Jennifer Doudna, PhD

Title(s)Professor, Cellular Molecular Pharmacology
SchoolSchool of Medicine
AddressLocation Required, #001
ORCID ORCID Icon0000-0001-9161-999X Additional info
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    Collapse Research 
    Collapse Research Activities and Funding
    Identifying and inhibiting the SARS-CoV-2 packaging mechanism
    NIH R21AI159666Jul 15, 2021 - Jun 30, 2023
    Role: Principal Investigator
    Cas9 RNP delivery to immune cells in vivo via molecular targeting
    NIH UG3AI150552Aug 28, 2019 - Jul 31, 2022
    Role: Co-Principal Investigator
    Expanding CRISPR-Cas editing technology through exploration of novel Cas proteins and DNA repair systems
    NIH U01AI142817Aug 24, 2018 - Jul 31, 2023
    Role: Principal Investigator
    Center for Genome Editing and Recording
    NIH RM1HG009490Aug 8, 2017 - May 31, 2022
    Role: Principal Investigator
    Minstrel HTUV Gallery 700 Automated Crystal Growth and Imaging System
    NIH S10OD016268Jun 1, 2013 - May 31, 2015
    Role: Principal Investigator
    HCV IRES Control of Human Translational Initiation
    NIH R56AI095687Sep 30, 2011 - Sep 29, 2012
    Role: Principal Investigator
    Program in Virus Translational Control
    NIH P01GM073732Jun 1, 2006 - May 31, 2012
    Role: Principal Investigator
    Structure and Function of RNAi-related Nucleases
    NIH R01GM073794Sep 1, 2005 - Mar 31, 2015
    Role: Principal Investigator
    Structure and Mechanism of Internal Ribosome Entry Sites
    NIH R01GM065942Sep 1, 2002 - Aug 31, 2006
    Role: Principal Investigator
    Nucleic Acids Gordon Research Conference
    NIH R13GM066300May 1, 2002 - Apr 30, 2003
    Role: Principal Investigator
    NIH R01GM056361Aug 1, 1997 - Jul 31, 2002
    Role: Principal Investigator

    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. 2023 Sep 19. Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ. PMID: 37738970.
      View in: PubMed   Mentions:    Fields:    
    2. Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes. bioRxiv. 2023 Aug 10. Yoon PH, Skopintsev P, Shi H, Chen LX, Adler BA, Al-Shimary M, Craig RJ, Li Z, Amerasekera J, Trinidad M, Nisonoff H, Chen K, Lahiri A, Boger R, Jacobsen S, Banfield JF, Doudna JA. PMID: 37609353; PMCID: PMC10441404.
      View in: PubMed   Mentions:
    3. Genome editing in the mouse brain with minimally immunogenic Cas9 RNPs. Mol Ther. 2023 08 02; 31(8):2422-2438. Stahl EC, Sabo JK, Kang MH, Allen R, Applegate E, Kim SE, Kwon Y, Seth A, Lemus N, Salinas-Rios V, Soczek KM, Trinidad M, Vo LT, Jeans C, Wozniak A, Morris T, Kimberlin A, Foti T, Savage DF, Doudna JA. PMID: 37403358; PMCID: PMC10422012.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    4. Genome expansion by a CRISPR trimmer-integrase. Nature. 2023 Jun; 618(7966):855-861. Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA. PMID: 37316664; PMCID: PMC10284694.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    5. Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6. Nat Commun. 2023 04 21; 14(1):2308. Taha TY, Chen IP, Hayashi JM, Tabata T, Walcott K, Kimmerly GR, Syed AM, Ciling A, Suryawanshi RK, Martin HS, Bach BH, Tsou CL, Montano M, Khalid MM, Sreekumar BK, Renuka Kumar G, Wyman S, Doudna JA, Ott M. PMID: 37085489; PMCID: PMC10120482.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    6. Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. bioRxiv. 2023 Mar 22. Tsuchida CA, Brandes N, Bueno R, Trinidad M, Mazumder T, Yu B, Hwang B, Chang C, Liu J, Sun Y, Hopkins CR, Parker KR, Qi Y, Satpathy AT, Stadtmauer EA, Cate JHD, Eyquem J, Fraietta JA, June CH, Chang HY, Ye CJ, Doudna JA. PMID: 36993359; PMCID: PMC10055432.
      View in: PubMed   Mentions:
    7. To TnpB or not TnpB? Cas12 is the answer. Nat Chem Biol. 2023 03; 19(3):263-264. Yoon PH, Adler BA, Doudna JA. PMID: 36797405.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    8. Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6. bioRxiv. 2023 Feb 09. Taha TY, Chen IP, Hayashi JM, Tabata T, Walcott K, Kimmerly GR, Syed AM, Ciling A, Suryawanshi RK, Martin HS, Bach BH, Tsou CL, Montano M, Khalid MM, Sreekumar BK, Kumar GR, Wyman S, Doudna JA, Ott M. PMID: 36798416; PMCID: PMC9934579.
      View in: PubMed   Mentions:
    9. Precise transcript targeting by CRISPR-Csm complexes. Nat Biotechnol. 2023 Jan 23. Colognori D, Trinidad M, Doudna JA. PMID: 36690762.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    10. CRISPR technology: A decade of genome editing is only the beginning. Science. 2023 01 20; 379(6629):eadd8643. Wang JY, Doudna JA. PMID: 36656942.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimalsCells
    11. Genome editing in plants using the compact editor CasΦ. Proc Natl Acad Sci U S A. 2023 01 24; 120(4):e2216822120. Li Z, Zhong Z, Wu Z, Pausch P, Al-Shayeb B, Amerasekera J, Doudna JA, Jacobsen SE. PMID: 36652483; PMCID: PMC9942878.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    12. Improved genome editing by an engineered CRISPR-Cas12a. Nucleic Acids Res. 2022 12 09; 50(22):12689-12701. Ma E, Chen K, Shi H, Stahl EC, Adler B, Trinidad M, Liu J, Zhou K, Ye J, Doudna JA. PMID: 36537251; PMCID: PMC9825149.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    13. Decorating chromatin for enhanced genome editing using CRISPR-Cas9. Proc Natl Acad Sci U S A. 2022 12 06; 119(49):e2204259119. Chen E, Lin-Shiao E, Trinidad M, Saffari Doost M, Colognori D, Doudna JA. PMID: 36459645; PMCID: PMC9894255.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    14. Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors. Cell. 2022 11 23; 185(24):4574-4586.e16. Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, Doudna JA. PMID: 36423580.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    15. Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing. Nat Microbiol. 2022 Dec; 7(12):1967-1979. Adler BA, Hessler T, Cress BF, Lahiri A, Mutalik VK, Barrangou R, Banfield J, Doudna JA. PMID: 36316451; PMCID: PMC9712115.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    16. Borgs are giant genetic elements with potential to expand metabolic capacity. Nature. 2022 10; 610(7933):731-736. Al-Shayeb B, Schoelmerich MC, West-Roberts J, Valentin-Alvarado LE, Sachdeva R, Mullen S, Crits-Christoph A, Wilkins MJ, Williams KH, Doudna JA, Banfield JF. PMID: 36261517; PMCID: PMC9605863.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    17. Conserved features of TERT promoter duplications reveal an activation mechanism that mimics hotspot mutations in cancer. Nat Commun. 2022 09 16; 13(1):5430. Barger CJ, Suwala AK, Soczek KM, Wang AS, Kim MY, Hong C, Doudna JA, Chang SM, Phillips JJ, Solomon DA, Costello JF. PMID: 36114166; PMCID: PMC9481613.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    18. Treatment of Genetic Diseases With CRISPR Genome Editing. JAMA. 2022 09 13; 328(10):980-981. Kan MJ, Doudna JA. PMID: 36098733.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    19. CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors. Nucleic Acids Res. 2022 Aug 26; 50(15):8986-8998. Otoupal PB, Cress BF, Doudna JA, Schoeniger JS. PMID: 35950485; PMCID: PMC9410913.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    20. Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Nat Biomed Eng. 2022 08; 6(8):944-956. Chandrasekaran SS, Agrawal S, Fanton A, Jangid AR, Charrez B, Escajeda AM, Son S, Mcintosh R, Tran H, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, Knott GJ, Dang Q, Van Dis E, Dugan E, Kim S, Liu TY, IGI Testing Consortium, Moehle EA, Kogut K, Eskenazi B, Harris E, Stanley SA, Lareau LF, Tan MX, Fletcher DA, Doudna JA, Savage DF, Hsu PD. PMID: 35953650; PMCID: PMC10367768.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    21. Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles. Proc Natl Acad Sci U S A. 2022 08 02; 119(31):e2200592119. Syed AM, Ciling A, Taha TY, Chen IP, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Suryawanshi R, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Spraggon L, Tabata T, Ott M, Doudna JA. PMID: 35858386; PMCID: PMC9351483.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansCells
    22. A naturally DNase-free CRISPR-Cas12c enzyme silences gene expression. Mol Cell. 2022 06 02; 82(11):2148-2160.e4. Huang CJ, Adler BA, Doudna JA. PMID: 35659325.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    23. Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination. Nature. 2022 07; 607(7918):351-355. Suryawanshi RK, Chen IP, Ma T, Syed AM, Brazer N, Saldhi P, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Montano M, Gascon R, Tsou CL, Garcia-Knight MA, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Soveg FW, George AF, Fang X, Maishan M, Matthay M, Morris MK, Wadford D, Hanson C, Greene WC, Andino R, Spraggon L, Roan NR, Chiu CY, Doudna JA, Ott M. PMID: 35584773; PMCID: PMC9279157.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    24. Structural biology of CRISPR-Cas immunity and genome editing enzymes. Nat Rev Microbiol. 2022 11; 20(11):641-656. Wang JY, Pausch P, Doudna JA. PMID: 35562427.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    25. Crystal structure of an RNA/DNA strand exchange junction. PLoS One. 2022; 17(4):e0263547. Cofsky JC, Knott GJ, Gee CL, Doudna JA. PMID: 35436289; PMCID: PMC9015157.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    26. CRISPR-Cas9 bends and twists DNA to read its sequence. Nat Struct Mol Biol. 2022 04; 29(4):395-402. Cofsky JC, Soczek KM, Knott GJ, Nogales E, Doudna JA. PMID: 35422516; PMCID: PMC9189902.
