-
2
-
-
0036529621
-
Comparative genomics and evolution of proteins involved in RNA metabolism
-
Anantharaman V, Koonin EV, Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res 2002; 30:1427-1464 (Pubitemid 34679722)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.7
, pp. 1427-1464
-
-
Anantharaman, V.1
Koonin, E.V.2
Aravind, L.3
-
3
-
-
58149191269
-
MODOMICS: A database of RNA modification pathways. 2008 update
-
Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, et al. MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res 2009; 37:118-121
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 118-121
-
-
Czerwoniec, A.1
Dunin-Horkawicz, S.2
Purta, E.3
Kaminska, K.H.4
Kasprzak, J.M.5
Bujnicki, J.M.6
-
4
-
-
33846078626
-
REBASE - Enzymes and genes for DNA restriction and modification
-
DOI 10.1093/nar/gkl891
-
Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE - enzymes and genes for DNA restriction and modification. Nucleic Acids Res 2007; 35:269-270 (Pubitemid 46056212)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Roberts, R.J.1
Vincze, T.2
Posfai, J.3
Macelis, D.4
-
6
-
-
0035883519
-
Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution
-
Kobayashi I. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 2001; 29:3742-3756 (Pubitemid 32910516)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.18
, pp. 3742-3756
-
-
Kobayashi, I.1
-
8
-
-
0019248608
-
Modified bases in bacteriophage DNAs
-
Warren RA. Modified bases in bacteriophage DNAs. Annu Rev Microbiol 1980; 34:137-158
-
(1980)
Annu Rev Microbiol
, vol.34
, pp. 137-158
-
-
Warren, R.A.1
-
9
-
-
33646008874
-
N6-methyl-adenine: An epigenetic signal for DNA-protein interactions
-
Wion D, Casadesus J. N6-methyl-adenine: an epigenetic signal for DNA-protein interactions. Nat Rev 2006; 4:183-192
-
(2006)
Nat Rev
, vol.4
, pp. 183-192
-
-
Wion, D.1
Casadesus, J.2
-
10
-
-
15744401773
-
Eukaryotic cytosine methyltransferases
-
DOI 10.1146/annurev.biochem.74.010904.153721
-
Goll MG, Bestor TH. Eukaryotic cytosine methyltransferases. Annu Rev Biochem 2005; 74:481-514. (Pubitemid 40995515)
-
(2005)
Annual Review of Biochemistry
, vol.74
, pp. 481-514
-
-
Goll, M.G.1
Bestor, T.H.2
-
11
-
-
37049002223
-
Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes
-
DOI 10.1016/j.ijpara.2007.07.018, PII S0020751907003001
-
Iyer LM, Anantharaman V, Wolf MY, Aravind L. Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. Int J Parasitol 2008; 38:1-31. (Pubitemid 350251386)
-
(2008)
International Journal for Parasitology
, vol.38
, Issue.1
, pp. 1-31
-
-
Iyer, L.M.1
Anantharaman, V.2
Wolf, M.Y.3
Aravind, L.4
-
12
-
-
43749098985
-
DNA methylation landscapes: Provocative insights from epigenomics
-
Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008; 9:465-476
-
(2008)
Nat Rev Genet
, vol.9
, pp. 465-476
-
-
Suzuki, M.M.1
Bird, A.2
-
14
-
-
0029145415
-
Hypermodified bases in DNA
-
Gommers-Ampt JH, Borst P. Hypermodified bases in DNA. Faseb J 1995; 9:1034-1042
-
(1995)
Faseb J
, vol.9
, pp. 1034-1042
-
-
Gommers-Ampt, J.H.1
Borst, P.2
-
15
-
-
0037083364
-
Requirement of the activation-induced deaminase (AID) gene for immunoglobulin gene conversion
-
DOI 10.1126/science.1067308
-
Arakawa H, Hauschild J, Buerstedde JM. Requirement of the activation-induced deaminase (AID) gene for immunoglobulin gene conversion. Science (New York, NY) 2002; 295:1301-1306 (Pubitemid 34157623)
-
(2002)
Science
, vol.295
, Issue.5558
, pp. 1301-1306
-
-
Arakawa, H.1
Hauschild, J.2
Buerstedde, J.-M.3
-
16
-
-
0034268780
-
Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme
-
Muramatsu M, Kinoshita K, Fagarasan S, Yamada S, Shinkai Y, Honjo T. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 2000; 102:553-563
