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Items: 1 to 50 of 59

1.

Advancement of the 5-Amino-1-(Carbamoylmethyl)-1H-1,2,3-Triazole-4-Carboxamide Scaffold to Disarm the Bacterial SOS Response.

Selwood T, Larsen BJ, Mo CY, Culyba MJ, Hostetler ZM, Kohli RM, Reitz AB, Baugh SDP.

Front Microbiol. 2018 Dec 18;9:2961. doi: 10.3389/fmicb.2018.02961. eCollection 2018.

2.

Exploiting Substrate Promiscuity to Develop Activity-Based Probes for TET Family Enzymes.

Ghanty U, DeNizio JE, Liu MY, Kohli RM.

J Am Chem Soc. 2018 Dec 6. doi: 10.1021/jacs.8b04722. [Epub ahead of print]

PMID:
30518204
3.

The SOS Response Mediates Sustained Colonization of the Mammalian Gut.

Samuels AN, Roggiani M, Zhu J, Goulian M, Kohli RM.

Infect Immun. 2018 Dec 3. pii: IAI.00711-18. doi: 10.1128/IAI.00711-18. [Epub ahead of print]

PMID:
30510108
4.

How reliable and valid are the self-reports of sexual behavior among HIV discordant couples in Pune, INDIA.

Kohli RM, Mehendale S, Brahme R, Bollinger B, Chidrawar S, Ghate M, Joglekar N, Sahay S.

Psychol Health Med. 2018 Jan - Dec;23(sup1):1333-1340. doi: 10.1080/13548506.2018.1499943.

PMID:
30486669
5.

Selectivity and Promiscuity in TET-Mediated Oxidation of 5-Methylcytosine in DNA and RNA.

DeNizio JE, Liu MY, Leddin EM, Cisneros GA, Kohli RM.

Biochemistry. 2019 Feb 5;58(5):411-421. doi: 10.1021/acs.biochem.8b00912. Epub 2018 Nov 14.

PMID:
30387995
6.

OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development.

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, Ecker JR, Goll M, Panning B.

Elife. 2018 Oct 16;7. pii: e34870. doi: 10.7554/eLife.34870.

7.

Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase.

Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM.

Nat Biotechnol. 2018 Oct 8. doi: 10.1038/nbt.4204. [Epub ahead of print]

PMID:
30295673
8.

Systematic Evaluation of Soluble Protein Expression Using a Fluorescent Unnatural Amino Acid Reveals No Reliable Predictors of Tolerability.

Hostetler ZM, Ferrie JJ, Bornstein MR, Sungwienwong I, Petersson EJ, Kohli RM.

ACS Chem Biol. 2018 Oct 19;13(10):2855-2861. doi: 10.1021/acschembio.8b00696. Epub 2018 Sep 20.

PMID:
30216041
9.

Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network.

Culyba MJ, Kubiak JM, Mo CY, Goulian M, Kohli RM.

PLoS Genet. 2018 Jun 1;14(6):e1007405. doi: 10.1371/journal.pgen.1007405. eCollection 2018 Jun.

10.

Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells.

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, Chen F, Everett JK, Alexander KA, Lin-Shiao E, Gee MH, Liu X, Young RM, Ambrose D, Wang Y, Xu J, Jordan MS, Marcucci KT, Levine BL, Garcia KC, Zhao Y, Kalos M, Porter DL, Kohli RM, Lacey SF, Berger SL, Bushman FD, June CH, Melenhorst JJ.

Nature. 2018 Jun;558(7709):307-312. doi: 10.1038/s41586-018-0178-z. Epub 2018 May 30.

11.

Harnessing natural DNA modifying activities for editing of the genome and epigenome.

DeNizio JE, Schutsky EK, Berrios KN, Liu MY, Kohli RM.

Curr Opin Chem Biol. 2018 Aug;45:10-17. doi: 10.1016/j.cbpa.2018.01.016. Epub 2018 Feb 13. Review.

