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SGTC - Center Publications

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› Patents & Technology Transfer
› Original Papers
› Reviews
› Short Communications
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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. Multiplex DNA Amplification.
    Dahl, F. Fredriksson, S. 2008. [Stanford Reference: S06-022]
  2. Coaxial Nanoneedle.
    Esfandyarpour, H. Parizi, K.B. Davis, R.W. 2008. [Stanford Docket S06-072]
  3. Microfluidic Chamber with Magnetic Bead for DNA Sequencing.
    Esfandyarpour, H. [Stanford Docket S07-067]
  4. 3-D DNA-Crossover-Network Porous Bead.
    Esfandyarpour, H. [Stanford Docket S07-374]
  5. Needle-Sequencing: Novel Ultra Sensitive Gene Sequencing Platform.
    Esfandyarpour, H. Davis, R.W. [Stanford Docket S06-080]
  6. Application of WiMax for remote Defibrillator interrogation, information transfer, and management.
    Rezaee, M. Nejah, A. Esfandyarpour, H. [Stanford Docket S07-361]
  7. Application of WiMax for Remote, Long Term ECG Recording and Automated Transfer.
    Rezaee, M. Nejah, A. Esfandyarpour, H. [Stanford Docket S07-379]
  8. Modification of Surface for Biomolecule Immobilization.
    Pourmand, N., Wang, S. and Yu, H. 2007. [Stanford Reference S06-325]
  9. 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]
  10. Use of Electric Field for Improved Biological Assays.
    Khurana, T. Ronaghi, M. Santiago, J. 2007. [Stanford Reference S06-449]
  11. 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 Reference: S05-208]
  12. Activated Nanopores for Biochemical Analysis.
    Davis, RW. Ronaghi, M. Talasaz, A. H. 2007. [Stanford Reference S03-098]
  13. Whole-Genome Sequencing and Assembly using High-Throughput Short-Read Technologies.
    Batzoglou, S. Ronaghi, M. Sundquist, A. [Stanford Reference: S06-059]
  14. A Novel Architecture for CMOS Sensor Chip.
    Agah, A. Ronaghi, M. 2007. [Stanford Reference S06-448]
  15. Bioluminescence regenerative cycle (BRC) for nucleic acid quantification.
    Pourmand, N. Hassibi, A. 2006. US Patent 7,141,370. [USPTO], [Stanford Ref S01-084]
  16. Single-Stranded DNA from Double-Stranded DNA.
    Mindrinos, MN. Krishnakumar, S. Davis, RW. 2006. [Stanford Reference S06-082]
  17. Chemically Cleavable Linker for Tandem Oligonucleotide Synthesis.
    Jensen, M. Anderson, K. 2006. [Stanford Docket S04-240]
  18. DNA Purification Scheme Using Acetic Anhydride Derivative.
    Jensen, M. 2006.
  19. Gene Assembly Using the Succinyl Phosphoramidite Linker.
    Jensen, M. 2006.
  20. Assay for Influenza Viruses, Including H5N1.
    Davis, RW. Diamond, L. Kumm, J. Pourmand, N. 2006. [Stanford Reference S06-155]
  21. Magnetic Sifter for Biomedical Detection.
    Pourmand, N. Wang, S. White, R. 2005. [Stanford Reference S05-306]
  22. A New Technology for Barcoded Clonal Amplification.
    Mashayekhi, F. Ronaghi, M. 2005. [Stanford Reference S04-127]
  23. Enzymatic Separation of Tandem Oligonucleotides by Chemical or Enzymatic Cleavage.
    Jensen, M. Anderson, K. 2005. [Stanford Docket S04-106]
  24. Methods of Improved Sensitivity for Proximity Ligation.
    Davis, RW. Fredriksson, S. 2005. [Stanford Reference S04-074]
  25. Clinical and Genomic/Proteomic Data Integration and QA/QC Analysis System.
    Davis, RW. Ji, H. Kumm, J. 2004. [Stanford Reference S04-255].
  26. Multiplex Pyrosequencing for typing.
    Pourmand, N., Ronaghi, M. 2004. [Stanford Reference S00-132]
  27. Specific Region Identification for Human Papilloma Virus.
    Pourmand, N., Gharizadeh, B., Davis, R.W. (2005) [Stanford Docket S05-177]
  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. 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]
  30. Apparatus and methods for parallel processing of micro-volume liquid reactions.
    O'Keefe, M., Foreman, PK., [USPTO]
  31. Microarray substrate with integrated photodetector and methods of use thereof.
    O'Keefe M., Patent Application
  32. Temperature-Modulated Array High-Performance Liquid Chromatography.
    Huber, C.G., O'Keefe, M., Oberacher H., Oefner P.J., Premstaller, A., Xiao, W., Provisional Patent filed
  33. 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]
  34. Microarray-based DNA fingerprinting using branch migration assay.
    Pourmand, N., Davis, R.W., Wang, S.X. 2004. PCT/US05/33838. [Stanford Docket S04-276]
  35. Reciprocal Hemizygous Scanning (RHS).
    Davis, R.W., McCusker, J., Steinmetz L.M., Patent Application.
  36. Concatenated Oligonucleotide Primer Synthesis for PCR.
    Davis, R.W., Hardenbol P., Willis T.
  37. 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]
  38. Universal Support for Oligonucleotide Synthesis with Enzymatic Release.
    Hardenbol P., Willis, T.
  39. 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
  40. 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]
  41. 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)
  42. 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)
  43. 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
  44. Methods for Expression Profiling and Drug Discovery.
    Pourmand, N., Hassibi, A. U.S. PTO No. 60/407,412. Filed on August 30, 2002
  45. 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
  46. 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]
  47. 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]
  48. 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]
  49. Microcentrifuge.
    Marziali A.,(2001), United States Patent 6,238,330. The Board of Trustees of the Leland Stanford Junior University, Palo Alto, CA. [USPTO]
  50. 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 Reference]
  51. 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]
  52. 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]
  53. 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]
  54. 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 Number 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]
  55. 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]
  56. 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]
  57. 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]

