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CRISPR-Mediated Activation of Endogenous Gene Expression in the Postnatal Heart.

Schoger E, Carroll KJ, Iyer LM, McAnally JR, Tan W, Liu N, Noack C, Shomroni O, Salinas G, Groß J, Herzog N, Doroudgar S, Bassel-Duby R, Zimmermann WH, Zelarayán LC.

Circ Res. 2020 Jan 3;126(1):6-24. doi: 10.1161/CIRCRESAHA.118.314522. Epub 2019 Nov 15.


KLF15-Wnt-Dependent Cardiac Reprogramming Up-Regulates SHISA3 in the Mammalian Heart.

Noack C, Iyer LM, Liaw NY, Schoger E, Khadjeh S, Wagner E, Woelfer M, Zafiriou MP, Milting H, Sossalla S, Streckfuss-Boemeke K, Hasenfuß G, Zimmermann WH, Zelarayán LC.

J Am Coll Cardiol. 2019 Oct 8;74(14):1804-1819. doi: 10.1016/j.jacc.2019.07.076.


The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis.

Zhang C, Hung YH, Rim HJ, Zhang D, Frost JM, Shin H, Jang H, Liu F, Xiao W, Iyer LM, Aravind L, Zhang XQ, Fischer RL, Huh JH, Hsieh TF.

Proc Natl Acad Sci U S A. 2019 Aug 27;116(35):17563-17571. doi: 10.1073/pnas.1907290116. Epub 2019 Aug 13.


Agonistic and antagonistic roles of fibroblasts and cardiomyocytes on viscoelastic stiffening of engineered human myocardium.

Schlick SF, Spreckelsen F, Tiburcy M, Iyer LM, Meyer T, Zelarayan LC, Luther S, Parlitz U, Zimmermann WH, Rehfeldt F.

Prog Biophys Mol Biol. 2019 Jul;144:51-60. doi: 10.1016/j.pbiomolbio.2018.11.011. Epub 2018 Dec 12.


Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile Elements.

Krishnan A, Burroughs AM, Iyer LM, Aravind L.

iScience. 2018 Nov 30;9:192-208. doi: 10.1016/j.isci.2018.10.017. Epub 2018 Oct 23.


Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes.

Kaur G, Iyer LM, Subramanian S, Aravind L.

Sci Rep. 2018 Apr 18;8(1):6196. doi: 10.1038/s41598-018-24467-z.


Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys.

Holland SJ, Berghuis LM, King JJ, Iyer LM, Sikora K, Fifield H, Peter S, Quinlan EM, Sugahara F, Shingate P, Trancoso I, Iwanami N, Temereva E, Strohmeier C, Kuratani S, Venkatesh B, Evanno G, Aravind L, Schorpp M, Larijani M, Boehm T.

Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):E3211-E3220. doi: 10.1073/pnas.1720871115. Epub 2018 Mar 19.


Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity.

Krishnan A, Iyer LM, Holland SJ, Boehm T, Aravind L.

Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):E3201-E3210. doi: 10.1073/pnas.1720897115. Epub 2018 Mar 19.


A context-specific cardiac β-catenin and GATA4 interaction influences TCF7L2 occupancy and remodels chromatin driving disease progression in the adult heart.

Iyer LM, Nagarajan S, Woelfer M, Schoger E, Khadjeh S, Zafiriou MP, Kari V, Herting J, Pang ST, Weber T, Rathjens FS, Fischer TH, Toischer K, Hasenfuss G, Noack C, Johnsen SA, Zelarayán LC.

Nucleic Acids Res. 2018 Apr 6;46(6):2850-2867. doi: 10.1093/nar/gky049.


A Nonhemolytic Group B Streptococcus Strain Exhibits Hypervirulence.

Gendrin C, Vornhagen J, Armistead B, Singh P, Whidbey C, Merillat S, Knupp D, Parker R, Rogers LM, Quach P, Iyer LM, Aravind L, Manning SD, Aronoff DM, Rajagopal L.

J Infect Dis. 2018 Mar 5;217(6):983-987. doi: 10.1093/infdis/jix646.


Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements.

Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L.

J Bacteriol. 2017 Jul 11;199(15). pii: e00245-17. doi: 10.1128/JB.00245-17. Print 2017 Aug 1.


Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors.

Zhang D, Burroughs AM, Vidal ND, Iyer LM, Aravind L.

Nucleic Acids Res. 2016 May 5;44(8):3513-33. doi: 10.1093/nar/gkw221. Epub 2016 Apr 8.


Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification.