PMID:
29452938
12.

Inhibitors of LexA Autoproteolysis and the Bacterial SOS Response Discovered by an Academic-Industry Partnership.

Mo CY, Culyba MJ, Selwood T, Kubiak JM, Hostetler ZM, Jurewicz AJ, Keller PM, Pope AJ, Quinn A, Schneck J, Widdowson KL, Kohli RM.

ACS Infect Dis. 2018 Mar 9;4(3):349-359. doi: 10.1021/acsinfecdis.7b00122. Epub 2018 Jan 8.

PMID:
29275629
13.

Solid-State Nanopore Analysis of Diverse DNA Base Modifications Using a Modular Enzymatic Labeling Process.

Wang F, Zahid OK, Swain BE, Parsonage D, Hollis T, Harvey S, Perrino FW, Kohli RM, Taylor EW, Hall AR.

Nano Lett. 2017 Nov 8;17(11):7110-7116. doi: 10.1021/acs.nanolett.7b03911. Epub 2017 Oct 5.

14.

A Small-Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage.

Kubiak JM, Culyba MJ, Liu MY, Mo CY, Goulian M, Kohli RM.

ACS Synth Biol. 2017 Nov 17;6(11):2067-2076. doi: 10.1021/acssynbio.7b00108. Epub 2017 Sep 1.

15.

APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA.

Schutsky EK, Nabel CS, Davis AKF, DeNizio JE, Kohli RM.

Nucleic Acids Res. 2017 Jul 27;45(13):7655-7665. doi: 10.1093/nar/gkx345.

16.

Improving target amino acid selectivity in a permissive aminoacyl tRNA synthetase through counter-selection.

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.

Org Biomol Chem. 2017 May 3;15(17):3603-3610. doi: 10.1039/c7ob00582b.

17.

DNA Methyltransferases Demonstrate Reduced Activity against Arabinosylcytosine: Implications for Epigenetic Instability in Acute Myeloid Leukemia.

Nabel CS, DeNizio JE, Carroll M, Kohli RM.

Biochemistry. 2017 Apr 25;56(16):2166-2169. doi: 10.1021/acs.biochem.7b00208. Epub 2017 Apr 12.

18.

Mechanisms for targeted, purposeful mutation revealed in an APOBEC-DNA complex.

Schutsky EK, Hostetler ZM, Kohli RM.

Nat Struct Mol Biol. 2017 Feb 6;24(2):97-98. doi: 10.1038/nsmb.3373. No abstract available.

PMID:
28169999
19.

Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine.

Liu MY, Torabifard H, Crawford DJ, DeNizio JE, Cao XJ, Garcia BA, Cisneros GA, Kohli RM.

Nat Chem Biol. 2017 Feb;13(2):181-187. doi: 10.1038/nchembio.2250. Epub 2016 Dec 5.

20.

Introduction: Genome Modifying Mechanisms.

Kohli RM, Van Duyne GD.

Chem Rev. 2016 Oct 26;116(20):12653-12654. No abstract available.

PMID:
27780353
21.

Systematically Altering Bacterial SOS Activity under Stress Reveals Therapeutic Strategies for Potentiating Antibiotics.

Mo CY, Manning SA, Roggiani M, Culyba MJ, Samuels AN, Sniegowski PD, Goulian M, Kohli RM.

mSphere. 2016 Aug 10;1(4). pii: e00163-16. doi: 10.1128/mSphere.00163-16. eCollection 2016 Jul-Aug.

22.

Quantification of Oxidized 5-Methylcytosine Bases and TET Enzyme Activity.

Liu MY, DeNizio JE, Kohli RM.

Methods Enzymol. 2016;573:365-85. doi: 10.1016/bs.mie.2015.12.006. Epub 2016 Feb 1.

23.

The expanding scope and impact of epigenetic cytosine modifications.

Liu MY, DeNizio JE, Schutsky EK, Kohli RM.

