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    Jonathan Weissman, PhD

    TitleProfessor
    SchoolUCSF School of Medicine
    DepartmentCellular Molecular Pharmacology
    Address1700 4th Street
    San Francisco CA 94158
    Phone415-502-7642
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      Other Positions
      TitleProfessor, School of Medicine


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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Jan CH, Williams CC, Weissman JS. Response to Comment on "Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling". Science. 2015 Jun 12; 348(6240):1217.
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      2. Sidrauski C, Tsai JC, Kampmann M, Hearn BR, Vedantham P, Jaishankar P, Sokabe M, Mendez AS, Newton BW, Tang EL, Verschueren E, Johnson JR, Krogan NJ, Fraser CS, Weissman JS, Renslo AR, Walter P. Pharmacological dimerization and activation of the exchange factor eIF2B antagonizes the integrated stress response. Elife. 2015 Apr 15; 4.
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      3. Kampmann M, Bassik MC, Weissman JS. Corrigendum: Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps. Nat Protoc. 2015 Apr; 10(4):644.
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      4. Baltimore D, Berg P, Botchan M, Carroll D, Charo RA, Church G, Corn JE, Daley GQ, Doudna JA, Fenner M, Greely HT, Jinek M, Martin GS, Penhoet E, Puck J, Sternberg SH, Weissman JS, Yamamoto KR. Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science. 2015 Apr 3; 348(6230):36-8.
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      5. Jovanovic M, Rooney MS, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach MR, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, Regev A. Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens. Science. 2015 Mar 6; 347(6226):1259038.
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      6. Li X, Colvin T, Rauch JN, Acosta-Alvear D, Kampmann M, Dunyak B, Hann B, Aftab BT, Murnane M, Cho M, Walter P, Weissman JS, Sherman MY, Gestwicki JE. Validation of the Hsp70-Bag3 Protein-Protein Interaction as a Potential Therapeutic Target in Cancer. Mol Cancer Ther. 2015 Jan 6.
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      7. Shen PS, Park J, Qin Y, Li X, Parsawar K, Larson MH, Cox J, Cheng Y, Lambowitz AM, Weissman JS, Brandman O, Frost A. Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains. Science. 2015 Jan 2; 347(6217):75-8.
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      8. Pop C, Rouskin S, Ingolia NT, Han L, Phizicky EM, Weissman JS, Koller D. Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Mol Syst Biol. 2014; 10(12):770.
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      9. Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH, La Russa M, Tsai JC, Weissman JS, Dueber JE, Qi LS, Lim WA. Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds. Cell. 2015 Jan 15; 160(1-2):339-50.
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      10. Williams CC, Jan CH, Weissman JS. Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling. Science. 2014 Nov 7; 346(6210):748-51.
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      11. Jan CH, Williams CC, Weissman JS. Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling. Science. 2014 Nov 7; 346(6210):1257521.
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      12. Kannan K, Kanabar P, Schryer D, Florin T, Oh E, Bahroos N, Tenson T, Weissman JS, Mankin AS. The general mode of translation inhibition by macrolide antibiotics. Proc Natl Acad Sci U S A. 2014 Nov 11; 111(45):15958-63.
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      13. Albert FW, Muzzey D, Weissman JS, Kruglyak L. Genetic influences on translation in yeast. PLoS Genet. 2014 Oct; 10(10):e1004692.
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      14. Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS. Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell. 2014 Oct 23; 159(3):647-61.
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      15. Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell. 2014 Oct 23; 159(3):635-46.
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      16. Julien O, Kampmann M, Bassik MC, Zorn JA, Venditto VJ, Shimbo K, Agard NJ, Shimada K, Rheingold AL, Stockwell BR, Weissman JS, Wells JA. Unraveling the mechanism of cell death induced by chemical fibrils. Nat Chem Biol. 2014 Nov; 10(11):969-76.
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      17. Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJ, Jackson SE, Wills MR, Weissman JS. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep. 2014 Sep 11; 8(5):1365-79.
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      18. Smith MH, Rodriguez EH, Weissman JS. Misfolded proteins induce aggregation of the lectin Yos9. J Biol Chem. 2014 Sep 12; 289(37):25670-7.
