-
2
-
-
0028800220
-
Myc and Max: Molecular evolution of a family of proto-oncogenes and their dimerization partner
-
ATCHLEY, W. R., and W. M. FITCH. 1995. Myc and Max: molecular evolution of a family of proto-oncogenes and their dimerization partner. Proc. Natl. Acad. Sci. USA 92:10217-10221.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 10217-10221
-
-
Atchley, W.R.1
Fitch, W.M.2
-
3
-
-
0031008399
-
A natural classification of the basic helix-loop-helix class of transcription factors
-
_. 1997. A natural classification of the basic helix-loop-helix class of transcription factors. Proc. Natl. Acad. Sci. USA 94:5172-5176.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 5172-5176
-
-
-
5
-
-
0032925848
-
Positional dependence, cliques and predictive motifs in the bHLH protein domain
-
ATCHLEY, W. R., W. TERHALLE, and A. DRESS. 1999. Positional dependence, cliques and predictive motifs in the bHLH protein domain. J. Mol. Evol. 48:501-516.
-
(1999)
J. Mol. Evol.
, vol.48
, pp. 501-516
-
-
Atchley, W.R.1
Terhalle, W.2
Dress, A.3
-
6
-
-
0031569798
-
The crystal structure of an intact human Max-DNA complex: New insights into mechanisms of transcriptional control
-
BROWNLIE, P., T. CESKA, M. LAMERS, C. ROMIER, G. STIER, H. TEO, and D. SUCK. 1997. The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control. Structure 5:509-520.
-
(1997)
Structure
, vol.5
, pp. 509-520
-
-
Brownlie, P.1
Ceska, T.2
Lamers, M.3
Romier, C.4
Stier, G.5
Teo, H.6
Suck, D.7
-
7
-
-
0029856518
-
Modeling residue usage in aligned protein sequences via maximum likelihood
-
BRUNO, W. 1996. Modeling residue usage in aligned protein sequences via maximum likelihood. Mol. Biol. Evol. 13: 1368-1374.
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 1368-1374
-
-
Bruno, W.1
-
8
-
-
0028832687
-
Covariation of residues in the homeo-domain sequence family
-
CLARKE, N. D. 1995. Covariation of residues in the homeo-domain sequence family. Protein Sci. 4:2269-2278.
-
(1995)
Protein Sci.
, vol.4
, pp. 2269-2278
-
-
Clarke, N.D.1
-
10
-
-
0028329080
-
Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer
-
ELLENBERGER, T., D. FASS, M. ARNAUD, and S. C. HARRISON. 1994. Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer. Genes Dev. 15:970-980.
-
(1994)
Genes Dev.
, vol.15
, pp. 970-980
-
-
Ellenberger, T.1
Fass, D.2
Arnaud, M.3
Harrison, S.C.4
-
11
-
-
0022203256
-
Phylogenies and the comparative method
-
FELSENSTEIN, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1-15.
-
(1985)
Am. Nat.
, vol.125
, pp. 1-15
-
-
Felsenstein, J.1
-
12
-
-
0027979220
-
Structure and function of the b/HLH/Z domain of USF
-
FERRE-D'AMARE, A. R., P. POGNONEC, R. G. ROEDER, and S. K. BURLEY. 1994. Structure and function of the b/HLH/Z domain of USF. EMBO J. 13:180-189.
-
(1994)
EMBO J.
, vol.13
, pp. 180-189
-
-
Ferre-D'Amare, A.R.1
Pognonec, P.2
Roeder, R.G.3
Burley, S.K.4
-
13
-
-
0027910469
-
Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain
-
FERRE-D'AMARE, A. R., G. C. PRENDERGAST, E. B. ZIFF, and S. K. BURLEY. 1993. Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363:38-45.
-
(1993)
Nature
, vol.363
, pp. 38-45
-
-
Ferre-D'Amare, A.R.1
Prendergast, G.C.2
Ziff, E.B.3
Burley, S.K.4
-
14
-
-
0027423317
-
Simple diagnostic statistical tests of models for DNA substitution
-
GOLDMAN, N. 1993. Simple diagnostic statistical tests of models for DNA substitution. J. Mol. Evol. 37:650-661.
-
(1993)
J. Mol. Evol.
, vol.37
, pp. 650-661
-
-
Goldman, N.1
-
15
-
-
0031805465
-
Assessing the impact of secondary structure and solvent accessibility on protein evolution
-
GOLDMAN N, J. L. THORNE, and D. T. JONES. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149:445-458.
-
(1998)
Genetics
, vol.149
, pp. 445-458
-
-
Goldman, N.1
Thorne, J.L.2
Jones, D.T.3
-
16
-
-
0001818891
-
Measuring correlations in symbol sequences
-
HERZEL, H., and I. GROSS. 1995. Measuring correlations in symbol sequences. Physica A 216:518-530.
