-
1
-
-
0037376655
-
Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell
-
J.J. Tyson, K.C. Chen, and B. Novak Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell Curr Opin Cell Biol 15 2003 221 231
-
(2003)
Curr Opin Cell Biol
, vol.15
, pp. 221-231
-
-
Tyson, J.J.1
Chen, K.C.2
Novak, B.3
-
2
-
-
0037686112
-
The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster
-
R. Albert, and H.G. Othmer The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster J Theor Biol 223 2003 1 18
-
(2003)
J Theor Biol
, vol.223
, pp. 1-18
-
-
Albert, R.1
Othmer, H.G.2
-
3
-
-
3142630279
-
Gene regulatory network controlling embryonic specification in the sea urchin
-
P. Oliveri, and E.H. Davidson Gene regulatory network controlling embryonic specification in the sea urchin Curr Opin Genet Dev 14 2004 351 360
-
(2004)
Curr Opin Genet Dev
, vol.14
, pp. 351-360
-
-
Oliveri, P.1
Davidson, E.H.2
-
4
-
-
3142740663
-
Comparative genomics
-
DOI: 10.1371/journal.pbio.0000058.
-
Hardison RC: Comparative genomics. PLoS Biol 2003, DOI: 10.1371/journal.pbio.0000058.
-
(2003)
PLoS Biol
-
-
Hardison, R.C.1
-
5
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
-
C. Li, and W.H. Wong Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection Proc Natl Acad Sci USA 98 2001 31 36
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
-
6
-
-
0344153725
-
Dissecting the transcription networks of a cell using computational genomics
-
H. Li, and W. Wang Dissecting the transcription networks of a cell using computational genomics Curr Opin Genet Dev 13 2003 611 616
-
(2003)
Curr Opin Genet Dev
, vol.13
, pp. 611-616
-
-
Li, H.1
Wang, W.2
-
7
-
-
10744226222
-
Computational discovery of gene modules and regulatory networks
-
Z. Bar-Joseph, G.K. Gerber, T.I. Lee, N.J. Rinaldi, J.Y. Yoo, F. Robert, D.B. Gordon, E. Fraenkel, T.S. Jaakkola, and R.A. Young Computational discovery of gene modules and regulatory networks Nat Biotechnol 21 2003 1337 1342
-
(2003)
Nat Biotechnol
, vol.21
, pp. 1337-1342
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Lee, T.I.3
Rinaldi, N.J.4
Yoo, J.Y.5
Robert, F.6
Gordon, D.B.7
Fraenkel, E.8
Jaakkola, T.S.9
Young, R.A.10
-
8
-
-
0037168519
-
A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae
-
W. Wang, J.M. Cherry, D. Botstein, and H. Li A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae Proc Natl Acad Sci USA 99 2002 16893 16898
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 16893-16898
-
-
Wang, W.1
Cherry, J.M.2
Botstein, D.3
Li, H.4
-
9
-
-
0036699526
-
Revealing modular organization in the yeast transcriptional network
-
J. Ihmels, G. Friedlander, S. Bergmann, O. Sarig, Y. Ziv, and N. Barkai Revealing modular organization in the yeast transcriptional network Nat Genet 31 2002 370 377
-
(2002)
Nat Genet
, vol.31
, pp. 370-377
-
-
Ihmels, J.1
Friedlander, G.2
Bergmann, S.3
Sarig, O.4
Ziv, Y.5
Barkai, N.6
-
10
-
-
1942453302
-
Predicting gene expression from sequence
-
M.A. Beer, and S. Tavazoie Predicting gene expression from sequence Cell 117 2004 185 198 The authors fit a Bayesian model to a wide spectrum of expression profiles in yeast and highlight for a particularly favorable case of the ribosomal genes (many genes tightly regulated) where strict position and orientation effects can be learned for several cooperating proteins.
-
(2004)
Cell
, vol.117
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
11
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
E. Segal, M. Shapira, A. Regev, D. Pe'er, D. Botstein, D. Koller, and N. Friedman Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data Nat Genet 34 2003 166 176 The authors describe a procedure to partition genes into disjoint coexpression sets and, for each of these, infer a tree of transcriptional regulation that best explains the sets. The potential regulators are the annotated transcription factors in the genome, and regulation is inferred only from co-variation (of either sign) between the expression of the regulator and its targets.
