Publications from the Snyder Lab

Here is a list of publications from the lab, later to be made sortable.

Right now this site is in progress, and the information is not up-to-date. Please be patient as these pages are slowly updated.

l. Drlica, K. and Snyder, M. (1978). Superhelical Escherichia coli DNA: Relaxation by Coumermycin. J. Mol. Biol.
120, 145-154.

2. Snyder, M. and Drlica, K. (1979). DNA Gyrase on the Bacterial Chromosome: DNA Cleavage Induced by Oxolinic Acid.
J. Mol. Biol. 131, 287-302.

3. Snyder, M., Hirsh, J. and Davidson, N. (1981). The Cuticle Genes of Drosophila: A Developmentally Regulated Gene
Cluster. Cell 25, 165-177.

4. Snyder, M., Hunkapiller, M., Yuen, D., Silvert, D., Fristrom, J. and Davidson, N. (1981).A Cluster of Drosophila
Cuticle Genes. In ICN-UCLA Symposium on Developmental Biology Using Purified Genes XXIII D. Brown and F. Fox, Eds.,
125-133.

5. Snyder, M., Kimbrell, D., Hunkapiller, M., Hill, R., Fristrom, J. and Davidson, N. (1982). A Transposable Element
that Splits the Promoter Region Inactivates a Drosophila Cuticle Protein Gene. Proc. Natl. Acad. Sci. USA 79,
7430-7434.

6. Snyder, M., Hunkapiller, M., Yuen, D., Silvert, D., Fristrom, J. and Davidson, N. (1982). Cuticle Protein Genes of
Drosophila: Structure, Organization and Evolution of Four Clustered Genes. Cell 29, 1027-1040.

7. Snyder, M. and Davidson, N. (1983). Two Gene Families Clustered in a Small Region of the Drosophila Genome. J.
Mol. Biol. 166, 101-118.

8. Snyder, M. (1983). Organization and Expression of a Cluster of Drosophila Cuticle Genes. Doctoral Dissertation,
California Institute of Technology, Pasadena, Ca.

9. Snyder, M. and Davis, R.W. (1985). Screening ?gt11 Expression Libraries with Antibody Probes. Hybridomas in
the Biosciences and Medicine. Timothy Springer, ed., Plenum Press, N.Y. 397-406.

10. Hieter, P., Mann, C., Snyder, M. and Davis, R.W. (1985). Mitotic Stability of Yeast Chromosomes: A Colony Color
Assay that Measures Nondisjunction and Chromosome Loss. Cell 40, 381-392.

11. Johnson, L.M., Snyder, M., Chang, L.M.S., Davis, R.W. and Campbell, J.L. (1985). Isolation of the Gene Encoding
Yeast DNA Polymerase I. Cell 43, 369-377.

12. Snyder, M., Elledge, S. and Davis, R.W. (1986). Rapid Mapping of Antigenic Coding Regions and Creating Insertion
Mutations in Yeast Genes by Mini-Tn10 Transplason Mutagenesis. Proc. Natl. Acad. Sci. USA 83, 730-734.

13. Davis, R.W., Vollrath, D., Thomas, M., Hieter, P., Snyder, M., Mann, C. and Fasullo, M. (1986). Genome Plasticity
in Saccharomyces cerevisiae. UCLA Symposium series.

14. Snyder, M., Buchman, A.R. and Davis, R.W. (1986). Bent DNA at a Yeast Autonomously Replicating Sequence. Nature
324, 87-89.

15. Snyder, M., Elledge, S., Sweetser, D., Young, R.A. and Davis, R.W. (1987). ?gt11: Gene Isolation with Antibody
Probes and Other Applications. Methods in Enzymology, R. Wu and L. Grossman, eds., Academic Press, N.Y., 154,
107-128.

16. Snyder, M., R. J. Sapolsky and R. W. Davis, Transcription interferes with elements important for chromosome
maintenance in Saccharomyces cerevisiae, Mol Cell Biol, 8 (5), 2184-94 (1988).]

17. Snyder, M. and R. W. Davis, SPA1: a gene important for chromosome segregation and other mitotic functions in S.
cerevisiae, Cell, 54 (6), 743-54]

18. Kolman, C. J., M. Snyder and D. Soll, Genomic organization of tRNA and aminoacyl-tRNA synthetase genes for two
amino acids in Saccharomyces cerevisiae, Genomics, 3 (3), 201-6 (1988).]

19. Snyder, M., The SPA2 protein of yeast localizes to sites of cell growth, J Cell Biol, 108 (4), 1419-29 (1989).]

20. Yang, C. H., E. J. Lambie, J. Hardin, J. Craft and M. Snyder, Higher order structure is present in the yeast
nucleus: autoantibody probes demonstrate that the nucleolus lies opposite the spindle pole body, Chromosoma, 98 (2),
123-8 (1989).]

21. Gehrung, S. and M. Snyder, The SPA2 gene of Saccharomyces cerevisiae is important for pheromone-induced
morphogenesis and efficient mating, J Cell Biol, 111 (4), 1451-64 (1990).]