-
(1995)
Physica A
, vol.216
, pp. 518-530
-
-
Herzel, H.1
Gross, I.2
-
17
-
-
0002410257
-
Parametric bootstrapping in molecular phylogenies: Applications and performance
-
J. D. FERRARIS and S. R. PALUMBI, eds. Wiley-Liss, New York
-
HUELSENBECK, J. P., D. M. HILLIS, and R. JONES. 1996. Parametric bootstrapping in molecular phylogenies: applications and performance. Pp. 19-45 in J. D. FERRARIS and S. R. PALUMBI, eds. Molecular zoology: advances, strategies, and protocols. Wiley-Liss, New York.
-
(1996)
Molecular Zoology: Advances, Strategies, and Protocols
, pp. 19-45
-
-
Huelsenbeck, J.P.1
Hillis, D.M.2
Jones, R.3
-
18
-
-
0032472955
-
A helix-turn-helix-structure unit in human centromere protein B (CENP-B)
-
IWAHARA, J., T. K. KIGAWA, H. KITAGAWA, T. MASUMOTO, T. OKAZAKI, and S. YOKOYAMA. 1998. A helix-turn-helix-structure unit in human centromere protein B (CENP-B). EMBO J. 17:827-837.
-
(1998)
EMBO J.
, vol.17
, pp. 827-837
-
-
Iwahara, J.1
Kigawa, T.K.2
Kitagawa, H.3
Masumoto, T.4
Okazaki, T.5
Yokoyama, S.6
-
19
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
JONES, D. T., W. R. TAYLOR, and J. M. THORNTON. 1992. The rapid generation of mutation data matrices from protein sequences. CABIOS 8:275-282.
-
(1992)
CABIOS
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
20
-
-
0027960477
-
Discovering structural correlations in alpha-helices
-
KLINGLER, T. M., and D. L. BRUTLAG. 1994. Discovering structural correlations in alpha-helices. Protein Sci. 3:1847-1857.
-
(1994)
Protein Sci.
, vol.3
, pp. 1847-1857
-
-
Klingler, T.M.1
Brutlag, D.L.2
-
21
-
-
0027297096
-
Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis
-
KORBER B. T., R. M. FARBER, D. H. WOLPERT, and A. S. LAPEDES. 1993. Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc. Natl. Acad. Sci. USA 90:7176-7180.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 7176-7180
-
-
Korber, B.T.1
Farber, R.M.2
Wolpert, D.H.3
Lapedes, A.S.4
-
22
-
-
0030931016
-
Mutation matrices and physical-chemical properties: Correlations and implications
-
KOSHI, J. M., and R. A. GOLDSTEIN. 1997. Mutation matrices and physical-chemical properties: correlations and implications. Proteins 27:336-344.
-
(1997)
Proteins
, vol.27
, pp. 336-344
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
23
-
-
0028215362
-
Crystal structure of MyoD bHLH domain-DNA complex: Perspectives on DNA recognition and implications for transcriptional activation
-
MA, P. C., M. A. ROULD, H. WEINTRAUB, and C. O. PABO. 1994. Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation. Cell 77:451-459.
-
(1994)
Cell
, vol.77
, pp. 451-459
-
-
Ma, P.C.1
Rould, M.A.2
Weintraub, H.3
Pabo, C.O.4
-
24
-
-
0032751751
-
Modular evolution of the bHLH family of transcription factors
-
MORGENSTERN, B., and W. R. ATCHLEY. 1999. Modular evolution of the bHLH family of transcription factors. Mol. Biol. Evol. 16:1654-1663.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1654-1663
-
-
Morgenstern, B.1
Atchley, W.R.2
-
25
-
-
0028307093
-
Structure and function of helix-loop-helix proteins
-
MURRE, C., G. BAIN, M. A. VAN DIJK, I. ENGEL, B. A. FURNARI, M. E. MASSARI, J. R. MATTHEWS, M. W. QUONG, R. R. RIVERA, and M. H. STUIVER. 1994. Structure and function of helix-loop-helix proteins. Biochim. Biophys. Acta 1218:129-135.
-
(1994)
Biochim. Biophys. Acta
, vol.1218
, pp. 129-135
-
-
Murre, C.1
Bain, G.2
Van Dijk, M.A.3
Engel, I.4
Furnari, B.A.5
Massari, M.E.6
Matthews, J.R.7
Quong, M.W.8
Rivera, R.R.9
Stuiver, M.H.10
-
26
-
-
0028174955
-
Functional characterization of the INO2 gene of Saccharomyces cerevisiae
-
NIKOLOFF, D. M., and S. A. HENRY. 1994. Functional characterization of the INO2 gene of Saccharomyces cerevisiae. J. Biol. Chem. 269:7402-7411.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 7402-7411
-
-
Nikoloff, D.M.1
Henry, S.A.2
-
27
-
-
0032524465
-
Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution
-
PARRAGA, A., L. BELLSOLELL, A. R. FERRE-D'AMARE, and S. K. BURLEY. 1998. Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution. Structure 6: 661-672.
