Publications of the Weissman lab

Verges KJ, Smith MH, Toyama BH, Weissman JS. (2011) Strain conformation, primary structure and the propagation of the yeast prion [PSI(+)]. Nat Struct Mol Biol, 18(4): 493-99.

Foo CK, Ohhashi Y, Kelly MJ, Tanaka M, Weissman JS. (2011) Radically Different Amyloid Conformations Dictate the Seeding Specificity of a Chimeric Sup35 Prion. J Mol Biol, 408(1): 1-8.

Ohhashi Y, Ito K, Toyama BH, Weissman JS, Tanaka M. (2010) Differences in prion strain conformations result from non-native interactions in a nucleus. Nature Chemical Biology, 6:225-30.

Collins SR, Weissman JS, Krogan NJ. (2009) From information to knowledge: new technologies for defining gene function. Nature Methods, 6:721-3.

Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, Mukherjee P, Silva AC, Shales M, Collins SR, van Wageningen S, Kemmeren P, vHolstege FC, Weissman JS, Keogh MC, Koller D, Shokat KM, Krogan NJ. (2009) Functional organization of the S. cerevisiae phosphorylation network. Cell, Mar 6;136(5):952-63.

Jonikas MC, Collins SR, Denic V, Oh E, Quan EM, Schmid V, Weibezahn J, Schwappach B, Walter P, Weissman JS, Schuldiner M. (2009) Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum. Science, Mar 27;323(5922):1693-7.

Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS. (2009) Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling. Science, April 10: 218-223.

Quan EM, Kamiya Y, Kamiya D, Denic V, Weibezahn J, Kato K, Weissman JS. (2008) Defining the glycan destruction signal for endoplasmic reticulum-associated degradation. Molecular Cell, Dec 26;32(6):870-7.

Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, Cagney G, Collins SR, Whitworth GB, Kress TL, Weissman JS, Ideker T, Guthrie C, Krogan NJ. (2008) A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Molecular Cell, Dec 5;32(5):735-46.

Tipton KA, Verges KJ, Weissman JS. (2008) In vivo monitoring of the prion replication cycle reveals a critical role for Sis1 in delivering substrates to Hsp104. Molecular Cell, Nov 21;32(4):584-91.

Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park HO, Hayles J, Hoe KL, Kim DU, Ideker T, Grewal SI, Weissman JS, Krogan NJ. (2008) Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science, Oct 17;322(5900):405-10.

Ingolia NT, Weissman JS. (2008) Systems biology: Reverse engineering the cell. Nature, 454:1059-62.

Schuldiner M, Metz J, Schmid V, Denic V, Rakwalska M, Schmitt HD, Schwappach B, Weissman JS. (2008) The GET complex mediates insertion of tail-anchored proteins into the ER membrane. Cell, 134:634-45.

Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL, Mori H, Weissman JS, Krogan NJ, Gross CA. (2008) High-throughput, quantitative analyses of genetic interactions in E. coli. Nature Methods, Sep;5(9):781-787.

Breslow DK, Cameron DM, Collins SR, Schuldiner M, Stewart-Ornstein J, Newman HW, Braun S, Madhani HD, Krogan NJ, Weissman JS. (2008) A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nature Methods, Aug;5(8):711-8.

McDonald M, Kendall A, Tanaka M, Weissman JS, Stubbs G. (2008) Enclosed chambers for humidity control and sample containment in fiber diffraction. Journal Applied Crystallography, 41:206-209.

Haass FA, Jonikas M, Walter P, Weissman JS, Jan YN, Jan LY, Schuldiner M. (2007) Identification of yeast proteins necessary for cell-surface function of a potassium channel. PNAS, 104:18079-84.

Ihmels J, Collins S, Schuldiner M, Krogan N, Weissman J. (2007) Genetic interactions reveal the cost of gene loss for singleton and duplicate genes. Molecular Systems Biology, 3:86.

Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ. (2007) Towards a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Molecular Cell Proteomics, 6:439-50.

Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, Greenblatt JF. (2006) Global landscape of protein complexes in the yeast saccharomyces cerevisiae. Nature, 440:7084.

Kulp MS, Frickel EM, Ellgaard L, Weissman JS. (2006) Domain architecture of protein disulfide isomerase facilitates its dual role as an oxidase and an isomerase in ERO1P-mediated disulfide formation. Journal Biological Chemistry, 281:876-884.

Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell, 123:4.

Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, Ihmels J, Andrews B, Boone C, Greenblatt JF, Weissman JS, Krogan NJ. (2005) Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell, 123:366-8.

Bhamidipati A, Denic V, Quan EM, Weissman JS. (2005) Exploration of the topological requirements of ERAD identifies Yos9p as a lectin sensor of misfolded glycoproteins in the ER lumen. Molecular Cell, 19:1-11.

Tanaka M, Chien P, Yonekura K, Weissman JS. (2005) Mechanism of cross-species prion transmission: An infectious conformation compatible with two highly divergent yeast prion proteins. Cell, 121:49-62.

Howson R, Huh W, Ghaemmaghami S, Falvo JV, Bower K, Belle A, Dephoure N, Wykoff DD, Weissman JS, OShea EK. (2005) Construction, verification and experimental use of two epitope-tagged collections of budding yeast strains (p 2-16). Comparative and Functional Genomics, 6(1-2):2-16.