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      19. Schrader JM, Zhou B, Li GW, Lasker K, Childers WS, Williams B, Long T, Crosson S, McAdams HH, Weissman JS, Shapiro L. The coding and noncoding architecture of the Caulobacter crescentus genome. PLoS Genet. 2014 Jul; 10(7):e1004463.
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      20. Kampmann M, Bassik MC, Weissman JS. Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps. Nat Protoc. 2014 Aug; 9(8):1825-47.
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      21. van de Weijer ML, Bassik MC, Luteijn RD, Voorburg CM, Lohuis MA, Kremmer E, Hoeben RC, LeProust EM, Chen S, Hoelen H, Ressing ME, Patena W, Weissman JS, McManus MT, Wiertz EJ, Lebbink RJ. A high-coverage shRNA screen identifies TMEM129 as an E3 ligase involved in ER-associated protein degradation. Nat Commun. 2014; 5:3832.
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      22. Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D, Gross CA, Block SM, Greenleaf WJ, Landick R, Weissman JS. A pause sequence enriched at translation start sites drives transcription dynamics in vivo. Science. 2014 May 30; 344(6187):1042-7.
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      23. Li GW, Burkhardt D, Gross C, Weissman JS. Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell. 2014 Apr 24; 157(3):624-35.
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      24. Muzzey D, Sherlock G, Weissman JS. Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans. Genome Res. 2014 Jun; 24(6):963-73.
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      25. Pfanner N, van der Laan M, Amati P, Capaldi RA, Caudy AA, Chacinska A, Darshi M, Deckers M, Hoppins S, Icho T, Jakobs S, Ji J, Kozjak-Pavlovic V, Meisinger C, Odgren PR, Park SK, Rehling P, Reichert AS, Sheikh MS, Taylor SS, Tsuchida N, van der Bliek AM, van der Klei IJ, Weissman JS, Westermann B, Zha J, Neupert W, Nunnari J. Uniform nomenclature for the mitochondrial contact site and cristae organizing system. J Cell Biol. 2014 Mar 31; 204(7):1083-6.
        View in: PubMed PMC3971754
      26. Wolff S, Weissman JS, Dillin A. Differential scales of protein quality control. Cell. 2014 Mar 27; 157(1):52-64.
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      27. Arias C, Weisburd B, Stern-Ginossar N, Mercier A, Madrid AS, Bellare P, Holdorf M, Weissman JS, Ganem D. KSHV 2.0: a comprehensive annotation of the Kaposi's sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features. PLoS Pathog. 2014 Jan; 10(1):e1003847.
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      28. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell. 2013 Dec 19; 155(7):1479-91.
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      29. Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature. 2014 Jan 30; 505(7485):701-5.
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      30. Dunn JG, Foo CK, Belletier NG, Gavis ER, Weissman JS. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. Elife. 2013; 2:e01179.
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      31. Stewart-Ornstein J, Nelson C, DeRisi J, Weissman JS, El-Samad H. Msn2 coordinates a stoichiometric gene expression program. Curr Biol. 2013 Dec 2; 23(23):2336-45.
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      32. Matheny CJ, Wei MC, Bassik MC, Donnelly AJ, Kampmann M, Iwasaki M, Piloto O, Solow-Cordero DE, Bouley DM, Rau R, Brown P, McManus MT, Weissman JS, Cleary ML. Next-generation NAMPT inhibitors identified by sequential high-throughput phenotypic chemical and functional genomic screens. Chem Biol. 2013 Nov 21; 20(11):1352-63.
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      33. Wiita AP, Ziv E, Wiita PJ, Urisman A, Julien O, Burlingame AL, Weissman JS, Wells JA. Global cellular response to chemotherapy-induced apoptosis. Elife. 2013; 2:e01236.
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      34. Becker AH, Oh E, Weissman JS, Kramer G, Bukau B. Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes. Nat Protoc. 2013 Nov; 8(11):2212-39.
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      35. Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc. 2013 Nov; 8(11):2180-96.
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      36. Berchowitz LE, Gajadhar AS, van Werven FJ, De Rosa AA, Samoylova ML, Brar GA, Xu Y, Xiao C, Futcher B, Weissman JS, White FM, Amon A. A developmentally regulated translational control pathway establishes the meiotic chromosome segregation pattern. Genes Dev. 2013 Oct 1; 27(19):2147-63.
