SGTC Publications

Following is a list of publications starting in 1993, when the Stanford Genome Technology Center was founded. The list is updated through September 2013 only.

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).

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Original Articles

  1. Community members in activated sludge as determined by molecular probe technology. Xu W, Brand VR, Suresh S, Jensen MA, Davis RW, Criddle CS, St.Onge RP, Hyman RW. 2020 January 1;168(115104). doi:
  2. Identification of polyketide biosynthetic gene clusters that harbor self-resistance target genes. Vandova GA, Nivina A, Khosla C, Davis RW, Fisher CR, Hillenmeyer ME. bioRxiv. 2020 June 2. doi:
  3. Automated motion tracking and data extraction for red blood cell biomechanics. Kumar A, Schmidt BR, Sanchez ZAC, Yazar F, Davis RW, Ramasubramanian AK, Saha AK.Curr Protoc Cytom. 2020 Jun;93(1):e75. doi:10.1002/cpcy.75.
  4. The IDO metabolic trap hypothesis for the etiology of ME/CFS. Kashi AA, Davis RW, Phair RD. Diagnostics (Basel). 2019 Jul 26;9(3). pii: E82. doi: 10.3390/diagnostics9030082.
  5. A nanoelectronics-blood-based diagnostic biomarker for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Esfandyarpour R, Kashi A, Nemat-Gorgani M, Wilhelmy J, Davis RW. Proc Natl Acad Sci U S A. 2019 May 21;116(21):10250-10257. doi: 10.1073/pnas.1901274116. Epub 2019 Apr 29.
  6. Red blood cell deformability is diminished in patients with Chronic Fatigue Syndrome. Saha AK, Schmidt BR, Wilhelmy J, Nguyen V, Abugherir A, Do JK, Nemat-Gorgani M, Davis RW, Ramasubramanian AK. Clin Hemorheol Microcirc. 2019;71(1):113-116. doi: 10.3233/CH-180469.
  7. A biosensor-based approach reveals links between efflux pump expression and cell cycle regulation in pleiotropic drug resistance of yeast. Li J, Kolberg K, Schlecht U, St Onge RP, Aparicio AM, Horecka J, Davis RW, Hillenmeyer ME, Harvey CJB. J Biol Chem. 2019 Jan 25;294(4):1257-1266. doi: 10.1074/jbc.RA118.003904. Epub 2018 Dec 4.
  8. Combining newborn metabolic and DNA analysis for second-tier testing of methylmalonic acidemia. Peng G, Shen P, Gandotra N, Le A, Fung E, Jelliffe-Pawlowski L, Davis RW, Enns GM, Zhao H, Cowan TM, Scharfe C. Genet Med. 2018 Sep 13. doi: 10.1038/s41436-018-0272-5.
  9. Multiplexed precision genome editing with trackable genomic barcodes in yeast. Roy KR, Smith JD, Vonesch SC, Lin G, Tu CS, Lederer AR, Chu A, Suresh S, Nguyuen M, Horecka J, Tripathi A, Burnett WT, Morgan MA, Schulz J, Orsley KM, Wei W, Aiyar RS, Davis RW, Bankaitis VA, Haber JE, Salit ML, St Onge RP, Steinmetz LM. Nat Biotechnol. 2018 Jul;36(6):512-520. doi: 10.1038/nbt.4137. Epub 2018 May 7.
  10. HEx: A heterologous expression platform for the discovery of fungal natural products. Harvey CJB, Tang M, Schlecht U, Horecka J, Fischer CR, Lin HC, Li J, Naughton B, Cherry J, Miranda M, Li YF, Chu AM, Hennessy JR, Vandova GA, Inglis D, Aiyar RS, Steinmetz LM, Davis RW, Medema MH, Sattely E, Khosla C, St Onge RP, Tang Y, Hillenmeyer ME. Sci Adv. 2018 Apr 11;4(4):eaar5459. doi: 10.1126/sciadv.aar5459. eCollection 2018 Apr.
  11. Template-independent enzymatic oligonucleotide synthesis (TiEOS): Its history, prospects, and challenges. Jensen MA, Davis RW. Biochemistry. 2018 Mar 27;57(12):1821-1832. doi: 10.1021/acs.biochem.7b00937. Epub 2018 Mar 13. Review.
  12. Streamlined circular proximity ligation assay provides high stringency and compatibility with low-affinity antibodies. Jalil R, Horecka J, Swartz JR, Davis RW, Persson HHJ. Proc Natl Acad Sci U S A. 2018 Jan 16. doi: 10.1073/pnas.1718283115.
  13. Quantitative analysis of protein interaction network dynamics in yeast. Celaj A, Schlecht U, Smith JD, Xu W, Suresh S, Miranda M, Aparicio AM, Proctor M, Davis RW, Roth FP, St Onge RP. Mol Syst Biol. 2017 Jul 13;13(7):934. doi: 10.15252/msb.20177532.
  14. Autonomous sweat extraction and analysis applied to cystic fibrosis and glucose monitoring using a fully integrated wearable platform. Emaminejad S, Gao W, Wu E, Davies ZA, Nyein HYY, Challa S, Ryan SP, Fahad HM, Chen K, Shahpar Z, Talebi S, Milla C, Javey A, Davis RW. Proc Natl Acad Sci U S A. 2017 May 2;114(18):4625-30 doi: 10.1073/pnas.1701740114.
  15. Heterologous expression of diverse propionyl-CoA carboxylases affects polyketide production in Escherichia coli. Vandova GA, O’Brien RV, Lowry B, Robbins TF, Fischer CR, Davis RW, Khosla C, Harvey CJB, Hillenmeyer ME. J Antibiot (Tokyo). 2017 Apr 12. doi: 10.1038/ja.2017.38.
  16. Multifunctional, inexpensive, and reusable nanoparticle-printed biochip for cell manipulation and diagnosis. Esfandyarpour R, DiDonato MJ, Yang Y, Durmus NG, Harris JS, Davis RW. Proc Natl Acad Sci USA. 2017 Feb 21;114(8):E1306-E1315. doi: 10.1073/pnas.1621318114.
  17. A method for high-throughput production of sequence-verified DNA libraries and strain collections. Smith JD, Schlecht U, Xu W, Suresh S, Horecka J, Proctor MJ, Aiyar RS, Bennett RA, Chu A, Li YF, Roy K, Davis RW, Steinmetz LM, Hyman RW, Levy SF, St Onge RP. Mol Syst Biol. 2017 Feb 13;13(2):913. doi: 10.15252/msb.20167233.
  18. Application of 3D printing for smart objects with embedded electronic sensors and systems. Ota H, Emaminejad S, Gao Y, Zhao A, Wu E, Challa S, Chen K, Fahad HM, Jha AK, Kiriya D, Gao W, Shiraki H, Morioka K, Ferguson AR, Healy KE, Davis RW, Javey A. Adv Mater. 2016;1(1600013):1-8. doi: 10.1002/admt.201600013.
  19. Systematic Mapping of Chemical-Genetic Interactions in Saccharomyces cerevisiae. Suresh S, Schlecht U, Xu W, Bray W, Miranda M, Davis RW, Nislow C, Giaever G, Lokey RS, St Onge RP. Cold Spring Harb Protoc. 2016 Sep 1;2016(9):pdb.top077701. doi: 10.1101/pdb.top077701.
  20. Identification of chemical-genetic interactions via parallel analysis of barcoded yeast strains. Suresh S, Schlecht U, Xu W, Miranda M, Davis RW, Nislow C, Giaever G, St Onge RP. Cold Spring Harb Protoc. 2016 Sep 1;2016(9):pdb.prot088054. doi: 10.1101/pdb.prot088054.
  21. Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae. Xie B, Horecka J, Chu A, Davis RW, Becker E, Primig M. RNA Biol. 2016 Sep;13(9):772-82. doi: 10.1080/15476286.2016.1191738.
  22. A wearable electrochemical platform for noninvasive simultaneous monitoring of Ca(2+) and pH. Nyein HY, Gao W, Shahpar Z, Emaminejad S, Challa S, Chen K, Fahad HM, Tai LC, Ota H, Davis RW, Javey A. ACS Nano. 2016 Jul 26;10(7):7216-24. doi: 10.1021/acsnano.6b04005.
  23. An electrochemical platform for localized pH control on demand. Fomina N, Johnson CA, Maruniak A, Bahrampour S, Lang C, Davis RW, Kavusi S, Ahmad H. Lab Chip. 2016 Jun 21;16(12):2236-44. doi: 10.1039/c6lc00421k.
  24. Nucleotide-specific contrast for DNA sequencing by electron spectroscopy. Mankos M, Persson HH, N'Diaye AT, Shadman K, Schmid AK, Davis RW. PLoS One. 2016 May 5;11(5):e0154707. doi: 10.1371/journal.pone.0154707.
