-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 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
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey, T.L. and Elkan, C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2: 28-36.
-
(1994)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
3
-
-
0036107903
-
Discovery of regulatory elements by a computational method for phylogenetic footprinting
-
Blanchette, M. and Tompa, M. 2002. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res. 12: 739-748.
-
(2002)
Genome Res.
, vol.12
, pp. 739-748
-
-
Blanchette, M.1
Tompa, M.2
-
4
-
-
0037142086
-
A global analysis of Caenorhabditis elegans operons
-
Blumenthal, T., Evans, D., Link, C.D., Guffanti, A., Lawson, D., Thierry-Mieg, J., Thierry-Mieg, D., Chiu, W.L., Duke, K., Kiraly, M., et al. 2002. A global analysis of Caenorhabditis elegans operons. Nature 417: 851-854.
-
(2002)
Nature
, vol.417
, pp. 851-854
-
-
Blumenthal, T.1
Evans, D.2
Link, C.D.3
Guffanti, A.4
Lawson, D.5
Thierry-Mieg, J.6
Thierry-Mieg, D.7
Chiu, W.L.8
Duke, K.9
Kiraly, M.10
-
5
-
-
0037398368
-
Lagan and Multi-Lagan: Efficient tools for large-scale multiple alignment of genomic DNA
-
Brudno, M., Do, C.B., Cooper, G.M., Kim, M.F., Davydov, E., Green, E.D., Sidow, A., and Batzoglou, S. 2003. Lagan and Multi-Lagan: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13: 721-731.
-
(2003)
Genome Res.
, vol.13
, pp. 721-731
-
-
Brudno, M.1
Do, C.B.2
Cooper, G.M.3
Kim, M.F.4
Davydov, E.5
Green, E.D.6
Sidow, A.7
Batzoglou, S.8
-
6
-
-
0038724989
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
-
Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B.A., and Johnston, M. 2003. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
-
(2003)
Science
, vol.301
, pp. 71-76
-
-
Cliften, P.1
Sudarsanam, P.2
Desikan, A.3
Fulton, L.4
Fulton, B.5
Majors, J.6
Waterston, R.7
Cohen, B.A.8
Johnston, M.9
-
7
-
-
0037015038
-
Genomic expression programs and the integration of the Cd28 costimulatory signal in T cell activation
-
Diehn, M., Alizadeh, A.A., Rando, O.J., Liu, C.L., Stankunas, K., Botstein, D., Crabtree, G.R., and Brown, P.O. 2002. Genomic expression programs and the integration of the Cd28 costimulatory signal in T cell activation. Proc. Natl. Acad. Sci. 99: 11796-11801.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 11796-11801
-
-
Diehn, M.1
Alizadeh, A.A.2
Rando, O.J.3
Liu, C.L.4
Stankunas, K.5
Botstein, D.6
Crabtree, G.R.7
Brown, P.O.8
-
8
-
-
0031789944
-
Regulation of touch receptor differentiation by the Caenorhabditis elegans Mec-3 and Unc-86 genes
-
Duggan, A., Ma, C., and Chalfie, M. 1998. Regulation of touch receptor differentiation by the Caenorhabditis elegans Mec-3 and Unc-86 genes. Development 125:4107-4119.
-
(1998)
Development
, vol.125
, pp. 4107-4119
-
-
Duggan, A.1
Ma, C.2
Chalfie, M.3
-
9
-
-
18344415808
-
Distinguishing regulatory DNA from neutral sites
-
Einitski, L., Hardison, R.C., Li, J., Yang, S., Kolbe, D., Eswara, P., O'Connor, M.J., Schwartz, S., Miller, W., and Chiaromonte, F. 2003. Distinguishing regulatory DNA from neutral sites. Genome Res. 13: 64-72.
-
(2003)
Genome Res.
, vol.13
, pp. 64-72
-
-
Einitski, L.1
Hardison, R.C.2
Li, J.3
Yang, S.4
Kolbe, D.5
Eswara, P.6
O'Connor, M.J.7
Schwartz, S.8
Miller, W.9
Chiaromonte, F.10
-
10
-
-
0036468361
-
Regulation of organogenesis by the Caenorhabditis elegans Foxa protein Pha-4
-
Gaudet, J. and Mango, S.E. 2002. Regulation of organogenesis by the Caenorhabditis elegans Foxa protein Pha-4. Science 295: 821-825.