22. Granot, D. and M. Snyder, Glucose induces cAMP-independent growth-related changes in stationary-phase cells of
Saccharomyces cerevisiae, Proc Natl Acad Sci U S A, 88 (13), 5724-8]

23. Padmanabha, R., S. Gehrung and M. Snyder, The KNS1 gene of Saccharomyces cerevisiae encodes a nonessential protein
kinase homologue that is distantly related to members of the CDC28/cdc2 gene family, Mol Gen Genet, 229 (1), 1-9
(1991).]

24. Snyder, M., S. Gehrung and B. D. Page, Studies concerning the temporal and genetic control of cell polarity in
Saccharomyces cerevisiae, J Cell Biol, 114 (3), 515-32 (1991).]

25. Granot, D. and M. Snyder, Segregation of the nucleolus during mitosis in budding and fission yeast, Cell Motil
Cytoskeleton, 20 (1), 47-54]

26. Madden, K., C. Costigan and M. Snyder, Cell polarity and morphogenesis in Saccharomyces cerevisiae, Trends Cell
Biol, 2 (1), 22-9]

27. Costigan, C., S. Gehrung and M. Snyder, A synthetic lethal screen identifies SLK1, a novel protein kinase homolog
implicated in yeast cell morphogenesis and cell growth, Mol Cell Biol, 12 (3), 1162-78 (1992).]

28. Yang, C. H., E. J. Lambie and M. Snyder, NuMA: an unusually long coiled-coil related protein in the mammalian
nucleus, J Cell Biol, 116 (6), 1303-17]

29. Mirzayan, C., C. S. Copeland and M. Snyder, The NUF1 gene encodes an essential coiled-coil related protein that is
a potential component of the yeast nucleoskeleton, J Cell Biol, 116 (6), 1319-32]

30. Page, B. D. and M. Snyder, CIK1: a developmentally regulated spindle pole body-associated protein important for
microtubule functions in Saccharomyces cerevisiae, Genes Dev, 6 (8), 1414-29 (1992).]

31. Madden, K. and M. Snyder, Specification of sites for polarized growth in Saccharomyces cerevisiae and the influence
of external factors on site selection, Mol Biol Cell, 3 (9), 1025-35]

32. Friedman, H., M. Goebel and M. Snyder, A homolog of the proteasome-related RING10 gene is essential for yeast cell
growth, Gene, 122 (1), 203-6 (1992).]

33. Yang, C. H. and M. Snyder, The nuclear-mitotic apparatus protein is important in the establishment and maintenance
of the bipolar mitotic spindle apparatus, Mol Biol Cell, 3 (11), 1259-67 (1992).]

34. Copeland, C. S. and M. Snyder, Nuclear pore complex antigens delineate nuclear envelope dynamics in vegetative and
conjugating Saccharomyces cerevisiae, Yeast, 9 (3), 235-49 (1993).]

35. Granot, D. and M. Snyder, Carbon source induces growth of stationary phase yeast cells, independent of carbon
source metabolism, Yeast, 9 (5), 465-79 (1993).]

36. Flescher, E. G., K. Madden and M. Snyder, Components required for cytokinesis are important for bud site selection
in yeast, J Cell Biol, 122 (2), 373-86 (1993).]

37. Page, B. D. and M. Snyder, Chromosome segregation in yeast, Annu Rev Microbiol, 47 231-61 (1993).]

38. Xie, K., E. J. Lambie and M. Snyder, Nuclear dot antigens may specify transcriptional domains in the nucleus, Mol
Cell Biol, 13 (10), 6170-9 (1993).]

39. Page, B. D., L. L. Satterwhite, M. D. Rose and M. Snyder, Localization of the Kar3 kinesin heavy chain-related
protein requires the Cik1 interacting protein, J Cell Biol, 124 (4), 507-19 (1994).]

40. Costigan, C., D. Kolodrubetz and M. Snyder, NHP6A and NHP6B, which encode HMG1-like proteins, are candidates for
downstream components of the yeast SLT2 mitogen-activated protein kinase pathway, Mol Cell Biol, 14 (4), 2391-403]

41. Friedman, H. and M. Snyder, Mutations in PRG1, a yeast proteasome-related gene, cause defects in nuclear division
and are suppressed by deletion of a mitotic cyclin gene, Proc Natl Acad Sci U S A, 91 (6), 2031-5 (1994).]

42. Burns, N., B. Grimwade, P. B. Ross-Macdonald, E. Y. Choi, K. Finberg, G. S. Roeder and M. Snyder, Large-scale
analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae, Genes Dev, 8
(9), 1087-105 (1994).] Featured in News and Views.

43. Costigan, C. and M. Snyder, SLK1, a yeast homolog of MAP kinase activators, has a RAS/cAMP-independent role in
nutrient sensing, Mol Gen Genet, 243 (3), 286-96]

44. Snyder, M., The spindle pole body of yeast, Chromosoma, 103 (6), 369-80 (1994).]

45. Xie, K. and M. Snyder, Two short autoepitopes on the nuclear dot antigen are similar to epitopes encoded by the
Epstein-Barr virus, Proc Natl Acad Sci U S A, 92 (5), 1639-43 (1995).]

46. Li, O., Heath, C.V., Amberg, D.C., Dockendorff, T.C., Copeland, C.S., Snyder, M . and Cole, C.N. (1995). Mutation
or Deletion of the Saccharomyces cerevisiae RAT3/NUP133 gene causes temperature-dependent nuclear accumulation of
poly(A)+ RNA and constitutive clustering of nuclear pore complexes. Mol. Biol. Cell 6, 401-417.

