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Jonathan Weissman, PhD

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


    Collapse Research 
    Collapse Research Activities and Funding
    The Cancer Target Discovery and Development Network at UCSF
    NIH/NCI U01CA217882Aug 10, 2017 - Jul 31, 2022
    Role: Co-Principal Investigator
    Harnessing CRISPR for Targeted and Inducible Epigenomic Reprogramming
    NIH/NIDA R01DA036858Sep 30, 2013 - May 31, 2018
    Role: Principal Investigator
    Structural Basis of Protein Homeostasis
    NIH/NIGMS U01GM098254Sep 30, 2012 - Jul 31, 2015
    Role: Co-Principal Investigator
    Human Gene Knockdowns that May Extend Lifespan
    NIH/NIA R01AG041826May 1, 2012 - Apr 30, 2017
    Role: Principal Investigator
    Bay Area Cancer Target Discovery and Development Network
    NIH/NCI U01CA168370May 1, 2012 - Apr 30, 2017
    Role: Co-Principal Investigator
    MECHANISM OF CHAPERONE MEDIATED PROTEIN FOLDING
    NIH/NIGMS R01GM055595May 1, 1997 - Apr 30, 2002
    Role: Principal Investigator
    Molecular Pathogenesis of Age-Dependent CNS Regeneration
    NIH/NIA P01AG010770Apr 1, 1993 - Mar 31, 2016
    Role: Co-Investigator
    Bio-Organic Biomedical Mass Spectrometry Resource
    NIH P41RR001614Mar 1, 1982 - May 31, 2015
    Role: Co-Investigator

    Collapse ORNG Applications 
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    Collapse In The News

    Collapse Bibliographic 
    Collapse Publications
    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. Ingolia NT, Hussmann JA, Weissman JS. Ribosome Profiling: Global Views of Translation. Cold Spring Harb Perspect Biol. 2018 Jul 23. PMID: 30037969.
      View in: PubMed
    2. Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, Adamson B, Chow ED, Kampmann M, Peterson TR, Nakamura K, Fischbach MA, Weissman JS, Gilbert LA. Mapping the Genetic Landscape of Human Cells. Cell. 2018 Jul 17. PMID: 30033366.
      View in: PubMed
    3. Roth TL, Puig-Saus C, Yu R, Shifrut E, Carnevale J, Li PJ, Hiatt J, Saco J, Krystofinski P, Li H, Tobin V, Nguyen DN, Lee MR, Putnam AL, Ferris AL, Chen JW, Schickel JN, Pellerin L, Carmody D, Alkorta-Aranburu G, Del Gaudio D, Matsumoto H, Morell M, Mao Y, Cho M, Quadros RM, Gurumurthy CB, Smith B, Haugwitz M, Hughes SH, Weissman JS, Schumann K, Esensten JH, May AP, Ashworth A, Kupfer GM, Greeley SAW, Bacchetta R, Meffre E, Roncarolo MG, Romberg N, Herold KC, Ribas A, Leonetti MD, Marson A. Reprogramming human T cell function and specificity with non-viral genome targeting. Nature. 2018 Jul 11. PMID: 29995861.
      View in: PubMed
    4. Li W, Okreglak V, Peschek J, Kimmig P, Zubradt M, Weissman JS, Walter P. Engineering ER-stress dependent non-conventional mRNA splicing. Elife. 2018 Jul 09; 7. PMID: 29985129.
      View in: PubMed
    5. Shao H, Li X, Moses MA, Gilbert LA, Kalyanaraman C, Young ZT, Chernova M, Journey SN, Weissman JS, Hann B, Jacobson MP, Neckers LM, Gestwicki JE. Exploration of Benzothiazole-Rhodacyanines as Allosteric Inhibitors of Protein-Protein Interactions with Heat Shock Protein 70 (Hsp70). J Med Chem. 2018 Jun 28. PMID: 29953808.
      View in: PubMed
    6. Guenther UP, Weinberg DE, Zubradt MM, Tedeschi FA, Stawicki BN, Zagore LL, Brar GA, Licatalosi DD, Bartel DP, Weissman JS, Jankowsky E. The helicase Ded1p controls use of near-cognate translation initiation codons in 5' UTRs. Nature. 2018 Jun 27. PMID: 29950728.
