Jennifer Doudna, PhD
Professor
Cellular Molecular Pharmacology
School of Medicine

Grants and Projects

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• Expanding CRISPR-Cas editing technology through exploration of novel Cas proteins and DNA repair systems, NIH, 2018-2023
• Identifying and inhibiting the SARS-CoV-2 packaging mechanism, NIH, 2021-2023
• Cas9 RNP delivery to immune cells in vivo via molecular targeting, NIH, 2019-2022
• Center for Genome Editing and Recording, NIH, 2017-2022
• Minstrel HTUV Gallery 700 Automated Crystal Growth and Imaging System, NIH, 2013-2015
• Structure and Function of RNAi-related Nucleases, NIH, 2005-2015
• HCV IRES Control of Human Translational Initiation, NIH, 2011-2012
• Program in Virus Translational Control, NIH, 2006-2012
• Structure and Mechanism of Internal Ribosome Entry Sites, NIH, 2002-2006
• Nucleic Acids Gordon Research Conference, NIH, 2002-2003
• Assembly of Higher Order Structure in Group I Ribozymes, NIH, 1997-2002

Publications (376)

Top publication keywords:
Ribonuclease IIIRNA, CatalyticCRISPR-Cas SystemsClustered Regularly Interspaced Short Palindromic RepeatsGenetic EngineeringEndodeoxyribonucleasesBacterial ProteinsRNA, BacterialEndonucleasesGene EditingCRISPR-Associated ProteinsRNANucleic Acid ConformationDNA CleavageIntegrases

• Assembly of SARS-CoV-2 nucleocapsid protein with nucleic acid.
  Nucleic acids research 2024 Zhao H, Syed AM, Khalid MM, Nguyen A, Ciling A, Wu D, Yau WM, Srinivasan S, Esposito D, Doudna JA, Piszczek G, Ott M, Schuck P
• A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.
  Nucleic acids research 2024 Enustun E, Armbruster EG, Lee J, Zhang S, Yee BA, Malukhina K, Gu Y, Deep A, Naritomi JT, Liang Q, Aigner S, Adler BA, Cress BF, Doudna JA, Chaikeeratisak V, Cleveland DW, Ghassemian M, Bintu B, Yeo …
• An essential and highly selective protein import pathway encoded by nucleus-forming phage.
  bioRxiv : the preprint server for biology 2024 Morgan CJ, Enustun E, Armbruster EG, Birkholz EA, Prichard A, Forman T, Aindow A, Wannasrichan W, Peters S, Inlow K, Shepherd IL, Razavilar A, Chaikeeratisak V, Adler BA, Cress BF, Doudna JA, Pogliano…
• Targeted nonviral delivery of genome editors in vivo.
  Proceedings of the National Academy of Sciences of the United States of America 2024 Tsuchida CA, Wasko KM, Hamilton JR, Doudna JA
• Hachiman is a genome integrity sensor.
  bioRxiv : the preprint server for biology 2024 Tuck OT, Adler BA, Armbruster EG, Lahiri A, Hu JJ, Zhou J, Pogliano J, Doudna JA

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• Engineering self-deliverable ribonucleoproteins for genome editing in the brain.
  Nature communications 2024 Chen K, Stahl EC, Kang MH, Xu B, Allen R, Trinidad M, Doudna JA
• In vivo human T cell engineering with enveloped delivery vehicles.
  Nature biotechnology 2024 Hamilton JR, Chen E, Perez BS, Sandoval Espinoza CR, Kang MH, Trinidad M, Ngo W, Doudna JA
• CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes.
  Nucleic acids research 2024 Adler BA, Trinidad MI, Bellieny-Rabelo D, Zhang E, Karp HM, Skopintsev P, Thornton BW, Weissman RF, Yoon PH, Chen L, Hessler T, Eggers AR, Colognori D, Boger R, Doherty EE, Tsuchida CA, Tran RV, …
• Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9.
  bioRxiv : the preprint server for biology 2023 Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Thornton BW, Xu B, Trinidad MI, Doudna JA
• Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes.
  Nucleic acids research 2023 Yoon PH, Skopintsev P, Shi H, Chen L, Adler BA, Al-Shimary M, Craig RJ, Loi KJ, DeTurk EC, Li Z, Amerasekera J, Trinidad M, Nisonoff H, Chen K, Lahiri A, Boger R, Jacobsen S, Banfield JF, Doudna JA
• Assembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acid.
  bioRxiv : the preprint server for biology 2023 Zhao H, Syed AM, Khalid MM, Nguyen A, Ciling A, Wu D, Yau WM, Srinivasan S, Esposito D, Doudna JA, Piszczek G, Ott M, Schuck P
• Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species.
  Nature communications 2023 Lou YC, Rubin BE, Schoelmerich MC, DiMarco KS, Borges AL, Rovinsky R, Song L, Doudna JA, Banfield JF
• Engineering self-deliverable ribonucleoproteins for genome editing in the brain.
  bioRxiv : the preprint server for biology 2023 Chen K, Stahl EC, Kang MH, Xu B, Allen R, Trinidad M, Doudna JA
• Lung and liver editing by lipid nanoparticle delivery of a stable CRISPR-Cas9 RNP.
  bioRxiv : the preprint server for biology 2023 Chen K, Han H, Zhao S, Xu B, Yin B, Trinidad M, Burgstone BW, Murthy N, Doudna JA
• Targeting the non-coding genome and temozolomide signature enables CRISPR-mediated glioma oncolysis.
  Cell reports 2023 Tan IL, Perez AR, Lew RJ, Sun X, Baldwin A, Zhu YK, Shah MM, Berger MS, Doudna JA, Fellmann C
• Previous exposure to Spike-providing parental strains confers neutralizing immunity to XBB lineage and other SARS-CoV-2 recombinants in the context of vaccination.
  Emerging microbes & infections 2023 Suryawanshi RK, Taha TY, McCavitt-Malvido M, Silva I, Khalid MM, Syed AM, Chen IP, Saldhi P, Sreekumar B, Montano M, Foresythe K, Tabata T, Kumar GR, Sotomayor-Gonzalez A, Servellita V, Gliwa A, …
• Assembly of SARS-CoV-2 ribonucleosomes by truncated N∗ variant of the nucleocapsid protein.
  The Journal of biological chemistry 2023 Adly AN, Bi M, Carlson CR, Syed AM, Ciling A, Doudna JA, Cheng Y, Morgan DO
• Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells.
  Cell 2023 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, Hofman L, Satpathy AT, Stadtmauer EA, Cate JHD, Eyquem J, Fraietta JA, June …
• A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.
  bioRxiv : the preprint server for biology 2023 Enustun E, Armbruster EG, Lee J, Zhang S, Yee BA, Gu Y, Deep A, Naritomi JT, Liang Q, Aigner S, Adler BA, Cress BF, Doudna JA, Chaikeeratisak V, Cleveland DW, Ghassemian M, Yeo GW, Pogliano J, Corbett…
• SARS-CoV-2 variants evolve convergent strategies to remodel the host response.
  Cell 2023 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, …
• Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection.
  bioRxiv : the preprint server for biology 2023 Armbruster EG, Lee J, Hutchings J, VanderWal AR, Enustun E, Adler BA, Aindow A, Deep A, Rodriguez ZK, Morgan CJ, Ghassemian M, Charles E, Cress BF, Savage DF, Doudna JA, Pogliano K, Corbett KD, Villa …
• Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes.
  bioRxiv : the preprint server for biology 2023 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
• Genome editing in the mouse brain with minimally immunogenic Cas9 RNPs.
  Molecular therapy : the journal of the American Society of Gene Therapy 2023 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
• Genome expansion by a CRISPR trimmer-integrase.
  Nature 2023 Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA
• Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6.
  Nature communications 2023 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, …
• Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells.
  bioRxiv : the preprint server for biology 2023 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 …
• To TnpB or not TnpB? Cas12 is the answer.
  Nature chemical biology 2023 Yoon PH, Adler BA, Doudna JA
• Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6.
  bioRxiv : the preprint server for biology 2023 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
• Precise transcript targeting by CRISPR-Csm complexes.
