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Items: 48

1.

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.

2.

Identifying and characterizing functional 3' nucleotide addition in the miRNA pathway.

Burroughs AM, Ando Y.

Methods. 2019 Jan 1;152:23-30. doi: 10.1016/j.ymeth.2018.08.006. Epub 2018 Aug 20. Review.

3.

Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes.

Verma R, Reichermeier KM, Burroughs AM, Oania RS, Reitsma JM, Aravind L, Deshaies RJ.

Nature. 2018 May;557(7705):446-451. doi: 10.1038/s41586-018-0022-5. Epub 2018 Apr 9.

4.

An integrated expression atlas of miRNAs and their promoters in human and mouse.

de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, Åström G, Babina M, Bertin N, Burroughs AM, Carlisle AJ, Daub CO, Detmar M, Deviatiiarov R, Fort A, Gebhard C, Goldowitz D, Guhl S, Ha TJ, Harshbarger J, Hasegawa A, Hashimoto K, Herlyn M, Heutink P, Hitchens KJ, Hon CC, Huang E, Ishizu Y, Kai C, Kasukawa T, Klinken P, Lassmann T, Lecellier CH, Lee W, Lizio M, Makeev V, Mathelier A, Medvedeva YA, Mejhert N, Mungall CJ, Noma S, Ohshima M, Okada-Hatakeyama M, Persson H, Rizzu P, Roudnicky F, Sætrom P, Sato H, Severin J, Shin JW, Swoboda RK, Tarui H, Toyoda H, Vitting-Seerup K, Winteringham L, Yamaguchi Y, Yasuzawa K, Yoneda M, Yumoto N, Zabierowski S, Zhang PG, Wells CA, Summers KM, Kawaji H, Sandelin A, Rehli M; FANTOM Consortium, Hayashizaki Y, Carninci P, Forrest ARR, de Hoon MJL.

Nat Biotechnol. 2017 Sep;35(9):872-878. doi: 10.1038/nbt.3947. Epub 2017 Aug 21.

5.

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.

6.

Novel clades of the HU/IHF superfamily point to unexpected roles in the eukaryotic centrosome, chromosome partitioning, and biologic conflicts.

Burroughs AM, Kaur G, Zhang D, Aravind L.

Cell Cycle. 2017 Jun 3;16(11):1093-1103. doi: 10.1080/15384101.2017.1315494. Epub 2017 Apr 25.

7.

An atlas of human long non-coding RNAs with accurate 5' ends.

Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M, Hasegawa A, Tang D, Lassmann T, Heutink P, Babina M, Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, de Hoon MJ, Arner E, Hayashizaki Y, Carninci P, Forrest AR.

Nature. 2017 Mar 9;543(7644):199-204. doi: 10.1038/nature21374. Epub 2017 Mar 1.

PMID:
28241135
8.

Global analysis of pre-mRNA subcellular localization following splicing inhibition by spliceostatin A.

Yoshimoto R, Kaida D, Furuno M, Burroughs AM, Noma S, Suzuki H, Kawamura Y, Hayashizaki Y, Mayeda A, Yoshida M.

RNA. 2017 Jan;23(1):47-57. Epub 2016 Oct 17.

9.

RNA damage in biological conflicts and the diversity of responding RNA repair systems.

Burroughs AM, Aravind L.

Nucleic Acids Res. 2016 Oct 14;44(18):8525-8555. Epub 2016 Aug 17. Review.

10.

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.

11.

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.

12.
13.

Analysis of two domains with novel RNA-processing activities throws light on the complex evolution of ribosomal RNA biogenesis.

Burroughs AM, Aravind L.

Front Genet. 2014 Dec 23;5:424. doi: 10.3389/fgene.2014.00424. eCollection 2014.

14.

Exploring allosteric activation of LigAB from Sphingobium sp. strain SYK-6 through kinetics, mutagenesis and computational studies.

Barry KP, Ngu A, Cohn EF, Cote JM, Burroughs AM, Gerbino JP, Taylor EA.

Arch Biochem Biophys. 2015 Feb 1;567:35-45. doi: 10.1016/j.abb.2014.12.019. Epub 2015 Jan 3.

PMID:
25562402
15.

PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.

Boele J, Persson H, Shin JW, Ishizu Y, Newie IS, Søkilde R, Hawkins SM, Coarfa C, Ikeda K, Takayama K, Horie-Inoue K, Ando Y, Burroughs AM, Sasaki C, Suzuki C, Sakai M, Aoki S, Ogawa A, Hasegawa A, Lizio M, Kaida K, Teusink B, Carninci P, Suzuki H, Inoue S, Gunaratne PH, Rovira C, Hayashizaki Y, de Hoon MJ.

Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11467-72. doi: 10.1073/pnas.1317751111. Epub 2014 Jul 21.

16.

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.

17.

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/j.sbi.2014.05.008. Epub 2014 Jun 19. Review.

18.

A promoter-level mammalian expression atlas.

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

19.

An atlas of active enhancers across human cell types and tissues.

Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A.

Nature. 2014 Mar 27;507(7493):455-461. doi: 10.1038/nature12787.

20.
21.

New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing.

Burroughs AM, Ando Y, Aravind L.

Wiley Interdiscip Rev RNA. 2014 Mar-Apr;5(2):141-81. doi: 10.1002/wrna.1210. Epub 2013 Dec 5. Review.

22.

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.

23.