      View in: PubMed
    7. Shurtleff MJ, Itzhak DN, Hussmann JA, Schirle Oakdale NT, Costa EA, Jonikas M, Weibezahn J, Popova KD, Jan CH, Sinitcyn P, Vembar SS, Hernandez H, Cox J, Burlingame AL, Brodsky J, Frost A, Borner GH, Weissman JS. The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins. Elife. 2018 May 29; 7. PMID: 29809151.
      View in: PubMed
    8. Yu Z, Surface LE, Park CY, Horlbeck MA, Wyant GA, Abu-Remaileh M, Peterson TR, Sabatini DM, Weissman JS, O'Shea EK. Identification of a transporter complex responsible for the cytosolic entry of nitrogen-containing-bisphosphonates. Elife. 2018 May 10; 7. PMID: 29745899.
      View in: PubMed
    9. Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY. Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. Cell. 2018 Apr 25. PMID: 29731168.
      View in: PubMed
    10. Zhang Y, Burkhardt DH, Rouskin S, Li GW, Weissman JS, Gross CA. A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation. Mol Cell. 2018 Apr 19; 70(2):274-286.e7. PMID: 29628307.
      View in: PubMed
    11. Jost M, Weissman JS. CRISPR Approaches to Small Molecule Target Identification. ACS Chem Biol. 2018 Feb 16; 13(2):366-375. PMID: 29261286.
      View in: PubMed
    12. Martinko AJ, Truillet C, Julien O, Diaz JE, Horlbeck MA, Whiteley G, Blonder J, Weissman JS, Bandyopadhyay S, Evans MJ, Wells JA. Targeting RAS-driven human cancer cells with antibodies to upregulated and essential cell-surface proteins. Elife. 2018 Jan 23; 7. PMID: 29359686.
      View in: PubMed
    13. Costa EA, Subramanian K, Nunnari J, Weissman JS. Defining the physiological role of SRP in protein-targeting efficiency and specificity. Science. 2018 02 09; 359(6376):689-692. PMID: 29348368.
      View in: PubMed
    14. Friedman JR, Kannan M, Toulmay A, Jan CH, Weissman JS, Prinz WA, Nunnari J. Lipid Homeostasis Is Maintained by Dual Targeting of the Mitochondrial PE Biosynthesis Enzyme to the ER. Dev Cell. 2018 Jan 22; 44(2):261-270.e6. PMID: 29290583.
      View in: PubMed
    15. Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N. The Human Cell Atlas. Elife. 2017 12 05; 6. PMID: 29206104.
      View in: PubMed
    16. Wangensteen KJ, Wang YJ, Dou Z, Wang AW, Mosleh-Shirazi E, Horlbeck MA, Gilbert LA, Weissman JS, Berger SL, Kaestner KH. Combinatorial genetics in liver repopulation and carcinogenesis with a novel in vivo CRISPR activation platform. Hepatology. 2017 Nov 01. PMID: 29091290.
      View in: PubMed
    17. Tak YE, Kleinstiver BP, Nuñez JK, Hsu JY, Horng JE, Gong J, Weissman JS, Joung JK. Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors. Nat Methods. 2017 Dec; 14(12):1163-1166. PMID: 29083402.
      View in: PubMed
    18. Jost M, Chen Y, Gilbert LA, Horlbeck MA, Krenning L, Menchon G, Rai A, Cho MY, Stern JJ, Prota AE, Kampmann M, Akhmanova A, Steinmetz MO, Tanenbaum ME, Weissman JS. Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent. Mol Cell. 2017 Oct 05; 68(1):210-223.e6. PMID: 28985505.
      View in: PubMed
    19. Kostova KK, Hickey KL, Osuna BA, Hussmann JA, Frost A, Weinberg DE, Weissman JS. CAT-tailing as a fail-safe mechanism for efficient degradation of stalled nascent polypeptides. Science. 2017 07 28; 357(6349):414-417. PMID: 28751611.
      View in: PubMed
    20. Kruth KA, Fang M, Shelton DN, Abu-Halawa O, Mahling R, Yang H, Weissman JS, Loh ML, Müschen M, Tasian SK, Bassik MC, Kampmann M, Pufall MA. Suppression of B-cell development genes is key to glucocorticoid efficacy in treatment of acute lymphoblastic leukemia. Blood. 2017 06 01; 129(22):3000-3008. PMID: 28424165.
