-
1
-
-
0002759539
-
Unsupervised learning of multiple motifs in biopolymers using expectation maximization
-
Bailey,T.L. and Elkan,C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learn., 21, 51-80.
-
(1995)
Machine Learn.
, vol.21
, pp. 51-80
-
-
Bailey, T.L.1
Elkan, C.2
-
2
-
-
0029146491
-
Identification of common motifs in unaligned DNA sequences: Application to Escherichia coli Lrp regulon
-
Fraenkel,Y.M., Mandel,Y., Friedberg,D. and Margalit,H. (1995) Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon. Comput. Appl. Biosci., 11, 379-387.
-
(1995)
Comput. Appl. Biosci.
, vol.11
, pp. 379-387
-
-
Fraenkel, Y.M.1
Mandel, Y.2
Friedberg, D.3
Margalit, H.4
-
3
-
-
0022358896
-
Rigorous pattern-recognition methods for DNA sequences: Analysis of promoter sequences from Escherichia coli
-
Galas,D.J., Eggert,M. and Waterman,M.S. (1985) Rigorous pattern-recognition methods for DNA sequences: analysis of promoter sequences from Escherichia coli. J. Mol. Biol., 186, 117-128.
-
(1985)
J. Mol. Biol.
, vol.186
, pp. 117-128
-
-
Galas, D.J.1
Eggert, M.2
Waterman, M.S.3
-
4
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
-
(1999)
Bioinformatics
, vol.15
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
5
-
-
0027912333
-
Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
-
Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wootton,J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.E.1
Altschul, S.F.2
Boguski, M.S.3
Liu, J.S.4
Neuwald, A.F.5
Wootton, J.C.6
-
6
-
-
0025320805
-
An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
-
Lawrence,C.E. and Reilly,A.A. (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins Struct. Funct. Genet., 7, 41-51.
-
(1990)
Proteins Struct. Funct. Genet.
, vol.7
, pp. 41-51
-
-
Lawrence, C.E.1
Reilly, A.A.2
-
7
-
-
0031651582
-
Motif discovery without alignment or enumeration
-
ACM Press, New York, NY
-
Rigoutsos,I. and Floratos,A. (1998) Motif discovery without alignment or enumeration. In RECOMB98: Proceedings of the Second Annual International Conference on Computational Molecular Biology. ACM Press, New York, NY, pp. 221-227.
-
(1998)
RECOMB98: Proceedings of the Second Annual International Conference on Computational Molecular Biology
, pp. 221-227
-
-
Rigoutsos, I.1
Floratos, A.2
-
8
-
-
0031655082
-
An algorithm for finding novel gapped motifs in DNA sequences
-
ACM Press, New York, NY
-
Rocke,E. and Tompa,M. (1998) An algorithm for finding novel gapped motifs in DNA sequences. In RECOMB98: Proceedings of the Second Annual International Conference on Computational Molecular Biology. ACM Press, New York, NY, pp. 228-233.
-
(1998)
RECOMB98: Proceedings of the Second Annual International Conference on Computational Molecular Biology
, pp. 228-233
-
-
Rocke, E.1
Tompa, M.2
-
9
-
-
0024385974
-
Methods for discovering novel motifs in nucleic acid sequences
-
Staden,R. (1989) Methods for discovering novel motifs in nucleic acid sequences. Comput. Appl. Biosci., 5, 293-298.
-
(1989)
Comput. Appl. Biosci.
, vol.5
, pp. 293-298
-
-
Staden, R.1
-
10
-
-
0032561246
-
The transcriptional program of sporulation in budding yeast
-
Chu,S., DeRisi,J., Eisen,M., Mulholland,J., Botstein,D., Brown,P.O. and Herskowitz,I. (1998) The transcriptional program of sporulation in budding yeast. Science, 282, 699-705.