47. Cid, V.J., Duran, A, del Rey, F., Snyder, M. Nombela, C. and Sanchez, M. (1995). Molecular Basis of Cell Integrity
and Morphogenesis in Saccharomyces cerevisiae, Microbiol. Rev. 59, 345-386.

48. Sobel, S. G. and M. Snyder, A highly divergent gamma-tubulin gene is essential for cell growth and proper
microtubule organization in Saccharomyces cerevisiae, J Cell Biol, 131 (6 Pt 2), 1775-88 (1995).]

49. Heath, C.V., Copeland, C.S., Amberg, D.C., Del Priore, V., Snyder, M. and Cole, C.N. (1995). Nuclear Pore Complex
Clustering and Nuclear Accumulation of Poly(A)+ RNA Associated with Mutation of the Saccharomyces cerevisiae
RAT2/NUP120 Gene. J. Cell Biol. 131, 1677-1697.

50. Ross-Macdonald, P., Burns, N., Malczynski, M., Sheehan, A., Roeder, S., and Snyder, M. (1995). Methods for
Large-Scale Analysis of Gene Expression, Protein Localization and Disruption Phenotypes in Saccharomyces cerevisiae.
Methods Mol. Cell. Biol. 5, 298-308.

51. Friedman-Einat, M., P. Einat, M. Snyder and F. Ruddle, Target gene identification: target specific transcriptional
activation by three murine homeodomain/VP16 hybrid proteins in Saccharomyces cerevisiae, J Exp Zool, 274 (3), 145-56
(1996).]

52. Burns, N., Ross-Macdonald, P., Roeder, G.S., and Snyder, M. (1996). Generation, Screening and Analysis of lacZ
Fusions in Yeast. in Microbial Genome Methods. K. Adolph, ed. CRC Press, New York p. 61-79.

53. Chen, C.-R., Malik, M., Snyder, M. and Drlica, K. (1996). DNA Gyrase and Topoisomerase IV on the Bacterial
Chromosome: Quinolone-Induced DNA Cleavage, J. Mol. Biol. 258, 627-637.

54. Roemer, T., K. Madden, J. Chang and M. Snyder, Selection of axial growth sites in yeast requires Axl2p, a novel
plasma membrane glycoprotein, Genes Dev, 10 (7), 777-93]

55. Roemer, T., L. G. Vallier and M. Snyder, Selection of polarized growth sites in yeast, Trends Cell Biol, 6 (11),
434-41]

56. Ross-Macdonald, P., A. Sheehan, G. S. Roeder and M. Snyder, A multipurpose transposon system for analyzing protein
production, localization, and function in Saccharomyces cerevisiae, Proc Natl Acad Sci U S A, 94 (1), 190-5 (1997).]

57. Santos, B. and M. Snyder, Targeting of chitin synthase 3 to polarized growth sites in yeast requires Chs5p and
Myo2p, J Cell Biol, 136 (1), 95-110 (1997).]

58. Madden, K., Y. J. Sheu, K. Baetz, B. Andrews and M. Snyder, SBF cell cycle regulator as a target of the yeast
PKC-MAP kinase pathway, Science, 275 (5307), 1781-4 (1997).]

59. Semenov, M. V. and M. Snyder, Human dishevelled genes constitute a DHR-containing multigene family, Genomics, 42
(2), 302-10 (1997).]

60. Manning, B. D., R. Padmanabha and M. Snyder, The Rho-GEF Rom2p localizes to sites of polarized cell growth and
participates in cytoskeletal functions in Saccharomyces cerevisiae, Mol Biol Cell, 8 (10), 1829-44 (1997).]

61. Ross-MacDonald, P., Sheehan, A., Friddle, C., Roeder, G.S. and Snyder, M. (1998). Transposon Tagging I: A Novel
System for Monitoring Protein Production, Function and Localization. in Methods in Microbiology: Yeast Gene
Analysis. M.F. Tuite & A.J.P. Brown, eds, Academic Press, London, Vol 26, 161-179.

62. Costigan, C. and Snyder, M. (1998). Cell Polarity in the Budding Yeast, Saccharomyces cerevisiae. Adv. Mol. Cell
Biol. 26, 1-66.

63. Erdman, S., L. Lin, M. Malczynski and M. Snyder, Pheromone-regulated genes required for yeast mating
differentiation, J Cell Biol, 140 (3), 461-83 (1998).]

64. Roemer, T., L. Vallier, Y. J. Sheu and M. Snyder, The Spa2-related protein, Sph1p, is important for polarized
growth in yeast, J Cell Sci, 111 ( Pt 4) 479-94 (1998).]

65. Sheu, Y. J., B. Santos, N. Fortin, C. Costigan and M. Snyder, Spa2p interacts with cell polarity proteins and
signaling components involved in yeast cell morphogenesis, Mol Cell Biol, 18 (7), 4053-69 (1998).]

