-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
17644425833
-
-
Aspergillus Sequencing Project. Broad Institute, MIT and Harvard Cambridge, MA
-
Aspergillus Sequencing Project (2003) Aspergillus Sequencing Project. Broad Institute, MIT and Harvard, Cambridge, MA
-
(2003)
Aspergillus Sequencing Project
-
-
-
3
-
-
0037811432
-
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
-
Chiang DY, Moses AM, Kellis M, Lander ES, Eisen MB (2003) Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol 4:R43
-
(2003)
Genome Biol
, vol.4
, pp. 43
-
-
Chiang, D.Y.1
Moses, A.M.2
Kellis, M.3
Lander, E.S.4
Eisen, M.B.5
-
4
-
-
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 BA, 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
-
5
-
-
0035986888
-
Evolution of transcription factor binding sites in Mammalian gene regulatory regions: Conservation and turnover
-
Dermitzakis ET, Clark AG (2002) Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover. Mol Biol Evol 19:1114-1121
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1114-1121
-
-
Dermitzakis, E.T.1
Clark, A.G.2
-
6
-
-
11144355642
-
The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome
-
Dietrich FS, Voegeli S, Brachat S, Choi S, et al. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-307
-
(2004)
Science
, vol.304
, pp. 304-307
-
-
Dietrich, F.S.1
Voegeli, S.2
Brachat, S.3
Choi, S.4
-
7
-
-
33745736295
-
Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution
-
Dujon B (2006) Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends Genet. 22:375-387
-
(2006)
Trends Genet.
, vol.22
, pp. 375-387
-
-
Dujon, B.1
-
8
-
-
3042720475
-
Genome evolution in yeasts
-
Dujon B, Sherman D, Fischer G, et al. (2004) Genome evolution in yeasts. Nature 430:35-44
-
(2004)
Nature
, vol.430
, pp. 35-44
-
-
Dujon, B.1
Sherman, D.2
Fischer, G.3
-
10
-
-
0035215378
-
Evolution of gene order in the genomes of two related yeast species
-
Fischer G, Neuveglise C, Durrens P, Gaillardin C, Dujon B (2001) Evolution of gene order in the genomes of two related yeast species. Genome Res 11:2009-2019
-
(2001)
Genome Res
, vol.11
, pp. 2009-2019
-
-
Fischer, G.1
Neuveglise, C.2
Durrens, P.3
Gaillardin, C.4
Dujon, B.5
-
11
-
-
33645787782
-
Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages
-
Fischer G, Rocha EP, Brunet F, Vergassola M, Dujon B (2006) Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages. PLoS Genet 2:e32
-
(2006)
PLoS Genet
, vol.2
, pp. 32
-
-
Fischer, G.1
Rocha, E.P.2
Brunet, F.3
Vergassola, M.4
Dujon, B.5
-
12
-
-
0037464589
-
The genome sequence of the filamentous fungus Neurospora crassa
-
Galagan JE, Calvo SE, Borkovitch KA, et al. (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422:859-868
-
(2003)
Nature
, vol.422
, pp. 859-868
-
-
Galagan, J.E.1
Calvo, S.E.2
Borkovitch, K.A.3
-
13
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241-4257
-
(2000)
Mol Biol Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
Storz, G.6
Botstein, D.7
Brown, P.O.8
-
14
-
-
14044252090
-
Conservation and evolution of cis-regulatory systems in ascomycete fungi
-
Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, Eisen MB (2004) Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol 2:e398
-
(2004)
PLoS Biol
, vol.2
, pp. 398
-
-
Gasch, A.P.1
Moses, A.M.2
Chiang, D.Y.3
Fraser, H.B.4
Berardini, M.5
Eisen, M.B.6
-
15
-
-
10244239321
-
Life with 6000 genes
-
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, et al. (1996) Life with 6000 genes. Science 274:563-567
-
(1996)
Science
, vol.274
, pp. 563-567
-
-
Goffeau, A.1
Barrell, B.G.2
Bussey, H.3
Davis, R.W.4
Dujon, B.5
Feldmann, H.6
Galibert, F.7
Hoheisel, J.D.8
Jacq, C.9
Johnston, M.10
-
16
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
Hughes JD, Estep PW, Tavazoie S, Church GM (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
-
17
-
-
0033772765
-
Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes
-
Jelinsky SA, Estep P, Church GM, Samson LD (2000) Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol 20:8157-8167
-
(2000)
Mol Cell Biol
, vol.20
, pp. 8157-8167
-
-
Jelinsky, S.A.1
Estep, P.2
Church, G.M.3
Samson, L.D.4
-
19
-
-
2642560445
-
Proteasomal degradation of RPN4 via two distinct mechanisms, ubiquitin-dependent and -independent
-
Ju D, Xie Y (2004) Proteasomal degradation of RPN4 via two distinct mechanisms, ubiquitin-dependent and -independent. J Biol Chem 279:23851-23854