-
(1998)
Science
, vol.282
, pp. 699-705
-
-
Chu, S.1
DeRisi, J.2
Eisen, M.3
Mulholland, J.4
Botstein, D.5
Brown, P.O.6
Herskowitz, I.7
-
11
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
12
-
-
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
-
13
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman,P.T., Sherlock,G., Zhang,M.Q., Iyer,V.R., Anders,K., Eisen,M.B., Brown,P.O., Botstein,D. and Futcher,B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
-
(1998)
Mol. Biol. Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
Eisen, M.B.6
Brown, P.O.7
Botstein, D.8
Futcher, B.9
-
14
-
-
0033028596
-
Systematic determination of genetic network architecture
-
Tavazoie,S., Hughes,J.D., Campbell,M.J., Cho,R.J. and Church,G.M. (1999) Systematic determination of genetic network architecture. Nature Genet., 22, 281-285.
-
(1999)
Nature Genet.
, vol.22
, pp. 281-285
-
-
Tavazoie, S.1
Hughes, J.D.2
Campbell, M.J.3
Cho, R.J.4
Church, G.M.5
-
15
-
-
0029960055
-
TRANSFAC: A database on transcription factors and their DNA binding sites
-
Wingender,E., Dietze,P., Karas,H. and Knuppel,R. (1996) TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res., 24, 238-241.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 238-241
-
-
Wingender, E.1
Dietze, P.2
Karas, H.3
Knuppel, R.4
-
16
-
-
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, 563-577.
-
(1999)
Bioinformatics
, vol.15
, pp. 563-577
-
-
Zhu, J.1
Zhang, M.Q.2
-
17
-
-
0032483307
-
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
-
van Helden,J., André,B. and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 827-842
-
-
van Helden, J.1
André, B.2
Collado-Vides, J.3
-
18
-
-
0034651804
-
Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals
-
van Helden,J., Olmo,M. and Pérez-Ortin,J. (2000) Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res., 28, 1000-1010.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1000-1010
-
-
van Helden, J.1
Olmo, M.2
Pérez-Ortin, J.3
-
19
-
-
0034656326
-
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
-
van Helden,J., Rios,A. and Collado-Vides,J. (2000) Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res., 28, 1808-1818.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1808-1818
-
-
van Helden, J.1
Rios, A.2
Collado-Vides, J.3
-
20
-
-
0033289316
-
An exact method for finding short motifs in sequences, with application to the ribosome binding site problem
-
AAAI Press, Menlo Park, CA
-
Tompa,M. (1999) An exact method for finding short motifs in sequences, with application to the ribosome binding site problem. In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 262-271.
-
(1999)
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
, pp. 262-271
-
-
Tompa, M.1
-
21
-
-
0032413411
-
Predicting gene regulatory elements in silico on a genomic scale
-
Brazma,A., Jonassen,I., Vilo,J. and Ukkonen,E. (1998) Predicting gene regulatory elements in silico on a genomic scale. Genome Res., 15, 1202-1215.
-
(1998)
Genome Res.
, vol.15
, pp. 1202-1215
-
-
Brazma, A.1
Jonassen, I.2
Vilo, J.3
Ukkonen, E.4
-
22
-
-
0000900670
-
Spelling approximate repeated or common motifs using a suffix tree
-
Springer-Verlag Lecture Notes in Computer Science no. 1380. Springer-Verlag, Heidelberg, Germany
-
Sagot,M. (1998) Spelling approximate repeated or common motifs using a suffix tree. In Latin '98: Theoretical Informatics, Springer-Verlag Lecture Notes in Computer Science no. 1380. Springer-Verlag, Heidelberg, Germany, pp. 111-127.
-
(1998)
Latin '98: Theoretical Informatics
, pp. 111-127
-
-
Sagot, M.1
-
23
-
-
0035224579
-
An algorithm for finding signals of unknown length in DNA sequences
-
Pavesi,G., Mauri,G. and Pesole,G. (2001) An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics, 17, S207-5214.
