Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile
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We present a strategy for generating and analyzing comprehensive genetic-interaction maps, termed E-MAPs (epistatic miniarray profiles), comprising quantitative measures of aggravating or alleviating interactions between gene pairs. Crucial to the interpretation of E-MAPs is their high-density nature made possible by focusing on logically connected gene subsets and including essential genes. Described here is the analysis of an E-MAP of genes acting in the yeast early secretory pathway. Hierarchical clustering, together with novel analytical strategies and experimental verification, revealed or clarified the role of many proteins involved in extensively studied processes such as sphingolipid metabolism and retention of HDEL proteins. At a broader level, analysis of the E-MAP delineated pathway organization and components of physical complexes and illustrated the interconnection between the various secretory processes. Extension of this strategy to other logically connected gene subsets in yeast and higher eukaryotes should provide critical insights into the functional/organizational principles of biological systems.
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Positive interactions were enriched between genes involved in mRNA decay and essential gene DAmP alleles.
“positive interactions were also enriched between genes involved in mRNA decay and essential gene DAmP alleles (13)”
From A global genetic interaction network maps a wiring diagram of cellular function (2016) · cites this paper as [13]
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Cites
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 12,617 · see citing works
Functional organization of the yeast proteome by systematic analysis of protein complexes
Gavin, A., Böesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A., Cruciat, C., et al. (2002) · Nature · doi:10.1038/415141a · Cited by 4,729 · see citing works
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706 · see citing works
Functional profiling of the Saccharomyces cerevisiae genome
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316 · see citing works
Global analysis of protein localization in budding yeast
Huh, W.-K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., & O'Shea, E. K. (2003) · Nature · doi:10.1038/nature02026 · Cited by 4,248 · cited 8× · see citing works
“…proteins revealed that most of the GET complex shifted in its localization from the ER to punctate structures (which in part but not entirely colocalize with the Golgi marker ANP1; Huh et al., 2003; data not shown) when cells were shifted from growth in rich to minimal medium (Figure 5B).”
BackgroundMethodInfluentialSelf-citationGlobal analysis of protein expression in yeast
Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750 · see citing works
Self-citationSystematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Ho, Y., Gruhler, A., Heilbut, A. M., Bader, G. D., Moore, L., Adams, S., Millar, A., Taylor, P. P., Bennett, K. L., Boutilier, K., et al. (2002) · Nature · doi:10.1038/415180a · Cited by 3,573 · see citing works
A comprehensive two-hybrid analysis to explore the yeast protein interactome
Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566 · see citing works
Functional Discovery via a Compendium of Expression Profiles
Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R. B., Armour, C. D., Bennett, H. A., Coffey, E. M., Dai, H. A., He, Y. D., et al. (2000) · Cell · doi:10.1016/s0092-8674(00)00015-5 · Cited by 2,534 · see citing works
Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
Tong, A. H. Y., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Pagé, N., Robinson, M., Raghibizadeh, S., Hogue, C. W. V., Bussey, H., et al. (2001) · Science · doi:10.1126/science.1065810 · Cited by 2,138 · see citing works
Self-citationGlobal Mapping of the Yeast Genetic Interaction Network
Tong, A. H. Y., Lesage, G., Bader, G. D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G. F., Brost, R. L., Chang, M., et al. (2004) · Science · doi:10.1126/science.1091317 · Cited by 2,070 · see citing works
Self-citationOxidative protein folding in eukaryotes
Tu, B. P., & Weissman, J. S. (2004) · The Journal of Cell Biology · doi:10.1083/jcb.200311055 · Cited by 1,041 · see citing works
Self-citationPatil, C., & Walter, P. (2001) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(00)00219-2 · Cited by 779 · see citing works
Subcellular localization of the yeast proteomePreprint
Kumar, A., Agarwal, S., Heyman, J. A., Matson, S., Heidtman, M. I., Piccirillo, S., Umansky, L., Drawid, A., Jansen, R., Liu, Y., et al. (2002) · Genes & Development · doi:10.1101/gad.970902 · Cited by 737 · see citing works
Cell Wall Architecture in Yeast: New Structure and New Challenges
Lipke, P. N., & Ovalle, R. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.15.3735-3740.1998 · Cited by 701 · see citing works
Parsons, A. B., Brost, R. L., Ding, H., Li, Z., Zhang, C., Sheikh, B., Brown, G. W., Kane, P. M., Hughes, T. R., & Boone, C. M. (2003) · Nature Biotechnology · doi:10.1038/nbt919 · Cited by 651 · see citing works
Self-citationExploration of Essential Gene Functions via Titratable Promoter Alleles
Mnaimneh, S., Davierwala, A. P., Haynes, J., Moffat, J., Peng, W.-T., Zhang, W., Yang, X., Pootoolal, J., Chua, G., Lopez, A., et al. (2004) · Cell · doi:10.1016/j.cell.2004.06.013 · Cited by 604 · see citing works
Self-citationModular epistasis in yeast metabolism
Segrè, D., DeLuna, A., Church, G. M., & Kishony, R. (2005) · Nature Genetics · doi:10.1038/ng1489 · Cited by 575 · see citing works
Epistasis and the Evolutionary Process
