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Ke Shi, Ph.D. - Publications

Affiliations: 
2012 Mathematics University of Minnesota, Twin Cities, Minneapolis, MN 
Area:
Applied Mathematics, Mathematics
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33 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
2019 Tang H, Shi K, Shi C, Aihara H, Zhang J, Du G. Enhancing subtilisin thermostability through a modified normalized B-factor analysis and loop-grafting strategy. The Journal of Biological Chemistry. PMID 31615894 DOI: 10.1074/Jbc.Ra119.010658  0.31
2019 Shi K, Cho S, Aukema KG, Lee T, Bera AK, Seffernick JL, Wackett LP, Aihara H. Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis. Plos One. 14: e0216979. PMID 31181074 DOI: 10.1371/Journal.Pone.0216979  0.302
2018 Lee JK, Bosnakovski D, Toso EA, Dinh T, Banerjee S, Bohl TE, Shi K, Orellana K, Kyba M, Aihara H. Crystal Structure of the Double Homeodomain of DUX4 in Complex with DNA. Cell Reports. 25: 2955-2962.e3. PMID 30540931 DOI: 10.1016/J.Celrep.2018.11.060  0.33
2018 Zeng Z, Deng F, Shi K, Ye G, Wang G, Fang L, Xiao S, Fu Z, Peng G. Dimerization of Coronavirus nsp9 with Diverse Modes Enhances Its Nucleic Acid Binding Affinity. Journal of Virology. PMID 29925659 DOI: 10.1128/Jvi.00692-18  0.306
2018 Kurniawan F, Shi K, Kurahashi K, Bielinsky AK, Aihara H. Crystal Structure of Cdc45 Suggests a Conformational Switch that May Regulate DNA Replication. Iscience. 3: 102-109. PMID 29901028 DOI: 10.1016/J.Isci.2018.04.011  0.335
2017 Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H. Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Scientific Reports. 7: 17415. PMID 29234087 DOI: 10.1038/S41598-017-17694-3  0.301
2017 Pandey KK, Bera S, Shi K, Aihara H, Grandgenett DP. A C-terminal Tail Region in the Rous Sarcoma Virus Integrase Provides High Plasticity of Functional Integrase Oligomerization during Intasome Assembly. The Journal of Biological Chemistry. PMID 28184005 DOI: 10.1074/Jbc.M116.773382  0.304
2016 Shi K, Carpenter MA, Banerjee S, Shaban NM, Kurahashi K, Salamango DJ, McCann JL, Starrett GJ, Duffy JV, Demir Ö, Amaro RE, Harki DA, Harris RS, Aihara H. Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nature Structural & Molecular Biology. PMID 27991903 DOI: 10.1038/Nsmb.3344  0.345
2016 Shaban NM, Shi K, Li M, Aihara H, Harris RS. 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure. Journal of Molecular Biology. PMID 27139641 DOI: 10.1016/J.Jmb.2016.04.026  0.311
2016 Yin Z, Shi K, Banerjee S, Pandey KK, Bera S, Grandgenett DP, Aihara H. Crystal structure of the Rous sarcoma virus intasome. Nature. 530: 362-6. PMID 26887497 DOI: 10.1107/S0108767317096970  0.305
2015 Shi K, Carpenter MA, Kurahashi K, Harris RS, Aihara H. Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain. The Journal of Biological Chemistry. PMID 26416889 DOI: 10.1074/Jbc.M115.679951  0.335
2014 Cho S, Shi K, Seffernick JL, Dodge AG, Wackett LP, Aihara H. Cyanuric acid hydrolase from Azorhizobium caulinodans ORS 571: crystal structure and insights into a new class of Ser-Lys dyad proteins. Plos One. 9: e99349. PMID 24915109 DOI: 10.1371/Journal.Pone.0099349  0.318
2014 Cockburn B, Shi K. Devising HDG methods for Stokes flow: An overview Computers and Fluids. 98: 221-229. DOI: 10.1016/J.Compfluid.2013.11.017  0.489
2013 Shi K, Pandey KK, Bera S, Vora AC, Grandgenett DP, Aihara H. A possible role for the asymmetric C-terminal domain dimer of Rous sarcoma virus integrase in viral DNA binding. Plos One. 8: e56892. PMID 23451105 DOI: 10.1371/Journal.Pone.0056892  0.31
2013 Shi K, Huang WM, Aihara H. An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation. Plos Biology. 11: e1001472. PMID 23382649 DOI: 10.1371/Journal.Pbio.1001472  0.304
2013 Chen L, Shi K, Yin Z, Aihara H. Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution. Nucleic Acids Research. 41: 648-56. PMID 23118486 DOI: 10.1093/Nar/Gks1015  0.311