      View in: PubMed
    21. Burkhardt DH, Rouskin S, Zhang Y, Li GW, Weissman JS, Gross CA. Operon mRNAs are organized into ORF-centric structures that predict translation efficiency. Elife. 2017 Jan 31; 6. PMID: 28139975.
      View in: PubMed
    22. Sendoel A, Dunn JG, Rodriguez EH, Naik S, Gomez NC, Hurwitz B, Levorse J, Dill BD, Schramek D, Molina H, Weissman JS, Fuchs E. Translation from unconventional 5' start sites drives tumour initiation. Nature. 2017 01 26; 541(7638):494-499. PMID: 28077873.
      View in: PubMed
    23. Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, Regev A. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016 Dec 15; 167(7):1853-1866.e17. PMID: 27984732.
      View in: PubMed
    24. Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, Pak RA, Gray AN, Gross CA, Dixit A, Parnas O, Regev A, Weissman JS. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016 Dec 15; 167(7):1867-1882.e21. PMID: 27984733.
      View in: PubMed
    25. Liu SJ, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, Weissman JS, Lim DA. CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science. 2017 01 06; 355(6320). PMID: 27980086.
      View in: PubMed
    26. Besnard E, Hakre S, Kampmann M, Lim HW, Hosmane NN, Martin A, Bassik MC, Verschueren E, Battivelli E, Chan J, Svensson JP, Gramatica A, Conrad RJ, Ott M, Greene WC, Krogan NJ, Siliciano RF, Weissman JS, Verdin E. The mTOR Complex Controls HIV Latency. Cell Host Microbe. 2016 Dec 14; 20(6):785-797. PMID: 27978436.
      View in: PubMed
    27. Aviram N, Ast T, Costa EA, Arakel EC, Chuartzman SG, Jan CH, Haßdenteufel S, Dudek J, Jung M, Schorr S, Zimmermann R, Schwappach B, Weissman JS, Schuldiner M. The SND proteins constitute an alternative targeting route to the endoplasmic reticulum. Nature. 2016 11 30; 540(7631):134-138. PMID: 27905431.
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    28. Dunn JG, Weissman JS. Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data. BMC Genomics. 2016 11 22; 17(1):958. PMID: 27875984.
      View in: PubMed
    29. Stewart-Ornstein J, Chen S, Bhatnagar R, Weissman JS, El-Samad H. Model-guided optogenetic study of PKA signaling in budding yeast. Mol Biol Cell. 2017 Jan 01; 28(1):221-227. PMID: 28035051.
      View in: PubMed
    30. Zubradt M, Gupta P, Persad S, Lambowitz AM, Weissman JS, Rouskin S. DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat Methods. 2017 01; 14(1):75-82. PMID: 27819661.
      View in: PubMed
    31. Schrader JM, Li GW, Childers WS, Perez AM, Weissman JS, Shapiro L, McAdams HH. Dynamic translation regulation in Caulobacter cell cycle control. Proc Natl Acad Sci U S A. 2016 11 01; 113(44):E6859-E6867. PMID: 27791168.
      View in: PubMed
    32. Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. Elife. 2016 09 23; 5. PMID: 27661255.
      View in: PubMed
    33. Sabnis AJ, Guerriero CJ, Olivas V, Sayana A, Shue J, Flanagan J, Asthana S, Paton AW, Paton JC, Gestwicki JE, Walter P, Weissman JS, Wipf P, Brodsky JL, Bivona TG. Combined chemical-genetic approach identifies cytosolic HSP70 dependence in rhabdomyosarcoma. Proc Natl Acad Sci U S A. 2016 08 09; 113(32):9015-20. PMID: 27450084; PMCID: PMC4987817 [Available on 02/09/17].
    34. Nguyen DP, Miyaoka Y, Gilbert LA, Mayerl SJ, Lee BH, Weissman JS, Conklin BR, Wells JA. Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity. Nat Commun. 2016 Jul 01; 7:12009. PMID: 27363581; PMCID: PMC4932181.
