Ronald Davis

Honors and Awards

• Recipient of, Dickson Prize in Medicine, University of Pittsburgh (2005-2004)
• Lifetime Achievement Award, Genetics Society of America (2004)
• Herbert A. Sober Award, ASBMB/IUBMB (2004)
• Senior Scholar Award in Global Infectious Disease, Ellison Medical Foundation (2002)
• Genetics Society of America Award, Genetics Society of America (1998)
• Biotechnology Research Award, Chiron Corporation (1998)
• Louis S. Rosentiel Award for, Distinguished Work in Basic Medical Research (1992)
• Distinguished Alumni Award, Eastern Illinois University (1984)
• Elected to the, National Academy of Sciences-Genetics (1983)
• Recipient of, United States Steel Award (1981)
• Chaired, Nucleic Acid Gordon Conference (1980)
• Award in Microbiology and Immunology, Eli Lilly and Co. (1976)
• Young Faculty Research Award, Society of the Sigma Xi (1976)
• Teacher-Scholar Grant, Dreyfus (1976)
• EMBO, European Lectureship (1976)

Postdoctoral Advisees

• Patrick Flaherty, Hong Gao, Maureen Hillenmeyer, Andy Mak, Janine Mok, Nader Nouri Zad, Ulrich Schlecht, Vincent Tabard Cossa, Wenyi Wang, Jacob Zahn, Yuping Zhang

Web Site Links

• Genome Technology Center

Industry Relationships

Stanford is committed to ethical and transparent interactions with our industry partners. It is our policy to disclose payments of $5,000 or more, equity valued at $5,000 or more in a publicly traded company, or any equity in a privately held company, to physicians and scientists employed by Stanford University from companies or other commercial entities with which they interact as part of their professional activities. 

• Consulting: Affymetrix, CellPoint
• Equity: Affymetrix, CellPoint

Research Interests

We are using Saccharomyces cerevisiae and Human to conduct whole genome analysis projects. The yeast genome sequence has approximately 6,000 genes. We have made a set of haploid and diploid strains (21,000) containing a complete deletion of each gene. In order to facilitate whole genome analysis each deletion is molecularly tagged with a unique 20-mer DNA sequence. This sequence acts as a molecular bar code and makes it easy to identify the presence of each deletion. The mixture of all such tag strains then allows for the analysis of the entire genome with the manipulation of a single culture. During growth under a variety of conditions the loss of a tag indicates the loss of a deletion from the population. The concentration of each tag is determined by PCR amplification of the tags and hybridization to an Affymetrix DNA chip that contains the complement to all of the DNA sequence tags. This approach is being applied to other microorganisms.

We have identified a number of wild isolates of yeast that grow at much higher temperatures than is typical for Saccharomyces cerevisiae and are pathogenic and can kill a mouse. Microarrays have been used to map complex genetic traits such as virulence traits in pathogenic Saccharomyces cerevisiae using hybridization to detect single nucleotide polymorphisms. We have developed a new technology termed Recipical Hemizygosity Scanning that allows the determination of the contribution to the phenotype of all pair wise alleles for the whole genome from 2 independent strains. Using this technology we can map and quantitate all of the alleles in the genome for any complex quantitative trait in a single tube assay. These technologies will allow us to explore allelic contributions in complex mixed culture real environments and to investigate ecology at the genome level.

We are conducting a whole genome analysis (transcriptome and proteome) from blood of Human trauma patients. In this large clinical study we are establishing the standards for clinical genomics. We have developed 2 new technologies, "Molecular Inversion Probes" (MIP) for massive multiplex analysis of SNP and DNA content in Human and, "Mismatch Repair Detection" for discovery of rare Human polymorphisms. Both technologies are being applied to numerous clinical investigations.

