Rahul Manu Kohli - Publications

2004 Harvard University, Cambridge, MA, United States 

56 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
2021 DeNizio JE, Dow BJ, Serrano JC, Ghanty U, Drohat AC, Kohli RM. TET-TDG active DNA demethylation at CpG and non-CpG sites. Journal of Molecular Biology. 166877. PMID 33561435 DOI: 10.1016/j.jmb.2021.166877  0.4
2021 Wang T, Luo M, Berrios KN, Schutsky EK, Wu H, Kohli RM. Bisulfite-Free Sequencing of 5-Hydroxymethylcytosine with APOBEC-Coupled Epigenetic Sequencing (ACE-Seq). Methods in Molecular Biology (Clifton, N.J.). 2198: 349-367. PMID 32822044 DOI: 10.1007/978-1-0716-0876-0_27  0.4
2020 Shen H, Ontiveros RJ, Owens MC, Liu MY, Ghanty U, Kohli RM, Liu KF. TET-mediated 5-methylcytosine oxidation in tRNA promotesĀ translation. The Journal of Biological Chemistry. 296: 100087. PMID 33460917 DOI: 10.1074/jbc.RA120.014226  0.4
2020 Caldwell BA, Liu MY, Prasasya RD, Wang T, DeNizio JE, Leu NA, Amoh NYA, Krapp C, Lan Y, Shields EJ, Bonasio R, Lengner CJ, Kohli RM, Bartolomei MS. Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency. Molecular Cell. PMID 33352108 DOI: 10.1016/j.molcel.2020.11.045  0.4
2020 Shen H, Ontiveros RJ, Owens MC, Liu MY, Ghanty U, Kohli RM, Liu KF. TET-mediated 5-methylcytosine oxidation in tRNA promotes translation. The Journal of Biological Chemistry. PMID 33199375 DOI: 10.1074/jbc.RA120.014226  0.4
2020 Wang T, Kohli RM. Discovery of an Unnatural DNA Modification Derived from a Natural Secondary Metabolite. Cell Chemical Biology. PMID 33053370 DOI: 10.1016/j.chembiol.2020.09.006  0.4
2020 Ghanty U, Wang T, Kohli RM. Nucleobase Modifiers Identify TET Enzymes as Bifunctional DNA Dioxygenases Capable of Direct N-Demethylation. Angewandte Chemie (International Ed. in English). PMID 32271979 DOI: 10.1002/Anie.202002751  0.4
2018 Ghanty U, DeNizio JE, Liu MY, Kohli RM. Exploiting Substrate Promiscuity to Develop Activity-Based Probes for TET Family Enzymes. Journal of the American Chemical Society. PMID 30518204 DOI: 10.1021/Jacs.8B04722  0.4
2018 DeNizio JE, Liu MY, Leddin E, Cisneros GA, Kohli RM. Selectivity and Promiscuity in TET-mediated oxidation of 5-methylcytosine in DNA and RNA. Biochemistry. PMID 30387995 DOI: 10.1021/Acs.Biochem.8B00912  0.4
2018 Hrit J, Goodrich L, Li C, Wang BA, Nie J, Cui X, Martin EA, Simental E, Fernandez J, Liu MY, Nery JR, Castanon R, Kohli RM, Tretyakova N, He C, et al. OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development. Elife. 7. PMID 30325306 DOI: 10.7554/Elife.34870  0.4
2018 Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM. Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase. Nature Biotechnology. PMID 30295673 DOI: 10.1038/Nbt.4204  0.4
2018 Fraietta JA, Nobles CL, Sammons MA, Lundh S, Carty SA, Reich TJ, Cogdill AP, Morrissette JJD, DeNizio JE, Reddy S, Hwang Y, Gohil M, Kulikovskaya I, Nazimuddin F, Gupta M, ... ... Kohli RM, et al. Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells. Nature. PMID 29849141 DOI: 10.1038/S41586-018-0178-Z  0.4
2018 DeNizio JE, Schutsky EK, Berrios KN, Liu MY, Kohli RM. Harnessing natural DNA modifying activities for editing of the genome and epigenome. Current Opinion in Chemical Biology. 45: 10-17. PMID 29452938 DOI: 10.1016/J.Cbpa.2018.01.016  0.4