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      37. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013 Jul 18; 154(2):442-51.
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      38. Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. Genome-wide annotation and quantitation of translation by ribosome profiling. Curr Protoc Mol Biol. 2013 Jul; Chapter 4:Unit 4.18.
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      39. Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell. 2013 Jul 3; 154(1):240-51.
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      40. Kampmann M, Bassik MC, Weissman JS. Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells. Proc Natl Acad Sci U S A. 2013 Jun 18; 110(25):E2317-26.
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      41. O'Connor PB, Li GW, Weissman JS, Atkins JF, Baranov PV. rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments. Bioinformatics. 2013 Jun 15; 29(12):1488-91.
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      42. Thorburn RR, Gonzalez C, Brar GA, Christen S, Carlile TM, Ingolia NT, Sauer U, Weissman JS, Amon A. Aneuploid yeast strains exhibit defects in cell growth and passage through START. Mol Biol Cell. 2013 May; 24(9):1274-89.
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      43. Schuldiner M, Weissman JS. The contribution of systematic approaches to characterizing the proteins and functions of the endoplasmic reticulum. Cold Spring Harb Perspect Biol. 2013 Mar; 5(3):a013284.
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      44. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013 Feb 28; 152(5):1173-83.
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      45. Bassik MC, Kampmann M, Lebbink RJ, Wang S, Hein MY, Poser I, Weibezahn J, Horlbeck MA, Chen S, Mann M, Hyman AA, Leproust EM, McManus MT, Weissman JS. A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell. 2013 Feb 14; 152(4):909-22.
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      46. Muzzey D, Schwartz K, Weissman JS, Sherlock G. Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure. Genome Biol. 2013; 14(9):R97.
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      47. 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. Decoding human cytomegalovirus. Science. 2012 Nov 23; 338(6110):1088-93.
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      48. 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. A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Cell. 2012 Nov 21; 151(5):1042-54.
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      49. Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc. 2012 Aug; 7(8):1534-50.
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      50. 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. Proto-genes and de novo gene birth. Nature. 2012 Jul 19; 487(7407):370-4.
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      51. 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. Functional repurposing revealed by comparing S. pombe and S. cerevisiae genetic interactions. Cell. 2012 Jun 8; 149(6):1339-52.
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      52. Radford SE, Weissman JS. Special issue: the molecular and cellular mechanisms of amyloidosis. J Mol Biol. 2012 Aug 10; 421(2-3):139-41.
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      53. Churchman LS, Weissman JS. Native elongating transcript sequencing (NET-seq). Curr Protoc Mol Biol. 2012 Apr; Chapter 4:Unit 4.14.1-17.
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      54. Li GW, Oh E, Weissman JS. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature. 2012 Apr 26; 484(7395):538-41.
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      55. Stewart-Ornstein J, Weissman JS, El-Samad H. Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae. Mol Cell. 2012 Feb 24; 45(4):483-93.
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      56. 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. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature. 2012 May 3; 485(7396):55-61.
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      57. Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science. 2012 Feb 3; 335(6068):552-7.
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      58. Oh E, Becker AH, Sandikci A, Huber D, Chaba R, Gloge F, Nichols RJ, Typas A, Gross CA, Kramer G, Weissman JS, Bukau B. Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell. 2011 Dec 9; 147(6):1295-308.
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      59. El-Samad H, Weissman JS. Genetics: Noise rules. Nature. 2011 Dec 8; 480(7376):188-9.
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      60. Smith MH, Ploegh HL, Weissman JS. Road to ruin: targeting proteins for degradation in the endoplasmic reticulum. Science. 2011 Nov 25; 334(6059):1086-90.
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      61. Roelants FM, Breslow DK, Muir A, Weissman JS, Thorner J. Protein kinase Ypk1 phosphorylates regulatory proteins Orm1 and Orm2 to control sphingolipid homeostasis in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2011 Nov 29; 108(48):19222-7.
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      62. Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell. 2011 Nov 11; 147(4):789-802.
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      63. Hoppins S, Collins SR, Cassidy-Stone A, Hummel E, Devay RM, Lackner LL, Westermann B, Schuldiner M, Weissman JS, Nunnari J. A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria. J Cell Biol. 2011 Oct 17; 195(2):323-40.