  Nature biotechnology 2023 Colognori D, Trinidad M, Doudna JA
• CRISPR technology: A decade of genome editing is only the beginning.
  Science (New York, N.Y.) 2023 Wang JY, Doudna JA
• Genome editing in plants using the compact editor CasΦ.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Li Z, Zhong Z, Wu Z, Pausch P, Al-Shayeb B, Amerasekera J, Doudna JA, Jacobsen SE
• Improved genome editing by an engineered CRISPR-Cas12a.
  Nucleic acids research 2022 Ma E, Chen K, Shi H, Stahl EC, Adler B, Trinidad M, Liu J, Zhou K, Ye J, Doudna JA
• Decorating chromatin for enhanced genome editing using CRISPR-Cas9.
  Proceedings of the National Academy of Sciences of the United States of America 2022 Chen E, Lin-Shiao E, Trinidad M, Saffari Doost M, Colognori D, Doudna JA
• Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors.
  Cell 2022 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
• Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing.
  Nature microbiology 2022 Adler BA, Hessler T, Cress BF, Lahiri A, Mutalik VK, Barrangou R, Banfield J, Doudna JA
• Borgs are giant genetic elements with potential to expand metabolic capacity.
  Nature 2022 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
• Conserved features of TERT promoter duplications reveal an activation mechanism that mimics hotspot mutations in cancer.
  Nature communications 2022 Barger CJ, Suwala AK, Soczek KM, Wang AS, Kim MY, Hong C, Doudna JA, Chang SM, Phillips JJ, Solomon DA, Costello JF
• Treatment of Genetic Diseases With CRISPR Genome Editing.
  JAMA 2022 Kan MJ, Doudna JA
• CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors.
  Nucleic acids research 2022 Otoupal PB, Cress BF, Doudna JA, Schoeniger JS
• Rapid detection of SARS-CoV-2 RNA in saliva via Cas13.
  Nature biomedical engineering 2022 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, …
• Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles.
  Proceedings of the National Academy of Sciences of the United States of America 2022 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 …
• A naturally DNase-free CRISPR-Cas12c enzyme silences gene expression.
  Molecular cell 2022 Huang CJ, Adler BA, Doudna JA
• Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination.
  Nature 2022 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, …
• Structural biology of CRISPR-Cas immunity and genome editing enzymes.
  Nature reviews. Microbiology 2022 Wang JY, Pausch P, Doudna JA
• Crystal structure of an RNA/DNA strand exchange junction.
  PloS one 2022 Cofsky JC, Knott GJ, Gee CL, Doudna JA
• CRISPR-Cas9 bends and twists DNA to read its sequence.
  Nature structural & molecular biology 2022 Cofsky JC, Soczek KM, Knott GJ, Nogales E, Doudna JA
• A functional map of HIV-host interactions in primary human T cells.
  Nature communications 2022 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, …
• Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants.
  Cell 2022 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, …
• Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity.
  Molecular cell 2022 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
• CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells.
  Nucleic acids research 2022 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
• Limited Cross-Variant Immunity after Infection with the SARS-CoV-2 Omicron Variant Without Vaccination.
  medRxiv : the preprint server for health sciences 2022 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, …
• Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles.
  medRxiv : the preprint server for health sciences 2022 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
• Species- and site-specific genome editing in complex bacterial communities.
  Nature microbiology 2021 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, …
• Optimizing COVID-19 control with asymptomatic surveillance testing in a university environment.
  Epidemics 2021 Brook CE, Northrup GR, Ehrenberg AJ, IGI SARS-CoV-2 Testing Consortium, Doudna JA, Boots M
• LuNER: Multiplexed SARS-CoV-2 detection in clinical swab and wastewater samples.
  PloS one 2021 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, …
• Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles.
  Science (New York, N.Y.) 2021 Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen PY, Hayashi JM, Soczek KM, Ott M, Doudna JA
• Publisher Correction: Accelerated RNA detection using tandem CRISPR nucleases.
  Nature chemical biology 2021 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, …
• Optimizing COVID-19 control with asymptomatic surveillance testing in a university environment.
  medRxiv : the preprint server for health sciences 2021 Brook CE, Northrup GR, Ehrenberg AJ, IGI SARS-CoV-2 Testing Consortium, Doudna JA, Boots M
• Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules.
  Nature communications 2021 Shams A, Higgins SA, Fellmann C, Laughlin TG, Oakes BL, Lew R, Kim S, Lukarska M, Arnold M, Staahl BT, Doudna JA, Savage DF
• Kinetic analysis of Cas12a and Cas13a RNA-Guided nucleases for development of improved CRISPR-Based diagnostics.
  iScience 2021 Nalefski EA, Patel N, Leung PJY, Islam Z, Kooistra RM, Parikh I, Marion E, Knott GJ, Doudna JA, Le Ny AM, Madan D
• Synthesis of Multi-Protein Complexes through Charge-Directed Sequential Activation of Tyrosine Residues.
  Journal of the American Chemical Society 2021 Mogilevsky CS, Lobba MJ, Brauer DD, Marmelstein AM, Maza JC, Gleason JM, Doudna JA, Francis MB
• DNA interference states of the hypercompact CRISPR-CasΦ effector.
  Nature structural & molecular biology 2021 Pausch P, Soczek KM, Herbst DA, Tsuchida CA, Al-Shayeb B, Banfield JF, Nogales E, Doudna JA
• Accelerated RNA detection using tandem CRISPR nucleases.
  Nature chemical biology 2021 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, …
• Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples.
  PloS one 2021 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, …
• Diverse ATPase Proteins in Mobilomes Constitute a Large Potential Sink for Prokaryotic Host ATP.
  Frontiers in microbiology 2021 Shim H, Shivram H, Lei S, Doudna JA, Banfield JF
• Targeted delivery of CRISPR-Cas9 and transgenes enables complex immune cell engineering.
  Cell reports 2021 Hamilton JR, Tsuchida CA, Nguyen DN, Shy BR, McGarrigle ER, Sandoval Espinoza CR, Carr D, Blaeschke F, Marson A, Doudna JA
• Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus.
  PloS one 2021 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, …
• Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex.
  Nature communications 2021 Wang JY, Hoel CM, Al-Shayeb B, Banfield JF, Brohawn SG, Doudna JA
• The NIH Somatic Cell Genome Editing program.
  Nature 2021 Saha K, Sontheimer EJ, Brooks PJ, Dwinell MR, Gersbach CA, Liu DR, Murray SA, Tsai SQ, Wilson RC, Anderson DG, Asokan A, Banfield JF, Bankiewicz KS, Bao G, Bulte JWM, Bursac N, Campbell JM, Carlson DF…
• A CRISPR-Cas9-integrase complex generates precise DNA fragments for genome integration.
  Nucleic acids research 2021 Jakhanwal S, Cress BF, Maguin P, Lobba MJ, Marraffini LA, Doudna JA
• Rapid, point-of-care molecular diagnostics with Cas13.
  medRxiv : the preprint server for health sciences 2021 Agrawal S, Fanton A, Chandrasekaran SS, Charrez B, Escajeda AM, Son S, Mcintosh R, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, …
• Cancer-specific loss of TERT activation sensitizes glioblastoma to DNA damage.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Amen AM, Fellmann C, Soczek KM, Ren SM, Lew RJ, Knott GJ, Park JE, McKinney AM, Mancini A, Doudna JA, Costello JF
• Accelerated RNA detection using tandem CRISPR nucleases.
  medRxiv : the preprint server for health sciences 2021 Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, de León Derby MD, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI…
• Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement.
  Science advances 2021 Boyle EA, Becker WR, Bai HB, Chen JS, Doudna JA, Greenleaf WJ
• Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.
  Cell 2021 Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA
• Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples.
  medRxiv : the preprint server for health sciences 2021 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, IGI SARS-CoV-2 …
• Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems.
  Nature microbiology 2021 He C, Keren R, Whittaker ML, Farag IF, Doudna JA, Cate JHD, Banfield JF
• Human Molecular Genetics and Genomics - Important Advances and Exciting Possibilities.
  The New England journal of medicine 2021 Collins FS, Doudna JA, Lander ES, Rotimi CN
• Controlling and enhancing CRISPR systems.