Publications

• Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. Wheeler HE,  Metter EJ, Tanaka T, Absher D, Higgins J, Zahn JM, Wilhelmy J, Davis RW, Singleton A, Myers RM, Ferrucci L, Kim SK.  PLoS Genet.  2009; 5 (10): e1000685
• A genome-wide screen for regulators of TORC1 in response to amino acid starvation reveals a conserved Npr2/3 complex. Neklesa TK,  Davis RW.  PLoS Genet.  2009; 5 (6): e1000515
• Whole genome survey of coding SNPs reveals a reproducible pathway determinant of Parkinson disease. Srinivasan BS,  Doostzadeh J, Absalan F, Mohandessi S, Jalili R, Bigdeli S, Wang J, Mahadevan J, Lee CL, Davis RW, William Langston J, Ronaghi M.  Hum Mutat.  2009; 30 (2): 228-38
• Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample. Qian WJ,  Liu T, Petyuk VA, Gritsenko MA, Petritis BO, Polpitiya AD, Kaushal A, Xiao W, Finnerty CC, Jeschke MG, Jaitly N, Monroe ME, Moore RJ, Moldawer LL, Davis RW, Tompkins RG, Herndon DN, Camp DG, Smith RD.  J Proteome Res.  2009; 8 (1): 290-9
• Alternative splicing of PTC7 in Saccharomyces cerevisiae determines protein localization. Juneau K,  Nislow C, Davis RW.  Genetics.  2009; 183 (1): 185-94
• Mapping gene associations in human mitochondria using clinical disease phenotypes. Scharfe C,  Lu HH, Neuenburg JK, Allen EA, Li GC, Klopstock T, Cowan TM, Enns GM, Davis RW.  PLoS Comput Biol.  2009; 5 (4): e1000374
• Meiotic recombination generates rich diversity in NK cell receptor genes, alleles, and haplotypes. Norman PJ,  Abi-Rached L, Gendzekhadze K, Hammond JA, Moesta AK, Sharma D, Graef T, McQueen KL, Guethlein LA, Carrington CV, Chandanayingyong D, Chang YH, Crespí C, Saruhan-Direskeneli G, Hameed K, Kamkamidze G, Koram KA, Layrisse Z, Matamoros N, Milà J, Park MH, Pitchappan RM, Ramdath DD, Shiau MY, Stephens HA, Struik S, Tyan D, Verity DH, Vaughan RW, Davis RW, Fraser PA, Riley EM, Ronaghi M, Parham P.  Genome Res.  2009; 19 (5): 757-69
• Electrical detection of protein biomarkers using bioactivated microfluidic channels. Javanmard M,  Talasaz AH, Nemat-Gorgani M, Pease F, Ronaghi M, Davis RW.  Lab Chip.  2009; 9 (10): 1429-34
• Conformational flexibility of a model protein upon immobilization on self-assembled monolayers. Bigdeli S,  Talasaz AH, Ståhl P, Persson HH, Ronaghi M, Davis RW, Nemat-Gorgani M.  Biotechnol Bioeng.  2008; 100 (1): 19-27
• 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.  2008; 32 (2): 190-7
• Multiplexed proximity ligation assays to profile putative plasma biomarkers relevant to pancreatic and ovarian cancer. Fredriksson S,  Horecka J, Brustugun OT, Schlingemann J, Koong AC, Tibshirani R, Davis RW.  Clin Chem.  2008; 54 (3): 582-9
• High-throughput creation of a whole-genome collection of yeast knockout strains. Chu AM,  Davis RW.  Methods Mol Biol.  2008; 416 205-20
• The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Hillenmeyer ME,  Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, St Onge RP, Tyers M, Koller D, Altman RB, Davis RW, Nislow C, Giaever G.  Science.  2008; 320 (5874): 362-5
• 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; 105 (27): 9296-301
• Pervasive and persistent redundancy among duplicated genes in yeast. Dean EJ,  Davis JC, Davis RW, Petrov DA.  PLoS Genet.  2008; 4 (7): e1000113
• An integrated platform of genomic assays reveals small-molecule bioactivities. Hoon S,  Smith AM, Wallace IM, Suresh S, Miranda M, Fung E, Proctor M, Shokat KM, Zhang C, Davis RW, Giaever G, St Onge RP, StOnge RP, Nislow C.  Nat Chem Biol.  2008; 4 (8): 498-506
• Superoxide anions regulate TORC1 and its ability to bind Fpr1:rapamycin complex. Neklesa TK,  Davis RW.  Proc Natl Acad Sci U S A.  2008; 105 (39): 15166-71
• A System for Multiplexed Direct Electrical Detection of DNA Synthesis. Anderson EP,  Daniels JS, Yu H, Karhanek M, Lee TH, Davis RW, Pourmand N.  Sens Actuators B Chem.  2008; 129 (1): 79-86
• High-resolution, in vivo magnetic resonance imaging of Drosophila at 18.8 Tesla. Null B,  Liu CW, Hedehus M, Conolly S, Davis RW.  PLoS One.  2008; 3 (7): e2817
• 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 WF, Davis RW, Ji H.  Proc Natl Acad Sci U S A.  2007; 104 (22): 9387-92
• A novel catechol-based universal support for oligonucleotide synthesis. Anderson KM,  Jaquinod L, Jensen MA, Ngo N, Davis RW.  J Org Chem.  2007; 72 (26): 9875-80
• Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Pierce SE,  Davis RW, Nislow C, Giaever G.  Nat Protoc.  2007; 2 (11): 2958-74
