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

1. Enrichment of target sequences with conserved sequence motif probes and probe design algorithm.
   Wang, C., B. Gharizadeh, and M. Ronaghi. 2008. [Stanford Docket S08-086]
2. Targeting sequences sequencing.
   Wang, C., Gharizadeh, B., Babrzadeh, F., Ronaghi, M. 2008. [Stanford Docket S08-102]
3. Multiplex DNA Amplification.
   Dahl, F. Fredriksson, S. 2008. [Stanford Reference S06-022]
4. Coaxial Nanoneedle.
   Esfandyarpour, H. Parizi, K.B. Davis, R.W. 2008. [Stanford Docket S06-072]
   
5. Microfluidic Chamber with Magnetic Bead for DNA Sequencing.
   Esfandyarpour, H. 2007. [Stanford Docket S07-067]
6. 3-D DNA-Crossover-Network Porous Bead.
   Esfandyarpour, H. 2007. [Stanford Docket S07-374]
7. DNA fingerprinting using a branch migration assay.
   Pourmand, N., R.W. Davis, and S.X. Wang. 2007. [USPTO, 7,238,486]
8. Application of WiMax for remote Defibrillator interrogation, information transfer, and management.
   Rezaee, M. Nejah, A. Esfandyarpour, H. [Stanford Docket S07-361]
9. Application of WiMax for Remote, Long Term ECG Recording and Automated Transfer.
   Rezaee, M. Nejah, A. Esfandyarpour, H. [Stanford Docket S07-379]
   
10. Modification of Surface for Biomolecule Immobilization.
    Pourmand, N., Wang, S. and Yu, H. 2007. [Stanford Reference S06-325]
11. 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], [Stanford Docket S00-157]
12. Use of Electric Field for Improved Biological Assays.
    Khurana, T. Ronaghi, M. Santiago, J. 2007. [Stanford Docket S06-449]
    
13. Heat and pH Measurement for Sequencing of DNA (Thermosequencing: A Novel DNA Sequencing Method).
    Esfandyarpour, H. Ronaghi, M. 2007. US patent application 3815.3. [Stanford Docket S05-208]
14. Activated Nanopores for Biochemical Analysis.
    Davis, RW. Ronaghi, M. Talasaz, A. H. 2007. [Stanford Docket S03-098]
15. Renaturation, reassociation, association and hybridization of nucleic acid molecules.
    Namsaraev, E., R.W. Davis, Karlin-Neumann, G. 2006. US Patent 7,129,044. [USPTO]
16. Whole-Genome Sequencing and Assembly using High-Throughput Short-Read Technologies.
    Batzoglou, S. Ronaghi, M. Sundquist, A. [Stanford Reference: S06-059]
17. A Novel Architecture for CMOS Sensor Chip.
    Agah, A. Ronaghi, M. 2007. [Stanford Reference S06-448]
18. Needle-Sequencing: Novel Ultra Sensitive Gene Sequencing Platform.
    Esfandyarpour, H. Davis, R.W. 2006. [Stanford Docket S06-080]
19. Bioluminescence regenerative cycle (BRC) for nucleic acid quantification.
    Pourmand, N. Hassibi, A. 2006. US Patent 7,141,370. [USPTO], [Stanford Ref S01-084]
20. Single-Stranded DNA from Double-Stranded DNA.
    Mindrinos, MN. Krishnakumar, S. Davis, RW. 2006. [Stanford Reference S06-082]
21. Renaturation, reassociation, association and hybridization of nucleic acid molecules.
    Namsaraev, E., R.W. Davis, and G. Karlin-Neumann. 2006. US Patent 7,129,044 [USPTO]
22. Increased read-length and synchronicity of Pyrosequencing technology by preogrammed dispensation of dideoxy nucleotides for termination of non-synchronized extensions.
    Gharizadeh, B., N. Nourizad. 2006 [Stanford Docket S06-038]
23. Chemically Cleavable Linker for Tandem Oligonucleotide Synthesis.
    Jensen, M. Anderson, K. 2006. [Stanford Docket S04-240]
24. DNA Purification Scheme Using Acetic Anhydride Derivative.
    Jensen, M. 2006.
25. Gene Assembly Using the Succinyl Phosphoramidite Linker.
    Jensen, M. 2006.
26. Assay for Influenza Viruses, Including H5N1.
    Davis, RW. Diamond, L. Kumm, J. Pourmand, N. 2006. [Stanford Reference S06-155]
27. Magnetic Sifter for Biomedical Detection.
    Pourmand, N. Wang, S. White, R. 2005. [Stanford Reference S05-306]
28. A New Technology for Barcoded Clonal Amplification.
    Mashayekhi, F. Ronaghi, M. 2005. [Stanford Reference S04-127]
29. Enzymatic Separation of Tandem Oligonucleotides by Chemical or Enzymatic Cleavage.
    Jensen, M. Anderson, K. 2005. [Stanford Docket S04-106]
30. Methods of Improved Sensitivity for Proximity Ligation.
    Davis, RW. Fredriksson, S. 2005. [Stanford Reference S04-074]
31. Specific Region Identification for Human Papilloma Virus.
    Pourmand, N., Gharizadeh, B., Davis, R.W. (2005) [Stanford Docket S05-177]
32. 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]
33. Dimeric flourescent polypeptides.
    Davis, R.W. and Vaillancourt, P. 2005. US Patent 6,936,428. Stratagene California (La Jolla, CA) USA. [USPTO]
34. Human Y Chromosome Specific Single Nucleotide Polymorphisms (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], [Stanford Reference]
35. Detection and identification assay for Stachybotrys species.
    Jejelowo, F. Gharizadeh, B. Pourmand, N. 2005. [Stanford Docket S05-177]
36. Dimeric flourescent polypeptides.
    Davis, R.W. Vaillancourt, P. 2005. US Patent US Patent 6,936,428. [USPTO]
    