  25. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Smith JD, Suresh S, Schlecht U, Wu M, Wagih O, Peltz G, Davis RW, Steinmetz LM, Parts L, St Onge RP. Genome Biol. 2016 Mar 8;17:45. doi: 10.1186/s13059-016-0900-9.
  26. Integrating cell phone imaging with magnetic levitation (i-LEV) for label-free blood analysis at the point-of-living. Baday M, Calamak S, Durmus NG, Davis RW, Steinmetz LM, Demirci U. Small. 2016 Mar 2;12(9):1222-9. doi: 10.1002/smll.201501845.
  27. Next-generation molecular testing of newborn dried blood spots for cystic fibrosis. Lefterova MI, Shen P, Odegaard JI, Fung E, Chiang T, Peng G, Davis RW, Wang W, Kharrazi M, Schrijver I, Scharfe C. J Mol Diagn. 2016 Mar;18(2):267-82. doi: 10.1016/j.jmoldx.2015.11.005.
  28. Nanoelectronic three-dimensional (3D) nanotip sensing array for real-time, sensitive, label-free sequence specific detection of nucleic acids. Esfandyarpour R, Yang L, Koochak Z, Harris JS, Davis RW. Biomed Microdevices. 2016 Feb;18(1):7. doi: 10.1007/s10544-016-0032-8.
  29. Fully integrated wearable sensor arrays for multiplexed in situ perspiration analysis. Gao W, Emaminejad S, Nyein HY, Challa S, Chen K, Peck A, Fahad HM, Ota H, Shiraki H, Kiriya D, Lien DH, Brooks GA, Davis RW, Javey A. Nature. 2016 Jan 28;529(7587):509-14. doi: 10.1038/nature16521.
  30. A rapid, high-quality, cost-effective, comprehensive and exapandable targeted next-generation sequencing assay for inherited heart diseases. Wilson KD, Shen P, Fung E, Karakikes I, Zhang A, InanlooRahatloo K, Odegaard J, Sallam K, Davis RW, Lui GK, Ashley EA, Scharfe C, Wu JC. Circ Res. 2015 Sep 11;117(7):603-11. doi: 10.1161/circresaha.115.306723.
  31. Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics. Inci F, Filippini C, Baday M, Ozen MO, Calamak S, Durmus NG, Wang S, Hanhauser E, Hobbs KS, Juillard F, Kuang PP, Vetter ML, Carocci M, Yamamoto HS, Takagi Y, Yildiz UH, Akin D, Wesemann DR, Singhal A, Yang PL, Nibert ML, Fichorova RN, Lau DT, Henrich TJ, Kaye KM, Schachter SC, Kuritzkes DR, Steinmetz LM, Gambhir SS, Davis RW, Demirci U. Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):E4354-63. doi: 10.1073/pnas.1510824112.
  32. Magnetic levitation of single cells. Durmus NG, Tekin HC, Guven S, Sridhar K, Arslan Yildiz A, Calibasi G, Ghiran I, Davis RW, Steinmetz LM, Demirci U. Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):E3661-8. doi: 10.1073/pnas.1509250112.
  33. RASA: Robust alternative splicing analysis for human transcriptome arrays. Seok J, Xu W, Davis RW, Xiao W. Sci Rep. 2015 Jul 6;5:11917. doi: 10.1038/srep11917.
  34. LBP19: Extended coverage by next generation sequencing methods refines the characterization of the common and well documented hla alleles. Fernandez-Vina A, Wang C, Krishnakumar S, Levinson DF, Davis RW, Mindrinos M. Hum Immunol. 2015 Apr;76(4):210-38. doi: 10.1016/j.humimm.2015.01.051.
  35. Integrating cell phone imaging with magnetic levitation (i-LEV) for label-free blood analysis at the point-of-living. Baday M, Calamak S, Durmus NG, Davis RW, Steinmetz LM, Dermirci U. Small. 2016 Mar 2;12(9):122-9. doi:10.1002/smll.201501845. Epub 2015 Nov 2.
  36. A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification. Bigdeli S, Dettloff RO, Frank CW, Davis RW, Crosby LD. PLoS One. 2015 Feb 17;10(2):e0117738. doi:10.1371/journal.pone.0117738. eCollection 2015.
  37. Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development. Becker E, Liu Y, Lardenois A, Walther T, Horecka J, Stuparevic I, Law MJ, Lavigne R, Evrard B, Demougin P, Riffle M, Strich R, Davis RW, Pineau C, Primig M. J Proteomics. 2015 Feb 4;119C:30-44. doi: 10.1016/j.jprot.2015.01.015.
  38. Tunable control of antibody immobilization using electric field. Emaminejad S, Javanmard M, Gupta C, Chang S, Davis RW, Howe RT. Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):1995-9. doi: 10.1073/pnas.1424592112. Epub 2015 Feb 3.
  39. Multielectrode sensing for extraction of signal from noise in impedance cytometry. Emaminejad S, Talebi S, Davis RW, Javanmard M. IEEE Sens J. 2015 Jan 8;15(5):2715-6. doi: 10.1109/jsen.2015.2389224.
  40. Mice are not men. Warren HS, Tompkins RG, Moldawer LL, Seok J, Xu W, Mindrinos MN, Maier RV, Xiao W, Davis RW. Proc Natl Acad Sci U S A. 2015 Jan 27;112(4):E345. doi: 10.1073/pnas.1414857111. Epub 2014 Dec 24.
  41. The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. Lardenois A, Stuparevic I, Liu Y, Law MJ, Becker E, Smagulova F, Waern K, Guilleux MH, Horecka J, Chu A, Kervarrec C, Strich R, Snyder M, Davis RW, Steinmetz LM, Primig M. Nucleic Acids Res. 2015 Jan;43(1):115-28. doi: 10.1093/nar/gku1185. Epub 2014 Dec 3.
  42. Single cell mutational analysis of PIK3CA in circulating tumor cells and metastases in breast cancer reveals heterogeneity, discordance, and mutation persistence in cultured disseminated tumor cells from bone marrow. Deng G, Krishnakumar S, Powell AA, Zhang H, Mindrinos MN, Telli ML, Davis RW, Jeffrey SS. BMC Cancer. 2014 Jun 19;14:456. doi: 10.1186/1471-2407-14-456.
  43. Detecting differential protein expression in large-scale population proteomics. Ryu SY, Qian WJ, Camp DG, Smith RD, Tompkins RG, Davis RW, Xiao W. Bioinformatics. 2014 Oct;30(19):2741-6. doi: 10.1093/bioinformatics/btu341. Epub 2014 Jun 12.
  44. Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Kuehl JV, Price MN, Ray J, Wetmore KM, Esquivel Z, Kazakov AE, Nguyen M, Kuehn R, Davis RW, Hazen TC, Arkin AP, Deutschbauer A.MBio. 2014 May 27;5(3):e01041-14. doi: 10.1128/mBio.01041-14.
  45. Multiplexed actuation using ultra dielectrophoresis for proteomics applications: a comprehensive electrical and electrothermal design methodology. Emaminejad S, Dutton RW, Davis RW, Javanmard M. Lab Chip. 2014 Jun 21;14(12):2105-14. doi: 10.1039/c4lc00036f. Epub 2014 May 7.
  46. Targeted and highly multiplexed detection of microorganisms by employing an ensemble of molecular probes. Xu W, Krishnakumar S, Miranda M, Jensen MA, Fukushima M, Palm C, Fung E, Davis RW, St Onge RP, Hyman RW. Appl Environ Microbiol. 2014 Jul;80(14):4153-61. doi: 10.1128/AEM.00666-14. Epub 2014 May 2.
  47. Mapping the cellular response to small molecules using chemogenomic fitness signatures. Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, Cheung-Ong K, Torres NP, Spear ED, Han MK, Schlecht U, Suresh S, Duby G, Heisler LE, Surendra A, Fung E, Urbanus ML, Gebbia M, Lissina E, Miranda M, Chiang JH, Aparicio AM, Zeghouf M, Davis RW, Cherfils J, Boutry M, Kaiser CA, Cummins CL, Trimble WS, Brown GW, Schimmer AD, Bankaitis VA, Nislow C, Bader GD, Giaever G. Science. 2014 Apr 11;344(6180):208-11. doi: 10.1126/science.1250217. Erratum in: Science. 2014 May 23;344(6186):1255771.
  48. A functional screen for copper homeostasis genes identifies a pharmacologically tractable cellular system. Schlecht U, Suresh S, Xu W, Aparicio AM, Chu A, Proctor MJ, Davis RW, Scharfe C, St Onge RP. BMC Genomics. 2014 Apr 5;15:263. doi: 10.1186/1471-2164-15-263.
  49. The 50:50 method for PCR-based seamless genome editing in yeast. Horecka J, Davis RW. Yeast. 2014 Mar;31(3):103-12. doi: 10.1002/yea.2992. Epub 2013 Dec 13.