    35. Liu YC, Fujimori DG, Weissman JS. Htm1p-Pdi1p is a folding-sensitive mannosidase that marks N-glycoproteins for ER-associated protein degradation. Proc Natl Acad Sci U S A. 2016 07 12; 113(28):E4015-24. PMID: 27357682; PMCID: PMC4948361 [Available on 01/12/17].
    36. Braun CJ, Bruno PM, Horlbeck MA, Gilbert LA, Weissman JS, Hemann MT. Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation. Proc Natl Acad Sci U S A. 2016 07 05; 113(27):E3892-900. PMID: 27325776.
      View in: PubMed
    37. Leonetti MD, Sekine S, Kamiyama D, Weissman JS, Huang B. A scalable strategy for high-throughput GFP tagging of endogenous human proteins. Proc Natl Acad Sci U S A. 2016 06 21; 113(25):E3501-8. PMID: 27274053; PMCID: PMC4922190 [Available on 12/21/16].
    38. Peters JM, Colavin A, Shi H, Czarny TL, Larson MH, Wong S, Hawkins JS, Lu CHS, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS, Huang KC, Gross CA. A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. Cell. 2016 Jun 02; 165(6):1493-1506. PMID: 27238023; PMCID: PMC4894308 [Available on 06/02/17].
    39. Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA. Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol. 2016 Apr 14; 17:67. PMID: 27081004; PMCID: PMC4831157.
    40. Kamiyama D, Sekine S, Barsi-Rhyne B, Hu J, Chen B, Gilbert LA, Ishikawa H, Leonetti MD, Marshall WF, Weissman JS, Huang B. Versatile protein tagging in cells with split fluorescent protein. Nat Commun. 2016 Mar 18; 7:11046. PMID: 26988139; PMCID: PMC4802074.
    41. Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tjian R, Weissman JS. Nucleosomes impede Cas9 access to DNA in vivo and in vitro. Elife. 2016 03 17; 5. PMID: 26987018; PMCID: PMC4861601.
    42. Mandegar MA, Huebsch N, Frolov EB, Shin E, Truong A, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP, Weissman JS, Qi LS, So PL, Conklin BR. CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs. Cell Stem Cell. 2016 Apr 07; 18(4):541-53. PMID: 26971820; PMCID: PMC4830697 [Available on 04/07/17].
    43. Fields AP, Rodriguez EH, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, Weissman JS. A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation. Mol Cell. 2015 Dec 03; 60(5):816-827. PMID: 26638175; PMCID: PMC4720255 [Available on 12/03/16].
    44. Suzuki G, Weissman JS, Tanaka M. [KIL-d] Protein Element Confers Antiviral Activity via Catastrophic Viral Mutagenesis. Mol Cell. 2015 Nov 19; 60(4):651-60. PMID: 26590718.
      View in: PubMed
    45. Anderson DJ, Le Moigne R, Djakovic S, Kumar B, Rice J, Wong S, Wang J, Yao B, Valle E, Kiss von Soly S, Madriaga A, Soriano F, Menon MK, Wu ZY, Kampmann M, Chen Y, Weissman JS, Aftab BT, Yakes FM, Shawver L, Zhou HJ, Wustrow D, Rolfe M. Targeting the AAA ATPase p97 as an Approach to Treat Cancer through Disruption of Protein Homeostasis. Cancer Cell. 2015 Nov 09; 28(5):653-665. PMID: 26555175; PMCID: PMC4941640.
    46. Brar GA, Weissman JS. Ribosome profiling reveals the what, when, where and how of protein synthesis. Nat Rev Mol Cell Biol. 2015 Nov; 16(11):651-64. PMID: 26465719.
      View in: PubMed
    47. Acosta-Alvear D, Cho MY, Wild T, Buchholz TJ, Lerner AG, Simakova O, Hahn J, Korde N, Landgren O, Maric I, Choudhary C, Walter P, Weissman JS, Kampmann M. Paradoxical resistance of multiple myeloma to proteasome inhibitors by decreased levels of 19S proteasomal subunits. Elife. 2015 Sep 01; 4:e08153. PMID: 26327694; PMCID: PMC4602331.
    48. Tanenbaum ME, Stern-Ginossar N, Weissman JS, Vale RD. Regulation of mRNA translation during mitosis. Elife. 2015 Aug 25; 4. PMID: 26305499; PMCID: PMC4548207.