• Connector inversion probe technology: a powerful one-primer multiplex DNA amplification system for numerous scientific applications. Akhras MS,  Unemo M, Thiyagarajan S, Nyrén P, Davis RW, Fire AZ, Pourmand N.  PLoS One.  2007; 2 (9): e915
• Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. McClellan AJ,  Xia Y, Deutschbauer AM, Davis RW, Gerstein M, Frydman J.  Cell.  2007; 131 (1): 121-35
• A high-resolution atlas of nucleosome occupancy in yeast. Lee W,  Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C.  Nat Genet.  2007; 39 (10): 1235-44
• Unusual selection on the KIR3DL1/S1 natural killer cell receptor in Africans. Norman PJ,  Abi-Rached L, Gendzekhadze K, Korbel D, Gleimer M, Rowley D, Bruno D, Carrington CV, Chandanayingyong D, Chang YH, Crespí C, Saruhan-Direskeneli G, Fraser PA, Hameed K, Kamkamidze G, Koram KA, Layrisse Z, Matamoros N, Milà J, Park MH, Pitchappan RM, Ramdath DD, Shiau MY, Stephens HA, Struik S, Verity DH, Vaughan RW, Tyan D, Davis RW, Riley EM, Ronaghi M, Parham P.  Nat Genet.  2007; 39 (9): 1092-9
• 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; 4 (4): 327-9
• 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 SX, Davis RW.  Proc Natl Acad Sci U S A.  2007; 104 (15): 6146-51
• PathogenMip assay: a multiplex pathogen detection assay. Akhras MS,  Thiyagarajan S, Villablanca AC, Davis RW, Nyrén P, Pourmand N.  PLoS One.  2007; 2 (2): e223
• Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector. Fredriksson S,  Banér J, Dahl F, Chu A, Ji H, Welch K, Davis RW.  Nucleic Acids Res.  2007; 35 (7): e47
• Accelerating the discovery of biologically active small molecules using a high-throughput yeast halo assay. Gassner NC,  Tamble CM, Bock JE, Cotton N, White KN, Tenney K, St Onge RP, Proctor MJ, Giaever G, Nislow C, Davis RW, Crews P, Holman TR, Lokey RS.  J Nat Prod.  2007; 70 (3): 383-90
• High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Juneau K,  Palm C, Miranda M, Davis RW.  Proc Natl Acad Sci U S A.  2007; 104 (5): 1522-7
• Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. St Onge RP,  Mani R, Oh J, Proctor M, Fung E, Davis RW, Nislow C, Roth FP, Giaever G.  Nat Genet.  2007; 39 (2): 199-206
• Prediction of protein orientation upon immobilization on biological and nonbiological surfaces. Talasaz AH,  Nemat-Gorgani M, Liu Y, Ståhl P, Dutton RW, Ronaghi M, Davis RW.  Proc Natl Acad Sci U S A.  2006; 103 (40): 14773-8
• 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; 7 500
• Cell trapping in activated micropores for functional analysis. Talasaz AH,  Powell AA, Stahl P, Ronaghi M, Jeffrey SS, Mindrinos M, Davis RW.  Conf Proc IEEE Eng Med Biol Soc.  2006; 1 1838-41
• Modeling of the bioactivated nanopore devices. Talasaz AH,  Liu Y, Ronaghi M, Davis RW.  Conf Proc IEEE Eng Med Biol Soc.  2006; 1 1830-3
• Rapid and highly informative diagnostic assay for H5N1 influenza viruses. Pourmand N,  Diamond L, Garten R, Erickson JP, Kumm J, Donis RO, Davis RW.  PLoS One.  2006; 1 e95
• Introns regulate RNA and protein abundance in yeast. Juneau K,  Miranda M, Hillenmeyer ME, Nislow C, Davis RW.  Genetics.  2006; 174 (1): 511-8
• Direct electrical detection of DNA synthesis. Pourmand N,  Karhanek M, Persson HH, Webb CD, Lee TH, Zahradníková A, Davis RW.  Proc Natl Acad Sci U S A.  2006; 103 (17): 6466-70
• A high-resolution map of transcription in the yeast genome. David L,  Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM.  Proc Natl Acad Sci U S A.  2006; 103 (14): 5320-5
• A haplotype framework for cystic fibrosis mutations in Iran. Elahi E,  Khodadad A, Kupershmidt I, Ghasemi F, Alinasab B, Naghizadeh R, Eason RG, Amini M, Esmaili M, Esmaeili Dooki MR, Sanati MH, Davis RW, Ronaghi M, Thorstenson YR.  J Mol Diagn.  2006; 8 (1): 119-27
• Current rectification with poly-l-lysine-coated quartz nanopipettes. Umehara S,  Pourmand N, Webb CD, Davis RW, Yasuda K, Karhanek M.  Nano Lett.  2006; 6 (11): 2486-92
• A unique and universal molecular barcode array. Pierce SE,  Fung EL, Jaramillo DF, Chu AM, Davis RW, Nislow C, Giaever G.  Nat Methods.  2006; 3 (8): 601-3
• 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 JM, Davis RW.  Cancer Res.  2006; 66 (16): 7910-9
• Transcriptional profiling of aging in human muscle reveals a common aging signature. Zahn JM,  Sonu R, Vogel H, Crane E, Mazan-Mamczarz K, Rabkin R, Davis RW, Becker KG, Owen AB, Kim SK.  PLoS Genet.  2006; 2 (7): e115