  Nature chemical biology 2020 Shivram H, Cress BF, Knott GJ, Doudna JA
• IGI-LuNER: single-well multiplexed RT-qPCR test for SARS-CoV-2.
  medRxiv : the preprint server for health sciences 2020 Stahl EC, Tsuchida CA, Hamilton JR, Lin-Shiao E, McDevitt SL, Moehle EA, Witkowsky LB, Tsui CK, Pestal K, Gildea HK, McElroy M, Keller A, Sylvain I, Williams C, Hirsh A, Ciling A, Ehrenberg AJ, IGI …
• Corrigendum to "Engineering of monosized lipid-coated mesoporous silica nanoparticles for CRISPR delivery" Acta Biomaterialia (2020), 114, 358-368.
  Acta biomaterialia 2020 Noureddine A, Maestas-Olguin A, Saada EA, LaBauve AE, Agola JO, Baty KE, Howard T, Sabo JK, Espinoza CRS, Doudna JA, Schoeniger JS, Butler KS, Negrete OA, Brinker CJ, Serda RE
• Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.
  Cell 2020 Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, …
• Attachment of a 32P-phosphate to the 3' Terminus of a DNA Oligonucleotide.
  Bio-protocol 2020 Cofsky JC, Doudna JA
• Reactions to the National Academies/Royal Society Report on Heritable Human Genome Editing.
  The CRISPR journal 2020 Angrist M, Barrangou R, Baylis F, Brokowski C, Burgio G, Caplan A, Chapman CR, Church GM, Cook-Deegan R, Cwik B, Doudna JA, Evans JH, Greely HT, Hercher L, Hurlbut JB, Hynes RO, Ishii T, Kiani S, Lee …
• Massively parallel kinetic profiling of natural and engineered CRISPR nucleases.
  Nature biotechnology 2020 Jones SK, Hawkins JA, Johnson NV, Jung C, Hu K, Rybarski JR, Chen JS, Doudna JA, Press WH, Finkelstein IJ
• Site-Specific Bioconjugation through Enzyme-Catalyzed Tyrosine-Cysteine Bond Formation.
  ACS central science 2020 Lobba MJ, Fellmann C, Marmelstein AM, Maza JC, Kissman EN, Robinson SA, Staahl BT, Urnes C, Lew RJ, Mogilevsky CS, Doudna JA, Francis MB
• Chemistry of Class 1 CRISPR-Cas effectors: Binding, editing, and regulation.
  The Journal of biological chemistry 2020 Liu TY, Doudna JA
• DNA capture by a CRISPR-Cas9-guided adenine base editor.
  Science (New York, N.Y.) 2020 Lapinaite A, Knott GJ, Palumbo CM, Lin-Shiao E, Richter MF, Zhao KT, Beal PA, Liu DR, Doudna JA
• Engineering of monosized lipid-coated mesoporous silica nanoparticles for CRISPR delivery.
  Acta biomaterialia 2020 Noureddine A, Maestas-Olguin A, Saada EA, LaBauve AE, Agola JO, Baty KE, Howard T, Sabo JK, Espinoza CRS, Doudna JA, Schoeniger JS, Butler KS, Negrete OA, Brinker CJ, Serda RE
• CRISPR-CasΦ from huge phages is a hypercompact genome editor.
  Science (New York, N.Y.) 2020 Pausch P, Al-Shayeb B, Bisom-Rapp E, Tsuchida CA, Li Z, Cress BF, Knott GJ, Jacobsen SE, Banfield JF, Doudna JA
• A scoutRNA Is Required for Some Type V CRISPR-Cas Systems.
  Molecular cell 2020 Harrington LB, Ma E, Chen JS, Witte IP, Gertz D, Paez-Espino D, Al-Shayeb B, Kyrpides NC, Burstein D, Banfield JF, Doudna JA
• Author Correction: Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity.
  Nature biotechnology 2020 Richter MF, Zhao KT, Eton E, Lapinaite A, Newby GA, Thuronyi BW, Wilson C, Koblan LW, Zeng J, Bauer DE, Doudna JA, Liu DR
• CRISPR-Cas12a exploits R-loop asymmetry to form double-strand breaks.
  eLife 2020 Cofsky JC, Karandur D, Huang CJ, Witte IP, Kuriyan J, Doudna JA
• Machine learning predicts new anti-CRISPR proteins.
  Nucleic acids research 2020 Eitzinger S, Asif A, Watters KE, Iavarone AT, Knott GJ, Doudna JA, Minhas FUAA
• Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity.
  Nature biotechnology 2020 Richter MF, Zhao KT, Eton E, Lapinaite A, Newby GA, Thuronyi BW, Wilson C, Koblan LW, Zeng J, Bauer DE, Doudna JA, Liu DR
• Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Watters KE, Shivram H, Fellmann C, Lew RJ, McMahon B, Doudna JA
• Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Ivanov IE, Wright AV, Cofsky JC, Aris KDP, Doudna JA, Bryant Z
• Clades of huge phages from across Earth's ecosystems.
  Nature 2020 Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, Castelle CJ, Olm MR, Bouma-Gregson K, Amano Y, He C, Méheust R, Brooks B, Thomas A, Lavy A, Matheus-Carnevali P, Sun C, Goltsman DSA, Borton…
• The promise and challenge of therapeutic genome editing.
  Nature 2020 Doudna JA
• Knocking out barriers to engineered cell activity.
  Science (New York, N.Y.) 2020 Hamilton JR, Doudna JA
• CRISPR's unwanted anniversary.
  Science (New York, N.Y.) 2019 Doudna J
• Reply to Nathamgari et al.: Nanopore electroporation for intracellular delivery of biological macromolecules.
  Proceedings of the National Academy of Sciences of the United States of America 2019 Cao Y, Ma E, Cestellos-Blanco S, Qiu R, Su Y, Doudna JA, Yang P
• Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a.
  eLife 2019 Knott GJ, Cress BF, Liu JJ, Thornton BW, Lew RJ, Al-Shayeb B, Rosenberg DJ, Hammel M, Adler BA, Lobba MJ, Xu M, Arkin AP, Fellmann C, Doudna JA
• Target preference of Type III-A CRISPR-Cas complexes at the transcription bubble.
  Nature communications 2019 Liu TY, Liu JJ, Aditham AJ, Nogales E, Doudna JA
• Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2.
  Nature communications 2019 Thavalingam A, Cheng Z, Garcia B, Huang X, Shah M, Sun W, Wang M, Harrington L, Hwang S, Hidalgo-Reyes Y, Sontheimer EJ, Doudna J, Davidson AR, Moraes TF, Wang Y, Maxwell KL
• Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs.
  Nature communications 2019 Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T
• Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems.
  Frontiers in microbiology 2019 Chen LX, Al-Shayeb B, Méheust R, Li WJ, Doudna JA, Banfield JF
• Author Correction: CasX enzymes comprise a distinct family of RNA-guided genome editors.
  Nature 2019 Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KLM, Chuck J, Tan D, Knott GJ, Harrington LB, Al-Shayeb B, Wagner A, Brötzmann J, Staahl BT, Taylor KL, Desmarais J, Nogales E, Doudna JA
• Broad-spectrum enzymatic inhibition of CRISPR-Cas12a.
  Nature structural & molecular biology 2019 Knott GJ, Thornton BW, Lobba MJ, Liu JJ, Al-Shayeb B, Watters KE, Doudna JA
• Nontoxic nanopore electroporation for effective intracellular delivery of biological macromolecules.
  Proceedings of the National Academy of Sciences of the United States of America 2019 Cao Y, Ma E, Cestellos-Blanco S, Zhang B, Qiu R, Su Y, Doudna JA, Yang P
• Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics.
  ACS central science 2019 Ricci CG, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G
• CasX enzymes comprise a distinct family of RNA-guided genome editors.
  Nature 2019 Liu JJ, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KLM, Chuck J, Tan D, Knott GJ, Harrington LB, Al-Shayeb B, Wagner A, Brötzmann J, Staahl BT, Taylor KL, Desmarais J, Nogales E, Doudna JA
• A Functional Mini-Integrase in a Two-Protein-type V-C CRISPR System.