-
(2003)
Nat Genet
, vol.34
, pp. 166-176
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
Pe'Er, D.4
Botstein, D.5
Koller, D.6
Friedman, N.7
-
12
-
-
2442446708
-
Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
-
E. Segal, R. Yelensky, and D. Koller Genome-wide discovery of transcriptional modules from DNA sequence and gene expression Bioinformatics 19 Suppl 1 2003 i273 i282
-
(2003)
Bioinformatics
, vol.19
, Issue.1 SUPPL.
-
-
Segal, E.1
Yelensky, R.2
Koller, D.3
-
13
-
-
0037398368
-
LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
-
M. Brudno, C.B. Do, G.M. Cooper, M.F. Kim, E. Davydov, E.D. Green, A. Sidow, and S. Batzoglou LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA Genome Res 13 2003 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
-
14
-
-
1842667852
-
MAVID: Constrained ancestral alignment of multiple sequences
-
N. Bray, and L. Pachter MAVID: constrained ancestral alignment of multiple sequences Genome Res 14 2004 693 699
-
(2004)
Genome Res
, vol.14
, pp. 693-699
-
-
Bray, N.1
Pachter, L.2
-
15
-
-
4944262040
-
Glocal alignment: Finding rearrangements during alignment
-
M. Brudno, S. Malde, A. Poliakov, C.B. Do, O. Couronne, I. Dubchak, and S. Batzoglou Glocal alignment: finding rearrangements during alignment Bioinformatics 19 Suppl 1 2003 i54 i62
-
(2003)
Bioinformatics
, vol.19
, Issue.1 SUPPL.
-
-
Brudno, M.1
Malde, S.2
Poliakov, A.3
Do, C.B.4
Couronne, O.5
Dubchak, I.6
Batzoglou, S.7
-
16
-
-
10744222156
-
Identification and characterization of multi-species conserved sequences
-
E.H. Margulies, M. Blanchette, D. Haussler, and E.D. Green Identification and characterization of multi-species conserved sequences Genome Res 13 2003 2507 2518
-
(2003)
Genome Res
, vol.13
, pp. 2507-2518
-
-
Margulies, E.H.1
Blanchette, M.2
Haussler, D.3
Green, E.D.4
-
17
-
-
1542748076
-
Aligning multiple genomic sequences with the threaded blockset aligner
-
M. Blanchette, W.J. Kent, C. Riemer, L. Elnitski, A.F. Smit, K.M. Roskin, R. Baertsch, K. Rosenbloom, H. Clawson, and E.D. Green Aligning multiple genomic sequences with the threaded blockset aligner Genome Res 14 2004 708 715
-
(2004)
Genome Res
, vol.14
, pp. 708-715
-
-
Blanchette, M.1
Kent, W.J.2
Riemer, C.3
Elnitski, L.4
Smit, A.F.5
Roskin, K.M.6
Baertsch, R.7
Rosenbloom, K.8
Clawson, H.9
Green, E.D.10
-
18
-
-
1042264827
-
A probabilistic method to detect regulatory modules
-
•] to exploit block-aligned multi-species data. Motifs in blocks are scored according to an evolution model for sequence constrained to bind a protein, whereas occurrences in unaligned regions are counted as independent events. Positional correlations between sites can also be learned and scored.
-
(2003)
Bioinformatics
, vol.19
, Issue.1 SUPPL.
-
-
Sinha, S.1
Van Nimwegen, E.2
Siggia, E.D.3
-
19
-
-
13244260826
-
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
-
DOI: 10.1186/1471-2105-5-170.
-
Sinha S, Blanchette M, Tompa M: PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics 2004, DOI: 10.1186/1471-2105-5-170.