• Data quality in genomics and microarrays. Ji H,  Davis RW.  Nat Biotechnol.  2006; 24 (9): 1112-3
• Analysis of hybridization on the molecular barcode GeneChip microarray. Walton SP,  Mindrinos MN, Davis RW.  Biochem Biophys Res Commun.  2006; 348 (2): 689-96
• Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Deutschbauer AM,  Jaramillo DF, Proctor M, Kumm J, Hillenmeyer ME, Davis RW, Nislow C, Giaever G.  Genetics.  2005; 169 (4): 1915-25
• Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach. Qian WJ,  Monroe ME, Liu T, Jacobs JM, Anderson GA, Shen Y, Moore RJ, Anderson DJ, Zhang R, Calvano SE, Lowry SF, Xiao W, Moldawer LL, Davis RW, Tompkins RG, Camp DG, Smith RD.  Mol Cell Proteomics.  2005; 4 (5): 700-9
• Multiplexed variation scanning for 1,000 amplicons in hundreds of patients using mismatch repair detection (MRD) on tag arrays. Faham M,  Zheng J, Moorhead M, Fakhrai-Rad H, Namsaraev E, Wong K, Wang Z, Chow SG, Lee L, Suyenaga K, Reichert J, Boudreau A, Eberle J, Bruckner C, Jain M, Karlin-Neumann G, Jones HB, Willis TD, Buxbaum JD, Davis RW.  Proc Natl Acad Sci U S A.  2005; 102 (41): 14717-22
• Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. Lee W,  St Onge RP, Proctor M, Flaherty P, Jordan MI, Arkin AP, Davis RW, Nislow C, Giaever G.  PLoS Genet.  2005; 1 (2): e24
• Single DNA molecule detection using nanopipettes and nanoparticles. Karhanek M,  Kemp JT, Pourmand N, Davis RW, Webb CD.  Nano Lett.  2005; 5 (2): 403-7
• A novel method for STR-based DNA profiling using microarrays. Kemp JT,  Davis RW, White RL, Wang SX, Webb CD.  J Forensic Sci.  2005; 50 (5): 1109-13
• Microbes on the human vaginal epithelium. Hyman RW,  Fukushima M, Diamond L, Kumm J, Giudice LC, Davis RW.  Proc Natl Acad Sci U S A.  2005; 102 (22): 7952-7
• Bioluminescence regenerative cycle (BRC) system: theoretical considerations for nucleic acid quantification assays. Hassibi A,  Contag C, Vlad MO, Hafezi M, Lee TH, Davis RW, Pourmand N.  Biophys Chem.  2005; 116 (3): 175-85
• Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae. Gu Z,  David L, Petrov D, Jones T, Davis RW, Steinmetz LM.  Proc Natl Acad Sci U S A.  2005; 102 (4): 1092-7
• Quantitative trait loci mapped to single-nucleotide resolution in yeast. Deutschbauer AM,  Davis RW.  Nat Genet.  2005; 37 (12): 1333-40
• Characterization of synthetic DNA bar codes in Saccharomyces cerevisiae gene-deletion strains. Eason RG,  Pourmand N, Tongprasit W, Herman ZS, Anthony K, Jejelowo O, Davis RW, Stolc V.  Proc Natl Acad Sci U S A.  2004; 101 (30): 11046-51
• The diploid genome sequence of Candida albicans. Jones T,  Federspiel NA, Chibana H, Dungan J, Kalman S, Magee BB, Newport G, Thorstenson YR, Agabian N, Magee PT, Davis RW, Scherer S.  Proc Natl Acad Sci U S A.  2004; 101 (19): 7329-34
• A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo. Wang QT,  Piotrowska K, Ciemerych MA, Milenkovic L, Scott MP, Davis RW, Zernicka-Goetz M.  Dev Cell.  2004; 6 (1): 133-44
• Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Giaever G,  Flaherty P, Kumm J, Proctor M, Nislow C, Jaramillo DF, Chu AM, Jordan MI, Arkin AP, Davis RW.  Proc Natl Acad Sci U S A.  2004; 101 (3): 793-8
• A multi-enzyme model for Pyrosequencing. Agah A,  Aghajan M, Mashayekhi F, Amini S, Davis RW, Plummer JD, Ronaghi M, Griffin PB.  Nucleic Acids Res.  2004; 32 (21): e166
• A transcriptional profile of aging in the human kidney. Rodwell GE,  Sonu R, Zahn JM, Lund J, Wilhelmy J, Wang L, Xiao W, Mindrinos M, Crane E, Segal E, Myers BD, Brooks JD, Davis RW, Higgins J, Owen AB, Kim SK.  PLoS Biol.  2004; 2 (12): e427
• Multiplexed genotyping with sequence-tagged molecular inversion probes. Hardenbol P,  Banér J, Jain M, Nilsson M, Namsaraev EA, Karlin-Neumann GA, Fakhrai-Rad H, Ronaghi M, Willis TD, Landegren U, Davis RW.  Nat Biotechnol.  2003; 21 (6): 673-8
• Contributions of ATM mutations to familial breast and ovarian cancer. Thorstenson YR,  Roxas A, Kroiss R, Jenkins MA, Yu KM, Bachrich T, Muhr D, Wayne TL, Chu G, Davis RW, Wagner TM, Oefner PJ.  Cancer Res.  2003; 63 (12): 3325-33
• Genotyping African haplotypes in ATM using a co-spotted single-base extension assay. Jain M,  Thorstenson YR, Faulkner DM, Pourmand N, Jones T, Au M, Oefner PJ, White KP, Davis RW.  Hum Mutat.  2003; 22 (3): 214-21
• Determination of hepatitis C virus genotype by Pyrosequencing. Elahi E,  Pourmand N, Chaung R, Rofoogaran A, Boisver J, Samimi-Rad K, Davis RW, Ronaghi M.  J Virol Methods.  2003; 109 (2): 171-6