-
(2004)
J Biol Chem
, vol.279
, pp. 23851-23854
-
-
Ju, D.1
Xie, Y.2
-
20
-
-
0035346389
-
Isolation and identification of PACE-binding protein rpn4-a new transcription activator, participating in regulation of 26S proteosome and other genes
-
Kapranov AB, Kuriatova MV, Preobrazhenskaia OV, Tiutiaeva VV, Stuka R, Feldmann H, Karpov VL, Karpov V (2001) Isolation and identification of PACE-binding protein rpn4-a new transcription activator, participating in regulation of 26S proteosome and other genes. Mol Biol (Mosk) 35:420-431
-
(2001)
Mol Biol (Mosk)
, vol.35
, pp. 420-431
-
-
Kapranov, A.B.1
Kuriatova, M.V.2
Preobrazhenskaia, O.V.3
Tiutiaeva, V.V.4
Stuka, R.5
Feldmann, H.6
Karpov, V.L.7
Karpov, V.8
-
21
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (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
-
22
-
-
1942452749
-
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
-
Kellis M, Birren BW, Lander ES (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428:617-624
-
(2004)
Nature
, vol.428
, pp. 617-624
-
-
Kellis, M.1
Birren, B.W.2
Lander, E.S.3
-
23
-
-
0034704325
-
Genome rearrangements in yeasts. Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae
-
Llorente B, Malpertuy A, Neuvéglise C, et al. (2000) Genome rearrangements in yeasts. Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae. FEBS Lett 487:101-112
-
(2000)
FEBS Lett
, vol.487
, pp. 101-112
-
-
Llorente, B.1
Malpertuy, A.2
Neuvéglise, C.3
-
24
-
-
18944392199
-
Identification and characterization of a Drosophila proteasome regulatory network
-
Lundgren J, Masson P, Mirzaei Z, Young P (2005) Identification and characterization of a Drosophila proteasome regulatory network. Mol Cell Biol 25:4662-4675
-
(2005)
Mol Cell Biol
, vol.25
, pp. 4662-4675
-
-
Lundgren, J.1
Masson, P.2
Mirzaei, Z.3
Young, P.4
-
25
-
-
0032483028
-
Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences
-
Makalowski W, Boguski MS (1998) Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc Natl Acad Sci USA 95:9407-9412
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 9407-9412
-
-
Makalowski, W.1
Boguski, M.S.2
-
26
-
-
0034704256
-
Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes
-
Malpertuy A, Tekaia F, Casaregola S, et al. (2000) Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes. FEBS Lett 487:113-121
-
(2000)
FEBS Lett
, vol.487
, pp. 113-121
-
-
Malpertuy, A.1
Tekaia, F.2
Casaregola, S.3
-
27
-
-
0033004441
-
Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast
-
Mannhaupt G, Schnall R, Karpov V, Vetter I, Feldmann H (1999) Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Lett 450:27-34
-
(1999)
FEBS Lett
, vol.450
, pp. 27-34
-
-
Mannhaupt, G.1
Schnall, R.2
Karpov, V.3
Vetter, I.4
Feldmann, H.5
-
28
-
-
0037821846
-
Inhibition of proteasome activity induces concerted expression of proteasome genes and de novo formation of mammalian proteasomes
-
Meiners S, Heyken D, Weller A, Ludwig A, Stangl K, Kloetzel K-P, Kruger E (2003) Inhibition of proteasome activity induces concerted expression of proteasome genes and de novo formation of mammalian proteasomes. J Biol Chem 278:21517-21525
-
(2003)
J Biol Chem
, vol.278
, pp. 21517-21525
-
-
Meiners, S.1
Heyken, D.2
Weller, A.3
Ludwig, A.4
Stangl, K.5
Kloetzel, K.-P.6
Kruger, E.7
-
30
-
-
0642368358
-
Position specific variation in the rate of evolution in transcription factor binding sites
-
Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB (2003) Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol 3:19
-
(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
-
31
-
-
22144491990
-
MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
-
Moses AM, Chiang DY, Pollard DA, Iyer VN, Eisen MB (2004) MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol 5:R98
-
(2004)
Genome Biol
, vol.5
, pp. 98
-
-
Moses, A.M.1
Chiang, D.Y.2
Pollard, D.A.3
Iyer, V.N.4
Eisen, M.B.5
-
32
-
-
28644434509
-
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
-
Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, et al. (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438:1092-1093
-
(2005)
Nature
, vol.438
, pp. 1092-1093
-
-
Nierman, W.C.1
Pain, A.2
Anderson, M.J.3
Wortman, J.R.4
Kim, H.S.5
Arroyo, J.6
Berriman, M.7
Abe, K.8
Archer, D.B.9
Bermejo, C.10
-
33
-
-
0036226237
-