66. Madden, K. and M. Snyder, Cell polarity and morphogenesis in budding yeast, Annu Rev Microbiol, 52 687-744 (1998).]

67. Ross-Macdonald, P., A. Sheehan, C. Friddle, G. S. Roeder and M. Snyder, Transposon mutagenesis for the analysis of
protein production, function, and localization, Methods Enzymol, 303 512-32]

68. Barral, Y., M. Parra, S. Bidlingmaier and M. Snyder, Nim1-related kinases coordinate cell cycle progression with
the organization of the peripheral cytoskeleton in yeast, Genes Dev, 13 (2), 176-87 (1999).
[http://www.genesdev.org/cgi/content/full/13/2/176] (Featured on Cover).

69. Hong, S.K., Han, S.B., Snyder, M. and Choi E.Y. (1999). SHC1, a High pH Inducible Gene Required for Growth at
Alkaline pH in Saccharomyces cerevisiae. Biochem. Biophys. Res. Comm. 255, 116-122.

70. Manning, B. D., J. G. Barrett, J. A. Wallace, H. Granok and M. Snyder, Differential regulation of the Kar3p
kinesin-related protein by two associated proteins, Cik1p and Vik1p, J Cell Biol, 144 (6), 1219-33 (1999).]

71. Winzeler, E.A., Astromoff, A., Liang, H., Shoemaker, D.D., Anderson, K., Bangham, R., Boeke, J.D., Bussey, H.,
Connelly, C., Davis, K., Dietrich, F., Foury, F., Friend, S., Gentalen, E., Giaever, G., Jones, T., Laub, M., Liao,
H., Lockhart, D., Lussier, M., Ross-Macdonald, P., Menard, P., Mittmann, M., Pai, C., Philippsen, P., Rebischung,
C., Riles, L., Rine, J., Roberts, C., Snyder, M., Stroms, R.K., Veronneau, S., Ward, T., Whelan, S., Yen, G., Yu,
K., Johnston, M., Davis, R.W. (1999) Functional characterization of the Saccharomyces cerevisiae genome by
comprehensive and precise gene deletion and massively parallel analysis. Science 285, 901-906.

72. Ross-Macdonald, P., P. S. Coelho, T. Roemer, S. Agarwal, A. Kumar, R. Jansen, K. H. Cheung, A. Sheehan, D.
Symoniatis, L. Umansky, M. Heidtman, F. K. Nelson, H. Iwasaki, K. Hager, M. Gerstein, P. Miller, G. S. Roeder and M.
Snyder, Large-scale analysis of the yeast genome by transposon tagging and gene disruption, Nature, 402 (6760),
413-8]

73. Vogel, J. and Snyder, M. (1999). The Centrosome in Cell Replication and Development. Curr. Topics in Devel. 49,
75-104.

74. des Etages, S.A., Kumar, A., and Snyder, M. (1999). Transposons as Tools. Encyclopedia of Genetics, S. Brenner
and J.H. Miller, eds. Academic Press, San Diego. 2034-2040.

75. Mattagajasingh, S.N, Huang, S.C., Hartenstein, J.S., Snyder, M., Marchesi, V.T., and Benz E.J. (1999) A nonerythroid
isoform of protein 4.1R interacts with the nuclear mitotic apparatus (NuMA) protein. J. Cell Biol. 145, 29-43.

76. Kumar, A., K. H. Cheung, P. Ross-Macdonald, P. S. Coelho, P. Miller and M. Snyder, TRIPLES: a database of gene
function in Saccharomyces cerevisiae, Nucleic Acids Res, 28 (1), 81-4]

77. Kumar, A., S. A. des Etages, P. S. Coelho, G. S. Roeder and M. Snyder, High-throughput methods for the large-scale
analysis of gene function by transposon tagging, Methods Enzymol, 328 550-74]

78. Santos, B. and M. Snyder, Sbe2p and sbe22p, two homologous Golgi proteins involved in yeast cell wall formation,
Mol Biol Cell, 11 (2), 435-52 (2000).]

79. Zhan X, Lee M, Abenes G, Von Reis I, Kittinunvorakoon C, Ross-Macdonald P, Snyder M, and Liu F (2000). Mutagenesis
of murine cytomegalovirus using a Tn3-based transposon. Virology 266:264-74.

80. Cheung, K. H., A. Kumar, M. Snyder and P. Miller, An integrated web interface for large-scale characterization of
sequence data, Funct Integr Genomics, 1 (1), 70-5]

81. Sheu, Y. J., Y. Barral and M. Snyder, Polarized growth controls cell shape and bipolar bud site selection in
Saccharomyces cerevisiae, Mol Cell Biol, 20 (14), 5235-47 (2000).]

82. Kumar, A. and Snyder, M. (2000). Genome-Wide Transposon Mutagenesis in Yeast. In Current Protocols in Mol. Biol.
(ed, Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D., Seidman, J.G., Smith, J.A., and Struhl, K.) Wiley and
Sons, N.Y., N.Y. Unit 13.3.

83. Barral, Y., V. Mermall, M. S. Mooseker and M. Snyder, Compartmentalization of the cell cortex by septins is
required for maintenance of cell polarity in yeast, Mol Cell, 5 (5), 841-51 (2000).
[http://www.molecule.org/content/article/abstract?uid=PIIS109727650080324X]

84. Barrett, J. G., B. D. Manning and M. Snyder, The Kar3p kinesin-related protein forms a novel heterodimeric
structure with its associated protein Cik1p, Mol Biol Cell, 11 (7), 2373-85 (2000).]

