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A strategy for extracting and analyzing large-scale quantitative epistatic interaction data
Sean R Collins, Maya Schuldiner, Nevan J Krogan, Jonathan S Weissman
Genome Biol. 2006; 7(7): R63. Published online 2006 July 21. doi: 10.1186/gb-2006-7-7-r63
PMCID:
PMC1779568
Abstract Full Text PDF–1.2M Supplementary Material

Is Cited by the Following 64 Articles in this Archive:

The Role of the Parkinson's Disease Gene PARK9 in Essential Cellular Pathways and the Manganese Homeostasis Network in Yeast
Alessandra Chesi, Austin Kilaru, Xiaodong Fang, Antony A. Cooper, Aaron D. Gitler
PLoS One. 2012; 7(3): e34178. Published online 2012 March 23. doi: 10.1371/journal.pone.0034178
PMCID:
PMC3311584
Abstract Full Text PDF–224K Supplementary Material
Scd6 targets eIF4G to repress translation: RGG-motif proteins as a class of eIF4G-binding proteins
Purusharth Rajyaguru, Meipei She, Roy Parker
Mol Cell. Author manuscript; available in PMC 2012 July 27.
Published in final edited form as: Mol Cell. 2012 January 27; 45(2): 244–254. doi: 10.1016/j.molcel.2011.11.026
PMCID:
PMC3277450
Free in PMC on 2012/07/27
A quantitative analysis of monochromaticity in genetic interaction networks
Chien-Hsiang Hsu, Tse-Yi Wang, Hsueh-Ting Chu, Cheng-Yan Kao, Kuang-Chi Chen
BMC Bioinformatics. 2011; 12(Suppl 13): S16. Published online 2011 November 30. doi: 10.1186/1471-2105-12-S13-S16
PMCID:
PMC3278832
Abstract Full Text PDF–3.9M Supplementary Material
Eisosome proteins assemble into a membrane scaffold
Lena Karotki, Juha T. Huiskonen, Christopher J. Stefan, Natasza E. Ziółkowska, Robyn Roth, Michal A. Surma, Nevan J. Krogan, Scott D. Emr, John Heuser, Kay Grünewald, Tobias C. Walther
J Cell Biol. 2011 November 28; 195(5): 889–902. doi: 10.1083/jcb.201104040
PMCID:
PMC3257569
Free in PMC on 2012/05/28
Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways
Mohan Babu, J. Javier Díaz-Mejía, James Vlasblom, Alla Gagarinova, Sadhna Phanse, Chris Graham, Fouad Yousif, Huiming Ding, Xuejian Xiong, Anaies Nazarians-Armavil, Md Alamgir, Mehrab Ali, Oxana Pogoutse, Asaf Pe'er, Roland Arnold, Magali Michaut, John Parkinson, Ashkan Golshani, Chris Whitfield, Shoshana J. Wodak, Gabriel Moreno-Hagelsieb, Jack F. Greenblatt, Andrew Emili
PLoS Genet. 2011 November; 7(11): e1002377. Published online 2011 November 17. doi: 10.1371/journal.pgen.1002377
PMCID:
PMC3219608
Abstract Full Text PDF–1.1M Supplementary Material
Genetic Dissection of Salicylic Acid-Mediated Defense Signaling Networks in Arabidopsis
Gina Ng, Savanna Seabolt, Chong Zhang, Sasan Salimian, Timley A. Watkins, Hua Lu
Genetics. 2011 November; 189(3): 851–859. doi: 10.1534/genetics.111.132332
PMCID:
PMC3213356
Free in PMC on 2012/11/01
A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria
Suzanne Hoppins, Sean R. Collins, Ann Cassidy-Stone, Eric Hummel, Rachel M. DeVay, Laura L. Lackner, Benedikt Westermann, Maya Schuldiner, Jonathan S. Weissman, Jodi Nunnari
J Cell Biol. 2011 October 17; 195(2): 323–340. doi: 10.1083/jcb.201107053
PMCID:
PMC3198156
Abstract Full Text PDF–4.1M Supplementary Material
Dominating Biological Networks
Tijana Milenković, Vesna Memišević, Anthony Bonato, Nataša Pržulj
PLoS One. 2011; 6(8): e23016. Published online 2011 August 26. doi: 10.1371/journal.pone.0023016
PMCID:
PMC3162560
Abstract Full Text PDF–779K
Putting genetic interactions in context through a global modular decomposition
Jeremy Bellay, Gowtham Atluri, Tina L. Sing, Kiana Toufighi, Michael Costanzo, Philippe Souza Moraes Ribeiro, Gaurav Pandey, Joshua Baller, Benjamin VanderSluis, Magali Michaut, Sangjo Han, Philip Kim, Grant W. Brown, Brenda J. Andrews, Charles Boone, Vipin Kumar, Chad L. Myers
Genome Res. 2011 August; 21(8): 1375–1387. doi: 10.1101/gr.117176.110
PMCID:
PMC3149503
Abstract Full Text PDF–1.3M