37. Apparatus and methods for parallel processing of micro-volume liquid reactions.
    O'Keefe, M., Foreman, PK., [USPTO]
38. Microarray substrate with integrated photodetector and methods of use thereof.
    O'Keefe M., Patent Application
39. Clinical and Genomic/Proteomic Data Integration and QA/QC Analysis System.
    Davis, RW. Ji, H. Kumm, J. 2004. [Stanford Reference S04-255].
    
40. Multiplex Pyrosequencing for typing.
    Pourmand, N., Ronaghi, M. 2004. [Stanford Reference S00-132]
41. Charge Alternation DNA Detection System.
    Pourmand, N., Karhanek, M., Davis, R.W. U.S. PTO No. 60/627,192. Filed Nov. 12, 2004 [Stanford Docket S04-291]
42. Microarray-based DNA fingerprinting using branch migration assay.
    Pourmand, N., Davis, R.W., Wang, S.X. 2004. PCT/US05/33838. [Stanford Docket S04-276]
43. 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]
44. Reciprocal Hemizygous Scanning (RHS).
    Davis, R.W., McCusker, J., Steinmetz L.M., 2001. [Stanford Docket 01-117]
45. Concatenated Oligonucleotide Primer Synthesis for PCR.
    Davis, R.W., Hardenbol P., Willis T. 2000. Stanford Docket S00-044.
46. Identification of drugs and drug targets by detection of the stress response.
    Davis, R.W., Giaever, G. 2004. United States Patent 6,743,583. [Stanford Reference], [USPTO]
47. Universal Support for Oligonucleotide Synthesis with Enzymatic Release.
    Hardenbol P., Willis, T.
48. Methods for Cellular or Microorganism Capture and Quantification using Bioluminescence Regenerative Cycle (BRC) Assays.
    Hassibi, A., Ghazvini, S., Pourmand, N. U.S. PTO No. 60/451,107. Filed on Feb. 27, 2003
49. Target-specific tagged multiple-oligonucleotide pool for specific detection, identification and quantification of microorganisms and viruses on genomic DNA/RNA and other target DNA/RNA.
    Pourmand, N., Gharizadeh, B. U.S. Patent Application. 2003. [Stanford Docket S03-176]
50. Transient electrical signal based methods and devices for characterizing molecular interaction and/or motion in a sample.
    Pourmand, N., Hassibi, A. U.S. Patent Application 20030152985 (2003)
51. Transient electrical signal based methods and devices for characterizing molecular interaction and/or motion in a sample.
    Pourmand, N., Hassibi, A. U.S. Patent Application 20020155476 (2003)
52. Bio-Molecular Sequencing Recovery Using Statistical Signal Processing.
    Hassibi, B., Hassibi, A., Pourmand, N. U.S. PTO No. 60/422,439. Filed on Oct. 29, 2002
53. Methods for Expression Profiling and Drug Discovery.
    Pourmand, N., Hassibi, A. U.S. PTO No. 60/407,412. Filed on August 30, 2002
54. Modulation of Luciferase Activity in the Bioluminescence Regenerative Cycle (BRC) Assay with a Peptide Linker.
    Pourmand, N. Hassibi, A. Ghazvini, S.. 2002. U.S PTO No. 60/435,924. Filed Dec. 20, 2002
    
