-
1
-
-
54949148332
-
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
-
Hogan, D.J., Riordan, D.P., Gerber, A.P., Herschlag, D. and Brown, P.O. (2008) Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol., 6, e255.
-
(2008)
PLoS Biol.
, vol.6
-
-
Hogan, D.J.1
Riordan, D.P.2
Gerber, A.P.3
Herschlag, D.4
Brown, P.O.5
-
2
-
-
34250735674
-
RNA regulons: Coordination of post-transcriptional events
-
DOI 10.1038/nrg2111, PII NRG2111
-
Keene, J.D. (2007) RNA regulons: coordination of post-transcriptional events. Nat. Rev. Genet., 8, 533-543. (Pubitemid 46955210)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.7
, pp. 533-543
-
-
Keene, J.D.1
-
3
-
-
19344365947
-
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
-
Gerber, A.P., Herschlag, D. and Brown, P.O. (2004) Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol., 2, E79.
-
(2004)
PLoS Biol.
, vol.2
-
-
Gerber, A.P.1
Herschlag, D.2
Brown, P.O.3
-
4
-
-
0037313537
-
Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery
-
DOI 10.1038/ng1080
-
Hieronymus, H. and Silver, P.A. (2003) Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat. Genet., 33, 155-161. (Pubitemid 36177066)
-
(2003)
Nature Genetics
, vol.33
, Issue.2
, pp. 155-161
-
-
Hieronymus, H.1
Silver, P.A.2
-
5
-
-
0141482078
-
Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts using DNA microarray analysis
-
DOI 10.1073/pnas.2033246100
-
Shepard, K.A., Gerber, A.P., Jambhekar, A., Takizawa, P.A., Brown, P.O., Herschlag, D., DeRisi, J.L. and Vale, R.D. (2003) Widespread cytoplasmic mRNA transport in yeast: identification of 22 bud-localized transcripts using DNA microarray analysis. Proc. Natl Acad. Sci. USA, 100, 11429-11434. (Pubitemid 37205952)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.20
, pp. 11429-11434
-
-
Shepard, K.A.1
Gerber, A.P.2
Jambhekar, A.3
Takizawa, P.A.4
Brown, P.O.5
Herschlag, D.6
DeRisi, J.L.7
Vale, R.D.8
-
6
-
-
0036289532
-
Eukaryotic mRNPs may represent posttranscriptional operons
-
DOI 10.1016/S1097-2765(02)00559-2
-
Keene, J.D. and Tenenbaum, S.A. (2002) Eukaryotic mRNPs may represent posttranscriptional operons. Mol. Cell, 9, 1161-1167. (Pubitemid 34722296)
-
(2002)
Molecular Cell
, vol.9
, Issue.6
, pp. 1161-1167
-
-
Keene, J.D.1
Tenenbaum, S.A.2
-
7
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
DOI 10.1093/nar/gkg500
-
Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G. and Thompson, J.D. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31, 3497-3500. (Pubitemid 37442184)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
Higgins, D.G.6
Thompson, J.D.7
-
8
-
-
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. Mach. Learn., 21, 51-80.
-
(1995)
Mach. Learn.
, vol.21
, pp. 51-80
-
-
Bailey, T.L.1
Elkan, C.2
-
9
-
-
35348955882
-
A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types
-
DOI 10.1016/j.molcel.2007.09.027, PII S1097276507006661
-
Elemento, O., Slonim, N. and Tavazoie, S. (2007) A universal framework for regulatory element discovery across all genomes and data types. Mol. Cell, 28, 337-350. (Pubitemid 47600005)
-
(2007)
Molecular Cell
, vol.28
, Issue.2
, pp. 337-350
-
-
Elemento, O.1
Slonim, N.2
Tavazoie, S.3
-
10
-
-
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
-
11
-
-
0031787969
-
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
-
DOI 10.1038/nbt1098-939
-
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. (Pubitemid 28483622)
-
(1998)
Nature Biotechnology
, vol.16
, Issue.10
, pp. 939-945
-
-
Roth, F.P.1
Hughes, J.D.2
Estep, P.W.3
Church, G.M.4
-
12
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
DOI 10.1038/nbt1053
-
Tompa, M., Li, N., Bailey, T.L., Church, G.M., De Moor, B., Eskin, E., Favorov, A.V., Frith, M.C., Fu, Y., Kent, W.J. et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144. (Pubitemid 41724640)
-
(2005)
Nature Biotechnology
, vol.23
, Issue.1
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
De Moor, B.5
Eskin, E.6
Favorov, A.V.7
Frith, M.C.8
Fu, Y.9
Kent, W.J.10
Makeev, V.J.11
Mironov, A.A.12
Noble, W.S.13
Pavesi, G.14
Pesole, G.15
Regnier, M.16
Simonis, N.17
Sinha, S.18
Thijs, G.19
Van Helden, J.20
Vandenbogaert, M.21
Weng, Z.22
Workman, C.23
Ye, C.24
Zhu, Z.25
more..
