Publications

Recent publication: Dharia et al. (2009) Use of high-density tiling microarrays to globally identify mutations and elucidate mechanisms of drug resistance in Plasmodium falciparum. [Genome Biology | PubMed]
  1. Dharia NV, Sidhu ABS, Cassera MB, Westenberger SJ, Bopp SER, Eastman RT, Plouffe D, Batalov S, Park, DJ, Volkman SK, Wirth DF, Zhou Y, Fidock DA, Winzeler EA. (2009) Use of high-density tiling microarrays to globally identify mutations and elucidate mechanisms of drug resistance in Plasmodium falciparum. Genome Biology, 10:R21.
    [PubMed]
  2. Le Roch KG, Johnson J, Ahiboh H, Plouffe D, Henson K, Chung DW, Prudhomme J, Zhou Y, Witola W, Yates J III, Ben Mamoun C, Winzeler EA, Vial H. (2008) A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum. BMC Genomics, 9(1):513.
    [PubMed]
  3. Winzeler EA. (2008) Malaria research in the post-genomic era. Nature, 455(7214):751-6. Review.
    [PubMed]
  4. Plouffe D, Brinker A, McNamara C, Henson K, Kato N, Kuhen K, Nagle A, Adrián F, Matzen JT, Anderson P, Nam TG, Gray NS, Chatterjee A, Janes J, Yan SF, Trager R, Caldwell JS, Schultz PG, Zhou Y, Winzeler EA. (2008) In silico activity profiling reveals the mechanism of action of antimalarials discovered in a high-throughput screen. PNAS, 105(26):9059-64.
    [PubMed]
  5. Kato N, Sakata T, Breton G, Le Roch KG, Nagle A, Andersen C, Bursulaya B, Henson K, Johnson J, Kumar KA, Marr F, Mason D, McNamara C, Plouffe D, Ramachandran V, Spooner M, Tuntland T, Zhou Y, Peters EC, Chatterjee A, Schultz PG, Ward GE, Gray N, Harper J, Winzeler EA. (2008) Gene expression signatures and small-molecule compounds link a protein kinase to Plasmodium falciparum motility. Nature Chemical Biology, 4(6):347-56.
    [PubMed]
  6. Zhou Y, Ramachandran V, Kumar KA, Westenberger S, Refour P, Zhou B, Li F, Young JA, Chen K, Plouffe D, Henson K, Nussenzweig V, Carlton J, Vinetz JM, Duraisingh MT, Winzeler EA. (2008) Evidence-based annotation of the malaria parasite's genome using comparative expression profiling. PLoS ONE, 3(2):e1570.
    [PubMed]
  7. Young JA, Johnson JR, Brenner C, Yan SF, Chen K, Le Roch KG, Zhou Y, Winzeler EA. (2008) In silico discovery of transcription regulator elements in Plasmodium falciparum. BMC Genomics, 9(1):70.
    [PubMed]
  8. Daily JP, Scanfeld D, Pochet N, Le Roch K, Plouffe D, Kamal M, Sarr O, Mboup S, Ndir O, Wypij D, Levasseur K, Thomas E, Tamayo P, Dong C, Zhou Y, Lander ES, Ndiaye D, Wirth D, Winzeler EA, Mesirov JP, Regev A. (2007) Distinct physiological states of Plasmodium falciparum in malaria-infected patients. Nature, 450(7172):1091-5.
    [PubMed]
  9. Sakata T, Winzeler EA. (2007) Genomics, systems biology and drug development for infectious diseases. Molecular BioSystems, 3(12):841-8. Review.
    [PubMed]
  10. Singh AP, Buscaglia CA, Wang Q, Levay A, Nussenzweig DR, Walker JR, Winzeler EA, Fujii H, Fontoura BM, Nussenzweig V. (2007) Plasmodium circumsporozoite protein promotes the development of the liver stages of the parasite. Cell, 131(3):492-504.
    [PubMed]
  11. Kumar KA, Garcia CR, Chandran VR, Van Rooijen N, Zhou Y, Winzeler E, Nussenzweig V. (2007) Exposure of Plasmodium sporozoites to the intracellular concentration of potassium enhances infectivity and reduces cell passage activity. Molecular and Biochemical Parasitology, 156(1):32-40.
    [PubMed]
  12. Deitsch K, Duraisingh M, Dzikowski R, Gunasekera A, Khan S, Le Roch K, Llinas M, Mair G, McGovern V, Roos D, Shock J, Sims J, Wiegand R, Winzeler E. (2007) Mechanisms of gene regulation in Plasmodium. The American Journal of Tropical Medicine and Hygiene, 77(2):201-8. Review.
