Bassik M, Kampmann M,
Lebbink RJ, Wang S, Hein MY, Poser I, Weibezahn J, Horlbeck MA, Mann M, Hyman AA, LeProust EM,
McManus MT, Weissman JS. (2013) A systematic Mammalian genetic interaction map reveals pathways
underlying ricin susceptibility. Cell, 152: 909-22.
Schuldiner M,
Weissman JS. (2013) The Contribution of Systematic Approaches to Characterizing the
Proteins and Functions of the Endoplasmic Reticulum. Cold Spring Harb Perspect Biol, 5(3).
Brandman O, Stewart-Ornstein J, Wong D, Larson A, Williams CC, Li GW, Zhou S, King
D, Shen PS, Weibezahn J, Dunn JG, Rouskin S,
Inada T, Frost A, Weissman JS. (2012) A ribosome-bound quality control complex triggers degradation of nascent peptides and signals
translation stress. Cell, 151: 1042-54.
Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, Ma M, Shen
B, Qian SB, Hengel H, Mann M, Ingolia
NT, Weissman JS. (2012) Decoding human cytomegalovirus. Science, 338: 1088-93.
Radford
SE, Weissman JS. (2012) Special Issue: the molecular and cellular mechanisms of
amyloidosis. J Mol Biol, 421: 139-41.
Carvunis AR, Rolland
T, Wapinski I, Calderwood MA, Yildirim MA, Simonis N, Charloteaux B, Hidalgo CA, Barbette J, Santhanam B,
Brar GA, Weissman JS, Regev A, Thierry-Mieg N, Cusick ME, Vidal M. (2012) Proto-genes and de novo gene
birth. Nature, 487: 370-4.
Ingolia NT, Brar GA,
Rouskin S, McGeachy AM, Weissman JS. (2012)
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of
ribosome-protected mRNA fragments. Nature Protocols, 7: 1534-50.
Frost A, Elgort MG, Brandman O, Ives C, Collins SR, Miller-Vedam L, Weibezahn J,
Hein MY, Poser I, Mann M, Hyman AA, Weissman JS. (2012) Functional repurposing revealed by comparing S. pombe and S. cerevisiae
genetic interactions. Cell, 149: 1339-52.
Li GW, Oh E, Weissman JS. (2012) The anti-Shine-Dalgamo
sequence drives translational pausing and codon choice in bacteria.
Nature, 484: 538-41.
Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, Sher A, Shi
EY, Stumpf CR, Christensen C, Bonham MJ, Wang S, Ren P, Martin M, Jessen K, Feldman ME, Weissman JS, Shokat KM, Rommel C, Ruggero D. (2012)
The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature, 485:
55-61.
Stewart-Ornstein J, Weissman JS, El-Samad H. (2012) Cellular
noise regulons underlie fluctuations in Saccharomyces cerevisiae.
Mol Cell, 45: 483-93.
Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. (2012)
High-resoltion view of the yeast meiotic program revealed
by ribosome profiling. Science, 335: 552-7.
El-Samad H, Weissman JS. (2011) Genetics: Noise rules. Nature, 480:
188-189.
Roelants FM, Breslow DK, Muir A, Weissman JS, Thorner J. (2011) Protein kinase Ypk1
phosphorylates regulatory proteins Orm1 and Orm2 to control
sphingolipid
homeostasis in Saccharomyces cerevisiae. PNAS, 108: 19222-27.
Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G,
Weissman JS, Bukau B. (2011) Selective ribosome
profiling
reveals the co-translational chaperone action of trigger factor in vivo. Cell, 147: 1295-1308.
Smith MH, Ploegh HL, Weissman JS. (2011) Road to ruin: targeting proteins for degradation in the
endoplasmic reticulum. Science, 334:
1086-90.
Ingolia NT, Lareau LF, Weissman JS. (2011) Ribosome profiling of mouse embryonic stem cells
reveals the complexity and dynamics of Mammalian
proteomes. Cell, 147: 789-802.
Hoppins S, Collins SR, Cassidy-Stone A, Hummel E, Devary RM, Lackner LL, Westermann B,
Schuldiner M, Weissman JS, Nunnari J. (2011) A
mitochondrial-focused
genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria. J Cell Biol, 195: 323-40.
Gracheva E, Cordero J, Weissman J, Infgolia N, Julius D. (2011) Ganglion-specific
splicing of TRPV1 underlies infrared sensation in vampire bats.
Nature,
476: 88-91.
Terzi N, Churchman LS, Vasilijeva L, Weissman J, Buratowski S. (2011) H3K4 trimethylation by Set1 promotes
efficient
termination by the Nrd1-Nab3-Sen1 pathway. Mol Cell Biol, 31: 3569-83.
Toyama
BH, Weissman JS. (2011) Amyloid Structure: Conformational Diversity and Consequences. Annual Review of
Biochemistry, Volume 80: 557-85.
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.
Churchman LS, Weissman JS. (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature,
469: 368-73.