Hurst, L. D. (2000) · Heredity · doi:10.1111/j.1365-2540.2000.0846b.pp.x · Cited by 563 · see citing works
Semenza, J. C., Hardwick, K., Dean, N., & Pelham, H. R. B. (1990) · Cell · doi:10.1016/0092-8674(90)90698-e · Cited by 539 · see citing works
Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast
Giaever, G. N., Flaherty, P., Kumm, J., Proctor, M. J., Nislow, C., Jaramillo, D. F., Chu, A. M., Jordan, M. I., Arkin, A. P., & Davis, R. W. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307490100 · Cited by 506 · see citing works
RNA Polymerase II Elongation Factors of Saccharomyces cerevisiae: a Targeted Proteomics Approach
Krogan, N. J., Kim, M., Ahn, S., Zhong, G., Kobor, M. S., Cagney, G., Emili, A., Shilatifard, A., Buratowski, S., & Greenblatt, J. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.20.6979-6992.2002 · Cited by 497 · see citing works
Self-citationVesicle tethering complexes in membrane traffic
Whyte, J. R. C., & Munro, S. (2002) · Journal of Cell Science · doi:10.1242/jcs.115.13.2627 · Cited by 457 · see citing works
Genetic Basis of Mitochondrial Function and Morphology in Saccharomyces cerevisiae
Dimmer, K. S., Fritz, S., Fuchs, F., Messerschmitt, M., Weinbach, N., Neupert, W., & Westermann, B. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.01-12-0588 · Cited by 443 · see citing works
Systematic interpretation of genetic interactions using protein networks
Kelley, R., & Ideker, T. (2005) · Nature Biotechnology · doi:10.1038/nbt1096 · Cited by 437 · see citing works
Epistasis and the Evolutionary Process
Wolf, J. B., Brodie, E. D., & Wade, M. J. (2000) · Cited by 434 · see citing works
Test of synergistic interactions among deleterious mutations in bacteria
Elena, S. F., & Lenski, R. E. (1997) · Nature · doi:10.1038/37108 · Cited by 416 · see citing works
A sphingosine-1-phosphate receptor regulates cell migration during vertebrate heart development
Kupperman, E., An, S. M., Osborne, N., Waldron, S., & Stainier, D. Y. R. (2000) · Nature · doi:10.1038/35018092 · Cited by 394 · see citing works
A Robust Toolkit for Functional Profiling of the Yeast Genome
Pan, X., Yuan, D., Xiang, D., Wang, X., Sookhai-Mahadeo, S., Bader, J. S., Hieter, P., Spencer, F. A., & Boeke, J. D. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.09.035 · Cited by 314 · see citing works
Large-Scale Functional Genomic Analysis of Sporulation and Meiosis in Saccharomyces cerevisiae
Enyenihi, A. H., & Saunders, W. S. (2003) · Genetics · doi:10.1093/genetics/163.1.47 · Cited by 252 · see citing works
Sütterlin, C., Hsu, P., Mallabiabarrena, A., & Malhotra, V. (2002) · Cell · doi:10.1016/s0092-8674(02)00720-1 · Cited by 252 · see citing works
Aberrant mRNAs with extended 3′ UTRs are substrates for rapid degradation by mRNA surveillance
Muhlrad, D., & Parker, R. (1999) · RNA · doi:10.1017/s1355838299990829 · Cited by 242 · see citing works
Bhamidipati, A., Denic, V., Toyama, E. Q., & Weissman, J. S. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.07.027 · Cited by 234 · see citing works
Self-citationGenetic Selection of Peptide Inhibitors of Biological Pathways
Norman, T., Smith, D. L., Sorger, P. K., Drees, B., O’Rourke, S. M., Hughes, T. R., Roberts, C. J., Friend, S. H., Fields, S., & Murray, A. W. (1999) · Science · doi:10.1126/science.285.5427.591 · Cited by 190 · see citing works
Ric1p and Rgp1p form a complex that catalyses nucleotide exchange on Ypt6p
Siniossoglou, S., Peak‐Chew, S. Y., & Pelham, H. R. B. (2000) · The EMBO Journal · doi:10.1093/emboj/19.18.4885 · Cited by 170 · see citing works
Sato, K., & Nakano, A. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-01-0027 · Cited by 115 · see citing works
Vashist, S., Frank, C. G., Jakob, C. A., & Ng, D. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.02-06-0090 · Cited by 97 · see citing works
Simons, J. F., Ebersold, M., & Helenius, A. (1998) · The EMBO Journal · doi:10.1093/emboj/17.2.396 · Cited by 93 · see citing works
The Saccharomyces cerevisiae Arr4p is involved in metal and heat tolerance*
Shen, J., Hsu, C., Kang, B.-K., Rosen, B. P., & Bhattacharjee, H. (2003) · BioMetals · doi:10.1023/a:1022504311669 · Cited by 75 · see citing works
Balakrishnan, R. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki023 · Cited by 70 · see citing works
Yeast Genes Controlling Responses to Topogenic Signals in a Model Transmembrane Protein
Tipper, D. J., & Harley, C. A. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.01-10-0488 · Cited by 63 · see citing works
Shahinian, S., Dijkgraaf, G. J. P., Sdicu, A., Thomas, D. Y., Jakob, C. A., Aebi, M., & Bussey, H. (1998) · Genetics · doi:10.1093/genetics/149.2.843 · Cited by 62 · see citing works
Lester, R. L., & Dickson, R. C. (2001) · Analytical Biochemistry · doi:10.1006/abio.2001.5368 · Cited by 55 · see citing works
de Martin, P. E., Du, Y., Novick, P., & Ferro‐Novick, S. (2004) · Journal of Cell Science · doi:10.1242/jcs.01583 · Cited by 53 · see citing works
Li, D., Gonzalez, O., Bachinski, L. L., & Roberts, R. (2000) · Gene · doi:10.1016/s0378-1119(00)00347-4 · Cited by 36 · see citing works
Flagged first, then by citations
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Sorted by citations
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A., et al. (2006) · Nature · doi:10.1038/nature04670 · Cited by 2,915 · see citing works
Self-citationMolecular mechanisms and physiological functions of mitophagy
Onishi, M., Yamano, K., Sato, M., Matsuda, N., & Okamoto, K. (2021) · The EMBO Journal · doi:10.15252/embj.2020104705 · Cited by 1,429 · see citing works
“The Get1/2 complex is important for insertion of tail-anchored proteins into the ER membrane (Schuldiner et al , 2005; Schuldiner et al , 2008; Wang et al , 2014).”