  Molecular cell 2019 Wright AV, Wang JY, Burstein D, Harrington LB, Paez-Espino D, Kyrpides NC, Iavarone AT, Banfield JF, Doudna JA
• Spacer Acquisition Rates Determine the Immunological Diversity of the Type II CRISPR-Cas Immune Response.
  Cell host & microbe 2019 Heler R, Wright AV, Vucelja M, Doudna JA, Marraffini LA
• CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification.
  Cell 2019 Oakes BL, Fellmann C, Rishi H, Taylor KL, Ren SM, Nadler DC, Yokoo R, Arkin AP, Doudna JA, Savage DF
• CRISPR-Cas9 genome engineering of primary CD4+ T cells for the interrogation of HIV-host factor interactions.
  Nature protocols 2019 Hultquist JF, Hiatt J, Schumann K, McGregor MJ, Roth TL, Haas P, Doudna JA, Marson A, Krogan NJ
• Temperature-Responsive Competitive Inhibition of CRISPR-Cas9.
  Molecular cell 2018 Jiang F, Liu JJ, Osuna BA, Xu M, Berry JD, Rauch BJ, Nogales E, Bondy-Denomy J, Doudna JA
• Programmed DNA destruction by miniature CRISPR-Cas14 enzymes.
  Science (New York, N.Y.) 2018 Harrington LB, Burstein D, Chen JS, Paez-Espino D, Ma E, Witte IP, Cofsky JC, Kyrpides NC, Banfield JF, Doudna JA
• A Unified Resource for Tracking Anti-CRISPR Names.
  The CRISPR journal 2018 Bondy-Denomy J, Davidson AR, Doudna JA, Fineran PC, Maxwell KL, Moineau S, Peng X, Sontheimer EJ, Wiedenheft B
• Disruption of the β1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner.
  Cancer cell 2018 Mancini A, Xavier-Magalhães A, Woods WS, Nguyen KT, Amen AM, Hayes JL, Fellmann C, Gapinske M, McKinney AM, Hong C, Jones LE, Walsh KM, Bell RJA, Doudna JA, Costa BM, Song JS, Perez-Pinera P, Costello…
• Systematic discovery of natural CRISPR-Cas12a inhibitors.
  Science (New York, N.Y.) 2018 Watters KE, Fellmann C, Bai HB, Ren SM, Doudna JA
• CRISPR-Cas guides the future of genetic engineering.
  Science (New York, N.Y.) 2018 Knott GJ, Doudna JA
• Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain.
  Quarterly reviews of biophysics 2018 Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA
• The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders.
  Cell 2018 Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, …
• RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a.
  Cell reports 2018 Tambe A, East-Seletsky A, Knott GJ, Doudna JA, O'Connell MR
• Applications of CRISPR-Cas Enzymes in Cancer Therapeutics and Detection.
  Trends in cancer 2018 Huang CH, Lee KC, Doudna JA
• Receptor-Mediated Delivery of CRISPR-Cas9 Endonuclease for Cell-Type-Specific Gene Editing.
  Journal of the American Chemical Society 2018 Rouet R, Thuma BA, Roy MD, Lintner NG, Rubitski DM, Finley JE, Wisniewska HM, Mendonsa R, Hirsh A, de Oñate L, Compte Barrón J, McLellan TJ, Bellenger J, Feng X, Varghese A, Chrunyk BA, Borzilleri K, …
• Correction: Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain.
  PLoS biology 2018 Lintner NG, McClure KF, Petersen D, Londregan AT, Piotrowski DW, Wei L, Xiao J, Bolt M, Loria PM, Maguire B, Geoghegan KF, Huang A, Rolph T, Liras S, Doudna JA, Dullea RG, Cate JHD
• Programmable RNA recognition using a CRISPR-associated Argonaute.
  Proceedings of the National Academy of Sciences of the United States of America 2018 Lapinaite A, Doudna JA, Cate JHD
• Genomes in Focus: Development and Applications of CRISPR-Cas9 Imaging Technologies.
  Angewandte Chemie (International ed. in English) 2018 Knight SC, Tjian R, Doudna JA
• Spotlight: A Conversation with Laura Kiessling and Jennifer Doudna.
  ACS chemical biology 2018 Kiessling LL, Doudna JA
• CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity.
  Science (New York, N.Y.) 2018 Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA
• RNA-dependent RNA targeting by CRISPR-Cas9.
  eLife 2018 Strutt SC, Torrez RM, Kaya E, Negrete OA, Doudna JA
• CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing.
  Nature communications 2017 Moreno-Mateos MA, Fernandez JP, Rouet R, Vejnar CE, Lane MA, Mis E, Khokha MK, Doudna JA, Giraldez AJ
• Widespread Translational Remodeling during Human Neuronal Differentiation.
  Cell reports 2017 Blair JD, Hockemeyer D, Doudna JA, Bateup HS, Floor SN
• A thermostable Cas9 with increased lifetime in human plasma.
  Nature communications 2017 Harrington LB, Paez-Espino D, Staahl BT, Chen JS, Ma E, Kyrpides NC, Doudna JA
• Nanoparticle delivery of Cas9 ribonucleoprotein and donor DNA in vivo induces homology-directed DNA repair.
  Nature biomedical engineering 2017 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, …
• Enhanced proofreading governs CRISPR-Cas9 targeting accuracy.
  Nature 2017 Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, Sternberg SH, Joung JK, Yildiz A, Doudna JA
• Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme.
  Nature structural & molecular biology 2017 Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O'Connell MR, Doudna JA
• A Broad-Spectrum Inhibitor of CRISPR-Cas9.
  Cell 2017 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
• A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9.
  Science advances 2017 Dagdas YS, Chen JS, Sternberg SH, Doudna JA, Yildiz A
• Structures of the CRISPR genome integration complex.
  Science (New York, N.Y.) 2017 Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna JA
• Disabling Cas9 by an anti-CRISPR DNA mimic.
  Science advances 2017 Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA
• Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery.
  Nucleic acids research 2017 Gaj T, Staahl BT, Rodrigues GMC, Limsirichai P, Ekman FK, Doudna JA, Schaffer DV
• DNA recognition by an RNA-guided bacterial Argonaute.
  PloS one 2017 Doxzen KW, Doudna JA
• High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Boyle EA, Andreasson JOL, Chircus LM, Sternberg SH, Wu MJ, Guegler CK, Doudna JA, Greenleaf WJ
• RNA Targeting by Functionally Orthogonal Type VI-A CRISPR-Cas Enzymes.
  Molecular cell 2017 East-Seletsky A, O'Connell MR, Burstein D, Knott GJ, Doudna JA
• Correction: RNA and DNA Targeting by a Reconstituted Thermus thermophilus Type III-A CRISPR-Cas System.
  PloS one 2017 Liu TY, Iavarone AT, Doudna JA
• CRISPR-Cas9 Structures and Mechanisms.
  Annual review of biophysics 2017 Jiang F, Doudna JA
• Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain.
  PLoS biology 2017 Lintner NG, McClure KF, Petersen D, Londregan AT, Piotrowski DW, Wei L, Xiao J, Bolt M, Loria PM, Maguire B, Geoghegan KF, Huang A, Rolph T, Liras S, Doudna JA, Dullea RG, Cate JH
• RNA-based recognition and targeting: sowing the seeds of specificity.
  Nature reviews. Molecular cell biology 2017 Gorski SA, Vogel J, Doudna JA
• Efficient genome editing in the mouse brain by local delivery of engineered Cas9 ribonucleoprotein complexes.
  Nature biotechnology 2017 Staahl BT, Benekareddy M, Coulon-Bainier C, Banfal AA, Floor SN, Sabo JK, Urnes C, Munares GA, Ghosh A, Doudna JA
• RNA and DNA Targeting by a Reconstituted Thermus thermophilus Type III-A CRISPR-Cas System.
  PloS one 2017 Liu TY, Iavarone AT, Doudna JA
• RNA Scanning of a Molecular Machine with a Built-in Ruler.
  Journal of the American Chemical Society 2016 Koh HR, Kidwell MA, Doudna J, Myong S
• Cornerstones of CRISPR-Cas in drug discovery and therapy.
  Nature reviews. Drug discovery 2016 Fellmann C, Gowen BG, Lin PC, Doudna JA, Corn JE
• Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response.
