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Ailong Ke, Ph.D. - Publications

Affiliations: 
2005- Molecular Biology and Genetics Cornell University, Ithaca, NY, United States 
Area:
RNA biology
Website:
https://mbg.cornell.edu/people/ailong-ke
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61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Hu C, Myers MT, Zhou X, Hou Z, Lozen ML, Nam KH, Zhang Y, Ke A. Exploiting activation and inactivation mechanisms in type I-C CRISPR-Cas3 for genome-editing applications. Molecular Cell. PMID 38242128 DOI: 10.1016/j.molcel.2023.12.034  0.332
2022 Hu C, Ke A. Reconstitution and biochemical characterization of the RNA-guided helicase-nuclease protein Cas3 from type I-A CRISPR-Cas system. Methods in Enzymology. 673: 405-424. PMID 35965014 DOI: 10.1016/bs.mie.2022.03.059  0.33
2022 Hu C, Ni D, Nam KH, Majumdar S, McLean J, Stahlberg H, Terns MP, Ke A. Allosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools. Molecular Cell. PMID 35835111 DOI: 10.1016/j.molcel.2022.06.007  0.315
2021 Lu C, Cai R, Grigg JC, Ke A. Using tRNA Scaffold to Assist RNA Crystallization. Methods in Molecular Biology (Clifton, N.J.). 2323: 39-47. PMID 34086272 DOI: 10.1007/978-1-0716-1499-0_4  0.739
2020 Budhathoki JB, Xiao Y, Schuler G, Hu C, Cheng A, Ding F, Ke A. Real-time observation of CRISPR spacer acquisition by Cas1-Cas2 integrase. Nature Structural & Molecular Biology. PMID 32367067 DOI: 10.1038/S41594-020-0415-7  0.334
2019 Battaglia RA, Grigg JC, Ke A. Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators. Nature Structural & Molecular Biology. PMID 31740853 DOI: 10.1038/S41594-019-0327-6  0.427
2019 Suddala KC, Price IR, Dandpat SS, Janeček M, Kührová P, Šponer J, Banáš P, Ke A, Walter NG. Local-to-global signal transduction at the core of a Mn sensing riboswitch. Nature Communications. 10: 4304. PMID 31541094 DOI: 10.1038/S41467-019-12230-5  0.416
2019 Cai R, Price IR, Ding F, Wu F, Chen T, Zhang Y, Liu G, Jardine PJ, Lu C, Ke A. ATP/ADP modulates gp16-pRNA conformational change in the Phi29 DNA packaging motor. Nucleic Acids Research. PMID 31396619 DOI: 10.1093/Nar/Gkz692  0.697
2019 Dolan AE, Hou Z, Xiao Y, Gramelspacher MJ, Heo J, Howden SE, Freddolino PL, Ke A, Zhang Y. Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas. Molecular Cell. PMID 30975459 DOI: 10.1016/J.Molcel.2019.03.014  0.371
2019 Dillard KE, Schaub JM, Brown MW, Saifuddin FA, Xiao Y, Hernandez E, Dahlhauser SD, Anslyn EV, Ke A, Finkelstein IJ. Sortase-mediated fluorescent labeling of CRISPR complexes. Methods in Enzymology. 616: 43-59. PMID 30691654 DOI: 10.1016/Bs.Mie.2018.10.031  0.313
2019 Xiao Y, Ke A. Reconstitution and biochemical characterization of ribonucleoprotein complexes in Type I-E CRISPR-Cas systems. Methods in Enzymology. 616: 27-41. PMID 30691647 DOI: 10.1016/Bs.Mie.2018.11.003  0.398
2018 Dillard KE, Brown MW, Johnson NV, Xiao Y, Dolan A, Hernandez E, Dahlhauser SD, Kim Y, Myler LR, Anslyn EV, Ke A, Finkelstein IJ. Assembly and Translocation of a CRISPR-Cas Primed Acquisition Complex. Cell. PMID 30343903 DOI: 10.1016/J.Cell.2018.09.039  0.38
2018 Xiao Y, Luo M, Dolan AE, Liao M, Ke A. Structure basis for RNA-guided DNA degradation by Cascade and Cas3. Science (New York, N.Y.). PMID 29880725 DOI: 10.1126/Science.Aat0839  0.481
2018 Battaglia RA, Ke A. Guanidine-sensing riboswitches: How do they work and what do they regulate? Wiley Interdisciplinary Reviews. Rna. e1482. PMID 29697203 DOI: 10.1002/Wrna.1482  0.487