-
(2001)
Bioinformatics
, vol.17
-
-
Pavesi, G.1
Mauri, G.2
Pesole, G.3
-
24
-
-
0034564539
-
A statistical method for finding transcription factor binding sites
-
AAAI Press, Menlo Park, CA
-
Sinha,S. and Tompa,M. (2000) A statistical method for finding transcription factor binding sites. In Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 344-354.
-
(2000)
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
, pp. 344-354
-
-
Sinha, S.1
Tompa, M.2
-
25
-
-
0030765448
-
MIPS: A database for protein sequences, homology data and yeast genome information
-
Mewes,H.W., Albermann,K., Heumann,K., Liebl,S. and Pfeiffer,F. (1997) MIPS: a database for protein sequences, homology data and yeast genome information. Nucleic Acids Res., 25, 28-30.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 28-30
-
-
Mewes, H.W.1
Albermann, K.2
Heumann, K.3
Liebl, S.4
Pfeiffer, F.5
-
26
-
-
0003965929
-
The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression
-
(eds) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
-
Jones,E.W., Pringle,J.R. and Broach,J.R. (eds) (1992) The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
-
(1992)
-
-
Jones, E.W.1
Pringle, J.R.2
Broach, J.R.3
-
27
-
-
0030979616
-
Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism
-
Blaiseau,P.-L., Isnard,A.-D., Surdin-Kerjan,Y. and Thomas,D. (1997) Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism. Mol. Cell. Biol., 17, 3640-3648.
-
(1997)
Mol. Cell. Biol.
, vol.17
, pp. 3640-3648
-
-
Blaiseau, P.-L.1
Isnard, A.-D.2
Surdin-Kerjan, Y.3
Thomas, D.4
-
28
-
-
0030868697
-
Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family
-
Mai,B. and Breeden,L. (1997) Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family. Mol. Cell. Biol., 17, 6491-6501.
-
(1997)
Mol. Cell. Biol.
, vol.17
, pp. 6491-6501
-
-
Mai, B.1
Breeden, L.2
-
30
-
-
0029058028
-
DNA binding specificity determinants in MADS-box transcription factors
-
Nurrish,S.J. and Treisman,R. (1995) DNA binding specificity determinants in MADS-box transcription factors. Mol. Cell. Biol., 15, 4076-4085.
-
(1995)
Mol. Cell. Biol.
, vol.15
, pp. 4076-4085
-
-
Nurrish, S.J.1
Treisman, R.2
-
31
-
-
0030574260
-
Regulation of phosphatase synthesis in Saccharomyces cerevisiae - A review
-
Oshima,Y., Nobuo,O. and Harashima,S. (1996) Regulation of phosphatase synthesis in Saccharomyces cerevisiae - a review. Gene, 179, 171-177.
-
(1996)
Gene.
, vol.179
, pp. 171-177
-
-
Oshima, Y.1
Nobuo, O.2
Harashima, S.3
-
32
-
-
0034615781
-
Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites
-
Roulet,E., Bucher,P., Schneider,R., Wingender,E., Dusserre,Y., Werner,T. and Mermod,N. (2000) Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites. J. Mol. Biol., 297, 833-848.
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 833-848
-
-
Roulet, E.1
Bucher, P.2
Schneider, R.3
Wingender, E.4
Dusserre, Y.5
Werner, T.6
Mermod, N.7
-
33
-
-
0028575444
-
Cadmium tolerance mediated by the yeast AP-1 protein requires the presence of an ATP-binding cassette transporter-encoding gene, YCS1
-
Wemmie,J.A., Szczypka,M.S., Thiele,D.J. and Moye-Rowley,W.S. (1994) Cadmium tolerance mediated by the yeast AP-1 protein requires the presence of an ATP-binding cassette transporter-encoding gene, YCS1. J. Biol. Chem., 269, 32592-32597.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 32592-32597
-
-
Wemmie, J.A.1
Szczypka, M.S.2
Thiele, D.J.3
Moye-Rowley, W.S.4
-
34
-
-
0029795578
-
Over- and underrepresentation of short DNA words in herpesvirus genomes
-
Leung,M.-Y., Marsh,G.M. and Speed,T.P. (1996) Over- and underrepresentation of short DNA words in herpesvirus genomes. J. Comput. Biol., 3, 345-360.