-
(2004)
BMC Bioinformatics
-
-
Sinha, S.1
Blanchette, M.2
Tompa, M.3
-
20
-
-
0031875569
-
Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies
-
A.L. Halpern, and W.J. Bruno Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies Mol Biol Evol 15 1998 910 917
-
(1998)
Mol Biol Evol
, vol.15
, pp. 910-917
-
-
Halpern, A.L.1
Bruno, W.J.2
-
21
-
-
0642368358
-
Position specific variation in the rate of evolution in transcription factor binding sites
-
A.M. Moses, D.Y. Chiang, M. Kellis, E.S. Lander, and M.B. Eisen Position specific variation in the rate of evolution in transcription factor binding sites BMC Evol Biol 3 2003 19
-
(2003)
BMC Evol Biol
, vol.3
, pp. 19
-
-
Moses, A.M.1
Chiang, D.Y.2
Kellis, M.3
Lander, E.S.4
Eisen, M.B.5
-
22
-
-
0032555671
-
Direct allelic variation scanning of the yeast genome
-
E.A. Winzeler, D.R. Richards, A.R. Conway, A.L. Goldstein, S. Kalman, M.J. McCullough, J.H. McCusker, D.A. Stevens, L. Wodicka, and D.J. Lockhart Direct allelic variation scanning of the yeast genome Science 281 1998 1194 1197
-
(1998)
Science
, vol.281
, pp. 1194-1197
-
-
Winzeler, E.A.1
Richards, D.R.2
Conway, A.R.3
Goldstein, A.L.4
Kalman, S.5
McCullough, M.J.6
McCusker, J.H.7
Stevens, D.A.8
Wodicka, L.9
Lockhart, D.J.10
-
23
-
-
0036532201
-
Deciphering gene expression regulatory networks
-
J.J. Wyrick, and R.A. Young Deciphering gene expression regulatory networks Curr Opin Genet Dev 12 2002 130 136
-
(2002)
Curr Opin Genet Dev
, vol.12
, pp. 130-136
-
-
Wyrick, J.J.1
Young, R.A.2
-
24
-
-
2942518343
-
Mapping global histone acetylation patterns to gene expression
-
S.K. Kurdistani, S. Tavazoie, and M. Grunstein Mapping global histone acetylation patterns to gene expression Cell 117 2004 721 733
-
(2004)
Cell
, vol.117
, pp. 721-733
-
-
Kurdistani, S.K.1
Tavazoie, S.2
Grunstein, M.3
-
25
-
-
0042736137
-
Epigenomic profiling using microarrays
-
van Steensel B, Henikoff S: Epigenomic profiling using microarrays. Biotechniques 2003, 35:346-50,352-4,356-7.
-
(2003)
Biotechniques
, vol.35
, pp. 346-350
-
-
Van Steensel, B.1
Henikoff, S.2
-
26
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
-
V.R. Iyer, C.E. Horak, C.S. Scafe, D. Botstein, M. Snyder, and P.O. Brown Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF Nature 409 2001 533 538
-
(2001)
Nature
, vol.409
, pp. 533-538
-
-
Iyer, V.R.1
Horak, C.E.2
Scafe, C.S.3
Botstein, D.4
Snyder, M.5
Brown, P.O.6
-
27
-
-
17944372930
-
Serial regulation of transcriptional regulators in the yeast cell cycle
-
I. Simon, J. Barnett, N. Hannett, C.T. Harbison, N.J. Rinaldi, T.L. Volkert, J.J. Wyrick, J. Zeitlinger, D.K. Gifford, and T.S. Jaakkola Serial regulation of transcriptional regulators in the yeast cell cycle Cell 106 2001 697 708
-
(2001)
Cell
, vol.106
, pp. 697-708
-
-
Simon, I.1
Barnett, J.2
Hannett, N.3
Harbison, C.T.4
Rinaldi, N.J.5
Volkert, T.L.6
Wyrick, J.J.7
Zeitlinger, J.8
Gifford, D.K.9
Jaakkola, T.S.10
-
28
-
-
0033672594
-
The core meiotic transcriptome in budding yeasts
-
M. Primig, R.M. Williams, E.A. Winzeler, G.G. Tevzadze, A.R. Conway, S.Y. Hwang, R.W. Davis, and R.E. Esposito The core meiotic transcriptome in budding yeasts Nat Genet 26 2000 415 423
-
(2000)
Nat Genet
, vol.26
, pp. 415-423
-
-
Primig, M.1
Williams, R.M.2
Winzeler, E.A.3
Tevzadze, G.G.4
Conway, A.R.5
Hwang, S.Y.6
Davis, R.W.7
Esposito, R.E.8
-
29
-
-
0032561246
-
The transcriptional program of sporulation in budding yeast
-
S. Chu, J. DeRisi, M. Eisen, J. Mulholland, D. Botstein, P.O. Brown, and I. Herskowitz The transcriptional program of sporulation in budding yeast Science 282 1998 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
-
30
-
-
0037177625
-
Genetic dissection of transcriptional regulation in budding yeast
-
R.B. Brem, G. Yvert, R. Clinton, and L. Kruglyak Genetic dissection of transcriptional regulation in budding yeast Science 296 2002 752 755
-
(2002)
Science
, vol.296
, pp. 752-755
-
-
Brem, R.B.1
Yvert, G.2
Clinton, R.3
Kruglyak, L.4
-
31
-
-
0042856391
-
Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors
-
G. Yvert, R.B. Brem, J. Whittle, J.M. Akey, E. Foss, E.N. Smith, R. Mackelprang, and L. Kruglyak Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors Nat Genet 35 2003 57 64 The authors make a case for linkage analysis as an approach for discovering regulatory groupings. Of the 2300 genes showing linkage, only 25% linked to a marker within 10 kb of the genes and, hence, most variation is trans; but the trans-acting loci do not correlate with recognized transcription factors. Several co-varying gene clusters were traced to mutations that are particular to a laboratory strain.