2018 Hrit J, Goodrich L, Li C, Wang B, Nie J, Cui X, Martin EA, Simental E, Fernandez J, Liu MY, Nery JR, Castanon R, Kohli RM, Tretyakova N, He C, et al. Author response: OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development Elife. DOI: 10.7554/Elife.34870.035  0.4
2017 Kubiak JM, Culyba MJ, Liu MY, Mo CY, Goulian M, Kohli RM. A small-molecule inducible synthetic circuit for control of the SOS gene network without DNA damage. Acs Synthetic Biology. PMID 28826208 DOI: 10.1021/Acssynbio.7B00108  0.4
2017 Schutsky EK, Nabel CS, Davis AKF, DeNizio JE, Kohli RM. APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA. Nucleic Acids Research. PMID 28472485 DOI: 10.1093/Nar/Gkx345  0.4
2017 Nabel CS, DeNizio JE, Carroll M, Kohli RM. DNA Methyltransferases Demonstrate Reduced Activity against Arabinosylcytosine: Implications for Epigenetic Instability in Acute Myeloid Leukemia. Biochemistry. PMID 28394581 DOI: 10.1021/Acs.Biochem.7B00208  0.4
2017 Schutsky EK, Hostetler ZM, Kohli RM. Mechanisms for targeted, purposeful mutation revealed in an APOBEC-DNA complex. Nature Structural & Molecular Biology. 24: 97-98. PMID 28169999 DOI: 10.1038/Nsmb.3373  0.4
2016 Liu MY, Torabifard H, Crawford DJ, DeNizio JE, Cao XJ, Garcia BA, Cisneros GA, Kohli RM. Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. Nature Chemical Biology. PMID 27918559 DOI: 10.1038/Nchembio.2250  0.4
2016 Liu MY, DeNizio JE, Kohli RM. Quantification of Oxidized 5-Methylcytosine Bases and TET Enzyme Activity. Methods in Enzymology. 573: 365-385. PMID 27372762 DOI: 10.1016/Bs.Mie.2015.12.006  0.4
2016 Liu MY, DeNizio JE, Schutsky EK, Kohli RM. The expanding scope and impact of epigenetic cytosine modifications. Current Opinion in Chemical Biology. 33: 67-73. PMID 27315338 DOI: 10.1016/J.Cbpa.2016.05.029  0.4
2016 Crawford DJ, Liu MY, Nabel CS, Cao XJ, Garcia BA, Kohli RM. Tet2 catalyzes stepwise 5-methylcytosine oxidation by an iterative and de novo mechanism. Journal of the American Chemical Society. PMID 26734843 DOI: 10.1021/Jacs.5B10554  1
2016 Liu MY, DeNizio JE, Kohli RM. Quantification of Oxidized 5-Methylcytosine Bases and TET Enzyme Activity Methods in Enzymology. DOI: 10.1016/bs.mie.2015.12.006  1
2015 Culyba MJ, Mo CY, Kohli RM. Targets for Combating the Evolution of Acquired Antibiotic Resistance. Biochemistry. 54: 3573-82. PMID 26016604 DOI: 10.1021/Acs.Biochem.5B00109  1
2014 Gajula KS, Huwe PJ, Mo CY, Crawford DJ, Stivers JT, Radhakrishnan R, Kohli RM. High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase. Nucleic Acids Research. 42: 9964-75. PMID 25064858 DOI: 10.1093/Nar/Gku689  1
2014 Stavrou S, Crawford D, Blouch K, Browne EP, Kohli RM, Ross SR. Different modes of retrovirus restriction by human APOBEC3A and APOBEC3G in vivo. Plos Pathogens. 10: e1004145. PMID 24851906 DOI: 10.1371/Journal.Ppat.1004145  1
2014 Mo CY, Birdwell LD, Kohli RM. Specificity determinants for autoproteolysis of LexA, a key regulator of bacterial SOS mutagenesis. Biochemistry. 53: 3158-68. PMID 24779472 DOI: 10.1021/Bi500026E  1
2014 Nabel CS, Schutsky EK, Kohli RM. Molecular targeting of mutagenic AID and APOBEC deaminases. Cell Cycle (Georgetown, Tex.). 13: 171-2. PMID 24241207 DOI: 10.4161/Cc.27036  1
2013 Kohli RM, Zhang Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature. 502: 472-9. PMID 24153300 DOI: 10.1038/Nature12750  1