2018 Battaglia RA, Ke A. Acting in tandem. Elife. 7. PMID 29683426 DOI: 10.7554/Elife.36489  0.439
2017 Xiao Y, Ng S, Nam KH, Ke A. How type II CRISPR-Cas establish immunity through Cas1-Cas2-mediated spacer integration. Nature. PMID 28869593 DOI: 10.1038/Nature24020  0.42
2017 Xiao Y, Luo M, Hayes RP, Kim J, Ng S, Ding F, Liao M, Ke A. Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System. Cell. 170: 48-60.e11. PMID 28666122 DOI: 10.1016/J.Cell.2017.06.012  0.397
2017 Jung C, Hawkins JA, Jones SK, Xiao Y, Rybarski JR, Dillard KE, Hussmann J, Saifuddin FA, Savran CA, Ellington AD, Ke A, Press WH, Finkelstein IJ. Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips. Cell. 170: 35-47.e13. PMID 28666121 DOI: 10.1016/J.Cell.2017.05.044  0.37
2017 Hameed U, Price I, Ikram-Ul-Haq, Ke A, Wilson DB, Mirza O. Functional characterization and crystal structure of thermostable amylase from Thermotoga petrophila, reveals high thermostability and an unusual form of dimerization. Biochimica Et Biophysica Acta. PMID 28648523 DOI: 10.1016/J.Bbapap.2017.06.015  0.343
2017 Battaglia RA, Price IR, Ke A. Structural Basis for Guanidine Sensing by the ykkC Family of Riboswitches. Rna (New York, N.Y.). PMID 28096518 DOI: 10.1261/Rna.060186.116  0.395
2016 Xiao Y, Ke A. PIWI Takes a Giant Step. Cell. 167: 310-312. PMID 27716504 DOI: 10.1016/J.Cell.2016.09.043  0.419
2016 Hayes RP, Xiao Y, Ding F, van Erp PB, Rajashankar K, Bailey S, Wiedenheft B, Ke A. Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli. Nature. PMID 26863189 DOI: 10.1038/Nature16995  0.686
2015 Grigg JC, Ke A. Structures of Large RNAs and RNA-Protein Complexes: Toward Structure Determination of Riboswitches. Methods in Enzymology. 558: 213-32. PMID 26068743 DOI: 10.1016/Bs.Mie.2015.02.009  0.488
2015 Nam KH, DeLisa MP, Ke A. Characterizing Metal-Dependent Nucleases of CRISPR-Cas Prokaryotic Adaptive Immunity Systems. Methods in Molecular Biology (Clifton, N.J.). 1311: 265-76. PMID 25981479 DOI: 10.1007/978-1-4939-2687-9_17  0.343
2015 Mizrachi D, Chen Y, Liu J, Peng HM, Ke A, Pollack L, Turner RJ, Auchus RJ, DeLisa MP. Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy. Nature Communications. 6: 6826. PMID 25851941 DOI: 10.1038/Ncomms7826  0.307
2015 Price IR, Gaballa A, Ding F, Helmann JD, Ke A. Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches. Molecular Cell. 57: 1110-23. PMID 25794619 DOI: 10.1016/J.Molcel.2015.02.016  0.402
2015 Hayes RP, Ke A. One more piece down to solve the III-A CRISPR puzzle. Journal of Molecular Biology. 427: 228-30. PMID 25451600 DOI: 10.1016/J.Jmb.2014.10.019  0.478
2014 Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A. Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation. Nature Structural & Molecular Biology. 21: 771-7. PMID 25132177 DOI: 10.1038/Nsmb.2875  0.466
2014 Price IR, Grigg JC, Ke A. Common themes and differences in SAM recognition among SAM riboswitches. Biochimica Et Biophysica Acta. 1839: 931-938. PMID 24863160 DOI: 10.1016/J.Bbagrm.2014.05.013  0.437
2014 Johnson CM, Chen Y, Lee H, Ke A, Weaver KE, Dunny GM. Identification of a conserved branched RNA structure that functions as a factor-independent terminator. Proceedings of the National Academy of Sciences of the United States of America. 111: 3573-8. PMID 24550474 DOI: 10.1073/Pnas.1315374111  0.451
