-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul S.F., T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller and D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, 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
-
2
-
-
0034077514
-
Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors?
-
Baliga N.S., Y.A. Goo, W.V. Ng, L. Hood, C.J. Daniels and S. DasSarma. 2000. Is gene expression in Halobacterium NRC-1 regulated by multiple TBP and TFB transcription factors? Mol. Microbiol. 36:1184-1185.
-
(2000)
Mol. Microbiol
, vol.36
, pp. 1184-1185
-
-
Baliga, N.S.1
Goo, Y.A.2
Ng, W.V.3
Hood, L.4
Daniels, C.J.5
DasSarma, S.6
-
3
-
-
9144257886
-
-
Bateman A., L. Coin, R. Durbin et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32 Database issue:D138-141.
-
Bateman A., L. Coin, R. Durbin et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32 Database issue:D138-141.
-
-
-
-
5
-
-
0034745386
-
The archaeal TFIIEalpha homologue facilitates transcription initiation by enhancing TATA-box recognition
-
2:133-138
-
Bell S.D., A.B. Brinkman, J. van der Oost and S.P. Jackson. 2001b. The archaeal TFIIEalpha homologue facilitates transcription initiation by enhancing TATA-box recognition. EMBO Rep. 2:133-138.
-
(2001)
EMBO Rep
-
-
Bell, S.D.1
Brinkman, A.B.2
van der Oost, J.3
Jackson, S.P.4
-
6
-
-
0037023326
-
The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation
-
Bell S.D., C.H. Botting, B.N. Wardleworth, S.P. Jackson and M.F. White. 2002. The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science 296:148-151.
-
(2002)
Science
, vol.296
, pp. 148-151
-
-
Bell, S.D.1
Botting, C.H.2
Wardleworth, B.N.3
Jackson, S.P.4
White, M.F.5
-
7
-
-
4544235395
-
Archaeal phylogeny based on proteins of the transcription and translation machineries: Tackling the Methanopyrus kandleri paradox
-
Brochier C., P. Forterre and S. Gribaldo. 2004. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol. 5:R17.01-12.
-
(2004)
Genome Biol
, vol.5
-
-
Brochier, C.1
Forterre, P.2
Gribaldo, S.3
-
8
-
-
0037665941
-
Transcription regulation and environmental adaptation in bacteria
-
Cases I., V. de Lorenzo and C.A. Ouzounis. 2003. Transcription regulation and environmental adaptation in bacteria. Trends Microbiol. 11:248-253.
-
(2003)
Trends Microbiol
, vol.11
, pp. 248-253
-
-
Cases, I.1
de Lorenzo, V.2
Ouzounis, C.A.3
-
9
-
-
0037440195
-
The phylogenetic diversity of eukaryotic transcription
-
Coulson R.M. and C.A. Ouzounis. 2003. The phylogenetic diversity of eukaryotic transcription. Nucleic Acids Res. 31:653-660.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 653-660
-
-
Coulson, R.M.1
Ouzounis, C.A.2
-
10
-
-
0035109743
-
Transcription- associated protein families are primarily taxon-specific
-
Coulson R.M., A.J. Enright and C.A. Ouzounis. 2001. Transcription- associated protein families are primarily taxon-specific. Bioinformatics 17:95-97.
-
(2001)
Bioinformatics
, vol.17
, pp. 95-97
-
-
Coulson, R.M.1
Enright, A.J.2
Ouzounis, C.A.3
-
11
-
-
4444339460
-
Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum
-
Coulson R.M., N. Hall and C.A. Ouzounis. 2004. Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res. 14:1548-1554.
-
(2004)
Genome Res
, vol.14
, pp. 1548-1554
-
-
Coulson, R.M.1
Hall, N.2
Ouzounis, C.A.3
-
12
-
-
0012606881
-
Extreme genomes
-
DeLong E.F. 2000. Extreme genomes. Genome Biol. 1:r10291-10293.
-
(2000)
Genome Biol
, vol.1
-
-
DeLong, E.F.1
-
13
-
-
0037308245
-
Archaea and their potential role in human disease
-
Eckburg P.B., P.W. Lepp and D.A. Relman. 2003. Archaea and their potential role in human disease. Infect. Immun. 71:591-596.