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      64. Gracheva EO, Cordero-Morales JF, González-Carcacía JA, Ingolia NT, Manno C, Aranguren CI, Weissman JS, Julius D. Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats. Nature. 2011 Aug 4; 476(7358):88-91.
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      65. Terzi N, Churchman LS, Vasiljeva L, Weissman J, Buratowski S. H3K4 trimethylation by Set1 promotes efficient termination by the Nrd1-Nab3-Sen1 pathway. Mol Cell Biol. 2011 Sep; 31(17):3569-83.
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      66. Verges KJ, Smith MH, Toyama BH, Weissman JS. Strain conformation, primary structure and the propagation of the yeast prion [PSI+]. Nat Struct Mol Biol. 2011 Apr; 18(4):493-9.
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      67. Foo CK, Ohhashi Y, Kelly MJ, Tanaka M, Weissman JS. Radically different amyloid conformations dictate the seeding specificity of a chimeric Sup35 prion. J Mol Biol. 2011 Apr 22; 408(1):1-8.
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      68. Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature. 2011 Jan 20; 469(7330):368-73.
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      69. Toyama BH, Weissman JS. Amyloid structure: conformational diversity and consequences. Annu Rev Biochem. 2011; 80:557-85.
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      70. Henry TC, Power JE, Kerwin CL, Mohammed A, Weissman JS, Cameron DM, Wykoff DD. Systematic screen of Schizosaccharomyces pombe deletion collection uncovers parallel evolution of the phosphate signal transduction pathway in yeasts. Eukaryot Cell. 2011 Feb; 10(2):198-206.
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      71. Weissman JS. The epistemology of cell biology. Mol Biol Cell. 2010 Nov 15; 21(22):3825.
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      72. Breslow DK, Weissman JS. Membranes in balance: mechanisms of sphingolipid homeostasis. Mol Cell. 2010 Oct 22; 40(2):267-79.
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      73. Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature. 2010 Aug 12; 466(7308):835-40.
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      74. Battle A, Jonikas MC, Walter P, Weissman JS, Koller D. Automated identification of pathways from quantitative genetic interaction data. Mol Syst Biol. 2010 Jun 8; 6:379.
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      75. Springer M, Weissman JS, Kirschner MW. A general lack of compensation for gene dosage in yeast. Mol Syst Biol. 2010 May 11; 6:368.
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      76. Vembar SS, Jonikas MC, Hendershot LM, Weissman JS, Brodsky JL. J domain co-chaperone specificity defines the role of BiP during protein translocation. J Biol Chem. 2010 Jul 16; 285(29):22484-94.
        View in: PubMed PMC2903355
      77. Gracheva EO, Ingolia NT, Kelly YM, Cordero-Morales JF, Hollopeter G, Chesler AT, Sánchez EE, Perez JC, Weissman JS, Julius D. Molecular basis of infrared detection by snakes. Nature. 2010 Apr 15; 464(7291):1006-11.
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      78. Breslow DK, Collins SR, Bodenmiller B, Aebersold R, Simons K, Shevchenko A, Ejsing CS, Weissman JS. Orm family proteins mediate sphingolipid homeostasis. Nature. 2010 Feb 25; 463(7284):1048-53.
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      79. Weissman J. Journal club. A biochemist looks at how DNA sequencing can reveal more than just sequences. Nature. 2009 Oct 29; 461(7268):1177.
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      80. Collins SR, Weissman JS, Krogan NJ. From information to knowledge: new technologies for defining gene function. Nat Methods. 2009 Oct; 6(10):721-23.
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      81. Hollien J, Lin JH, Li H, Stevens N, Walter P, Weissman JS. Regulated Ire1-dependent decay of messenger RNAs in mammalian cells. J Cell Biol. 2009 Aug 10; 186(3):323-31.
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      82. Kornmann B, Currie E, Collins SR, Schuldiner M, Nunnari J, Weissman JS, Walter P. An ER-mitochondria tethering complex revealed by a synthetic biology screen. Science. 2009 Jul 24; 325(5939):477-81.
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      83. Bassik MC, Lebbink RJ, Churchman LS, Ingolia NT, Patena W, LeProust EM, Schuldiner M, Weissman JS, McManus MT. Rapid creation and quantitative monitoring of high coverage shRNA libraries. Nat Methods. 2009 Jun; 6(6):443-5.