2013 Nabel CS, Lee JW, Wang LC, Kohli RM. Nucleic acid determinants for selective deamination of DNA over RNA by activation-induced deaminase. Proceedings of the National Academy of Sciences of the United States of America. 110: 14225-30. PMID 23942124 DOI: 10.1073/Pnas.1306345110  1
2013 MacMillan AL, Kohli RM, Ross SR. APOBEC3 inhibition of mouse mammary tumor virus infection: the role of cytidine deamination versus inhibition of reverse transcription. Journal of Virology. 87: 4808-17. PMID 23449789 DOI: 10.1128/Jvi.00112-13  1
2012 Nabel CS, Jia H, Ye Y, Shen L, Goldschmidt HL, Stivers JT, Zhang Y, Kohli RM. AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nature Chemical Biology. 8: 751-8. PMID 22772155 DOI: 10.1038/Nchembio.1042  1
2012 Nabel CS, Manning SA, Kohli RM. The curious chemical biology of cytosine: deamination, methylation, and oxidation as modulators of genomic potential. Acs Chemical Biology. 7: 20-30. PMID 22004246 DOI: 10.1021/Cb2002895  1
2011 Nabel CS, Kohli RM. Molecular biology. Demystifying DNA demethylation. Science (New York, N.Y.). 333: 1229-30. PMID 21885763 DOI: 10.1126/Science.1211917  1
2010 Kohli RM. Grand challenge commentary: The chemistry of a dynamic genome. Nature Chemical Biology. 6: 866-8. PMID 21079591 DOI: 10.1038/Nchembio.471  1
2010 Kohli RM, Maul RW, Guminski AF, McClure RL, Gajula KS, Saribasak H, McMahon MA, Siliciano RF, Gearhart PJ, Stivers JT. Local sequence targeting in the AID/APOBEC family differentially impacts retroviral restriction and antibody diversification. The Journal of Biological Chemistry. 285: 40956-64. PMID 20929867 DOI: 10.1074/Jbc.M110.177402  1
2010 McMahon MA, Siliciano JD, Kohli RM, Siliciano RF. Sensitivity of V75I HIV-1 reverse transcriptase mutant selected in vitro by acyclovir to anti-HIV drugs. Aids (London, England). 24: 319-23. PMID 20009920 DOI: 10.1097/Qad.0B013E32833424E5  1
2009 Kohli RM, Abrams SR, Gajula KS, Maul RW, Gearhart PJ, Stivers JT. A portable hot spot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase. The Journal of Biological Chemistry. 284: 22898-904. PMID 19561087 DOI: 10.1074/Jbc.M109.025536  1
2009 Ho RS, Kohli RM, Maragakis LL. When to think of zebras. The American Journal of Medicine. 122: 424-6. PMID 19375549 DOI: 10.1016/J.Amjmed.2009.01.008  1
2008 McMahon MA, Siliciano JD, Lai J, Liu JO, Stivers JT, Siliciano RF, Kohli RM. The antiherpetic drug acyclovir inhibits HIV replication and selects the V75I reverse transcriptase multidrug resistance mutation. The Journal of Biological Chemistry. 283: 31289-93. PMID 18818198 DOI: 10.1074/Jbc.C800188200  1
2004 Yeh E, Lin H, Clugston SL, Kohli RM, Walsh CT. Enhanced macrocyclizing activity of the thioesterase from tyrocidine synthetase in presence of nonionic detergent. Chemistry & Biology. 11: 1573-82. PMID 15556008 DOI: 10.1016/J.Chembiol.2004.09.003  1
2004 Yeh E, Kohli RM, Bruner SD, Walsh CT. Type II thioesterase restores activity of a NRPS module stalled with an aminoacyl-S-enzyme that cannot be elongated. Chembiochem : a European Journal of Chemical Biology. 5: 1290-3. PMID 15368584 DOI: 10.1002/Cbic.200400077  1