-
(2000)
Cell
, vol.102
, pp. 553-563
-
-
Muramatsu, M.1
Kinoshita, K.2
Fagarasan, S.3
Yamada, S.4
Shinkai, Y.5
Honjo, T.6
-
17
-
-
34249065874
-
Evolution and diversification of lamprey antigen receptors: Evidence for involvement of an AID-APOBEC family cytosine deaminase
-
DOI 10.1038/ni1463, PII NI1463
-
Rogozin IB, Iyer LM, Liang L, Glazko GV, Liston VG, Pavlov YI, et al. Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase. Nat Immunol 2007; 8:647-656 (Pubitemid 46785129)
-
(2007)
Nature Immunology
, vol.8
, Issue.6
, pp. 647-656
-
-
Rogozin, I.B.1
Iyer, L.M.2
Liang, L.3
Glazko, G.V.4
Liston, V.G.5
Pavlov, Y.I.6
Aravind, L.7
Pancer, Z.8
-
18
-
-
53849113697
-
Base J: Discovery, biosynthesis and possible functions
-
Borst P, Sabatini R. Base J: discovery, biosynthesis and possible functions. Annual review of microbiology 2008; 62:235-251
-
(2008)
Annual Review of Microbiology
, vol.62
, pp. 235-251
-
-
Borst, P.1
Sabatini, R.2
-
19
-
-
34548603504
-
Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation
-
DOI 10.1038/nature06146, PII NATURE06146
-
Jia D, Jurkowska RZ, Zhang X, Jeltsch A, Cheng X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 2007; 449:248-251 (Pubitemid 47402375)
-
(2007)
Nature
, vol.449
, Issue.7159
, pp. 248-251
-
-
Jia, D.1
Jurkowska, R.Z.2
Zhang, X.3
Jeltsch, A.4
Cheng, X.5
-
20
-
-
33646088737
-
Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase
-
Horton JR, Liebert K, Bekes M, Jeltsch A, Cheng X. Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase. J Mol Biol 2006; 358:559-570
-
(2006)
J Mol Biol
, vol.358
, pp. 559-570
-
-
Horton, J.R.1
Liebert, K.2
Bekes, M.3
Jeltsch, A.4
Cheng, X.5
-
21
-
-
0032535109
-
Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniae bound to S-adenosylmethionine
-
Tran PH, Korszun ZR, Cerritelli S, Springhorn SS, Lacks SA. Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine. Structure 1998; 6:1563-1575 (Pubitemid 29000533)
-
(1998)
Structure
, vol.6
, Issue.12
, pp. 1563-1575
-
-
Tran, P.H.1
Korszun, Z.R.2
Cerritelli, S.3
Springhorn, S.S.4
Lacks, S.A.5
-
22
-
-
0029068629
-
The crystal structure of HaeIII methyltransferase convalently complexed to DNA: An extrahelical cytosine and rearranged base pairing
-
Reinisch KM, Chen L, Verdine GL, Lipscomb WN. The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell 1995; 82:143-153
-
(1995)
Cell
, vol.82
, pp. 143-153
-
-
Reinisch, K.M.1
Chen, L.2
Verdine, G.L.3
Lipscomb, W.N.4
-
23
-
-
0033105429
-
Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex
-
Song HK, Sohn SH, Suh SW. Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex. EMBO J 1999; 18:1104-1113 (Pubitemid 29110296)
-
(1999)
EMBO Journal
, vol.18
, Issue.5
, pp. 1104-1113
-
-
Song, H.K.1
Sohn, S.H.2
Suh, S.W.3
-
24
-
-
0028969335
-
Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme
-
Holm L, Sander C. Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme. EMBO J 1995; 14:1287-1293
-
(1995)
EMBO J
, vol.14
, pp. 1287-1293
-
-
Holm, L.1
Sander, C.2
-
25
-
-
0035902864
-
High resolution crystal structures of T4 phage beta-glucosyltransferase: Induced fit and effect of substrate and metal binding
-
DOI 10.1006/jmbi.2001.4905
-
Morera S, Lariviere L, Kurzeck J, Aschke-Sonnenborn U, Freemont PS, Janin J, Ruger W. High resolution crystal structures of T4 phage beta- glucosyltransferase: induced fit and effect of substrate and metal binding. J Mol Biol 2001; 311:569-577 (Pubitemid 32816590)
-
(2001)
Journal of Molecular Biology
, vol.311
, Issue.3
, pp. 569-577
-
-
Morera, S.1
Lariviere, L.2
Kurzeck, J.3
Aschke-Sonnenborn, U.4
Freemont, P.S.5
Janin, J.6
Ruger, W.7
-
26
-
-
38349118270
-
Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily
-
Georgetown, Tex
-
Kaminska KH, Bujnicki JM. Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily. Cell cycle (Georgetown, Tex) 2008; 7:120-121
-
(2008)
Cell Cycle
, vol.7
, pp. 120-121
-
-
Kaminska, K.H.1
Bujnicki, J.M.2
-
27
-
-
59649125285
-
Evidence that J-binding protein 2 is a thymidine hydroxylase catalyzing the first step in the biosynthesis of DNA base J
-
Vainio S, Genest PA, Ter Riet B, van Luenen H, Borst P. Evidence that J-binding protein 2 is a thymidine hydroxylase catalyzing the first step in the biosynthesis of DNA base J. Mol Biochem Parasitol 2009; 164:157-161
-
(2009)
Mol Biochem Parasitol
, vol.164
, pp. 157-161
-
-
Vainio, S.1
Genest, P.A.2
Ter Riet, B.3
Van Luenen, H.4
Borst, P.5
-
28
-
-
34249845812
-
The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase
-
Yu Z, Genest PA, ter Riet B, Sweeney K, DiPaolo C, Kieft R, et al. The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. Nucleic Acids Res 2007; 35:2107-2115
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 2107-2115
-
-
Yu, Z.1
Genest, P.A.2
Ter Riet, B.3
Sweeney, K.4
DiPaolo, C.5
Kieft, R.6
-
29
-
-
0030726204
-
Identification of strictly conserved histidine and arginine residues as part of the active site in Petunia hybrida flavanone 3beta-hydroxylase
-
Lukacin R, Britsch L. Identification of strictly conserved histidine and arginine residues as part of the active site in Petunia hybrida flavanone 3beta-hydroxylase. Eur J Biochem 1997; 249:748-757
-
(1997)
Eur J Biochem
, vol.249
, pp. 748-757
-
-
Lukacin, R.1
Britsch, L.2
-
30
-
-
0035663669
-
Structure of proline 3-hydroxylase: Evolution of the family of 2-oxoglutarate dependent oxygenases
-
DOI 10.1046/j.0014-2956.2001.02617.x
-
Clifton IJ, Hsueh LC, Baldwin JE, Harlos K, Schofield CJ. Structure of proline 3-hydroxylase. Evolution of the family of 2-oxoglutarate dependent oxygenases. Eur J Biochem 2001; 268:6625-6636 (Pubitemid 34014770)
-
(2001)
European Journal of Biochemistry
, vol.268
, Issue.24
, pp. 6625-6636
-
-
Clifton, I.J.1
Hsueh, L.-C.2
Baldwin, J.E.3
Harlos, K.4
Schofield, C.J.5
-
31
-
-
0029038392
-
Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes
-
Roach PL, Clifton IJ, Fulop V, Harlos K, Barton GJ, Hajdu J, et al. Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes. Nature 1995; 375:700-704
-
(1995)
Nature
, vol.375
, pp. 700-704
-
-
Roach, P.L.1
Clifton, I.J.2
Fulop, V.3
Harlos, K.4
Barton, G.J.5
Hajdu, J.6
-
32
-
-
19744376088
-
Genes of the thymidine salvage pathway: Thymine-7-hydroxylase from a Rhodotorula glutinis cDNA library and iso-orotate decarboxylase from Neurospora crassa
-
DOI 10.1016/j.bbagen.2005.02.001, PII S0304416505000322
-
Smiley JA, Kundracik M, Landfried DA, Barnes VR, Sr., Axhemi AA. Genes of the thymidine salvage pathway: thymine-7-hydroxylase from a Rhodotorula glutinis cDNA library and iso-orotate decarboxylase from Neurospora crassa. Biochim Biophys Acta 2005; 1723:256-264 (Pubitemid 40744694)
-
(2005)
Biochimica et Biophysica Acta - General Subjects
, vol.1723
, Issue.1-3
, pp. 256-264
-
-
Smiley, J.A.1
Kundracik, M.2
Landfried, D.A.3
Barnes Sr., V.R.4
Axhemi, A.A.5
-
33
-
-
0037068446
-
Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage
-
Trewick SC, Henshaw TF, Hausinger RP, Lindahl T, Sedgwick B. Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage. Nature 2002; 419:174-178
-
(2002)
Nature
, vol.419
, pp. 174-178
-
-
Trewick, S.C.1
Henshaw, T.F.2
Hausinger, R.P.3
Lindahl, T.4
Sedgwick, B.5
-
34
-
-
0035221419
-
The DNA-repair protein AlkB, EGL-9 and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases
-
Aravind L, Koonin EV. The DNA-repair protein AlkB, EGL-9 and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Genome Biol 2001; 2:7.