An ER-Mitochondria Tethering Complex Revealed by a Synthetic Biology Screen
Kornmann, B., Currie, E., Collins, S. R., Schuldiner, M., Nunnari, J., Weissman, J. S., & Walter, P. (2009) · Science · doi:10.1126/science.1175088 · Cited by 1,275 · see citing works
Self-citationA global genetic interaction network maps a wiring diagram of cellular function
Costanzo, M., VanderSluis, B., Koch, E. N., Baryshnikova, A., Pons, C., Tan, G., Wang, W., Usaj, M., Hanchard, J., Lee, S. D., et al. (2016) · Science · doi:10.1126/science.aaf1420 · Cited by 1,240 · see citing works
“In a similar regulatory relationship, positive interactions were also enriched between genes involved in mRNA decay and essential gene DAmP alleles (13), which often affect mRNA stability via disruption of their 3′ untranslated region (fig.”
BackgroundSelf-citationGlobal analysis of the yeast lipidome by quantitative shotgun mass spectrometry
Ejsing, C. S., Sampaio, J. L., Surendranath, V., Duchoslav, E., Ekroos, K., Klemm, R. W., Simons, K., & Shevchenko, A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811700106 · Cited by 1,071 · see citing works
Horlbeck, M. A., Gilbert, L. A., Villalta, J. E., Adamson, B., Pak, R. A., Chen, Y., Fields, A. P., Park, C. Y., Corn, J. E., Kampmann, M., et al. (2016) · eLife · doi:10.7554/elife.19760 · Cited by 894 · see citing works
“, 2015) will allow for simultaneous control of several genes, facilitating dissection of cellular pathways and systematic mapping of mammalian genetic interactions (Bassik et al., 2013; Costanzo et al., 2010; Schuldiner et al., 2005).”
BackgroundSelf-citationvan Opijnen, T., Bodi, K. L., & Camilli, A. (2009) · Nature Methods · doi:10.1038/nmeth.1377 · Cited by 926 · see citing works
Gene essentiality and synthetic lethality in haploid human cells
Blomen, V. A., Májek, P., Jae, L. T., Bigenzahn, J. W., Nieuwenhuis, J., Staring, J., Sacco, R., van Diemen, F. R., Olk, N., Stukalov, A., et al. (2015) · Science · doi:10.1126/science.aac7557 · Cited by 857 · see citing works
Ideker, T., & Sharan, R. (2008) · Genome Research · doi:10.1101/gr.071852.107 · Cited by 817 · see citing works
Ideker, T., & Krogan, N. J. (2012) · Molecular Systems Biology · doi:10.1038/msb.2011.99 · Cited by 784 · see citing works
“…of genetic interactions, where both positive (alleviating) and negative (aggravating) interactions are observed along with their interaction strengths, was initially accomplished in budding yeast using the E-MAP (epistatic miniarray profile) approach (Schuldiner et al , 2005; Beltrao et al , 2010).”
MethodSelf-citationCotranscriptional Set2 Methylation of Histone H3 Lysine 36 Recruits a Repressive Rpd3 Complex
Keogh, M., Kurdistani, S. K., Morris, S. A., Ahn, S., Podolny, V., Collins, S. R., Schuldiner, M., Chin, K., Punna, T., Thompson, N. J., et al. (2005) · Cell · doi:10.1016/j.cell.2005.10.025 · Cited by 780 · see citing works
“The 384 deletion strains in our transcription/chromatin miniarray were crossed against a similar miniarray carrying a different marker, thereby creating a 384 × 384 E-MAP matrix of double-mutant haploid strains (Schuldiner et al., 2005).”
Self-citationCollins, S. R., Miller, K. M., Maas, N. L., Roguev, A., Fillingham, J., Chu, C. S., Schuldiner, M., Gebbia, M., Recht, J., Shales, M., et al. (2007) · Nature · doi:10.1038/nature05649 · Cited by 869 · see citing works
Self-citationComprehensive Characterization of Genes Required for Protein Folding in the Endoplasmic Reticulum
Jonikas, M. C., Collins, S. R., Denic, V., Oh, E., Toyama, E. Q., Schmid, V., Weibezahn, J., Schwappach, B., Walter, P., Weissman, J. S., et al. (2009) · Science · doi:10.1126/science.1167983 · Cited by 713 · see citing works
Self-citationPhenotypic Landscape of a Bacterial Cell
Nichols, R. J., Sen, Ś., Choo, Y. J., Beltrão, P., Zietek, M., Chaba, R., Lee, S., Kazmierczak, K. M., Lee, K. J., Wong, A., et al. (2010) · Cell · doi:10.1016/j.cell.2010.11.052 · Cited by 702 · see citing works
Self-citationAnatomical Profiling of G Protein-Coupled Receptor Expression
Regard, J. B., Sato, I. T., & Coughlin, S. R. (2008) · Cell · doi:10.1016/j.cell.2008.08.040 · Cited by 696 · see citing works
Histone Variant H2A.Z Marks the 5′ Ends of Both Active and Inactive Genes in Euchromatin
Raisner, R. M., Hartley, P. D., Meneghini, M. D., Bao, M. Z., Liu, C. L., Schreiber, S. L., Rando, O. J., & Madhani, H. D. (2005) · Cell · doi:10.1016/j.cell.2005.10.002 · Cited by 676 · see citing works
Exploring genetic interactions and networks with yeast
Boone, C., Bussey, H., & Andrews, B. J. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2085 · Cited by 661 · see citing works
“For example, replacing the 3′ UTR of an essential gene with a selectable marker often leads to lower transcript levels and a resultant phenotyp”
BackgroundclusterMaker: a multi-algorithm clustering plugin for Cytoscape
Morris, J. H., Apeltsin, L., Newman, A. M., Baumbach, J., Wittkop, T., Su, G., Bader, G. D., & Ferrin, T. E. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-436 · Cited by 609 · see citing works
“Hierarchical, k-medoid, and k-means algorithms are commonly used for clustering gene expression data [1] and genetic interaction profiles [2].”