-
(1996)
J. Comput. Biol.
, vol.3
, pp. 345-360
-
-
Leung, M.-Y.1
Marsh, G.M.2
Speed, T.P.3
-
35
-
-
84958051478
-
Motif statistics
-
Springer-Verlag Lecture Notes in Computer Science no. 1643. Springer-Verlag, Heidelberg, Germany
-
Nicodème,P., Salvy,B. and Flajolet,P. (1999) Motif statistics. In 7th Annual European Symposium on Algorithms-ESA99. Springer-Verlag Lecture Notes in Computer Science no. 1643. Springer-Verlag, Heidelberg, Germany, pp. 194-211.
-
(1999)
7th Annual European Symposium on Algorithms-ESA99
, pp. 194-211
-
-
Nicodème, P.1
Salvy, B.2
Flajolet, P.3
-
36
-
-
0012621510
-
Separating real motifs from their artifacts
-
Blanchette,M. and Sinha,S. (2001) Separating real motifs from their artifacts. Bioinformatics, 17, S30-S38.
-
(2001)
Bioinformatics
, vol.17
-
-
Blanchette, M.1
Sinha, S.2
-
37
-
-
0034098727
-
Systematic management and analysis of yeast gene expression data
-
Aach,J., Rindone,W. and Church,G.M. (2000) Systematic management and analysis of yeast gene expression data. Genome Res., 10, 431-445.
-
(2000)
Genome Res.
, vol.10
, pp. 431-445
-
-
Aach, J.1
Rindone, W.2
Church, G.M.3
-
38
-
-
0028851909
-
Functional characterization of an inositol-sensitive upstream activation sequence in yeast. A cis-regulatory element responsible for inositol-choline mediated regulation of phospholipid biosynthesis
-
Bachhawat,N., Ouyang,Q. and Henry,S.A. (1995) Functional characterization of an inositol-sensitive upstream activation sequence in yeast. A cis-regulatory element responsible for inositol-choline mediated regulation of phospholipid biosynthesis. J. Biol. Chem., 270, 25087-25095.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 25087-25095
-
-
Bachhawat, N.1
Ouyang, Q.2
Henry, S.A.3
-
39
-
-
0029149344
-
DNA binding site of the yeast heteromeric Ino2p/Ino4p basic helix-loop-helix transcription factor; structural requirements as defined by saturation mutagenesis
-
Schüller,H.-J., Richter,K., Hoffman,B., Ebbert,R. and Schweizer,E. (1995) DNA binding site of the yeast heteromeric Ino2p/Ino4p basic helix-loop-helix transcription factor; structural requirements as defined by saturation mutagenesis. FEBS Lett., 370, 149-152.
-
(1995)
FEBS Lett.
, vol.370
, pp. 149-152
-
-
Schüller, H.-J.1
Richter, K.2
Hoffman, B.3
Ebbert, R.4
Schweizer, E.5
-
40
-
-
0032812984
-
Overproduction of the Opi1 repressor inhibits transcriptional activation of structural genes required for phospholipid biosynthesis in the yeast Saccharomyces cerevisiae
-
Wagner,C., Blank,M., Strohmann,B. and Schüller,H.-J. (1999) Overproduction of the Opi1 repressor inhibits transcriptional activation of structural genes required for phospholipid biosynthesis in the yeast Saccharomyces cerevisiae. Yeast, 15, 843-854.
-
(1999)
Yeast
, vol.15
, pp. 843-854
-
-
Wagner, C.1
Blank, M.2
Strohmann, B.3
Schüller, H.-J.4
-
41
-
-
0025883649
-
RPC19, the gene for a subunit common to yeast RNA polymerases A (I) and C (III)
-
Dequard-Chablat,M., Riva,M., Carles,C. and Sentenac,A. (1991) RPC19, the gene for a subunit common to yeast RNA polymerases A (I) and C (III). J. Biol. Chem., 266, 15300-15307.