-
(2003)
Infect. Immun
, vol.71
, pp. 591-596
-
-
Eckburg, P.B.1
Lepp, P.W.2
Relman, D.A.3
-
14
-
-
0031743421
-
Profile hidden Markov models
-
Eddy S.R. 1998. Profile hidden Markov models. Bioinformatics 14:755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
15
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright A.J., S. Van Dongen and C.A. Ouzounis. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:1575-1584.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
16
-
-
0029967362
-
SRS: Information retrieval system for molecular biology data banks
-
Etzold T., A. Ulyanov and P. Argos. 1996. SRS: information retrieval system for molecular biology data banks. Methods Enzymol. 266:114-128.
-
(1996)
Methods Enzymol
, vol.266
, pp. 114-128
-
-
Etzold, T.1
Ulyanov, A.2
Argos, P.3
-
17
-
-
0036225678
-
The genome of M. acetivorans reveals extensive metabolic and physiological diversity
-
Galagan J.E., C. Nusbaum, A. Roy et al. 2002. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12:532-542.
-
(2002)
Genome Res
, vol.12
, pp. 532-542
-
-
Galagan, J.E.1
Nusbaum, C.2
Roy, A.3
-
18
-
-
20344386725
-
Archaeal transcription and its regulators
-
Geiduschek E.P. and M. Ouhammouch. 2005. Archaeal transcription and its regulators. Mol. Microbiol. 56:1397-1407.
-
(2005)
Mol. Microbiol
, vol.56
, pp. 1397-1407
-
-
Geiduschek, E.P.1
Ouhammouch, M.2
-
19
-
-
2442659081
-
Low-pass sequencing for microbial comparative genomics
-
Goo Y.A., J. Roach, G. Glusman et al. 2004. Low-pass sequencing for microbial comparative genomics. BMC Genomics 5:3.
-
(2004)
BMC Genomics
, vol.5
, pp. 3
-
-
Goo, Y.A.1
Roach, J.2
Glusman, G.3
-
20
-
-
0030271631
-
Activation and repression of E. coli promoters
-
Gralla J.D. 1996. Activation and repression of E. coli promoters. Curr. Opin. Genet. Dev. 6:526-530.
-
(1996)
Curr. Opin. Genet. Dev
, vol.6
, pp. 526-530
-
-
Gralla, J.D.1
-
21
-
-
0035116309
-
TFE, an archaeal transcription factor in Methanobacterium thermoautotrophicum related to eucaryal transcription factor TFIIEalpha
-
Hanzelka B.L., T.J. Darcy and J.N. Reeve. 2001. TFE, an archaeal transcription factor in Methanobacterium thermoautotrophicum related to eucaryal transcription factor TFIIEalpha. J. Bacteriol. 183:1813-1818.
-
(2001)
J. Bacteriol
, vol.183
, pp. 1813-1818
-
-
Hanzelka, B.L.1
Darcy, T.J.2
Reeve, J.N.3
-
22
-
-
22244437571
-
The genome of the kinetoplastid parasite, Leishmania major
-
Ivens A.C., C.S. Peacock, E.A. Worthey et al. 2005. The genome of the kinetoplastid parasite, Leishmania major. Science 309:436-442.
-
(2005)
Science
, vol.309
, pp. 436-442
-
-
Ivens, A.C.1
Peacock, C.S.2
Worthey, E.A.3
-
23
-
-
0042594458
-
COmplete GENome Tracking (COGENT): A flexible data environment for computational genomics
-
Janssen P., A.J. Enright, B. Audit, I. Cases, L. Goldovsky, N. Harte, V. Kunin and C.A. Ouzounis. 2003. COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics 19:1451-1452.