  50. IpO: plasmids and methods for simplified, PCR-based DNA transplant in yeast. Horecka J, Chu AM, Davis RW. Yeast. 2014 May;31(5):185-93. doi: 10.1002/yea.3006. Epub 2014 Mar 20.
  51. Scan statistics analysis for detection of introns in time-course tiling array data. Reiner-Benaim A, Davis RW, Juneau K. Stat Appl Genet Mol Biol. 2014 Apr 1;13(2):173-90. doi: 10.1515/sagmb-2013-0038.
  52. A novel low energy electron microscope for DNA sequencing and surface analysis. Mankos M, Shadman K, Persson HH, N'Diaye AT, Schmid AK, Davis RW. Ultramicroscopy. 2014 Oct;145:36-49. doi: 10.1016/j.ultramic.2014.01.007. Epub 2014 Jan 31.
  53. Digital microfluidic assay for protein detection. Mok J, Mindrinos MN, Davis RW, Javanmard M. Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2110-5. doi: 10.1073/pnas.1323998111. Epub 2014 Jan 21.
  54. Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations. Fu GK, Xu W, Wilhelmy J, Mindrinos MN, Davis RW, Xiao W, Fodor SP. Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1891-6. doi: 10.1073/pnas.1323732111. Epub 2014 Jan 21.
  55. Label-free electronic probing of nucleic acids and proteins at the nanoscale using the nanoneedle biosensor. Esfandyarpour R, Javanmard M, Koochak Z, Esfandyarpour H, Harris JS, Davis RW. Biomicrofluidics. 2013 Aug 6;7(4):44114. doi: 10.1063/1.4817771. eCollection 2013. Erratum in: Biomicrofluidics. 2014;8(2):029901.
  56. Nanoelectronic impedance detection of target cells. Esfandyarpour R, Javanmard M, Koochak Z, Harris JS, Davis RW. Biotechnol Bioeng. 2014 Jun;111(6):1161-9. doi: 10.1002/bit.25171. Epub 2013 Dec 28.
  57. Computational identification and analysis of orphan assembly-line polyketide synthases. O'Brien RV, Davis RW, Khosla C, Hillenmeyer ME. J Antibiot (Tokyo). 2014 Jan;67(1):89-97. doi: 10.1038/ja.2013.125. Epub 2013 Dec 4.
  58. Ceftriaxone increases glutamate uptake and reduces striatal tyrosine hydroxylase loss in 6-OHDA Parkinson's model. Chotibut T, Davis RW, Arnold JC, Frenchek Z, Gurwara S, Bondada V, Geddes JW, Salvatore MF. Mol Neurobiol. 2014 Jun;49(3):1282-92. doi: 10.1007/s12035-013-8598-0. Epub 2013 Dec 3.
  59. PITPs as targets for selectively interfering with phosphoinositide signaling in cells. Nile AH, Tripathi A, Yuan P, Mousley CJ, Suresh S, Wallace IM, Shah SD, Pohlhaus DT, Temple B, Nislow C, Giaever G, Tropsha A, Davis RW, St Onge RP, Bankaitis VA. Nat Chem Biol. 2014 Jan;10(1):76-84. doi: 10.1038/nchembio.1389. Epub 2013 Nov 24.
  60. Treadmill exercise inhibits apoptotic neuronal cell death with suppressed vascular endothelial growth factor expression in the retinas of the diabetic rats. Ji ES, Ko IG, Cho JW, Davis RW, Hwang GY, Jee YS, Lim BV. J Exerc Rehabil. 2013 Jun 30;9(3):348-53. doi: 10.12965/jer.130043. eCollection 2013.
  61. Simulation and fabrication of a new novel 3D injectable biosensor for high throughput genomics and proteomics in a lab-on-a-chip device. Esfandyarpour R, Esfandyarpour H, Harris JS, Davis RW. Nanotechnology. 2013 Nov 22;24(46):465301. doi: 10.1088/0957-4484/24/46/465301. Epub 2013 Oct 22.
  62. To study human inflammatory diseases in humans.
    Tompkins RG, Warren HS, Mindrinos MN, Xiao W, Davis RW. Proc Natl Acad Sci USA. 2013 Sep 3;110(36):E3371.
  63. Of men, not mice, and inflammation.
    Warren HS, Tompkins RG, Mindrinos MN, Xiao W, Davis RW. Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):E3151.
  64. The Sequencing Bead Array (SBA), a next-generation digital suspension array.
    Akhras MS, Pettersson E, Diamond L, Unemo M, Okamoto J, Davis RW, Pourmand N. PLoS One. 2013 Oct 7;8(10):e76696. doi: 10.1371/journal.pone.0076696. eCollection 2013.
  65. Determination of burn patient outcome by large-scale quantitative discovery proteomics.
    Finnerty CC, Jeschke MG, Qian WJ, Kaushal A, Xiao W, Liu T, Gritsenko MA, Moore RJ, Camp DG 2nd, Moldawer LL, Elson C, Schoenfeld D, Gamelli R, Gibran N, Klein M, Arnoldo B, Remick D, Smith RD, Davis R, Tompkins RG, Herndon DN; Investigators of the Inflammation and the Host Response Glue Grant. Crit Care Med. 2013 Jun;41(6):1421-34. doi: 10.1097/CCM.0b013e31827c072e.
  66. Direct oligonucleotide synthesis onto super-paramagnetic beads.
    Jensen MA, Akhras MS, Fukushima M, Pourmand N, Davis RW. J Biotechnol. 2013 Aug 11;167(4):448-453. doi: 10.1016/j.jbiotec.2013.08.006.
  67. Progress toward an aberration-corrected low energy electron microscope for DNA sequencing and surface analysis.  
    Mankos M, Shadman K, N'diaye AT, Schmid AK, Persson HH, Davis RW.  J Vac Sci Technol B Nanotechnol Microelectron. 2012 Nov;30(6):6F402. Epub 2012 Oct 26.
  68. Diversity of the Vaginal Microbiome Correlates With Preterm Birth.
    Hyman, RW., Fukushima, M., Jiang, H., Fung, E., Rand, L., Johnson, B., Vo, KC., Caughey, AB., Hilton, JF., Davis, RW, Guidice, LC. Reproductive Sciences 2014, 21:32, published online 28 May 2013. DOI: 10.1177/1933719113488838. [PubMed]
  69. Multiplex target capture with double-stranded DNA probes.
    Shen, P., Wang, W., Chi, AK., Fan, Y., Davis, RW., Scharfe, C. Genome Medicine 2013, 5:50 doi:10.1186/gm454. [PubMed]
  70. Multiplex target capture with double-stranded DNA probesBenchmarking outcomes in the critically injured trauma patient and the effect of implementing standard operating procedures.
    Cuschieri, J., Johnson, J. L., Sperry, J., West, M. A., Moore, E. E., Minei, J. P., Bankey, P. E., Nathens, A. B., Cuenca, A. G., Efron, P. A., Hennessy, L., Xiao, W., Mindrinos, M. N., McDonald-Smith, G. P., Mason, P. H., Billiar, T. R., Schoenfeld, D. A., Warren, H. S., Cobb, J. P., Moldawer, L. L., Davis, R. W., Maier, R. V., Tompkins, R. G., Ann Surg. 2012;255(5):993-9. PMCID: 3327791. [PubMed]
  71. Microfluidic diagnostic tool for the developing world: contactless impedance flow cytometry.
    Emaminejad S, Javanmard M, Dutton RW, Davis RW. Lab on a chip. 2012. [PubMed]
  72. Control of DNA capture by nanofluidic transistors.
    Paik, K. H., Liu, Y., Tabard-Cossa, V., Waugh, M. J., Huber, D. E., Provine, J., Howe, R. T., Dutton, R.W., Davis, R.W. ACS Nano. 2012;6(8):6767-75. PMCID: 3429714. [PubMed]
  73. Cationic amphiphilic drugs are potent inhibitors of yeast sporulation.
    Schlecht, U., St Onge, RP,. Walther, T., Francois, J. M., Davis, RW. PLoS ONE. 2012;7(8):e42853. PMCID: 3414501. [PubMed]
  74. Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies.
    Xu, W., Gao, H., Seok, J., Wilhelmy, J., Mindrinos, M. N., Davis, R. W., Xiao, W. BioTechniques. 2012;52(6):386-8. [PubMed]
  75. High-throughput, high-fidelity HLA genotyping with deep sequencing.
    Wang, C., Krishnakumar, S., Wilhelmy, J., Babrzadeh, F., Stepanyan, L., Su, L. F. Levinson, D. Fernandez-Vina, M. A. Davis, R. W. Davis, M. M. Mindrinos, M. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(22):8676-81. PMCID: 3365218. [PubMed]
  76. Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research.