Control of 26S proteasome expression by transcription factors regulating multidrug resistance in Saccharomyces cerevisiae
-
Owsianik G, Balzi L, Ghislain M (2002) Control of 26S proteasome expression by transcription factors regulating multidrug resistance in Saccharomyces cerevisiae. Mol Microbiol 43:1295-1308
-
(2002)
Mol Microbiol
, vol.43
, pp. 1295-1308
-
-
Owsianik, G.1
Balzi, L.2
Ghislain, M.3
-
34
-
-
0034923498
-
Design and selection of novel Cys2His2 zinc finger proteins
-
Pabo CO, Peisach E, Grant RA (2001) Design and selection of novel Cys2His2 zinc finger proteins. Annu Rev Biochem 70:313-340
-
(2001)
Annu Rev Biochem
, vol.70
, pp. 313-340
-
-
Pabo, C.O.1
Peisach, E.2
Grant, R.A.3
-
35
-
-
2942516151
-
Benchmarking tools for the alignment of functional noncoding DNA
-
Pollard DA, Bergman CM, Stoye J, Celniker S, Eisen MB (2004) Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinform 5:6
-
(2004)
BMC Bioinform
, vol.5
, pp. 6
-
-
Pollard, D.A.1
Bergman, C.M.2
Stoye, J.3
Celniker, S.4
Eisen, M.B.5
-
36
-
-
1542316919
-
Integrated molecular network control
-
Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, Galitski T (2004) Integrated molecular network control. Genome Res 14:380-390
-
(2004)
Genome Res
, vol.14
, pp. 380-390
-
-
Prinz, S.1
Avila-Campillo, I.2
Aldridge, C.3
Srinivasan, A.4
Dimitrov, K.5
Siegel, A.F.6
Galitski, T.7
-
37
-
-
33645023614
-
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
-
Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH (2006) Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440:341-345
-
(2006)
Nature
, vol.440
, pp. 341-345
-
-
Scannell, D.R.1
Byrne, K.P.2
Gordon, J.L.3
Wong, S.4
Wolfe, K.H.5
-
38
-
-
0034704310
-
Genomic exploration of the hemiascomycetous yeasts: 1. a set of yeast species for molecular evolution studies
-
Souciet JL, Aigle M, Artiguenave F, et al. (2000) Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett 487:3-12
-
(2000)
FEBS Lett
, vol.487
, pp. 3-12
-
-
Souciet, J.L.1
Aigle, M.2
Artiguenave, F.3
-
39
-
-
0034649566
-
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
-
The Arabidopsis Genome Initiative
-
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
-
(2000)
Nature
, vol.408
, pp. 796-815
-
-
-
40
-
-
0041620271
-
Regulatory sequence analysis tools
-
van Helden J (2003) Regulatory sequence analysis tools. Nucleic Acids Res 31:3593-3596
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3593-3596
-
-
Van Helden, J.1
-
41
-
-
11244343965
-
Rpn4 is a physiological substrate of the Ubr2 ubiquitin ligase
-
Wang L, Mao X, Ju D, Xie Y (2004) Rpn4 is a physiological substrate of the Ubr2 ubiquitin ligase. J Biol Chem 279:55218-55223
-
(2004)
J Biol Chem
, vol.279
, pp. 55218-55223
-
-
Wang, L.1
Mao, X.2
Ju, D.3
Xie, Y.4
-
42
-
-
9644300915
-
The proteasome: A proteolytic nanomachine of cell regulation and waste disposal
-
Wolf DH, Hilt W (2004) The proteasome: a proteolytic nanomachine of cell regulation and waste disposal. Biochim Biophys Acta 1695:19-31
-
(2004)
Biochim Biophys Acta
, vol.1695
, pp. 19-31
-
-
Wolf, D.H.1
Hilt, W.2
-
43
-
-
0030947344
-
Molecular evidence for an ancient duplication of the entire yeast genome
-
Wolfe KH, Shields DC (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713
-
(1997)
Nature
, vol.387
, pp. 708-713
-
-
Wolfe, K.H.1
Shields, D.C.2
-
45
-
-
0037155196
-
Analysis of Drosophila 26 S proteasome using RNA interference
-
Wojcik C, DeMartino GN (2002) Analysis of Drosophila 26 S proteasome using RNA interference. J Biol Chem 277:6188-6197
-
(2002)
J Biol Chem
, vol.277
, pp. 6188-6197
-
-
Wojcik, C.1
Demartino, G.N.2
-
46
-
-
0037148758
-
The genome sequence of Schizosaccharomyces pombe
-
Wood V, Gwilliam R, Rajandream MA, 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
-
47
-
-
0042697343
-
The evolution of transcriptional regulation in eukaryotes
-
Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV, Romano LA (2003) The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20:1377-1419
-
(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
-
48
-
-
0035853037
-
RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: A negative feedback circuit
-
Xie Y, Varshavsky A (2001) RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a negative feedback circuit. Proc Natl Acad Sci USA 98:3056-3061
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 3056-3061
-
-
Xie, Y.1
Varshavsky, A.2
|