-
(2003)
Bioinformatics
, vol.19
, pp. 1451-1452
-
-
Janssen, P.1
Enright, A.J.2
Audit, B.3
Cases, I.4
Goldovsky, L.5
Harte, N.6
Kunin, V.7
Ouzounis, C.A.8
-
24
-
-
0028953815
-
The eubacterial transcriptional activator Lrp is present in the archaeon Pyrococcus furiosus
-
Kyrpides N.C. and C.A. Ouzounis. 1995. The eubacterial transcriptional activator Lrp is present in the archaeon Pyrococcus furiosus. Trends Biochem. Sci. 20:140-141.
-
(1995)
Trends Biochem. Sci
, vol.20
, pp. 140-141
-
-
Kyrpides, N.C.1
Ouzounis, C.A.2
-
25
-
-
0031308505
-
Bacterial sigma 70 transcription factor DNA-binding domains in the archaeon Methanococcus jannaschii
-
Kyrpides N.C. and C.A. Ouzounis. 1997. Bacterial sigma 70 transcription factor DNA-binding domains in the archaeon Methanococcus jannaschii. J. Mol. Evol. 45:706-707.
-
(1997)
J. Mol. Evol
, vol.45
, pp. 706-707
-
-
Kyrpides, N.C.1
Ouzounis, C.A.2
-
28
-
-
1942535726
-
Transcriptional regulation in Archaea
-
Ouhammouch M. 2004. Transcriptional regulation in Archaea. Curr. Opin. Genet. Dev. 14:133-138.
-
(2004)
Curr. Opin. Genet. Dev
, vol.14
, pp. 133-138
-
-
Ouhammouch, M.1
-
29
-
-
0031282970
-
ThiD-TenA: A gene pair fusion in eukaryotes
-
Ouzounis C.A. and N.C. Kyrpides. 1997. ThiD-TenA: a gene pair fusion in eukaryotes. J. Mol. Evol. 45:708-711.
-
(1997)
J. Mol. Evol
, vol.45
, pp. 708-711
-
-
Ouzounis, C.A.1
Kyrpides, N.C.2
-
30
-
-
0026754364
-
TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes
-
Ouzounis C. and C. Sander. 1992. TFIIB, an evolutionary link between the transcription machineries of archaebacteria and eukaryotes. Cell 71:189-190.
-
(1992)
Cell
, vol.71
, pp. 189-190
-
-
Ouzounis, C.1
Sander, C.2
-
31
-
-
0033638015
-
CAST: An iterative algorithm for the complexity analysis of sequence tracts
-
Promponas V.J., A.J. Enright, S. Tsoka, D.P. Kreil, C. Leroy, S. Hamodrakas, C. Sander and C.A. Ouzounis. 2000. CAST: an iterative algorithm for the complexity analysis of sequence tracts. Bioinformatics 16:915-922.
-
(2000)
Bioinformatics
, vol.16
, pp. 915-922
-
-
Promponas, V.J.1
Enright, A.J.2
Tsoka, S.3
Kreil, D.P.4
Leroy, C.5
Hamodrakas, S.6
Sander, C.7
Ouzounis, C.A.8
-
32
-
-
0030960672
-
-
Ptashne M. and A. Gann. 1997. Transcriptional activation by recruitment. Nature 386:569-577.
-
Ptashne M. and A. Gann. 1997. Transcriptional activation by recruitment. Nature 386:569-577.
-
-
-
-
33
-
-
0039985557
-
Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome
-
Puhler G., H. Leffers, F. Gropp, P. Palm, H.P. Klenk, F. Lottspeich, R.A. Garrett and W. Zillig. 1989. Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome. Proc. Natl. Acad. Sci. USA 86:4569-4573.
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 4569-4573
-
-
Puhler, G.1
Leffers, H.2
Gropp, F.3
Palm, P.4
Klenk, H.P.5
Lottspeich, F.6
Garrett, R.A.7
Zillig, W.8
-
34
-
-
0030974754
-
Factor requirements for transcription in the archaeon Sulfolobus shibatae
-
Qureshi S.A., S.D. Bell and S.P. Jackson. 1997. Factor requirements for transcription in the archaeon Sulfolobus shibatae. EMBO J. 16:2927-2936.