      View in: PubMed   Mentions: 16     Fields:    
    27. A functional map of HIV-host interactions in primary human T cells. Nat Commun. 2022 04 01; 13(1):1752. Hiatt J, Hultquist JF, McGregor MJ, Bouhaddou M, Leenay RT, Simons LM, Young JM, Haas P, Roth TL, Tobin V, Wojcechowskyj JA, Woo JM, Rathore U, Cavero DA, Shifrut E, Nguyen TT, Haas KM, Malik HS, Doudna JA, May AP, Marson A, Krogan NJ. PMID: 35365639; PMCID: PMC8976027.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    28. Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants. Cell. 2022 04 28; 185(9):1539-1548.e5. Servellita V, Syed AM, Morris MK, Brazer N, Saldhi P, Garcia-Knight M, Sreekumar B, Khalid MM, Ciling A, Chen PY, Kumar GR, Gliwa AS, Nguyen J, Sotomayor-Gonzalez A, Zhang Y, Frias E, Prostko J, Hackett J, Andino R, Wadford DA, Hanson C, Doudna J, Ott M, Chiu CY. PMID: 35429436; PMCID: PMC8930394.
      View in: PubMed   Mentions: 63     Fields:    Translation:HumansCells
    29. Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity. Mol Cell. 2022 03 17; 82(6):1199-1209.e6. Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brötzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG. PMID: 35219382; PMCID: PMC9189900.
      View in: PubMed   Mentions: 11     Fields:    Translation:Animals
    30. CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells. Nucleic Acids Res. 2022 02 22; 50(3):1256-1268. Lin-Shiao E, Pfeifer WG, Shy BR, Saffari Doost M, Chen E, Vykunta VS, Hamilton JR, Stahl EC, Lopez DM, Sandoval Espinoza CR, Deyanov AE, Lew RJ, Poirer MG, Marson A, Castro CE, Doudna JA. PMID: 35104875; PMCID: PMC8860605.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    31. Limited Cross-Variant Immunity after Infection with the SARS-CoV-2 Omicron Variant Without Vaccination. medRxiv. 2022 Feb 09. Suryawanshi RK, Chen IP, Ma T, Syed AM, Brazer N, Saldhi P, Simoneau CR, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Montano M, Garcia-Knight MA, Sotomayor-Gonzalez A, Servellita V, Gliwa A, Nguyen J, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Soveg FW, George AF, Fang X, Maishan M, Matthay M, Greene WC, Andino R, Spraggon L, Roan NR, Chiu CY, Doudna J, Ott M. PMID: 35075459; PMCID: PMC8786226.
      View in: PubMed   Mentions:
    32. Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles. medRxiv. 2022 Jan 02. Syed AM, Ciling A, Khalid MM, Sreekumar B, Chen PY, Kumar GR, Silva I, Milbes B, Kojima N, Hess V, Shacreaw M, Lopez L, Brobeck M, Turner F, Spraggon L, Taha TY, Tabata T, Chen IP, Ott M, Doudna JA. PMID: 34981067; PMCID: PMC8722610.
      View in: PubMed   Mentions:
    33. Species- and site-specific genome editing in complex bacterial communities. Nat Microbiol. 2022 01; 7(1):34-47. Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinsky R, Smock DCJ, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM, Banfield JF, Doudna JA. PMID: 34873292; PMCID: PMC9261505.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansCellsPHPublic Health
    34. Optimizing COVID-19 control with asymptomatic surveillance testing in a university environment. Epidemics. 2021 12; 37:100527. Brook CE, Northrup GR, Ehrenberg AJ, IGI SARS-CoV-2 Testing Consortium, Doudna JA, Boots M. PMID: 34814094; PMCID: PMC8591900.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCellsPHPublic Health
    35. LuNER: Multiplexed SARS-CoV-2 detection in clinical swab and wastewater samples. PLoS One. 2021; 16(11):e0258263. Stahl EC, Gopez AR, Tsuchida CA, Fan VB, Moehle EA, Witkowsky LB, Hamilton JR, Lin-Shiao E, McElroy M, McDevitt SL, Ciling A, Tsui CK, Pestal K, Gildea HK, Keller A, Sylvain IA, Williams C, Hirsh A, Ehrenberg AJ, Kantor R, Metzger M, Nelson KL, Urnov FD, Ringeisen BR, Giannikopoulos P, Doudna JA, IGI Testing Consortium. PMID: 34758033; PMCID: PMC8580221.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCellsPHPublic Health
    36. Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. Science. 2021 Dec 24; 374(6575):1626-1632. Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen PY, Hayashi JM, Soczek KM, Ott M, Doudna JA. PMID: 34735219; PMCID: PMC9005165.
      View in: PubMed   Mentions: 113     Fields:    Translation:HumansAnimalsCells
    37. Publisher Correction: Accelerated RNA detection using tandem CRISPR nucleases. Nat Chem Biol. 2021 Nov; 17(11):1210. Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim S, Dugan EJ, IGI Testing Consortium, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. PMID: 34616098; PMCID: PMC8493939.
      View in: PubMed   Mentions:    Fields:    
    38. Optimizing COVID-19 control with asymptomatic surveillance testing in a university environment. medRxiv. 2021 Oct 27. Brook CE, Northrup GR, Ehrenberg AJ, IGI SARS-CoV-2 Testing Consortium, Doudna JA, Boots M. PMID: 33442708; PMCID: PMC7805470.
      View in: PubMed   Mentions:
    39. Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules. Nat Commun. 2021 09 27; 12(1):5664. Shams A, Higgins SA, Fellmann C, Laughlin TG, Oakes BL, Lew R, Kim S, Lukarska M, Arnold M, Staahl BT, Doudna JA, Savage DF. PMID: 34580310; PMCID: PMC8476515.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    40. Kinetic analysis of Cas12a and Cas13a RNA-Guided nucleases for development of improved CRISPR-Based diagnostics. iScience. 2021 Sep 24; 24(9):102996. Nalefski EA, Patel N, Leung PJY, Islam Z, Kooistra RM, Parikh I, Marion E, Knott GJ, Doudna JA, Le Ny AM, Madan D. PMID: 34505008; PMCID: PMC8411246.
      View in: PubMed   Mentions: 18  
    41. Synthesis of Multi-Protein Complexes through Charge-Directed Sequential Activation of Tyrosine Residues. J Am Chem Soc. 2021 09 01; 143(34):13538-13547. Mogilevsky CS, Lobba MJ, Brauer DD, Marmelstein AM, Maza JC, Gleason JM, Doudna JA, Francis MB. PMID: 34382787; PMCID: PMC9274618.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    42. DNA interference states of the hypercompact CRISPR-CasΦ effector. Nat Struct Mol Biol. 2021 08; 28(8):652-661. Pausch P, Soczek KM, Herbst DA, Tsuchida CA, Al-Shayeb B, Banfield JF, Nogales E, Doudna JA. PMID: 34381246; PMCID: PMC8496406.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    43. Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples. PLoS One. 2021; 16(8):e0255690. Hamilton JR, Stahl EC, Tsuchida CA, Lin-Shiao E, Tsui CK, Pestal K, Gildea HK, Witkowsky LB, Moehle EA, McDevitt SL, McElroy M, Keller A, Sylvain I, Hirsh A, Ciling A, Ehrenberg AJ, Ringeisen BR, Huberty G, Urnov FD, Giannikopoulos P, Doudna JA, IGI SARS-CoV-2 Consortium. PMID: 34351984; PMCID: PMC8341588.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCellsPHPublic Health
    44. Accelerated RNA detection using tandem CRISPR nucleases. Nat Chem Biol. 2021 09; 17(9):982-988. Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim S, Dugan EJ, IGI Testing Consortium, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. PMID: 34354262; PMCID: PMC10184463.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansCells
    45. Diverse ATPase Proteins in Mobilomes Constitute a Large Potential Sink for Prokaryotic Host ATP. Front Microbiol. 2021; 12:691847. Shim H, Shivram H, Lei S, Doudna JA, Banfield JF. PMID: 34305853; PMCID: PMC8297831.