Curr Opin Chem Biol. 2016 Aug;33:67-73. doi: 10.1016/j.cbpa.2016.05.029. Epub 2016 Jun 14. Review.

24.

Tet2 Catalyzes Stepwise 5-Methylcytosine Oxidation by an Iterative and de novo Mechanism.

Crawford DJ, Liu MY, Nabel CS, Cao XJ, Garcia BA, Kohli RM.

J Am Chem Soc. 2016 Jan 27;138(3):730-3. doi: 10.1021/jacs.5b10554. Epub 2016 Jan 13.

25.

Targets for Combating the Evolution of Acquired Antibiotic Resistance.

Culyba MJ, Mo CY, Kohli RM.

Biochemistry. 2015 Jun 16;54(23):3573-82. doi: 10.1021/acs.biochem.5b00109. Epub 2015 Jun 5. Review.

26.

High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase.

Gajula KS, Huwe PJ, Mo CY, Crawford DJ, Stivers JT, Radhakrishnan R, Kohli RM.

Nucleic Acids Res. 2014 Sep;42(15):9964-75. doi: 10.1093/nar/gku689. Epub 2014 Jul 26.

27.

Different modes of retrovirus restriction by human APOBEC3A and APOBEC3G in vivo.

Stavrou S, Crawford D, Blouch K, Browne EP, Kohli RM, Ross SR.

PLoS Pathog. 2014 May 22;10(5):e1004145. doi: 10.1371/journal.ppat.1004145. eCollection 2014 May.

28.

Specificity determinants for autoproteolysis of LexA, a key regulator of bacterial SOS mutagenesis.

Mo CY, Birdwell LD, Kohli RM.

Biochemistry. 2014 May 20;53(19):3158-68. doi: 10.1021/bi500026e. Epub 2014 May 8.

29.

Molecular targeting of mutagenic AID and APOBEC deaminases.

Nabel CS, Schutsky EK, Kohli RM.

Cell Cycle. 2014;13(2):171-2. doi: 10.4161/cc.27036. Epub 2013 Nov 15. No abstract available.

30.

TET enzymes, TDG and the dynamics of DNA demethylation.

Kohli RM, Zhang Y.

Nature. 2013 Oct 24;502(7472):472-9. doi: 10.1038/nature12750. Review.

31.

Nucleic acid determinants for selective deamination of DNA over RNA by activation-induced deaminase.

Nabel CS, Lee JW, Wang LC, Kohli RM.

Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14225-30. doi: 10.1073/pnas.1306345110. Epub 2013 Aug 13.

32.

APOBEC3 inhibition of mouse mammary tumor virus infection: the role of cytidine deamination versus inhibition of reverse transcription.

MacMillan AL, Kohli RM, Ross SR.

J Virol. 2013 May;87(9):4808-17. doi: 10.1128/JVI.00112-13. Epub 2013 Feb 28.

33.

AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation.

Nabel CS, Jia H, Ye Y, Shen L, Goldschmidt HL, Stivers JT, Zhang Y, Kohli RM.

Nat Chem Biol. 2012 Sep;8(9):751-8. doi: 10.1038/nchembio.1042. Epub 2012 Jul 8.

34.

The curious chemical biology of cytosine: deamination, methylation, and oxidation as modulators of genomic potential.

Nabel CS, Manning SA, Kohli RM.

ACS Chem Biol. 2012 Jan 20;7(1):20-30. doi: 10.1021/cb2002895. Epub 2011 Oct 31. Review.

35.

Molecular biology. Demystifying DNA demethylation.

Nabel CS, Kohli RM.

Science. 2011 Sep 2;333(6047):1229-30. doi: 10.1126/science.1211917. No abstract available.

PMID:
21885763
36.

Grand challenge commentary: The chemistry of a dynamic genome.

Kohli RM.

Nat Chem Biol. 2010 Dec;6(12):866-8. doi: 10.1038/nchembio.471.

