Select Publications

Kainth P, Andrews B. Quantitative cell array screening to identify regulators of gene expression. Brief Funct Genomic Proteomic. 2009 Dec 1. [Epub ahead of print]

Huang D, Kaluarachchi S, van Dyk D, Friesen H, Sopko R, Ye W, Bastajian N, Moffat J, Sassi H, Costanzo M, Andrews BJ. Dual regulation by pairs of cyclin-dependent protein kinases and histone deacetylases controls G1 transcription in budding yeast. PLoS Biol. 2009 Sep;7(9):e1000188.

Zou J, Friesen H, Larson J, Huang D, Cox M, Tatchell K, Andrews B. Regulation of cell polarity through phosphorylation of Bni4 by Pho85 G1 cyclin-dependent kinases in Saccharomyces cerevisiae. Mol Biol Cell. 2009 Jul;20(14):3239-50

Fillingham J, Kainth P, Lambert JP, van Bakel H, Tsui K, Peña-Castillo L, Nislow C, Figeys D, Hughes TR, Greenblatt J, Andrews BJ. Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. Mol Cell. 2009 Aug 14;35(3):340-51.

Kainth P, Sassi HE, Peña-Castillo L, Chua G, Hughes TR, Andrews B.Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast. Methods. 2009 Jul;48(3):258-64.

Sassi HE, Bastajian N, Kainth P, Andrews BJ. Reporter-based synthetic genetic array analysis: a functional genomics approach for investigating the cell cycle in Saccharomyces cerevisiae. Methods Mol Biol. 2009;548:55-73.

Roth FP, Lipshitz HD, Andrews BJ. Q&A: epistasis. J Biol. 2009;8(4):35. Epub 2009 May 22.

Zou J, Friesen H, Larson J, Huang D, Cox M, Tatchell K, Andrews B. Regulation of Cell Polarity through Phosphorylation of Bni4 by Pho85 G1 Cdks in Saccharomyces cerevisiae. Mol Biol Cell. 2009 May 20. [Epub ahead of print]
Vizeacoumar FJ, Chong Y, Boone C, Andrews BJ. A picture is worth a thousand words: genomics to phenomics in the yeast Saccharomyces cerevisiae. FEBS Lett. 2009 Jun 5;583(11):1656-61. Epub 2009 Apr 5. Review.

Ho CH, Magtanong L, Barker SL, Gresham D, Nishimura S, Natarajan P, Koh JL, Porter J, Gray CA, Andersen RJ, Giaever G, Nislow C, Andrews B, Botstein D, Graham TR, Yoshida M, Boone C. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nat Biotechnol. 2009 Apr;27(4):369-77. Epub 2009 Apr 6.

Kainth P, Sassi HE, Peña-Castillo L, Chua G, Hughes TR, Andrews B. Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast. Methods. 2009 Mar 6. [Epub ahead of print]

Makhnevych T, Sydorskyy Y, Xin X, Srikumar T, Vizeacoumar FJ, Jeram SM, Li Z, Bahr S, Andrews BJ, Boone C, Raught B. Global map of SUMO function revealed by protein-protein interaction and genetic networks. Mol Cell. 2009 Jan 16;33(1):124-35.

Kurat CF, Wolinski H, Petschnigg J, Kaluarachchi S, Andrews B, Natter K, Kohlwein SD. Cdk1/Cdc28-dependent activation of the major triacylglycerol lipase Tgl4 in yeast links lipolysis to cell-cycle progression. Mol Cell. 2009 Jan 16;33(1):53-63.

Dixon SJ, Fedyshyn Y, Koh JL, Prasad TS, Chahwan C, Chua G, Toufighi K, Baryshnikova A, Hayles J, Hoe KL, Kim DU, Park HO, Myers CL, Pandey A, Durocher D, Andrews BJ, Boone C. Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16653-8. Epub 2008 Oct 17.

Sopko R, Andrews BJ. Linking the kinome and phosphorylome--a comprehensive review of approaches to find kinase targets. Mol Biosyst. 2008 Sep;4(9):920-33. Epub 2008 Jul 17. Review.

Butland G, Babu M, Díaz-Mejía JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H, Sheikh B, Moreno-Hagelseib G, Greenblatt JF, Emili A. eSGA: E. coli synthetic genetic array analysis. Nat Methods. 2008 5(9):789-95.