Henry TC, Power JE, Kerwin CL, Mohammed A, Weissman JS, Cameron DM, Wykoff
DD. (2011) Systematic screen of
Schizosaccharomyces pombe deletion collection uncovers parallel evolution of the phosphate signal transduction pathway in yeasts.
Eukarot Cell, 10(2): 198-206.
Guo H, Ingolia NT, Weissman JS, Bartel DP. (2010) Mammalian microRNAs
predominately act to decrease target mRNA levels. Nature,
466:835-40.
Vembar SS, Jonikas MC, Hendershot LM, Weissman JS, Brodsky JL. (2010) J domain
co-chaperone specificity defines the role of BIP during protein
translocation. Journal Biological Chemistry, 285:22484-94.
Battle A, Jonikas MC, Walter P, Weissman JS, Koller D. (2010)
Automated identification of pathways from quantitative genetic interaction data. Molecular Systems Biology, 6:397.
Springer M, Weissman JS, Kirschner MW. (2010) A general lack of compensation for gene dosage in
yeast. Molecular Systems Biology,
6:368.
Gracheva EO, Ingolia NT, Kelly YM, Cordero-Morales JF, Hollopeter G, Chesler AT,
Sanchez EE, Perez JC, Weissman JS, Julius DJ. (2010)
Molecular basis of infrared detection by snakes. Nature, 464:1006-11.
Breslow DK, Collins SR, Bodenmiller B, Aebersold R, Simons K, Shevchenko A, Ejsing CS,
Weissman JS. (2010) ORM family proteins
mediate sphingolipid homeostasis. Nature, 463:1048-53.
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.
Hollien J, Lin JH, Li H, Stevens N, Walter P, Weissman JS. (2009) Regulated Ire
1-dependent decay of messenger RNAs in mammalian
cells. Journal Cell Biology, 186:323-31.
Kornmann B, Currie E, Collins SR, Schuldiner M, Nunnari J, Weissman JS, Walter P.
(2009) An ER-mitochondria tethering complex revealed by a
synthetic biology screen. Science, 325:477-81.
Bassik MC, Lebbink RJ, Churchman LS, Ingolia NT, Patena W, LeProust
EM, Schuldiner M, Weissman JS, McManus MT. (2009) Rapid
creation and quantitative monitoring of high coverage shRNA libraries. Nature Methods, 6:443-5.
Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB,
Weissman J, Shoichet BK. (2009) Small-molecule aggregates inhibit amyloid polymerization. Nature Chemical Biology, 4:197-9.
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.
Roguev A, Wiren M, Weissman JS, Krogan NJ. (2007) High-throughput genetic interaction mapping in the fission yeast Schizosaccaromyces pombe.
Nature
Methods, 10:861-866.
Morrison AJ, Kim J-A, Person MD, Highland J, Xiao J, Wehr TS, Hensley S, Bao Y, Shen J, Collins SR,
Weissman JS, Delrow J, Krogan NJ, Haber JE, Shen X. (2007) Mec1/Tel1 phosphorylation of the INO80 chromatin
remodeling complex influences DNA damage checkpoint responses. Cell,
130:499-511.
Denic V, Weissman JS. (2007) A molecular caliper mechanism for determining very long-chain fatty acid length.
Cell, Aug 24;130(4):663-77
Laribee NR, Yoichiro S, Mersman DP, Collins SR, Kemmeren P, Roguev A, Weissman J, Briggs SD, Krogan NJ, Strahl BD. (2007) CCR4/NOT complex
associates with the proteasome and regulates histone methylation. PNAS, 104:5836-41.
Toyama BH, Kelly MJS, Gross JD, Weissman JS. (2007) The structural basis of yeast prion strain variants. Nature, 449: 233-7.
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. (2007) Functional dissection of yeast chromosome biology complexes using a genetic interaction map. Nature, 446:806-810.
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.
Schuldiner M, Collins SR, Weissman JS, Krogan NJ. (2006) Quantitative genetic analysis in S. cerevisiae using epistatic miniarray profiles (E-MAPs)
and its application to chromatin functions. Methods, 40:344-52.
Newman JR, Weissman JS. (2006) Systems Biology: many things from one. Nature, 444:561-2.
Tanaka M, Collins SR, Toyama BH, Weissman JS. (2006) The physical basis of how prion conformations determine strain phenotypes. Nature,
442:585-9.
Denic V, Quan EM, Weissman JS. (2006) A luminal surveillance complex that selects misfolded glycoproteins for ER-associated degradation.
Cell, 126:349-59.
Hollien J, Weissman JS. (2006) Decay of endoplasmic reticulum-localized mRNAs during the unfolded protein response. Science, 313:104-7.
Collins SR, Schuldiner MB, Krogan NJ, Weissman JS. (2006) A strategy for extracting and analyzing large-scale quantitative epistatic interaction
data. Genome Biology, 7:R63.
Newman JRS, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. (2006) Single-cell proteomics of the budding yeast saccharomyces
cerevisiae. Nature, 144:840-846.
Bukau B, Weissman J, Horwich A. (2006) Molecular chaperones and protein quality control. Cell, 125:3.
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.