MethodOrm family proteins mediate sphingolipid homeostasis
Breslow, D. K., Collins, S. R., Bodenmiller, B., Aebersold, R. H., Simons, K., Shevchenko, A., Ejsing, C. S., & Weissman, J. S. (2010) · Nature · doi:10.1038/nature08787 · Cited by 599 · see citing works
Self-citationNext-generation genomics: an integrative approach
Hawkins, R. D., Hon, G. C., & Ren, B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2795 · Cited by 591 · see citing works
“In yeast, genetic interaction pathways are being identified through large-scale epistasis screens ( epistatic miniarray profiles (E-MAPs)”
Getting connected: analysis and principles of biological networksPreprint
Zhu, X., Gerstein, M., & Snyder, M. P. (2007) · Genes & Development · doi:10.1101/gad.1528707 · Cited by 549 · see citing works
“In fact, interactions that when combined either enhance or reduce growth have been investigated to generate a detailed genetic interaction map, E-MAPs (for epistatic miniarray profiles), for genes involved in the yeast early secretory pathway (Schuldiner et al. 2005).”
BackgroundComputed structures of core eukaryotic protein complexes
Humphreys, I. R., Pei, J., Baek, M., Krishnakumar, A., Anishchenko, I., Ovchinnikov, S., Zhang, J., Ness, T. J., Banjade, S., Bagde, S. R., et al. (2021) · Science · doi:10.1126/science.abm4805 · Cited by 542 · see citing works
“The tether is thought to participate in COPII vesicle capture ( 78 , 79 ), but the mechanism remains unclear.”
A Class of Dynamin-like GTPases Involved in the Generation of the Tubular ER Network
Hu, J., Shibata, Y., Zhu, P., Voss, C., Rismanchi, N., Prinz, W. A., Rapoport, T. A., & Blackstone, C. D. (2009) · Cell · doi:10.1016/j.cell.2009.05.025 · Cited by 540 · see citing works
“A large-scale screen for genetic interaction partners also demonstrated synthetic effects of yop1 and sey1 deletions (Schuldiner et al., 2005).”
BackgroundA DNA Integrity Network in the Yeast Saccharomyces cerevisiae
Pan, X., Ye, P., Yuan, D., Wang, X., Bader, J. S., & Boeke, J. D. (2006) · Cell · doi:10.1016/j.cell.2005.12.036 · Cited by 538 · see citing works
A comprehensive strategy enabling high-resolution functional analysis of the yeast genome
Breslow, D. K., Cameron, D. M., Collins, S. R., Schuldiner, M., Stewart-Ornstein, J., Newman, H. W., Braun, S. J., Madhani, H. D., Krogan, N. J., & Weissman, J. S. (2008) · Nature Methods · doi:10.1038/nmeth.1234 · Cited by 517 · see citing works
Self-citationThe GET Complex Mediates Insertion of Tail-Anchored Proteins into the ER Membrane
Schuldiner, M., Metz, J., Schmid, V., Denic, V., Rakwalska, M., Schmitt, H. D., Schwappach, B., & Weissman, J. S. (2008) · Cell · doi:10.1016/j.cell.2008.06.025 · Cited by 522 · see citing works
“…damage response (Zewail et al., 2003) and V-type ATPase dysfunction (Sambade et al., 2005) for Dget2 (Dhur2/Drmd7); sensitivity to toxic metal ions (Shen et al., 2003) and effects on protein degradation machinery (Auld et al., 2006) for Dget3 (Darr4); and defects in meiotic spore formation (Auld…”
BackgroundSelf-citationExploring the Mode-of-Action of Bioactive Compounds by Chemical-Genetic Profiling in Yeast
Parsons, A. B., López, A., Givoni, I. E., Williams, D. E., Gray, C. A., Porter, J., Chua, G., Sopko, R., Brost, R. L., Ho, C.-H., et al. (2006) · Cell · doi:10.1016/j.cell.2006.06.040 · Cited by 500 · see citing works
“In particular, we show that tamoxifen, a breast cancer therapeutic, disrupts calcium homeostasis, and we identify PS as a target for papuamide B, a cytotoxic cyclic lipopeptide with antifungal and anti-HIV activity (Ford et al., 1999).”
BackgroundSelf-citationHan, K., Jeng, E., Hess, G., Morgens, D., Li, A., & Bassik, M. (2017) · Nature Biotechnology · doi:10.1038/nbt.3834 · Cited by 482 · see citing works
“These maps have been useful tools for predicting gene function, allowing dissection of complexes and pathways 6–10 in a range of organisms 5,7,9,11–15 .”
InfluentialTransposon insertion sequencing: a new tool for systems-level analysis of microorganisms
van Opijnen, T., & Camilli, A. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3033 · Cited by 495 · see citing works
Mani, R., St.Onge, R. P., Hartman, J. L., Giaever, G. N., & Roth, F. P. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712255105 · Cited by 471 · see citing works
Hoppins, S. C., Collins, S. R., Cassidy-Stone, A., Hummel, E., DeVay, R. M., Lackner, L. L., Westermann, B., Schuldiner, M., Weissman, J. S., & Nunnari, J. M. (2011) · The Journal of Cell Biology · doi:10.1083/jcb.201107053 · Cited by 473 · see citing works
“Consistent with earlier studies (Schuldiner et al., 2005), there was considerable”
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Nagai, S., Dubrana, K., Tsai-Pflugfelder, M., Davidson, M. B., Roberts, T. M., Brown, G. W., Varela, E., Hediger, F., Gasser, S. M., & Krogan, N. J. (2008) · Science · doi:10.1126/science.1162790 · Cited by 451 · see citing works
Self-citationA Luminal Surveillance Complex that Selects Misfolded Glycoproteins for ER-Associated Degradation
Denic, V., Toyama, E. Q., & Weissman, J. S. (2006) · Cell · doi:10.1016/j.cell.2006.05.045 · Cited by 419 · see citing works
“Deletions in the Y3656 background were generated using the pFA6-NATMX3 cassette using standard methods (Goldstein and McCusker, 1999; Schuldiner et al., 2005).”