      View in: PubMed   Mentions: 5  
    46. Targeted delivery of CRISPR-Cas9 and transgenes enables complex immune cell engineering. Cell Rep. 2021 06 01; 35(9):109207. Hamilton JR, Tsuchida CA, Nguyen DN, Shy BR, McGarrigle ER, Sandoval Espinoza CR, Carr D, Blaeschke F, Marson A, Doudna JA. PMID: 34077734; PMCID: PMC8236216.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    47. Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus. PLoS One. 2021; 16(5):e0251296. Ehrenberg AJ, Moehle EA, Brook CE, Doudna Cate AH, Witkowsky LB, Sachdeva R, Hirsh A, Barry K, Hamilton JR, Lin-Shiao E, McDevitt S, Valentin-Alvarado L, Letourneau KN, Hunter L, Keller A, Pestal K, Frankino PA, Murley A, Nandakumar D, Stahl EC, Tsuchida CA, Gildea HK, Murdock AG, Hochstrasser ML, O'Brien E, Ciling A, Tsitsiklis A, Worden K, Dugast-Darzacq C, Hays SG, Barber CC, McGarrigle R, Lam EK, Ensminger DC, Bardet L, Sherry C, Harte A, Nicolette G, Giannikopoulos P, Hockemeyer D, Petersen M, Urnov FD, Ringeisen BR, Boots M, Doudna JA, IGI SARS-CoV-2 Testing Consortium. PMID: 34038425; PMCID: PMC8153421.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    48. Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex. Nat Commun. 2021 05 06; 12(1):2571. Wang JY, Hoel CM, Al-Shayeb B, Banfield JF, Brohawn SG, Doudna JA. PMID: 33958590; PMCID: PMC8102632.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
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    109. Programmable RNA recognition using a CRISPR-associated Argonaute. Proc Natl Acad Sci U S A. 2018 03 27; 115(13):3368-3373. Lapinaite A, Doudna JA, Cate JHD. PMID: 29531059; PMCID: PMC5879674.
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    110. Genomes in Focus: Development and Applications of CRISPR-Cas9 Imaging Technologies. Angew Chem Int Ed Engl. 2018 04 09; 57(16):4329-4337. Knight SC, Tjian R, Doudna JA. PMID: 29080263; PMCID: PMC6014596.
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    111. Spotlight: A Conversation with Laura Kiessling and Jennifer Doudna. ACS Chem Biol. 2018 Feb 16; 13(2):290-295. Kiessling LL, Doudna JA. PMID: 29448761.
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    112. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018 04 27; 360(6387):436-439. Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA. PMID: 29449511; PMCID: PMC6628903.
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    113. RNA-dependent RNA targeting by CRISPR-Cas9. Elife. 2018 01 05; 7. Strutt SC, Torrez RM, Kaya E, Negrete OA, Doudna JA. PMID: 29303478; PMCID: PMC5796797.
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    114. CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing. Nat Commun. 2017 12 08; 8(1):2024. Moreno-Mateos MA, Fernandez JP, Rouet R, Vejnar CE, Lane MA, Mis E, Khokha MK, Doudna JA, Giraldez AJ. PMID: 29222508; PMCID: PMC5722943.
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    115. Widespread Translational Remodeling during Human Neuronal Differentiation. Cell Rep. 2017 Nov 14; 21(7):2005-2016. Blair JD, Hockemeyer D, Doudna JA, Bateup HS, Floor SN. PMID: 29141229; PMCID: PMC5759054.
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    116. A thermostable Cas9 with increased lifetime in human plasma. Nat Commun. 2017 11 10; 8(1):1424. Harrington LB, Paez-Espino D, Staahl BT, Chen JS, Ma E, Kyrpides NC, Doudna JA. PMID: 29127284; PMCID: PMC5681539.
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    117. Nanoparticle delivery of Cas9 ribonucleoprotein and donor DNA in vivo induces homology-directed DNA repair. Nat Biomed Eng. 2017; 1:889-901. Lee K, Conboy M, Park HM, Jiang F, Kim HJ, Dewitt MA, Mackley VA, Chang K, Rao A, Skinner C, Shobha T, Mehdipour M, Liu H, Huang WC, Lan F, Bray NL, Li S, Corn JE, Kataoka K, Doudna JA, Conboy I, Murthy N. PMID: 29805845; PMCID: PMC5968829.
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    118. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature. 2017 10 19; 550(7676):407-410. Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, Sternberg SH, Joung JK, Yildiz A, Doudna JA. PMID: 28931002; PMCID: PMC5918688.
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    119. Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme. Nat Struct Mol Biol. 2017 Oct; 24(10):825-833. Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O'Connell MR, Doudna JA. PMID: 28892041; PMCID: PMC5961731.
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    120. A Broad-Spectrum Inhibitor of CRISPR-Cas9. Cell. 2017 Sep 07; 170(6):1224-1233.e15. Harrington LB, Doxzen KW, Ma E, Liu JJ, Knott GJ, Edraki A, Garcia B, Amrani N, Chen JS, Cofsky JC, Kranzusch PJ, Sontheimer EJ, Davidson AR, Maxwell KL, Doudna JA. PMID: 28844692; PMCID: PMC5875921.
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    121. A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9. Sci Adv. 2017 08; 3(8):eaao0027. Dagdas YS, Chen JS, Sternberg SH, Doudna JA, Yildiz A. PMID: 28808686; PMCID: PMC5547770.
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    122. Structures of the CRISPR genome integration complex. Science. 2017 09 15; 357(6356):1113-1118. Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna JA. PMID: 28729350; PMCID: PMC5748385.
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    123. Disabling Cas9 by an anti-CRISPR DNA mimic. Sci Adv. 2017 07; 3(7):e1701620. Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA. PMID: 28706995; PMCID: PMC5507636.
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    124. Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery. Nucleic Acids Res. 2017 Jun 20; 45(11):e98. Gaj T, Staahl BT, Rodrigues GMC, Limsirichai P, Ekman FK, Doudna JA, Schaffer DV. PMID: 28334779; PMCID: PMC5499784.
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    125. DNA recognition by an RNA-guided bacterial Argonaute. PLoS One. 2017; 12(5):e0177097. Doxzen KW, Doudna JA. PMID: 28520746; PMCID: PMC5435312.
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    126. High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding. Proc Natl Acad Sci U S A. 2017 05 23; 114(21):5461-5466. Boyle EA, Andreasson JOL, Chircus LM, Sternberg SH, Wu MJ, Guegler CK, Doudna JA, Greenleaf WJ. PMID: 28495970; PMCID: PMC5448226.
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    127. RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes. Mol Cell. 2017 May 04; 66(3):373-383.e3. East-Seletsky A, O'Connell MR, Burstein D, Knott GJ, Doudna JA. PMID: 28475872; PMCID: PMC5999320.
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    128. Correction: RNA and DNA Targeting by a Reconstituted Thermus thermophilus Type III-A CRISPR-Cas System. PLoS One. 2017; 12(4):e0175612. Liu TY, Iavarone AT, Doudna JA. PMID: 28384323; PMCID: PMC5383342.
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    129. CRISPR-Cas9 Structures and Mechanisms. Annu Rev Biophys. 2017 05 22; 46:505-529. Jiang F, Doudna JA. PMID: 28375731.
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    131. RNA-based recognition and targeting: sowing the seeds of specificity. Nat Rev Mol Cell Biol. 2017 04; 18(4):215-228. Gorski SA, Vogel J, Doudna JA. PMID: 28196981.
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    132. Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes. Nat Biotechnol. 2017 05; 35(5):431-434. Staahl BT, Benekareddy M, Coulon-Bainier C, Banfal AA, Floor SN, Sabo JK, Urnes C, Munares GA, Ghosh A, Doudna JA. PMID: 28191903; PMCID: PMC6649674.
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    134. RNA Scanning of a Molecular Machine with a Built-in Ruler. J Am Chem Soc. 2017 01 11; 139(1):262-268. Koh HR, Kidwell MA, Doudna J, Myong S. PMID: 27958730; PMCID: PMC8670420.
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    135. Cornerstones of CRISPR-Cas in drug discovery and therapy. Nat Rev Drug Discov. 2017 02; 16(2):89-100. Fellmann C, Gowen BG, Lin PC, Doudna JA, Corn JE. PMID: 28008168; PMCID: PMC5459481.
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    136. Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response. Mol Cell. 2017 Jan 05; 65(1):168-175. Heler R, Wright AV, Vucelja M, Bikard D, Doudna JA, Marraffini LA. PMID: 28017588; PMCID: PMC5218886.
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    137. New CRISPR-Cas systems from uncultivated microbes. Nature. 2017 02 09; 542(7640):237-241. Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF. PMID: 28005056; PMCID: PMC5300952.
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    138. A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells. Cell Rep. 2016 10 25; 17(5):1438-1452. Hultquist JF, Schumann K, Woo JM, Manganaro L, McGregor MJ, Doudna J, Simon V, Krogan NJ, Marson A. PMID: 27783955; PMCID: PMC5123761.
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    139. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nat Methods. 2016 Dec; 13(12):1013-1020. Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY. PMID: 27749837; PMCID: PMC5509561.
