. (2001) Journal of Bacteriology Feb, 183(3):865-872. [Publisher Full Text].
  330. Functional analysis of the yeast genome by precise deletion and parallel phenotypic characterization.
    Winzeler, E.A., Liang, H., Shoemaker, D.D., Davis, R.W., (2000). Novartis Found Symp, 229:105-109; discussion 109-111.
  331. Attitude towards prophylactic surgery and effects of genetic counselling in families with BRCA mutations.
    Austrian Hereditary Breast and Ovarian Cancer Group. Wagner, T.M., Moslinger, R., Langbauer, G., Ahner, R., Fleischmann, E., Auterith, A., Friedmann, A., Helbich, T., Zielinski, C., Pittermann, E., Seifert, M., Oefner, P., (2000). Apr, Br J Cancer, 82(7):1249-1253. [Publisher]
  332. Y chromosome sequence variation and the history of human populations.
    Underhill, P.A., Shen, P., Lin, A.A., Jin, L., Passarino, G., Yang, W.H., Kauffman, E., Bonne-Tamir, B., Bertranpetit, J., Francalacci, P., Ibrahim, M., Jenkins, T., Kidd, J.R., Mehdi, S.Q., Seielstad, M.T., Wells, R.S., Piazza, A., Davis, R.W., Feldman, M.W., Cavalli-Sforza, L.L., Oefner, P.J., (2000). Nov, Nat Genet, 26(3):358-361. [Publisher Full Text].
  333. Recent common ancestry of human Y chromosomes: evidence from DNA sequence data.
    Thomson, R., Pritchard, J.K., Shen, P., Oefner, P.J., Feldman, M.W., (2000). Jun 20, Proc Natl Acad Sci U S A, 97(13):7360-7365. [Publisher Full Text].
  334. Analysis of the genome of the flowering plant Arabidopsis thaliana. The Arabidopsis Genome Initiative (AGI). (2000) Nature. 408(6814):796-815. [Publisher Full Text]
  335. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.
    Theologis, A., Ecker, J.R., Palm, C.J., Federspiel, N.A., Kaul, S., White, O., Alonso, J., Altafi, H., Araujo, R., Bowman, C.L., Brooks, S.Y., Buehler, E., Chan, A., Chao, Q., Chen, H., Cheuk, R.F., Chin, C.W., Chung, M.K., Conn, L., Conway, A.B., Conway, A.R., Creasy, T.H., Dewar, K., Dunn, P., Etgu, P., et al., (2000). Dec 14, Nature, 408(6814):816-820. [Publisher Full Text].
  336. Polynesian origins: insights from the Y chromosome.
    Su, B., Jin, L., Underhill, P., Martinson, J., Saha, N., McGarvey, S.T., Shriver, M.D., Chu, J., Oefner, P., Chakraborty, R., Deka, R., (2000). Jul 18, Proc Natl Acad Sci U S A, 97(15):8225-8228. [Publisher Full Text].
  337. High-accuracy DNA sequence variation screening by DHPLC.
    Spiegelman, J.I., Mindrinos, M.N., Oefner, P.J., (2000). Nov, Biotechniques, 29(5):1084-1090, 1092. [PubMed Abstract].
  338. Cloning of the Arabidopsis RSF1 gene by using a mapping strategy based on high-density DNA arrays and denaturing high-performance liquid chromatography.
    Spiegelman, J.I., Mindrinos, M.N., Fankhauser, C., Richards, D., Lutes, J., Chory, J., Oefner, P.J., (2000). Dec, Plant Cell, 12(12):2485-2498. [Publisher Full Text].
  339. Mutational analyses of BRCA1 and BRCA2 in Ashkenazi and non-Ashkenazi Jewish women with familial breast and ovarian cancer.
    Shiri-Sverdlov, R., Oefner, P., Green, L., Baruch, R.G., Wagner, T., Kruglikova, A., Haitchick, S., Hofstra, R.M., Papa, M.Z., Mulder, I., Rizel, S., Bar Sade, R.B., Dagan, E., Abdeen, Z., Goldman, B., Friedman, E., (2000). Dec, Hum Mutat, 16(6):491-501. [PubMed Abstract].
  340. Population genetic implications from sequence variation in four Y chromosome genes.
    Shen, P., Wang, F., Underhill, P.A., Franco, C., Yang, W.H., Roxas, A., Sung, R., Lin, A.A., Hyman, R.W., Vollrath, D., Davis, R.W., Cavalli-Sforza, L.L., Oefner, P.J., (2000). Jun 20, Proc Natl Acad Sci U S A, 97(13):7354-7359. [Publisher Full Text].