    [PubMed]
  13. Zhou Y, Zhou B, Chen K, Yan SF, King FJ, Jiang S, Winzeler EA. (2007) Large-scale annotation of small-molecule libraries using public databases. Journal of Chemical Information and Modeling, 47(4):1386-94.
    [PubMed]
  14. Gunasekera AM, Myrick A, Le Roch K, Winzeler EA, Wirth DF. (2007) Plasmodium falciparum: Genome wide perturbations in transcript profiles among mixed stage cultures after chloroquine treatment. Experimental Parasitology, 117(1):87-92.
    [PubMed]
  15. Gunasekera AM, Myrick A, Militello KT, Sims JS, Dong CK, Gierahn T, Le Roch K, Winzeler EA, Wirth DF. (2007) Regulatory motifs uncovered among gene expression clusters in Plasmodium falciparum. Molecular and Biochemical Parasitology, 153(1):19-30.
    [PubMed]
  16. Kidgell C, Winzeler EA. (2006) Using the genome to dissect the molecular basis of drug resistance. Future Microbiology, 1(2):185-199. Review.
    [PubMed]
  17. Kidgell C, Volkman SK, Daily J, Borevitz JO, Plouffe D, Zhou Y, Johnson JR, Le Roch KG, Sarr O, Ndir O, Mboup S, Batalov S, Wirth DF, Winzeler EA. (2006) A systematic map of genetic variation in Plasmodium falciparum. PLoS Pathogens, 2(6):e57.
    [PubMed]
  18. Winzeler EA. (2006) Applied systems biology and malaria. Nature Reviews Microbiology, 4(2):145-51. Review.
    [PubMed]
  19. Le Roch KG, Winzeler EA. (2005) Molecular approaches to malaria: The transcriptome of the malaria parasite, Plasmodium falciparum. ASM Press, 5:68-84.
  20. Carret C, Horrocks P, Konfortov B, Winzeler EA, Qureshi M, Newbold C, Ivens A. (2005) Microarray-based comparative genomic analyses of the human malaria parasite Plasmodium falciparum using Affymetrix arrays. Molecular and Biochemical Parasitology, 144(2):177-86.
    [PubMed]
  21. Young JA, Fivelman QL, Blair P, de la Vega P, Le Roch KG, Zhou Y, Carucci DJ, Baker DA, Winzeler EA. (2005) The Plasmodium falciparum sexual development transcriptome: A microarray analysis using ontology-based pattern identification. Molecular and Biochemical Parasitology, 143(1):67-79.
    [PubMed]
  22. Stubbs J, Simpson K, Triglia T, Plouffe D, Tonkin CJ, Duraisingh MT, Maier AG, Winzeler EA, Cowman AF. (2005) Molecular mechanism for switching of P. falciparum invasion pathways into human erythrocytes. Science, 309(5739):1384-7.
    [PubMed]
  23. Kidgell C, Winzeler EA. (2005) Elucidating genetic diversity with oligonucleotide arrays. Chromosome Research, 13:225-235. Review.
    [PubMed]
  24. Simpson KM, Baum J, Good RT, Winzeler EA, Cowman AF, Speed TP. (2005) A comparison of match-only algorithms for the analysis of Plasmodium falciparum oligonucleotide arrays. International Journal for Parasitology, 35(5):523-31.
    [PubMed]
  25. Young JA, Winzeler EA. (2005) Using expression information to discover new drug and vaccine targets in the malaria parasite Plasmodium falciparum. Pharmacogenomics, 6(1):17-26. Review.
    [PubMed]
  26. Daily JP, Le Roch KG, Sarr O, Ndiaye D, Lukens A, Zhou Y, Ndir O, Mboup S, Sultan A, Winzeler EA, Wirth DF. (2005) In vivo transcriptome of P. falciparum reveals over expression of transcripts encoding surface proteins. The Journal of Infectious Diseases, 191:1196-1203.
    [PubMed]
  27. Zhou Y, Young JA, Santrosyan A, Kaisheng C, Yan F, Winzeler EA. (2005) In silico gene function prediction using ontology-based pattern identification. Bioinformatics, 21(7):1237-45.
    [PubMed]
  28. O’Neill BM, Hanway D, Winzeler EA. (2004) Coordinated functions of WSS1, PSY2 and TOF1 in the DNA damage response. Nucleic Acids Research, 32(22):6519-30.
    [PubMed]
  29. Le Roch KG, Winzeler EA. (2004) Biochip in malaria for anti-parasitic discovery. Biochips as Pathways to Drugs, In Press.
  30. Le Roch KG, Florens L, Johnson JR, Zhou Y, Santrosyan A, Grainger M, Williamson KC, Holder AA, Carucci DJ, Yates III JR, Winzeler EA. (2004) Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Research, 14:2308-18.