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    140. Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. Elife. 2016 10 12; 5. Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH. PMID: 27731797; PMCID: PMC5072841.
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    141. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature. 2016 Oct 13; 538(7624):270-273. East-Seletsky A, O'Connell MR, Knight SC, Burstein D, Cate JH, Tjian R, Doudna JA. PMID: 27669025; PMCID: PMC5576363.
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    142. Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9. Nat Commun. 2016 09 14; 7:12778. Singh D, Sternberg SH, Fei J, Doudna JA, Ha T. PMID: 27624851; PMCID: PMC5027287.
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    143. Applications of CRISPR technologies in research and beyond. Nat Biotechnol. 2016; 34(9):933-941. Barrangou R, Doudna JA. PMID: 27606440.
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    145. DNA Targeting by a Minimal CRISPR RNA-Guided Cascade. Mol Cell. 2016 09 01; 63(5):840-51. Hochstrasser ML, Taylor DW, Kornfeld JE, Nogales E, Doudna JA. PMID: 27588603; PMCID: PMC5111854.
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    146. eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature. 2016 08 04; 536(7614):96-9. Lee AS, Kranzusch PJ, Doudna JA, Cate JH. PMID: 27462815; PMCID: PMC5003174.
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    147. Reconstitution of selective HIV-1 RNA packaging in vitro by membrane-bound Gag assemblies. Elife. 2016 06 25; 5. Carlson LA, Bai Y, Keane SC, Doudna JA, Hurley JH. PMID: 27343348; PMCID: PMC4946900.
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    148. CRISPR Immunological Memory Requires a Host Factor for Specificity. Mol Cell. 2016 06 16; 62(6):824-833. Nuñez JK, Bai L, Harrington LB, Hinder TL, Doudna JA. PMID: 27211867.
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    149. Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. Oncotarget. 2016 May 10; 7(19):28169-82. Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfister SM, Taylor MD, Chang HY, Cho YJ. PMID: 27058758; PMCID: PMC5053718.
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    150. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. Nat Biotechnol. 2016 06; 34(6):646-51. Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna JA, Savage DF. PMID: 27136077; PMCID: PMC4900928.
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    151. Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. Elife. 2016 04 28; 5. Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ, Almeida R. PMID: 27130520; PMCID: PMC4880442.
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    152. A bacterial Argonaute with noncanonical guide RNA specificity. Proc Natl Acad Sci U S A. 2016 Apr 12; 113(15):4057-62. Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC, Kranzusch PJ, Doudna JA. PMID: 27035975; PMCID: PMC4839417.
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    153. Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell. 2016 Apr 07; 165(2):488-96. Nelles DA, Fang MY, O'Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW. PMID: 26997482; PMCID: PMC4826288.
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    154. Voices of biotech. Nat Biotechnol. 2016 Mar; 34(3):270-5. Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M, Junca H, June C, Kamb S, Khvorova A, Kim DH, Kim JS, Krishnan Y, Lakadamyali M, Lappalainen T, Lewin S, Liao J, Loman N, Lundberg E, Lynd L, Martin C, Mellman I, Miyawaki A, Mummery C, Nelson K, Paz J, Peralta-Yahya P, Picotti P, Polyak K, Prather K, Qin J, Quake S, Regev A, Rogers JA, Shetty R, Sommer M, Stevens M, Stolovitzky G, Takahashi M, Tang F, Teichmann S, Torres-Padilla ME, Tripathi L, Vemula P, Verdine G, Vollmer F, Wang J, Ying JY, Zhang F, Zhang T. PMID: 26963549.
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    155. Chemical and Biophysical Modulation of Cas9 for Tunable Genome Engineering. ACS Chem Biol. 2016 Mar 18; 11(3):681-8. Nuñez JK, Harrington LB, Doudna JA. PMID: 26857072.
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    156. Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering. Cell. 2016 Jan 14; 164(1-2):29-44. Wright AV, Nuñez JK, Doudna JA. PMID: 26771484.
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    158. Tunable protein synthesis by transcript isoforms in human cells. Elife. 2016 Jan 06; 5. Floor SN, Doudna JA. PMID: 26735365; PMCID: PMC4764583.
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    159. Analog sensitive chemical inhibition of the DEAD-box protein DDX3. Protein Sci. 2016 Mar; 25(3):638-49. Floor SN, Barkovich KJ, Condon KJ, Shokat KM, Doudna JA. PMID: 26650549; PMCID: PMC4815421.
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    160. Genome-editing revolution: My whirlwind year with CRISPR. Nature. 2015 Dec 24; 528(7583):469-71. Doudna J. PMID: 26701037.
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    161. Genome editing: the end of the beginning. Genome Biol. 2015 Dec 23; 16:292. Doudna JA, Gersbach CA. PMID: 26700220; PMCID: PMC4699356.
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    162. Get in LINE: Competition for Newly Minted Retrotransposon Proteins at the Ribosome. Mol Cell. 2015 Dec 03; 60(5):712-714. Floor SN, Doudna JA. PMID: 26638173.
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    163. Perspective: Embryo editing needs scrutiny. Nature. 2015 Dec 03; 528(7580):S6. Doudna J. PMID: 26630598.
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    164. Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3. J Biol Chem. 2016 Jan 29; 291(5):2412-21. Floor SN, Condon KJ, Sharma D, Jankowsky E, Doudna JA. PMID: 26598523; PMCID: PMC4732223.
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    165. Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science. 2015 Nov 13; 350(6262):823-6. Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M, Liu Z, Doudna JA, Tjian R. PMID: 26564855.
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    166. Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes. Mol Cell. 2015 Nov 05; 60(3):398-407. Ma E, Harrington LB, O'Connell MR, Zhou K, Doudna JA. PMID: 26545076; PMCID: PMC4636735.
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    167. Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System. Cell. 2015 Nov 05; 163(4):854-65. Redding S, Sternberg SH, Marshall M, Gibb B, Bhat P, Guegler CK, Wiedenheft B, Doudna JA, Greene EC. PMID: 26522594; PMCID: PMC4636941.
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    168. Conformational control of DNA target cleavage by CRISPR-Cas9. Nature. 2015 Nov 05; 527(7576):110-3. Sternberg SH, LaFrance B, Kaplan M, Doudna JA. PMID: 26524520; PMCID: PMC4859810.
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    169. Foreign DNA capture during CRISPR-Cas adaptive immunity. Nature. 2015 Nov 26; 527(7579):535-8. Nuñez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA. PMID: 26503043; PMCID: PMC4662619.
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    170. Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2',3' cGAMP Signaling. Mol Cell. 2015 Sep 17; 59(6):891-903. Kranzusch PJ, Wilson SC, Lee AS, Berger JM, Doudna JA, Vance RE. PMID: 26300263; PMCID: PMC4575873.
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    173. Expanding the Biologist's Toolkit with CRISPR-Cas9. Mol Cell. 2015 May 21; 58(4):568-74. Sternberg SH, Doudna JA. PMID: 26000842.
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    175. Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning. Science. 2015 May 01; 348(6234):581-5. Taylor DW, Zhu Y, Staals RH, Kornfeld JE, Shinkai A, van der Oost J, Nogales E, Doudna JA. PMID: 25837515; PMCID: PMC4582657.
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    176. Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science. 2015 Apr 03; 348(6230):36-8. 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. PMID: 25791083; PMCID: PMC4394183.
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    179. Rational design of a split-Cas9 enzyme complex. Proc Natl Acad Sci U S A. 2015 Mar 10; 112(10):2984-9. Wright AV, Sternberg SH, Taylor DW, Staahl BT, Bardales JA, Kornfeld JE, Doudna JA. PMID: 25713377; PMCID: PMC4364227.
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    180. Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature. 2015 Mar 12; 519(7542):193-8. Nuñez JK, Lee AS, Engelman A, Doudna JA. PMID: 25707795; PMCID: PMC4359072.
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    181. Dicer-TRBP complex formation ensures accurate mammalian microRNA biogenesis. Mol Cell. 2015 Feb 05; 57(3):397-407. Wilson RC, Tambe A, Kidwell MA, Noland CL, Schneider CP, Doudna JA. PMID: 25557550; PMCID: PMC4320653.
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    182. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife. 2014 Dec 15; 3:e04766. Lin S, Staahl BT, Alla RK, Doudna JA. PMID: 25497837; PMCID: PMC4383097.
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    183. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014 Nov 28; 346(6213):1258096. Doudna JA, Charpentier E. PMID: 25430774.
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    184. Cutting it close: CRISPR-associated endoribonuclease structure and function. Trends Biochem Sci. 2015 Jan; 40(1):58-66. Hochstrasser ML, Doudna JA. PMID: 25468820.
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    185. RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus. Mol Cell. 2014 Nov 20; 56(4):518-30. Staals RH, Zhu Y, Taylor DW, Kornfeld JE, Sharma K, Barendregt A, Koehorst JJ, Vlot M, Neupane N, Varossieau K, Sakamoto K, Suzuki T, Dohmae N, Yokoyama S, Schaap PJ, Urlaub H, Heck AJ, Nogales E, Doudna JA, Shinkai A, van der Oost J. PMID: 25457165; PMCID: PMC4342149.