Iyer LM, Zhang D, Aravind L.

Bioessays. 2016 Jan;38(1):27-40. doi: 10.1002/bies.201500104. Epub 2015 Dec 12. Review.


Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling.

Burroughs AM, Zhang D, Schäffer DE, Iyer LM, Aravind L.

Nucleic Acids Res. 2015 Dec 15;43(22):10633-54. doi: 10.1093/nar/gkv1267. Epub 2015 Nov 20.


Transcription factors, chromatin proteins and the diversification of Hemiptera.

Vidal NM, Grazziotin AL, Iyer LM, Aravind L, Venancio TM.

Insect Biochem Mol Biol. 2016 Feb;69:1-13. doi: 10.1016/j.ibmb.2015.07.001. Epub 2015 Jul 29.


Proteasomal control of cytokinin synthesis protects Mycobacterium tuberculosis against nitric oxide.

Samanovic MI, Tu S, Novák O, Iyer LM, McAllister FE, Aravind L, Gygi SP, Hubbard SR, Strnad M, Darwin KH.

Mol Cell. 2015 Mar 19;57(6):984-994. doi: 10.1016/j.molcel.2015.01.024. Epub 2015 Feb 26.


Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea.

Chavez L, Huang Y, Luong K, Agarwal S, Iyer LM, Pastor WA, Hench VK, Frazier-Bowers SA, Korol E, Liu S, Tahiliani M, Wang Y, Clark TA, Korlach J, Pukkila PJ, Aravind L, Rao A.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):E5149-58. doi: 10.1073/pnas.1419513111. Epub 2014 Nov 18.


Multiple enzymatic activities of ParB/Srx superfamily mediate sexual conflict among conjugative plasmids.

Maindola P, Raina R, Goyal P, Atmakuri K, Ojha A, Gupta S, Christie PJ, Iyer LM, Aravind L, Arockiasamy A.

Nat Commun. 2014 Oct 31;5:5322. doi: 10.1038/ncomms6322.


Selection of the lamprey VLRC antigen receptor repertoire.

Holland SJ, Gao M, Hirano M, Iyer LM, Luo M, Schorpp M, Cooper MD, Aravind L, Mariuzza RA, Boehm T.

Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14834-9. doi: 10.1073/pnas.1415655111. Epub 2014 Sep 16.


Genomic donor cassette sharing during VLRA and VLRC assembly in jawless vertebrates.

Das S, Li J, Holland SJ, Iyer LM, Hirano M, Schorpp M, Aravind L, Cooper MD, Boehm T.

Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14828-33. doi: 10.1073/pnas.1415580111. Epub 2014 Sep 16.


The natural history of ADP-ribosyltransferases and the ADP-ribosylation system.

Aravind L, Zhang D, de Souza RF, Anand S, Iyer LM.

Curr Top Microbiol Immunol. 2015;384:3-32. doi: 10.1007/82_2014_414. Review.


Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics.

Aravind L, Burroughs AM, Zhang D, Iyer LM.

Cold Spring Harb Perspect Biol. 2014 Jul 1;6(7):a016063. doi: 10.1101/cshperspect.a016063. Review.


Resilience of biochemical activity in protein domains in the face of structural divergence.

Zhang D, Iyer LM, Burroughs AM, Aravind L.

Curr Opin Struct Biol. 2014 Jun;26:92-103. doi: 10.1016/ Epub 2014 Jun 19. Review.


A TET homologue protein from Coprinopsis cinerea (CcTET) that biochemically converts 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine.

Zhang L, Chen W, Iyer LM, Hu J, Wang G, Fu Y, Yu M, Dai Q, Aravind L, He C.

J Am Chem Soc. 2014 Apr 2;136(13):4801-4. doi: 10.1021/ja500979k. Epub 2014 Mar 25.


Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes.

Iyer LM, Zhang D, de Souza RF, Pukkila PJ, Rao A, Aravind L.

Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1676-83. doi: 10.1073/pnas.1321818111. Epub 2014 Jan 7.


Gene networks and chromatin and transcriptional regulation of the phaseolin promoter in Arabidopsis.

Sundaram S, Kertbundit S, Shakirov EV, Iyer LM, Jurícek M, Hall TC.

Plant Cell. 2013 Jul;25(7):2601-17. doi: 10.1105/tpc.113.112714. Epub 2013 Jul 19.


Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA.

Iyer LM, Zhang D, Burroughs AM, Aravind L.

Nucleic Acids Res. 2013 Sep;41(16):7635-55. doi: 10.1093/nar/gkt573. Epub 2013 Jun 28.