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      84. Passos DO, Doma MK, Shoemaker CJ, Muhlrad D, Green R, Weissman J, Hollien J, Parker R. Analysis of Dom34 and its function in no-go decay. Mol Biol Cell. 2009 Jul; 20(13):3025-32.
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      85. Jonikas MC, Collins SR, Denic V, Oh E, Quan EM, Schmid V, Weibezahn J, Schwappach B, Walter P, Weissman JS, Schuldiner M. Comprehensive characterization of genes required for protein folding in the endoplasmic reticulum. Science. 2009 Mar 27; 323(5922):1693-7.
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      86. Fiedler D, Braberg H, Mehta M, Chechik G, Cagney G, Mukherjee P, Silva AC, Shales M, Collins SR, van Wageningen S, Kemmeren P, Holstege FC, Weissman JS, Keogh MC, Koller D, Shokat KM, Krogan NJ. Functional organization of the S. cerevisiae phosphorylation network. Cell. 2009 Mar 6; 136(5):952-63.
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      87. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009 Apr 10; 324(5924):218-23.
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      88. Quan EM, Kamiya Y, Kamiya D, Denic V, Weibezahn J, Kato K, Weissman JS. Defining the glycan destruction signal for endoplasmic reticulum-associated degradation. Mol Cell. 2008 Dec 26; 32(6):870-7.
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      89. 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. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell. 2008 Dec 5; 32(5):735-46.
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      90. Tipton KA, Verges KJ, Weissman JS. In vivo monitoring of the prion replication cycle reveals a critical role for Sis1 in delivering substrates to Hsp104. Mol Cell. 2008 Nov 21; 32(4):584-91.
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      91. Chechik G, Oh E, Rando O, Weissman J, Regev A, Koller D. Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Nat Biotechnol. 2008 Nov; 26(11):1251-9.
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      92. 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. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science. 2008 Oct 17; 322(5900):405-10.
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      93. 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. High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods. 2008 Sep; 5(9):781-7.
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      94. Ingolia NT, Weissman JS. Systems biology: Reverse engineering the cell. Nature. 2008 Aug 28; 454(7208):1059-62.
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      95. Schuldiner M, Metz J, Schmid V, Denic V, Rakwalska M, Schmitt HD, Schwappach B, Weissman JS. The GET complex mediates insertion of tail-anchored proteins into the ER membrane. Cell. 2008 Aug 22; 134(4):634-45.
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      96. Breslow DK, Cameron DM, Collins SR, Schuldiner M, Stewart-Ornstein J, Newman HW, Braun S, Madhani HD, Krogan NJ, Weissman JS. A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods. 2008 Aug; 5(8):711-8.
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      97. Feng BY, Toyama BH, Wille H, Colby DW, Collins SR, May BC, Prusiner SB, Weissman J, Shoichet BK. Small-molecule aggregates inhibit amyloid polymerization. Nat Chem Biol. 2008 Mar; 4(3):197-9.
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      98. Haass FA, Jonikas M, Walter P, Weissman JS, Jan YN, Jan LY, Schuldiner M. Identification of yeast proteins necessary for cell-surface function of a potassium channel. Proc Natl Acad Sci U S A. 2007 Nov 13; 104(46):18079-84.
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      99. Roguev A, Wiren M, Weissman JS, Krogan NJ. High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe. Nat Methods. 2007 Oct; 4(10):861-6.
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      100. Toyama BH, Kelly MJ, Gross JD, Weissman JS. The structural basis of yeast prion strain variants. Nature. 2007 Sep 13; 449(7159):233-7.
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      101. Denic V, Weissman JS. A molecular caliper mechanism for determining very long-chain fatty acid length. Cell. 2007 Aug 24; 130(4):663-77.
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      102. Morrison AJ, Kim JA, 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. Mec1/Tel1 phosphorylation of the INO80 chromatin remodeling complex influences DNA damage checkpoint responses. Cell. 2007 Aug 10; 130(3):499-511.
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      103. Ihmels J, Collins SR, Schuldiner M, Krogan NJ, Weissman JS. Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss. Mol Syst Biol. 2007; 3:86.