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    186. New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. Nucleic Acids Res. 2014 Nov 10; 42(20):12833-46. Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS. PMID: 25326328; PMCID: PMC4227795.
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    187. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature. 2014 Dec 11; 516(7530):263-6. O'Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA. PMID: 25274302; PMCID: PMC4268322.
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    188. RNA-guided assembly of Rev-RRE nuclear export complexes. Elife. 2014 Aug 27; 3:e03656. Bai Y, Tambe A, Zhou K, Doudna JA. PMID: 25163983; PMCID: PMC4142337.
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    189. Evolutionarily conserved roles of the dicer helicase domain in regulating RNA interference processing. J Biol Chem. 2014 Oct 10; 289(41):28352-62. Kidwell MA, Chan JM, Doudna JA. PMID: 25135636; PMCID: PMC4192488.
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    190. Structure-guided reprogramming of human cGAS dinucleotide linkage specificity. Cell. 2014 Aug 28; 158(5):1011-1021. Kranzusch PJ, Lee ASY, Wilson SC, Solovykh MS, Vance RE, Berger JM, Doudna JA. PMID: 25131990; PMCID: PMC4157622.
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    191. Insights into RNA structure and function from genome-wide studies. Nat Rev Genet. 2014 Jul; 15(7):469-79. Mortimer SA, Kidwell MA, Doudna JA. PMID: 24821474.
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    192. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol. 2014 Jun; 21(6):528-34. Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA. PMID: 24793649; PMCID: PMC4075942.
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    193. CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference. Proc Natl Acad Sci U S A. 2014 May 06; 111(18):6618-23. Hochstrasser ML, Taylor DW, Bhat P, Guegler CK, Sternberg SH, Nogales E, Doudna JA. PMID: 24748111; PMCID: PMC4020112.
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    194. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science. 2014 Mar 14; 343(6176):1247997. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA. PMID: 24505130; PMCID: PMC4184034.
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    195. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. 2014 Mar 06; 507(7490):62-7. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. PMID: 24476820; PMCID: PMC4106473.
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    196. Methods in Enzymology. The use of CRISPR/Cas9, ZFNs, and TALENs in generating site-specific genome alterations. Preface. Methods Enzymol. 2014; 546:xix-xx. Doudna JA, Sontheimer EJ. PMID: 25398356.
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    197. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Res. 2014 Jan; 42(2):1341-53. Niewoehner O, Jinek M, Doudna JA. PMID: 24150936; PMCID: PMC3902920.
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    198. Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus. Mol Cell. 2013 Oct 10; 52(1):135-145. Staals RHJ, Agari Y, Maki-Yonekura S, Zhu Y, Taylor DW, van Duijn E, Barendregt A, Vlot M, Koehorst JJ, Sakamoto K, Masuda A, Dohmae N, Schaap PJ, Doudna JA, Heck AJR, Yonekura K, van der Oost J, Shinkai A. PMID: 24119403; PMCID: PMC4006948.
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    199. Enhancement of hepatitis C viral RNA abundance by precursor miR-122 molecules. RNA. 2013 Dec; 19(12):1825-32. Cox EM, Sagan SM, Mortimer SA, Doudna JA, Sarnow P. PMID: 24106328; PMCID: PMC3884667.
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    200. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol. 2013 Sep; 31(9):839-43. Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR. PMID: 23934178; PMCID: PMC3782611.
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    201. Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions. Genetics. 2013 Oct; 195(2):331-48. Lo TW, Pickle CS, Lin S, Ralston EJ, Gurling M, Schartner CM, Bian Q, Doudna JA, Meyer BJ. PMID: 23934893; PMCID: PMC3781963.
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    202. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013 Jul 18; 154(2):442-51. 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. PMID: 23849981; PMCID: PMC3770145.
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    203. Activating silent argonautes. Nat Struct Mol Biol. 2013 Jul; 20(7):769-71. Kidwell MA, Doudna JA. PMID: 23984440.
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    204. Hepatitis C virus 3'UTR regulates viral translation through direct interactions with the host translation machinery. Nucleic Acids Res. 2013 Sep; 41(16):7861-74. Bai Y, Zhou K, Doudna JA. PMID: 23783572; PMCID: PMC3763534.
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    205. Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation. Nucleic Acids Res. 2013 Aug; 41(15):7512-21. Sun C, Querol-Audí J, Mortimer SA, Arias-Palomo E, Doudna JA, Nogales E, Cate JH. PMID: 23766293; PMCID: PMC3753635.
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    206. Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity. Cell Rep. 2013 May 30; 3(5):1362-8. Kranzusch PJ, Lee AS, Berger JM, Doudna JA. PMID: 23707061; PMCID: PMC3800681.
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    207. Differential roles of human Dicer-binding proteins TRBP and PACT in small RNA processing. Nucleic Acids Res. 2013 Jul; 41(13):6568-76. Lee HY, Zhou K, Smith AM, Noland CL, Doudna JA. PMID: 23661684; PMCID: PMC3711433.
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    208. Substrate-specific structural rearrangements of human Dicer. Nat Struct Mol Biol. 2013 Jun; 20(6):662-70. Taylor DW, Ma E, Shigematsu H, Cianfrocco MA, Noland CL, Nagayama K, Nogales E, Doudna JA, Wang HW. PMID: 23624860; PMCID: PMC3676429.
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    209. Multiple sensors ensure guide strand selection in human RNAi pathways. RNA. 2013 May; 19(5):639-48. Noland CL, Doudna JA. PMID: 23531496; PMCID: PMC3677279.
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    210. RNA-protein analysis using a conditional CRISPR nuclease. Proc Natl Acad Sci U S A. 2013 Apr 02; 110(14):5416-21. Lee HY, Haurwitz RE, Apffel A, Zhou K, Smart B, Wenger CD, Laderman S, Bruhn L, Doudna JA. PMID: 23493562; PMCID: PMC3619310.
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    211. Biotechnology: Rewriting a genome. Nature. 2013 Mar 07; 495(7439):50-1. Charpentier E, Doudna JA. PMID: 23467164.
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    212. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013 Feb 28; 152(5):1173-83. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. PMID: 23452860; PMCID: PMC3664290.
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    213. Unconventional miR-122 binding stabilizes the HCV genome by forming a trimolecular RNA structure. Nucleic Acids Res. 2013 Apr; 41(7):4230-40. Mortimer SA, Doudna JA. PMID: 23416544; PMCID: PMC3627571.
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    214. RNA-programmed genome editing in human cells. Elife. 2013 Jan 29; 2:e00471. Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J. PMID: 23386978; PMCID: PMC3557905.
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    215. Molecular mechanisms of RNA interference. Annu Rev Biophys. 2013; 42:217-39. Wilson RC, Doudna JA. PMID: 23654304; PMCID: PMC5895182.
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    216. ATP-independent diffusion of double-stranded RNA binding proteins. Proc Natl Acad Sci U S A. 2013 Jan 02; 110(1):151-6. Koh HR, Kidwell MA, Ragunathan K, Doudna JA, Myong S. PMID: 23251028; PMCID: PMC3538233.
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    217. TRBP alters human precursor microRNA processing in vitro. RNA. 2012 Nov; 18(11):2012-9. Lee HY, Doudna JA. PMID: 23006623; PMCID: PMC3479391.
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    218. RNA processing enables predictable programming of gene expression. Nat Biotechnol. 2012 Oct; 30(10):1002-6. Qi L, Haurwitz RE, Shao W, Doudna JA, Arkin AP. PMID: 22983090.
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    219. Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa. Mol Cell Proteomics. 2012 Nov; 11(11):1430-41. van Duijn E, Barbu IM, Barendregt A, Jore MM, Wiedenheft B, Lundgren M, Westra ER, Brouns SJ, Doudna JA, van der Oost J, Heck AJ. PMID: 22918228; PMCID: PMC3494201.
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    220. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012 Aug 17; 337(6096):816-21. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. PMID: 22745249; PMCID: PMC6286148.
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    221. Coordinated activities of human dicer domains in regulatory RNA processing. J Mol Biol. 2012 Sep 28; 422(4):466-76. Ma E, Zhou K, Kidwell MA, Doudna JA. PMID: 22727743; PMCID: PMC3461841.
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    222. Biochemistry. Guided tour to the heart of RISC. Science. 2012 May 25; 336(6084):985-6. Kaya E, Doudna JA. PMID: 22628640.
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    223. Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA. EMBO J. 2012 Jun 13; 31(12):2824-32. Haurwitz RE, Sternberg SH, Doudna JA. PMID: 22522703; PMCID: PMC3380207.
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    224. Mechanism of foreign DNA selection in a bacterial adaptive immune system. Mol Cell. 2012 Jun 08; 46(5):606-15. Sashital DG, Wiedenheft B, Doudna JA. PMID: 22521690; PMCID: PMC3397241.
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    225. Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. RNA. 2012 Apr; 18(4):661-72. Sternberg SH, Haurwitz RE, Doudna JA. PMID: 22345129; PMCID: PMC3312554.
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    226. RNA-guided genetic silencing systems in bacteria and archaea. Nature. 2012 Feb 15; 482(7385):331-8. Wiedenheft B, Sternberg SH, Doudna JA. PMID: 22337052.