2014 Liu JJ, Bratkowski MA, Liu X, Niu CY, Ke A, Wang HW. Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Nature Structural & Molecular Biology. 21: 95-102. PMID 24336220 DOI: 10.1038/Nsmb.2736  0.465
2013 Grigg JC, Ke A. Sequence, structure, and stacking: specifics of tRNA anchoring to the T box riboswitch. Rna Biology. 10: 1761-4. PMID 24356646 DOI: 10.4161/Rna.26996  0.414
2013 Grigg JC, Ke A. Structural determinants for geometry and information decoding of tRNA by T box leader RNA. Structure (London, England : 1993). 21: 2025-32. PMID 24095061 DOI: 10.1016/J.Str.2013.09.001  0.395
2013 Grigg JC, Chen Y, Grundy FJ, Henkin TM, Pollack L, Ke A. T box RNA decodes both the information content and geometry of tRNA to affect gene expression Proceedings of the National Academy of Sciences of the United States of America. 110: 7240-7245. PMID 23589841 DOI: 10.1073/Pnas.1222214110  0.47
2013 Grigg JC, Ke A. One platform, five brands: how nature cuts the cost on riboswitches. Journal of Molecular Biology. 425: 1593-5. PMID 23542340 DOI: 10.1016/J.Jmb.2013.03.036  0.361
2013 Chen Y, Hyun Nam K, Ke A, Pollack L. A SAXS Study of the CRISPR Associated Gene (Cas) Csn2 in the Presence and Absence of Calcium Ions Biophysical Journal. 104: 252a-253a. DOI: 10.1016/J.Bpj.2012.11.1420  0.337
2012 Nam KH, Huang Q, Ke A. Nucleic acid binding surface and dimer interface revealed by CRISPR-associated CasB protein structures. Febs Letters. 586: 3956-61. PMID 23079036 DOI: 10.1016/J.Febslet.2012.09.041  0.436
2012 Nam KH, Ding F, Haitjema C, Huang Q, DeLisa MP, Ke A. Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein. The Journal of Biological Chemistry. 287: 35943-52. PMID 22942283 DOI: 10.1074/Jbc.M112.382598  0.472
2012 Zhao W, Saha M, Ke A, Morais MC, Jardine PJ, Grimes S. A three-helix junction is the interface between two functional domains of prohead RNA in 29 DNA packaging. Journal of Virology. 86: 11625-32. PMID 22896620 DOI: 10.1128/Jvi.01370-12  0.493
2012 Nam KH, Haitjema C, Liu X, Ding F, Wang H, DeLisa MP, Ke A. Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system. Structure (London, England : 1993). 20: 1574-84. PMID 22841292 DOI: 10.1016/J.Str.2012.06.016  0.421
2012 Lee G, Bratkowski MA, Ding F, Ke A, Ha T. Elastic coupling between RNA degradation and unwinding by an exoribonuclease. Science (New York, N.Y.). 336: 1726-9. PMID 22745434 DOI: 10.1126/Science.1216848  0.481
2012 Karlsson AJ, Lim HK, Xu H, Rocco MA, Bratkowski MA, Ke A, DeLisa MP. Engineering antibody fitness and function using membrane-anchored display of correctly folded proteins. Journal of Molecular Biology. 416: 94-107. PMID 22197376 DOI: 10.1016/J.Jmb.2011.12.021  0.358
2011 Nam KH, Kurinov I, Ke A. Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity. The Journal of Biological Chemistry. 286: 30759-68. PMID 21697083 DOI: 10.1074/Jbc.M111.256263  0.424
2011 Lu C, Smith AM, Ding F, Chowdhury A, Henkin TM, Ke A. Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch. Journal of Molecular Biology. 409: 786-99. PMID 21549712 DOI: 10.1016/J.Jmb.2011.04.039  0.742
2011 Ding F, Lu C, Zhao W, Rajashankar KR, Anderson DL, Jardine PJ, Grimes S, Ke A. Structure and assembly of the essential RNA ring component of a viral DNA packaging motor. Proceedings of the National Academy of Sciences of the United States of America. 108: 7357-62. PMID 21471452 DOI: 10.1073/Pnas.1016690108  0.727
2011 Ataide SF, Schmitz N, Shen K, Ke A, Shan SO, Doudna JA, Ban N. The crystal structure of the signal recognition particle in complex with its receptor. Science (New York, N.Y.). 331: 881-6. PMID 21330537 DOI: 10.1126/Science.1196473  0.77