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      104. Laribee RN, Shibata Y, Mersman DP, Collins SR, Kemmeren P, Roguev A, Weissman JS, Briggs SD, Krogan NJ, Strahl BD. CCR4/NOT complex associates with the proteasome and regulates histone methylation. Proc Natl Acad Sci U S A. 2007 Apr 3; 104(14):5836-41.
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      105. 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. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature. 2007 Apr 12; 446(7137):806-10.
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      106. Collins SR, Kemmeren P, Zhao XC, Greenblatt JF, Spencer F, Holstege FC, Weissman JS, Krogan NJ. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics. 2007 Mar; 6(3):439-50.
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      107. Schuldiner M, Collins SR, Weissman JS, Krogan NJ. Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions. Methods. 2006 Dec; 40(4):344-52.
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      108. Newman JR, Weissman JS. Systems biology: many things from one. Nature. 2006 Nov 30; 444(7119):561-2.
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      109. Denic V, Quan EM, Weissman JS. A luminal surveillance complex that selects misfolded glycoproteins for ER-associated degradation. Cell. 2006 Jul 28; 126(2):349-59.
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      110. Hollien J, Weissman JS. Decay of endoplasmic reticulum-localized mRNAs during the unfolded protein response. Science. 2006 Jul 7; 313(5783):104-7.
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      111. Tanaka M, Collins SR, Toyama BH, Weissman JS. The physical basis of how prion conformations determine strain phenotypes. Nature. 2006 Aug 3; 442(7102):585-9.
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      112. Newman JR, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, DeRisi JL, Weissman JS. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature. 2006 Jun 15; 441(7095):840-6.
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      113. Bukau B, Weissman J, Horwich A. Molecular chaperones and protein quality control. Cell. 2006 May 5; 125(3):443-51.
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      114. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-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. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006 Mar 30; 440(7084):637-43.
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      115. Collins SR, Schuldiner M, Krogan NJ, Weissman JS. A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol. 2006; 7(7):R63.
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      116. Tanaka M, Weissman JS. An efficient protein transformation protocol for introducing prions into yeast. Methods Enzymol. 2006; 412:185-200.
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      117. Kulp MS, Frickel EM, Ellgaard L, Weissman JS. Domain architecture of protein-disulfide isomerase facilitates its dual role as an oxidase and an isomerase in Ero1p-mediated disulfide formation. J Biol Chem. 2006 Jan 13; 281(2):876-84.
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      118. 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. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell. 2005 Nov 18; 123(4):593-605.
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      119. Schuldiner M, Collins SR, Thompson NJ, Denic V, Bhamidipati A, Punna T, Ihmels J, Andrews B, Boone C, Greenblatt JF, Weissman JS, Krogan NJ. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell. 2005 Nov 4; 123(3):507-19.
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      120. Bhamidipati A, Denic V, Quan EM, Weissman JS. Exploration of the topological requirements of ERAD identifies Yos9p as a lectin sensor of misfolded glycoproteins in the ER lumen. Mol Cell. 2005 Sep 16; 19(6):741-51.
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      121. Tanaka M, Chien P, Yonekura K, Weissman JS. Mechanism of cross-species prion transmission: an infectious conformation compatible with two highly divergent yeast prion proteins. Cell. 2005 Apr 8; 121(1):49-62.
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      122. Howson R, Huh WK, Ghaemmaghami S, Falvo JV, Bower K, Belle A, Dephoure N, Wykoff DD, Weissman JS, O'Shea EK. Construction, verification and experimental use of two epitope-tagged collections of budding yeast strains. Comp Funct Genomics. 2005; 6(1-2):2-16.
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      123. Weissman JS, O'Shea EK. 2004 Irving Sigal Young Investigator Award. Protein Sci. 2004 Dec; 13(12):3333-5.
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      124. Collins SR, Douglass A, Vale RD, Weissman JS. Mechanism of prion propagation: amyloid growth occurs by monomer addition. PLoS Biol. 2004 Oct; 2(10):e321.
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      125. Osherovich LZ, Cox BS, Tuite MF, Weissman JS. Dissection and design of yeast prions. PLoS Biol. 2004 Apr; 2(4):E86.
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      126. Tanaka M, Chien P, Naber N, Cooke R, Weissman JS. Conformational variations in an infectious protein determine prion strain differences. Nature. 2004 Mar 18; 428(6980):323-8.