Integrating multiple types of data to predict novel cell cycle-related genes
Lin Wang, Lin Hou, Minping Qian, Fangting Li, Minghua Deng
BMC Syst Biol. 2011; 5(Suppl 1): S9. Published online 2011 June 20. doi: 10.1186/1752-0509-5-S1-S9
PMCID:
PMC3121125
Abstract Full Text PDF–1.1M Supplementary Material
Noise reduction in genome-wide perturbation screens using linear mixed-effect models
Danni Yu, John Danku, Ivan Baxter, Sungjin Kim, Olena K. Vatamaniuk, David E. Salt, Olga Vitek
Bioinformatics. 2011 August 15; 27(16): 2173–2180. Published online 2011 June 17. doi: 10.1093/bioinformatics/btr359
PMCID:
PMC3150043
Free in PMC on 2012/08/15
A yeast model for polyalanine-expansion aggregation and toxicity
Catherine A. Konopka, Melissa N. Locke, Pamela S. Gallagher, Ngan Pham, Michael P. Hart, Claire J. Walker, Aaron D. Gitler, Richard G. Gardner
Mol Biol Cell. 2011 June 15; 22(12): 1971–1984. doi: 10.1091/mbc.E11-01-0037
PMCID:
PMC3113764
Abstract Full Text PDF–5.6M
Improved functional overview of protein complexes using inferred epistatic relationships
Colm Ryan, Derek Greene, Aude Guénolé, Haico van Attikum, Nevan J Krogan, Pádraig Cunningham, Gerard Cagney
BMC Syst Biol. 2011; 5: 80. Published online 2011 May 23. doi: 10.1186/1752-0509-5-80
PMCID:
PMC3117733
Abstract Full Text PDF–1.4M Supplementary Material
Molecular Determinants and Genetic Modifiers of Aggregation and Toxicity for the ALS Disease Protein FUS/TLS
Zhihui Sun, Zamia Diaz, Xiaodong Fang, Michael P. Hart, Alessandra Chesi, James Shorter, Aaron D. Gitler
PLoS Biol. 2011 April; 9(4): e1000614. Published online 2011 April 26. doi: 10.1371/journal.pbio.1000614
PMCID:
PMC3082519
Abstract Full Text PDF–2.1M Supplementary Material
Quantitative maps of genetic interactions in yeast - Comparative evaluation and integrative analysis
Rolf O Lindén, Ville-Pekka Eronen, Tero Aittokallio
BMC Syst Biol. 2011; 5: 45. Published online 2011 March 24. doi: 10.1186/1752-0509-5-45
PMCID:
PMC3079637
Abstract Full Text PDF–1.4M Supplementary Material
Protein Complexes are Central in the Yeast Genetic Landscape
Magali Michaut, Anastasia Baryshnikova, Michael Costanzo, Chad L. Myers, Brenda J. Andrews, Charles Boone, Gary D. Bader
PLoS Comput Biol. 2011 February; 7(2): e1001092. Published online 2011 February 24. doi: 10.1371/journal.pcbi.1001092
PMCID:
PMC3044758
Abstract Full Text PDF–710K Supplementary Material
Modular analysis of the probabilistic genetic interaction network
Lin Hou, Lin Wang, Minping Qian, Dong Li, Chao Tang, Yunping Zhu, Minghua Deng, Fangting Li
Bioinformatics. 2011 March 15; 27(6): 853–859. Published online 2011 January 28. doi: 10.1093/bioinformatics/btr031
PMCID:
PMC3051332
Abstract Full Text PDF–398K
Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action
Laura Kapitzky, Pedro Beltrao, Theresa J Berens, Nadine Gassner, Chunshui Zhou, Arthur Wüster, Julie Wu, M Madan Babu, Stephen J Elledge, David Toczyski, R Scott Lokey, Nevan J Krogan
Mol Syst Biol. 2010; 6: 451. Published online 2010 December 21. doi: 10.1038/msb.2010.107
PMCID:
PMC3018166
Abstract Full Text PDF–2.2M Supplementary Material
Rewiring of Genetic Networks in Response to DNA Damage
Sourav Bandyopadhyay, Monika Mehta, Dwight Kuo, Min-Kyung Sung, Ryan Chuang, Eric J. Jaehnig, Bernd Bodenmiller, Katherine Licon, Wilbert Copeland, Michael Shales, Dorothea Fiedler, Janusz Dutkowski, Aude Guénolé, Haico van Attikum, Kevan M. Shokat, Richard D. Kolodner, Won-Ki Huh, Ruedi Aebersold, Michael-Christopher Keogh, Nevan J. Krogan, Trey Ideker
Science. Author manuscript; available in PMC 2010 December 21.
Published in final edited form as: Science. 2010 December 3; 330(6009): 1385–1389. doi: 10.1126/science.1195618
PMCID:
PMC3006187
Abstract Full Text PDF–1.9M Supplementary Material
TDP-43 toxicity in yeast
Maria Armakola, Michael P. Hart, Aaron D. Gitler
Methods. Author manuscript; available in PMC 2012 March 1.