-
(1991)
J. Biol. Chem.
, vol.266
, pp. 15300-15307
-
-
Dequard-Chablat, M.1
Riva, M.2
Carles, C.3
Sentenac, A.4
-
42
-
-
0035313452
-
DDSE: Downstream targets of the SNF3 signal transduction pathway
-
Theodoris,G. and Bisson,L.F. (2001) DDSE: downstream targets of the SNF3 signal transduction pathway. FEBS Microbiol. Lett., 197, 73-77.
-
(2001)
FEBS Microbiol. Lett.
, vol.197
, pp. 73-77
-
-
Theodoris, G.1
Bisson, L.F.2
-
43
-
-
0032865543
-
Function and regulation of yeast hexose transporters
-
Ozcan,S. and Johnston,M. (1999) Function and regulation of yeast hexose transporters. Microbiol. Mol. Biol. Rev., 63, 554-569.
-
(1999)
Microbiol. Mol. Biol. Rev.
, vol.63
, pp. 554-569
-
-
Ozcan, S.1
Johnston, M.2
-
44
-
-
0035723369
-
The role of the yeast plasma membrane SPS nutrient sensor in the metabolic response to extracellular amino acids
-
Forsberg,H., Gilstring,C.F., Zargari,A., Martinez,P. and Ljungdahl,P.O. (2001) The role of the yeast plasma membrane SPS nutrient sensor in the metabolic response to extracellular amino acids. Mol. Microbiol., 42, 215-228.
-
(2001)
Mol. Microbiol.
, vol.42
, pp. 215-228
-
-
Forsberg, H.1
Gilstring, C.F.2
Zargari, A.3
Martinez, P.4
Ljungdahl, P.O.5
-
45
-
-
0026611051
-
SWI6 protein is required for transcription of the periodically expressed DNA synthesis genes in budding yeast
-
Lowndes,N.F., Johnson,A.L., Breeden,L. and Johnston,L.H. (1992) SWI6 protein is required for transcription of the periodically expressed DNA synthesis genes in budding yeast. Nature, 357, 505-508.
-
(1992)
Nature
, vol.357
, pp. 505-508
-
-
Lowndes, N.F.1
Johnson, A.L.2
Breeden, L.3
Johnston, L.H.4
-
46
-
-
0030768053
-
Plasma membrane translocation of fluorescent-labeled phosphatidylethanolamine is controlled by transcription regulators, PDR1 and PDR3
-
Kean,L.S., Grant,A.M., Angeletti,C., Mahe,Y., Kuchler,K., Fuller,R.S. and Nichols,J.W. (1997) Plasma membrane translocation of fluorescent-labeled phosphatidylethanolamine is controlled by transcription regulators, PDR1 and PDR3. J. Cell Biol., 138, 255-270.
-
(1997)
J. Cell Biol.
, vol.138
, pp. 255-270
-
-
Kean, L.S.1
Grant, A.M.2
Angeletti, C.3
Mahe, Y.4
Kuchler, K.5
Fuller, R.S.6
Nichols, J.W.7
-
47
-
-
0028271865
-
Identification of potential target genes for Adr1p through characterization of essential nucleotides in UAS1
-
Cheng,C., Kacherovsky,N., Dombek,K.M., Camier,S., Thukral,S.K., Rhim,E. and Young,E.T. (1994) Identification of potential target genes for Adr1p through characterization of essential nucleotides in UAS1 Mol. Cell. Biol., 14, 3842-3852.
-
(1994)
Mol. Cell. Biol.
, vol.14
, pp. 3842-3852
-
-
Cheng, C.1
Kacherovsky, N.2
Dombek, K.M.3
Camier, S.4
Thukral, S.K.5
Rhim, E.6
Young, E.T.7
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