-
(1998)
Structure
, vol.6
, pp. 661-672
-
-
Parraga, A.1
Bellsolell, L.2
Ferre-D'Amare, A.R.3
Burley, S.K.4
-
28
-
-
0001775540
-
Folded and unfolded proteins: An introduction
-
T. E. CREIGHTON, ed. W. H. Freeman and Co., New York
-
RICHARDS, F. M. 1992. Folded and unfolded proteins: an introduction. Pp. 1-58 in T. E. CREIGHTON, ed. Protein folding. W. H. Freeman and Co., New York.
-
(1992)
Protein Folding
, pp. 1-58
-
-
Richards, F.M.1
-
29
-
-
0030196610
-
Application of information theory to DNA sequence analysis: A review
-
ROMAN-ROLDAN, R., P. BERNAOLA-GAVAN, and J. L. OLIVER. 1996. Application of information theory to DNA sequence analysis: a review. Patt. Recog. 29:1187-1194.
-
(1996)
Patt. Recog.
, vol.29
, pp. 1187-1194
-
-
Roman-Roldan, R.1
Bernaola-Gavan, P.2
Oliver, J.L.3
-
30
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
SAITOU, N., and M. NEI. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
31
-
-
0029806673
-
Reading of DNA sequence logos: Prediction of major groove binding by information theory
-
SCHNEIDER, T. D. 1996. Reading of DNA sequence logos: prediction of major groove binding by information theory. Methods Enzymol. s:445-455.
-
(1996)
Methods Enzymol.
, vol.S
, pp. 445-455
-
-
Schneider, T.D.1
-
32
-
-
0030794453
-
Crystal structure of PHO4 bHLH domain-DNA complex: Flanking base recognition
-
SHIMIZU, T., A. TOUMOTO, K. IHARA, M. SHIMIZU, Y. KYOGOKU, N. OGAWA, Y. OSHIMA, and T. HAKOSHIMA. 1997. Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition. EMBO J. 16:4689-4697.
-
(1997)
EMBO J.
, vol.16
, pp. 4689-4697
-
-
Shimizu, T.1
Toumoto, A.2
Ihara, K.3
Shimizu, M.4
Kyogoku, Y.5
Ogawa, N.6
Oshima, Y.7
Hakoshima, T.8
-
35
-
-
0029938188
-
The Shannon information entropy of protein sequences
-
STRAIT, B. J., and T. G. DEWEY. 1996. The Shannon information entropy of protein sequences. Biophys. J. 71:148-155.
-
(1996)
Biophys. J.
, vol.71
, pp. 148-155
-
-
Strait, B.J.1
Dewey, T.G.2
-
36
-
-
0026550149
-
Anti-helix-loop-helix domain antibodies: Discovery of antibodies that inhibit DNA binding activity of human centromere protein B (CENP-B)
-
SUGIMOTO, K., Y. MURO, and M. HIMENO. 1992. Anti-helix-loop-helix domain antibodies: discovery of antibodies that inhibit DNA binding activity of human centromere protein B (CENP-B). J. Biochem. 111:478-483.
-
(1992)
J. Biochem.
, vol.111
, pp. 478-483
-
-
Sugimoto, K.1
Muro, Y.2
Himeno, M.3
-
37
-
-
0025864579
-
CENP-B is a highly conserved mammalian centromere protein with homology to the helix-loop-helix family of proteins
-
SULLIVAN, K. F., and C. A. GLASS. 1991. CENP-B is a highly conserved mammalian centromere protein with homology to the helix-loop-helix family of proteins. Chromosoma 100:360-370.
-
(1991)
Chromosoma
, vol.100
, pp. 360-370
-
-
Sullivan, K.F.1
Glass, C.A.2
-
38
-
-
0001336205
-
Phylogenetic inference
-
D. M. HILLIS, C. MORITZ, and B. K. MABLE, eds. Sinauer, Sunderland, Mass
-
SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, and D. M. HILLIS. 1996. Phylogenetic inference. Pp. 407-514 in D. M. HILLIS, C. MORITZ, and B. K. MABLE, eds. Molecular systematics. 2nd edition. Sinauer, Sunderland, Mass.
-
(1996)
Molecular Systematics. 2nd Edition
, pp. 407-514
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
39
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
THOMPSON, J. D., D. G. HIGGINS, and T. J. GIBSON. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
40
-
-
0028181528
-
Protein classification by stochastic modeling and optimal filtering of amino-acid sequences
-
WHITE, J. V., C. M. STULTZ, and T. F. SMITH. 1994. Protein classification by stochastic modeling and optimal filtering of amino-acid sequences. Math. Biosci. 119:35-75.
-
(1994)
Math. Biosci.
, vol.119
, pp. 35-75
-
-
White, J.V.1
Stultz, C.M.2
Smith, T.F.3
-
41
-
-
0034724418
-
Separation of phylogenetic and functional associations in biological sequences using the parametric bootstrap
-
in press
-
WOLLENBERG, K., and W. R. ATCHLEY. 2000. Separation of phylogenetic and functional associations in biological sequences using the parametric bootstrap. Proc. Natl. Acad. Sci. USA (in press).
-
(2000)
Proc. Natl. Acad. Sci. USA
-
-
Wollenberg, K.1
Atchley, W.R.2
|