2012 2011 2010 2009 2008 2007
 

Selected Publications:              



2012

Douglas AC, Smith AM, Sharifpoor S, Yan Z, Durbic T, Heisler LE, Lee AY, Ryan O, Göttert H, Surendra A, van Dyk D, Giaever G, Boone C, Nislow C, Andrews BJ. Functional analysis with a barcoder yeast gene overexpression system. G3: Genes, Genomes, Genetics. 2012 Oct;2(10):1279-89. PMID:23050238

Kaluarachchi Duffy S,Friesen H, Baryshnikova A, Lambert JP, Chong YT, Figeys D, Andrews BJ. Exploring the yeast acetylome using functional genomics.  Cell. 2012 May 11;149(4):936-48. PMID:22579291

Nguyen Ba AN, Yeh BJ, van Dyk D, Davidson AR, Andrews BJ, Weiss EL, Moses AM. Proteome-wide discovery of evolutionary conserved sequences in disordered regions.  Sci Signal. 2012 Mar 13; 15(215):rs1. PMID: 22416277

Sharifpoor S, van Dyk D, Costanzo M, Baryshnikova A, Friesen H, Douglas AC, Youn JY, Vandersluis B, Myers CL, Papp B, Boone C, Andrews BJ. Functional wiring of the yeast kinome revealed by global analysis of network motifs. Genome Res. 2012 Apr;22(4):791-801. PMID: 22282571


[Top]
2011

Kurat CF, Lambert JP, van Dyk D, Tsui K, van Bakel H, Kaluarachchi S, Friesen H, Kainth P, Nislow C, Figeys D, Fillingham J, Andrews BJ. Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundry protein.  Genes Dev. 2011 Dec 1;25 (23):2489-501. PMID: 22156209

Sharifpoor S, Nguyen Ba AN, Youn JY, van Dyk D, Friesen H, Douglas AC, Kurat CF, Chong YT, Founk K, Moses AM, Andrews BJ. A quantitative literature-curated gold standard for kinase-substrate pairs.  Genome Biol. 2011 Apr 14;12(4):R39. PMID: 21492431

Li Z, Vizeacoumar FJ, Bahr S, Li J, Warringer J, Vizeacoumar FS, Min R, Vandersluis B, Bellay J, Devit M, Fleming JA, Stephens A, Haase J, Lin ZY, Baryshnikova A, Lu H, Yan Z, Jin K, Barker S, Datti A, Giaever G, Nislow C, Bulawa C, Myers CL, Costanzo M, Gingras AC, Zhang Z, Blomberg A, Bloom K, Andrews B, Boone C. Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat Biotechnol. 2011 Apr;29(4):361-7. Epub 2011 Mar 27. PMID: 21441928

Magtanong L, Ho CH, Barker SL, Jiao W, Baryshnikova A, Bahr S, Smith AM, Heisler LE, Choy JS, Kuzmin E, Andrusiak K, Kobylianski A, Li Z, Costanzo M, Basrai MA, Giaever G, Nislow C, Andrews B, Boone C.Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell. Nat Biotechnol. 2011, May 15;29(6):505-11. PMID: 21572441


[Top]
2010
Youn JY, Friesen H, Kishimoto T, Henne WM, Kurat CF, Ye W, Ceccarelli DF, Sicheri F, Kohlwein SD, McMahon HT, Andrews BJ. Dissecting BAR domain function in the yeast Amphiphysins Rvs161 and Rvs167 during endocytosis. Mol Biol Cell. 2010 Sep 1;21(17):3054-69. Epub 2010 Jul 7.PMID:20610658

Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C. , The genetic landscape of a cell. , Science. 2010 Jan 22;327(5964):425-31. PMID: 20093466

VanderSluis B, Bellay J, Musso G, Costanzo M, Papp B, Vizeacoumar FJ, Baryshnikova A, Andrews B, Boone C, Myers CL. Genetic interactions reveal the evolutionary trajectories of duplicate genes. Mol Syst Biol. 2010 Nov 16;6:429. PMID: 21081923

Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL.Quantitative analysis of fitness and genetic interactions in yeast on a genome scale , Nat Methods. 2010 Dec;7(12):1017-24. Epub 2010 Nov 14. PMID: 21076421

Vizeacoumar FJ, van Dyk N, S Vizeacoumar F, Cheung V, Li J, Sydorskyy Y, Case N, Li Z, Datti A, Nislow C, Raught B, Zhang Z, Frey B, Bloom K, Boone C, Andrews BJ., Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis., J Cell Biol. 2010 Jan 11;188(1):69-81.PMID: 20065090

Baryshnikova A, Costanzo M, Dixon S, Vizeacoumar FJ, Myers CL, Andrews B, Boone C. Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Methods Enzymol. 2010;470:145-79. Epub 2010 Mar 1. PMID: 20946810

Kainth P, Andrews B. Quantitative cell array screening to identify regulators of gene expression. Brief Funct Genomics. 2010 Jan;9(1):13-23. Epub 2009 Dec 1. Review. PMID: 19952074.

Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C. DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res. 2010; Jan;38(Database issue):D502-7. Epub 2009 Oct 30. PMID: 19880385

Baryshnikova A, Costanzo M, Dixon S, Vizeacoumar FJ, Myers CL, Andrews B, Boone C. Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Methods Enzymol. 2010;470:145-79. Epub 2010 Mar 1. PMID: 20946810

Kahana S, Pnueli L, Kainth P, Sassi HE, Andrews B, Kassir Y. Functional dissection of IME1 transcription using quantitative promoter-reporter screening. Genetics. 2010 Nov;186(3):829-41. Epub 2010 Aug 25. PMID: 20739709

Liu C, van Dyk D, Xu P, Choe V, Pan H, Peng J, Andrews B, Rao H. Ubiquitin chain elongation enzyme Ufd2 regulates a subset of Doa10 substrates. J Biol Chem. 2010 Apr 2;285(14):10265-72. Epub 2010 Feb 16. PMID:20159987

Kainth P, Andrews B. Quantitative cell array screening to identify regulators of gene expression. Brief Funct Genomics. 2010 Jan;9(1):13-23. Epub 2009 Dec 1. Review. PMID: 19952074.
Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C. DRYGIN: a database of quantitative genetic interaction networks in yeast. Nucleic Acids Res. 2010 Jan;38(Database issue):D502-7. Epub 2009 Oct 30. PubMed PMID: 19880385.

Traven A, Lo TL, Pike BL, Friesen H, Guzzo J, Andrews B, Heierhorst J. Dual functions of Mdt1 in genome maintenance and cell integrity pathways in Saccharomyces cerevisiae. Yeast. 2010 Jan;27(1):41-52. PMID: 19894211

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 Sep;5(9):789-95. PubMed PMID: 18677321.

[Top]
2009

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. Epub 2009 Sep 8. PMID: 19823668

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. PMID: 19683497

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. Epub 2009 Mar 6. PMID: 19269327

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. PMID:19521819

Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C. Systematic mapping of genetic interaction networks. Annu Rev Genet. 2009; 43:601-25. Review. PMID: 19712041

Dixon SJ, Andrews BJ, Boone C.
Exploring the conservation of synthetic lethal genetic interaction networks. Commun Integr Biol. 2009; 2(2):78-81. PubMed PMID:19704894.

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. PubMed PMID:19521819.

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. Epub 2009 May 20.PMID: 19458192.

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. PubMed PMID: 19351535.

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. PMID: 19150427

Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C. Systematic mapping of genetic interaction networks. Annu Rev Genet. 2009;43:601-25. Review. PMID: 19712041
Dixon SJ, Andrews BJ, Boone C. Exploring the conservation of synthetic lethal genetic interaction networks. Commun Integr Biol. 2009;2(2):78-81. PubMed PMID:19704894.

Dhillon N, Raab J, Guzzo J, Szyjka SJ, Gangadharan S, Aparicio OM, Andrews B, Kamakaka RT. DNA polymerase epsilon, acetylases and remodellers cooperate to form a specialized chromatin structure at a tRNA insulator.EMBO J. 2009 Sep 2;28(17):2583-600. Epub 2009 Jul 23. PMID: 19629037

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. Epub 2009 May 20.PMID: 19458192.
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. PubMed PMID: 19351535.

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. PMID: 19349972

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. Epub 2009 Mar 6. PMID: 19269327
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. PubMed PMID: 19150434.

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. PMID: 19150427

 

[Top]
2008

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. PubMed PMID: 18931302.

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; Aug;5(8):719-25. Epub 2008 Jul 11. PubMed PMID: 18622398.



[Top]
2007
Sopko R, Huang D, Smith JC, Figeys D, Andrews BJ. Activation of the Cdc42pGTPase by cyclin-dependent protein kinases in budding yeast EMBO J. 2007; Oct 31;26(21):4487-500. Epub 2007 Sep 13. PubMed PMID: 17853895.

Huang D, Friesen H, Andrews B. Pho85, a multifunctional cyclin-dependent protein kinase in budding yeast. Mol Microbiol. 2007; Oct;66(2):303-14. Epub 2007 Sep 10. Review. PMID: 17850263

Boone C, Bussey H, Andrews BJ.
Exploring genetic interactions and networks with yeast. Nat Rev Genet. 2007; Jun;8(6):437-49. Review. PubMed PMID: 17510664.

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; May;176(1):193-208. Epub 2007 Apr 3. PubMed PMID: 17409071.

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; Apr 12;446(7137):806-10. Epub 2007 Feb 21. PMID: 17314980



Full list of publications can be downloaded from PubMED.