Tu BP, Weissman JS. (2004) Oxidative protein folding in eukaryotes: mechanisms and consequences. Journal of Cell Biology, 164:341-346.

Weissman JS, OShea EK. (2004) Irving Sigal Young Investigator Award Address. Protein Science, 13:3333-3335.

Collins SR, Douglass A, Vale RD, Weissman JS. (2004) Mechanism of prion propagation: Amyloid growth occurs by monomer addition. PloS Biology, 2:1499-1500.

Osherovich LZ, Cox BS, Tuite MF, Weissman JS. (2004) Dissection and design of yeast prions. PloS Biology, 2:0442-0451.

Tanaka M, Chien P, Naber N, Cooke R, Weissman JS. (2004) Conformational variations in an infectious protein determine prion strain differences. Nature, 428:323-28.

Chien P, Weissman JS, DePace AH. (2004) Emerging principles of conformation-based prion inheritance. Annual Review of Biochemistry, 73:617-56.

Ghaemmaghami S, Huh W-K, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. (2003) Global analysis of protein expression in yeast. Nature, 425:737-41.

Huh W-K, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK. (2003) Global analysis of protein localization in budding yeast. Nature, 425:686-91.

Chien P, DePace AH, Collins S, Weissman JS. (2003) Generation of prion transmission barriers by mutational control of amyloid conformations. Nature, 424:948-51.

Wang JD, Herman C, Tipton KA, Gross CA, Weissman JS. (2002) Directed evolution of substrate-optimized GroEL/S chaperonins. Cell, 111:1027-1039.

Tu BP, Weissman JS. (2002) The FAD- and O2-dependent reaction cycle of Ero1-mediated oxidative protein folding in the endoplasmic reticulum. Molecular Cell, 10:983-994.

DePace AH, Weissman JS. (2002) Origins and kinetic consequences of diversity in Sup35 yeast prion fibers. Nature Structural Biology, 9:389-395.

Osherovich LZ, Weissman JS. (2002) The utility of prions. Developmental Cell, 2:143-152.

Weissman JS, Hood JK. (2001) Prion diseases. A rogue protein. Lancet, 358:s53.

Weissman JS. (2001) The ins and outs of GroEL-mediated folding. Molecular Cell, 8:730-732.

Travers KT, Patil CP, Weissman JS. (2001) Functional genomic approaches to understanding molecular chaperones and stress responses. Advanced Protein Chemistry, 59:345-390.

Fewell SW, Travers KT, Weissman JS, Brodsky JL. (2001) The action of molecular chaperones in the early secretory pathway. Annual Review of Genetics, 35:149-91.

Osherovich LZ, Weissman JS. (2001) Multiple Gln/Asn-Rich prion domains confer susceptibility to induction of the yeast [PSI+] prion. Cell, 106:183-194.

Chien PC, Weissman JS. (2001) Conformational diversity in a yeast prion dictates its seeding specificity. Nature, 410:223-227.

Tu BP, Ho-Scheleyer SC, Travers KJ, Weissman JS. (2000) Biochemical basis of oxidative protein folding in the endoplasmic reticulum. Science, 290:1571-1574.

Michelitsch MD, Weissman JS. (2000) A census of glutamine/asparagine-rich regions: Implications for their conserved function and the prediction of novel prions. PNAS, 97:11910-11915.

Sparrer HE, Santoso A, Szoka Jr FC, Weissman JS. (2000) Evidence for the prion hypothesis: Induction of the yeast [PSI+] factor by in vitro-converted Sup35 protein. Science, 289:595-599.

Travers KT, Patil CP, Wodicka L, Lockhart DJ, Weissman JS, Walter P. (2000) Functional and genomic analyses reveal essential coordination between the unfolded protein response and ER-associated degradation. Cell, 101:249-258.

Santoso A, Chien P, Weissman JS. (2000) Molecular basis of a yeast prion species barrier. Cell, 100:277-288.

Wang JD, Weissman JS. (1999) Thinking outside the box: new insights into the mechanism of GroEL-mediated folding. Nature Structural Biology, 6:597-600.

DePace AH, Santoso A, Hillner P, Weissman JS. (1998) A critical role for amino-terminal glutamine/asparagine repeats in the formation and propagation of a yeast prion. Cell, 93:1241-1252.

Wang JD, Michelitsch MD, Weissman JS. (1998) GroEL-GroES-mediated protein folding requires an intact central cavity. PNAS, 95:12163-12168.

Horwich AL, Burston SG, Rye HS, Weissman JS, Fenton WA. (1998) Construction of single-ring and two-ring hybrid versions of bacterial chaperonin GroEL. Methods in Enzymology; 290:141-146.

Pollard M, Travers KT, Weissman JS. (1998) Ero1p: a novel and ubiquitous protein with an essential role in oxidative protein folding in the endoplasmic reticulum. Molecular Cell, 1:171-182.

Horwich AL, Weissman JS. (1997) Deadly conformations--protein misfolding in prion disease. Cell, 89:499-510.

Fenton WA, Weissman JS, Horwich AL. (1996) Putting a lid on protein folding: structure and function of GroES. Chemical Biology, 3:157-161.