  Molecular cell 2016 Heler R, Wright AV, Vucelja M, Bikard D, Doudna JA, Marraffini LA
• New CRISPR-Cas systems from uncultivated microbes.
  Nature 2016 Burstein D, Harrington LB, Strutt SC, Probst AJ, Anantharaman K, Thomas BC, Doudna JA, Banfield JF
• A Cas9 Ribonucleoprotein Platform for Functional Genetic Studies of HIV-Host Interactions in Primary Human T Cells.
  Cell reports 2016 Hultquist JF, Schumann K, Woo JM, Manganaro L, McGregor MJ, Doudna J, Simon V, Krogan NJ, Marson A
• ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.
  Nature methods 2016 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
• Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex.
  eLife 2016 Schulze-Gahmen U, Echeverria I, Stjepanovic G, Bai Y, Lu H, Schneidman-Duhovny D, Doudna JA, Zhou Q, Sali A, Hurley JH
• Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection.
  Nature 2016 East-Seletsky A, O'Connell MR, Knight SC, Burstein D, Cate JH, Tjian R, Doudna JA
• Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9.
  Nature communications 2016 Singh D, Sternberg SH, Fei J, Doudna JA, Ha T
• Applications of CRISPR technologies in research and beyond.
  Nature biotechnology 2016 Barrangou R, Doudna JA
• Protecting genome integrity during CRISPR immune adaptation.
  Nature structural & molecular biology 2016 Wright AV, Doudna JA
• DNA Targeting by a Minimal CRISPR RNA-Guided Cascade.
  Molecular cell 2016 Hochstrasser ML, Taylor DW, Kornfeld JE, Nogales E, Doudna JA
• eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation.
  Nature 2016 Lee AS, Kranzusch PJ, Doudna JA, Cate JH
• Reconstitution of selective HIV-1 RNA packaging in vitro by membrane-bound Gag assemblies.
  eLife 2016 Carlson LA, Bai Y, Keane SC, Doudna JA, Hurley JH
• CRISPR Immunological Memory Requires a Host Factor for Specificity.
  Molecular cell 2016 Nuñez JK, Bai L, Harrington LB, Hinder TL, Doudna JA
• Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress.
  Oncotarget 2016 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, …
• Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch.
  Nature biotechnology 2016 Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna JA, Savage DF
• Nucleosome breathing and remodeling constrain CRISPR-Cas9 function.
  eLife 2016 Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ, Almeida R
• A bacterial Argonaute with noncanonical guide RNA specificity.
  Proceedings of the National Academy of Sciences of the United States of America 2016 Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC, Kranzusch PJ, Doudna JA
• Programmable RNA Tracking in Live Cells with CRISPR/Cas9.
  Cell 2016 Nelles DA, Fang MY, O'Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW
• Voices of biotech.
  Nature biotechnology 2016 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, …
• Chemical and Biophysical Modulation of Cas9 for Tunable Genome Engineering.
  ACS chemical biology 2016 Nuñez JK, Harrington LB, Doudna JA
• Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering.
  Cell 2016 Wright AV, Nuñez JK, Doudna JA
• Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage.
  Science (New York, N.Y.) 2016 Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K, Thompson AJ, Nogales E, Doudna JA
• Tunable protein synthesis by transcript isoforms in human cells.
  eLife 2016 Floor SN, Doudna JA
• Analog sensitive chemical inhibition of the DEAD-box protein DDX3.
  Protein science : a publication of the Protein Society 2015 Floor SN, Barkovich KJ, Condon KJ, Shokat KM, Doudna JA
• Genome-editing revolution: My whirlwind year with CRISPR.
  Nature 2015 Doudna J
• Genome editing: the end of the beginning.
  Genome biology 2015 Doudna JA, Gersbach CA
• Get in LINE: Competition for Newly Minted Retrotransposon Proteins at the Ribosome.
  Molecular cell 2015 Floor SN, Doudna JA
• Perspective: Embryo editing needs scrutiny.
  Nature 2015 Doudna J
• Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3.
  The Journal of biological chemistry 2015 Floor SN, Condon KJ, Sharma D, Jankowsky E, Doudna JA
• Dynamics of CRISPR-Cas9 genome interrogation in living cells.
  Science (New York, N.Y.) 2015 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
• Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes.
  Molecular cell 2015 Ma E, Harrington LB, O'Connell MR, Zhou K, Doudna JA
• Surveillance and Processing of Foreign DNA by the Escherichia coli CRISPR-Cas System.
  Cell 2015 Redding S, Sternberg SH, Marshall M, Gibb B, Bhat P, Guegler CK, Wiedenheft B, Doudna JA, Greene EC
• Conformational control of DNA target cleavage by CRISPR-Cas9.
  Nature 2015 Sternberg SH, LaFrance B, Kaplan M, Doudna JA
• Foreign DNA capture during CRISPR-Cas adaptive immunity.
  Nature 2015 Nuñez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA
• Ancient Origin of cGAS-STING Reveals Mechanism of Universal 2',3' cGAMP Signaling.
  Molecular cell 2015 Kranzusch PJ, Wilson SC, Lee AS, Berger JM, Doudna JA, Vance RE
• Generation of knock-in primary human T cells using Cas9 ribonucleoproteins.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Schumann K, Lin S, Boyer E, Simeonov DR, Subramaniam M, Gate RE, Haliburton GE, Ye CJ, Bluestone JA, Doudna JA, Marson A
• STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition.
  Science (New York, N.Y.) 2015 Jiang F, Zhou K, Ma L, Gressel S, Doudna JA
• Expanding the Biologist's Toolkit with CRISPR-Cas9.
  Molecular cell 2015 Sternberg SH, Doudna JA
• CRISPR germline engineering--the community speaks.
  Nature biotechnology 2015 Bosley KS, Botchan M, Bredenoord AL, Carroll D, Charo RA, Charpentier E, Cohen R, Corn J, Doudna J, Feng G, Greely HT, Isasi R, Ji W, Kim JS, Knoppers B, Lanphier E, Li J, Lovell-Badge R, Martin GS, …
• Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning.
  Science (New York, N.Y.) 2015 Taylor DW, Zhu Y, Staals RH, Kornfeld JE, Shinkai A, van der Oost J, Nogales E, Doudna JA
• Biotechnology. A prudent path forward for genomic engineering and germline gene modification.
  Science (New York, N.Y.) 2015 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
• Genomic engineering and the future of medicine.
  JAMA 2015 Doudna JA
• The structural biology of CRISPR-Cas systems.
  Current opinion in structural biology 2015 Jiang F, Doudna JA
• Rational design of a split-Cas9 enzyme complex.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Wright AV, Sternberg SH, Taylor DW, Staahl BT, Bardales JA, Kornfeld JE, Doudna JA
• Integrase-mediated spacer acquisition during CRISPR-Cas adaptive immunity.
  Nature 2015 Nuñez JK, Lee AS, Engelman A, Doudna JA
• Dicer-TRBP complex formation ensures accurate mammalian microRNA biogenesis.
  Molecular cell 2014 Wilson RC, Tambe A, Kidwell MA, Noland CL, Schneider CP, Doudna JA
• Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery.
  eLife 2014 Lin S, Staahl BT, Alla RK, Doudna JA
• Genome editing. The new frontier of genome engineering with CRISPR-Cas9.
  Science (New York, N.Y.) 2014 Doudna JA, Charpentier E
• Cutting it close: CRISPR-associated endoribonuclease structure and function.
  Trends in biochemical sciences 2014 Hochstrasser ML, Doudna JA
• RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus.
  Molecular cell 2014 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, …
• New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
  Nucleic acids research 2014 Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS
• Programmable RNA recognition and cleavage by CRISPR/Cas9.
  Nature 2014 O'Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA
• RNA-guided assembly of Rev-RRE nuclear export complexes.
  eLife 2014 Bai Y, Tambe A, Zhou K, Doudna JA
• Evolutionarily conserved roles of the dicer helicase domain in regulating RNA interference processing.
  The Journal of biological chemistry 2014 Kidwell MA, Chan JM, Doudna JA
• Structure-guided reprogramming of human cGAS dinucleotide linkage specificity.