    Seok J, Xu W, Jiang H, Davis RW, Xiao W. PLoS ONE. 2012;7(2):e31440. PMCID: 3270033. [PubMed]
  77. JETTA: junction and exon toolkits for transcriptome analysis.
    Seok J, Xu W, Gao H, Davis RW, Xiao W. Bioinformatics. 2012;28(9):1274-5. PMCID: 3338022. [PubMed]. JETTA and its demonstrations are freely available at
  78. Multiplex assay for condition-dependent changes in protein-protein interactions.
    Schlecht U, Miranda M, Suresh S, Davis RW, St Onge RP. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(23):9213-8. [PubMed]
  79. Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines.
    Powell, A. A. Talasaz, A. H. Zhang, H. Coram, M. A. Reddy, A. Deng, G. Telli, M. L. Advani, R. H. Carlson, R. W. Mollick, J. A. Sheth, S. Kurian, A. W. Ford, J. M. Stockdale, F. E. Quake, S. R. Pease, R. F. Mindrinos, M. N. Bhanot, G. Dairkee, S. H. Davis, R. W. Jeffrey, S. S. PLoS ONE. 2012;7(5):e33788. PMCID: 3346739. [PubMed]
  80. Molecular probe technology detects bacteria without culture.
    Hyman, R. W. St Onge, R. P. Kim, H. Tamaresis, J. S. Miranda, M. Aparicio, A. M. Fukushima, M. Pourmand, N. Giudice, L. C. Davis, R. W. BMC microbiology. 2012;12:29. PMCID: 3316761. [PubMed]
  81. The dynamics of the vaginal microbiome during infertility therapy with in vitro fertilization-embryo transfer.
    Richard W. Hyman, Christopher N. Herndon, Hui Jiang, Curtis Palm, Marilyn Fukushima, Denise Bernstein, Kim Chi Vo, Zara Zelenko, Ronald W. Davis and Linda C. Giudice. J Assist Reprod Genet. 2012;29(2):105-15. PMCID: 3270134. [Epub ahead of print] DOI: 10.1007/s10815-011-9694-6. [Publisher], [PubMed]
  82. A rapid, cost-effective method of assembly and purification of synthetic DNA probes >100 bp.
    Jensen MA, Jauregui L, Davis RW. PLoS ONE. 2012;7(4):e34373. PMCID: 3321010. [PubMed]
  83. Competitive Genomic Screens of Barcoded Yeast Libraries.
    Smith, A. M., Durbic, T., Oh, J., Urbanus, M., Proctor, M., Heisler, L. E., et al. J. Vis. Exp. (54), e2864, DOI: 10.3791/2864 (2011).
  84. Bacteria on Human Skin.
    Hyman, RW., Babrzadeh, F., Palm, C., Wang, C., Fukushima, M., Davis, RW. American Journal of Microbiology 2 (2): 25-34, 2011. DOI: 10.3844/ajmsp.2011.25.34 [Publisher]
  85. The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome.
    Newburger DE, Natsoulis G, Grimes S, Bell JM, Davis RW, Batzoglou S, Ji HP. Nucleic Acids Res. 2012 Jan;40(Database issue):D1137-43. Epub 2011 Nov 18. [PubMed], Human OligoGenome Resource at
  86. High-throughput VDJ sequencing for quantification of minimal residual disease in chronic lymphocytic leukemia and immune reconstitution assessment.
    Logan AC, Gao H, Wang C, Sahaf B, Jones CD, Marshall EL, Buño I, Armstrong R, Fire AZ, Weinberg KI, Mindrinos M, Zehnder JL, Boyd SD, Xiao W, Davis RW, Miklos DB. Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21194-9. Epub 2011 Dec 12. [PubMed]
  87. A genomic storm in critically injured humans.
    Xiao W, Mindrinos MN, Seok J, Cuschieri J, Cuenca AG, Gao H, Hayden DL, Hennessy L, Moore EE, Minei JP, Bankey PE, Johnson JL, Sperry J, Nathens AB, Billiar TR, West MA, Brownstein BH, Mason PH, Baker HV, Finnerty CC, Jeschke MG, López MC, Klein MB, Gamelli RL, Gibran NS, Arnoldo B, Xu W, Zhang Y, Calvano SE, McDonald-Smith GP, Schoenfeld DA, Storey JD, Cobb JP, Warren HS, Moldawer LL, Herndon DN, Lowry SF, Maier RV, Davis RW, Tompkins RG; and the Inflammation and Host Response to Injury Large-Scale Collaborative Research Program. J Exp Med. 2011 Dec 19;208(13):2581-90. Epub 2011 Nov 21. [PubMed], [Publisher]
  88. Performance comparison of whole-genome sequencing platforms.
    Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. Nat Biotechnol. 2011 Dec 18;30(1):78-82. doi: 10.1038/nbt.2065. [PubMed]
  89. Use of Negative Dielectrophoresis for Selective Elution of Protein-bound Particles.
    Javanmard M, Emaminejad S, Dutton RW, Davis RW. Analytical chemistry. 2012;84(3):1432-8. PMCID: 3278233. [Epub ahead of print], [PubMed]
  90. Improvement in cell capture throughput using parallel bioactivated microfluidic channels.
    Javanmard M, Babrzadeh F, Nyren P, Davis RW. Biomed Microdevices. 2012;14(4):625-9. PMCID: 3414683. [PubMed]
  91. Targeted sequencing library preparation by genomic DNA circularization.
    Myllykanagas S, Natsoulis G, Bell JM, Ji HP. BMC Biotechnol. 2011 Dec 14;11(1):122. [Epub ahead of print] [PubMed]
  92. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions.
    Deutschbauer A, Price MN, Wetmore KM, Shao W, Baumohl JK, Xu Z, Nguyen M, Tamse R, Davis RW, Arkin AP. PLoS Genet. 2011 Nov;7(11):e1002385. Epub 2011 Nov 17. [PubMed]
  93. Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms.
    Wallace IM, Urbanus ML, Luciani GM, Burns AR, Han MKL, Wang H, Arora K, Heisler LE, Proctor M, St Onge RP, Roemer T, Roy PJ, Cummins CL, Bader GD, Nislow C, Giaever G. Chemistry & Biology, Volume 18, Issue 10, 1273-1283, 28 October 2011. [Article]
  94. Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing.
    Myllykangas S, Buenrostro J, Natsoulis G, Bell JM, Ji HP. Nature Biotechnology (2011) doi:10.1038/nbt.1996. [Publisher]
  95. Ultrasensitive detection of rare mutations using next-generation targeted resequencing.
    Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, Bell J, Brown S, Holodniy M, Zhang N, Ji HP. Nucleic Acids Res. 2012;40(1):e2. PMCID: 3245950. [Epub ahead of print], [PubMed]
  96. Benchmarking outcomes in the critically injured trauma patient and the effect of implementing standard operating procedures.
    Cuschieri, J. Johnson, J. L. Sperry, J. West, M. A. Moore, E. E. Minei, J. P. Bankey, P. E. Nathens, A. B. Cuenca, A. G. Efron, P. A. Hennessy, L. Xiao, W. Mindrinos, M. N. McDonald-Smith, G. P. Mason, P. H. Billiar, T. R. Schoenfeld, D. A. Warren, H. S. Cobb, J. P. Moldawer, L. L. Davis, R. W. Maier, R. V. Tompkins, R. G. Ann Surg. 2012;255(5):993-9. PMCID: 3327791. [PubMed]
  97. Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1.
    Babrzadeh, F. Jalili, R. Wang, C. Shokralla, S. Pierce, S. Robinson-Mosher, A. Nyren, P. Shafer, R. W. Basso, L. C. de Amorim, H. V. de Oliveira, A. J. Davis, R. W. Ronaghi, M. Gharizadeh, B. Stambuk, B. U. Mol Genet Genomics. 2012;287(6):485-94. [PubMed]
  98. Competitive Genomic Screens of Barcoded Yeast Libraries.
    Smith AM, Durbic T, Oh J, Urbanus M, Proctor M, Heisler LE, Giaever G, Nislow C. J Vis Exp. 2011 Aug 11;(54). pii: 2864. doi: 10.3791/2864. [PubMed], [Video]
  99. The Automated Cell: Compound and Environment Screening System (ACCESS) for Chemogenomic Screening.
    Proctor M, Urbanus ML, Fung EL, Jaramillo DF, Davis RW, Nislow C, Giaever G. Methods Mol Biol. 2011;759:239-69. [PubMed]
  100. A flexible approach for highly multiplexed candidate gene targeted resequencing.
    Natsoulis G, Bell JM, Xu H, Buenrostro JD, Ordonez H, Grimes S, Newburger D, Jensen M, Zahn JM, Zhang N, Ji HP. PLoS One. 2011;6(6):e21088. Epub 2011 Jun 30. [PubMed]
  101. Combining magnetic resonance spectroscopy and molecular genomics offers better accuracy in brain tumor typing and prediction of survival than either methodology alone.
