-
1
-
-
1942453302
-
Predicting gene expression from sequence
-
DOI 10.1016/S0092-8674(04)00304-6, PII S0092867404003046
-
Beer MA, Tavazoie S. 2004. Predicting gene expression from sequence. Cell 117: 185-198. (Pubitemid 38496239)
-
(2004)
Cell
, vol.117
, Issue.2
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
2
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
Margulies, E.H.6
Weng, Z.7
Snyder, M.8
Dermitzakis, E.T.9
Thurman, R.E.10
-
3
-
-
0032579440
-
Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications
-
DOI 10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2- 2
-
Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD. 1998. Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115-132. (Pubitemid 28062863)
-
(1998)
Yeast
, vol.14
, Issue.2
, pp. 115-132
-
-
Brachmann, C.B.1
Davies, A.2
Cost, G.J.3
Caputo, E.4
Li, J.5
Hieter, P.6
Boeke, J.D.7
-
4
-
-
66149118241
-
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
-
Calvo SE, Pagliarini DJ, Mootha VK. 2009. Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc Natl Acad Sci 106: 7507-7512.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 7507-7512
-
-
Calvo, S.E.1
Pagliarini, D.J.2
Mootha, V.K.3
-
5
-
-
26944478233
-
Evolutionary conservation suggests a regulatory function of AUG triplets in 5′-UTRs of eukaryotic genes
-
DOI 10.1093/nar/gki847
-
Churbanov A, Rogozin IB, Babenko VN, Ali H, Koonin EV. 2005. Evolutionary conservation suggests a regulatory function of AUG triplets in 5′-UTRs of eukaryotic genes. Nucleic Acids Res 33: 5512-5520. (Pubitemid 41548817)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.17
, pp. 5512-5520
-
-
Churbanov, A.1
Rogozin, I.B.2
Babenko, V.N.3
Ali, H.4
Koonin, E.V.5
-
6
-
-
0038724989
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting
-
DOI 10.1126/science.1084337
-
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. (Pubitemid 36801562)
-
(2003)
Science
, vol.301
, Issue.5629
, 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
-
8
-
-
0037119587
-
Stochastic gene expression in a single cell
-
DOI 10.1126/science.1070919
-
Elowitz MB, Levine AJ, Siggia ED, Swain PS. 2002. Stochastic gene expression in a single cell. Science 297: 1183-1186. (Pubitemid 36193353)
-
(2002)
Science
, vol.297
, Issue.5584
, pp. 1183-1186
-
-
Elowitz, M.B.1
Levine, A.J.2
Siggia, E.D.3
Swain, P.S.4
-
9
-
-
0031978181
-
Base-calling of automated sequencer traces using phred. II. Error probabilities
-
Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194. (Pubitemid 28177230)
-
(1998)
Genome Research
, vol.8
, Issue.3
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
10
-
-
0142215475
-
Global analysis of protein expression in yeast
-
DOI 10.1038/nature02046
-
Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. 2003. Global analysis of protein expression in yeast. Nature 425: 737-741. (Pubitemid 37314318)
-
(2003)
Nature
, vol.425
, Issue.6959
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.-K.2
Bower, K.3
Howson, R.W.4
Belle, A.5
Dephoure, N.6
O'Shea, E.K.7
Weissman, J.S.8
-
11
-
-
0036270543
-
Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method
-
DOI 10.1016/S0076-6879(02)50957-5
-
Gietz RD, Woods RA. 2002. Transformation of yeast by lithium acetate/ single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol 350: 87-96. (Pubitemid 34619485)
-
(2002)
Methods in Enzymology
, vol.350
, pp. 87-96
-
-
Gietz, R.D.1
Woods, R.A.2
-
12
-
-
0021924399
-
Specific DNA binding of GAL4, a positive regulatory protein of yeast
-
Giniger E, Varnum SM, Ptashne M. 1985. Specific DNA binding of GAL4, a positive regulatory protein of yeast. Cell 40: 767-774. (Pubitemid 15240282)
-
(1985)
Cell
, vol.40
, Issue.4
, pp. 767-774
-
-
Giniger, E.1
Varnum, S.M.2
Ptashne, M.3
-
13
-
-
0031955116
-
Consed: A graphical tool for sequence finishing
-
Gordon D, Abajian C, Green P. 1998. Consed: A graphical tool for sequence finishing. Genome Res 8: 195-202. (Pubitemid 28177231)
-
(1998)
Genome Research
, vol.8
, Issue.3
, pp. 195-202
-
-
Gordon, D.1
Abajian, C.2
Green, P.3
-
14
-
-
0347416978
-
Genome-Wide Analysis of mRNAs Regulated by the Nonsense-Mediated and 5′ to 3′ mRNA Decay Pathways in Yeast
-
DOI 10.1016/S1097-2765(03)00446-5
-
He F, Li X, Spatrick P, Casillo R, Dong S, Jacobson A. 2003. Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5′ to 3′ mRNA decay pathways in yeast. Mol Cell 12: 1439-1452. (Pubitemid 38037013)
-
(2003)
Molecular Cell
, vol.12
, Issue.6
, pp. 1439-1452
-
-
He, F.1
Li, X.2
Spatrick, P.3
Casillo, R.4
Dong, S.5
Jacobson, A.6
-
15
-
-
67249117049
-
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
-
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci 106: 9362-9367.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 9362-9367
-
-
Hindorff, L.A.1
Sethupathy, P.2
Junkins, H.A.3
Ramos, E.M.4
Mehta, J.P.5
Collins, F.S.6
Manolio, T.A.7
-
16
-
-
27144510561
-
Translational regulation of GCN4 and the general amino acid control of yeast
-
DOI 10.1146/annurev.micro.59.031805.133833
-
Hinnebusch AG. 2005. Translational regulation of GCN4 and the general amino acid control of yeast. Annu Rev Microbiol 59: 407-450. (Pubitemid 41507438)
-
(2005)
Annual Review of Microbiology
, vol.59
, pp. 407-450
-
-
Hinnebusch, A.G.1
-
17
-
-
70349536104
-
Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi
-
Hood HM, Neafsey DE, Galagan J, Sachs MS. 2009. Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi. Annu Rev Microbiol 63: 385-409.