    [PubMed]
  31. Le Roch KG, Winzeler EA. (2004) Genome-wide analysis of gene expression. Encyclopedia of Biological Chemistry. Elseivier, 2:175-180.
  32. Daily JP, Le Roch KG, Sarr O, Fang X, Zhou Y, Ndir O, Mboup S, Sultan A, Winzeler EA, Wirth DF. (2004) In vivo transcriptional profiling of Plasmodium falciparum. Malarial Journal, 3:30.
    [PubMed]
  33. Barrera L, Benner C, Tao YC, Winzeler EA, Zhou Y. (2004) Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays. BMC Bioinformatics, 5(1):42.
    [PubMed]
  34. Sam-Yellowe TY, Florens L, Johnson JR, Wang T, Le Roch KG, Zhou Y, Batalov S, Carucci DJ, Winzeler EA, Yates III JR. (2004) A Plasmodium gene family encoding Maurer’s cleft membrane proteins: Structural properties and expression profile. Genome Research, 14(6):1052-9.
    [PubMed]
  35. Le Roch KG, Zhou Y, Blair PL, Grainger M, Moch JK, Haynes JD, De la Vega P, Holder AA, Batalov S, Carucci DJ, Winzeler EA. (2003) Discovery of gene function by expression profiling of the malaria parasite lifecycle. Science, 301 (5639): 1503-8.
    [PubMed]
  36. Washburn MP, Oshiro G, Koller A, Ulaszek RR, Plouffe D, Deciu C, Winzeler E, Yates III JR. (2003) Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. PNAS, 100(6):3107-12.
    [PubMed]
  37. Borevitz JO, Liang D, Plouffe D, Chang H-S, Zhu T, Weigel D, Berry CC, Winzeler E, Choryl J. (2003) Large scale identification of single feature polymorphisms in complex genomes. Genome Research, 13(3):513-523.
    [PubMed]
  38. Winzeler EA, Castillo-Davis CI, Oshiro G, Liang D, Richards DR, Zhou Y, Hartl DL. (2003) Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays. Genetics, 163(1):79-89.
    [PubMed]
  39. Volkman S, Hartl D, Wirth DF, Nielsen KM, Choi M, Batalov S, Zhou Y, Plouffe D, Le Roch KG, Abagyan R, Winzeler EA. (2002) Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science, 298(5591):216-218.
    [PubMed]
  40. Williams RM, Primig M, Washburn BK, Winzeler EA, Bellis M, Sarrauste de Menthiere C, Davis RW, Esposito RE. (2002) The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast. PNAS, 99(21):13431-6.
    [PubMed]
  41. Le Roch KG, Zhou Y, Batalov S, Winzeler EA. (2002) Monitoring the chromosome 2 interythrocytic transcriptome of Plasmodium falciparum using oligonucleotide arrays. The American Journal of Tropical Medicine and Hygiene, 67(3):233-243.
    [PubMed]
  42. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian K-D, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter 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 C, 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. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418(6896):387-391.
    [PubMed]
  43. Grünenfelder B, Winzeler EA. (2002) Treasures and traps in genome-wide data sets: case examples from yeast. Nature Review Genetics, 3(9):653-661. Review.
    [PubMed]
  44. Hanway D, Chin JK, Xia G, Oshiro G, Winzeler EA, Romesberg FE. (2002) Previously uncharacterized genes in the UV- and MMS- induced DNA damage response in yeast. PNAS, 99(16):10605-10.
    [PubMed]
  45. Karlyshev AV, Dorrell N, Winzeler E, Wren BW. (2002) Further strategies for signature-tagged mutagenesis and the application of oligonucleotide microarrays for the quantitation of DNA-tagged strains. Functional Microbial Genomics in Methods in Microbiology: London, United Kingdom, Vol33 edited by Wren, BW, Dorrell, N, Elsevier.
  46. Oshiro G, Wodicka LM, Washburn MP, Yates III JR, Lockhart DJ, Winzeler EA. (2002) Parallel identification of new genes in Saccharomyces cerevisiae. Genome Research, 12(8):1210-20.
    [PubMed]
  47. Que QQ, Winzeler EA. (2002) Large-scale mutagenesis and functional genomics in yeast. Functional & Integrative Genomics, 2(4-5):193-198. Review.
    [PubMed]
  48. Hartl DL, Volkman SK, Neilsen KM, Barry AE, Day KP, Wirth DF, Winzeler EA. (2002) The paradoxical population genetics of Plasmodium falciparum. Trends in Parasitology, 18(6):266-272. Review.
    [PubMed]
  49. Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, Conway A, Lockhart DJ, Davis RW, Brewer BJ, Fangman WL. (2001) Replication dynamics of the yeast genome. Science, 294(5540):115-21.