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      127. Tu BP, Weissman JS. Oxidative protein folding in eukaryotes: mechanisms and consequences. J Cell Biol. 2004 Feb 2; 164(3):341-6.
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      128. Chien P, Weissman JS, DePace AH. Emerging principles of conformation-based prion inheritance. Annu Rev Biochem. 2004; 73:617-56.
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      129. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK. Global analysis of protein localization in budding yeast. Nature. 2003 Oct 16; 425(6959):686-91.
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      130. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. Global analysis of protein expression in yeast. Nature. 2003 Oct 16; 425(6959):737-41.
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      131. Chien P, DePace AH, Collins SR, Weissman JS. Generation of prion transmission barriers by mutational control of amyloid conformations. Nature. 2003 Aug 21; 424(6951):948-51.
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      132. Wang JD, Herman C, Tipton KA, Gross CA, Weissman JS. Directed evolution of substrate-optimized GroEL/S chaperonins. Cell. 2002 Dec 27; 111(7):1027-39.
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      133. Tu BP, Weissman JS. The FAD- and O(2)-dependent reaction cycle of Ero1-mediated oxidative protein folding in the endoplasmic reticulum. Mol Cell. 2002 Nov; 10(5):983-94.
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      134. DePace AH, Weissman JS. Origins and kinetic consequences of diversity in Sup35 yeast prion fibers. Nat Struct Biol. 2002 May; 9(5):389-96.
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      135. Osherovich LZ, Weissman JS. The utility of prions. Dev Cell. 2002 Feb; 2(2):143-51.
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      136. Weissman JS, Hood JK. Prion diseases. A rogue protein. Lancet. 2001 Dec; 358 Suppl:S53.
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      137. Weissman JS. The ins and outs of GroEL-mediated protein folding. Mol Cell. 2001 Oct; 8(4):730-2.
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      138. Osherovich LZ, Weissman JS. Multiple Gln/Asn-rich prion domains confer susceptibility to induction of the yeast [PSI(+)] prion. Cell. 2001 Jul 27; 106(2):183-94.
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      139. Chien P, Weissman JS. Conformational diversity in a yeast prion dictates its seeding specificity. Nature. 2001 Mar 8; 410(6825):223-7.
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      140. Aridor M, Fish KN, Bannykh S, Weissman J, Roberts TH, Lippincott-Schwartz J, Balch WE. The Sar1 GTPase coordinates biosynthetic cargo selection with endoplasmic reticulum export site assembly. J Cell Biol. 2001 Jan 8; 152(1):213-29.
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      141. Travers KJ, Patil CK, Weissman JS. Functional genomic approaches to understanding molecular chaperones and stress responses. Adv Protein Chem. 2001; 59:345-90.
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      142. Fewell SW, Travers KJ, Weissman JS, Brodsky JL. The action of molecular chaperones in the early secretory pathway. Annu Rev Genet. 2001; 35:149-91.
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      143. Tu BP, Ho-Schleyer SC, Travers KJ, Weissman JS. Biochemical basis of oxidative protein folding in the endoplasmic reticulum. Science. 2000 Nov 24; 290(5496):1571-4.
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      144. Michelitsch MD, Weissman JS. A census of glutamine/asparagine-rich regions: implications for their conserved function and the prediction of novel prions. Proc Natl Acad Sci U S A. 2000 Oct 24; 97(22):11910-5.
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      145. Sparrer HE, Santoso A, Szoka FC, Weissman JS. Evidence for the prion hypothesis: induction of the yeast [PSI+] factor by in vitro- converted Sup35 protein. Science. 2000 Jul 28; 289(5479):595-9.
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      146. Travers KJ, Patil CK, Wodicka L, Lockhart DJ, Weissman JS, Walter P. Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell. 2000 Apr 28; 101(3):249-58.
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      147. Allan BB, Weissman J, Aridor M, Moyer B, Chen CD, Yoo JS, Balch WE. Stage-specific assays to study biosynthetic cargo selection and role of SNAREs in export from the endoplasmic reticulum and delivery to the Golgi. Methods. 2000 Apr; 20(4):411-6.