55. Cloned Sequence Insert Detection Using BRC (Bioluminescence Regenerative Cycle).
    Pourmand, N., A. Hassibi, and S. Ghazvini. 2002. U.S Patent application 60/435,934.
56. Detection of polymorphisms by denaturing high-performance liquid chromatography.
    Oefner, P.J. 2002. United States Patent 6,453,244. Stanford University, Palo Alto, CA. [USPTO]
57. High-density random-order array of magnetic beads for genotyping.
    Jain, M., Roberts, L., White, R.L., (2002). Patent Pending, The Board of Trustees of the Leland Stanford Junior University, Stanford, CA. Patents Pending, [Stanford Reference S99-142].
58. Selecting tag nucleic acids.
    Morris, M.S., Shoemaker, D.D., Davis, R.W. Mittmann, M.P. 2002. US Patent 6,458,530. [USPTO]
59. Recombinant mycobacteria.
    Bloom, B.R., Davis, R.W., Jacobs, Jr., R., Young, R.A., Husson, R.N. 2002. US Patent 6,372,478. [USPTO]
60. Method for simultaneous centrifugation of samples.
    Marziali, A., (2001). United States Patent 6,273,848. The Board of Trustees of the Leland Stanford Junior University, Palo Alto, CA. [USPTO]
61. Microcentrifuge.
    Marziali A.,(2001), United States Patent 6,238,330. The Board of Trustees of the Leland Stanford Junior University, Palo Alto, CA. [USPTO]
62. Temperature-Modulated Array High-Performance Liquid Chromatography.
    Huber, C.G., O'Keefe, M., Oberacher H., Oefner P.J., Premstaller, A., Xiao, W. 2001. Stanford Docket S01-147.
63. 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]
64. 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. The Board of Trustees of the Leland Stanford Junior University. [USPTO], [Stanford Docket S97-157]
65. Thermocycling apparatus and method.
    Hunicke-Smith S.P., (2000). United States Patent 6,132,996. The Board of Trustees of the Leland Stanford Junior University. [USPTO]
66. Thermocycling apparatus and method.
    Hunicke-Smith S.P., (1999). United States Patent 5,985,651. The Board of Trustees of the Leland Stanford Junior University. [USPTO]
67. 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]
68. Cleaved amplified RFLP detection methods.
    Ausubel, F., Davis, R.W., Preuss, D. 1999. US Patent, 6,004,783. [USPTO]
69. Apparatus and method for shear breakage of polynucleotides.
    Oefner, P.J., Hunicke-Smith S.P. 1998. United States Patent 5,846,832. The Board of Trustees of the Leland Stanford Junior University (Stanford, CA). Licensed to GeneMachines, San Carlos, CA, USA. [USPTO], [Stanford Reference]
70. Detection of nucleic acid heteroduplex molecules by denaturing high-performance liquid chromatography and methods for comparative sequencing.
    Oefner, P.J., Underhill, P.A., (1998). United States Patent 5,795,976. The Board of Trustees of the Leland Stanford Junior University, Stanford, CA. 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], [Stanford Reference]
71. 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). [Stanford Reference]
72. 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]
73. 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]
74. Recombinant mycobacterial vaccine.
    Bloom, B.R., Davis, R.W., Jacobs, Jr., W.R., Young, R.A., Husson, R.N. 1996. US Patent 5,504,005. [USPTO]
75. Electrophoresis using contour-clamped electric fields.
    Chu, G., Vollrath, D., Davis, R., (1996). United States Patent 5,549,796. The Board of Trustees of the Leland Stanford Junior University. [USPTO]
76. 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]
    

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Original Papers

1. Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes.
   Scharf, C., Horng-Shing Lu, H., Neuenburg, JK., Allen, EA., Li4, G-C., Klopstock, T., Cowan, TM., Enns, GM., Davis, RW. [Publisher Full Text]
2. 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]
   
3. 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]
4. 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]
5. 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]
6. 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]
7. 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]
   
8. 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]
   
9. 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. I.E.E.E. Transactions on Magnetics [submitted]
   
10. 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]
11. Identification of Small Molecule Inhibitors of Pseudomonas aeruginosa Exoenzyme S Using a Yeast Phenotypic Screen.
    Arnoldo A, Curak J, Kittanakom S, Chevelev I, Lee VT, et al. (2008). PLoS Genet 4(2): e1000005.
12. 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]
13. 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]
14. 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]
15. 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]
16. 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]
    
17. 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]
18. 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]
    
19. 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]
    
20. 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]
21. 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.
22. 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]
    
23. 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, submitted
    
24. 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]
25. 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]
    
26. 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.
27. 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.
28. 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).
29. 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).
30. Label-free impedance biosensors: Opportunities and challenges.
    Daniels, J. S. Pourmand, N. (2008). Electroanalysis 19(12):1239.
    