    [PubMed]
  50. Karlyshev AV, Oyston PC, Williams K, Clark GC, Titball RW, Winzeler EA, Wren BW. (2001) Application of high-density array based signature-tagged mutagenesis to discover novel yersinia virulence-associated genes. Infection & Immunology, 69(12):7809-10.
    [PubMed]
  51. Winzeler EA, Liang H, Shoemaker DD, Davis RW. (2000) Functional analysis of the yeast genome by precise deletion and parallel phenotypic characterization. Novartis Foundation Symposium, 229:105-9.
  52. Primig M, Williams RM, Winzeler EA, Tevzadze GG, Conway AR, Hwang SY, Davis RW, Esposito RE. (2000) The core meiotic transcriptome in budding yeasts. Nature Genetics, 26:415-23.
    [PubMed]
  53. Soll DR, Winzeler EA. (2000) Editorial overview: Genome-wide approaches to cell function. Current Opinion in Microbiology, 3(3):283-4.
  54. Lockhart DJ, Winzeler EA. (2000) Genomics, gene expression and DNA arrays. Nature, 405:827-36. Review.
    [PubMed]
  55. Oshiro G, Winzeler EA. (2000) Aneuploidy — it’s more common than you think. Nature Biotechnology, 18:715-16.
    [PubMed]
  56. Winzeler E, Shoemaker D, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke J, Bussey H, Chu A, Connelly C, Davis K, Dietrich F, Dow S, El B, Foury MFG, Friend S, Gentalen E, Giaever G, Hegemann J, Jones T, Laub M, Liao H, Liebundguth N, Lockhart D, Lucau-Danila A, Lussier M, M’Rabet N, Menard P, Mittmann M, Pai C, Rebischung C, Revuelta J, Riles L, Roberts C, Ross-MacDonald P, Scherens B, Snyder M, Sookhai-Mhadeo S, Storms R, Veronneau S, Voet M, Volckaert G, Ward T, Wysocki R, Yen G, Yu K, Zimmermann K, Philippsen P, Johnston M, Davis R. (1999) Functional characterization of the Saccharomyces cervisiae genome by precise deletion and parallel analysis. Science, 285:901-6.
    [PubMed]
  57. Winzeler EA, Schena M, Davis RW. (1999) Flourescence-based expression monitoring using microarrays. Methods in Enzymology, 309:3-18. Review.
    [PubMed]
  58. Giaever G, Shoemaker DS, Jones TW, Liang H, Winzeler EA, Astromoff A, Davis RW. (1999) Genomic profiling of drug and toxin sensitivities via induced haploinsufficiency. Nature Genetics, 21:278-83.
    [PubMed]
  59. Winzeler EA, Lee B, McCusker JH, Davis RW. (1999) Whole genome genetic-typing using high-density oligonucleotide arrays. Parasitology, 118 Suppl:S73-80
    [PubMed]
  60. Winzeler EA, Richards DR, Conway AR, Goldstein AL, Kalman S, McCullough MJ, McCusker JH, Stevens DA, Wodicka L, Lockhart DJ, Davis RW. (1998) Direct allelic variation scanning of the yeast genome. Science, 281:1194-7.
    [PubMed  |  Science Cover]
  61. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway AR, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell, 2:65-73.
    [PubMed]
  62. Winzeler E, Wheeler R, Shapiro L. (1997) Transcriptional analysis of the Caulobacter 4.5S RNA and the physiological basis of a ffs mutant with a Ts phenotype. Journal of Molecular Biology, 272:665-76.
    [PubMed]
  63. Winzeler E. (1997) Functional genomics of Saccharomyces cerevisiae. ASM News, 63:312-17.
  64. Winzeler E, Davis R. (1997) Functional analysis of the yeast genome. Current Opinions in Genetics and Development, 7:771-76. Review.
    [PubMed]
  65. Winzeler E, Shapiro L. (1997) Translation of the leaderless Caulobacter dnaX mRNA. The Journal of Bacteriology, 179:3981-8.
    [PubMed]
  66. Winzeler E, Shapiro L. (1996) A novel promoter motif for Caulobacter cell cycle-controlled DNA replication promoters. Journal of Molecular Biology, 264:412-25.
    [PubMed]
  67. Winzeler E, Shapiro L. (1995) Use of flow cytometry to identify a Caulobacter 4.5S RNA temperature-sensitive mutant defective in the cell cycle. Journal of Molecular Biology, 251:346-65.
    [PubMed]
  68. Winzeler E, Small EW. (1991) Flourescence anisotropy decay of ethidium bound to nucleosome core particles: The torsional motion of the DNA is highly constrained and sensitive to pH. Biochemistry, 30:5304-13.
    [PubMed]