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Norman, T. M., Horlbeck, M. A., Replogle, J. M., Ge, A. Y., Xu, A., Jost, M., Gilbert, L. A., & Weissman, J. S. (2019) · Science · doi:10.1126/science.aax4438 · Cited by 392 · see citing works
Self-citationSystematic exploration of essential yeast gene function with temperature-sensitive mutants
Li, Z., Vizeacoumar, F. J., Bahr, S., Li, J., Warringer, J., Vizeacoumar, F. S., Min, R., VanderSluis, B., Bellay, J., DeVit, M. J., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1832 · Cited by 404 · see citing works
“and decreased abundance by mRNA perturbation allele”
Self-citationIdentification of a Targeting Factor for Posttranslational Membrane Protein Insertion into the ER
Stefanovic, S., & Hegde, R. S. (2007) · Cell · doi:10.1016/j.cell.2007.01.036 · Cited by 406 · see citing works
“Considered together, these results indicate that the ATPase-deficient TRC40 dominantly inhibits the principal TA protein insertion pathway without substantial effects on the known cotranslational (Gorlich and Rapoport, 1993), posttranslational ( Panzner et al., 1995 ), or spontaneous (Brambillasca et al., 2005) transl…”
CRISPRi and CRISPRa Screens in Mammalian Cells for Precision Biology and Medicine
Kampmann, M. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00657 · Cited by 371 · see citing works
Drug interactions and the evolution of antibiotic resistance
Yeh, P. J., Hegreness, M. J., Aiden, A. P., & Kishony, R. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2133 · Cited by 350 · see citing works
Data-driven modelling of signal-transduction networks
Janes, K. A., & Yaffe, M. B. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2041 · Cited by 356 · see citing works
The Cost of Protein Production
Kafri, M., Metzl-Raz, E., Jona, G., & Barkai, N. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.12.015 · Cited by 348 · see citing works
“To this end, we generated an additional library in which mCherry was expressed from a destabilized mRNA (DAmP [decreased abundance by mRNA perturbation]; Figure 4A) (Muhlrad and Parker, 1999; Schuldiner et al., 2005), thereby reducing the translation load while maintaining the same transcription burden.”
BackgroundMethodConservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast
Roguev, A., Bandyopadhyay, S., Zofall, M., Zhang, K., Fischer, T., Collins, S. R., Qu, H., Shales, M., Park, H.-O., Hayles, J., et al. (2008) · Science · doi:10.1126/science.1162609 · Cited by 352 · see citing works
Self-citationTrait Variation in Yeast Is Defined by Population History
Warringer, J., Zörgö, E., Cubillos, F. A., Zia, A., Gjuvsland, A. B., Simpson, J. T., Forsmark, A., Durbin, R. M., Omholt, S. W., Louis, E. J., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002111 · Cited by 338 · see citing works
Secretory Protein Biogenesis and Traffic in the Early Secretory Pathway
Barlowe, C. K., & Miller, E. A. (2013) · Genetics · doi:10.1534/genetics.112.142810 · Cited by 321 · see citing works
<i>APOE4</i> disrupts intracellular lipid homeostasis in human iPSC-derived glia
Sienski, G., Narayan, P., Bonner, J. M., Kory, N., Boland, S., Arczewska, A. A., Ralvenius, W. T., Akay, L., Lockshin, E., He, L., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.aaz4564 · Cited by 336 · see citing works
Molecular mechanisms of epistasis within and between genes
Lehner, B. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.05.007 · Cited by 325 · see citing works
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B.-J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., et al. (2006) · Journal of Biology · doi:10.1186/jbiol36 · Cited by 326 · see citing works
“Although the current LC dataset captures basic data about physical and genetic interactions, much other information remains to be extracted and compiled, including quantitative measures of protein and genetic interactions [67,85], spatio-temporal aspects of network organization [54,68], protein-DNA interactions [72] a…”
BackgroundSelf-citationMapping the Genetic Landscape of Human Cells
Horlbeck, M. A., Xu, A., Wang, M., Bennett, N. K., Park, C. Y., Bogdanoff, D., Adamson, B., Chow, E. D., Kampmann, M., Peterson, T. R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.010 · Cited by 319 · see citing works
Self-citationChuang, H., Hofree, M., & Ideker, T. (2010) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100109-104122 · Cited by 316 · see citing works
“The development of rapid screening techniques for genetic interactions, such as synthetic genetic arrays (SGAs) (Tong et al. 2001, 2004), diploid synthetic lethality analysis by microarray (dSLAM) (Ooi et al. 2003), and epistatic miniarray profiles (E-MAP) (Schuldiner et al. 2005), have allowed the quantification of g…”
InfluentialA strategy for extracting and analyzing large-scale quantitative epistatic interaction data
Collins, S. R., Schuldiner, M., Krogan, N. J., & Weissman, J. S. (2006) · Genome biology · doi:10.1186/gb-2006-7-7-r63 · Cited by 300 · see citing works
Self-citationSystematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions
St.Onge, R. P., Mani, R., Oh, J., Proctor, M. J., Fung, E., Davis, R. W., Nislow, C., Roth, F. P., & Giaever, G. N. (2007) · Nature Genetics · doi:10.1038/ng1948 · Cited by 306 · see citing works
A new era in functional genomics screens
Przybyla, L., & Gilbert, L. A. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-021-00409-w · Cited by 281 · see citing works
Merksamer, P. I., Trusina, A., & Papa, F. R. (2008) · Cell · doi:10.1016/j.cell.2008.10.011 · Cited by 302 · see citing works
“Strains were from the Yeast Consortium Deletion Library (Giaever et al., 2002) or from the DAmP library (Schuldiner et al., 2005) (Table S1).”
Systematic Mapping of Genetic Interaction Networks
Dixon, S. J., Costanzo, M., Baryshnikova, A., Andrews, B., & Boone, C. M. (2008) · Annual Review of Genetics · doi:10.1146/annurev.genet.39.073003.114751 · Cited by 290 · see citing works
“Most of the existing systematic studies examining positive interactions have used loss-of-function (LOF) alleles (112, 119).”