• Functional profiling of the Saccharomyces cerevisiae genome. Giaever G,  Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Güldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kötter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M.  Nature.  2002; 418 (6896): 387-91
• Systematic screen for human disease genes in yeast. Steinmetz LM,  Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, Jones T, Chu AM, Giaever G, Prokisch H, Oefner PJ, Davis RW.  Nat Genet.  2002; 31 (4): 400-4
• Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Birrell GW,  Brown JA, Wu HI, Giaever G, Chu AM, Davis RW, Brown JM.  Proc Natl Acad Sci U S A.  2002; 99 (13): 8778-83
• Gene expression during the life cycle of Drosophila melanogaster. Arbeitman MN,  Furlong EE, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP.  Science.  2002; 297 (5590): 2270-5
• Sequence of Plasmodium falciparum chromosome 12. Hyman RW,  Fung E, Conway A, Kurdi O, Mao J, Miranda M, Nakao B, Rowley D, Tamaki T, Wang F, Davis RW.  Nature.  2002; 419 (6906): 534-7
• Yeast tRNA as carrier in the isolation of microscale RNA for global amplification and expression profiling. Wang QT,  Xiao W, Mindrinos M, Davis RW.  Biotechniques.  2002; 33 (4): 788, 790, 792 passim
• Parallel phenotypic analysis of sporulation and postgermination growth in Saccharomyces cerevisiae. Deutschbauer AM,  Williams RM, Chu AM, Davis RW.  Proc Natl Acad Sci U S A.  2002; 99 (24): 15530-5
• Multiplex Pyrosequencing. Pourmand N,  Elahi E, Davis RW, Ronaghi M.  Nucleic Acids Res.  2002; 30 (7): e31
• Identification and preliminary characterization of mouse Adam33. Gunn TM,  Azarani A, Kim PH, Hyman RW, Davis RW, Barsh GS.  BMC Genet.  2002; 3 2
• Dissecting the architecture of a quantitative trait locus in yeast. Steinmetz LM,  Sinha H, Richards DR, Spiegelman JI, Oefner PJ, McCusker JH, Davis RW.  Nature.  2002; 416 (6878): 326-30
• A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity. Birrell GW,  Giaever G, Chu AM, Davis RW, Brown JM.  Proc Natl Acad Sci U S A.  2001; 98 (22): 12608-13
• Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Barnett MJ,  Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR.  Proc Natl Acad Sci U S A.  2001; 98 (17): 9883-8
• Global analysis of ATM polymorphism reveals significant functional constraint. Thorstenson YR,  Shen P, Tusher VG, Wayne TL, Davis RW, Chu G, Oefner PJ.  Am J Hum Genet.  2001; 69 (2): 396-412
• Transcriptional regulation and function during the human cell cycle. Cho RJ,  Huang M, Campbell MJ, Dong H, Steinmetz L, Sapinoso L, Hampton G, Elledge SJ, Davis RW, Lockhart DJ.  Nat Genet.  2001; 27 (1): 48-54
• DAtA: database of Arabidopsis thaliana annotation. Palm CJ,  Federspiel NA, Davis RW.  Nucleic Acids Res.  2000; 28 (1): 102-3
• Prevalence of small inversions in yeast gene order evolution. Seoighe C,  Federspiel N, Jones T, Hansen N, Bivolarovic V, Surzycki R, Tamse R, Komp C, Huizar L, Davis RW, Scherer S, Tait E, Shaw DJ, Harris D, Murphy L, Oliver K, Taylor K, Rajandream MA, Barrell BG, Wolfe KH.  Proc Natl Acad Sci U S A.  2000; 97 (26): 14433-7
• Functional analysis of the yeast genome by precise deletion and parallel phenotypic characterization. Winzeler EA,  Liang H, Shoemaker DD, Davis RW.  Novartis Found Symp.  2000; 229 105-9; discussion 109-11
• Population genetic implications from sequence variation in four Y chromosome genes. Shen P,  Wang F, Underhill PA, Franco C, Yang WH, Roxas A, Sung R, Lin AA, Hyman RW, Vollrath D, Davis RW, Cavalli-Sforza LL, Oefner PJ.  Proc Natl Acad Sci U S A.  2000; 97 (13): 7354-9
• Y chromosome sequence variation and the history of human populations. Underhill PA,  Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonné-Tamir B, Bertranpetit J, Francalacci P, Ibrahim M, Jenkins T, Kidd JR, Mehdi SQ, Seielstad MT, Wells RS, Piazza A, Davis RW, Feldman MW, Cavalli-Sforza LL, Oefner PJ.  Nat Genet.  2000; 26 (3): 358-61
• High-density arrays and insights into genome function. Steinmetz LM,  Davis RW.  Biotechnol Genet Eng Rev.  2000; 17 109-46
• Whole genome genetic-typing in yeast using high-density oligonucleotide arrays. Winzeler EA,  Lee B, McCusker JH, Davis RW.  Parasitology.  1999; 118 Suppl S73-80
• Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Cho RJ,  Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N, Theologis A, Yang WH, Hubbell E, Au M, Chung EY, Lashkari D, Lemieux B, Dean C, Lipshutz RJ, Ausubel FM, Davis RW, Oefner PJ.  Nat Genet.  1999; 23 (2): 203-7
• Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Winzeler EA,  Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Liebundguth N, Lockhart DJ, Lucau-Danila A, Lussier M, M'Rabet N, Menard P, Mittmann M, Pai C, Rebischung C, Revuelta JL, Riles L, Roberts CJ, Ross-MacDonald P, Scherens B, Snyder M, Sookhai-Mahadeo S, Storms RK, Véronneau S, Voet M, Volckaert G, Ward TR, Wysocki R, Yen GS, Yu K, Zimmermann K, Philippsen P, Johnston M, Davis RW.  Science.  1999; 285 (5429): 901-6
• Fluorescence-based expression monitoring using microarrays. Winzeler EA,  Schena M, Davis RW.  Methods Enzymol.  1999; 306 3-18
• An automated sample preparation system for large-scale DNA sequencing. Marziali A,  Willis TD, Federspiel NA, Davis RW.  Genome Res.  1999; 9 (5): 457-62
• Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Kalman S,  Mitchell W, Marathe R, Lammel C, Fan J, Hyman RW, Olinger L, Grimwood J, Davis RW, Stephens RS.  Nat Genet.  1999; 21 (4): 385-9
• An arrayable flow-through microcentrifuge for high-throughput instrumentation. Marziali A,  Willis TD, Davis RW.  Proc Natl Acad Sci U S A.  1999; 96 (1): 61-6
• The mouse mahogany locus encodes a transmembrane form of human attractin. Gunn TM,  Miller KA, He L, Hyman RW, Davis RW, Azarani A, Schlossman SF, Duke-Cohan JS, Barsh GS.  Nature.  1999; 398 (6723): 152-6
• Genomic profiling of drug sensitivities via induced haploinsufficiency. Giaever G,  Shoemaker DD, Jones TW, Liang H, Winzeler EA, Astromoff A, Davis RW.  Nat Genet.  1999; 21 (3): 278-83
• On the in vivo function of the RecA ATPase. Campbell MJ,  Davis RW.  J Mol Biol.  1999; 286 (2): 437-45
• Toxic mutations in the recA gene of E. coli prevent proper chromosome segregation. Campbell MJ,  Davis RW.  J Mol Biol.  1999; 286 (2): 417-35
• Imaging of apoptosis (programmed cell death) with 99mTc annexin V. Blankenberg FG,  Katsikis PD, Tait JF, Davis RE, Naumovski L, Ohtsuki K, Kopiwoda S, Abrams MJ, Strauss HW.  J Nucl Med.  1999; 40 (1): 184-91
• Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations. Jin L,  Underhill PA, Doctor V, Davis RW, Shen P, Cavalli-Sforza LL, Oefner PJ.  Proc Natl Acad Sci U S A.  1999; 96 (7): 3796-800
• An automated hydrodynamic process for controlled, unbiased DNA shearing. Thorstenson YR,  Hunicke-Smith SP, Oefner PJ, Davis RW.  Genome Res.  1998; 8 (8): 848-55
• Direct allelic variation scanning of the yeast genome. Winzeler EA,  Richards DR, Conway AR, Goldstein AL, Kalman S, McCullough MJ, McCusker JH, Stevens DA, Wodicka L, Lockhart DJ, Davis RW.  Science.  1998; 281 (5380): 1194-7
• Parallel analysis of genetic selections using whole genome oligonucleotide arrays. Cho RJ,  Fromont-Racine M, Wodicka L, Feierbach B, Stearns T, Legrain P, Lockhart DJ, Davis RW.  Proc Natl Acad Sci U S A.  1998; 95 (7): 3752-7
• Microarrays: biotechnology's discovery platform for functional genomics. Schena M,  Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW.  Trends Biotechnol.  1998; 16 (7): 301-6
• A genome-wide transcriptional analysis of the mitotic cell cycle. Cho RJ,  Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW.  Mol Cell.  1998; 2 (1): 65-73
• Functional analysis of the yeast genome. Winzeler EA,  Davis RW.  Curr Opin Genet Dev.  1997; 7 (6): 771-6
• Yeast microarrays for genome wide parallel genetic and gene expression analysis. Lashkari DA,  DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW.  Proc Natl Acad Sci U S A.  1997; 94 (24): 13057-62
• Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Underhill PA,  Jin L, Lin AA, Mehdi SQ, Jenkins T, Vollrath D, Davis RW, Cavalli-Sforza LL, Oefner PJ.  Genome Res.  1997; 7 (10): 996-1005
• Whole genome analysis: experimental access to all genome sequenced segments through larger-scale efficient oligonucleotide synthesis and PCR. Lashkari DA,  McCusker JH, Davis RW.  Proc Natl Acad Sci U S A.  1997; 94 (17): 8945-7
• Application of DNA typing methods and genetic analysis to epidemiology and taxonomy of Saccharomyces isolates. Clemons KV,  Park P, McCusker JH, McCullough MJ, Davis RW, Stevens DA.  J Clin Microbiol.  1997; 35 (7): 1822-8
• The nucleotide sequence of Saccharomyces cerevisiae chromosome V. Dietrich FS,  Mulligan J, Hennessy K, Yelton MA, Allen E, Araujo R, Aviles E, Berno A, Brennan T, Carpenter J, Chen E, Cherry JM, Chung E, Duncan M, Guzman E, Hartzell G, Hunicke-Smith S, Hyman RW, Kayser A, Komp C, Lashkari D, Lew H, Lin D, Mosedale D, Davis RW.  Nature.  1997; 387 (6632 Suppl): 78-81
• Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Heller RA,  Schena M, Chai A, Shalon D, Bedilion T, Gilmore J, Woolley DE, Davis RW.  Proc Natl Acad Sci U S A.  1997; 94 (6): 2150-5
• Efficient random subcloning of DNA sheared in a recirculating point-sink flow system. Oefner PJ,  Hunicke-Smith SP, Chiang L, Dietrich F, Mulligan J, Davis RW.  Nucleic Acids Res.  1996; 24 (20): 3879-86
• Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Shoemaker DD,  Lashkari DA, Morris D, Mittmann M, Davis RW.  Nat Genet.  1996; 14 (4): 450-6
• CDP1, a novel Saccharomyces cerevisiae gene required for proper nuclear division and chromosome segregation. Foreman PK,  Davis RW.  Genetics.  1996; 144 (4): 1387-97
• Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Schena M,  Shalon D, Heller R, Chai A, Brown PO, Davis RW.  Proc Natl Acad Sci U S A.  1996; 93 (20): 10614-9
• An automated multiplex oligonucleotide synthesizer: development of high-throughput, low-cost DNA synthesis. Lashkari DA,  Hunicke-Smith SP, Norgren RM, Davis RW, Brennan T.  Proc Natl Acad Sci U S A.  1995; 92 (17): 7912-5
• Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Schena M,  Shalon D, Davis RW, Brown PO.  Science.  1995; 270 (5235): 467-70
• Sliding-plate gel caster. Lashkari DA,  Norgren RM, Davis RW.  Biotechniques.  1995; 18 (4): 625-6
• Pathogenicity of Saccharomyces cerevisiae in complement factor five-deficient mice. Byron JK,  Clemons KV, McCusker JH, Davis RW, Stevens DA.  Infect Immun.  1995; 63 (2): 478-85
• Structure of homeobox-leucine zipper genes suggests a model for the evolution of gene families. Schena M,  Davis RW.  Proc Natl Acad Sci U S A.  1994; 91 (18): 8393-7
• Epidermal cell fate determination in Arabidopsis: patterns defined by a steroid-inducible regulator. Lloyd AM,  Schena M, Walbot V, Davis RW.  Science.  1994; 266 (5184): 436-9
• Saccharomyces cerevisiae virulence phenotype as determined with CD-1 mice is associated with the ability to grow at 42 degrees C and form pseudohyphae. McCusker JH,  Clemons KV, Stevens DA, Davis RW.  Infect Immun.  1994; 62 (12): 5447-55
• Cloning vectors for the synthesis of epitope-tagged, truncated and chimeric proteins in Saccharomyces cerevisiae. Foreman PK,  Davis RW.  Gene.  1994; 144 (1): 63-8
• Tetrad analysis possible in Arabidopsis with mutation of the QUARTET (QRT) genes. Preuss D,  Rhee SY, Davis RW.  Science.  1994; 264 (5164): 1458-60
• Genetic characterization of pathogenic Saccharomyces cerevisiae isolates. McCusker JH,  Clemons KV, Stevens DA, Davis RW.  Genetics.  1994; 136 (4): 1261-9
• Functional expression of the yeast FLP/FRT site-specific recombination system in Nicotiana tabacum. Lloyd AM,  Davis RW.  Mol Gen Genet.  1994; 242 (6): 653-7
• Point mutations that separate the role of Saccharomyces cerevisiae centromere binding factor 1 in chromosome segregation from its role in transcriptional activation. Foreman PK,  Davis RW.  Genetics.  1993; 135 (2): 287-96
• A conditional sterile mutation eliminates surface components from Arabidopsis pollen and disrupts cell signaling during fertilization. Preuss D,  Lemieux B, Yen G, Davis RW.  Genes Dev.  1993; 7 (6): 974-85
• The HAT4 gene of Arabidopsis encodes a developmental regulator. Schena M,  Lloyd AM, Davis RW.  Genes Dev.  1993; 7 (3): 367-79
• A dominant truncation allele identifies a gene, STE20, that encodes a putative protein kinase necessary for mating in Saccharomyces cerevisiae. Ramer SW,  Davis RW.  Proc Natl Acad Sci U S A.  1993; 90 (2): 452-6
• ATP hydrolysis and the displaced strand are two factors that determine the polarity of RecA-promoted DNA strand exchange. Konforti BB,  Davis RW.  J Mol Biol.  1992; 227 (1): 38-53
• Dominant genetics using a yeast genomic library under the control of a strong inducible promoter. Ramer SW,  Elledge SJ, Davis RW.  Proc Natl Acad Sci U S A.  1992; 89 (23): 11589-93
• Arabidopsis and Nicotiana anthocyanin production activated by maize regulators R and C1. Lloyd AM,  Walbot V, Davis RW.  Science.  1992; 258 (5089): 1773-5
• HD-Zip proteins: members of an Arabidopsis homeodomain protein superfamily. Schena M,  Davis RW.  Proc Natl Acad Sci U S A.  1992; 89 (9): 3894-8