-
(2002)
Science
, vol.295
, pp. 821-825
-
-
Gaudet, J.1
Mango, S.E.2
-
11
-
-
0034284481
-
Conserved noncoding sequences are reliable guides to regulatory elements
-
Hardison, R.C. 2000. Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16: 369-372.
-
(2000)
Trends Genet.
, vol.16
, pp. 369-372
-
-
Hardison, R.C.1
-
12
-
-
0025372992
-
Identification of consensus patterns in unaligned DNA sequences known to be functionally related
-
Hertz, G.Z., Hartzell III, G.W., and Stormo, G.D. 1990. Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Appl. Biosci. 6: 81-92.
-
(1990)
Comput. Appl. Biosci.
, vol.6
, pp. 81-92
-
-
Hertz, G.Z.1
Hartzell III, G.W.2
Stormo, G.D.3
-
13
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E.S. 2003. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
14
-
-
0036226603
-
BLAT - The BLAST-like alignment tool
-
Kent, W.J. 2002. BLAT - The BLAST-like alignment tool. Genome Res. 12: 656-664.
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
15
-
-
0033832676
-
Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment
-
Kent, W.J. and Zahler, A.M. 2000. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 10:1115-1125.
-
(2000)
Genome Res.
, vol.10
, pp. 1115-1125
-
-
Kent, W.J.1
Zahler, A.M.2
-
16
-
-
84950424966
-
Bayesian Models for multiple local sequence alignment and Gibbs sampling strategies
-
Liu, J.S., Neuwald, A.F., and Lawrence, C.E. 1995. Bayesian Models for multiple local sequence alignment and Gibbs sampling strategies. J. Am. Stat. Assoc. 90: 1156-1170.
-
(1995)
J. Am. Stat. Assoc.
, vol.90
, pp. 1156-1170
-
-
Liu, J.S.1
Neuwald, A.F.2
Lawrence, C.E.3
-
17
-
-
0035228215
-
Bioprospector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
-
Liu, X., Brutlag, D.L., and Liu, J.S. 2001. Bioprospector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 127-138.
-
(2001)
Pac. Symp. Biocomput.
, pp. 127-138
-
-
Liu, X.1
Brutlag, D.L.2
Liu, J.S.3
-
18
-
-
0035253676
-
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
-
McCue, L., Thompson, W., Carmack, C., Ryan, M.P., Liu, J.S., Derbyshire, V., and Lawrence, C.E. 2001. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res. 29: 774-782.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 774-782
-
-
McCue, L.1
Thompson, W.2
Carmack, C.3
Ryan, M.P.4
Liu, J.S.5
Derbyshire, V.6
Lawrence, C.E.7
-
19
-
-
0033918228
-
Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes
-
McGuire, A.M., Hughes, J.D., and Church, G.M. 2000. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res. 10: 744-757.
-
(2000)
Genome Res.
, vol.10
, pp. 744-757
-
-
McGuire, A.M.1
Hughes, J.D.2
Church, G.M.3
-
20
-
-
0028353904
-
The DNA-binding specificity of the hepatocyte nuclear factor 3/Forkhead domain is influenced by amino-acid residues adjacent to the recognition helix
-
Overdier, D.G., Porcella, A., and Costa, R.H. 1994. The DNA-binding specificity of the hepatocyte nuclear factor 3/Forkhead domain is influenced by amino-acid residues adjacent to the recognition helix. Mol. Cell. Biol. 14: 2755-2766.
-
(1994)
Mol. Cell. Biol.
, vol.14
, pp. 2755-2766
-
-
Overdier, D.G.1
Porcella, A.2
Costa, R.H.3
-
21
-
-
0035261381
-
Genomic strategies to identify mammalian regulatory sequences
-
Pennacchio, L.A. and Rubin, E.M. 2001. Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet. 2: 100-109.
-
(2001)
Nat. Rev. Genet.
, vol.2
, pp. 100-109
-
-
Pennacchio, L.A.1
Rubin, E.M.2
-
22
-
-
0035162594
-
RefSeq and LocusLink: NCBI gene-centered resources
-
Pruitt, K.D. and Maglott, D.R. 2001. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 29: 137-140.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 137-140
-
-
Pruitt, K.D.1
Maglott, D.R.2
-
23
-
-
12244259677
-
Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites
-
Qin, Z.S., McCue, L.A., Thompson, W., Mayerhofer, L., Lawrence, C.E., and Liu, J.S. 2003. Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat. Biotechnol. 21: 435-439.