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    227. Reconsidering movement of eukaryotic mRNAs between polysomes and P bodies. Mol Cell. 2011 Dec 09; 44(5):745-58. Arribere JA, Doudna JA, Gilbert WV. PMID: 22152478; PMCID: PMC3240842.
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    228. Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3). Proc Natl Acad Sci U S A. 2011 Dec 20; 108(51):20473-8. Sun C, Todorovic A, Querol-Audí J, Bai Y, Villa N, Snyder M, Ashchyan J, Lewis CS, Hartland A, Gradia S, Fraser CS, Doudna JA, Nogales E, Cate JH. PMID: 22135459; PMCID: PMC3251073.
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    229. Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. J Virol. 2012 Feb; 86(3):1750-7. Mehle A, Dugan VG, Taubenberger JK, Doudna JA. PMID: 22090127; PMCID: PMC3264373.
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    230. Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning. Structure. 2011 Oct 12; 19(10):1456-66. Berry KE, Waghray S, Mortimer SA, Bai Y, Doudna JA. PMID: 22000514; PMCID: PMC3209822.
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    231. Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature. 2011 Sep 21; 477(7365):486-489. Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJJ, van der Oost J, Doudna JA, Nogales E. PMID: 21938068; PMCID: PMC4165517.
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    232. siRNA repositioning for guide strand selection by human Dicer complexes. Mol Cell. 2011 Jul 08; 43(1):110-21. Noland CL, Ma E, Doudna JA. PMID: 21726814; PMCID: PMC3143821.
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    233. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A. 2011 Jul 05; 108(27):11063-8. Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. PMID: 21642531; PMCID: PMC3131332.
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    234. Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A. 2011 Jul 05; 108(27):11069-74. Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. PMID: 21642536; PMCID: PMC3131376.
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    235. An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3. Nat Struct Mol Biol. 2011 Jun; 18(6):680-7. Sashital DG, Jinek M, Doudna JA. PMID: 21572442.
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    236. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions. Proc Natl Acad Sci U S A. 2011 Jun 21; 108(25):10092-7. Wiedenheft B, van Duijn E, Bultema JB, Bultema J, Waghmare SP, Waghmare S, Zhou K, Barendregt A, Westphal W, Heck AJ, Heck A, Boekema EJ, Boekema E, Dickman MJ, Dickman M, Doudna JA. PMID: 21536913; PMCID: PMC3121849.
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    237. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol. 2011 May; 18(5):529-36. Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ. PMID: 21460843.
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    238. Coupled 5' nucleotide recognition and processivity in Xrn1-mediated mRNA decay. Mol Cell. 2011 Mar 04; 41(5):600-8. Jinek M, Coyle SM, Doudna JA. PMID: 21362555; PMCID: PMC3090138.
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    239. The crystal structure of the signal recognition particle in complex with its receptor. Science. 2011 Feb 18; 331(6019):881-6. Ataide SF, Schmitz N, Shen K, Ke A, Shan SO, Doudna JA, Ban N. PMID: 21330537; PMCID: PMC3758919.
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    240. Optimized high-throughput screen for hepatitis C virus translation inhibitors. J Biomol Screen. 2011 Feb; 16(2):211-20. Berry KE, Peng B, Koditek D, Beeman D, Pagratis N, Perry JK, Parrish J, Zhong W, Doudna JA, Shih IH. PMID: 21297107; PMCID: PMC3260011.
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    241. Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity. Biochemistry. 2010 Nov 02; 49(43):9269-79. Weeks AM, Coyle SM, Jinek M, Doudna JA, Chang MC. PMID: 20836570; PMCID: PMC3461317.
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    242. Substrate-specific kinetics of Dicer-catalyzed RNA processing. J Mol Biol. 2010 Dec 03; 404(3):392-402. Chakravarthy S, Sternberg SH, Kellenberger CA, Doudna JA. PMID: 20932845; PMCID: PMC3005596.
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    243. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science. 2010 Sep 10; 329(5997):1355-8. Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA. PMID: 20829488; PMCID: PMC3133607.
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    244. The HCV IRES pseudoknot positions the initiation codon on the 40S ribosomal subunit. RNA. 2010 Aug; 16(8):1559-69. Berry KE, Waghray S, Doudna JA. PMID: 20584896; PMCID: PMC2905755.
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    245. Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae. PLoS One. 2010 Feb 09; 5(2):e9114. Clarkson BK, Gilbert WV, Doudna JA. PMID: 20161741; PMCID: PMC2817733.
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    246. A host of factors regulating influenza virus replication. Viruses. 2010 Feb; 2(2):566-573. Mehle A, Doudna JA. PMID: 21994648; PMCID: PMC3185602.
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    247. Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation. Nat Struct Mol Biol. 2010 Feb; 17(2):238-40. Jinek M, Fabian MR, Coyle SM, Sonenberg N, Doudna JA. PMID: 20098421; PMCID: PMC2920127.
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    248. Structural insights into RNA interference. Curr Opin Struct Biol. 2010 Feb; 20(1):90-7. Sashital DG, Doudna JA. PMID: 20053548; PMCID: PMC2855239.
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    249. Adaptive strategies of the influenza virus polymerase for replication in humans. Proc Natl Acad Sci U S A. 2009 Dec 15; 106(50):21312-6. Mehle A, Doudna JA. PMID: 19995968; PMCID: PMC2789757.
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    250. Structural insights into RNA processing by the human RISC-loading complex. Nat Struct Mol Biol. 2009 Nov; 16(11):1148-53. Wang HW, Noland C, Siridechadilok B, Taylor DW, Ma E, Felderer K, Doudna JA, Nogales E. PMID: 19820710; PMCID: PMC2845538.
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    251. Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell. 2009 Sep 24; 35(6):868-80. Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohlschlegel J, Doudna JA, Chen CY, Shyu AB, Yates JR, Hannon GJ, Filipowicz W, Duchaine TF, Sonenberg N. PMID: 19716330; PMCID: PMC2803087.
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    252. Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense. Structure. 2009 Jun 10; 17(6):904-12. Wiedenheft B, Zhou K, Jinek M, Coyle SM, Ma W, Doudna JA. PMID: 19523907.
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    253. The pathway of hepatitis C virus mRNA recruitment to the human ribosome. Nat Struct Mol Biol. 2009 Apr; 16(4):397-404. Fraser CS, Hershey JW, Doudna JA. PMID: 19287397; PMCID: PMC2689074.
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    254. A three-dimensional view of the molecular machinery of RNA interference. Nature. 2009 Jan 22; 457(7228):405-12. Jinek M, Doudna JA. PMID: 19158786.
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    255. dsRNA with 5' overhangs contributes to endogenous and antiviral RNA silencing pathways in plants. EMBO J. 2009 Mar 04; 28(5):545-55. Fukunaga R, Doudna JA. PMID: 19165150; PMCID: PMC2657584.
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    256. Direct link between RACK1 function and localization at the ribosome in vivo. Mol Cell Biol. 2009 Mar; 29(6):1626-34. Coyle SM, Gilbert WV, Doudna JA. PMID: 19114558; PMCID: PMC2648249.
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    257. An inhibitory activity in human cells restricts the function of an avian-like influenza virus polymerase. Cell Host Microbe. 2008 Aug 14; 4(2):111-22. Mehle A, Doudna JA. PMID: 18692771; PMCID: PMC2597520.
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    258. Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3. Proc Natl Acad Sci U S A. 2008 Nov 25; 105(47):18139-44. Zhou M, Sandercock AM, Fraser CS, Ridlova G, Stephens E, Schenauer MR, Yokoi-Fong T, Barsky D, Leary JA, Hershey JW, Doudna JA, Robinson CV. PMID: 18599441; PMCID: PMC2587604.
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    259. Nucleic acids and their protein partners. Curr Opin Struct Biol. 2008 Jun; 18(3):279-81. Puglisi JD, Doudna JA. PMID: 18547801.
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    260. Autoinhibition of human dicer by its internal helicase domain. J Mol Biol. 2008 Jun 27; 380(1):237-43. Ma E, MacRae IJ, Kirsch JF, Doudna JA. PMID: 18508075; PMCID: PMC2927216.
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    261. In vitro reconstitution of the human RISC-loading complex. Proc Natl Acad Sci U S A. 2008 Jan 15; 105(2):512-7. MacRae IJ, Ma E, Zhou M, Robinson CV, Doudna JA. PMID: 18178619; PMCID: PMC2206567.
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    262. Structural determinants of RNA recognition and cleavage by Dicer. Nat Struct Mol Biol. 2007 Oct; 14(10):934-40. MacRae IJ, Zhou K, Doudna JA. PMID: 17873886.
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    263. Cap-independent translation is required for starvation-induced differentiation in yeast. Science. 2007 Aug 31; 317(5842):1224-7. Gilbert WV, Zhou K, Butler TK, Doudna JA. PMID: 17761883.
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    264. An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer. Acta Crystallogr D Biol Crystallogr. 2007 Sep; 63(Pt 9):993-9. MacRae IJ, Doudna JA. PMID: 17704568.