PMID:
21079591
37.

Local sequence targeting in the AID/APOBEC family differentially impacts retroviral restriction and antibody diversification.

Kohli RM, Maul RW, Guminski AF, McClure RL, Gajula KS, Saribasak H, McMahon MA, Siliciano RF, Gearhart PJ, Stivers JT.

J Biol Chem. 2010 Dec 24;285(52):40956-64. doi: 10.1074/jbc.M110.177402. Epub 2010 Oct 6.

38.

Sensitivity of V75I HIV-1 reverse transcriptase mutant selected in vitro by acyclovir to anti-HIV drugs.

McMahon MA, Siliciano JD, Kohli RM, Siliciano RF.

AIDS. 2010 Jan 16;24(2):319-23. doi: 10.1097/QAD.0b013e32833424e5.

PMID:
20009920
39.

A portable hot spot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase.

Kohli RM, Abrams SR, Gajula KS, Maul RW, Gearhart PJ, Stivers JT.

J Biol Chem. 2009 Aug 21;284(34):22898-904. doi: 10.1074/jbc.M109.025536. Epub 2009 Jun 26.

40.

When to think of zebras.

Ho RS, Kohli RM, Maragakis LL.

Am J Med. 2009 May;122(5):424-6. doi: 10.1016/j.amjmed.2009.01.008. No abstract available.

PMID:
19375549
41.

The antiherpetic drug acyclovir inhibits HIV replication and selects the V75I reverse transcriptase multidrug resistance mutation.

McMahon MA, Siliciano JD, Lai J, Liu JO, Stivers JT, Siliciano RF, Kohli RM.

J Biol Chem. 2008 Nov 14;283(46):31289-93. doi: 10.1074/jbc.C800188200. Epub 2008 Sep 24.

42.

Modification of medical outcome study (MOS) instrument for quality of life assessment & its validation in HIV infected individuals in India.

Kohli RM, Sane S, Kumar K, Paranjape RS, Mehendale SM.

Indian J Med Res. 2005 Oct;122(4):297-304.

PMID:
16394320
43.

Assessment of quality of life among HIV-infected persons in Pune, India.

Kohli RM, Sane S, Kumar K, Paranjape RS, Mehendale SM.

Qual Life Res. 2005 Aug;14(6):1641-7.

PMID:
16110943
44.

Enhanced macrocyclizing activity of the thioesterase from tyrocidine synthetase in presence of nonionic detergent.

Yeh E, Lin H, Clugston SL, Kohli RM, Walsh CT.

Chem Biol. 2004 Nov;11(11):1573-82.

45.

Type II thioesterase restores activity of a NRPS module stalled with an aminoacyl-S-enzyme that cannot be elongated.

Yeh E, Kohli RM, Bruner SD, Walsh CT.

Chembiochem. 2004 Sep 6;5(9):1290-3. No abstract available.

PMID:
15368584
46.

Chemoenzymatic route to macrocyclic hybrid peptide/polyketide-like molecules.

Kohli RM, Burke MD, Tao J, Walsh CT.

J Am Chem Soc. 2003 Jun 18;125(24):7160-1.

PMID:
12797773
47.

Enzymology of acyl chain macrocyclization in natural product biosynthesis.

Kohli RM, Walsh CT.

Chem Commun (Camb). 2003 Feb 7;(3):297-307. Review.

PMID:
12613585
48.

Characterization of the surfactin synthetase C-terminal thioesterase domain as a cyclic depsipeptide synthase.

Tseng CC, Bruner SD, Kohli RM, Marahiel MA, Walsh CT, Sieber SA.

Biochemistry. 2002 Nov 12;41(45):13350-9.

PMID:
12416979
49.

Biomimetic synthesis and optimization of cyclic peptide antibiotics.

Kohli RM, Walsh CT, Burkart MD.

Nature. 2002 Aug 8;418(6898):658-61.

PMID:
12167866
50.

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