31. 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
32. 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]
33. 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]
    
34. The Role of NanoBiotechnology in the Detection of Infectious Diseases.
    Esfandyarpour, H., submitted to the Journal of Nanotechnology, Sep. 2007.
35. A Novel Receptacle for Gene Sequencing.
    Esfandyarpour, H., Davis, R.W., NSTI-Nanotech 2007, Vol.3, pp. 422-425.
36. 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.
37. Gate-Controlled Microfluidic Chamber with magnetic bead for DNA Sequencing-by-synthesis Technology.
    Esfandyarpour, H. and Davis R.W., ICNMM2007, ref- 3119.
38. 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.
39. Nano-Biotechnology toward Diagnostic Industry: Obstacles and Opportunities.
    Esfandyarpour, H., ”NSTI-Nanotech 2007, Vol. 4, pp 421-423.
40. 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]
41. 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]
42. 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]
43. 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]
    
44. 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]
45. Connector inversion probe technology: a powerful one-primer multiplex DNA amplification system for numerous scientific applications.
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46. A high-resolution atlas of nucleosome occupancy in yeast.
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48. Multigene amplification and massively parallel sequencing for cancer mutation discovery.
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49. Branch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays.
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51. PathogenMip assay: a multiplex pathogen detection assay.
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53. Molecular characterization of Neisseria gonorrhoeae identifies transmission and resistance of one ciprofloxacin-resistant strain.
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54. Analysis of read length limiting factors in Pyrosequencing chemistry.
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56. Patterns of known and novel small RNAs in human cervical cancer.
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57. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance.
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61. Human papillomavirus (HPV), DNA aberrations and cell cycle progression in anal squamous cell carcinoma patients.
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63. Does HPV-status 6-12 months after treatment of high grade dysplasia in the uterine cervix predict long term recurrence?
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65. Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789.
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66. INCREASED SIZE EXCLUSION LIMIT2 Encodes a Putative DEVH Box RNA Helicase Involved in Plasmodesmata Function during Arabidopsis Embryogenesis.
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67. Label-Free Impedance Biosensors: Opportunities and Challenges.
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90. Spin valve sensors for ultra sensitive detection of super paramagnetic nanoparticles for biological applications.
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91. One-Pot Synthesis of Mono-disperse Iron Oxide Nanoparticles for Potential Biomedical Applications
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279. Method enabling pyrosequencing on double-stranded DNA.
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280. 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].
281. 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.
282. 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].
283. 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].
284. 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].
285. 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].
286. 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].
287. 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].
288. 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].
289. 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].
290. 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].
291. 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.
292. 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].
293. 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].
294. 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.
295. 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].
296. 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].
297. 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].
298. 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].
299. 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].
300. 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].
301. 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].
302. 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].
303. 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].
304. 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].
305. 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].
306. 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].
307. 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
308. 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].
309. 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].
310. 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].
311. 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].
312. 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].
313. 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].
314. 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].
315. 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].
316. 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].
317. 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].
318. 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].
319. Mapping cloned sequences on YACs.
     Agyare, F.D., Lagos, G., Lashkari, D., Davis, R.W., Lemieux, B., (1998). Methods Mol Biol, 82:199-208.
320. 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].
321. Capillary electrophoresis measurement of metabolites in glycolysis.
     Shen, P., Hauri, D., Ross, J., Oefner, P.J., (1997). J. Cap. Elec, 3:155-163.
322. 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].
323. 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.
324. 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.
325. Automation for the Arabidopsis genome sequencing project.
     Marziali, A., Federspiel, N., and Davis, R.W., (1997). Trends in Plant Science, 2:71-74.
326. 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].
327. 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].
328. 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].
329. 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].
330. The nucleotide sequence of chromosome IV.
     Jacq, C., Davis, R.W., et al. (144 co-authors). (1997). Nature 387 suppl:75-78. [PubMed Abstract]
331. 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].
332. 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].
333. 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
334. 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].
335. 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].
336. 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].
337. 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].
338. 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].
339. 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].
340. 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.
341. 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].
342. 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].
343. 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].
344. 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.
345. 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
346. 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].
347. 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].
348. 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]
349. 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
350. 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]
351. 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
352. Surface-charge reversed capillary zone electrophoresis of inorganic and organic anions.
     Oefner, P.J. (1995). Electrophoresis. 1995 Jan;16(1):46-56. [PubMed Abstract]
353. Sliding-plate gel caster.
     Lashkari, D. A., Norgren, R. M., Davis, R. W. (1995). Biotechniques Apr 18(4):625-6
354. 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]
355. 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
356. 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]
357. 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]
358. 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]
359. 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]
360. 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]
361. 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]
362. 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]
363. 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]
364. 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]
365. 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]
366. 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]
367. 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]
368. 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]
369. 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]
370. 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]
371. 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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Reviews

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

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Short Communications

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

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Books & Book Chapters

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

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Proceedings

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

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Letters

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

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Submissions to GenBank

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

updated April 24, 2009