Self-citationA molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds
Ho, C. H., Magtanong, L., Barker, S. L., Gresham, D., Nishimura, S., Natarajan, P., Koh, J. L. Y., Porter, J., Gray, C. A., Andersen, R. J., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1534 · Cited by 281 · see citing works
“Similarly, a strain carrying a different MVD1 hypomorphic allele—an mvd1-DAmP mutant expressing less wild-type protein owing to a deletion of the 3′ untranslated region of MVD1 that reduces mRNA tenfol”
BackgroundSelf-citationMembrane Protein Insertion at the Endoplasmic Reticulum
Shao, S., & Hegde, R. S. (2011) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-092910-154125 · Cited by 287 · see citing works
“The original and subsequent synthetic genetic array analysis of yeast genes (Battle et al. 2010; Costanzo et al. 2010; Jonikas et al. 2009; Schuldiner et al. 2005, 2008) clustered Get3 with five other genes whose products are the membrane proteins Get1 and Get2 and the cytosolic proteins Get4,…”
Yeger‐Lotem, E., Riva, L., Su, L. J., Gitler, A. D., Cashikar, A. G., King, O. D., Auluck, P. K., Geddie, M. L., Valastyan, J. S., Karger, D. R., et al. (2009) · Nature Genetics · doi:10.1038/ng.337 · Cited by 284 · see citing works
A Molecular Caliper Mechanism for Determining Very Long-Chain Fatty Acid Length
Denic, V., & Weissman, J. S. (2007) · Cell · doi:10.1016/j.cell.2007.06.031 · Cited by 279 · see citing works
“…Elongation Cycle Dehydratase In our previous large-scale genetic interactions study of the yeast early secretory pathway, we identified Phs1p as a highly conserved ER protein with six predicted transmembrane segments that plays an essential role in sphingolipid metabolism (Schuldiner et al., 2005).”
Self-citationHan, S., Lone, M. A., Schneiter, R., & Chang, A. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0911617107 · Cited by 278 · see citing works
Oliveira, D. L., Nakayasu, E. S., Joffe, L. S., Guimaraes, A. J., Sobreira, T. J. P., Nosanchuk, J. D., Cordero, R. J. B., Frasés, S., Casadevall, A., de Almeida, I. C., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011113 · Cited by 268 · see citing works
“Similarly, Pma1p and its isoform Pma2p interact with several elements of Golgi-associated pathways of cellular traffic, including Ric1p, a protein involved in retrograde transport to the cis-Golgi network, and Vps29p, which is essential for endosome-to-Golgi retrograde transport [59,60].”
BackgroundGlobal Genetic Networks and the Genotype-to-Phenotype Relationship
Costanzo, M., Kuzmin, E., van Leeuwen, J., Mair, B., Moffat, J., Boone, C., & Andrews, B. (2019) · Cell · doi:10.1016/j.cell.2019.01.033 · Cited by 241 · see citing works
“However, comprehensive SGA analysis has been the most extensively used method for GI studies (for example, Collins et al., 2007; Schuldiner et al., 2005; Tong et al., 2004) and its large-scale application enabled mapping of a global GI network for budding yeast (Costanzo et al.”
InfluentialSelf-citationWilmes, G. M., Bergkessel, M., Bandyopadhyay, S., Shales, M., Braberg, H., Cagney, G., Collins, S. R., Whitworth, G. B., Kress, T. L., Weissman, J. S., et al. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.11.012 · Cited by 265 · see citing works
“E-MAP Analysis Strains were constructed and E-MAP experiments were performed as previously described (Collins et al., 2006, 2007b; Schuldiner et al., 2005).”
MethodInfluentialSelf-citationFunctions and metabolism of sphingolipids in Saccharomyces cerevisiae
Dickson, R. C., Sumanasekera, C., & Lester, R. L. (2006) · Progress in Lipid Research · doi:10.1016/j.plipres.2006.03.004 · Cited by 262 · see citing works
Bach, L., Michaelson, L. V., Haslam, R. P., Bellec, Y., Gissot, L., Marion, J., Costa, M. D., Boutin, J., Miquel, M., Tellier, F., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805089105 · Cited by 263 · see citing works
“PHS1 had the strongest epistatic interaction in yeast with the LCB phosphatase LCB3 (6).”
BackgroundTail-anchored membrane protein insertion into the endoplasmic reticulum
Hegde, R. S., & Keenan, R. J. (2011) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3226 · Cited by 258 · see citing works
“, and mutant phenotypes in other organisms were related to processes that involved TA protein”
Cyclic changes in metabolic state during the life of a yeast cell
Tu, B. P., Mohler, R. E., Liu, J. C., Dombek, K. M., Young, E. T., Synovec, R. E., & McKnight, S. L. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708365104 · Cited by 260 · see citing works
Functional Organization of the S. cerevisiae Phosphorylation Network
Fiedler, D., Braberg, H., Mehta, M., Chechik, G., Cagney, G., Mukherjee, P., Silva, A. C., Shales, M., Collins, S. R., van Wageningen, S., et al. (2009) · Cell · doi:10.1016/j.cell.2008.12.039 · Cited by 251 · see citing works
“Abovedashedline:Theptonratiosofpreviouslypublisheddatasets (early secretory pathway [ESP] [Schuldiner et al., 2005] and chromosome function [Collins et al., 2007b]), the signaling E-MAP, only protein kinases and protein phosphatases (K versus K or P versus P), and protein kinases versus protein…”
InfluentialSelf-citationInhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models
Armakola, M., Higgins, M., Figley, M. D., Barmada, S. J., Scarborough, E. A., Diaz, Z., Fang, X., Shorter, J., Krogan, N. J., Finkbeiner, S. M., et al. (2012) · Nature Genetics · doi:10.1038/ng.2434 · Cited by 250 · see citing works
Self-citationEvolution of protein phosphatases in plants and animals
Moorhead, G. B. G., Wever, V. D., Templeton, G. W., & Kerk, D. (2008) · Biochemical Journal · doi:10.1042/bj20081986 · Cited by 254 · see citing works
Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae
Babu, M., Vlasblom, J., Pu, S., Guo, X., Graham, C., Bean, B. D. M., Burston, H. E., Vizeacoumar, F. J., Snider, J. D., Phanse, S., et al. (2012) · Nature · doi:10.1038/nature11354 · Cited by 251 · see citing works
Self-citationDefenouillère, Q., Yao, Y., Mouaikel, J., Namane, A., Galopier, A., Decourty, L., Doyen, A., Malabat, C., Saveanu, C., Jacquier, A., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221724110 · Cited by 246 · see citing works
High-throughput, quantitative analyses of genetic interactions in E. coli
Typas, A., Nichols, R. J., Siegele, D. A., Shales, M., Collins, S. R., Lim, B., Braberg, H., Yamamoto, N., Takeuchi, R., Wanner, B. L., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1240 · Cited by 236 · see citing works
Self-citationBhamidipati, A., Denic, V., Toyama, E. Q., & Weissman, J. S. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.07.027 · Cited by 234 · see citing works
Self-citationHierarchical Modularity and the Evolution of Genetic Interactomes across Species
Ryan, C. J., Roguev, A., Patrick, K. L., Xu, J., Jahari, H., Tong, Z., Beltrão, P., Shales, M., Qu, H., Collins, S. R., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.028 · Cited by 230 · see citing works
“Frameworks for modeling and scoring genetic interactions are normally centered at zero (i.e., a neutral gene pair) (Schuldiner et al., 2005; Collins et al., 2006, 2010; Baryshnikova et al., 2010; Horn et al., 2011) and have been developed to capture a continuous spectrum of phenotype strengths.”
