Selected Publications

2011

Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell.

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.
Nat Biotechnol. 2011
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Systematic exploration of essential yeast gene function with temperature-sensitive mutants.

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, et al.
Nat Biotechnol. 2011
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Bringing order to protein disorder through comparative genomics and genetic interactions.

Bellay J, Han S, Michaut M, Kim T, Costanzo M, Andrews BJ, Boone C, Bader GD, Myers CL, Kim PM.
Genome Biol. 2011 Feb 16;12(2):R14
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Combining functional genomics and chemical biology to identify targets of bioactive compounds.

Ho CH, Piotrowski J, Dixon SJ, Baryshnikova A, Costanzo M, Boone C.
Curr Opin Chem Biol. 2011 Feb;15(1):66-78
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Charting the genetic interaction map of a cell.

Costanzo M, Baryshnikova A, Myers CL, Andrews B, Boone C.
Curr Opin Biotechnol. 2011 Feb;22(1):66-74
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Microarray-based target identification using drug hypersensitive fission yeast expressing ORFeome.

Arita Y, Nishimura S, Matsuyama A, Yashiroda Y, Usui T, Boone C, Yoshida M.
Mol Biosyst. 2011 Feb 22
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2010

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.

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.
Nat Methods. 2010 Dec;7(12):1017-24
PDF, Supplementary website

The genetic landscape of a cell.

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, et al.
Science. 2010 Jan 22;327(5964):425-31
PDF, Supplementary website

DRYGIN: a database of quantitative genetic interaction networks in yeast.

Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C.
Nucleic Acids Res. 2010 Jan;38(Database issue):D502-7

Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis.

Vizeacoumar FJ, van Dyk N, Vizeacoumar FS, 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.
J Cell Biol. 2010 Jan 11;188(1):69-81

Genotype to phenotype: a complex problem.

Dowell RD, Ryan O, Jansen A, Cheung D, Agarwala S, Danford T, Bernstein DA, Rolfe PA, Heisler LE, Chin B, Nislow C, Giaever G, Phillips PC, Fink GR, Gifford DK, Boone C.
Science. 2010 Apr 23;328(5977):469

Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe.

Baryshnikova A, Costanzo M, Dixon S, Vizeacoumar FJ, Myers CL, Andrews B, Boone C.
Methods Enzymol. 2010;470:145-79

Genetic interactions reveal the evolutionary trajectories of duplicate genes.

VanderSluis B, Bellay J, Musso G, Costanzo M, Papp B, Vizeacoumar FJ, Baryshnikova A, Andrews B, Boone C, Myers CL.
Mol Syst Biol. 2010 Nov 16;6:429

2009

A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.

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.
Nat Biotechnol. 2009 Apr;27(4):369-77

Systematic mapping of genetic interaction networks.

Dixon SJ, Costanzo M, Baryshnikova A, Andrews B, Boone C.
Annu Rev Genet. 2009;43:601-25. Review.

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.

Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Currell B, Seshagiri S, Yu H, Winsor B, Vidal M, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C.
PLoS Biol. 2009 Oct;7(10):e1000218

2008

Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes.

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.
Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16653-8

2007

Exploring genetic interactions and networks with yeast.

Boone C, Bussey H, Andrews BJ.
Nat Rev Genet. 2007 Jun;8(6):437-49. Review.

2006

Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast.

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, et al.
Cell. 2006 Aug 11;126(3):611-25
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2004

Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways.

Parsons AB, Brost RL, Ding H, Li Z, Zhang C, Sheikh B, Brown GW, Kane PM, Hughes TR, Boone C.
Nat Biotechnol. 2004 Jan;22(1):62-9
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Global mapping of the yeast genetic interaction network.

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, et al.
Science. 2004 Feb 6;303(5659):808-13
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2002

A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.

Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G.
Science. 2002 Jan 11;295(5553):321-4
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2001

Systematic genetic analysis with ordered arrays of yeast deletion mutants.

Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Pagé N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C.
Science. 2001 Dec 14;294(5550):2364-8
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