-
(2003)
Nat Genet
, vol.35
, pp. 57-64
-
-
Yvert, G.1
Brem, R.B.2
Whittle, J.3
Akey, J.M.4
Foss, E.5
Smith, E.N.6
MacKelprang, R.7
Kruglyak, L.8
-
32
-
-
0037313182
-
Evolution of gene expression in the Drosophila melanogaster subgroup
-
S.A. Rifkin, J. Kim, and K.P. White Evolution of gene expression in the Drosophila melanogaster subgroup Nat Genet 33 2003 138 144 The authors compare gene expression changes accompanying metamorphosis among four strains of D. melanogaster, Drosophila simulans and Drosophila yakuba - the latter two are diverged from D. melanogaster by 2.3 and 5 million years, respectively. Approximately half of the annotated genes varied during this transition and half of these showed some variation among the lineages. The data permit simple models of selection and drift to be fit, and the correlation between magnitude of change and evolutionary stability was also highlighted.
-
(2003)
Nat Genet
, vol.33
, pp. 138-144
-
-
Rifkin, S.A.1
Kim, J.2
White, K.P.3
-
33
-
-
2642580659
-
Duplicate genes increase gene expression diversity within and between species
-
Z. Gu, S.A. Rifkin, K.P. White, and W.H. Li Duplicate genes increase gene expression diversity within and between species Nat Genet 36 2004 577 579
-
(2004)
Nat Genet
, vol.36
, pp. 577-579
-
-
Gu, Z.1
Rifkin, S.A.2
White, K.P.3
Li, W.H.4
-
34
-
-
3042722019
-
Evolutionary changes in cis and trans gene regulation
-
P.J. Wittkopp, B.K. Haerum, and A.G. Clark Evolutionary changes in cis and trans gene regulation Nature 430 2004 85 88 The authors mate D. simulans and D. melanogaster and then examined transcripts for genes that are differentially expressed between the two species. In the hybrid, their sequencing technology permitted them to determine the level of each allele (cis differences), whereas comparison with the parent species defined trans changes.
-
(2004)
Nature
, vol.430
, pp. 85-88
-
-
Wittkopp, P.J.1
Haerum, B.K.2
Clark, A.G.3
-
35
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
M. Kellis, N. Patterson, M. Endrizzi, B. Birren, and E.S. Lander Sequencing and comparison of yeast species to identify genes and regulatory elements Nature 423 2003 241 254 To screen for regulatory sequence, the authors ranked all six-base (with a gap) core motifs as to whether they were contained in four-way aligned blocks in the upstream regions of the species they sequenced. They subsequently filtered out motifs with significant occurrence in coding regions and 3′ of genes.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
36
-
-
1942452749
-
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
-
M. Kellis, B.W. Birren, and E.S. Lander Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae Nature 428 2004 617 624
-
(2004)
Nature
, vol.428
, pp. 617-624
-
-
Kellis, M.1
Birren, B.W.2
Lander, E.S.3
-
37
-
-
0038724989
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
-
P. Cliften, P. Sudarsanam, A. Desikan, L. Fulton, B. Fulton, J. Majors, R. Waterston, B.A. Cohen, and M. Johnston Finding functional features in Saccharomyces genomes by phylogenetic footprinting Science 301 2003 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
-
38
-
-
11144355642
-
The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome
-
F.S. Dietrich, S. Voegeli, S. Brachat, A. Lerch, K. Gates, S. Steiner, C. Mohr, R. Pohlmann, P. Luedi, and S. Choi The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome Science 304 2004 304 307
-
(2004)
Science
, vol.304
, pp. 304-307
-
-
Dietrich, F.S.1
Voegeli, S.2
Brachat, S.3
Lerch, A.4
Gates, K.5
Steiner, S.6
Mohr, C.7
Pohlmann, R.8
Luedi, P.9
Choi, S.10
-
39
-
-
3142592324
-