    49. Kampmann M, Horlbeck MA, Chen Y, Tsai JC, Bassik MC, Gilbert LA, Villalta JE, Kwon SC, Chang H, Kim VN, Weissman JS. Next-generation libraries for robust RNA interference-based genome-wide screens. Proc Natl Acad Sci U S A. 2015 Jun 30; 112(26):E3384-91. PMID: 26080438; PMCID: PMC4491794.
    50. Jan CH, Williams CC, Weissman JS. LOCAL TRANSLATION. Response to Comment on "Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling". Science. 2015 Jun 12; 348(6240):1217. PMID: 26068842.
      View in: PubMed
    51. 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:e07314. PMID: 25875391; PMCID: PMC4426669.
    52. 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):643. PMID: 25811902.
      View in: PubMed
    53. 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 03; 348(6230):36-8. PMID: 25791083; PMCID: PMC4394183.
    54. 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 06; 347(6226):1259038. PMID: 25745177; PMCID: PMC4506746.
    55. 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 Mar; 14(3):642-8. PMID: 25564440; PMCID: PMC4456214.
    56. 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 02; 347(6217):75-8. PMID: 25554787; PMCID: PMC4451101.
    57. 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 Dec 23; 10:770. PMID: 25538139; PMCID: PMC4300493.
    58. 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. PMID: 25533786; PMCID: PMC4297522.
    59. Williams CC, Jan CH, Weissman JS. Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling. Science. 2014 Nov 07; 346(6210):748-51. PMID: 25378625; PMCID: PMC4263316.
    60. Jan CH, Williams CC, Weissman JS. Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling. Science. 2014 Nov 07; 346(6210):1257521. PMID: 25378630; PMCID: PMC4285348.
    61. 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. PMID: 25349425; PMCID: PMC4234590.
    62. Albert FW, Muzzey D, Weissman JS, Kruglyak L. Genetic influences on translation in yeast. PLoS Genet. 2014 Oct; 10(10):e1004692. PMID: 25340754; PMCID: PMC4207643.
    63. 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. PMID: 25307933; PMCID: PMC4252608.
    64. 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. PMID: 25307932; PMCID: PMC4253859.
    65. 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. PMID: 25262416; PMCID: PMC4201873.
    66. 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. PMID: 25159147; PMCID: PMC4216110.
    67. Smith MH, Rodriguez EH, Weissman JS. Misfolded proteins induce aggregation of the lectin Yos9. J Biol Chem. 2014 Sep 12; 289(37):25670-7. PMID: 25086047; PMCID: PMC4162170.
    68. 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. PMID: 25078267; PMCID: PMC4117421.
    69. 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. PMID: 24992097; PMCID: PMC4144868.
    70. 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 May 08; 5:3832. PMID: 24807418; PMCID: PMC4024746.
    71. 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. PMID: 24789973; PMCID: PMC4108260.
    72. 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. PMID: 24766808; PMCID: PMC4006352.
    73. 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. PMID: 24732588; PMCID: PMC4032860.
    74. 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. PMID: 24687277; PMCID: PMC3971754.
    75. Wolff S, Weissman JS, Dillin A. Differential scales of protein quality control. Cell. 2014 Mar 27; 157(1):52-64. PMID: 24679526.
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    77. 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. PMID: 24360272; PMCID: PMC3918502.
    78. 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. PMID: 24336214; PMCID: PMC3966492.
    79. Dunn JG, Foo CK, Belletier NG, Gavis ER, Weissman JS. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. Elife. 2013 Dec 03; 2:e01179. PMID: 24302569; PMCID: PMC3840789.
    80. Stewart-Ornstein J, Nelson C, DeRisi J, Weissman JS, El-Samad H. Msn2 coordinates a stoichiometric gene expression program. Curr Biol. 2013 Dec 02; 23(23):2336-45. PMID: 24210615; PMCID: PMC4072881.
    81. 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. PMID: 24183972.
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    82. 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 Oct 29; 2:e01236. PMID: 24171104; PMCID: PMC3808542.
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    84. 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. PMID: 24136345; PMCID: PMC3922765.
    85. 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 01; 27(19):2147-63. PMID: 24115771; PMCID: PMC3850098.
    86. 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. PMID: 23849981; PMCID: PMC3770145.
    87. 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. PMID: 23821443; PMCID: PMC3775365.