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Original Papers

  1. 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]
  2. 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.
  3. 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 Mar 28; [Epub ahead of print]
  4. 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]
  5. Identification of Genes Involved in the Toxic Response of Saccharomyces cerevisiae against Iron and Copper Overload by Parallel Analysis of Deletion Mutants.
    Jo WJ, Loguinov A, Chang M, Wintz H, Nislow C, Arkin AP, Giaever G, Vulpe CD. Toxicol Sci. 2008 Mar;102(1):205.
  6. 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.
  7. 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.
  8. 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]
  9. 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.
  10. 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]
  11. 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
  12. 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]
  13. 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.
  14. 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.
  15. 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).
  16. 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).
  17. Label-free impedance biosensors: Opportunities and challenges.
    Daniels, J. S. Pourmand, N. (2008). Electroanalysis 19(12):1239.
  18. 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
  19. 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]
  20. 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]
  21. The Role of NanoBiotechnology in the Detection of Infectious Diseases.
    Esfandyarpour, H., submitted to the Journal of Nanotechnology, Sep. 2007.
  22. A Novel Receptacle for Gene Sequencing.
    Esfandyarpour, H., Davis, R.W., NSTI-Nanotech 2007, Vol.3, pp. 422-425.
  23. 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.
  24. Gate-Controlled Microfluidic Chamber with magnetic bead for DNA Sequencing-by-synthesis Technology.
    Esfandyarpour, H. and Davis R.W., ICNMM2007, ref- 3119.
  25. 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.
  26. Nano-Biotechnology toward Diagnostic Industry: Obstacles and Opportunities.
    Esfandyarpour, H., ”NSTI-Nanotech 2007, Vol. 4, pp 421-423.
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
  38. 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]
  39. 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].
  40. 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]
  41. Analysis of read length limiting factors in Pyrosequencing chemistry.
    Mashayekhi, F. Ronaghi, M. Anal Biochem 363(2):275-87 (2007). [PubMed], [Publisher Full Text]
  42. 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]
  43. 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]
  44. 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]
  45. Pyrosequencing for discovery and analysis of DNA sequence variations.
    Ronaghi, M., Shokralla, S., Gharizadeh, B. Pharmacogenomics 8(10):1437-41 (2007). [PubMed], [Full Text]
  46. 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]
  47. 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]
  48. 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]
  49. 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]
  50. 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]
  51. 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]
  52. 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]
  53. 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]
  54. Label-Free Impedance Biosensors: Opportunities and Challenges.
    Daniels, J. S. Pourmand, N. Electroanalysis 19(12):1239-1257 (2007). [PubMed], [Full Text]
  55. 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]
  56. Accelerating the discovery of biologically active small molecules using a high-throughput yeast halo assay.
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