Methods in comparative genomics: Genome correspondence, gene identification and regulatory motif discovery
-
M. Kellis, N. Patterson, B. Birren, B. Berger, and E.S. Lander Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery J Comput Biol 11 2004 319 355
-
(2004)
J Comput Biol
, vol.11
, pp. 319-355
-
-
Kellis, M.1
Patterson, N.2
Birren, B.3
Berger, B.4
Lander, E.S.5
-
40
-
-
0042697343
-
The evolution of transcriptional regulation in eukaryotes
-
G.A. Wray, M.W. Hahn, E. Abouheif, J.P. Balhoff, M. Pizer, M.V. Rockman, and L.A. Romano The evolution of transcriptional regulation in eukaryotes Mol Biol Evol 20 2003 1377 1419
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1377-1419
-
-
Wray, G.A.1
Hahn, M.W.2
Abouheif, E.3
Balhoff, J.P.4
Pizer, M.5
Rockman, M.V.6
Romano, L.A.7
-
41
-
-
0034730161
-
Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis
-
H.J. Bussemaker, H. Li, and E.D. Siggia Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis Proc Natl Acad Sci USA 97 2000 10096 10100
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 10096-10100
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
42
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
C.T. Harbison, D.B. Gordon, T.I. Lee, N.J. Rinaldi, K.D. Macisaac, T.W. Danford, N.M. Hannett, J.B. Tagne, D.B. Reynolds, and J. Yoo Transcriptional regulatory code of a eukaryotic genome Nature 431 2004 99 104 In this study, ChIP and interspecies conservation data are used to predict sequence motifs for over 200 yeast transcription factors. The motifs are then used to identify binding sites in promoters bound by the corresponding factor, and further filtered by presence in several other species. Regulatory inputs are found for 1300 genes.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
MacIsaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.B.8
Reynolds, D.B.9
Yoo, J.10
-
43
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
P.T. Spellman, G. Sherlock, M.Q. Zhang, V.R. Iyer, K. Anders, M.B. Eisen, P.O. Brown, D. Botstein, and B. Futcher Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization Mol Biol Cell 9 1998 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
-
45
-
-
19344365135
-
Ras and gpa2 mediate one branch of a redundant glucose signaling pathway in yeast
-
DOI: 10.1371/journal.pbio.0020128.
-
Wang Y, Pierce M, Schneper L, Guldal CG, Zhang X, Tavazoie S, Broach JR: Ras and gpa2 mediate one branch of a redundant glucose signaling pathway in yeast. PLoS Biol 2004, DOI: 10.1371/journal.pbio.0020128.
-
(2004)
PLoS Biol
-
-
Wang, Y.1
Pierce, M.2
Schneper, L.3
Guldal, C.G.4
Zhang, X.5
Tavazoie, S.6
Broach, J.R.7
-
46
-
-
0037722938
-
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling
-
J. Zeitlinger, I. Simon, C.T. Harbison, N.M. Hannett, T.L. Volkert, G.R. Fink, and R.A. Young Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling Cell 113 2003 395 404
-
(2003)
Cell
, vol.113
, pp. 395-404
-
-
Zeitlinger, J.1
Simon, I.2
Harbison, C.T.3
Hannett, N.M.4
Volkert, T.L.5
Fink, G.R.6
Young, R.A.7
-
48
-
-
18344415808
-
Distinguishing regulatory DNA from neutral sites
-
L. Elnitski, R.C. Hardison, J. Li, S. Yang, D. Kolbe, P. Eswara, M.J. O'Connor, S. Schwartz, W. Miller, and F. Chiaromonte Distinguishing regulatory DNA from neutral sites Genome Res 13 2003 64 72
-
(2003)
Genome Res
, vol.13
, pp. 64-72
-
-
Elnitski, 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
-
49
-
-
2942517986
-
Conservation of regulatory elements between two species of Drosophila
-
DOI: 10.1186/1471-2105-4-57.
-
Emberly E, Rajewsky N, Siggia ED: Conservation of regulatory elements between two species of Drosophila. BMC Bioinformatics 2003. DOI: 10.1186/1471-2105-4-57.