85. Manning, B. D. and M. Snyder, Drivers and passengers wanted! the role of kinesin-associated proteins, Trends Cell
Biol, 10 (7), 281-9 (2000).]

86. Deng, Y., Lee, J.P., Tianasoa-Ramamonjy, M., Snyder, J.K., Des Etages, S.A., Kanada, D., Snyder, M.P., and Turner,
C.J. (2000). New Anitimicrobial Flavanones from Physena madagascariensis, J. Natural Products, in press.

87. Coelho, P. S., A. Kumar and M. Snyder, Genome-wide mutant collections: toolboxes for functional genomics, Curr Opin
Microbiol, 3 (3), 309-15 (2000).]

88. Vogel, J. and M. Snyder, The carboxy terminus of Tub4p is required for gamma-tubulin function in budding yeast, J
Cell Sci, 113 Pt 21 3871-82 (2000).

89. Bouquin N, Barral Y, Courbeyrette R, Blondel M, Snyder, M, and Mann, C. (2000). Regulation of cytokinesis by the
Elm1 protein kinase in Saccharomyces cerevisiae. J. Cell Sci. 113:1435-45.

90. Zhu, H., J. F. Klemic, S. Chang, P. Bertone, A. Casamayor, K. G. Klemic, D. Smith, M. Gerstein, M. A. Reed and M.
Snyder, Analysis of yeast protein kinases using protein chips, Nat Genet, 26 (3), 283-9 (2000).]

91. Cheung, K. H., P. Miller, A. Sherman, S. Weston, E. Stratmann, M. Schultz, M. Snyder and A. Kumar,
Graphically-enabled integration of bioinformatics tools allowing parallel execution, Proc AMIA Symp, 141-5]

92. Erdman, S. and M. Snyder, A filamentous growth response mediated by the yeast mating pathway, Genetics, 159 (3),
919-28 (2001).

93. Zhu, H. and M. Snyder, Protein arrays and microarrays, Curr Opin Chem Biol, 5 (1), 40-5 (2001).

94. Vidan, S. and M. Snyder, Large-scale mutagenesis: yeast genetics in the genome era, Curr Opin Biotechnol, 12 (1),
28-34 (2001).

95. Iyer, V.I.*, Horak, C.A*, Scafe, C.S., Botstein, D., Snyder, M., and Brown, P.O. (2001). Genomic binding
distribution of the yeast cell-cycle transcription factors SBF and MBF. Nature, 409, 533-538. * co first authors.

96. Bidlingmaier, S., E. L. Weiss, C. Seidel, D. G. Drubin and M. Snyder, The Cbk1p pathway is important for polarized
cell growth and cell separation in Saccharomyces cerevisiae, Mol Cell Biol, 21 (7), 2449-62 (2001).

97. Kumar, A. and M. Snyder, Emerging technologies in yeast genomics, Nat Rev Genet, 2 (4), 302-12 (2001).

98. Ni, L. and M. Snyder, A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae, Mol
Biol Cell, 12 (7), 2147-70 (2001).

99. Cheung, K. H., J. Hager, K. Nelson, K. White, Y. Li, M. Snyder, K. Williams and P. Miller, A dynamic approach to
mapping coordinates between microplates and microarrays, J Biomed Inform, 35 (5-6), 306-12 (2002).

100. Sheu, Y.-J. and Snyder, M. (2001). Control of Cell Polarity and Shape in S. cerevisiae. Howard and N. Gow eds.
Springer, Heidelberg Mycota Vol VIII The Biology of the Fungal Cell p.19-53.

101. Zhu, H., M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek,
T. Mitchell, P. Miller, R. A. Dean, M. Gerstein and M. Snyder, Global analysis of protein activities using proteome
chips, Science, 293 (5537), 2101-5 (2001). (Featured in many journals, websites and newspapers)

102. Zhu, H. and Snyder, M. (2001). Biochemical Assays in a Chip Format. Current Drug Discovery 31-34.

103. Vogel, J., B. Drapkin, J. Oomen, D. Beach, K. Bloom and M. Snyder, Phosphorylation of gamma-tubulin regulates
microtubule organization in budding yeast, Dev Cell, 1 (5), 621-31 (2001).

104. Vidan, S. and Snyder, M. (2001). Making Drug Addicts Out of Yeast. Nature Biotech. 19, 1022-1023.

105. Kumar, A., P. M. Harrison, K. H. Cheung, N. Lan, N. Echols, P. Bertone, P. Miller, M. B. Gerstein and M. Snyder,
An integrated approach for finding overlooked genes in yeast, Nat Biotechnol, 20 (1), 58-63 (2002). (Featured in
Nature. Biotech., News and Views).

106. Bidlingmaier, S. and M. Snyder, Large-scale identification of genes important for apical growth in Saccharomyces
cerevisiae by directed allele replacement technology (DART) screening, Funct Integr Genomics, 1 (6), 345-56 (2002).

107. Horak, C. E. and M. Snyder, ChIP-chip: a genomic approach for identifying transcription factor binding sites,
Methods Enzymol, 350 469-83 (2002).

108. Kumar, A., S. Vidan and M. Snyder, Insertional mutagenesis: transposon-insertion libraries as mutagens in yeast,
Methods Enzymol, 350 219-29 (2002).