Yan Z, Costanzo M, Heisler LE, Paw J, Kaper F, Andrews BJ, Boone C, Giaever G, Nislow C. Yeast Barcoders: a chemogenomic application of a universal donor-strain collection carrying bar-code identifiers. Nat Methods. 2008 5:719-25.

Hoke SM, Guzzo J, Andrews B, Brandl CJ. Systematic genetic array analysis links the Saccharomyces cerevisiae SAGA/SLIK and NuA4 component Tra1 to multiple cellular processes. BMC Genet. 2008 9:46.

Sopko R, Huang D, Smith JC, Figeys D, Andrews BJ. Activation of the Cdc42p GTPase by cyclin-dependent protein kinases in budding yeast. EMBO J. 2007 26:4487-500.

Huang D, Friesen H, Andrews B.Pho85, a multifunctional cyclin-dependent protein kinase in budding yeast. Mol Microbiol. 2007 66:303-14.

Mutiu AI, Hoke SM, Genereaux J, Hannam C, MacKenzie K, Jobin-Robitaille O, Guzzo J, Côté J, Andrews B, Haniford DB, Brandl CJ. Structure/function analysis of the phosphatidylinositol-3-kinase domain of yeast tra1. Genetics. 2007 177:151-66.

Boone C, Bussey H, Andrews BJ. Exploring genetic interactions and networks with yeast. Nat Rev Genet. 2007 8:437-49.

Haynes J, Garcia B, Stollar EJ, Rath A, Andrews BJ, Davidson AR. The biologically relevant targets and binding affinity requirements for the function of the yeast actin-binding protein 1 Src-homology 3 domain vary with genetic context. Genetics. 2007 176:193-208.

Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature. 2007 446:806-10.

Costanzo M, Giaever G, Nislow C, Andrews B. Experimental approaches to identify genetic networks. Curr Opin Biotechnol. 2006 17:472-80.

Parsons AB, Lopez A, Givoni IE, Williams DE, Gray CA, Porter J, Chua G, Sopko R, Brost RL, Ho CH, Wang J, Ketela T, Brenner C, Brill JA, Fernandez GE, Lorenz TC, Payne GS, Ishihara S, Ohya Y, Andrews B, Hughes TR, Frey BJ, Graham TR, Andersen RJ, Boone C. Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast. Cell. 2006 126:611-25.

Chua G, Morris QD, Sopko R, Robinson MD, Ryan O, Chan ET, Frey BJ, Andrews BJ, Boone C, Hughes TR. Identifying transcription factor functions and targets by phenotypic activation. Proc Natl Acad Sci U S A. 2006 103:12045-50

Bussey H, Andrews B, Boone C. From worm genetic networks to complex human diseases. Nat Genet. 2006 38:862-3.

Sopko R, Papp B, Oliver SG, Andrews BJ. Phenotypic activation to discover biological pathways and kinase substrates. Cell Cycle. 2006 5:1397-402.

Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol. 2006  5:11.

Baetz K, Measday V, Andrews B. Revealing hidden relationships among yeast genes involved in chromosome segregation using systematic synthetic lethal and synthetic dosage lethal screens. Cell Cycle. 2006 5:592-5.

Sopko R, Andrews B. Small open reading frames: not so small anymore. Genome Res. 2006 16:314-5

Friesen, H., Humphries, C., Ho, Y., Schub, O. Collwill, K. and Andrews, B. (2006).  Genetic characterization of the yeast amphiphysins RVS161 and RVS167 reveals roles for the Rvs heterodimer in vivo.  Mol. Biol. Cell 17, 1306-1321

Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K., Snyder, M., Oliver, S.G., Cyert, M., Hughes, T.R., Boone, C., Andrews, B. (2006).  Mapping pathways and phenotypes by systematic gene overexpression.  Mol. Cell 21: 319-330

Measday, V., Baetz, K., Guzzo, J., Yuen, K., Kwok, T., Shiekh, B., Ding, H., Ueta, R.,  Hoac, T., Cheng, B., Pot, I., Tong, A., Yamaguchi-Iwai, Y., Boone, C., Hieter, P.,  Andrews, B. (2005).   Systematic yeast synthetic lethal and synthetic dosage lethality screens identify genes required for chromosome segregation.  Proc Natl Acad Sci USA 102: 13956-13961