-
(2003)
BMC Bioinformatics
-
-
Emberly, E.1
Rajewsky, N.2
Siggia, E.D.3
-
50
-
-
19344375742
-
Transcriptional control in the segmentation gene network of Drosophila
-
DOI: 10.1371/journal.pbio.0020271.
-
Schroeder MD, Pearce M, Fak J, Fan H, Unnerstall U, Emberly E, Rajewsky N, Siggia ED, Gaul U: Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol 2004, DOI: 10.1371/journal.pbio.0020271. This study enlarges the number of confirmed regulatory modules for the anterior-posterior patterning network by 40% by using a computational screen for binding site clusters to target experiments. The authors demonstrate a strong correlation between computed module composition and where it is expressed. In addition, the presence of both activators and repressors distinguishes functional modules from other regions with comparable scores.
-
(2004)
PLoS Biol
-
-
Schroeder, M.D.1
Pearce, M.2
Fak, J.3
Fan, H.4
Unnerstall, U.5
Emberly, E.6
Rajewsky, N.7
Siggia, E.D.8
Gaul, U.9
-
51
-
-
0012301705
-
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome
-
DOI: 10.1186/gb-2002-3-12-research0086.
-
Bergman CM, Pfeiffer BD, Rincon-Limas DE, Hoskins RA, Gnirke A, Mungall CJ, Wang AM, Kronmiller B, Pacleb J, Park S et al.: Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol 2002 DOI: 10.1186/gb-2002-3-12-research0086.
-
(2002)
Genome Biol
-
-
Bergman, C.M.1
Pfeiffer, B.D.2
Rincon-Limas, D.E.3
Hoskins, R.A.4
Gnirke, A.5
Mungall, C.J.6
Wang, A.M.7
Kronmiller, B.8
Pacleb, J.9
Park, S.10
-
52
-
-
0031891484
-
High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups
-
D.A. Petrov, and D.L. Hartl High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups Mol Biol Evol 15 1998 293 302
-
(1998)
Mol Biol Evol
, vol.15
, pp. 293-302
-
-
Petrov, D.A.1
Hartl, D.L.2
-
53
-
-
16344388566
-
Sequence turnover and tandem repeats in cis-regulatory modules in Drosophila
-
DOI:10.1093/molbev/msi090.
-
Sinha S, Siggia ED: Sequence turnover and tandem repeats in cis-regulatory modules in Drosophila. Mol Biol Evol 2004, DOI:10.1093/molbev/ msi090.
-
(2004)
Mol Biol Evol
-
-
Sinha, S.1
Siggia, E.D.2
-
54
-
-
0036608206
-
Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin
-
C.H. Yuh, C.T. Brown, C.B. Livi, L. Rowen, P.J. Clarke, and E.H. Davidson Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin Dev Biol 246 2002 148 161
-
(2002)
Dev Biol
, vol.246
, pp. 148-161
-
-
Yuh, C.H.1
Brown, C.T.2
Livi, C.B.3
Rowen, L.4
Clarke, P.J.5
Davidson, E.H.6
-
55
-
-
0344153727
-
Genomic regulatory regions: Insights from comparative sequence analysis
-
G.M. Cooper, and A. Sidow Genomic regulatory regions: insights from comparative sequence analysis Curr Opin Genet Dev 13 2003 604 610
-
(2003)
Curr Opin Genet Dev
, vol.13
, pp. 604-610
-
-
Cooper, G.M.1
Sidow, A.2
-
56
-
-
0037184519
-
Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo
-
A. Stathopoulos, M. Van Drenth, A. Erives, M. Markstein, and M. Levine Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo Cell 111 2002 687 701
-
(2002)
Cell
, vol.111
, pp. 687-701
-
-
Stathopoulos, A.1
Van Drenth, M.2
Erives, A.3
Markstein, M.4
Levine, M.5
-
57
-
-
2942576308
-
Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo
-
DOI: 10.1186/1471-2105-3-30.
-
Rajewsky N, Vergassola M, Gaul U, Siggia ED: Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 2002, DOI: 10.1186/1471-2105-3-30.
-
(2002)
BMC Bioinformatics
-
-
Rajewsky, N.1
Vergassola, M.2
Gaul, U.3
Siggia, E.D.4
-
58
-
-
4644363054
-
Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster
-
J. Jaeger, M. Blagov, D. Kosman, K.N. Kozlov, Manu, E. Myasnikova, S. Surkova, C.E. Vanario-Alonso, M. Samsonova, and D.H. Sharp Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster Genetics 167 2004 1721 1737 The authors fit a model for the gap gene protein network using an empirical response function whose argument is the fitting matrix of protein interactions. They fit this to data at ∼7 minute time intervals, and over most of the embryo (pole-specific factors are missing). They do not fit mutant data.