109. Kumar, A., S. Agarwal, J. A. Heyman, S. Matson, M. Heidtman, S. Piccirillo, L. Umansky, A. Drawid, R. Jansen, Y.
Liu, K. H. Cheung, P. Miller, M. Gerstein, G. S. Roeder and M. Snyder, Subcellular localization of the yeast
proteome, Genes Dev, 16 (6), 707-19 (2002).

110. Kumar, A. and Snyder, M. (2002). Protein Complexes Take the Bait. Nature 415: 123-124.

111. Kumar, A., K. H. Cheung, N. Tosches, P. Masiar, Y. Liu, P. Miller and M. Snyder, The TRIPLES database: a community
resource for yeast molecular biology, Nucleic Acids Res, 30 (1), 73-5 (2002).

112. Harrison, P., A. Kumar, N. Lan, N. Echols, M. Snyder and M. Gerstein, A small reservoir of disabled ORFs in the
yeast genome and its implications for the dynamics of proteome evolution, J Mol Biol, 316 (3), 409-19 (2002).

113. Kumar, A., Cheung, K.-H., Marenco, L., Tosches, N., Masiar, P., Liu, Y., Miller, P., and Snyder, M. (2002). The
TRIPLES Database of Yeast Protein Function. In Analyzing Gene Expression (ed., Lorkowski, S. and Cullen, P., et
al.) Wiley-VCH Verlag GmbH, Weinheim, Germany. in press.

114. Harrison, P. M., A. Kumar, N. Lang, M. Snyder and M. Gerstein, A question of size: the eukaryotic proteome and the
problems in defining it, Nucleic Acids Res, 30 (5), 1083-90 (2002).

115. Casamayor, A. and M. Snyder, Bud-site selection and cell polarity in budding yeast, Curr Opin Microbiol, 5 (2),
179-86 (2002).

116. Zhu, H. and M. Snyder, "Omic" approaches for unraveling signaling networks, Curr Opin Cell Biol, 14 (2), 173-9
(2002).

117. Kusch, J., Meyer, A., Snyder, M. and Barral, Y. (2002). Proper positioning of the spindle and the cleavage plane
relative to each other involves microtubule capture by the cleavage apparatus in yeast. Gen. Dev. 16: 1627-1639

118. Horak, C. E., M. C. Mahajan, N. M. Luscombe, M. Gerstein, S. M. Weissman and M. Snyder, GATA-1 binding sites
mapped in the beta-globin locus by using mammalian chIp-chip analysis, Proc Natl Acad Sci U S A, 99 (5), 2924-9
(2002).

119. Bidlingmaier, S. and M. Snyder, Carbohydrate analysis prepares to enter the "Omics" era, Chem Biol, 9 (4), 400-1
(2002).

120. Snyder, M. and Kumar, A. (2002). Yeast genomics: past, present, and future promise. Funct. Integr. Genomics 2:
135-137.

121. Horak, C. E. and M. Snyder, Global analysis of gene expression in yeast, Funct Integr Genomics, 2 (4-5), 171-80
(2002).

122. Giaever G, Chu A.M., Ni L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre,
B., Arkin, A.P., 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, D.J., Gerstein, M., Gotte, D.,
Guldener, U., Hegemann, J.H., Hempel, S., Herman, Z., Jaramillo, D.F., Kelly, D.E., Kelly, S.L., Kotter, P.,
LaBonte, D., Lamb, D.C., Lan, N., Liang, H., Liao, H., Liu, L., Luo, C., Lussier, M., Mao, R., Menard, P., Ooi,
S.L., Revuelt,a J.L., Roberts, C.J., Rose, M., Ross-Macdonald, P., Scherensm B., Schimmack, G., Shafer, B.,
Shoemaker, D.D., Sookhai-Mahadeo, S., Storms, R.K., Strathern, J.N., Valle, G., Voet, M., Volckaert, G., Wang, C.Y.,
Ward, T.R., Wilhelmy, J., Winzeler, E.A., Yang, Y., Yen, G., Youngman, E., Yu, K., Bussey, H., Boeke, J.D., Snyder,
M., Philippsen, P., Davis, R.W., and Johnston, M. (2002). Functional profiling of the Saccharomyces cerevisiae
genome. Nature 418:387-91.

122. Vallier, L. G., J. E. Segall and M. Snyder, The alpha-factor receptor C-terminus is important for mating
projection formation and orientation in Saccharomyces cerevisiae, Cell Motil Cytoskeleton, 53 (4), 251-66 (2002).

123. Coelho, P. S., A. C. Bryan, A. Kumar, G. S. Shadel and M. Snyder, A novel mitochondrial protein, Tar1p, is encoded
on the antisense strand of the nuclear 25S rDNA, Genes Dev, 16 (21), 2755-60 (2002).

124. Horak, C.E., Luscombe, N.M., Qian, J., Piccirrillo, S., Gerstein, M, and Snyder., M. (2002). Complex
Transcriptional Circuitry at the G1/S Transition in Saccharomyces cerevisiae. Genes Dev. 16; 3017-33.

125. Michaud, G. A. and M. Snyder, Proteomic approaches for the global analysis of proteins, Biotechniques, 33 (6),
1308-16 (2002).