-
(2003)
Nat. Biotechnol.
, vol.21
, pp. 435-439
-
-
Qin, Z.S.1
McCue, L.A.2
Thompson, W.3
Mayerhofer, L.4
Lawrence, C.E.5
Liu, J.S.6
-
24
-
-
0030973579
-
Transcription factors of the NFAT family: Regulation and function
-
Rao, A., Luo, C., and Hogan, P.G. 1997. Transcription factors of the NFAT family: Regulation and function. Annu. Rev. Immunol. 15: 707-747.
-
(1997)
Annu. Rev. Immunol.
, vol.15
, pp. 707-747
-
-
Rao, A.1
Luo, C.2
Hogan, P.G.3
-
25
-
-
0031787969
-
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
-
Roth, F.P., Hughes, J.D., Estep, P.W., and Church, G.M. 1998. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol. 16: 939-945.
-
(1998)
Nat. Biotechnol.
, vol.16
, pp. 939-945
-
-
Roth, F.P.1
Hughes, J.D.2
Estep, P.W.3
Church, G.M.4
-
26
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., and Miller, W. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13: 103-107.
-
(2003)
Genome Res.
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smit, A.3
Zhang, Z.4
Baertsch, R.5
Hardison, R.C.6
Haussler, D.7
Miller, W.8
-
27
-
-
0033775978
-
Human-mouse genome comparisons to locate regulatory sites
-
Wasserman, W.W., Palumbo, M., Thompson, W., Fickett, J.W., and Lawrence, C.E. 2000. Human-mouse genome comparisons to locate regulatory sites. Nat. Genet. 26: 225-228.
-
(2000)
Nat. Genet.
, vol.26
, pp. 225-228
-
-
Wasserman, W.W.1
Palumbo, M.2
Thompson, W.3
Fickett, J.W.4
Lawrence, C.E.5
-
28
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
Lindblad-Toh, K.2
Birney, E.3
Rogers, J.4
Abril, J.F.5
Agarwal, P.6
Agarwala, R.7
Ainscough, R.8
Alexandersson, M.9
An, P.10
-
29
-
-
0033976586
-
Transfac: An integrated system for gene expression regulation
-
Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V., Meinhardt, T., Pruss, M., Reuter, I., and Schacherer, F. 2000. Transfac: An integrated system for gene expression regulation. Nucleic Acids Res. 28: 316-319.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 316-319
-
-
Wingender, E.1
Chen, X.2
Hehl, R.3
Karas, H.4
Liebich, I.5
Matys, V.6
Meinhardt, T.7
Pruss, M.8
Reuter, I.9
Schacherer, F.10
-
30
-
-
0037148758
-
The genome sequence of Schizosaccharomyces pombe
-
Wood, V., Gwilliam, R., Rajandream, M.A., Lyne, M., Lyne, R., Stewart, A., Sgouros, J.., Peat, N., Hayles, J., Baker, S., et al. 2002. The genome sequence of Schizosaccharomyces pombe. Nature 415: 871-880.
-
(2002)
Nature
, vol.415
, pp. 871-880
-
-
Wood, V.1
Gwilliam, R.2
Rajandream, M.A.3
Lyne, M.4
Lyne, R.5
Stewart, A.6
Sgouros, J.7
Peat, N.8
Hayles, J.9
Baker, S.10
-
31
-
-
0027100450
-
Regulation of the Mec-3 gene by the C. elegans homeoproteins Unc-86 and Mec-3
-
Xue, D., Finney, M., Ruvkun, G., and Chalfie, M. 1992. Regulation of the Mec-3 gene by the C. elegans homeoproteins Unc-86 and Mec-3. EMBO J. 11: 4969-4979.
-
(1992)
EMBO J.
, vol.11
, pp. 4969-4979
-
-
Xue, D.1
Finney, M.2
Ruvkun, G.3
Chalfie, M.4
-
32
-
-
0032861774
-
SCPD: A promoter database of the yeast Saccharomyces cerevisiae
-
Zhu, J. and Zhang, M.Q. 1999. SCPD: A promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15: 607-611.
-
(1999)
Bioinformatics
, vol.15
, pp. 607-611
-
-
Zhu, J.1
Zhang, M.Q.2
|