-
(2004)
Genetics
, vol.167
, pp. 1721-1737
-
-
Jaeger, J.1
Blagov, M.2
Kosman, D.3
Kozlov, K.N.4
Manu5
Myasnikova, E.6
Surkova, S.7
Vanario-Alonso, C.E.8
Samsonova, M.9
Sharp, D.H.10
-
59
-
-
12744263842
-
Computational identification of developmental enhancers: Conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
-
B.P. Berman, B.D. Pfeiffer, T.R. Laverty, S.L. Salzberg, G.M. Rubin, M.B. Eisen, and S.E. Celniker Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura Genome Biol 5 2004 R61 The authors examine the expression patterns of 28 uncharacterized modules found within their top 37 predictions for anterior-posterior patterned genes. Six of the 28 are active in the embryo, and mirror the expression of a neighboring gene, although two of these are neuroblast specific. They consider various criteria that would discriminate their active from inactive modules and find that binding site conservation in D. pseudoobscura works best.
-
(2004)
Genome Biol
, vol.5
, pp. 61
-
-
Berman, B.P.1
Pfeiffer, B.D.2
Laverty, T.R.3
Salzberg, S.L.4
Rubin, G.M.5
Eisen, M.B.6
Celniker, S.E.7
-
60
-
-
3042710549
-
A regulatory code for neurogenic gene expression in the Drosophila embryo
-
M. Markstein, R. Zinzen, P. Markstein, K.P. Yee, A. Erives, A. Stathopoulos, and M. Levine A regulatory code for neurogenic gene expression in the Drosophila embryo Development 131 2004 2387 2394 The authors test 15 genome-wide predictions of strong dorsal binding site clusters, generated by regular expression matches. This scan recovered one out of seven dorsal-regulated modules known at the time. Of the fifteen, five are functional and expressed at various levels in the nuclear dorsal gradient. The authors then predicted and tested other binding sites (two of which corresponded to Twist and Su(H)) common to three neural ectoderm genes, and scanned the genome with the entire set, recovering several functional modules that expressed in the expected region. From the data in this article, modules do not read their position in the dorsal gradient by the strength of the dorsal binding sites.
-
(2004)
Development
, vol.131
, pp. 2387-2394
-
-
Markstein, M.1
Zinzen, R.2
Markstein, P.3
Yee, K.P.4
Erives, A.5
Stathopoulos, A.6
Levine, M.7
-
61
-
-
0037154218
-
Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo
-
M. Markstein, P. Markstein, V. Markstein, and M.S. Levine Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo Proc Natl Acad Sci USA 99 2002 763 768
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 763-768
-
-
Markstein, M.1
Markstein, P.2
Markstein, V.3
Levine, M.S.4
-
62
-
-
13244271362
-
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
-
S. Sinha, M.D. Schroeder, U. Unnerstall, U. Gaul, and E.D. Siggia Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila BMC Bioinformatics 5 2004 129
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 129
-
-
Sinha, S.1
Schroeder, M.D.2
Unnerstall, U.3
Gaul, U.4
Siggia, E.D.5
-
63
-
-
8844270153
-
Prediction of similarly-acting cis-regulatory modules by subsequence profiling and comparative genomics in D. melanogaster and D. pseudoobscura
-
Y.H. Grad, F.P. Roth, M.S. Halfon, and G.M. Church Prediction of similarly-acting cis-regulatory modules by subsequence profiling and comparative genomics in D. melanogaster and D. pseudoobscura Bioinformatics 20 2004 2738 2750 Without using prior knowledge about factor binding sites, the authors determine modules common to a set of co-expressed genes. They first screen rather liberally for regions of strongest interspecies conservation, and then use a Gibbs-like search that models the current set of modules as a fifth order Markov model, searches for similar modules within the filtered sequence, and then updates the Markov model. Validation was done against the fly in situ set.