126. Rinn, J. L., G. Euskirchen, P. Bertone, R. Martone, N. M. Luscombe, S. Hartman, P. M. Harrison, F. K. Nelson, P.
Miller, M. Gerstein, S. Weissman and M. Snyder, The transcriptional activity of human Chromosome 22, Genes Dev, 17
(4), 529-40 (2003).

127. Zhu, H. and M. Snyder, Protein chip technology, Curr Opin Chem Biol, 7 (1), 55-63 (2003).

128. Cheung, K. H., K. White, J. Hager, M. Gerstein, V. Reinke, K. Nelson, P. Masiar, R. Srivastava, Y. Li, J. Li, H.
Zhao, D. B. Allison, M. Snyder, P. Miller and K. Williams, YMD: a microarray database for large-scale gene
expression analysis, Proc AMIA Symp, 140-4 (2002).

129. Casamayor, A. and M. Snyder, Molecular dissection of a yeast septin: distinct domains are required for septin
interaction, localization, and function, Mol Cell Biol, 23 (8), 2762-77 (2003).

130. Snyder, M. and M. Gerstein, Genomics. Defining genes in the genomics era, Science, 300 (5617), 258-60 (2003).

131. Zhu, H., M. Bilgin and M. Snyder, Proteomics, Annu Rev Biochem, 72 783-812]

132. Luscombe, N. M., T. E. Royce, P. Bertone, N. Echols, C. E. Horak, J. T. Chang, M. Snyder and M. Gerstein,
ExpressYourself: A modular platform for processing and visualizing microarray data, Nucleic Acids Res, 31 (13),
3477-82 (2003).

133. Reboul, J, Vaglio, P, Rual, JF, Lamesch, P, Martinez, M, Armstrong, CM, Li, S, Jacotot, L, Bertin, N, Janky, R,
Moore, T, Hudson, JR Jr, Hartley, JL, Brasch, MA, Vandenhaute, J, Boulton, S, Endress, GA, Jenna, S, Chevet, E,
Papasotiropoulos, V, Tolias, PP, Ptacek, J, Snyder, M, Huang, R, Chance, MR, Lee, H, Doucette-Stamm, L, Hill, DE,
Vidal, M. (2003). C. elegans ORFeome Version 1.1: Experimental Verification of the Genome Annotation and
Resource for Proteome-Scale Protein Expression. Nat Genet. 34:35-41.

134. Santos, B. and M. Snyder, Specific protein targeting during cell differentiation: polarized localization of Fus1p
during mating depends on Chs5p in Saccharomyces cerevisiae, Eukaryot Cell, 2 (4), 821-5 (2003).

135. Jona, G. and M. Snyder, Recent developments in analytical and functional protein microarrays, Curr Opin Mol Ther,
5 (3), 271-7 (2003).

136. Hanrahan, J. and M. Snyder, Cytoskeletal activation of a checkpoint kinase, Mol Cell, 12 (3), 663-73 (2003).
(Featured on cover)

137. Phizicky, E., Bastiaens, P.I., Zhu, H, Snyder, M, and Fields, S. (2003). Protein Analysis on a Proteomic Scale.
Nature. 422: 208-15.

138. Huang, J., Zhu, H, Haggarty, S.J., Spring, D.R. Snyder, M., and S. Schreiber. (2004). Finding New Components of
the TOR Signaling Pathway using Chemical Genetics and Proteome Chips, submitted.

139. Ball, J., Schweitzer, B., Predki, P., and Snyder, M., (2003). Development and Applications of Functional Protein
Arrays. M. Schena ed. Jones and Bartlett Publishers, Boston Protein Microarrays 421-440.

140. Schweitzer, B., Predki, P., and Snyder, M. (2003). Microarrays to Characterize Protein Interactions on a
Whole-Proteome Scale. Proteomics 3:2190-9.

141. Martone, R., G. Euskirchen, P. Bertone, S. Hartman, T. E. Royce, N. M. Luscombe, J. L. Rinn, F. K. Nelson, P.
Miller, M. Gerstein, S. Weissman and M. Snyder, Distribution of NF-kappaB-binding sites across human chromosome 22,
Proc Natl Acad Sci U S A, 100 (21), 12247-52 (2003).

142. Kafadar, K.A., Zhu, H., Snyder, M., and M. Cyert. (2003). Negative Regulation of Calcineurin Signaling by
Hrr25p, a Yeast Homolog of Casein Kinase I. Genes Devel. 17: 2698-708.

143. Michaud GA, Salcius M, Zhou F, Bangham R, Bonin J, Guo H, Snyder M, Predki PF, Schweitzer BI. (2003). Analyzing
antibody specificity with whole proteome microarrays. (2003). Nat. Biotechnol. 21:1509-12.

144. Jansen, R., H. Yu, D. Greenbaum, Y. Kluger, N. J. Krogan, S. Chung, A. Emili, M. Snyder, J. F. Greenblatt and M.
Gerstein, A Bayesian networks approach for predicting protein-protein interactions from genomic data, Science, 302
(5644), 449-53 (2003).