2011 Perez-Rodriguez R, Haitjema C, Huang Q, Nam KH, Bernardis S, Ke A, DeLisa MP. Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli. Molecular Microbiology. 79: 584-99. PMID 21255106 DOI: 10.1111/J.1365-2958.2010.07482.X  0.395
2011 Lee G, Bratkowski MA, Ding F, Ke A, Ha T. Single Molecule Analysis of yeast Rrp44 Exonuclease reveals a Spring-Loaded Mechanism of RNA Unwinding Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.3628  0.482
2010 Lu C, Ding F, Chowdhury A, Pradhan V, Tomsic J, Holmes WM, Henkin TM, Ke A. SAM Recognition and Conformational Switching Mechanism in the Bacillus subtilis yitJ S Box/SAM-I Riboswitch Journal of Molecular Biology. 404: 803-818. PMID 20951706 DOI: 10.1016/J.Jmb.2010.09.059  0.754
2010 Lu C, Ding F, Ke A. Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring. Plos One. 5: e8739. PMID 20090900 DOI: 10.1371/Journal.Pone.0008739  0.757
2008 Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar K, Henkin TM, Ke A. Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism Nature Structural and Molecular Biology. 15: 1076-1083. PMID 18806797 DOI: 10.1038/Nsmb.1494  0.716
2008 Wang HW, Wang J, Ding F, Callahan K, Bratkowski MA, Butler JS, Nogales E, Ke A. Single particle reconstruction of yeast RNA degradation machine, exosome, using electron microscopy Microscopy and Microanalysis. 14: 162-163. DOI: 10.1017/S1431927608082202  0.353
2007 Wang HW, Wang J, Ding F, Callahan K, Bratkowski MA, Butler JS, Nogales E, Ke A. Architecture of the yeast Rrp44 exosome complex suggests routes of RNA recruitment for 3' end processing. Proceedings of the National Academy of Sciences of the United States of America. 104: 16844-9. PMID 17942686 DOI: 10.1073/Pnas.0705526104  0.469
2007 Ke A, Ding F, Batchelor JD, Doudna JA. Structural roles of monovalent cations in the HDV ribozyme. Structure (London, England : 1993). 15: 281-7. PMID 17355864 DOI: 10.1016/J.Str.2007.01.017  0.546
2007 Wu S, Ke A, Doudna JA. A fast and efficient procedure to produce scFvs specific for large macromolecular complexes. Journal of Immunological Methods. 318: 95-101. PMID 17126854 DOI: 10.1016/J.Jim.2006.10.005  0.452
2006 Ke A, Doudna JA. 5 Catalytic Strategies of Self-Cleaving Ribozymes: Relics of an RNA World? Cold Spring Harbor Monograph Archive. 43: 109-131. DOI: 10.1101/087969739.43.109  0.491
2005 Spanggord RJ, Siu F, Ke A, Doudna JA. RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle. Nature Structural & Molecular Biology. 12: 1116-22. PMID 16299512 DOI: 10.1038/Nsmb1025  0.753
2004 Ke A, Doudna JA. Crystallization of RNA and RNA-protein complexes. Methods (San Diego, Calif.). 34: 408-14. PMID 15325657 DOI: 10.1016/J.Ymeth.2004.03.027  0.633
2004 Ke A, Zhou K, Ding F, Cate JH, Doudna JA. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature. 429: 201-5. PMID 15141216 DOI: 10.1038/Nature02522  0.724
2003 Ke A, Wolberger C. Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera. Protein Science : a Publication of the Protein Society. 12: 306-12. PMID 12538894 DOI: 10.1110/Ps.0219103  0.633
2002 Ke A, Mathias JR, Vershon AK, Wolberger C. Structural and thermodynamic characterization of the DNA binding properties of a triple alanine mutant of MATalpha2. Structure (London, England : 1993). 10: 961-71. PMID 12121651 DOI: 10.1016/S0969-2126(02)00790-6  0.595
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