-
(2009)
Annu Rev Microbiol
, vol.63
, pp. 385-409
-
-
Hood, H.M.1
Neafsey, D.E.2
Galagan, J.3
Sachs, M.S.4
-
18
-
-
17044409660
-
UAUG and uORFs in human and rodent 59untranslated mRNAs
-
Iacono M, Mignone F, Pesole G. 2005. uAUG and uORFs in human and rodent 59untranslated mRNAs. Gene 349: 97-105.
-
(2005)
Gene
, vol.349
, pp. 97-105
-
-
Iacono, M.1
Mignone, F.2
Pesole, G.3
-
19
-
-
0021471049
-
Sequences that regulate the divergent GAL1- GAL10 promoter in Saccharomyces cerevisiae
-
Johnston M, Davis RW. 1984. Sequences that regulate the divergent GAL1- GAL10 promoter in Saccharomyces cerevisiae. Mol Cell Biol 4: 1440-1448.
-
(1984)
Mol Cell Biol
, vol.4
, pp. 1440-1448
-
-
Johnston, M.1
Davis, R.W.2
-
20
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, et al. 2009. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366.
-
(2009)
Nature
, vol.458
, pp. 362-366
-
-
Kaplan, N.1
Moore, I.K.2
Fondufe-Mittendorf, Y.3
Gossett, A.J.4
Tillo, D.5
Field, Y.6
LeProust, E.M.7
Hughes, T.R.8
Lieb, J.D.9
Widom, J.10
-
21
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
DOI 10.1038/nature01644
-
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. (Pubitemid 40852689)
-
(2003)
Nature
, vol.423
, Issue.6937
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
22
-
-
0023656915
-
The regulatory protein GAL80 is a determinant of the chromatin structure of the yeast GAL1-10 control region
-
Lohr D, Torchia T, Hopper J. 1987. The regulatory protein GAL80 is a determinant of the chromatin structure of the yeast GAL1-10 control region. J Biol Chem 262: 15589-15597.
-
(1987)
J Biol Chem
, vol.262
, pp. 15589-15597
-
-
Lohr, D.1
Torchia, T.2
Hopper, J.3
-
23
-
-
0037208166
-
TRANSFAC: Transcriptional regulation, from patterns to profiles
-
DOI 10.1093/nar/gkg108
-
Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, et al. 2003. TRANSFAC: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31: 374-378. (Pubitemid 36150406)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gossling, E.4
Haubrock, M.5
Hehl, R.6
Hornischer, K.7
Karas, D.8
Kel, A.E.9
Kel-Margoulis, O.V.10
Kloos, D.-U.11
Land, S.12
Lewicki-Potapov, B.13
Michael, H.14
Munch, R.15
Reuter, I.16
Rotert, S.17
Saxel, H.18
Scheer, M.19
Thiele, S.20
Wingender, E.21
more..
-
24
-
-
79958276198
-
Translational control via protein-regulated upstream open reading frames
-
Medenbach J, Seiler M, Hentze MW. 2011. Translational control via protein-regulated upstream open reading frames. Cell 145: 902-913.