• The use of proline as a nitrogen source causes hypersensitivity to, and allows more economical use of 5FOA in Saccharomyces cerevisiae. McCusker JH,  Davis RW.  Yeast.  1991 Aug-Sep; 7 (6): 607-8
• DNA substrate requirements for stable joint molecule formation by the RecA and single-stranded DNA-binding proteins of Escherichia coli. Konforti BB,  Davis RW.  J Biol Chem.  1991; 266 (16): 10112-21
• A steroid-inducible gene expression system for plant cells. Schena M,  Lloyd AM, Davis RW.  Proc Natl Acad Sci U S A.  1991; 88 (23): 10421-5
• The Saccharomyces cerevisiae RPB4 gene is tightly linked to the TIF2 gene. Foreman PK,  Davis RW, Sachs AB.  Nucleic Acids Res.  1991; 19 (10): 2781
• Translation initiation and ribosomal biogenesis: involvement of a putative rRNA helicase and RPL46. Sachs AB,  Davis RW.  Science.  1990; 247 (4946): 1077-9
• The preference for a 3' homologous end is intrinsic to RecA-promoted strand exchange. Konforti BB,  Davis RW.  J Biol Chem.  1990; 265 (12): 6916-20
• Yeast centromere binding protein CBF1, of the helix-loop-helix protein family, is required for chromosome stability and methionine prototrophy. Cai M,  Davis RW.  Cell.  1990; 61 (3): 437-46
• Rain-, wind-, and touch-induced expression of calmodulin and calmodulin-related genes in Arabidopsis. Braam J,  Davis RW.  Cell.  1990; 60 (3): 357-64
• Gene targeting at the human CD4 locus by epitope addition. Jasin M,  Elledge SJ, Davis RW, Berg P.  Genes Dev.  1990; 4 (2): 157-66
• The poly(A) binding protein is required for poly(A) shortening and 60S ribosomal subunit-dependent translation initiation. Sachs AB,  Davis RW.  Cell.  1989; 58 (5): 857-67
• Rapid screening of a human genomic library in yeast artificial chromosomes for single-copy sequences. Traver CN,  Klapholz S, Hyman RW, Davis RW.  Proc Natl Acad Sci U S A.  1989; 86 (15): 5898-902
• Purification of a yeast centromere-binding protein that is able to distinguish single base-pair mutations in its recognition site. Cai MJ,  Davis RW.  Mol Cell Biol.  1989; 9 (6): 2544-50
• Genetic selection for genes encoding sequence-specific DNA-binding proteins. Elledge SJ,  Sugiono P, Guarente L, Davis RW.  Proc Natl Acad Sci U S A.  1989; 86 (10): 3689-93
• Position and density effects on repression by stationary and mobile DNA-binding proteins. Elledge SJ,  Davis RW.  Genes Dev.  1989; 3 (2): 185-97
• Strategies for genetic modification of parasites. Davis RW,  Ann N Y Acad Sci.  1989; 569 104-17
• Direction of chromosome rearrangements in Saccharomyces cerevisiae by use of his3 recombinational substrates. Fasullo MT,  Davis RW.  Mol Cell Biol.  1988; 8 (10): 4370-80
• Physical mapping of large DNA by chromosome fragmentation. Vollrath D,  Davis RW, Connelly C, Hieter P.  Proc Natl Acad Sci U S A.  1988; 85 (16): 6027-31
• Sequence and nitrate regulation of the Arabidopsis thaliana mRNA encoding nitrate reductase, a metalloflavoprotein with three functional domains. Crawford NM,  Smith M, Bellissimo D, Davis RW.  Proc Natl Acad Sci U S A.  1988; 85 (14): 5006-10
• Tandem array of human visual pigment genes at Xq28. Vollrath D,  Nathans J, Davis RW.  Science.  1988; 240 (4859): 1669-72
• An electrophoretic karyotype of Neurospora crassa. Orbach MJ,  Vollrath D, Davis RW, Yanofsky C.  Mol Cell Biol.  1988; 8 (4): 1469-73
• A family of versatile centromeric vectors designed for use in the sectoring-shuffle mutagenesis assay in Saccharomyces cerevisiae. Elledge SJ,  Davis RW.  Gene.  1988; 70 (2): 303-12
• Resolution of DNA molecules greater than 5 megabases by contour-clamped homogeneous electric fields. Vollrath D,  Davis RW.  Nucleic Acids Res.  1987; 15 (19): 7865-76
• A single domain of yeast poly(A)-binding protein is necessary and sufficient for RNA binding and cell viability. Sachs AB,  Davis RW, Kornberg RD.  Mol Cell Biol.  1987; 7 (9): 3268-76
• Identification and isolation of the gene encoding the small subunit of ribonucleotide reductase from Saccharomyces cerevisiae: DNA damage-inducible gene required for mitotic viability. Elledge SJ,  Davis RW.  Mol Cell Biol.  1987; 7 (8): 2783-93
• Plant defense genes are regulated by ethylene. Ecker JR,  Davis RW.  Proc Natl Acad Sci U S A.  1987; 84 (15): 5202-5206
• Nitrate reductase from squash: cDNA cloning and nitrate regulation. Crawford NM,  Campbell WH, Davis RW.  Proc Natl Acad Sci U S A.  1986; 83 (21): 8073-8076
• Inhibition of gene expression in plant cells by expression of antisense RNA. Ecker JR,  Davis RW.  Proc Natl Acad Sci U S A.  1986; 83 (15): 5372-5376