Armaity P. Davierwala*, Jennifer Haynes*, Zhijian Li, Renée L. Brost, Mark D. Robinson, Lisa Yu, Sanie Mnaimneh, Huiming Ding, Hongwei Zhu, Yiqun Chen, Xin Cheng,  Grant W. Brown, Charles Boone§, Brenda J. Andrews§ and Timothy R. Hughes§.  (2005).  The synthetic genetic    interaction spectrum of essential genes,  Nature Genetics  37, 1147-1152  §Co-corresponding authors

Friesen, H., Colwill, K., Robertson, K., Schub, O., and Andrews, B.J. (2005).  Interaction of the Saccharomyces cerevisiae cortical actin patch protein Rvs167p with proteins involved in ER to Golgi vesicle trafficking.  Genetics 170, 555-568

Menon, B.B., Sarma, N.J., Pasula, S., Deminoff, S.J., Willis, K.A., Barbara, K.E., Andrews, B., Santangelo, G.M. (2005).  Reverse recruitment: The Nup84 nuclear pore subcomplex mediates Rap1/Gcr1/Gcr2 transcriptional activation.  Proc. Natl. Acad. Sci  USA 102, 5749-5754

Mnaimneh, S*., Davierwala, A.P*., Haynes, J*., Moffat, J., Peng, W.T., Zhang, W., Yang, X, Pootoolal, J., Chua, G., Lopez, A., Trochesset, M., Morse, D., Krogan, N.J., Hiley, S.L., Li, Z., Morris, Q., Grigull, J., Mitsakakis, N., Roberts, C.J., Greenblatt, J.F., Boone, C., Kaiser, C.A., Andrews, B.J., Hughes, T.R. (2004).  Exploration of essential gene functions via titratable promoter alleles.  Cell 118, 31-44 {*co-first authors)

Marles JA, Dahesh S, Haynes J, Andrews BJ, Davidson AR. (2004). Protein-Protein Interaction Afinity Plays a Crucial Role in Conrolling the Sho1p-Mediated Signal Transduction Pathway in Yeast. Mol. Cell. 2004 Jun 18; 14:813-823.

Friesen H, Millman JS, Andrews BJ. (2003). Yeast functional genomics and cell biology: no longer in the dark. Genome Biol. 2003;4(12):352.

Costanzo M, Nishikawa JL, Tang X, Millman JS, Schub O, Breitkreuz K, Dewar D, Rupes I, Andrews BJ, Tyers M. (2004). CDK Activity Antagonizes Whi5, an Inhibitor of G1/S Trancription in Yeast. Cell. 2004 Jun 25; 117:899-913.

Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C. (2004). Global mapping of the yeast genetic interaction network. Science. 2004 Feb 6;303(5659):808-13.

Moffat J, Andrews B. (2004). Late-G1 cyclin-CDK activity is essential for control of cell morphogenesis in budding yeast. Nat Cell Biol. 2004 Jan;6(1):59-66.

Costanzo M, Schub O, Andrews B. (2003). G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1. Mol Cell Biol. 2003 Jul;23(14):5064-77.

Friesen H, Murphy K, Breitkreutz A, Tyers M, Andrews B. (2003). Regulation of the yeast amphiphysin homologue Rvs167p by phosphorylation. Mol Biol Cell. 2003 Jul;14(7):3027-40.

Humphries, C., Balser, H., D'Agostino, J., Winsor, B., Drubin, D., Barnes, G., Andrews, B, and Goode, B. (2002). Direct regulation of Arp2/3 complex activity and function by the actin binding protein coronin. J Cell Biol. 2002 Dec 23;159(6):993-1004.

Huang, D., Moffat, J. and Andrews, B. (2002). Dissection of a complex
phenotype by functional genomics reveals roles for the yeast
cyclin-dependent protein kinase Pho85 in stress adaptation and cell
integrity. Mol. Cell. Biol. 22, 5076-5088.

Tong, A., Evangelista, M., Parsons, A., Xu, H., Bader, G., Page, N., Robinson, M.,
Raghibizadeh, S., Hogue, C., Bussey, H., Andrews, B., Tyers, M., and Boone, C. (2001). Systematic genetic: analysis with ordered arrays of yeast deletion mutants, Science. 2001 Dec 14;294(5550):2364-8.

McBride, H., Sil, A., Measday, V., Yu, Y., Moffat, J., Maxon, M., Herskowitz, I.,
Andrews, B. and Stillman, D. (2001) The Pho85 cyclin dependent protein kinase is required for proper daughter cell-specific localization of the Ash1 protein in Saccharomyces cerevisiae, Mol. Micro.42, 345-353.