-
(2011)
Cell
, vol.145
, pp. 902-913
-
-
Medenbach, J.1
Seiler, M.2
Hentze, M.W.3
-
25
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
DOI 10.1126/science.1158441
-
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349. (Pubitemid 351929471)
-
(2008)
Science
, vol.320
, Issue.5881
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
Gerstein, M.6
Snyder, M.7
-
26
-
-
34249818182
-
Tissue-specific transcriptional regulation has diverged significantly between human and mouse
-
DOI 10.1038/ng2047, PII NG2047
-
Odom DT, Dowell RD, Jacobsen ES, Gordon W, Danford TW, MacIsaac KD, Rolfe PA, Conboy CM, Gifford DK, Fraenkel E. 2007. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet 39: 730-732. (Pubitemid 46848594)
-
(2007)
Nature Genetics
, vol.39
, Issue.6
, pp. 730-732
-
-
Odom, D.T.1
Dowell, R.D.2
Jacobsen, E.S.3
Gordon, W.4
Danford, T.W.5
MacIsaac, K.D.6
Rolfe, P.A.7
Conboy, C.M.8
Gifford, D.K.9
Fraenkel, E.10
-
27
-
-
2942718723
-
Control of stochasticity in eukaryotic gene expression
-
DOI 10.1126/science.1098641
-
Raser JM, O'Shea EK. 2004. Control of stochasticity in eukaryotic gene expression. Science 304: 1811-1814. (Pubitemid 38787899)
-
(2004)
Science
, vol.304
, Issue.5678
, pp. 1811-1814
-
-
Raser, J.M.1
O'Shea, E.K.2
-
28
-
-
0031658081
-
The chromatin structure of the GAL1 promoter forms independently of Reb1p in Saccharomyces cerevisiae
-
DOI 10.1007/s004380050799
-
Reagan MS, Majors JE. 1998. The chromatin structure of the GAL1 promoter forms independently of Reb1p in Saccharomyces cerevisiae. Mol Gen Genet 259: 142-149. (Pubitemid 28431638)
-
(1998)
Molecular and General Genetics
, vol.259
, Issue.2
, pp. 142-149
-
-
Reagan, M.S.1
Majors, J.E.2
-
29
-
-
77953062527
-
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
-
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, et al. 2010. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328: 1036-1040.
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
Wilson, M.D.2
Ballester, B.3
Schwalie, P.C.4
Brown, G.D.5
Marshall, A.6
Kutter, C.7
Watt, S.8
Martinez-Jimenez, C.P.9
Mackay, S.10
-
30
-
-
1542537849
-
Combining phylogenetic and hidden Markov models in biosequence analysis
-
DOI 10.1089/1066527041410472
-
Siepel A, Haussler D. 2004. Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol 11: 413-428. (Pubitemid 38901670)
-
(2004)
Journal of Computational Biology
, vol.11
, Issue.2-3
, pp. 413-428
-
-
Siepel, A.1
Haussler, D.2
-
32
-
-
0024669291
-
A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae
-
Sikorski RS, Hieter P. 1989. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27.
-
(1989)
Genetics
, vol.122
, pp. 19-27
-
-
Sikorski, R.S.1
Hieter, P.2
-
33
-
-
0032494751
-
Information content and free energy in DNA-protein interactions [1]
-
DOI 10.1006/jtbi.1998.0785
-
Stormo GD. 1998. Information content and free energy in DNA-protein interactions. J Theor Biol 195: 135-137. (Pubitemid 28521914)
-
(1998)
Journal of Theoretical Biology
, vol.195
, Issue.1
, pp. 135-137
-
-
Stormo, G.D.1
-
34
-
-
0042065288
-
Regulation of fungal gene expression via short open reading frames in the mRNA 5′untranslated region
-
DOI 10.1046/j.1365-2958.2003.03622.x
-
Vilela C, McCarthy JE. 2003. Regulation of fungal gene expression via short open reading frames in the mRNA 59untranslated region. Mol Microbiol 49: 859-867. (Pubitemid 36981334)
-
(2003)
Molecular Microbiology
, vol.49
, Issue.4
, pp. 859-867
-
-
Vilela, C.1
McCarthy, J.E.G.2
-
35
-
-
0021723295
-
Saccharomyces cerevisiae GAL1-GAL10 divergent promoter region: Location and function of the upstream activating sequence UAS(G)
-
West RW Jr, Yocum RR, Ptashne M. 1984. Saccharomyces cerevisiae GAL1-GAL10 divergent promoter region: Location and function of the upstream activating sequence UASG. Mol Cell Biol 4: 2467-2478. (Pubitemid 15212262)
-
(1984)
Molecular and Cellular Biology
, vol.4
, Issue.11
, pp. 2467-2478
-
-
West Jr., R.W.1
Yocum, R.R.2
Ptashne, M.3
-
36
-
-
63849315606
-
High-resolution DNA-binding specificity analysis of yeast transcription factors
-
Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, et al. 2009. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19: 556-566.
-
(2009)
Genome Res
, vol.19
, pp. 556-566
-
-
Zhu, C.1
Byers, K.J.2
McCord, R.P.3
Shi, Z.4
Berger, M.F.5
Newburger, D.E.6
Saulrieta, K.7
Smith, Z.8
Shah, M.V.9
Radhakrishnan, M.10
|