-
(2001)
Genome Biol
, vol.2
, pp. 7
-
-
Aravind, L.1
Koonin, E.V.2
-
35
-
-
13244251108
-
Regulation of Trypanosome DNA Glycosylation by a SWI2/SNF2-like Protein
-
DOI 10.1016/j.molcel.2004.12.022, PII S1097276505010099
-
DiPaolo C, Kieft R, Cross M, Sabatini R. Regulation of trypanosome DNA glycosylation by a SWI2/SNF2-like protein. Mol Cell 2005; 17:441-451 (Pubitemid 40193314)
-
(2005)
Molecular Cell
, vol.17
, Issue.3
, pp. 441-451
-
-
Dipaolo, C.1
Kieft, R.2
Cross, M.3
Sabatini, R.4
-
36
-
-
32844455577
-
Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB
-
DOI 10.1038/nature04561, PII NATURE04561
-
Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF. Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature 2006; 439:879-884 (Pubitemid 43255709)
-
(2006)
Nature
, vol.439
, Issue.7078
, pp. 879-884
-
-
Yu, B.1
Edstrom, W.C.2
Benach, J.3
Hamuro, Y.4
Weber, P.C.5
Gibney, B.R.6
Hunt, J.F.7
-
37
-
-
0037350661
-
TET1, a member of a novel protein family, is fused to MLL in acute myeloid leukemia containing the t(10;11)(q22;23) [3]
-
DOI 10.1038/sj.leu.2402834
-
Lorsbach RB, Moore J, Mathew S, Raimondi SC, Mukatira ST, Downing JR. TET1, a member of a novel protein family, is fused to MLL in acute myeloid leukemia containing the t(10;11)(q22;q23). Leukemia 2003; 17:637-641 (Pubitemid 36395661)
-
(2003)
Leukemia
, vol.17
, Issue.3
, pp. 637-641
-
-
Lorsback, R.B.1
Moore, J.2
Mathew, S.3
Raimondi, S.C.4
Mukatira, S.T.5
Downing, J.R.6
-
38
-
-
85011941017
-
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by the MLL fusion partner
-
In Press
-
Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by the MLL fusion partner, TET1 2009; In Press.