    Astrakas L, Blekas KD, Constantinou C, Andronesi OC, Mindrinos MN, Likas AC, et al. Int J Oncol. 2011;38(4):1113-27. PMID: 21274507. [PubMed]
  102. Human transcriptome array for high-throughput clinical studies.
    Xu, W., Seok, J., Mindrinos, M.N., Schweitzer, A.C., Jiang, H., Wilhelmy, J., Clark, T.A., Kapur, K., Xing, Y., Faham, M., Storey, J.D., Moldawer, L.L., Maier, R.V., Tompkins, R.G., Wong, W.H., Davis, R.W. and Xiao, W. PNAS. (2011) 108 (9):I3707-3712. PMCID: 3048146. [PubMed]
  103. Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing.
    Wang W, Shen P, Thiyagarajan S, Lin S, Palm C, Horvath R, Klopstock T, Cutler D, Pique L, Schrijver I, Davis RW, Mindrinos M, Speed TP, Scharfe C. Nucleic Acids Res. 39: 44-58. 2011. PMCID: 3017602. [Epub ahead of print] [PubMed]
  104. Distinctive responsiveness to stromal signaling accompanies histologic grade programming of cancer cells.
    Luciani MG, Seok J, Sayeed A, Champion S, Goodson WH, Jeffrey SS, Xiao W, Mindrinos M, Davis RW, Dairkee SH. PLoS One. 2011;6(5):e20016. Epub 2011 May 19. [PubMed]
  105. High-quality DNA sequence capture of 524 disease candidate genes.
    Shen, P., Wang, W., Krishnakumar, S., Palm, C., Chi, A.K., Enns, G., Davis, RW., Speed, T.P., Mindrinos, MN., Scharfe, C. (2011). Published online ahead of print April 5, 2011, doi: 10.1073/pnas.1018981108. PMCID: 3080966. [PubMed]
  106. Targeted deep resequencing of the human cancer genome using next-generation technologies.
    Myllykangas S, Ji HP. Biotechnol Genet Eng Rev. 2010;27:135-58. Review. [PubMed]
  107. Predicting patient survival from longitudinal gene expression.
    Zhang Y, Tibshirani RJ, Davis RW. Stat Appl Genet Mol Biol. 2010;9(1):Article41. PMCID: 3004784. [PubMed]
  108. Analysis of factorial time-course microarrays with application to a clinical study of burn injury.
    Zhou, B., Xu, W., Herndon, D., Tompkins, R., Davis, R., Xiao, W., Wong, W.H., Toner, M., Warren, H.S., Schoenfeld, D.A., Rahme, L., McDonald-Smith, G.P., Hayden, D., Mason, P., Fagan, S., Yu, Y.M., Cobb, J.P., Remick, D.G., Mannick, J.A., Lederer, J.A., Gamelli, R.L., Silver, G.M., West, M.A., Shapiro, M.B., Smith, R., Camp, D.G., 2nd, Qian, W., Storey, J., Mindrinos, M., Tibshirani, R., Lowry, S., Calvano, S., Chaudry, I., Cohen, M., Moore, E.E., Johnson, J., Moldawer, L.L., Baker, H.V., Efron, P.A., Balis, U.G., Billiar, T.R., Ochoa, J.B., Sperry, J.L., Miller-Graziano, C.L., De, A.K., Bankey, P.E., Finnerty, C.C., Jeschke, M.G., Minei, J.P., Arnoldo, B.D., Hunt, J.L., Horton, J., Brownstein, B., Freeman, B., Maier, R.V., Nathens, A.B., Cuschieri, J., Gibran, N., Klein, M. and O'Keefe, G. PNAS. (2010) 107 (22):I9923-8. PMCID: 2890487. [PubMed]
  109. Gas-phase cleavage and dephosphorylation of universal linker-bound oligodeoxynucleotides.
    Jensen MA, Anderson KM, Davis RW. (2010). Nucleosides, nucleotides & nucleic acids. (2010) 29 (11):I867-78. PMID: 21128173. [PubMed]
  110. DMSO and Betaine Greatly Improve Amplification of GC-Rich Constructs in De Novo Synthesis.
    Jensen, MA, Fukushima, M, Davis RW. (2010). PLoS ONE 5(6): e11024. doi:10.1371/journal.pone.0011024. PMCID: 2883997. [Full Text]
  111. A molecular inversion probe assay for detecting alternative splicing.
    Lin, S., Wang, W., Palm, C,Davis, RW., Juneau, K.BMC Genomics 2010, 11:712, doi:10.1186/1471-2164-11-712. PMCID: 3022918. [PubMed]
  112. Semi-automated library preparation for high-throughput DNA sequencing platforms.
    Farias-Hesson E, Erikson J, Atkins A, Shen P, Davis RW, Scharfe C, Pourmand N. J Biomed Biotechnol. 2010;2010:617469. Epub 2010 Jun 8. PMCID: 2896710.. [PubMed]
  113. Multiplex Identification of Microbes.
    Hyman, RW., St.Onge, RP., Allen, EA., Miranda, M., Aparicio, AM., Fukushima, M. and Davis, RW. Applied and environmental biology, June 2010, p. 3904–3910 Vol. 76, No. 12, doi:10.1128/AEM.02785-09. PMCID: 2893500. [PubMed]
  114. A direct comparison of the KB Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry.
    Hyman, R.W., Jiang, H., Fukushima, M. and Davis, RW. BMC research notes. (2010) 3 257. PMCID: 3020662. [PubMed]
  115. Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation.
    Wadia, P.P., Coram, M., Armstrong, R.J., Mindrinos, M., Butte, A.J. and Miklos, D.B. Blood. (2010) 115 2077-87. PMCID:2837325. [PubMed]
  116. Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples.
    Smith, A.M., Heisler, L.E., St Onge, R.P., Farias-Hesson, E., Wallace, I.M., Bodeau, J., Harris, A.N., Perry, K.M., Giaever, G., Pourmand, N. and Nislow, C. Nucleic Acids Res. (2010) 38 (13):Ie142. PMCID: 2910071. [PubMed]
  117. Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships.
    Seok, J., Kaushal, A., Davis, R.W. and Xiao, W. BMC Bioinformatics. (2010) 11 Suppl 1 S8. PMCID: 3009543. [PubMed]
  118. Gene annotation and drug target discovery in Candida albicans with a tagged transposon mutant collection.
    Oh, J., Fung, E., Schlecht, U., Davis, R.W., Giaever, G., St Onge, R.P., Deutschbauer, A. and Nislow, C. PLoS pathogens. (2010) 6 (10):I. PMCID: 2951378. [PubMed]
  119. A universal TagModule collection for parallel genetic analysis of microorganisms.
    Oh, J., Fung, E., Price, M.N., Dehal, P.S., Davis, R.W., Giaever, G., Nislow, C., Arkin, A.P. and Deutschbauer, A. Nucleic acids research. (2010) 38 (14):Ie146. [PubMed]
  120. Sensitive giant magnetoresistive-based immunoassay for multiplex mycotoxin detection.
    Mak, A.C., Osterfeld, S.J., Yu, H., Wang, S.X., Davis, R.W., Jejelowo, O.A. and Pourmand, N. Biosens Bioelectron. (2010) 25 1635-9. [PubMed]
  121. Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action.
    Hillenmeyer, M.E., Ericson, E., Davis, R.W., Nislow, C., Koller, D. and Giaever, G. Genome Biol. (2010) 11 R30. [PubMed]
  122. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets.
    Wang, C., Sanders, C.M., Yang, Q., Schroeder, H.W., Jr., Wang, E., Babrzadeh, F., Gharizadeh, B., Myers, R.M., Hudson, J.R., Jr., Davis, R.W. and Han, J. Proc Natl Acad Sci U S A. (2010) 107 1518-23. PMCID:2824416. [PubMed]
  123. The genetic landscape of a cell.
    Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E.D., Sevier, C.S., Ding, H., Koh, J.L., Toufighi, K., Mostafavi, S., Prinz, J., St Onge, R.P., VanderSluis, B., Makhnevych, T., Vizeacoumar, F.J., Alizadeh, S., Bahr, S., Brost, R.L., Chen, Y., Cokol, M., Deshpande, R., Li, Z., Lin, Z.Y., Liang, W., Marback, M., Paw, J., San Luis, B.J., Shuteriqi, E., Tong, A.H., van Dyk, N., Wallace, I.M., Whitney, J.A., Weirauch, M.T., Zhong, G., Zhu, H., Houry, W.A., Brudno, M., Ragibizadeh, S., Papp, B., Pal, C., Roth, F.P., Giaever, G., Nislow, C., Troyanskaya, O.G., Bussey, H., Bader, G.D., Gingras, A.C., Morris, Q.D., Kim, P.M., Kaiser, C.A., Myers, C.L., Andrews, B.J. and Boone, C. Science. (2010) 327 425-31. [PubMed]
  124. Molecular inversion probes reveal patterns of 9p21 deletion and copy number aberrations in childhood leukemia.
    Schiffman JD, Wang Y, McPherson LA, Welch K, Zhang N, Davis R, Lacayo NJ, Dahl GV, Faham M, Ford JM, Ji HP. Cancer Genet Cytogenet. 2009 Aug;193(1):9-18. [PubMed]
  125. Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample.