Baetz, K., Moffat, J., Haynes, J., Chang, M. and Andrews, B. (2001). Transcriptional
coregulation by the cell integrity MAP kinase Slt2 and the cell cycle regulator Swi4, Mol. Cell Biol., 21, 6515-6528

Moffat, J., Huang, D. and Andrews, B. (2000). Functions of Pho85 cyclin-
dependent kinases in budding yeast, Progress in Cell Cycle Research 4, 97-107, Plenum Publishing.

Macpherson, N., Measday, V. Moore, L. and Andrews, B. (2000). A yeast TAF17 mutant requires the Swi6 transcriptional activator for viability and shows defects in cell cycle-regulated transcription, Genetics 154, 1561-1576.

Measday, V., McBride, H., Moffat, J., Stillman, D. and Andrews, B. (2000).
Interactions between Pho85 cyclin-dependent kinase complexes and the Swi5 transcription factor in budding yeast, Molecular Microbiology 35, 825-834.

Huang, D., Patrick, G., Moffat, J., Tsai, L-H. and Andrews, B. (1999). Mammalian Cdk5 is a functional homologue of the budding yeast Pho85 cyclin-dependent protein kinase, Proc. Natl. Acad. Sci., USA,14445-14450.

Baetz, K. and Andrews, B. (1999). Regulation of the cell cycle transcription factor
Swi4 through auto-inhibiton of DNA binding, Mol. Cell. Biol. 19, 6729-6741

Ho, Y., Costanzo, M., Moore, L., Kobayashi, R. and Andrews, B. (1999).
Regulation of transcription at the S. cerevisiae Start transition by Stb1, a Swi6-binding protein, Mol. Cell. Biol., 19, 5267-5278.

Colwill, K., Field, D., Moore, L., Friesen, J. and Andrews, B. (1999). In vivo
analysis of the domains of yeast Rvs167p suggests Rvs167p function is mediated through multiple protein interactions, Genetics 152, 881-893.

Lee, J., Colwill, K., Aneliunas, V., Tennyson, C., Moore, L., Ho, Y. and Andrews,
B. (1998). Interaction of the yeast Rvs167 protein and Pho85 cyclin-dependent kinase complexes may link the cell cycle to the actin cytoskeleton, Current Biology 8. 1310-1321.

Huang, D., Moffat, J., Wilson, W., Moore, L. Roach, P. and Andrews, B. (1998).
Cyclin partners determine Pho85 protein kinase substrate specificity in vitro and in vivo: control of glycogen biosynthesis by Pcl8/Pcl10. Mol. Cell. Biol., 18, 3289-3299.

Tennyson, C., Lee, J. and Andrews, B. (1998). A role for the Pcl9-Pho85 cyclin-
cdk complex at the M/G1 boundary in S. cerevisiae, Molecular Microbiology, 28, 69-79

Measday, V. and Andrews, B. (1998). The cyclin family of budding yeast:
abundant use of a good idea, Trends in Genetics, 14, 66-72 (peer-reviewed review article).

Madden, K., Sheu, Yi-Jun, Baetz, K., Andrews, B. and Snyder, M. (1997) SBF Cell cycle regulator as a downstream target of the yeast PKC-MAP kinase pathway, Science, 275, 1781-1784.

Measday, V., Moore, L., Retnakaran, R., Lee, J., Donoviel, M., Neiman, A. and
Andrews, B. (1997) A family of cyclin-like proteins that interact with the cyclin-dependent kinase, Pho85, Mol. Cell. Biol., 17, 1212-1223.

Ho, Y., Mason, S., Kobayashi, R., Hoekstra, M. and Andrews, B. (1997). Role of
the casein kinase I isoform, Hrr25, and the cell-cycle regulatory transcription factor, SBF, in the transcriptional response to DNA damage in Saccharomyces cerevisiae, Proc. Natl. Acad. Sci, USA, 94, 581-586.

Harrington, L. and Andrews, B. (1996). Binding to the Swi4,6-dependent cell cycle
box (SCB) is cell cycle-regulated in vivo, Nucleic Acids Rsch., 24, 558-565.

Measday, V., Moore, L., Ogas, J., Tyers, M. and Andrews, B. (1994). The Pcl2
(OrfD)-Pho85 cyclin-dependent kinase complex, a cell cycle regulator in yeast, Science, 266, 1391-1395.