-
1
-
-
64549112146
-
Predicting the binding preference of transcription factors to individual DNA k-mers
-
Alleyne,T.M. et al. (2009) Predicting the binding preference of transcription factors to individual DNA k-mers. Bioinformatics, 25, 1012-1018.
-
(2009)
Bioinformatics
, vol.25
, pp. 1012-1018
-
-
Alleyne, T.M.1
-
2
-
-
0031008399
-
A natural classification of the basic helix-loophelix class of transcription factors
-
Atchley,W.R. and Fitch,W.M. (1997) A natural classification of the basic helix-loophelix class of transcription factors. Proc. Natl Acad. Sci. USA, 94, 5172-5176.
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 5172-5176
-
-
Atchley, W.R.1
Fitch, W.M.2
-
3
-
-
0030707656
-
Structural plasticity in a remodeled protein-protein interface
-
Atwell,S. et al. (1997) Structural plasticity in a remodeled protein-protein interface. Science, 278, 1125-1128.
-
(1997)
Science
, vol.278
, pp. 1125-1128
-
-
Atwell, S.1
-
4
-
-
0031569798
-
The crystal structure of an intact human Max-DNA complex: new insights into mechanisms of transcriptional control
-
Brownlie,P. et al. (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
-
5
-
-
0033305023
-
Basic helix-loop-helix proteins can act at the Ebox within the serum response element of the c-fos promoter to influence hormoneinduced promoter activation in Sertoli cells
-
Chaudhary,J. and Skinner,M.K. (1999) Basic helix-loop-helix proteins can act at the Ebox within the serum response element of the c-fos promoter to influence hormoneinduced promoter activation in Sertoli cells. Mol. Endocrinol., 13, 774-786.
-
(1999)
Mol. Endocrinol.
, vol.13
, pp. 774-786
-
-
Chaudhary, J.1
Skinner, M.K.2
-
7
-
-
77952862003
-
Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself?
-
Fernandes,A.D. and Gloor,G.B. (2010) Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself?. Bioinformatics, 26, 1135-1139.
-
(2010)
Bioinformatics
, vol.26
, pp. 1135-1139
-
-
Fernandes, A.D.1
Gloor, G.B.2
-
8
-
-
0027979220
-
Structure and function of the b/HLH/Z domain of USF
-
Ferre-D'Amare,A.R. et al. (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
-
9
-
-
0034595516
-
Co-evolution of proteins with their interaction partners
-
Goh,C.S. et al. (2000) Co-evolution of proteins with their interaction partners. J. Mol. Biol., 299, 283-293.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 283-293
-
-
Goh, C.S.1
-
10
-
-
67650594823
-
A multiparameter network reveals extensive divergence between C. elegans bhlh transcription factors
-
Grove,C.A. et al. (2009) A multiparameter network reveals extensive divergence between C. elegans bhlh transcription factors. Cell, 138, 314-327.
-
(2009)
Cell
, vol.138
, pp. 314-327
-
-
Grove, C.A.1
-
11
-
-
44349109637
-
Eukaryotic transcription factor binding sites-modeling and integrative search methods
-
Hannenhalli,S. (2008) Eukaryotic transcription factor binding sites-modeling and integrative search methods. Bioinformatics, 24, 1325-1331.
-
(2008)
Bioinformatics
, vol.24
, pp. 1325-1331
-
-
Hannenhalli, S.1
-
12
-
-
67649986228
-
Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism
-
Huang,N. et al. (2009) Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure, 17, 939-951.
-
(2009)
Structure
, vol.17
, pp. 939-951
-
-
Huang, N.1
-
13
-
-
33747860890
-
TSEMA: interactive prediction of protein pairings between interacting families
-
Izarzugaza,J.M.G. et al. (2006) TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Res., 34, W315-W319.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Izarzugaza, J.M.G.1
-
14
-
-
4043141372
-
An overview of the basic helix-loop-helix proteins
-
Jones,S. (2004) An overview of the basic helix-loop-helix proteins. Genome Biol., 5, 226.
-
(2004)
Genome Biol.
, vol.5
, pp. 226
-
-
Jones, S.1
-
15
-
-
44649193565
-
The RNA polymerase II core promoter - the gateway to transcription
-
Juven-Gershon,T. et al. (2008) The RNA polymerase II core promoter - the gateway to transcription, Curr. Opin. Cell Biol., 20, 253-259.
-
(2008)
Curr. Opin. Cell Biol.
, vol.20
, pp. 253-259
-
-
Juven-Gershon, T.1
-
16
-
-
18744421788
-
Phylogenetic analysis of the human basic helix-loop-helix proteins
-
RESEARCH0030
-
Ledent,V. et al. (2002) Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome Biol., 3, RESEARCH0030.
-
(2002)
Genome Biol.
, vol.3
-
-
Ledent, V.1
-
17
-
-
78149251209
-
FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution
-
Li,M.J. et al. (2010) FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution. Bioinformatics, 26, 2897-2899.