InfluentialSelf-citationWyce, A., Xiao, T., Whelan, K. A., Kosman, C., Walter, W., Eick, D., Hughes, T. R., Krogan, N. J., Strahl, B. D., & Berger, S. L. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.01.035 · Cited by 229 · see citing works
“Images were taken after 2 days of growth at 30 C. Genetic Interaction and Gene Expression Profiling Genetic interaction profiles using E-MAP technology (Schuldiner et al., 2005) and effects of deletions on gene expression were identified as previously described (Keogh et al., 2005).”
MethodSelf-citationProbing Nucleosome Function: A Highly Versatile Library of Synthetic Histone H3 and H4 Mutants
Dai, J., Hyland, E. M., Yuan, D., Huang, H., Bader, J. S., & Boeke, J. D. (2008) · Cell · doi:10.1016/j.cell.2008.07.019 · Cited by 229 · see citing works
A fine scale phenotype–genotype virulence map of a bacterial pathogenPreprint
van Opijnen, T., & Camilli, A. (2012) · Genome Research · doi:10.1101/gr.137430.112 · Cited by 220 · see citing works
“A reverse genetics approach based on genome-wide ordered arrays of single gene knockouts (Tong et al. 2001; Schuldiner et al. 2005) has been applied to several model organisms (Giaever et al.”
BackgroundMethodThe KDEL receptor: New functions for an old protein
Capitani, M., & Sallese, M. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.10.053 · Cited by 215 · see citing works
“pathway in yeast, another study reported that two subunits of the co-chaperone complex involved in the folding of microtubules (GIM3 and GIM4) have epistatic relationships with the KDEL receptor [72].”
BackgroundDickson, R. C. (2008) · Journal of Lipid Research · doi:10.1194/jlr.r800003-jlr200 · Cited by 216 · see citing works
Ben‐Aroya, S., Coombes, C. E., Kwok, T., O’Donnell, K. A., Boeke, J. D., & Hieter, P. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.02.021 · Cited by 213 · see citing works
“…by the yeast community for the study of essential genes, which resulted in a few collections that are already available to the community: DAmP alleles (Schuldiner et al., 2005), the N-degron (Kanemaki et al., 2003; Labib et al., 2000), and the tet promoter collections (Mnaimneh et al., 2004).”
BackgroundInfluentialPitre, S., Dehne, F., Chan, A., Cheetham, J., Duong, A., Emili, A., Gebbia, M., Greenblatt, J. F., Jessulat, M. G., Krogan, N. J., et al. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-365 · Cited by 213 · see citing works
Self-citationIntegrating physical and genetic maps: from genomes to interaction networks
Beyer, A., Bandyopadhyay, S., & Ideker, T. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2144 · Cited by 207 · see citing works
“Conversely, alleviating interactions have been thought to indicate genes within the same pathwa”
BackgroundGenome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures
Pierce, S. E., Davis, R. W., Nislow, C., & Giaever, G. N. (2007) · Nature Protocols · doi:10.1038/nprot.2007.427 · Cited by 208 · see citing works
Synthetic Genetic Array (SGA) Analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe
Baryshnikova, A., Costanzo, M., Dixon, S. J., Vizeacoumar, F. J., Myers, C. L., Andrews, B., & Boone, C. M. (2010) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(10)70007-0 · Cited by 201 · see citing works
Self-citationGreen, R. A., Kao, H.-L., Audhya, A., Arur, S., Mayers, J. R., Fridolfsson, H. N., Schulman, M., Schloissnig, S., Niessen, S., Laband, K., et al. (2011) · Cell · doi:10.1016/j.cell.2011.03.037 · Cited by 201 · see citing works
“, 2010), and maps have also been generated for subsets of gene implicated in specific processes—such as RNA processing, chromosome biology, proteasome function, and the secretory pathway (Breslow et al., 2008; Collins et al., 2007; Schuldiner et al., 2005; Wilmes et al., 2008).”
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, M. J., Jelasity, M., Myers, C. L., et al. (2011) · Nature Genetics · doi:10.1038/ng.846 · Cited by 206 · see citing works
“as well as genetic networks underlying specific biological processe”
Self-citationTargeting pathways of C-tail-anchored proteins
Borgese, N., & Fasana, E. (2010) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2010.07.010 · Cited by 203 · see citing works
One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy
Yofe, I., Weill, U., Meurer, M., Chuartzman, S. G., Zalckvar, E., Goldman, O., Ben‐Dor, S., Schütze, C., Wiedemann, N., Knop, M., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3795 · Cited by 202 · see citing works
Self-citationA Network of Cytosolic Factors Targets SRP-Independent Proteins to the Endoplasmic Reticulum
Ast, T., Cohen, G., & Schuldiner, M. (2013) · Cell · doi:10.1016/j.cell.2013.02.003 · Cited by 193 · see citing works
“Genetic interaction studies (Costanzo et al., 2010; Jonikas et al., 2009; Schuldiner et al., 2005) revealed that the deletion of Ydj1 was synthetically lethal when combined with deletions of the GET pathway (Figure S5), hinting that the two might have parallel cellular functions.”