  Cell 2014 Kranzusch PJ, Lee ASY, Wilson SC, Solovykh MS, Vance RE, Berger JM, Doudna JA
• Insights into RNA structure and function from genome-wide studies.
  Nature reviews. Genetics 2014 Mortimer SA, Kidwell MA, Doudna JA
• Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity.
  Nature structural & molecular biology 2014 Nuñez JK, Kranzusch PJ, Noeske J, Wright AV, Davies CW, Doudna JA
• CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Hochstrasser ML, Taylor DW, Bhat P, Guegler CK, Sternberg SH, Nogales E, Doudna JA
• Structures of Cas9 endonucleases reveal RNA-mediated conformational activation.
  Science (New York, N.Y.) 2014 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
• DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.
  Nature 2014 Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA
• Methods in Enzymology. The use of CRISPR/Cas9, ZFNs, and TALENs in generating site-specific genome alterations. Preface.
  Methods in enzymology 2014 Doudna JA, Sontheimer EJ
• Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases.
  Nucleic acids research 2013 Niewoehner O, Jinek M, Doudna JA
• Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus.
  Molecular cell 2013 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, …
• Enhancement of hepatitis C viral RNA abundance by precursor miR-122 molecules.
  RNA (New York, N.Y.) 2013 Cox EM, Sagan SM, Mortimer SA, Doudna JA, Sarnow P
• High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity.
  Nature biotechnology 2013 Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR
• Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions.
  Genetics 2013 Lo TW, Pickle CS, Lin S, Ralston EJ, Gurling M, Schartner CM, Bian Q, Doudna JA, Meyer BJ
• CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.
  Cell 2013 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
• Activating silent argonautes.
  Nature structural & molecular biology 2013 Kidwell MA, Doudna JA
• Hepatitis C virus 3'UTR regulates viral translation through direct interactions with the host translation machinery.
  Nucleic acids research 2013 Bai Y, Zhou K, Doudna JA
• Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation.
  Nucleic acids research 2013 Sun C, Querol-Audí J, Mortimer SA, Arias-Palomo E, Doudna JA, Nogales E, Cate JH
• Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity.
  Cell reports 2013 Kranzusch PJ, Lee AS, Berger JM, Doudna JA
• Differential roles of human Dicer-binding proteins TRBP and PACT in small RNA processing.
  Nucleic acids research 2013 Lee HY, Zhou K, Smith AM, Noland CL, Doudna JA
• Substrate-specific structural rearrangements of human Dicer.
  Nature structural & molecular biology 2013 Taylor DW, Ma E, Shigematsu H, Cianfrocco MA, Noland CL, Nagayama K, Nogales E, Doudna JA, Wang HW
• Multiple sensors ensure guide strand selection in human RNAi pathways.
  RNA (New York, N.Y.) 2013 Noland CL, Doudna JA
• RNA-protein analysis using a conditional CRISPR nuclease.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Lee HY, Haurwitz RE, Apffel A, Zhou K, Smart B, Wenger CD, Laderman S, Bruhn L, Doudna JA
• Biotechnology: Rewriting a genome.
  Nature 2013 Charpentier E, Doudna JA
• Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.
  Cell 2013 Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA
• Unconventional miR-122 binding stabilizes the HCV genome by forming a trimolecular RNA structure.
  Nucleic acids research 2013 Mortimer SA, Doudna JA
• RNA-programmed genome editing in human cells.
  eLife 2013 Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J
• Molecular mechanisms of RNA interference.
  Annual review of biophysics 2013 Wilson RC, Doudna JA
• ATP-independent diffusion of double-stranded RNA binding proteins.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Koh HR, Kidwell MA, Ragunathan K, Doudna JA, Myong S
• TRBP alters human precursor microRNA processing in vitro.
  RNA (New York, N.Y.) 2012 Lee HY, Doudna JA
• RNA processing enables predictable programming of gene expression.
  Nature biotechnology 2012 Qi L, Haurwitz RE, Shao W, Doudna JA, Arkin AP
• 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.
  Molecular & cellular proteomics : MCP 2012 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
• A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
  Science (New York, N.Y.) 2012 Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E
• Coordinated activities of human dicer domains in regulatory RNA processing.
  Journal of molecular biology 2012 Ma E, Zhou K, Kidwell MA, Doudna JA
• Biochemistry. Guided tour to the heart of RISC.
  Science (New York, N.Y.) 2012 Kaya E, Doudna JA
• Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA.
  The EMBO journal 2012 Haurwitz RE, Sternberg SH, Doudna JA
• Mechanism of foreign DNA selection in a bacterial adaptive immune system.
  Molecular cell 2012 Sashital DG, Wiedenheft B, Doudna JA
• Mechanism of substrate selection by a highly specific CRISPR endoribonuclease.
  RNA (New York, N.Y.) 2012 Sternberg SH, Haurwitz RE, Doudna JA
• RNA-guided genetic silencing systems in bacteria and archaea.
  Nature 2012 Wiedenheft B, Sternberg SH, Doudna JA
• Reconsidering movement of eukaryotic mRNAs between polysomes and P bodies.
  Molecular cell 2011 Arribere JA, Doudna JA, Gilbert WV
• Functional reconstitution of human eukaryotic translation initiation factor 3 (eIF3).
  Proceedings of the National Academy of Sciences of the United States of America 2011 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
• Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers.
  Journal of virology 2011 Mehle A, Dugan VG, Taubenberger JK, Doudna JA
• Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning.
  Structure (London, England : 1993) 2011 Berry KE, Waghray S, Mortimer SA, Bai Y, Doudna JA
• Structures of the RNA-guided surveillance complex from a bacterial immune system.
  Nature 2011 Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJJ, van der Oost J, Doudna JA, Nogales E
• siRNA repositioning for guide strand selection by human Dicer complexes.
  Molecular cell 2011 Noland CL, Ma E, Doudna JA
• Modeling and automation of sequencing-based characterization of RNA structure.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L
• Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).
  Proceedings of the National Academy of Sciences of the United States of America 2011 Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP
• An RNA-induced conformational change required for CRISPR RNA cleavage by the endoribonuclease Cse3.
  Nature structural & molecular biology 2011 Sashital DG, Jinek M, Doudna JA
• RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions.
  Proceedings of the National Academy of Sciences of the United States of America 2011 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
• Structural basis for CRISPR RNA-guided DNA recognition by Cascade.
  Nature structural & molecular biology 2011 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, …
• Coupled 5' nucleotide recognition and processivity in Xrn1-mediated mRNA decay.
  Molecular cell 2011 Jinek M, Coyle SM, Doudna JA
• The crystal structure of the signal recognition particle in complex with its receptor.
  Science (New York, N.Y.) 2011 Ataide SF, Schmitz N, Shen K, Ke A, Shan SO, Doudna JA, Ban N
• Optimized high-throughput screen for hepatitis C virus translation inhibitors.
  Journal of biomolecular screening 2011 Berry KE, Peng B, Koditek D, Beeman D, Pagratis N, Perry JK, Parrish J, Zhong W, Doudna JA, Shih IH
• Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity.
  Biochemistry 2010 Weeks AM, Coyle SM, Jinek M, Doudna JA, Chang MC
• Substrate-specific kinetics of Dicer-catalyzed RNA processing.
  Journal of molecular biology 2010 Chakravarthy S, Sternberg SH, Kellenberger CA, Doudna JA
• Sequence- and structure-specific RNA processing by a CRISPR endonuclease.
  Science (New York, N.Y.) 2010 Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA
• The HCV IRES pseudoknot positions the initiation codon on the 40S ribosomal subunit.
  RNA (New York, N.Y.) 2010 Berry KE, Waghray S, Doudna JA
• Functional overlap between eIF4G isoforms in Saccharomyces cerevisiae.
  PloS one 2010 Clarkson BK, Gilbert WV, Doudna JA
• A host of factors regulating influenza virus replication.
  Viruses 2010 Mehle A, Doudna JA
• Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation.
  Nature structural & molecular biology 2010 Jinek M, Fabian MR, Coyle SM, Sonenberg N, Doudna JA
• Structural insights into RNA interference.
  Current opinion in structural biology 2010 Sashital DG, Doudna JA
• Adaptive strategies of the influenza virus polymerase for replication in humans.