2003 Kohli RM, Burke MD, Tao J, Walsh CT. Chemoenzymatic route to macrocyclic hybrid peptide/polyketide-like molecules. Journal of the American Chemical Society. 125: 7160-1. PMID 12797773 DOI: 10.1021/Ja0352202  1
2003 Kohli RM, Walsh CT. Enzymology of acyl chain macrocyclization in natural product biosynthesis. Chemical Communications (Cambridge, England). 297-307. PMID 12613585 DOI: 10.1039/B208333G  1
2002 Tseng CC, Bruner SD, Kohli RM, Marahiel MA, Walsh CT, Sieber SA. Characterization of the surfactin synthetase C-terminal thioesterase domain as a cyclic depsipeptide synthase. Biochemistry. 41: 13350-9. PMID 12416979 DOI: 10.1021/Bi026592A  1
2002 Kohli RM, Walsh CT, Burkart MD. Biomimetic synthesis and optimization of cyclic peptide antibiotics. Nature. 418: 658-61. PMID 12167866 DOI: 10.1038/Nature00907  1
2002 Luo L, Kohli RM, Onishi M, Linne U, Marahiel MA, Walsh CT. Timing of epimerization and condensation reactions in nonribosomal peptide assembly lines: kinetic analysis of phenylalanine activating elongation modules of tyrocidine synthetase B. Biochemistry. 41: 9184-96. PMID 12119033 DOI: 10.1021/Bi026047+  1
2002 Bruner SD, Weber T, Kohli RM, Schwarzer D, Marahiel MA, Walsh CT, Stubbs MT. Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain SrfTE. Structure (London, England : 1993). 10: 301-10. PMID 12005429 DOI: 10.1016/S0969-2126(02)00716-5  1
2002 Kohli RM, Takagi J, Walsh CT. The thioesterase domain from a nonribosomal peptide synthetase as a cyclization catalyst for integrin binding peptides. Proceedings of the National Academy of Sciences of the United States of America. 99: 1247-52. PMID 11805307 DOI: 10.1073/Pnas.251668398  1
2001 Keating TA, Ehmann DE, Kohli RM, Marshall CG, Trauger JW, Walsh CT. Chain termination steps in nonribosomal peptide synthetase assembly lines: directed acyl-S-enzyme breakdown in antibiotic and siderophore biosynthesis. Chembiochem : a European Journal of Chemical Biology. 2: 99-107. PMID 11828432 DOI: 10.1002/1439-7633(20010202)2:2<99::Aid-Cbic99>3.0.Co;2-3  1
2001 Kohli RM, Trauger JW, Schwarzer D, Marahiel MA, Walsh CT. Generality of peptide cyclization catalyzed by isolated thioesterase domains of nonribosomal peptide synthetases. Biochemistry. 40: 7099-108. PMID 11401555 DOI: 10.1021/Bi010036J  1
2001 Trauger JW, Kohli RM, Walsh CT. Cyclization of backbone-substituted peptides catalyzed by the thioesterase domain from the tyrocidine nonribosomal peptide synthetase. Biochemistry. 40: 7092-8. PMID 11401554 DOI: 10.1021/Bi010035R  1
2000 Trauger JW, Kohli RM, Mootz HD, Marahiel MA, Walsh CT. Peptide cyclization catalysed by the thioesterase domain of tyrocidine synthetase. Nature. 407: 215-8. PMID 11001063 DOI: 10.1038/35025116  1
1999 Xu D, Kohli RM, Massey V. The role of threonine 37 in flavin reactivity of the old yellow enzyme. Proceedings of the National Academy of Sciences of the United States of America. 96: 3556-61. PMID 10097075 DOI: 10.1073/Pnas.96.7.3556  1
1998 Kohli RM, Massey V. The oxidative half-reaction of Old Yellow Enzyme. The role of tyrosine 196. The Journal of Biological Chemistry. 273: 32763-70. PMID 9830020 DOI: 10.1074/Jbc.273.49.32763  1
1998 Kohli RM. Site-directed mutagenesis using PCR-mediated introduction of silent mutations. Biotechniques. 25: 184-8. PMID 9714873 DOI: 10.2144/98252Bm01  1
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