-
(2010)
Bioinformatics
, vol.26
, pp. 2897-2899
-
-
Li, M.J.1
-
18
-
-
0028215362
-
Crystal structure of MyoD bHLH domain-DNA complex: perspectives on DNA recognition and implications for transcriptional activation
-
Ma,P.C. et al. (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
-
19
-
-
0028330517
-
Co-evolution of ligand-receptor pairs
-
Moyle,W.R. et al. (1994) Co-evolution of ligand-receptor pairs. Nature, 368, 251-255.
-
(1994)
Nature
, vol.368
, pp. 251-255
-
-
Moyle, W.R.1
-
20
-
-
45449111373
-
Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
-
Noyes,M.B. et al. (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell, 133, 1277-1289.
-
(2008)
Cell
, vol.133
, pp. 1277-1289
-
-
Noyes, M.B.1
-
21
-
-
0030821675
-
Correlated mutations contain information about protein-protein interaction
-
Pazos,F. et al. (1997) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol., 271, 511-523.
-
(1997)
J. Mol. Biol.
, vol.271
, pp. 511-523
-
-
Pazos, F.1
-
22
-
-
0035177259
-
Similarity of phylogenetic trees as indicator of proteinprotein interaction
-
Pazos,F. and Valencia,A. (2001) Similarity of phylogenetic trees as indicator of proteinprotein interaction. Protein Eng., 14, 609-614.
-
(2001)
Protein Eng.
, vol.14
, pp. 609-614
-
-
Pazos, F.1
Valencia, A.2
-
23
-
-
54349091030
-
Protein co-evolution, co-adaptation and interactions
-
Pazos,F. and Valencia,A. (2008) Protein co-evolution, co-adaptation and interactions. EMBO J., 27, 2648-2655.
-
(2008)
EMBO J.
, vol.27
, pp. 2648-2655
-
-
Pazos, F.1
Valencia, A.2
-
24
-
-
0029789461
-
Searching databases of conserved sequence regions by aligning protein multiple-alignments
-
Pietrokovski,S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24, 3836-3845.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 3836-3845
-
-
Pietrokovski, S.1
-
25
-
-
75549083247
-
JASPAR 2010: the greatly expanded openaccess database of transcription factor binding profiles
-
Portales-Casamar,E. et al. (2010) JASPAR 2010: the greatly expanded openaccess database of transcription factor binding profiles. Nucleic Acids Res., 38, D105-D110.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Portales-Casamar, E.1
-
26
-
-
79959930131
-
ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
-
Qin, J. et al. (2011) ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res., 39, W430-W436.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Qin, J.1
-
27
-
-
0030794453
-
Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition
-
Shimizu,T. et al. (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
-
28
-
-
14644388890
-
Making connections between novel transcription factors and their DNA motifs
-
Tan,K. et al. (2005) Making connections between novel transcription factors and their DNA motifs. Genome Res., 15, 312-320.
-
(2005)
Genome Res.
, vol.15
, pp. 312-320
-
-
Tan, K.1
-
29
-
-
33646822044
-
Codep: maximizing co-evolutionary interdependencies to discover interacting proteins
-
Tillier,E.R.M. et al. (2006) Codep: maximizing co-evolutionary interdependencies to discover interacting proteins. Proteins, 63, 822-831.
-
(2006)
Proteins
, vol.63
, pp. 822-831
-
-
Tillier, E.R.M.1
-
30
-
-
21644454183
-
Scoring docking models with evolutionary information
-
Tress,M. et al. (2005) Scoring docking models with evolutionary information. Proteins, 60, 275-280.
-
(2005)
Proteins
, vol.60
, pp. 275-280
-
-
Tress, M.1
-
31
-
-
18944373328
-
Highly efficient endogenous human gene correction using designed zinc-finger nucleases
-
Urnov,F.D. et al. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature, 435, 646-651.
-
(2005)
Nature
, vol.435
, pp. 646-651
-
-
Urnov, F.D.1
-
32
-
-
33745744510
-
Amammalian promoter model links cis elements to genetic networks
-
Wang,J.W. and Hannenhalli,S. (2006)Amammalian promoter model links cis elements to genetic networks. Biochem. Bioph. Res. Co., 347, 166-177.
-
(2006)
Biochem. Bioph. Res. Co.
, vol.347
, pp. 166-177
-
-
Wang, J.W.1
Hannenhalli, S.2
-
33
-
-
38049156077
-
MetaProm: a neural network based meta-predictor for alternative human promoter prediction
-
Wang,J.W. et al. (2007) MetaProm: a neural network based meta-predictor for alternative human promoter prediction. BMC Genomics, 8, 374.
-
(2007)
BMC Genomics
, vol.8
, pp. 374
-
-
Wang, J.W.1
-
34
-
-
58549114185
-
Identification of direct residue contacts in protein-protein interaction by message passing
-
Weigt,M. et al. (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc. Natl Acad. Sci. USA, 106, 67-72.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 67-72
-
-
Weigt, M.1
-
35
-
-
70449726432
-
Estimating sufficient statistics in co-evolutionary analysis by mutual information
-
Weil,P. et al. (2009) Estimating sufficient statistics in co-evolutionary analysis by mutual information. Comput. Biol. Chem., 33, 440-444.
-
(2009)
Comput. Biol. Chem.
, vol.33
, pp. 440-444
-
-
Weil, P.1
|