Published in final edited form as: Methods. 2011 March; 53(3): 238–245. Published online 2010 November 27. doi: 10.1016/j.ymeth.2010.11.006
PMCID:
PMC3073690
Abstract Full Text PDF–1.0M
Quantitative analysis of fitness and genetic interactions in yeast on a genome scale
Anastasia Baryshnikova, Michael Costanzo, Yungil Kim, Huiming Ding, Judice Koh, Kiana Toufighi, Ji-Young Youn, Jiongwen Ou, Bryan-Joseph San Luis, Sunayan Bandyopadhyay, Matthew Hibbs, David Hess, Anne-Claude Gingras, Gary D Bader, Olga G Troyanskaya, Grant W Brown, Brenda Andrews, Charles Boone, Chad L Myers
Nat Methods. Author manuscript; available in PMC 2011 June 17.
Published in final edited form as: Nat Methods. 2010 December; 7(12): 1017–1024. Published online 2010 November 14. doi: 10.1038/nmeth.1534
PMCID:
PMC3117325
Abstract Full Text PDF–1.4M Supplementary Material
Epistatic relationships reveal the functional organization of yeast transcription factors
Jiashun Zheng, Joris J Benschop, Michael Shales, Patrick Kemmeren, Jack Greenblatt, Gerard Cagney, Frank Holstege, Hao Li, Nevan J Krogan
Mol Syst Biol. 2010; 6: 420. Published online 2010 October 19. doi: 10.1038/msb.2010.77
PMCID:
PMC2990640
Abstract Full Text PDF–3.5M Supplementary Material
Individual Lysine Acetylations on the N Terminus of Saccharomyces cerevisiae H2A.Z Are Highly but Not Differentially Regulated
Monika Mehta, Hannes Braberg, Shuyi Wang, Anita Lozsa, Michael Shales, Alejandra Solache, Nevan J. Krogan, Michael-Christopher Keogh
J Biol Chem. 2010 December 17; 285(51): 39855–39865. Published online 2010 October 14. doi: 10.1074/jbc.M110.185967
PMCID:
PMC3000967
Abstract Full Text Supplementary Material
Identification of response-modulated genetic interactions by sensitivity-based epistatic analysis
Cory Batenchuk, Lioudmila Tepliakova, Mads Kærn
BMC Genomics. 2010; 11: 493. Published online 2010 September 10. doi: 10.1186/1471-2164-11-493
PMCID:
PMC2996989
Abstract Full Text PDF–2.9M Supplementary Material
Genome-Wide Scoring of Positive and Negative Epistasis through Decomposition of Quantitative Genetic Interaction Fitness Matrices
Ville-Pekka Eronen, Rolf O. Lindén, Anna Lindroos, Mirella Kanerva, Tero Aittokallio
PLoS One. 2010; 5(7): e11611. Published online 2010 July 15. doi: 10.1371/journal.pone.0011611
PMCID:
PMC2904709
Abstract Full Text PDF–841K Supplementary Material
Introduction to Focus Issue: Genetic Interactions
Daniel Segrè, Christopher J. Marx
Chaos. 2010 June; 20(2): 026101. Published online 2010 June 30. doi: 10.1063/1.3456057
PMCID:
PMC2909308
Abstract Full Text PDF–77K
Recursive expectation-maximization clustering: A method for identifying buffering mechanisms composed of phenomic modules
Jingyu Guo, Dehua Tian, Brett A. McKinney, John L. Hartman, IV
Chaos. 2010 June; 20(2): 026103. Published online 2010 June 30. doi: 10.1063/1.3455188
PMCID:
PMC2909310
Abstract Full Text PDF–1.1M
ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data
John C Dittmar, Robert JD Reid, Rodney Rothstein
BMC Bioinformatics. 2010; 11: 353. Published online 2010 June 28. doi: 10.1186/1471-2105-11-353
PMCID:
PMC2909220
Abstract Full Text PDF–1.7M Supplementary Material
A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking
Pablo S Aguilar, Florian Fröhlich, Michael Rehman, Mike Shales, Igor Ulitsky, Agustina Olivera-Couto, Hannes Braberg, Ron Shamir, Peter Walter, Matthias Mann, Christer S Ejsing, Nevan J Krogan, Tobias C Walther
Nat Struct Mol Biol. Author manuscript; available in PMC 2011 July 1.
Published in final edited form as: Nat Struct Mol Biol. 2010 July; 17(7): 901–908. Published online 2010 June 6. doi: 10.1038/nsmb.1829
PMCID:
PMC3073498
Abstract Full Text PDF–1.9M Supplementary Material
Colonyzer: automated quantification of micro-organism growth characteristics on solid agar
Conor Lawless, Darren J Wilkinson, Alexander Young, Stephen G Addinall, David A Lydall
BMC Bioinformatics. 2010; 11: 287. Published online 2010 May 28. doi: 10.1186/1471-2105-11-287
PMCID:
PMC2901369
Abstract Full Text PDF–2.9M
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