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    265. eIF3j is located in the decoding center of the human 40S ribosomal subunit. Mol Cell. 2007 Jun 22; 26(6):811-9. Fraser CS, Berry KE, Hershey JW, Doudna JA. PMID: 17588516.
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    266. Quantitative studies of ribosome conformational dynamics. Q Rev Biophys. 2007 May; 40(2):163-89. Fraser CS, Doudna JA. PMID: 18072984.
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    267. A higher degree of difficulty. ACS Chem Biol. 2007 Apr 24; 2(4):197-9. Kiessling LL, Doudna JA, Johnsson K, Mapp AK, Marletta MA, Seeberger PH, Williamson JR, Wedde SG. PMID: 17455890.
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    268. Structural roles of monovalent cations in the HDV ribozyme. Structure. 2007 Mar; 15(3):281-7. Ke A, Ding F, Batchelor JD, Doudna JA. PMID: 17355864.
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    269. Structural characterization of the human eukaryotic initiation factor 3 protein complex by mass spectrometry. Mol Cell Proteomics. 2007 Jul; 6(7):1135-46. Damoc E, Fraser CS, Zhou M, Videler H, Mayeur GL, Hershey JW, Doudna JA, Robinson CV, Leary JA. PMID: 17322308.
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    270. Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr Opin Struct Biol. 2007 Feb; 17(1):138-45. MacRae IJ, Doudna JA. PMID: 17194582.
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    271. SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting. RNA. 2007 Feb; 13(2):240-50. Siu FY, Spanggord RJ, Doudna JA. PMID: 17164479; PMCID: PMC1781372.
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    272. Structural and mechanistic insights into hepatitis C viral translation initiation. Nat Rev Microbiol. 2007 Jan; 5(1):29-38. Fraser CS, Doudna JA. PMID: 17128284.
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    273. A fast and efficient procedure to produce scFvs specific for large macromolecular complexes. J Immunol Methods. 2007 Jan 10; 318(1-2):95-101. Wu S, Ke A, Doudna JA. PMID: 17126854; PMCID: PMC2920608.
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    274. RNAs regulate biology. ACS Chem Biol. 2006 Jul 21; 1(6):335-8. Green R, Doudna JA. PMID: 17163766.
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    275. Distinct contributions of KH domains to substrate binding affinity of Drosophila P-element somatic inhibitor protein. RNA. 2006 Feb; 12(2):283-91. Chmiel NH, Rio DC, Doudna JA. PMID: 16428607; PMCID: PMC1370908.
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    276. Structural basis for double-stranded RNA processing by Dicer. Science. 2006 Jan 13; 311(5758):195-8. Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. PMID: 16410517.
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    277. Structure of Dicer and mechanistic implications for RNAi. Cold Spring Harb Symp Quant Biol. 2006; 71:73-80. Macrae IJ, Li F, Zhou K, Cande WZ, Doudna JA. PMID: 17381283.
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    278. GTP-dependent formation of a ribonucleoprotein subcomplex required for ribosome biogenesis. J Mol Biol. 2006 Feb 17; 356(2):432-43. Karbstein K, Doudna JA. PMID: 16376378.
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    279. Structural roles for human translation factor eIF3 in initiation of protein synthesis. Science. 2005 Dec 02; 310(5753):1513-5. Siridechadilok B, Fraser CS, Hall RJ, Doudna JA, Nogales E. PMID: 16322461.
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    280. An essential GTPase promotes assembly of preribosomal RNA processing complexes. Mol Cell. 2005 Nov 23; 20(4):633-43. Karbstein K, Jonas S, Doudna JA. PMID: 16307926.
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    281. RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle. Nat Struct Mol Biol. 2005 Dec; 12(12):1116-22. Spanggord RJ, Siu F, Ke A, Doudna JA. PMID: 16299512.
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    282. Chemical biology at the crossroads of molecular structure and mechanism. Nat Chem Biol. 2005 Nov; 1(6):300-3. Doudna JA. PMID: 16408062.
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    283. Identification and analysis of U5 snRNA variants in Drosophila. RNA. 2005 Oct; 11(10):1473-7. Chen L, Lullo DJ, Ma E, Celniker SE, Rio DC, Doudna JA. PMID: 16199758; PMCID: PMC1370830.
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    284. Ro's role in RNA reconnaissance. Cell. 2005 May 20; 121(4):495-496. MacRae IJ, Doudna JA. PMID: 15907458.
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    285. Mass spectrometric analysis of the human 40S ribosomal subunit: native and HCV IRES-bound complexes. Protein Sci. 2005 Jun; 14(6):1438-46. Yu Y, Ji H, Doudna JA, Leary JA. PMID: 15883184; PMCID: PMC2253395.
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    286. Ribozyme catalysis: not different, just worse. Nat Struct Mol Biol. 2005 May; 12(5):395-402. Doudna JA, Lorsch JR. PMID: 15870731.
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    287. Protein-nucleic acid interactions: unlocking mysteries old and new. Curr Opin Struct Biol. 2005 Feb; 15(1):65-67. Aggarwal AK, Doudna JA. PMID: 34650322; PMCID: PMC8513794.
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    288. Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA. Proc Natl Acad Sci U S A. 2004 Dec 07; 101(49):16990-5. Ji H, Fraser CS, Yu Y, Leary J, Doudna JA. PMID: 15563596; PMCID: PMC534415.
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    289. Crystallization of RNA and RNA-protein complexes. Methods. 2004 Nov; 34(3):408-14. Ke A, Doudna JA. PMID: 15325657.
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    290. Assembly of an active group II intron-maturase complex by protein dimerization. Biochemistry. 2004 Jun 01; 43(21):6486-97. Rambo RP, Doudna JA. PMID: 15157082.
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    291. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature. 2004 May 13; 429(6988):201-5. Ke A, Zhou K, Ding F, Cate JH, Doudna JA. PMID: 15141216.
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    292. Conserved but nonessential interaction of SRP RNA with translation factor EF-G. RNA. 2004 May; 10(5):772-8. Sagar MB, Lucast L, Doudna JA. PMID: 15100432; PMCID: PMC1370567.
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    293. Distinct sites of phosphorothioate substitution interfere with folding and splicing of the Anabaena group I intron. Nucleic Acids Res. 2004; 32(7):2272-80. Lupták A, Doudna JA. PMID: 15107495; PMCID: PMC407829.
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    294. RNA: primed for packing? Chem Biol. 2004 Feb; 11(2):149-51. Karbstein K, Doudna JA. PMID: 15123272.
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    295. Structural insights into the signal recognition particle. Annu Rev Biochem. 2004; 73:539-57. Doudna JA, Batey RT. PMID: 15189152.
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    296. The j-subunit of human translation initiation factor eIF3 is required for the stable binding of eIF3 and its subcomplexes to 40 S ribosomal subunits in vitro. J Biol Chem. 2004 Mar 05; 279(10):8946-56. Fraser CS, Lee JY, Mayeur GL, Bushell M, Doudna JA, Hershey JW. PMID: 14688252.
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    297. Protein-nucleic acid interactions. Curr Opin Struct Biol. 2003 Feb; 13(1):3-5. Aggarwal AK, Doudna JA. PMID: 34276144; PMCID: PMC8284994.
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    298. The chemical repertoire of natural ribozymes. Nature. 2002 Jul 11; 418(6894):222-8. Doudna JA, Cech TR. PMID: 12110898.
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    299. Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nat Struct Biol. 2002 May; 9(5):370-4. Kieft JS, Zhou K, Grech A, Jubin R, Doudna JA. PMID: 11927953.
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    300. Structure and function of the eukaryotic ribosome: the next frontier. Cell. 2002 Apr 19; 109(2):153-6. Doudna JA, Rath VL. PMID: 12007402.
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    301. Structural insights into group II intron catalysis and branch-site selection. Science. 2002 Mar 15; 295(5562):2084-8. Zhang L, Doudna JA. PMID: 11859154.
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    302. Creative catalysis: pieces of the RNA world jigsaw. Trends Biochem Sci. 2001 Dec; 26(12):699-701. Murray JM, Doudna JA. PMID: 11738588.
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    303. A universal mode of helix packing in RNA. Nat Struct Biol. 2001 Apr; 8(4):339-43. Doherty EA, Batey RT, Masquida B, Doudna JA. PMID: 11276255.
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    304. Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle. J Mol Biol. 2001 Mar 16; 307(1):229-46. Batey RT, Sagar MB, Doudna JA. PMID: 11243816.
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    305. Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit. Science. 2001 Mar 09; 291(5510):1959-62. Spahn CM, Kieft JS, Grassucci RA, Penczek PA, Zhou K, Doudna JA, Frank J. PMID: 11239155.
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    306. Large-scale purification of a stable form of recombinant tobacco etch virus protease. Biotechniques. 2001 Mar; 30(3):544-6, 548, 550 passim. Lucast LJ, Batey RT, Doudna JA. PMID: 11252791.
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    307. Mechanism of ribosome recruitment by hepatitis C IRES RNA. RNA. 2001 Feb; 7(2):194-206. Kieft JS, Zhou K, Jubin R, Doudna JA. PMID: 11233977; PMCID: PMC1370078.
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    308. Ribozyme structures and mechanisms. Annu Rev Biophys Biomol Struct. 2001; 30:457-75. Doherty EA, Doudna JA. PMID: 11441810.