  Proceedings of the National Academy of Sciences of the United States of America 2009 Mehle A, Doudna JA
• Structural insights into RNA processing by the human RISC-loading complex.
  Nature structural & molecular biology 2009 Wang HW, Noland C, Siridechadilok B, Taylor DW, Ma E, Felderer K, Doudna JA, Nogales E
• Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation.
  Molecular cell 2009 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
• Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense.
  Structure (London, England : 1993) 2009 Wiedenheft B, Zhou K, Jinek M, Coyle SM, Ma W, Doudna JA
• The pathway of hepatitis C virus mRNA recruitment to the human ribosome.
  Nature structural & molecular biology 2009 Fraser CS, Hershey JW, Doudna JA
• A three-dimensional view of the molecular machinery of RNA interference.
  Nature 2009 Jinek M, Doudna JA
• dsRNA with 5' overhangs contributes to endogenous and antiviral RNA silencing pathways in plants.
  The EMBO journal 2009 Fukunaga R, Doudna JA
• Direct link between RACK1 function and localization at the ribosome in vivo.
  Molecular and cellular biology 2008 Coyle SM, Gilbert WV, Doudna JA
• An inhibitory activity in human cells restricts the function of an avian-like influenza virus polymerase.
  Cell host & microbe 2008 Mehle A, Doudna JA
• Mass spectrometry reveals modularity and a complete subunit interaction map of the eukaryotic translation factor eIF3.
  Proceedings of the National Academy of Sciences of the United States of America 2008 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
• Nucleic acids and their protein partners.
  Current opinion in structural biology 2008 Puglisi JD, Doudna JA
• Autoinhibition of human dicer by its internal helicase domain.
  Journal of molecular biology 2008 Ma E, MacRae IJ, Kirsch JF, Doudna JA
• In vitro reconstitution of the human RISC-loading complex.
  Proceedings of the National Academy of Sciences of the United States of America 2008 MacRae IJ, Ma E, Zhou M, Robinson CV, Doudna JA
• Structural determinants of RNA recognition and cleavage by Dicer.
  Nature structural & molecular biology 2007 MacRae IJ, Zhou K, Doudna JA
• Cap-independent translation is required for starvation-induced differentiation in yeast.
  Science (New York, N.Y.) 2007 Gilbert WV, Zhou K, Butler TK, Doudna JA
• An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer.
  Acta crystallographica. Section D, Biological crystallography 2007 MacRae IJ, Doudna JA
• eIF3j is located in the decoding center of the human 40S ribosomal subunit.
  Molecular cell 2007 Fraser CS, Berry KE, Hershey JW, Doudna JA
• Quantitative studies of ribosome conformational dynamics.
  Quarterly reviews of biophysics 2007 Fraser CS, Doudna JA
• A higher degree of difficulty.
  ACS chemical biology 2007 Kiessling LL, Doudna JA, Johnsson K, Mapp AK, Marletta MA, Seeberger PH, Williamson JR, Wedde SG
• Structural roles of monovalent cations in the HDV ribozyme.
  Structure (London, England : 1993) 2007 Ke A, Ding F, Batchelor JD, Doudna JA
• Structural characterization of the human eukaryotic initiation factor 3 protein complex by mass spectrometry.
  Molecular & cellular proteomics : MCP 2007 Damoc E, Fraser CS, Zhou M, Videler H, Mayeur GL, Hershey JW, Doudna JA, Robinson CV, Leary JA
• Ribonuclease revisited: structural insights into ribonuclease III family enzymes.
  Current opinion in structural biology 2006 MacRae IJ, Doudna JA
• SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting.
  RNA (New York, N.Y.) 2006 Siu FY, Spanggord RJ, Doudna JA
• Structural and mechanistic insights into hepatitis C viral translation initiation.
  Nature reviews. Microbiology 2006 Fraser CS, Doudna JA
• A fast and efficient procedure to produce scFvs specific for large macromolecular complexes.
  Journal of immunological methods 2006 Wu S, Ke A, Doudna JA
• RNAs regulate biology.
  ACS chemical biology 2006 Green R, Doudna JA
• Distinct contributions of KH domains to substrate binding affinity of Drosophila P-element somatic inhibitor protein.
  RNA (New York, N.Y.) 2006 Chmiel NH, Rio DC, Doudna JA
• Structural basis for double-stranded RNA processing by Dicer.
  Science (New York, N.Y.) 2006 Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA
• Structure of Dicer and mechanistic implications for RNAi.
  Cold Spring Harbor symposia on quantitative biology 2006 Macrae IJ, Li F, Zhou K, Cande WZ, Doudna JA
• GTP-dependent formation of a ribonucleoprotein subcomplex required for ribosome biogenesis.
  Journal of molecular biology 2005 Karbstein K, Doudna JA
• Structural roles for human translation factor eIF3 in initiation of protein synthesis.
  Science (New York, N.Y.) 2005 Siridechadilok B, Fraser CS, Hall RJ, Doudna JA, Nogales E
• An essential GTPase promotes assembly of preribosomal RNA processing complexes.
  Molecular cell 2005 Karbstein K, Jonas S, Doudna JA
• RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle.
  Nature structural & molecular biology 2005 Spanggord RJ, Siu F, Ke A, Doudna JA
• Chemical biology at the crossroads of molecular structure and mechanism.
  Nature chemical biology 2005 Doudna JA
• Identification and analysis of U5 snRNA variants in Drosophila.
  RNA (New York, N.Y.) 2005 Chen L, Lullo DJ, Ma E, Celniker SE, Rio DC, Doudna JA
• Ro's role in RNA reconnaissance.
  Cell 2005 MacRae IJ, Doudna JA
• Mass spectrometric analysis of the human 40S ribosomal subunit: native and HCV IRES-bound complexes.
  Protein science : a publication of the Protein Society 2005 Yu Y, Ji H, Doudna JA, Leary JA
• Ribozyme catalysis: not different, just worse.
  Nature structural & molecular biology 2005 Doudna JA, Lorsch JR
• Protein-nucleic acid interactions: unlocking mysteries old and new.
  Current opinion in structural biology 2005 Aggarwal AK, Doudna JA
• Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA.
  Proceedings of the National Academy of Sciences of the United States of America 2004 Ji H, Fraser CS, Yu Y, Leary J, Doudna JA
• Crystallization of RNA and RNA-protein complexes.
  Methods (San Diego, Calif.) 2004 Ke A, Doudna JA
• Assembly of an active group II intron-maturase complex by protein dimerization.
  Biochemistry 2004 Rambo RP, Doudna JA
• A conformational switch controls hepatitis delta virus ribozyme catalysis.
  Nature 2004 Ke A, Zhou K, Ding F, Cate JH, Doudna JA
• Conserved but nonessential interaction of SRP RNA with translation factor EF-G.
  RNA (New York, N.Y.) 2004 Sagar MB, Lucast L, Doudna JA
• Distinct sites of phosphorothioate substitution interfere with folding and splicing of the Anabaena group I intron.
  Nucleic acids research 2004 Lupták A, Doudna JA
• RNA: primed for packing?
  Chemistry & biology 2004 Karbstein K, Doudna JA
• Structural insights into the signal recognition particle.
  Annual review of biochemistry 2004 Doudna JA, Batey RT
• 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.
  The Journal of biological chemistry 2003 Fraser CS, Lee JY, Mayeur GL, Bushell M, Doudna JA, Hershey JW
• Protein-nucleic acid interactions.
  Current opinion in structural biology 2003 Aggarwal AK, Doudna JA
• Specificity of RNA-RNA helix recognition.
  Proceedings of the National Academy of Sciences of the United States of America 2002 Battle DJ, Doudna JA
• The chemical repertoire of natural ribozymes.
  Nature 2002 Doudna JA, Cech TR
• Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation.
  Nature structural biology 2002 Kieft JS, Zhou K, Grech A, Jubin R, Doudna JA
• Structure and function of the eukaryotic ribosome: the next frontier.
  Cell 2002 Doudna JA, Rath VL
• Structural insights into group II intron catalysis and branch-site selection.
  Science (New York, N.Y.) 2002 Zhang L, Doudna JA
• Creative catalysis: pieces of the RNA world jigsaw.
