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Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets.

Lu X, Kensche PR, Huynen MA, Notebaart RA.

Nat Commun. 2013;4:2124. doi: 10.1038/ncomms3124.


Exploring genetic interactions and networks with yeast.

Boone C, Bussey H, Andrews BJ.

Nat Rev Genet. 2007 Jun;8(6):437-49. Review.


Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks.

He X, Qian W, Wang Z, Li Y, Zhang J.

Nat Genet. 2010 Mar;42(3):272-6. doi: 10.1038/ng.524. Epub 2010 Jan 24.


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, 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.

Science. 2010 Jan 22;327(5964):425-31. doi: 10.1126/science.1180823.


Evolutionary plasticity of genetic interaction networks.

Tischler J, Lehner B, Fraser AG.

Nat Genet. 2008 Apr;40(4):390-1. doi: 10.1038/ng.114. Epub 2008 Mar 23.


Modeling synthetic lethality.

Le Meur N, Gentleman R.

Genome Biol. 2008;9(9):R135. doi: 10.1186/gb-2008-9-9-r135. Epub 2008 Sep 12.


An integrated approach to characterize genetic interaction networks in yeast metabolism.

Szappanos B, Kovács K, Szamecz B, Honti F, Costanzo M, Baryshnikova A, Gelius-Dietrich G, Lercher MJ, Jelasity M, Myers CL, Andrews BJ, Boone C, Oliver SG, Pál C, Papp B.

Nat Genet. 2011 May 29;43(7):656-62. doi: 10.1038/ng.846.


Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions.

Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS.

Genome Res. 2008 Dec;18(12):1991-2004. doi: 10.1101/gr.077693.108. Epub 2008 Oct 2.


Preferential attachment in the protein network evolution.

Eisenberg E, Levanon EY.

Phys Rev Lett. 2003 Sep 26;91(13):138701. Epub 2003 Sep 26.


Genetic architecture of growth traits revealed by global epistatic interactions.

Xu L, Jiang H, Chen H, Gu Z.

Genome Biol Evol. 2011;3:909-14. doi: 10.1093/gbe/evr065. Epub 2011 Aug 22.


Saccharomyces cerevisiae genetics predicts candidate therapeutic genetic interactions at the mammalian replication fork.

van Pel DM, Stirling PC, Minaker SW, Sipahimalani P, Hieter P.

G3 (Bethesda). 2013 Feb;3(2):273-82. doi: 10.1534/g3.112.004754. Epub 2013 Feb 1.


Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.

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.

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


The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication.

Presser A, Elowitz MB, Kellis M, Kishony R.

Proc Natl Acad Sci U S A. 2008 Jan 22;105(3):950-4. doi: 10.1073/pnas.0707293105. Epub 2008 Jan 16.


Improved functional overview of protein complexes using inferred epistatic relationships.

Ryan C, Greene D, Guénolé A, van Attikum H, Krogan NJ, Cunningham P, Cagney G.

BMC Syst Biol. 2011 May 23;5:80. doi: 10.1186/1752-0509-5-80.


Evolution of protein complexes by duplication of homomeric interactions.

Pereira-Leal JB, Levy ED, Kamp C, Teichmann SA.

Genome Biol. 2007;8(4):R51.


An in vivo map of the yeast protein interactome.

Tarassov K, Messier V, Landry CR, Radinovic S, Serna Molina MM, Shames I, Malitskaya Y, Vogel J, Bussey H, Michnick SW.

Science. 2008 Jun 13;320(5882):1465-70. doi: 10.1126/science.1153878. Epub 2008 May 8.


Transcriptional regulatory networks in Saccharomyces cerevisiae.

Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA.

Science. 2002 Oct 25;298(5594):799-804.


An in silico approach combined with in vivo experiments enables the identification of a new protein whose overexpression can compensate for specific respiratory defects in Saccharomyces cerevisiae.

Glatigny A, Mathieu L, Herbert CJ, Dujardin G, Meunier B, Mucchielli-Giorgi MH.

BMC Syst Biol. 2011 Oct 25;5:173. doi: 10.1186/1752-0509-5-173.


Computational architecture of the yeast regulatory network.

Maslov S, Sneppen K.

Phys Biol. 2005 Nov 9;2(4):S94-100.

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