RNA-interference components are dispensable for transcriptional silencing of the drosophila bithorax-complex.

Cernilogar FM, Burroughs AM, Lanzuolo C, Breiling A, Imhof A, Orlando V.

PLoS One. 2013 Jun 13;8(6):e65740. doi: 10.1371/journal.pone.0065740. Print 2013.

24.

Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing.

Anantharaman V, Makarova KS, Burroughs AM, Koonin EV, Aravind L.

Biol Direct. 2013 Jun 15;8:15. doi: 10.1186/1745-6150-8-15.

25.
26.

Structural and functional characterization of MppR, an enduracididine biosynthetic enzyme from streptomyces hygroscopicus: functional diversity in the acetoacetate decarboxylase-like superfamily.

Burroughs AM, Hoppe RW, Goebel NC, Sayyed BH, Voegtline TJ, Schwabacher AW, Zabriskie TM, Silvaggi NR.

Biochemistry. 2013 Jul 2;52(26):4492-506. doi: 10.1021/bi400397k. Epub 2013 Jun 21.

27.

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.

PMID:
22350875
28.

Nonimmunoglobulin target loci of activation-induced cytidine deaminase (AID) share unique features with immunoglobulin genes.

Kato L, Begum NA, Burroughs AM, Doi T, Kawai J, Daub CO, Kawaguchi T, Matsuda F, Hayashizaki Y, Honjo T.

Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2479-84. doi: 10.1073/pnas.1120791109. Epub 2012 Jan 30.

29.

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.

30.

pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns.

Burroughs AM, Kawano M, Ando Y, Daub CO, Hayashizaki Y.

Nucleic Acids Res. 2012 Feb;40(4):1424-37. doi: 10.1093/nar/gkr903. Epub 2011 Nov 3.

31.

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila.

Cernilogar FM, Onorati MC, Kothe GO, Burroughs AM, Parsi KM, Breiling A, Lo Sardo F, Saxena A, Miyoshi K, Siomi H, Siomi MC, Carninci P, Gilmour DS, Corona DF, Orlando V.

Nature. 2011 Nov 6;480(7377):391-5. doi: 10.1038/nature10492.

32.

Nuclear pore complex protein mediated nuclear localization of dicer protein in human cells.

Ando Y, Tomaru Y, Morinaga A, Burroughs AM, Kawaji H, Kubosaki A, Kimura R, Tagata M, Ino Y, Hirano H, Chiba J, Suzuki H, Carninci P, Hayashizaki Y.

PLoS One. 2011;6(8):e23385. doi: 10.1371/journal.pone.0023385. Epub 2011 Aug 15.

33.

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.

34.

Two-step cleavage of hairpin RNA with 5' overhangs by human DICER.

Ando Y, Maida Y, Morinaga A, Burroughs AM, Kimura R, Chiba J, Suzuki H, Masutomi K, Hayashizaki Y.

BMC Mol Biol. 2011 Feb 9;12:6. doi: 10.1186/1471-2199-12-6.

35.

Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin.

Burroughs AM, Ando Y, de Hoon MJ, Tomaru Y, Suzuki H, Hayashizaki Y, Daub CO.

RNA Biol. 2011 Jan-Feb;8(1):158-77. Epub 2011 Jan 1.

36.

A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness.

Burroughs AM, Ando Y, de Hoon MJ, Tomaru Y, Nishibu T, Ukekawa R, Funakoshi T, Kurokawa T, Suzuki H, Hayashizaki Y, Daub CO.

Genome Res. 2010 Oct;20(10):1398-410. doi: 10.1101/gr.106054.110. Epub 2010 Aug 18.

37.

Natural history of the E1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation.

Burroughs AM, Iyer LM, Aravind L.

Proteins. 2009 Jun;75(4):895-910. doi: 10.1002/prot.22298.

38.

Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination.

Iyer LM, Burroughs AM, Aravind L.

Biol Direct. 2008 Nov 3;3:45. doi: 10.1186/1745-6150-3-45.

39.

Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems.

Burroughs AM, Iyer LM, Aravind L.

Genome Dyn. 2007;3:48-65. doi: 10.1159/000107603. Review.

40.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M.

Nature. 2008 Apr 24;452(7190):991-6. doi: 10.1038/nature06856.

41.

Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation.

Burroughs AM, Jaffee M, Iyer LM, Aravind L.

J Struct Biol. 2008 May;162(2):205-18. doi: 10.1016/j.jsb.2007.12.006. Epub 2008 Jan 1.

42.

The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function.

Peisach E, Wang L, Burroughs AM, Aravind L, Dunaway-Mariano D, Allen KN.

Proteins. 2008 Jan 1;70(1):197-207.

PMID:
17654544
43.

Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.

Burroughs AM, Balaji S, Iyer LM, Aravind L.

Biol Direct. 2007 Jul 2;2:18.

44.

A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands.

Burroughs AM, Balaji S, Iyer LM, Aravind L.

Biol Direct. 2007 Jan 24;2:4.

45.

Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes.

Burroughs AM, Allen KN, Dunaway-Mariano D, Aravind L.

J Mol Biol. 2006 Sep 1;361(5):1003-34. Epub 2006 Jul 7.

PMID:
16889794
48.

The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism.

Iyer LM, Burroughs AM, Aravind L.

Bioinformatics. 2006 Feb 1;22(3):257-63. Epub 2005 Dec 1.

PMID:
16322048

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