145. Lian, Z., G. Euskirchen, J. Rinn, R. Martone, P. Bertone, S. Hartman, T. Royce, K. Nelson, F. Sayward, N.
Luscombe, J. Yang, J. L. Li, P. Miller, A. E. Urban, M. Gerstein, S. Weissman and M. Snyder, Identification of novel
functional elements in the human genome, Cold Spring Harb Symp Quant Biol, 68 317-22 (2003).

146. Bidlingmaier, S. and M. Snyder, Regulation of polarized growth initiation and termination cycles by the polarisome
and Cdc42 regulators, J Cell Biol, 164 (2), 207-18 (2004). (Featured on cover).

147. Smith, M. G., S. G. Des Etages and M. Snyder, Microbial synergy via an ethanol-triggered pathway, Mol Cell Biol,
24 (9), 3874-84 (2004).]

148. Euskirchen, G., T. E. Royce, P. Bertone, R. Martone, J. L. Rinn, F. K. Nelson, F. Sayward, N. M. Luscombe, P.
Miller, M. Gerstein, S. Weissman and M. Snyder, CREB binds to multiple loci on human chromosome 22, Mol Cell Biol,
24 (9), 3804-14 (2004).

149. Rinn, J. L., J. S. Rozowsky, I. J. Laurenzi, P. H. Petersen, K. Zou, W. Zhong, M. Gerstein and M. Snyder, Major
molecular differences between mammalian sexes are involved in drug metabolism and renal function, Dev Cell, 6 (6),
791-800 (2004).]

150. Euskirchen G. and M. Snyder (2004). A Plethora of Sites. Nature Gen. 36, 325-326.

151. Hall, D. A., H. Zhu, X. Zhu, T. Royce, M. Gerstein and M. Snyder, Regulation of gene expression by a metabolic
enzyme, Science, 306 (5695), 482-4 (2004).

152. Luscombe, N. M., M. M. Babu, H. Yu, M. Snyder, S. A. Teichmann and M. Gerstein, Genomic analysis of regulatory
network dynamics reveals large topological changes, Nature, 431 (7006), 308-12 (2004).

153. White, E. J., O. Emanuelsson, D. Scalzo, T. Royce, S. Kosak, E. J. Oakeley, S. Weissman, M. Gerstein, M. Groudine,
M. Snyder and D. Schubeler, DNA replication-timing analysis of human chromosome 22 at high resolution and different
developmental states, Proc Natl Acad Sci U S A, 101 (51), 17771-6 (2004).]

154. Bertone, P., V. Stolc, T. E. Royce, J. S. Rozowsky, A. E. Urban, X. Zhu, J. L. Rinn, W. Tongprasit, M. Samanta, S.
Weissman, M. Gerstein and M. Snyder, Global identification of human transcribed sequences with genome tiling arrays,
Science, 306 (5705), 2242-6 (2004).

155. Kumar, A., M. Seringhaus, M. C. Biery, R. J. Sarnovsky, L. Umansky, S. Piccirillo, M. Heidtman, K. H. Cheung, C.
J. Dobry, M. B. Gerstein, N. L. Craig and M. Snyder, Large-scale mutagenesis of the yeast genome using a Tn7-derived
multipurpose transposon, Genome Res, 14 (10A), 1975-86 (2004).

156. Bertone, P. and M. Snyder, Prospects and challenges in proteomics, Plant Physiol, 138 (2), 560-2 (2005).
[http://www.plantphysiol.org/cgi/content/full/138/2/560]

157. Bertone, P., M. Gerstein and M. Snyder, Applications of DNA tiling arrays to experimental genome annotation and
regulatory pathway discovery, Chromosome Res, 13 (3), 259-74 (2005).
[http://www.springerlink.com/app/home/contribution.asp?wasp=d7fa7fe6254543e18eb51435e721d29d&referrer=parent&backto=
issue,5,12;journal,3,73;linkingpublicationresults,1:101771,1]

158. Rinn, J. L. and M. Snyder, Sexual dimorphism in mammalian gene expression, Trends Genet, 21 (5), 298-305 (2005).
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-4FTXXKH-3&_coverDate=05%2F31%2F2005&_alid=306589824&
_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5183&_sort=d&view=c&_acct=C000022720&_version=1&_urlVersion=0&_userid=483692&
md5=0b6c713d22f65db34186eecc377db4c1]

159. Royce, T. E., J. S. Rozowsky, P. Bertone, M. Samanta, V. Stolc, S. Weissman, M. Snyder and M. Gerstein, Issues in
the analysis of oligonucleotide tiling microarrays for transcript mapping, Trends Genet, 21 (8), 466-75 (2005).
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-4GG2HK4-2&_coverDate=08%2F31%2F2005&_alid=306581565&
_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5183&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=
8f0408ce7b60d60fa469b439412b69b5]

160. Smith, M. G., G. Jona, J. Ptacek, G. Devgan, H. Zhu, X. Zhu and M. Snyder, Global analysis of protein function
using protein microarrays, Mech Ageing Dev, 126 (1), 171-5 (2005).
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T31-4DM23HJ-2&_coverDate=01%2F01%2F2005&_alid=306577344&
_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=4933&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=
abf65c8d2d0f6fb513b0f0cb9cbc1667]Snyder, M., R. J. Sapolsky and R. W. Davis, Transcription interferes with elements
important for chromosome maintenance in Saccharomyces cerevisiae, Mol Cell Biol, 8 (5), 2184-94 (1988).