    Qian, W.J., Liu, T., Petyuk, V.A., Gritsenko, M.A., Petritis, B.O., Polpitiya, A.D., Kaushal, A., Xiao, W., Finnerty, C.C., Jeschke, M.G., Jaitly, N., Monroe, M.E., Moore, R.J., Moldawer, L.L., Davis, R.W., Tompkins, R.G., Herndon, D.N., Camp, D.G. and Smith, R.D. J Proteome Res. (2009) 8 290-9. PMCID:2752204. [PubMed]
  126. Whole genome survey of coding SNPs reveals a reproducible pathway determinant of Parkinson disease.
    Srinivasan, B.S., Doostzadeh, J., Absalan, F., Mohandessi, S., Jalili, R., Bigdeli, S., Wang, J., Mahadevan, J., Lee, C.L., Davis, R.W., William Langston, J. and Ronaghi, M. Hum Mutat. (2009) 30 228-38. PMCID:2793088. [PubMed]
  127. Chemogenomic approaches to elucidation of gene function and genetic pathways.
    Pierce, S.E., Davis, R.W., Nislow, C. and Giaever, G. Methods Mol Biol. (2009) 548 115-43. [PubMed]
  128. Label-free biosensing with functionalized nanopipette probes.
    Umehara, S., Karhanek, M., Davis, R.W. and Pourmand, N. Proc Natl Acad Sci U S A. (2009) 106 4611-6. PMCID:2651834. [PubMed]
  129. Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device.
    Talasaz, A.H., Powell, A.A., Huber, D.E., Berbee, J.G., Roh, K.H., Yu, W., Xiao, W., Davis, M.M., Pease, R.F., Mindrinos, M.N., Jeffrey, S.S. and Davis, R.W. Proc Natl Acad Sci U S A. (2009) 106 3970-5. PMCID:2645911. [PubMed]
  130. High-throughput, high-accuracy array-based resequencing.
    Zheng, J., Moorhead, M., Weng, L., Siddiqui, F., Carlton, V.E., Ireland, J.S., Lee, L., Peterson, J., Wilkins, J., Lin, S., Kan, Z., Seshagiri, S., Davis, R.W. and Faham, M. Proc Natl Acad Sci U S A. (2009) 106 6712-7. PMCID:2672536. [PubMed]
  131. Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes.
    Norman, P.J., Abi-Rached, L., Gendzekhadze, K., Hammond, J.A., Moesta, A.K., Sharma, D., Graef, T., McQueen, K.L., Guethlein, L.A., Carrington, C.V., Chandanayingyong, D., Chang, Y.H., Crespi, C., Saruhan-Direskeneli, G., Hameed, K., Kamkamidze, G., Koram, K.A., Layrisse, Z., Matamoros, N., Mila, J., Park, M.H., Pitchappan, R.M., Ramdath, D.D., Shiau, M.Y., Stephens, H.A., Struik, S., Tyan, D., Verity, D.H., Vaughan, R.W., Davis, R.W., Fraser, P.A., Riley, E.M., Ronaghi, M. and Parham, P. Genome Res. (2009) 19 757-69. PMCID:2675964. [PubMed]
  132. Electrical detection of protein biomarkers using bioactivated microfluidic channels.
    Javanmard, M., Talasaz, A.H., Nemat-Gorgani, M., Pease, F., Ronaghi, M. and Davis, R.W. Lab Chip. (2009) 9 1429-34. PMCID:2778468. [PubMed]
  133. A genome-wide screen for regulators of TORC1 in response to amino acid starvation reveals a conserved Npr2/3 complex.
    Neklesa, T.K. and Davis, R.W. PLoS Genet. (2009) 5 e1000515. PMCID:2686269. [PubMed]
  134. Alternative splicing of PTC7 in Saccharomyces cerevisiae determines protein localization.
    Juneau, K., Nislow, C. and Davis, R.W. Genetics. (2009) 183 185-94. PMCID:2746143. [PubMed]
  135. A dynamic network of transcription in LPS-treated human subjects.
    Seok, J. Xiao, W. Moldawer, L. L. Davis, R. W. Covert, M. W. BMC Syst Biol. (2009) 3 78. PMCID:2729748. [PubMed]
  136. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging.
    Wheeler, H. E. Metter, E. J. Tanaka, T. Absher, D. Higgins, J. Zahn, J. M. Wilhelmy, J. Davis, R. W. Singleton, A. Myers, R. M. Ferrucci, L. Kim, S. K. [PubMed]
  137. Genome-wide transcriptome analysis of 150 cell samples.
    Irimia, D. Mindrinos, M. Russom, A., Xiao, W., Wilhelmy, J., Wang, S., Heath, J. D., Kurn, N., Tompkins, R. G., Davis, R. W., Toner, M. Integr Biol (Camb). (2009) 1 99-107. [PubMed]
  138. Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes.
    Scharfe, C., Horng-Shing Lu, H., Neuenburg, JK., Allen, EA., Li4, G-C., Klopstock, T., Cowan, TM., Enns, GM., Davis, RW. PLoS Comput Biol. (2009) 5 e1000374. PMCID:2668170. [Publisher Full Text]
  139. 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]
  140. 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]
  141. 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]
  142. 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]
  143. 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]
  144. 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]
  145. 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]
  146. Magnetic Bar Array with Linker Technology for Detection and Investigation of Non-magnetic Molecules.
    Lee, D.W. Roberts, L.A. Peroziello, E. Fontana, R. Maat, S. Boone, T. Nemat-Gorgani, M. Hoon, S. Huber, D. White, R.L. EEE Transactions on Magnetics, vol. 44, issue 11, pp. 4468-4471.DOI: 10.1109/TMAG.2008.2001517
  147. 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]
  148. Identification of Small Molecule Inhibitors of Pseudomonas aeruginosa Exoenzyme S Using a Yeast Phenotypic Screen.
    Arnoldo, A. Curak, J. Kittanakom, S. Chevelev, I. Lee, V. T. Sahebol-Amri, M. Koscik, B. Ljuma, L. Roy, P. J. Bedalov, A. Giaever, G. Nislow, C. Merrill, A. R. Lory, S. Stagljar, I. (2008). PLoS Genet 4(2): e1000005. [PubMed]
  149. 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]
  150. 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]
  151. 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]
  152. 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]
  153. 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]
  154. 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]
  155. 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]
  156. 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]
  157. 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]
  158. A system for multiplexed direct electrical detection of DNA synthesis.
    Anderson, E. P. Daniels, J. S. Yu, H. Karhanek, M. Lee, T. H. Davis, R. W. Pourmand, N. (2008). Sensors & Actuators: B. Chemical, 129(1):79. [PubMed]
  159. 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]
  160. Magnetic Bar Array with Linker Technology for Detection and Investigation of Non-magnetic Molecules.
    Lee, D.W. Roberts, L.A. Peroziello, E. Fontana, R. Maat, S. Boone, T. Nemat-Gorgani, M. Hoon, S. Huber, D. White, R.L (2008). I.E.E.E. Transactions on Magnetics, Vol. 44, No. 11, November 2008. [Publisher Full Text, PDF]
  161. 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]
  162. 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]
  163. 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.
  164. 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.
  165. 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).
  166. 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).
  167. Label-free impedance biosensors: Opportunities and challenges.
    Daniels, J. S. Pourmand, N. (2008). Electroanalysis 19(12):1239. [PubMed]
  168. Involvement of skeletal muscle gene regulatory network in susceptibility to wound infection following trauma.
    Apidianakis Y, Mindrinos MN, Xiao W, Tegos GP, Papisov MI, Hamblin MR, Davis RW, Tompkins RG, Rahme LG. PLoS ONE. 2007 Dec 26;2(12):e1356. [PubMed]
  169. 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]
  170. 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]
  171. The Role of NanoBiotechnology in the Detection of Infectious Diseases.
    Esfandyarpour, H., submitted to the Journal of Nanotechnology, Sep. 2007.
  172. A Novel Receptacle for Gene Sequencing.
    Esfandyarpour, H., Davis, R.W., NSTI-Nanotech 2007, Vol.3, pp. 422-425.
  173. 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.
  174. Gate-Controlled Microfluidic Chamber with magnetic bead for DNA Sequencing-by-synthesis Technology.
    Esfandyarpour, H. and Davis R.W., ICNMM2007, ref- 3119.
  175. 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.