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      148. Santoso A, Chien P, Osherovich LZ, Weissman JS. Molecular basis of a yeast prion species barrier. Cell. 2000 Jan 21; 100(2):277-88.
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      149. Wang JD, Weissman JS. Thinking outside the box: new insights into the mechanism of GroEL-mediated protein folding. Nat Struct Biol. 1999 Jul; 6(7):597-600.
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      150. Wang JD, Michelitsch MD, Weissman JS. GroEL-GroES-mediated protein folding requires an intact central cavity. Proc Natl Acad Sci U S A. 1998 Oct 13; 95(21):12163-8.
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      151. DePace AH, Santoso A, Hillner P, Weissman JS. A critical role for amino-terminal glutamine/asparagine repeats in the formation and propagation of a yeast prion. Cell. 1998 Jun 26; 93(7):1241-52.
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      152. Aridor M, Weissman J, Bannykh S, Nuoffer C, Balch WE. Cargo selection by the COPII budding machinery during export from the ER. J Cell Biol. 1998 Apr 6; 141(1):61-70.
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      153. Horwich AL, Burston SG, Rye HS, Weissman JS, Fenton WA. Construction of single-ring and two-ring hybrid versions of bacterial chaperonin GroEL. Methods Enzymol. 1998; 290:141-6.
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      154. Pollard MG, Travers KJ, Weissman JS. Ero1p: a novel and ubiquitous protein with an essential role in oxidative protein folding in the endoplasmic reticulum. Mol Cell. 1998 Jan; 1(2):171-82.
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      155. Horwich AL, Weissman JS. Deadly conformations--protein misfolding in prion disease. Cell. 1997 May 16; 89(4):499-510.
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      156. Burston SG, Weissman JS, Farr GW, Fenton WA, Horwich AL. Release of both native and non-native proteins from a cis-only GroEL ternary complex. Nature. 1996 Sep 5; 383(6595):96-9.
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      157. Fenton WA, Weissman JS, Horwich AL. Putting a lid on protein folding: structure and function of the co-chaperonin, GroES. Chem Biol. 1996 Mar; 3(3):157-61.
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      158. Weissman JS, Rye HS, Fenton WA, Beechem JM, Horwich AL. Characterization of the active intermediate of a GroEL-GroES-mediated protein folding reaction. Cell. 1996 Feb 9; 84(3):481-90.
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      159. Weissman JS, Kim PS. A kinetic explanation for the rearrangement pathway of BPTI folding. Nat Struct Biol. 1995 Dec; 2(12):1123-30.
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      160. Weissman JS, Hohl CM, Kovalenko O, Kashi Y, Chen S, Braig K, Saibil HR, Fenton WA, Horwich AL. Mechanism of GroEL action: productive release of polypeptide from a sequestered position under GroES. Cell. 1995 Nov 17; 83(4):577-87.
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      161. Yu MH, Weissman JS, Kim PS. Contribution of individual side-chains to the stability of BPTI examined by alanine-scanning mutagenesis. J Mol Biol. 1995 Jun 2; 249(2):388-97.
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      162. Weissman JS. All roads lead to Rome? The multiple pathways of protein folding. Chem Biol. 1995 May; 2(5):255-60.
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      163. Weissman JS, Sigler PB, Horwich AL. From the cradle to the grave: ring complexes in the life of a protein. Science. 1995 Apr 28; 268(5210):523-4.
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      164. Horwich AL, Weissman JS, Fenton WA. Kinesis of polypeptide during GroEL-mediated folding. Cold Spring Harb Symp Quant Biol. 1995; 60:435-40.
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      165. Weissman JS, Kashi Y, Fenton WA, Horwich AL. GroEL-mediated protein folding proceeds by multiple rounds of binding and release of nonnative forms. Cell. 1994 Aug 26; 78(4):693-702.
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      166. Craig EA, Weissman JS, Horwich AL. Heat shock proteins and molecular chaperones: mediators of protein conformation and turnover in the cell. Cell. 1994 Aug 12; 78(3):365-72.
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      167. Weissman JS, Kim PS. Efficient catalysis of disulphide bond rearrangements by protein disulphide isomerase. Nature. 1993 Sep 9; 365(6442):185-8.
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      168. Weissman JS, Kim PS. The pro region of BPTI facilitates folding. Cell. 1992 Nov 27; 71(5):841-51.
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