2013 Cockburn B, Shi K. Superconvergent HDG methods for linear elasticity with weakly symmetric stresses Ima Journal of Numerical Analysis. 33: 747-770. DOI: 10.1093/Imanum/Drs020  0.492
2013 Cockburn B, Shi K. Conditions for superconvergence of HDG methods for stokes flow Mathematics of Computation. 82: 651-671. DOI: 10.1090/S0025-5718-2012-02644-5  0.485
2012 Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA, Pommier Y, Aihara H. Structural basis for recognition of 5′-phosphotyrosine adducts by Tdp2 Nature Structural and Molecular Biology. 19: 1372-1377. PMID 23104058 DOI: 10.1038/Nsmb.2423  0.33
2012 Cockburn B, Qiu W, Shi K. Superconvergent hdg methods on isoparametric elements for second-order elliptic problems Siam Journal On Numerical Analysis. 50: 1417-1432. DOI: 10.1137/110840790  0.491
2012 Cockburn B, Qiu W, Shi K. Conditions for superconvergence of HDG methods for second-order elliptic problems Mathematics of Computation. 81: 1327-1353. DOI: 10.1090/S0025-5718-2011-02550-0  0.501
2011 Celiker F, Cockburn B, Shi K. A projection-based error analysis of HDG methods for Timoshenko beams Mathematics of Computation. 81: 131-151. DOI: 10.1090/S0025-5718-2011-02522-6  0.687
2010 Celiker F, Cockburn B, Shi K. Hybridizable discontinuous galerkin methods for timoshenko beams Journal of Scientific Computing. 44: 1-37. DOI: 10.1007/S10915-010-9357-2  0.685
2004 Pan B, Shi K, Sundaralingam M. Synthesis, Purification and Crystallization of Guanine-rich RNA Oligonucleotides. Biological Procedures Online. 6: 257-262. PMID 15562298 DOI: 10.1251/Bpo96  0.304
2004 Premraj BJ, Raja S, Bhavesh NS, Shi K, Hosur RV, Sundaralingam M, Yathindra N. Solution structure of 2',5' d(G4C4). Relevance to topological restrictions and nature's choice of phosphodiester links. European Journal of Biochemistry / Febs. 271: 2956-66. PMID 15233791 DOI: 10.1111/J.1432-1033.2004.04225.X  0.324
2004 Shi K, Pan B, Tippin D, Sundaralingam M. Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers. Acta Crystallographica. Section D, Biological Crystallography. 60: 61-5. PMID 14684893 DOI: 10.1107/S0907444903021899  0.308
2003 Shi K, Pan B, Sundaralingam M. Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5 A resolution. Acta Crystallographica. Section D, Biological Crystallography. 59: 1377-83. PMID 12876339 DOI: 10.1107/S0907444903011788  0.322
2003 Pan B, Xiong Y, Shi K, Sundaralingam M. An eight-stranded helical fragment in RNA crystal structure: implications for tetraplex interaction. Structure (London, England : 1993). 11: 825-31. PMID 12842045 DOI: 10.1016/S0969-2126(03)00108-4  0.333
2003 Shi K, Pan B, Sundaralingam M. The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs. Nucleic Acids Research. 31: 1392-7. PMID 12595546 DOI: 10.1093/Nar/Gkg226  0.313
2002 Shi K, Mitra SN, Sundaralingam M. Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin. Acta Crystallographica. Section D, Biological Crystallography. 58: 601-6. PMID 11914483 DOI: 10.1107/S0907444902001889  0.301
2001 Deng J, Xiong Y, Sudarsanakumar C, Shi K, Sundaralingam M. Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple. Rna (New York, N.Y.). 7: 1425-31. PMID 11680847 DOI: 10.2210/Pdb1Fuf/Pdb  0.332
2000 Mitra SN, Biswas R, Shi K, Sundaralingam M. Crystal Structure of an RNA Duplex [r(gugcaca)dC](2) with 3'-Dinucleoside Overhangs Forming a Superhelix. Journal of Biomolecular Structure & Dynamics. 17: 189-94. PMID 22607423 DOI: 10.1080/07391102.2000.10506620  0.315
2000 Shi K, Biswas R, Mitra SN, Sundaralingam M. The crystal structure of the octamer [r(guauaca)dC]2 with six Watson-Crick base-pairs and two 3' overhang residues. Journal of Molecular Biology. 299: 113-22. PMID 10860726 DOI: 10.1006/Jmbi.2000.3751  0.302
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