| Year |
Citation |
Score |
| 2024 |
Berríos KN, Barka A, Gill J, Serrano JC, Bailer PF, Parker JB, Evitt NH, Gajula KS, Shi J, Kohli RM. Cooperativity between Cas9 and hyperactive AID establishes broad and diversifying mutational footprints in base editors. Nucleic Acids Research. PMID 38261989 DOI: 10.1093/nar/gkae024 |
0.398 |
|
| 2023 |
Lee SM, Loo CE, Prasasya RD, Bartolomei MS, Kohli RM, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. Biorxiv : the Preprint Server For Biology. PMID 37786695 DOI: 10.1101/2023.09.18.558252 |
0.319 |
|
| 2023 |
Loo CE, Hix MA, Wang T, Cisneros GA, Kohli RM. Revealing Drivers for Carboxy--adenosyl-l-methionine Use by Neomorphic Variants of a DNA Methyltransferase. Acs Chemical Biology. PMID 37379458 DOI: 10.1021/acschembio.3c00184 |
0.415 |
|
| 2023 |
Wang T, Fowler JM, Liu L, Loo CE, Luo M, Schutsky EK, Berríos KN, DeNizio JE, Dvorak A, Downey N, Montermoso S, Pingul BY, Nasrallah M, Gosal WS, Wu H, ... Kohli RM, et al. Direct enzymatic sequencing of 5-methylcytosine at single-base resolution. Nature Chemical Biology. PMID 37322153 DOI: 10.1038/s41589-023-01318-1 |
0.804 |
|
| 2022 |
Serrano JC, von Trentini D, Berríos KN, Barka A, Dmochowski IJ, Kohli RM. Structure-Guided Design of a Potent and Specific Inhibitor against the Genomic Mutator APOBEC3A. Acs Chemical Biology. PMID 36475588 DOI: 10.1021/acschembio.2c00796 |
0.431 |
|
| 2022 |
Jaramillo AVC, Cory MB, Li A, Kohli RM, Wuest WM. Exploration of inhibitors of the bacterial LexA repressor-protease. Bioorganic & Medicinal Chemistry Letters. 65: 128702. PMID 35351585 DOI: 10.1016/j.bmcl.2022.128702 |
0.576 |
|
| 2022 |
Barka A, Berríos KN, Bailer P, Schutsky EK, Wang T, Kohli RM. The Base-Editing Enzyme APOBEC3A Catalyzes Cytosine Deamination in RNA with Low Proficiency and High Selectivity. Acs Chemical Biology. 17: 629-636. PMID 35262324 DOI: 10.1021/acschembio.1c00919 |
0.804 |
|
| 2021 |
Berríos KN, Evitt NH, DeWeerd RA, Ren D, Luo M, Barka A, Wang T, Bartman CR, Lan Y, Green AM, Shi J, Kohli RM. Controllable genome editing with split-engineered base editors. Nature Chemical Biology. 17: 1262-1270. PMID 34663942 DOI: 10.1038/s41589-021-00880-w |
0.428 |
|
| 2021 |
Wang T, Loo CE, Kohli RM. Enzymatic Approaches for Profiling Cytosine Methylation and Hydroxymethylation. Molecular Metabolism. 101314. PMID 34375743 DOI: 10.1016/j.molmet.2021.101314 |
0.343 |
|
| 2021 |
Ghanty U, Serrano JC, Kohli RM. Harnessing Alternative Substrates to Probe TET Family Enzymes. Methods in Molecular Biology (Clifton, N.J.). 2272: 265-280. PMID 34009620 DOI: 10.1007/978-1-0716-1294-1_16 |
0.442 |
|
| 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 |
0.351 |
|
| 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 |
0.768 |
|
| 2021 |
Huang Z, Meng Y, Szabó PE, Kohli RM, Pfeifer GP. High-Resolution Analysis of 5-Hydroxymethylcytosine by TET-Assisted Bisulfite Sequencing. Methods in Molecular Biology (Clifton, N.J.). 2198: 321-331. PMID 32822042 DOI: 10.1007/978-1-0716-0876-0_25 |
0.461 |
|
| 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 |
0.358 |
|
| 2020 |
Wang F, Zahid OK, Ghanty U, Kohli RM, Hall AR. Modular affinity-labeling of the cytosine demethylation base elements in DNA. Scientific Reports. 10: 20253. PMID 33219273 DOI: 10.1038/s41598-020-76544-x |
0.371 |
|
| 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 |
0.464 |
|
| 2020 |
Hostetler ZM, Cory MB, Jones CM, Petersson EJ, Kohli RM. The Kinetic and Molecular Basis for the Interaction of LexA and Activated RecA Revealed by a Fluorescent Amino Acid Probe. Acs Chemical Biology. PMID 31999086 DOI: 10.1021/Acschembio.9B00886 |
0.388 |
|
| 2019 |
Xue JH, Chen GD, Hao F, Chen H, Fang Z, Chen FF, Pang B, Yang QL, Wei X, Fan QQ, Xin C, Zhao J, Deng X, Wang BA, Zhang XJ, ... ... Kohli RM, et al. A vitamin-C-derived DNA modification catalysed by an algal TET homologue. Nature. PMID 31043749 DOI: 10.1038/S41586-019-1160-0 |
0.46 |
|
| 2018 |
Sungwienwong I, Ferrie JJ, Jun JV, Liu C, Barrett TM, Hostetler ZM, Ieda N, Hendricks A, Muthusamy AK, Kohli RM, Chenoweth DM, Petersson GA, Petersson EJ. Improving the Fluorescent Probe Acridonylalanine Through a Combination of Theory and Experiment. Journal of Physical Organic Chemistry. 31. PMID 30983696 DOI: 10.1002/Poc.3813 |
0.3 |
|
| 2018 |
Selwood T, Larsen BJ, Mo CY, Culyba MJ, Hostetler ZM, Kohli RM, Reitz AB, Baugh SDP. Advancement of the 5-Amino-1-(Carbamoylmethyl)-1H-1,2,3-Triazole-4-Carboxamide Scaffold to Disarm the Bacterial SOS Response. Frontiers in Microbiology. 9: 2961. PMID 30619111 DOI: 10.3389/Fmicb.2018.02961 |