  176. Nano-Biotechnology toward Diagnostic Industry: Obstacles and Opportunities.
    Esfandyarpour, H., ”NSTI-Nanotech 2007, Vol. 4, pp 421-423.
  177. 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]
  178. 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]
  179. 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]
  180. 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]
  181. 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]
  182. 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]
  183. 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]
  184. 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]
  185. 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]
  186. 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]
  187. 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]
  188. 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]
  189. 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].
  190. 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]
  191. Analysis of read length limiting factors in Pyrosequencing chemistry.
    Mashayekhi, F. Ronaghi, M. Anal Biochem 363(2):275-87 (2007). [PubMed], [Publisher Full Text]
  192. 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]
  193. 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]
  194. 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]
  195. Pyrosequencing for discovery and analysis of DNA sequence variations.
    Ronaghi, M., Shokralla, S., Gharizadeh, B. Pharmacogenomics 8(10):1437-41 (2007). [PubMed], [Full Text]
  196. 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]
  197. 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]
  198. 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]
  199. 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]
  200. 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]
  201. 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]
  202. 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]
  203. 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]
  204. Label-Free Impedance Biosensors: Opportunities and Challenges.
    Daniels, J. S. Pourmand, N. Electroanalysis 19(12):1239-1257 (2007). [PubMed], [Full Text]
  205. 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]
  206. Accelerating the discovery of biologically active small molecules using a high-throughput yeast halo assay.
    Gassner N.C., Tamble C.M., Bock J.E., Cotton N., White K.N., Tenney K., St Onge R.P., Proctor M.J., Giaever G., Nislow C., Davis R.W., Crews P., Holman T.R., Lokey R.S.
    J Nat Prod 70(3):383-90 (2007). [PubMed], [Publisher Full Text]
  207. Inhibition of amyloid fibrillation of lysozyme by indole derivatives--possible mechanism of action.
    Morshedi, D. Rezaei-Ghaleh, N. Ebrahim-Habibi, A. Ahmadian, S. Nemat-Gorgani, M. (2007). Febs J 274(24):6415-25. [PubMed]
  208. Effect of polyamines on the structure, thermal stability and 2,2,2-trifluoroethanol-induced aggregation of alpha-chymotrypsin.
    Rezaei-Ghaleh, N. Ebrahim-Habibi, A. Moosavi-Movahedi, A. A. Nemat-Gorgani, M. (2007). Int J Biol Macromol 41(5):597-604. [PubMed]
  209. Examining protein protein interactions using endogenously tagged yeast arrays: the cross-and-capture system.
    Suter B, Fetchko MJ, Imhof R, Graham CI, Stoffel-Studer I, Zbinden C, Raghavan M, Lopez L, Beneti L, Hort J, Fillingham J, Greenblatt JF, Giaever G, Nislow C, Stagljar I. Genome Res. 2007 Dec;17(12):1774-82. Epub 2007 Nov 7. [PubMed]
  210. Role of electrostatic interactions in 2,2,2-trifluoroethanol-induced structural changes and aggregation of alpha-chymotrypsin.
    Rezaei-Ghaleh, N. Ebrahim-Habibi, A. Moosavi-Movahedi, A. A. Nemat-Gorgani, M. (2007). Arch Biochem Biophys 457(2):160-9. [PubMed]
  211. Thermostabilization of Bacillus amyloliquefaciens alpha-amylase by chemical cross-linking.
    Habibi, A. E. Khajeh, K. Naderi-Manesh, H. Ranjbar, B. Nemat-Gorgani, M. (2006). J Biotechnol 123(4):434-42. [PubMed]
  212. Shot Noise Models for Sequential Processes and the Role of Lateral Mixing.
    Neureuther, A, Pease, R.F.W., Pope, W., Parizi, K.B., Esfandyarpour, H., Liddle A., Anderson, E., et al., J. Vac Sci. and Technol. B, 24 (4), pp. 1902-1908 (2006).
  213. Chemical genomic profiling for identifying intracellular targets of toxicants producing Parkinson's disease.
    Doostzadeh J, Davis RW, Giaever GN, Nislow C, Langston JW. Toxicol Sci. 2007 Jan;95(1):182-7. Epub 2006 Oct 16. [PubMed]
  214. Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions.
    St.Onge, R.P., Mani, R., Oh, J., Proctor, M, Fung, E., Davis, R.W., Nislow, C., Roth, F.P., Giaever, G. Nat Genet 39(2): 199-206 (2007) (Subject of Highlight in Nat Rev Genet 8: 87 (2007). [PubMed Abstract], [Publisher Full Text]
  215. Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae strain YJM789.
    Wu Wei, John H. McCusker, Richard W. Hyman, Ted Jones, Ye Ning, Zhiwei Cao, Zhenglong Gu, Dan Bruno, Molly Miranda, Michelle Nguyen, Julie Wilhelmy, Caridad Komp, Raquel Tamse, Xiaojing Wang, Peilin Jia, Philippe Luedi, Peter J. Oefner, Lior David, Fred S. Dietrich, Yixue Li, Ronald W. Davis, and Lars M. Steinmetz. Proc. Natl. Acad. Sci. U.S.A. 104: 12,825-12,830. 2007. [PubMed]
  216. Uncoupling protein 3 expression and intramyocellular lipid accumulation by NMR following local burn trauma.
    Zhang Q, Cao H, Astrakas LG, Mintzopoulos D, Mindrinos MN, Schulz J 3rd, Tompkins RG, Rahme LG, Tzika AA. Int J Mol Med. 2006 Dec;18(6):1223-9. [PubMed]
  217. Rapid and highly informative diagnostic assay for H5N1 influenza viruses.
    Pourmand N., Diamond L., Garten R., Erickson J.P., Kumm J., Donis R.O., Davis R.W. PLoS ONE. 2006 Dec 20;1:e95. [Publisher Full Text]
  218. Interaction of native and apo-carbonic anhydrase with hydrophobic adsorbents: A comparative structure-function study.
    Salemi, Z. Hosseinkhani, S. Ranjbar, B. Nemat-Gorgani, M. (2006). J Biochem Mol Biol 39(5):636-41. [PubMed]
  219. Prediction of protein orientation upon immobilization on biological and nonbiological surfaces.
    Talasaz, A. H. Nemat-Gorgani, M. Liu, Y. Stahl, P. Dutton, R. W. Ronaghi, M. Davis, R. W. (2006). Proc Natl Acad Sci U S A 103(40):14773-8. [PubMed]
  220. Pyrosequencing of the DNA gyrase gene in Neisseria species: effective indicator of ciprofloxacin resistance in Neisseria gonorrhoeae.
    Lindbäck E, Unemo M, Akhras M, Gharizadeh B, Fredlund H, Pourmand N, Wretlind B. APMIS. 2006 Dec;114(12):837-41. [PubMed]
  221. Commonality and differences in leukocyte gene expression patterns among three models of inflammation and injury.
    Brownstein BH, Logvinenko T, Lederer JA, Cobb JP, Hubbard WJ, Chaudry IH, Remick DG, Baker HV, Xiao W, Mannick JA. Physiol Genomics. 2006 Feb 14;24(3):298-309. Epub 2005 Dec 20. [PubMed]
  222. PathogenMIPer: A tool for the design of molecular inversion probes to detect multiple pathogens.
    Thiyagarajan S, Karhanek M, Akhras M, Davis RW, Pourmand N. BMC Bioinformatics. 2006 Nov 14;7(1):500 [Epub ahead of print] [PubMed]
  223. Current Rectification with Poly-l-Lysine-Coated Quartz Nanopipettes.
    Umehara S, Pourmand N, Webb CD, Davis RW, Yasuda K, Karhanek M. Nano Lett. 2006 Nov 8;6(11):2486-2492. [PubMed]
  224. Linking Hydrophilic Macromolecules to Monodisperse Magnetite (Fe3O4) Nanoparticles via Trichloro-s-triazine.
    Jin Xie, Chenjie Xu, Zhichuan Xu, Yanglong Hou, Kaylie L. Young, S. X. Wang, N. Pourmand, and Shouheng Sun. Chem. Mater., 18 (23), 5401 -5403, 2006. [Publisher Full Text]
  225. Cell-specific expression and pathway analyses reveal alterations in trauma-related human T cell and monocyte pathways.