    88. 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 03; 154(1):240-51. PMID: 23810193; PMCID: PMC3756563.
    89. 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. PMID: 23739767; PMCID: PMC3690882.
    90. 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. PMID: 23603333; PMCID: PMC3673220.
    91. 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. PMID: 23468524; PMCID: PMC3639041.
    92. 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 01; 5(3):a013284. PMID: 23359093; PMCID: PMC3578357.
    93. 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. PMID: 23452860; PMCID: PMC3664290.
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    95. 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. PMID: 24025428; PMCID: PMC4054093.
    96. 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. PMID: 23180859; PMCID: PMC3817102.
    97. 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. PMID: 23178123; PMCID: PMC3534965.
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    99. 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. PMID: 22722833; PMCID: PMC3401362.
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    104. 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. PMID: 22365828; PMCID: PMC3327736.
    105. 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 Feb 22; 485(7396):55-61. PMID: 22367541; PMCID: PMC3663483.
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    107. 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 09; 147(6):1295-308. PMID: 22153074; PMCID: PMC3277850.
    108. El-Samad H, Weissman JS. Genetics: Noise rules. Nature. 2011 Dec 07; 480(7376):188-9. PMID: 22158239.
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    110. 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. PMID: 22080611; PMCID: PMC3228448.
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    112. 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. PMID: 21987634; PMCID: PMC3198156.
    113. 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 03; 476(7358):88-91. PMID: 21814281; PMCID: PMC3535012.
    114. 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. PMID: 21709022; PMCID: PMC3165552.
    115. 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. PMID: 21423194; PMCID: PMC3490428.
    116. 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. PMID: 21333653; PMCID: PMC3070826.
    117. Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature. 2011 Jan 20; 469(7330):368-73. PMID: 21248844; PMCID: PMC3880149.
    118. Toyama BH, Weissman JS. Amyloid structure: conformational diversity and consequences. Annu Rev Biochem. 2011; 80:557-85. PMID: 21456964; PMCID: PMC3817101.
    119. 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. PMID: 21169418; PMCID: PMC3067400.
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    122. 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. PMID: 20703300; PMCID: PMC2990499.
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    124. Springer M, Weissman JS, Kirschner MW. A general lack of compensation for gene dosage in yeast. Mol Syst Biol. 2010 May 11; 6:368. PMID: 20461075; PMCID: PMC2890323.
    125. 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. PMID: 20430885; PMCID: PMC2903355.
    126. 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. PMID: 20228791; PMCID: PMC2855400.
    127. 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. PMID: 20182505; PMCID: PMC2877384.
    128. Ohhashi Y, Ito K, Toyama BH, Weissman JS, Tanaka M. Differences in prion strain conformations result from non-native interactions in a nucleus. Nat Chem Biol. 2010 Mar; 6(3):225-230. PMID: 20081853.
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    131. 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. PMID: 19651891; PMCID: PMC2728407.
    132. 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. PMID: 19556461; PMCID: PMC2933203.
    133. 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. PMID: 19448642; PMCID: PMC2783737.
    134. 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. PMID: 19420139; PMCID: PMC2704154.
    135. 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. PMID: 19325107.
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    136. 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 06; 136(5):952-63. PMID: 19269370; PMCID: PMC2856666.
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    138. 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. PMID: 19111666; PMCID: PMC2873636.
    139. 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 05; 32(5):735-46. PMID: 19061648; PMCID: PMC2644724.
    140. 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. PMID: 19026788; PMCID: PMC2875781.
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    142. 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. PMID: 18818364; PMCID: PMC2753251.
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    144. Ingolia NT, Weissman JS. Systems biology: Reverse engineering the cell. Nature. 2008 Aug 28; 454(7208):1059-62. PMID: 18756243.
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    145. 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. PMID: 18724936.
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    147. 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. PMID: 18223646; PMCID: PMC2730835.
    148. 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. PMID: 17989219; PMCID: PMC2084299.
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    151. Denic V, Weissman JS. A molecular caliper mechanism for determining very long-chain fatty acid length. Cell. 2007 Aug 24; 130(4):663-77. PMID: 17719544.
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    154. 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 03; 104(14):5836-41. PMID: 17389396; PMCID: PMC1851578.
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    167. 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. PMID: 16368681.
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