-
(2004)
Bioinformatics
, vol.20
, pp. 2738-2750
-
-
Grad, Y.H.1
Roth, F.P.2
Halfon, M.S.3
Church, G.M.4
-
64
-
-
1842505125
-
Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics
-
A. Sandelin, and W.W. Wasserman Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics J Mol Biol 338 2004 207 215
-
(2004)
J Mol Biol
, vol.338
, pp. 207-215
-
-
Sandelin, A.1
Wasserman, W.W.2
-
65
-
-
0037386626
-
Analysis of the eye developmental pathway in Drosophila using DNA microarrays
-
L. Michaut, S. Flister, M. Neeb, K.P. White, U. Certa, and W.J. Gehring Analysis of the eye developmental pathway in Drosophila using DNA microarrays Proc Natl Acad Sci USA 100 2003 4024 4029
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 4024-4029
-
-
Michaut, L.1
Flister, S.2
Neeb, M.3
White, K.P.4
Certa, U.5
Gehring, W.J.6
-
66
-
-
0037327164
-
Discovery of genes with highly restricted expression patterns in the Drosophila wing disc using DNA oligonucleotide microarrays
-
M.J. Butler, T.L. Jacobsen, D.M. Cain, M.G. Jarman, M. Hubank, J.R. Whittle, R. Phillips, and A. Simcox Discovery of genes with highly restricted expression patterns in the Drosophila wing disc using DNA oligonucleotide microarrays Development 130 2003 659 670
-
(2003)
Development
, vol.130
, pp. 659-670
-
-
Butler, M.J.1
Jacobsen, T.L.2
Cain, D.M.3
Jarman, M.G.4
Hubank, M.5
Whittle, J.R.6
Phillips, R.7
Simcox, A.8
-
67
-
-
7444233156
-
A gene expression map for the euchromatic genome of Drosophila melanogaster
-
V. Stolc, Z. Gauhar, C. Mason, G. Halasz, M.F. van Batenburg, S.A. Rifkin, S. Hua, T. Herreman, W. Tongprasit, and P.E. Barbano A gene expression map for the euchromatic genome of Drosophila melanogaster Science 306 2004 655 660 The authors built custom arrays with probes to individual exons in addition to intergenic sequence, and monitored RNA expression using whole animals during six developmental stages. They found extensive expression of genomic regions that are not coding, and correlation of gene expression within domains syntenic with D. pseudoobscura.
-
(2004)
Science
, vol.306
, pp. 655-660
-
-
Stolc, V.1
Gauhar, Z.2
Mason, C.3
Halasz, G.4
Van Batenburg, M.F.5
Rifkin, S.A.6
Hua, S.7
Herreman, T.8
Tongprasit, W.9
Barbano, P.E.10
-
68
-
-
0037188521
-
Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics
-
E. van Nimwegen, M. Zavolan, N. Rajewsky, and E.D. Siggia Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics Proc Natl Acad Sci USA 99 2002 7323 7328
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 7323-7328
-
-
Van Nimwegen, E.1
Zavolan, M.2
Rajewsky, N.3
Siggia, E.D.4
-
69
-
-
15744375391
-
Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches
-
in press.
-
Chandonia JM, Brenner SE: Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins 2004, in press.
-
(2004)
Proteins
-
-
Chandonia, J.M.1
Brenner, S.E.2
-
70
-
-
4644367204
-
Positive selection on MMP3 regulation has shaped heart disease risk
-
M.V. Rockman, M.W. Hahn, N. Soranzo, D.A. Loisel, D.B. Goldstein, and G.A. Wray Positive selection on MMP3 regulation has shaped heart disease risk Curr Biol 14 2004 1531 1539
-
(2004)
Curr Biol
, vol.14
, pp. 1531-1539
-
-
Rockman, M.V.1
Hahn, M.W.2
Soranzo, N.3
Loisel, D.A.4
Goldstein, D.B.5
Wray, G.A.6
-
71
-
-
0033636013
-
A space-efficient algorithm for aligning large genomic sequences
-
B. Morgenstern A space-efficient algorithm for aligning large genomic sequences Bioinformatics 16 2000 948 949
-
(2000)
Bioinformatics
, vol.16
, pp. 948-949
-
-
Morgenstern, B.1
-
72
-
-
0032861774
-
SCPD: A promoter database of the yeast Saccharomyces cerevisiae
-
J. Zhu, and M.Q. Zhang SCPD: a promoter database of the yeast Saccharomyces cerevisiae Bioinformatics 15 1999 607 611
-
(1999)
Bioinformatics
, vol.15
, pp. 607-611
-
-
Zhu, J.1
Zhang, M.Q.2
|