  Trends in biochemical sciences 2001 Murray JM, Doudna JA
• A universal mode of helix packing in RNA.
  Nature structural biology 2001 Doherty EA, Batey RT, Masquida B, Doudna JA
• Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle.
  Journal of molecular biology 2001 Batey RT, Sagar MB, Doudna JA
• Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit.
  Science (New York, N.Y.) 2001 Spahn CM, Kieft JS, Grassucci RA, Penczek PA, Zhou K, Doudna JA, Frank J
• Large-scale purification of a stable form of recombinant tobacco etch virus protease.
  BioTechniques 2001 Lucast LJ, Batey RT, Doudna JA
• Mechanism of ribosome recruitment by hepatitis C IRES RNA.
  RNA (New York, N.Y.) 2001 Kieft JS, Zhou K, Jubin R, Doudna JA
• Mechanisms of internal ribosome entry in translation initiation.
  Cold Spring Harbor symposia on quantitative biology 2001 Kieft JS, Grech A, Adams P, Doudna JA
• Ribozyme structures and mechanisms.
  Annual review of biophysics and biomolecular structure 2001 Doherty EA, Doudna JA
• A phosphoramidate substrate analog is a competitive inhibitor of the Tetrahymena group I ribozyme.
  Chemistry & biology 2000 Hanna RL, Gryaznov SM, Doudna JA
• Hepatitis C virus internal ribosome entry site (IRES) stem loop IIId contains a phylogenetically conserved GGG triplet essential for translation and IRES folding.
  Journal of virology 2000 Jubin R, Vantuno NE, Kieft JS, Murray MG, Doudna JA, Lau JY, Baroudy BM
• Structural genomics of RNA.
  Nature structural biology 2000 Doudna JA
• Metal ions in ribozyme folding and catalysis.
  Current opinion in chemical biology 2000 Hanna R, Doudna JA
• The P5abc peripheral element facilitates preorganization of the tetrahymena group I ribozyme for catalysis.
  Biochemistry 2000 Engelhardt MA, Doherty EA, Knitt DS, Doudna JA, Herschlag D
• Crystal structure of the ribonucleoprotein core of the signal recognition particle.
  Science (New York, N.Y.) 2000 Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA
• Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module.
  Journal of molecular biology 2000 Ferré-D'Amaré AR, Doudna JA
• Ribozyme structures and mechanisms.
  Annual review of biochemistry 2000 Doherty EA, Doudna JA
• Solving large RNA structures by X-ray crystallography.
  Methods in enzymology 2000 Cate JH, Doudna JA
• Cashing in on crystals.
  Current biology : CB 1999 Doudna JA
• The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold.
  Journal of molecular biology 1999 Kieft JS, Zhou K, Jubin R, Murray MG, Lau JY, Doudna JA
• A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes.
  RNA (New York, N.Y.) 1999 Wadkins TS, Perrotta AT, Ferré-D'Amaré AR, Doudna JA, Been MD
• Assembly of an exceptionally stable RNA tertiary interface in a group I ribozyme.
  Biochemistry 1999 Doherty EA, Herschlag D, Doudna JA
• RNA folds: insights from recent crystal structures.
  Annual review of biophysics and biomolecular structure 1999 Ferré-D'Amaré AR, Doudna JA
• A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor.
  Nature structural biology 1998 Basu S, Rambo RP, Strauss-Soukup J, Cate JH, Ferré-D'Amaré AR, Strobel SA, Doudna JA
• Crystal structure of a hepatitis delta virus ribozyme.
  Nature 1998 Ferré-D'Amaré AR, Zhou K, Doudna JA
• Ribozymes: the hammerhead swings into action.
  Current biology : CB 1998 Doudna JA
• A general module for RNA crystallization.
  Journal of molecular biology 1998 Ferré-D'Amaré AR, Zhou K, Doudna JA
• The parallel universe of RNA folding.
  Nature structural biology 1998 Batey RT, Doudna JA
• A magnesium ion core at the heart of a ribozyme domain.
  Nature structural biology 1997 Cate JH, Hanna RL, Doudna JA
• RNA seeing double: close-packing of helices in RNA tertiary structure.
  Trends in biochemical sciences 1997 Strobel SA, Doudna JA
• RNA structure: crystal clear?
  Current opinion in structural biology 1997 Doudna JA, Cate JH
• The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core.
  Biochemistry 1997 Doherty EA, Doudna JA
• A sparse matrix approach to crystallizing ribozymes and RNA motifs.
  Methods in molecular biology (Clifton, N.J.) 1997 Cate JH, Doudna JA
• Emerging themes in RNA folding.
  Folding & design 1997 Doudna JA, Doherty EA
• Establishing suitability of RNA preparations for crystallization. Determination of polydispersity.
  Methods in molecular biology (Clifton, N.J.) 1997 Ferré-d'Amaré AR, Doudna JA
• Preparation of homogeneous ribozyme RNA for crystallization.
  Methods in molecular biology (Clifton, N.J.) 1997 Doudna JA
• Metal-binding sites in the major groove of a large ribozyme domain.
  Structure (London, England : 1993) 1996 Cate JH, Doudna JA
• Crystal structure of a group I ribozyme domain: principles of RNA packing.
  Science (New York, N.Y.) 1996 Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR, Doudna JA
• RNA tertiary structure mediation by adenosine platforms.
  Science (New York, N.Y.) 1996 Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna JA
• Use of cis- and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed RNA.
  Nucleic acids research 1996 Ferré-D'Amaré AR, Doudna JA
• Hammerhead ribozyme structure: U-turn for RNA structural biology.
  Structure (London, England : 1993) 1995 Doudna JA
• Selection of an RNA molecule that mimics a major autoantigenic epitope of human insulin receptor.
  Proceedings of the National Academy of Sciences of the United States of America 1995 Doudna JA, Cech TR, Sullenger BA
• Self-assembly of a group I intron active site from its component tertiary structural domains.
  RNA (New York, N.Y.) 1995 Doudna JA, Cech TR
• Hammering out the shape of a ribozyme.
  Structure (London, England : 1993) 1994 Doudna JA
• Crystallization of ribozymes and small RNA motifs by a sparse matrix approach.
  Proceedings of the National Academy of Sciences of the United States of America 1993 Doudna JA, Grosshans C, Gooding A, Kundrot CE
• Ribozyme-catalyzed primer extension by trinucleotides: a model for the RNA-catalyzed replication of RNA.
  Biochemistry 1993 Doudna JA, Usman N, Szostak JW
• Template-directed primer extension catalyzed by the Tetrahymena ribozyme.
  Molecular and cellular biology 1991 Bartel DP, Doudna JA, Usman N, Szostak JW
• A multisubunit ribozyme that is a catalyst of and template for complementary strand RNA synthesis.
  Science (New York, N.Y.) 1991 Doudna JA, Couture S, Szostak JW
• Chemical synthesis of oligoribonucleotides containing 2-aminopurine: substrates for the investigation of ribozyme function.
  The Journal of organic chemistry 1990 Doudna JA, Szostak JW, Rich A, Usman N
• Mutational analysis of conserved nucleotides in a self-splicing group I intron.
  Journal of molecular biology 1990 Couture S, Ellington AD, Gerber AS, Cherry JM, Doudna JA, Green R, Hanna M, Pace U, Rajagopal J, Szostak JW
• Miniribozymes, small derivatives of the sunY intron, are catalytically active.
  Molecular and cellular biology 1989 Doudna JA, Szostak JW
• RNA structure, not sequence, determines the 5' splice-site specificity of a group I intron.
  Proceedings of the National Academy of Sciences of the United States of America 1989 Doudna JA, Cormack BP, Szostak JW
• RNA-catalysed synthesis of complementary-strand RNA.
  Nature 1989 Doudna JA, Szostak JW
• Stereochemical course of catalysis by the Tetrahymena ribozyme.
  Science (New York, N.Y.) 1989 Rajagopal J, Doudna JA, Szostak JW
• Genetic dissection of an RNA enzyme.
  Cold Spring Harbor symposia on quantitative biology 1987 Doudna JA, Gerber AS, Cherry JM, Szostak JW