-
(2009)
TET1
-
-
Tahiliani, M.1
Koh, K.P.2
Shen, Y.3
Pastor, W.A.4
Bandukwala, H.5
Brudno, Y.6
-
39
-
-
0030977310
-
A component of the transcriptional repressor MeCP1 shares a motif with DNA methyltransferase and HRX proteins
-
DOI 10.1038/ng0797-256
-
Cross SH, Meehan RR, Nan X, Bird A. A component of the transcriptional repressor MeCP1 shares a motif with DNA methyltransferase and HRX proteins. Nature Genet 1997; 16:256-259 (Pubitemid 27280208)
-
(1997)
Nature Genetics
, vol.16
, Issue.3
, pp. 256-257
-
-
Cross, S.H.1
Meehan, R.R.2
Nan, X.3
Bird, A.4
-
40
-
-
33749369772
-
Solution structure of the nonmethyl-CpG-binding CXXC domain of the leukaemia-associated MLL histone methyltransferase
-
DOI 10.1038/sj.emboj.7601340, PII 7601340
-
Allen MD, Grummitt CG, Hilcenko C, Min SY, Tonkin LM, Johnson CM, et al. Solution structure of the nonmethyl-CpG-binding CXXC domain of the leukaemia-associated MLL histone methyltransferase. EMBO J 2006; 25:4503-4512 (Pubitemid 44498124)
-
(2006)
EMBO Journal
, vol.25
, Issue.19
, pp. 4503-4512
-
-
Allen, M.D.1
Grummitt, C.G.2
Hilcenko, C.3
Min, S.Y.4
Tonkin, L.M.5
Johnson, C.M.6
Freund, S.M.7
Bycroft, M.8
Warren, A.J.9
-
41
-
-
0034749352
-
Inhibition of the Wnt signaling pathway by Idax, a novel Dvl-binding protein
-
Hino S, Kishida S, Michiue T, Fukui A, Sakamoto I, Takada S, et al. Inhibition of the Wnt signaling pathway by Idax, a novel Dvl-binding protein. Mol Cell Biol 2001; 21:330-342
-
(2001)
Mol Cell Biol
, vol.21
, pp. 330-342
-
-
Hino, S.1
Kishida, S.2
Michiue, T.3
Fukui, A.4
Sakamoto, I.5
Takada, S.6
-
42
-
-
33646338187
-
Assembling the bacterial segrosome
-
DOI 10.1016/j.tibs.2006.03.002, PII S096800040600079X
-
Hayes F, Barilla D. Assembling the bacterial segrosome. Trends Biochem Sci 2006; 31:247-250 (Pubitemid 43674355)
-
(2006)
Trends in Biochemical Sciences
, vol.31
, Issue.5
, pp. 247-250
-
-
Hayes, F.1
Barilla, D.2
-
43
-
-
6044247519
-
Genome of bacteriophage P1
-
Lobocka MB, Rose DJ, Plunkett G, 3rd, Rusin M, Samojedny A, Lehnherr H, et al. Genome of bacteriophage P1. J Bacteriol 2004; 186:7032-7068
-
(2004)
J Bacteriol
, vol.186
, pp. 7032-7068
-
-
Lobocka, M.B.1
Rose, D.J.2
Plunkett III, G.3
Rusin, M.4
Samojedny, A.5
Lehnherr, H.6
-
44
-
-
7544240563
-
Shape-selective RNA recognition by cysteinyl-tRNA synthetase
-
DOI 10.1038/nsmb849
-
Hauenstein S, Zhang CM, Hou YM, Perona JJ. Shape-selective RNA recognition by cysteinyl-tRNA synthetase. Nat Struct Mol Biol 2004; 11:1134-1141 (Pubitemid 39453344)
-
(2004)
Nature Structural and Molecular Biology
, vol.11
, Issue.11
, pp. 1134-1141
-
-
Hauenstein, S.1
Zhang, C.-M.2
Hou, Y.-M.3
Perona, J.J.4
-
45
-
-
0029402597
-
The pseudouridine residues of ribosomal RNA
-
Ofengand J, Bakin A, Wrzesinski J, Nurse K, Lane BG. The pseudouridine residues of ribosomal RNA. Biochem Cell Biol 1995; 73:915-924
-
(1995)
Biochem Cell Biol
, vol.73
, pp. 915-924
-
-
Ofengand, J.1
Bakin, A.2
Wrzesinski, J.3
Nurse, K.4
Lane, B.G.5
-
46
-
-
0031000649
-
An evolutionary treasure: Unification of a broad set of amidohydrolases related to urease
-
DOI 10.1002/(SICI)1097-0134(199705)28:1<72::AID-PROT7>3.0.CO;2-L
-
Holm L, Sander C. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins 1997; 28:72-82. (Pubitemid 27194020)
-
(1997)
Proteins: Structure, Function and Genetics
, vol.28
, Issue.1
, pp. 72-82
-
-
Holm, L.1
Sander, C.2
-
47
-
-
0742305875
-
Repairing DNA-methylation damage
-
DOI 10.1038/nrm1312
-
Sedgwick B. Repairing DNA-methylation damage. Nat Rev Mol Cell Biol 2004; 5:148-157 (Pubitemid 38160257)
-
(2004)
Nature Reviews Molecular Cell Biology
, vol.5
, Issue.2
, pp. 148-157
-
-
Sedgwick, B.1
-
48
-
-
0035102449
-
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics
-
DOI 10.1128/MMBR.65.1.44-79.2001
-
Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ. Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev 2001; 65:44-79. (Pubitemid 32204287)
-
(2001)
Microbiology and Molecular Biology Reviews
, vol.65
, Issue.1
, pp. 44-79
-
-
Makarova, K.S.1
Aravind, L.2
Wolf, Y.I.3
Tatusov, R.L.4
Minton, K.W.5
Koonin, E.V.6
Daly, M.J.7
-
49
-
-
33846931283
-
The SRA Methyl-Cytosine-Binding Domain Links DNA and Histone Methylation
-
DOI 10.1016/j.cub.2007.01.009, PII S096098220700810X
-
Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 2007; 17:379-384 (Pubitemid 46241885)
-
(2007)
Current Biology
, vol.17
, Issue.4
, pp. 379-384
-
-
Johnson, L.M.1
Bostick, M.2
Zhang, X.3
Kraft, E.4
Henderson, I.5
Callis, J.6
Jacobsen, S.E.7
-
50
-
-
0032167733
-
The R3H motif: A domain that binds single-stranded nucleic acids
-
DOI 10.1016/S0968-0004(98)01258-4, PII S0968000498012584
-
Grishin NV. The R3H motif: a domain that binds single-stranded nucleic acids. Trends Biochem Sci 1998; 23:329-330 (Pubitemid 28461863)
-
(1998)
Trends in Biochemical Sciences
, vol.23
, Issue.9
, pp. 329-330
-
-
Grishin, N.V.1
-
51
-
-
0036066765
-
The role of lineage-specific gene family expansion in the evolution of eukaryotes
-
DOI 10.1101/gr.174302
-
Lespinet O, Wolf YI, Koonin EV, Aravind L. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res 2002; 12:1048-1059 (Pubitemid 34785197)
-
(2002)
Genome Research
, vol.12
, Issue.7
, pp. 1048-1059
-
-
Lespinet, O.1
Wolf, Y.I.2
Koonin, E.V.3
Aravind, L.4
-
52
-
-
0033575886
-
The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites
-
Hendrich B, Hardeland U, Ng HH, Jiricny J, Bird A. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature 1999; 401:301-304 (Pubitemid 129515547)
-
(1999)
Nature
, vol.401
, Issue.6750
, pp. 301-304
-
-
Hendrich, B.1
Hardeland, U.2
Ng, H.-H.3
Jiricny, J.4
Bird, A.5
-
54
-
-
0037352528
-
Maelstrom, a Drosophila spindle-class gene, encodes a protein that colocalizes with Vasa and RDE1/AGO1 homolog, aubergine, in nuage
-
DOI 10.1242/dev.00310
-
Findley SD, Tamanaha M, Clegg NJ, Ruohola-Baker H. Maelstrom, a Drosophila spindle-class gene, encodes a protein that colocalizes with Vasa and RDE1/AGO1 homolog, Aubergine, in nuage. Development (Cambridge, England) 2003; 130:859-871 (Pubitemid 36367507)
-
(2003)
Development
, vol.130
, Issue.5
, pp. 859-871
-
-
Findley, S.D.1
Tamanaha, M.2
Clegg, N.J.3
Ruohola-Baker, H.4
-
55
-
-
0034664813
-
SURVEY and SUMMARY: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories
-
Aravind L, Makarova KS, Koonin EV. SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res 2000; 28:3417-3432
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 3417-3432
-
-
Aravind, L.1
Makarova, K.S.2
Koonin, E.V.3
-
56
-
-
33646267428
-
Targeted gene silencing in the model mushroom Coprinopsis cinerea (Coprinus cinereus) by expression of homologous hairpin RNAs
-
Walti MA, Villalba C, Buser RM, Grunler A, Aebi M, Kunzler M. Targeted gene silencing in the model mushroom Coprinopsis cinerea (Coprinus cinereus) by expression of homologous hairpin RNAs. Eukaryot Cell 2006; 5:732-744
-
(2006)
Eukaryot Cell
, vol.5
, pp. 732-744
-
-
Walti, M.A.1
Villalba, C.2
Buser, R.M.3
Grunler, A.4
Aebi, M.5
Kunzler, M.6
-
57
-
-
48549092573
-
Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis
-
Soper SF, van der Heijden GW, Hardiman TC, Goodheart M, Martin SL, de Boer P, Bortvin A. Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis. Dev Cell 2008; 15:285-297
-
(2008)
Dev Cell
, vol.15
, pp. 285-297
-
-
Soper, S.F.1
Van Der Heijden, G.W.2
Hardiman, T.C.3
Goodheart, M.4
Martin, S.L.5
De Boer, P.6
Bortvin, A.7
-
58
-
-
32044470027
-
DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation
-
DOI 10.1016/j.cell.2005.12.034, PII S0092867406000687
-
Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, Harada JJ, et al. DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 2006; 124:495-506. (Pubitemid 43199436)
-
(2006)
Cell
, vol.124
, Issue.3
, pp. 495-506
-
-
Gehring, M.1
Huh, J.H.2
Hsieh, T.-F.3
Penterman, J.4
Choi, Y.5
Harada, J.J.6
Goldberg, R.B.7
Fischer, R.L.8
-
59
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389-3402 (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
60
-
-
0035878724
-
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
-
Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 2001; 29:2994-3005. (Pubitemid 32685225)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.14
, pp. 2994-3005
-
-
Schaffer, A.A.1
Aravind, L.2
Madden, T.L.3
Shavirin, S.4
Spouge, J.L.5
Wolf, Y.I.6
Koonin, E.V.7
Altschul, S.F.8
-
61
-
-
66749127100
-
Kalign2: High-performance multiple alignment of protein and nucleotide sequences allowing external features
-
Lassmann T, Frings O, Sonnhammer EL. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acids Res 2008.
-
(2008)
Nucleic Acids Res
-
-
Lassmann, T.1
Frings, O.2
Sonnhammer, E.L.3
-
62
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR. Profile hidden Markov models. Bioinformatics (Oxford, England) 1998; 14:755-763 (Pubitemid 28552108)
-
(1998)
Bioinformatics
, vol.14
, Issue.9
, pp. 755-763
-
-
Eddy, S.R.1
-
63
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
DOI 10.1093/nar/gki408
-
Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005; 33:244-248 (Pubitemid 44529917)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS
-
-
Soding, J.1
Biegert, A.2
Lupas, A.N.3
-
64
-
-
0034663597
-
Application of multiple sequence alignment profiles to improve protein secondary structure prediction
-
DOI 10.1002/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q
-
Cuff JA, Barton GJ. Application of multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 2000; 40:502-511 (Pubitemid 30624459)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.40
, Issue.3
, pp. 502-511
-
-
Cuff, J.A.1
Barton, G.J.2
-
65
-
-
33747788700
-
Comparative analysis of coiled-coil prediction methods
-
DOI 10.1016/j.jsb.2006.03.009, PII S1047847706000815, Fibrous Protein Structure
-
Gruber M, Soding J, Lupas AN. Comparative analysis of coiled-coil prediction methods. J Struct Biol 2006; 155:140-145 (Pubitemid 44278640)
-
(2006)
Journal of Structural Biology
, vol.155
, Issue.2
, pp. 140-145
-
-
Gruber, M.1
Soding, J.2
Lupas, A.N.3
-
66
-
-
0028501914
-
Non-globular domains in protein sequences: Automated segmentation using complexity measures
-
Wootton JC. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem 1994; 18:269-285
-
(1994)
Comput Chem
, vol.18
, pp. 269-285
-
-
Wootton, J.C.1
-
67
-
-
0031473847
-
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
-
DOI 10.1002/elps.1150181505
-
Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997; 18:2714-2723 (Pubitemid 28059943)
-
(1997)
Electrophoresis
, vol.18
, Issue.15
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
68
-
-
85011938394
-
-
Delano WL. San Carlos, CA: USA DeLano Scientific 2002
-
Delano WL. San Carlos, CA: USA DeLano Scientific 2002.
-
-
-
-
69
-
-
46649115430
-
Splign: Algorithms for computing spliced alignments with identification of paralogs
-
Kapustin Y, Souvorov A, Tatusova T, Lipman D. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol Direct 2008; 3:20.
-
(2008)
Biol Direct
, vol.3
, pp. 20
-
-
Kapustin, Y.1
Souvorov, A.2
Tatusova, T.3
Lipman, D.4
-
70
-
-
34548167888
-
-
BLASTCLUST program ftp://ftp.ncbi.nih.gov/blast/documents/blastclust. html.
-
BLASTCLUST Program
-
-
|