A hemolytic pigment of Group B Streptococcus allows bacterial penetration of human placenta.

Whidbey C, Harrell MI, Burnside K, Ngo L, Becraft AK, Iyer LM, Aravind L, Hitti J, Adams Waldorf KM, Rajagopal L.

J Exp Med. 2013 Jun 3;210(6):1265-81. doi: 10.1084/jem.20122753. Epub 2013 May 27.


Discovery of Novel DENN Proteins: Implications for the Evolution of Eukaryotic Intracellular Membrane Structures and Human Disease.

Zhang D, Iyer LM, He F, Aravind L.

Front Genet. 2012 Dec 13;3:283. doi: 10.3389/fgene.2012.00283. eCollection 2012.


Gene flow and biological conflict systems in the origin and evolution of eukaryotes.

Aravind L, Anantharaman V, Zhang D, de Souza RF, Iyer LM.

Front Cell Infect Microbiol. 2012 Jun 29;2:89. doi: 10.3389/fcimb.2012.00089. eCollection 2012.


Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms.

Zhang D, Iyer LM, Aravind L.

Bioinformatics. 2012 Oct 1;28(19):2407-11. Epub 2012 Jul 24.


Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics.

Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L.

Biol Direct. 2012 Jun 25;7:18. doi: 10.1186/1745-6150-7-18.


Structure and evolution of ubiquitin and ubiquitin-related domains.

Burroughs AM, Iyer LM, Aravind L.

Methods Mol Biol. 2012;832:15-63. doi: 10.1007/978-1-61779-474-2_2.


Insights from the architecture of the bacterial transcription apparatus.

Iyer LM, Aravind L.

J Struct Biol. 2012 Sep;179(3):299-319. doi: 10.1016/j.jsb.2011.12.013. Epub 2011 Dec 24.


The natural history of ubiquitin and ubiquitin-related domains.

Burroughs AM, Iyer LM, Aravind L.

Front Biosci (Landmark Ed). 2012 Jan 1;17:1433-60. Review.


The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications.

Aravind L, Iyer LM.

Cell Cycle. 2012 Jan 1;11(1):119-31. doi: 10.4161/cc.11.1.18475. Epub 2012 Jan 1.


Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems.

Iyer LM, Zhang D, Rogozin IB, Aravind L.

Nucleic Acids Res. 2011 Dec;39(22):9473-97. doi: 10.1093/nar/gkr691. Epub 2011 Sep 3.


Functional diversification of the RING finger and other binuclear treble clef domains in prokaryotes and the early evolution of the ubiquitin system.

Burroughs AM, Iyer LM, Aravind L.

Mol Biosyst. 2011 Jul;7(7):2261-77. doi: 10.1039/c1mb05061c. Epub 2011 May 6.


Natural history of the eukaryotic chromatin protein methylation system.

Aravind L, Abhiman S, Iyer LM.

Prog Mol Biol Transl Sci. 2011;101:105-76. doi: 10.1016/B978-0-12-387685-0.00004-4.


Natural history of eukaryotic DNA methylation systems.

Iyer LM, Abhiman S, Aravind L.

Prog Mol Biol Transl Sci. 2011;101:25-104. doi: 10.1016/B978-0-12-387685-0.00002-0.


A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems.

Zhang D, Iyer LM, Aravind L.

Nucleic Acids Res. 2011 Jun;39(11):4532-52. doi: 10.1093/nar/gkr036. Epub 2011 Feb 8.


Predicted class-I aminoacyl tRNA synthetase-like proteins in non-ribosomal peptide synthesis.

Aravind L, de Souza RF, Iyer LM.

Biol Direct. 2010 Aug 2;5:48. doi: 10.1186/1745-6150-5-48.


A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey.

Deng L, Velikovsky CA, Xu G, Iyer LM, Tasumi S, Kerzic MC, Flajnik MF, Aravind L, Pancer Z, Mariuzza RA.

Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13408-13. doi: 10.1073/pnas.1005475107. Epub 2010 Jul 8.


Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase.

Iyer LM, Abhiman S, de Souza RF, Aravind L.

Nucleic Acids Res. 2010 Sep;38(16):5261-79. doi: 10.1093/nar/gkq265. Epub 2010 Apr 27.


Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins.

Iyer LM, Abhiman S, Maxwell Burroughs A, Aravind L.

Mol Biosyst. 2009 Dec;5(12):1636-60. doi: 10.1039/b917682a. Epub 2009 Oct 13.

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