    Laudanski K, Miller-Graziano C, Xiao W, Mindrinos MN, Richards DR, De A, Moldawer LL, Maier RV, Bankey P, Baker HV, Brownstein BH, Cobb JP, Calvano SE, Davis RW, Tompkins RG. Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15564-9. Epub 2006 Oct 10. [PubMed], [Publisher Full Text]
  226. Large-scale pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing.
    Gharizadeh, B., Herman Z.S., Eason R.G., Jejelowo, O., Pourmand, N. Electrophoresis. 2006 Aug;27(15):3042-7. [PubMed]
  227. Spin valve sensors for ultra sensitive detection of super paramagnetic nanoparticles for biological applications.
    Guanxiong Li, Shouheng Sun, Robert J. Wilson, Robert L. White, Nader Pourmand, Shan X. Wang. Sensors and Actuators A 126 (2006)98-106. [PubMed]
  228. One-Pot Synthesis of Mono-disperse Iron Oxide Nanoparticles for Potential Biomedical Applications.
    Jin Xie, Sheng Peng, Nathan Brower, Nader Pourmand, Shan X. Wang, Shouheng Sun. Pure Appl. Chem. Vol 78, No. 5 1003-1014, 2006
  229. Introns regulate RNA and protein abundance in yeast.
    Juneau K, Miranda M, Hillenmeyer ME, Nislow C, Davis RW. Genetics. 2006 Sep;174(1):511-8. Epub 2006 Jul 2. [PubMed]
  230. Local and distant burn injury alter immuno-inflammatory gene expression in skeletal muscle.
    Padfield, KE., Zhang, Q., Gopalan, S., Tzika, AA., Mindrinos, MN., Tompkins, RG., Rahme, LG. J Trauma. 2006 Aug;61(2):280-92. [PubMed]
  231. Analysis of hybridization on the molecular barcode GeneChip microarray.
    Walton, SP., Mindrinos MN., Davis RW. Biochem Biophys Res Commun. 2006 Sep 22;348(2):689-96. Epub 2006 Jul 28. [PubMed], [Publisher Full Text]
  232. Microfluidic isolation of leukocytes from whole blood for phenotype and gene expression analysis.
    Sethu, P., Moldawer, LL., Mindrinos, MN., Scumpia, PO., Tannahill, CL., Wilhelmy, J., Efron, PA., Brownstein, BH., Tompkins, RG., Toner, M. Anal Chem. 2006 Aug 1;78(15):5453-61. [PubMed], [Publisher Full Text]
  233. Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma.
    Ji, H., Kumm, J., Zhang, M., Farnam, K., Salari, K., Faham, M., Ford, J.M., Davis, R.W. Cancer Res. 2006 Aug 15;66(16):7910-9. [PubMed], [Publisher Full Text]
  234. Large-scale pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing.
    Gharizadeh, B., Herman Z.S., Eason R.G., Jejelowo, O., Pourmand, N. Electrophoresis. 2006 Aug;27(15):3042-7. [PubMed]
  235. A unique and universal molecular barcode array.
    Pierce, SE, Fung, EL, Jaramillo, DF, Chu AM, Davis, RW, Nislow, C., Giaever, G. Nat Methods, 2006 Aug;3(8):601-3. [PubMed]
  236. The role of selection in the evolution of human mitochondrial genomes.
    Kivisild, T., Shen, P., Wall, D.P., Do, B., Sung, R., Davis, K., Passarino, G., Underhill, P.A., Scharfe, C., Torroni, A., Scozzari, R., Modiano, D., Coppa, A., de Knijff, P., Feldman, M., Cavalli-Sforza, L.L. & Oefner, P.J. Genetics 172, 373-87 (2006). [PubMed], [Publisher Full Text]
  237. Proteome analysis of mitochondrial outer membrane from Neurospora crassa.
    Schmitt, S., Prokisch, H., Schlunck, T., Camp, D.G., Ahting, U., Waizenegger, T., Scharfe, C., Meitinger, T., Imhof, A., Neupert, W., Oefner, P.J. & Rapaport, D. Proteomics 6(1), 72-80 (2006). [PubMed]
  238. MitoP2: the mitochondrial proteome database--now including mouse data.
    Prokisch, H., Andreoli, C., Ahting, U., Heiss, K., Ruepp, A., Scharfe, C. & Meitinger, T. Nucleic Acids Res 34, D705-11 (2006). [PubMed], [Publisher Full Text]
  239. A haplotype framework for cystic fibrosis mutations in Iran.
    Elahi, E., Khodadad, A., Kupershmidt, I., Ghasemi, F., Alinasab, B., Naghizadeh, R., Eason, R.G., Amini, M., Esmaili, M., Esmaeili Dooki, M.R., Sanati, M.H., Davis, R.W., Ronaghi, M. & Thorstenson, Y.R. J Mol Diagn 8, 119-27 (2006). [PubMed]
  240. A high-resolution map of transcription in the yeast genome.
    David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C.J., Bofkin, L., Jones, T., Davis, R.W. & Steinmetz, L.M. Proc Natl Acad Sci U S A 103, 5320-5 (2006). [PubMed], [Publisher Full Text]
  241. High dynamic range characterization of the trauma patient plasma proteome.
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  409. The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective.
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  411. The core meiotic transcriptome in budding yeasts.
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  412. DAtA: database of Arabidopsis thaliana annotation.
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  414. Polymorphism in the pertussis toxin promoter region affecting the DNA-based diagnosis of Bordetella infection.
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  415. Direct analysis of single-nucleotide polymorphism on double-stranded DNA by pyrosequencing.
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  416. Method enabling pyrosequencing on double-stranded DNA.
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  417. Mutation detection by pyrosequencing: sequencing of exons 5-8 of the p53 tumor suppressor gene.
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  418. Real-time PCR-based method for assaying the purity of bacterial artificial chromosome preparations.
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  419. A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis.
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  420. Analysis of the p53 tumor suppressor gene by pyrosequencing.
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  421. Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays.
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  422. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.
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  423. Whole genome genetic-typing in yeast using high-density oligonucleotide arrays.
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  424. Global sequence diversity of BRCA2: analysis of 71 breast cancer families and 95 control individuals of worldwide populations.
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  425. Denaturing high-performance liquid chromatography detects reliably BRCA1 and BRCA2 mutations.
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  426. Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae.
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  427. Y-Chromosome evidence for a northward migration of modern humans into Eastern Asia during the last Ice Age.
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  428. Analyses of secondary structures in DNA by pyrosequencing.
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  429. An arrayable flow-through microcentrifuge for high-throughput instrumentation.
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  430. An automated sample preparation system for large-scale DNA sequencing.
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  431. Production, purification, and luminometric analysis of recombinant Saccharomyces cerevisiae MET3 adenosine triphosphate sulfurylase expressed in Escherichia coli.
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  432. 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].
  433. 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].
  434. 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].
  435. 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].
  436. 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].
  437. 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].
  438. 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].
  439. 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].
  440. 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].
  441. Toxic mutations in the recA gene of E. coli prevent proper chromosome segregation.
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  442. On the in vivo function of the RecA ATPase.
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  443. 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].
  444. 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
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  446. 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].
  447. A sequencing method based on real-time pyrophosphate.
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  448. PCR-introduced loop structure as primer in DNA sequencing.
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  449. Phylogeny of the family Moraxellaceae by 16S rDNA sequence analysis, with special emphasis on differentiation of Moraxella species.
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  450. Blind analysis of denaturing high-performance liquid chromatography as a tool for mutation detection.
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  451. Bioluminometric method for real-time detection of reverse transcriptase activity.
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  452. 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].
  453. Modeling and analysis of competitive RT-PCR.
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  454. Parallel analysis of genetic selections using whole genome oligonucleotide arrays.
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  455. A genome-wide transcriptional analysis of the mitotic cell cycle.
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  456. Mapping cloned sequences on YACs.
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  457. Hepatitis G virus infection in hemodialysis patients and the effects of interferon treatment.
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  458. Capillary electrophoresis measurement of metabolites in glycolysis.
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  459. Quantification of alternatively spliced RUSH mRNA isoforms by QRT-PCR and IP-RP-HPLC analysis: a new approach to measuring regulated splicing efficiency.
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  460. A crtB Homolog Essential for Photochromogenicity in Mycobacterium marinum: Isolation, Characterization, and Gene Disruption via Homologous Recombination.
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  461. Detection of single-base changes using a bioluminometric primer extension assay.
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  462. Automation for the Arabidopsis genome sequencing project.
    Marziali, A., Federspiel, N., and Davis, R.W., (1997). Trends in Plant Science, 2:71-74.
  463. Denaturing HPLC-identified novel FBN1 mutations, polymorphisms, and sequence variants in Marfan syndrome and related connective tissue disorders.
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  464. Ca(2+)-activated anion channels and membrane depolarizations induced by blue light and cold in Arabidopsis seedlings.
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  465. Whole genome analysis: experimental access to all genome sequenced segments through larger-scale efficient oligonucleotide synthesis and PCR.
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  466. Yeast microarrays for genome wide parallel genetic and gene expression analysis.
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  467. The nucleotide sequence of chromosome IV.
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  468. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays.
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  469. A pre-Columbian Y chromosome-specific transition and its implications for human evolutionary history.
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  470. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy.
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  471. Analysis of glycolysis metabolites by capillary zone electrophoresis with indirect UV detection.
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  472. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.
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    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].

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.

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.


  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.


  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].

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)