0.395 |
|
| 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 |
0.523 |
|
| 2018 |
Samuels AN, Roggiani M, Zhu J, Goulian M, Kohli RM. The SOS Response Mediates Sustained Colonization of the Mammalian Gut. Infection and Immunity. PMID 30510108 DOI: 10.1128/Iai.00711-18 |
0.306 |
|
| 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 |
0.498 |
|
| 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 |
0.365 |
|
| 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 |
0.795 |
|
| 2018 |
Culyba MJ, Kubiak JM, Mo CY, Goulian M, Kohli RM. Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network. Plos Genetics. 14: e1007405. PMID 29856734 DOI: 10.1371/Journal.Pgen.1007405 |
0.382 |
|
| 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 |
0.806 |
|
| 2017 |
Mo CY, Culyba MJ, Selwood T, Kubiak JM, Hostetler ZM, Jurewicz AJ, Keller PM, Pope AJ, Quinn A, Schneck JL, Widdowson KL, Kohli RM. Inhibitors of LexA autoproteolysis and the bacterial SOS response discovered by an academic-industry partnership. Acs Infectious Diseases. PMID 29275629 DOI: 10.1021/Acsinfecdis.7B00122 |
0.424 |
|
| 2017 |
Wang F, Zahid OK, Swain B, Parsonage D, Hollis T, Harvey S, Perrino DF, Kohli RM, Taylor EW, Hall AR. Solid-state nanopore analysis of diverse DNA base modifications using a modular enzymatic labeling process. Nano Letters. PMID 28967259 DOI: 10.1021/Acs.Nanolett.7B03911 |
0.49 |
|
| 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 |
0.385 |
|
| 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 |
0.807 |
|
| 2017 |
Sungwienwong I, Hostetler ZM, Blizzard RJ, Porter JJ, Driggers CM, Mbengi LZ, Villegas JA, Speight LC, Saven JG, Perona JJ, Kohli RM, Mehl RA, Petersson EJ. Improving target amino acid selectivity in a permissive aminoacyl tRNA synthetase through counter-selection. Organic & Biomolecular Chemistry. PMID 28397914 DOI: 10.1039/C7Ob00582B |
0.301 |
|
| 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 |
0.443 |
|
| 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 |
0.788 |
|
| 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 |
0.382 |
|
| 2016 |
Kohli RM, Van Duyne GD. Introduction: Genome Modifying Mechanisms. Chemical Reviews. 116: 12653-12654. PMID 27780353 DOI: 10.1021/Acs.Chemrev.6B00584 |
0.31 |
|
| 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 |
0.534 |
|
| 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 |
0.793 |
|
| 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 |
0.425 |
|
| 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 |
0.515 |
|
| 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 |
0.355 |
|
| 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 |
0.795 |
|
| 2013 |
Kohli RM, Zhang Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature. 502: 472-9. PMID 24153300 DOI: 10.1038/Nature12750 |
0.515 |
|
| 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 |
0.504 |
|
| 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 |
0.336 |
|
| 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 |
0.518 |
|
| 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 |
0.503 |
|
| 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 |
0.49 |
|
| 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 |
0.458 |
|
| 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 |
0.458 |
|
| 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 |
0.445 |
|
| 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 |
0.356 |
|
| 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 |
0.714 |
|
| 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 |
0.603 |
|
| 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 |
0.485 |
|
| 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 |
0.493 |
|
| 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 |
0.723 |
|
| 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 |
0.623 |
|
| 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+ |
0.469 |
|
| 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 |
0.509 |
|
| 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 |
0.481 |
|
| 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 |
0.693 |
|
| 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 |
0.494 |
|
| 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 |
0.492 |
|
| 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 |
0.473 |
|
| 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 |
0.366 |
|
| 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 |
0.36 |
|
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