-
(1997)
EMBO J
, vol.16
, pp. 2927-2936
-
-
Qureshi, S.A.1
Bell, S.D.2
Jackson, S.P.3
-
35
-
-
0038575389
-
Archaeal chromatin and transcription
-
Reeve J.N. 2003. Archaeal chromatin and transcription. Mol. Microbiol. 48:587-598.
-
(2003)
Mol. Microbiol
, vol.48
, pp. 587-598
-
-
Reeve, J.N.1
-
36
-
-
0028361219
-
The TATA-binding protein: A general transcription factor in eukaryotes and archaebacteria
-
Rowlands T., P. Baumann and S.P. Jackson. 1994. The TATA-binding protein: a general transcription factor in eukaryotes and archaebacteria. Science 264:1326-1329.
-
(1994)
Science
, vol.264
, pp. 1326-1329
-
-
Rowlands, T.1
Baumann, P.2
Jackson, S.P.3
-
37
-
-
3342959174
-
Modulation of DNA conformations through the formation of alternative high-order HU-DNA complexes
-
Sagi D., N. Friedman, C. Vorgias, A.B. Oppenheim and J. Stavans. 2004. Modulation of DNA conformations through the formation of alternative high-order HU-DNA complexes. J. Mol. Biol. 341:419-428.
-
(2004)
J. Mol. Biol
, vol.341
, pp. 419-428
-
-
Sagi, D.1
Friedman, N.2
Vorgias, C.3
Oppenheim, A.B.4
Stavans, J.5
-
38
-
-
5444225805
-
Elongation by RNA polymerase II: The short and long of it
-
Sims R.J., 3rd, R. Belotserkovskaya and D. Reinberg. 2004. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18:2437-2468.
-
(2004)
Genes Dev
, vol.18
, pp. 2437-2468
-
-
Sims 3rd, R.J.1
Belotserkovskaya, R.2
Reinberg, D.3
-
39
-
-
0037007150
-
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens
-
Slesarev A.I., K.V. Mezhevaya, K.S. Makarova et al. 2002. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl. Acad. Sci. USA 99:4644-4649.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 4644-4649
-
-
Slesarev, A.I.1
Mezhevaya, K.V.2
Makarova, K.S.3
-
40
-
-
0033052407
-
Transcription initiation in Archaea: Facts, factors and future aspects
-
Soppa J. 1999. Transcription initiation in Archaea: facts, factors and future aspects. Mol. Microbiol. 31:1295-1305.
-
(1999)
Mol. Microbiol
, vol.31
, pp. 1295-1305
-
-
Soppa, J.1
-
41
-
-
0033538531
-
Fundamentally different logic of gene regulation in eukaryotes and prokaryotes
-
Struhl K. 1999. Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98:1-4.
-
(1999)
Cell
, vol.98
, pp. 1-4
-
-
Struhl, K.1
-
42
-
-
0036753399
-
A recombinant RNA polymerase II-like enzyme capable of promoter-specific transcription
-
Werner F. and R.O. Weinzierl. 2002. A recombinant RNA polymerase II-like enzyme capable of promoter-specific transcription. Mol. Cell 10:635-646.
-
(2002)
Mol. Cell
, vol.10
, pp. 635-646
-
-
Werner, F.1
Weinzierl, R.O.2
-
43
-
-
0034326829
-
Archaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12
-
Werner F., J.J. Eloranta and R.O. Weinzierl. 2000. Archaeal RNA polymerase subunits F and P are bona fide homologs of eukaryotic RPB4 and RPB12. Nucleic Acids Res. 28:4299-4305.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 4299-4305
-
-
Werner, F.1
Eloranta, J.J.2
Weinzierl, R.O.3
-
44
-
-
0024396228
-
RNA polymerase II subunit RPB4 is essential for high- and low-temperature yeast cell growth
-
Woychik N.A. and R.A. Young. 1989. RNA polymerase II subunit RPB4 is essential for high- and low-temperature yeast cell growth. Mol. Cell. Biol. 9:2854-2859.
-
(1989)
Mol. Cell. Biol
, vol.9
, pp. 2854-2859
-
-
Woychik, N.A.1
Young, R.A.2
|