  341. Prevalence of small inversions in yeast gene order evolution.
    Seoighe, C., Federspiel, N., Jones, T., Hansen, N., Bivolarovic, V., Surzycki, R., Tamse, R., Komp, C., Huizar, L., Davis, R.W., Scherer, S., Tait, E., Shaw, D.J., Harris, D., Murphy, L., Oliver, K., Taylor, K., Rajandream, M.A., Barrell, B.G., Wolfe, K.H., (2000). Dec 19, Proc Natl Acad Sci U S A, 97(26):14433-14437. [Publisher Full Text].
  342. The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective.
    Semino, O., Passarino, G., Oefner, P.J., Lin, A.A., Arbuzova, S., Beckman, L.E., De Benedictis, G., Francalacci, P., Kouvatsi, A., Limborska, S., Marcikiae, M., Mika, A., Mika, B., Primorac, D., Santachiara-Benerecetti, A.S., Cavalli-Sforza, L.L., Underhill, P.A., (2000). Nov 10, Science, 290(5494):1155-1159. [Publisher Full Text]. Historical Article
  343. Improved performance of pyrosequencing using single-stranded DNA-binding protein.
    Ronaghi, M., (2000). Nov 15, Anal Biochem, 286(2):282-288. [PubMed Abstract] DOI: 10.1006/abio.2000.4808.
  344. The core meiotic transcriptome in budding yeasts.
    Primig, M., Williams, R.M., Winzeler, E.A., Tevzadze, G.G., Conway, A.R., Hwang, S.Y., Davis, R.W., Esposito, R.E., (2000). Dec, Nat Genet, 26(4):415-423. [Publisher Full Text].
  345. DAtA: database of Arabidopsis thaliana annotation.
    Palm, C.J., Federspiel, N.A., Davis, R.W., (2000). Jan 1, Nucleic Acids Res, 28(1):102-103. [Publisher Full Text].
  346. Allelic discrimination by denaturing high-performance liquid chromatography.
    Oefner, P.J., (2000). Mar 10, J Chromatogr B Biomed Sci Appl, 739(2):345-355. [PubMed Abstract].
  347. Polymorphism in the pertussis toxin promoter region affecting the DNA-based diagnosis of Bordetella infection.
    Nygren, M., Reizenstein, E., Ronaghi, M., Lundeberg, J., (2000). Jan, J Clin Microbiol, 38(1):55-60. [Publisher Full Text].
  348. Direct analysis of single-nucleotide polymorphism on double-stranded DNA by pyrosequencing.
    Nordstrom, T., Ronaghi, M., Forsberg, L., de Faire, U., Morgenstern, R., Nyren, P., (2000). Apr, Biotechnol Appl Biochem, 31 ( Pt 2):107-112. [Publisher].
  349. Method enabling pyrosequencing on double-stranded DNA.
    Nordstrom, T., Nourizad, K., Ronaghi, M., Nyren, P., (2000). Jul 1, Anal Biochem, 282(2):186-193. [Publisher] DOI: 10.1006/abio.2000.4603.
  350. Mutation detection by pyrosequencing: sequencing of exons 5-8 of the p53 tumor suppressor gene.
    Garcia, C.A., Ahmadian, A., Gharizadeh, B., Lundeberg, J., Ronaghi, M., Nyren, P., (2000). Aug 8, Gene, 253(2):249-257. [Publisher].
  351. Real-time PCR-based method for assaying the purity of bacterial artificial chromosome preparations.
    Foreman, P.K., Davis, R.W., (2000). Sep, Biotechniques, 29(3):410-412.
  352. A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis.
    Drenkard, E., Richter, B.G., Rozen, S., Stutius, L.M., Angell, N.A., Mindrinos, M., Cho, R.J., Oefner, P.J., Davis, R.W., Ausubel, F.M., (2000). Dec, Plant Physiol, 124(4):1483-1492. [Publisher Full Text].
  353. Analysis of the p53 tumor suppressor gene by pyrosequencing.
    Ahmadian, A., Lundeberg, J., Nyren, P., Uhlen, M., Ronaghi, M., (2000). Jan, Biotechniques, 28(1):140-144, 146-147. [PubMed Abstract].
  354. Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays.
    Aharoni, A., Keizer, L.C., Bouwmeester, H.J., Sun, Z., Alvarez-Huerta, M., Verhoeven, H.A., Blaas, J., van Houwelingen, A.M., De Vos, R.C., van der Voet, H., Jansen, R.C., Guis, M., Mol, J., Davis, R.W., Schena, M., van Tunen, A.J., O'Connell, A.P., (2000). May, Plant Cell, 12(5):647-662. [Publisher Full Text].
  355. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.
    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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