BackgroundSelf-citationLearning a Prior on Regulatory Potential from eQTL Data
Lee, S., Dudley, A. M., Drubin, D. A., Silver, P. A., Krogan, N. J., Pe’er, D., & Koller, D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000358 · Cited by 191 · see citing works
“In particular, all of the data sets that we used to produce our benchmark set of regulator-target interactions (such as differential expression subject to regulator deletion or over-expression) can also be used as meta-features, as can other high-throughput data such as signaling interactions [50,51] or genetic intera…”
MethodSelf-citationSpokoini, R., Moldavski, O., Nahmias, Y., England, J. L., Schuldiner, M., & Kaganovich, D. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.024 · Cited by 191 · see citing works
Self-citationPaumi, C. M., Chuk, M., Snider, J. D., Štagljar, I., & Michaelis, S. (2009) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00020-09 · Cited by 189 · see citing works
“and for defining cellular pathways (12, 45, 67, 87, 140, 152).”
A gene ontology inferred from molecular networks
Dutkowski, J., Kramer, M., Surma, M. A., Balakrishnan, R., Cherry, J. M., Krogan, N. J., & Ideker, T. (2013) · Nature Biotechnology · doi:10.1038/nbt.2463 · Cited by 184 · see citing works
Exploring genetic suppression interactions on a global scale
van Leeuwen, J. S., Pons, C., Mellor, J. C., Yamaguchi, T. N., Friesen, H., Koschwanez, J. H., Ušaj, M. M., Pechlaner, M., Takar, M., Ušaj, M., et al. (2016) · Science · doi:10.1126/science.aag0839 · Cited by 176 · see citing works
“Although no significant functional enrichment was found for genes involved in RNA processing, nonsense-mediatedmRNA decay genes suppressed several DAmP alleles of essential genes (generated by decreased abundance by mRNA perturbation, DAmP) (22), which affect mRNA stability throughdisruption of their 3′untranslated re…”
BackgroundSelf-citationEvolution of phosphoregulation: comparison of phosphorylation patterns across yeast species
Beltrao, P., Trinidad, J. C., Fiedler, D., Roguev, A., Lim, W. A., Shokat, K. M., Burlingame, A. L., & Krogan, N. J. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000134 · Cited by 188 · see citing works
“using the E-MAP method as previously described, adding an additional 2,000 genetic interactions to the dataset”
Self-citationZhao, R., Kakihara, Y., Gribun, A., Huen, J., Yang, G., Khanna, M., Costanzo, M., Brost, R. L., Boone, C. M., Hughes, T. R., et al. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200709061 · Cited by 185 · see citing works
“When both Tah1 and Pih1 were mixed with the Rvb1/2 complex, coelution of Rvb1, Rvb2, Tah1, and Pih1 was observed over several fractions, indicating that the complex might be dynamic ( Fig.”
BackgroundMethodSelf-citationExposing the fitness contribution of duplicated genes
DeLuna, A., Vetsigian, K., Noam Shoresh, F., Hegreness, M., Colón‐González, M., Chao, S., & Kishony, R. (2008) · Nature Genetics · doi:10.1038/ng.123 · Cited by 177 · see citing works
“The functional overlap between members of duplicate pairs manifests as deviations of the fitness cost of double deletions from the additive expectation based on the effects of single deletion”
BackgroundNetwork Inference, Analysis, and Modeling in Systems Biology
Albert, R. (2007) · The Plant Cell · doi:10.1105/tpc.107.054700 · Cited by 179 · see citing works
“Most applications derive biological insight through ‘‘guilt by association;’’ that is, they predict the function of unknown gene products by their association with recognized clusters (Schuldiner et al., 2005; Bjorklund et al., 2006).”
BackgroundCharacterization of mycobacterial virulence genes through genetic interaction mapping
Joshi, S. M., Pandey, A. K., Capite, N., Fortune, S. M., Rubin, E. J., & Sassetti, C. M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603179103 · Cited by 176 · see citing works
Arsenic Metabolism in Prokaryotic and Eukaryotic Microbes
Bhattacharjee, H., & Rosen, B. P. (2007) · Springer eBooks · doi:10.1007/7171_2006_086 · Cited by 177 · see citing works
A global analysis of genetic interactions in Caenorhabditis elegans
Byrne, A. B., Weirauch, M. T., Wong, V., Koeva, M., Dixon, S. J., Stuart, J. M., & Roy, P. J. (2007) · Journal of Biology · doi:10.1186/jbiol58 · Cited by 172 · see citing works
- Authors
- Schuldiner, M., Collins, S. R., Thompson, N. J., Denic, V., Bhamidipati, A., Punna, T., Ihmels, J., Andrews, B., Boone, C., Greenblatt, J. F., Weissman, J. S., & Krogan, N. J.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of Toronto (CA)
- Corresponding author
- Weissman, Jonathan S.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2005-11
- Volume
- 123
- Issue
- 3
- Pages
- 507-519
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2042688172
- Cited by
- 870
- References
- 45
- Citations by year
- 2026: 12 · 2025: 12 · 2024: 15 · 2023: 19 · 2022: 23 · 2021: 30 · 2020: 34 · 2019: 30 · 2018: 36 · 2017: 41 · 2016: 25 · 2015: 47 · 2014: 54 · 2013: 57 · 2012: 61
- FWCI
- 20.53
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
- Keywords
- genetic interaction mapping, sphingolipid metabolism, protein complex formation, essential genes, hierarchical clustering, Saccharomyces cerevisiae
- MeSH terms
- Endoplasmic Reticulum, Epistasis, Genetic, Glycosylation, Membrane Proteins, Mutation, Saccharomyces cerevisiae, Cluster Analysis, Receptors, Peptide, Computational Biology, Gene Expression Profiling, Protein Transport, Protein Interaction Mapping, Saccharomyces cerevisiae Proteins
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