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    309. Mechanisms of internal ribosome entry in translation initiation. Cold Spring Harb Symp Quant Biol. 2001; 66:277-83. Kieft JS, Grech A, Adams P, Doudna JA. PMID: 12762029.
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    310. Structural genomics of RNA. Nat Struct Biol. 2000 Nov; 7 Suppl:954-6. Doudna JA. PMID: 11103998.
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    311. A phosphoramidate substrate analog is a competitive inhibitor of the Tetrahymena group I ribozyme. Chem Biol. 2000 Nov; 7(11):845-54. Hanna RL, Gryaznov SM, Doudna JA. PMID: 11094338.
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    312. Hepatitis C virus internal ribosome entry site (IRES) stem loop IIId contains a phylogenetically conserved GGG triplet essential for translation and IRES folding. J Virol. 2000 Nov; 74(22):10430-7. Jubin R, Vantuno NE, Kieft JS, Murray MG, Doudna JA, Lau JY, Baroudy BM. PMID: 11044087; PMCID: PMC110917.
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    313. Metal ions in ribozyme folding and catalysis. Curr Opin Chem Biol. 2000 Apr; 4(2):166-70. Hanna R, Doudna JA. PMID: 10742186.
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    314. The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis. Biochemistry. 2000 Mar 14; 39(10):2639-51. Engelhardt MA, Doherty EA, Knitt DS, Doudna JA, Herschlag D. PMID: 10704214.
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    315. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science. 2000 Feb 18; 287(5456):1232-9. Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA. PMID: 10678824.
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    316. Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module. J Mol Biol. 2000 Jan 21; 295(3):541-56. Ferré-D'Amaré AR, Doudna JA. PMID: 10623545.
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    317. Solving large RNA structures by X-ray crystallography. Methods Enzymol. 2000; 317:169-80. Cate JH, Doudna JA. PMID: 10829280.
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    318. Ribozyme structures and mechanisms. Annu Rev Biochem. 2000; 69:597-615. Doherty EA, Doudna JA. PMID: 10966470.
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    319. Cashing in on crystals. Curr Biol. 1999 Oct 07; 9(19):R731-4. Doudna JA. PMID: 10530999.
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    320. The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold. J Mol Biol. 1999 Sep 24; 292(3):513-29. Kieft JS, Zhou K, Jubin R, Murray MG, Lau JY, Doudna JA. PMID: 10497018.
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    321. A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. RNA. 1999 Jun; 5(6):720-7. Wadkins TS, Perrotta AT, Ferré-D'Amaré AR, Doudna JA, Been MD. PMID: 10376872; PMCID: PMC1369799.
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    322. Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme. Biochemistry. 1999 Mar 09; 38(10):2982-90. Doherty EA, Herschlag D, Doudna JA. PMID: 10074350.
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    323. RNA folds: insights from recent crystal structures. Annu Rev Biophys Biomol Struct. 1999; 28:57-73. Ferré-D'Amaré AR, Doudna JA. PMID: 10410795.
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    324. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat Struct Biol. 1998 Nov; 5(11):986-92. Basu S, Rambo RP, Strauss-Soukup J, Cate JH, Ferré-D'Amaré AR, Strobel SA, Doudna JA. PMID: 9808044.
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    325. Crystal structure of a hepatitis delta virus ribozyme. Nature. 1998 Oct 08; 395(6702):567-74. Ferré-D'Amaré AR, Zhou K, Doudna JA. PMID: 9783582.
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    326. Ribozymes: the hammerhead swings into action. Curr Biol. 1998 Jul 02; 8(14):R495-7. Doudna JA. PMID: 9663384.
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    327. A general module for RNA crystallization. J Mol Biol. 1998 Jun 12; 279(3):621-31. Ferré-D'Amaré AR, Zhou K, Doudna JA. PMID: 9641982.
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    328. The parallel universe of RNA folding. Nat Struct Biol. 1998 May; 5(5):337-40. Batey RT, Doudna JA. PMID: 9586989.
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    329. A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol. 1997 Jul; 4(7):553-8. Cate JH, Hanna RL, Doudna JA. PMID: 9228948.
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    330. RNA seeing double: close-packing of helices in RNA tertiary structure. Trends Biochem Sci. 1997 Jul; 22(7):262-6. Strobel SA, Doudna JA. PMID: 9255068.
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    331. RNA structure: crystal clear? Curr Opin Struct Biol. 1997 Jun; 7(3):310-6. Doudna JA, Cate JH. PMID: 9204271.
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    332. The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core. Biochemistry. 1997 Mar 18; 36(11):3159-69. Doherty EA, Doudna JA. PMID: 9115992.
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    333. A sparse matrix approach to crystallizing ribozymes and RNA motifs. Methods Mol Biol. 1997; 74:379-86. Cate JH, Doudna JA. PMID: 9204453.
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    334. Preparation of homogeneous ribozyme RNA for crystallization. Methods Mol Biol. 1997; 74:365-70. Doudna JA. PMID: 9204451.
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    335. Emerging themes in RNA folding. Fold Des. 1997; 2(5):R65-70. Doudna JA, Doherty EA. PMID: 9377708.
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    336. Establishing suitability of RNA preparations for crystallization. Determination of polydispersity. Methods Mol Biol. 1997; 74:371-7. Ferré-d'Amaré AR, Doudna JA. PMID: 9204452.
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    337. Metal-binding sites in the major groove of a large ribozyme domain. Structure. 1996 Oct 15; 4(10):1221-9. Cate JH, Doudna JA. PMID: 8939748.
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    338. RNA tertiary structure mediation by adenosine platforms. Science. 1996 Sep 20; 273(5282):1696-9. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna JA. PMID: 8781229.
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    339. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 1996 Sep 20; 273(5282):1678-85. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA. PMID: 8781224.
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    340. Use of cis- and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res. 1996 Mar 01; 24(5):977-8. Ferré-D'Amaré AR, Doudna JA. PMID: 8600468; PMCID: PMC145725.
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    341. Hammerhead ribozyme structure: U-turn for RNA structural biology. Structure. 1995 Aug 15; 3(8):747-50. Doudna JA. PMID: 7582890.
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    342. Selection of an RNA molecule that mimics a major autoantigenic epitope of human insulin receptor. Proc Natl Acad Sci U S A. 1995 Mar 14; 92(6):2355-9. Doudna JA, Cech TR, Sullenger BA. PMID: 7534420; PMCID: PMC42482.
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    343. Self-assembly of a group I intron active site from its component tertiary structural domains. RNA. 1995 Mar; 1(1):36-45. Doudna JA, Cech TR. PMID: 7489486; PMCID: PMC1369057.
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    344. Hammering out the shape of a ribozyme. Structure. 1994 Dec 15; 2(12):1271-2. Doudna JA. PMID: 7704535.
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    345. Crystallization of ribozymes and small RNA motifs by a sparse matrix approach. Proc Natl Acad Sci U S A. 1993 Aug 15; 90(16):7829-33. Doudna JA, Grosshans C, Gooding A, Kundrot CE. PMID: 8356090; PMCID: PMC47236.
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    346. Ribozyme-catalyzed primer extension by trinucleotides: a model for the RNA-catalyzed replication of RNA. Biochemistry. 1993 Mar 02; 32(8):2111-5. Doudna JA, Usman N, Szostak JW. PMID: 7680575.
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    347. Template-directed primer extension catalyzed by the Tetrahymena ribozyme. Mol Cell Biol. 1991 Jun; 11(6):3390-4. Bartel DP, Doudna JA, Usman N, Szostak JW. PMID: 2038341; PMCID: PMC360195.
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    348. A multisubunit ribozyme that is a catalyst of and template for complementary strand RNA synthesis. Science. 1991 Mar 29; 251(5001):1605-8. Doudna JA, Couture S, Szostak JW. PMID: 1707185.
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    349. Chemical synthesis of oligoribonucleotides containing 2-aminopurine: substrates for the investigation of ribozyme function. J Org Chem. 1990 Oct 12; 55(21):5547-9. Doudna JA, Szostak JW, Rich A, Usman N. PMID: 11540922.
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    350. Mutational analysis of conserved nucleotides in a self-splicing group I intron. J Mol Biol. 1990 Oct 05; 215(3):345-58. Couture S, Ellington AD, Gerber AS, Cherry JM, Doudna JA, Green R, Hanna M, Pace U, Rajagopal J, Szostak JW. PMID: 1700131.
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    351. Miniribozymes, small derivatives of the sunY intron, are catalytically active. Mol Cell Biol. 1989 Dec; 9(12):5480-3. Doudna JA, Szostak JW. PMID: 2685567; PMCID: PMC363717.
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    352. RNA structure, not sequence, determines the 5' splice-site specificity of a group I intron. Proc Natl Acad Sci U S A. 1989 Oct; 86(19):7402-6. Doudna JA, Cormack BP, Szostak JW. PMID: 2678103; PMCID: PMC298070.
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    353. RNA-catalysed synthesis of complementary-strand RNA. Nature. 1989 Jun 15; 339(6225):519-22. Doudna JA, Szostak JW. PMID: 2660003.
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