-
13
-
-
0042490664
-
The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators
-
DOI 10.1038/nsb956
-
Aviv, T., Lin, Z., Lau, S., Rendl, L.M., Sicheri, F. and Smibert, C.A. (2003) The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. Nat. Struct. Biol., 10, 614-621. (Pubitemid 36944714)
-
(2003)
Nature Structural Biology
, vol.10
, Issue.8
, pp. 614-621
-
-
Aviv, T.1
Lin, Z.2
Lau, S.3
Rendl, L.M.4
Sicheri, F.5
Smibert, C.A.6
-
14
-
-
55549092781
-
Distinct roles for Khd1p in the localization and expression of bud-localized mRNAs in yeast
-
Hasegawa, Y., Irie, K. and Gerber, A.P. (2008) Distinct roles for Khd1p in the localization and expression of bud-localized mRNAs in yeast. RNA, 14, 2333-2347.
-
(2008)
RNA
, vol.14
, pp. 2333-2347
-
-
Hasegawa, Y.1
Irie, K.2
Gerber, A.P.3
-
15
-
-
0038487811
-
Poly(A)-binding proteins: Multifunctional scaffolds for the post-transcriptional control of gene expression
-
Mangus, D.A., Evans, M.C. and Jacobson, A. (2003) Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol., 4, 223.
-
(2003)
Genome Biol.
, vol.4
, pp. 223
-
-
Mangus, D.A.1
Evans, M.C.2
Jacobson, A.3
-
16
-
-
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. and 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
-
17
-
-
0035921929
-
RNA-binding protein Nrd1 directs poly(A)-independent 3-end formation of RNA polymerase II transcripts
-
DOI 10.1038/35095090
-
0-end formation of RNA polymerase II transcripts. Nature, 413, 327-331. (Pubitemid 32905855)
-
(2001)
Nature
, vol.413
, Issue.6853
, pp. 327-331
-
-
Steinmetz, E.J.1
Conrad, N.K.2
Brow, D.A.3
Corden, J.L.4
-
18
-
-
33744790273
-
Prediction of RNA secondary structure by free energy minimization
-
DOI 10.1016/j.sbi.2006.05.010, PII S0959440X06000819
-
Mathews, D.H. and Turner, D.H. (2006) Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol., 16, 270-278. (Pubitemid 43831654)
-
(2006)
Current Opinion in Structural Biology
, vol.16
, Issue.3
, pp. 270-278
-
-
Mathews, D.H.1
Turner, D.H.2
-
19
-
-
0025074907
-
Vitro selection of RNA molecules that bind specific ligands
-
Ellington, A.D. and Szostak, J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
-
(1990)
Nature
, vol.346
, pp. 818-822
-
-
Ellington, A.D.1
Szostak, J.W.2
-
20
-
-
0025194307
-
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
-
Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
-
(1990)
Science
, vol.249
, pp. 505-510
-
-
Tuerk, C.1
Gold, L.2
-
21
-
-
0142215475
-
Global analysis of protein expression in yeast
-
DOI 10.1038/nature02046
-
Ghaemmaghami, S., Huh, W.K., Bower, K., Howson, R.W., Belle, A., Dephoure, N., O'Shea, E.K. and Weissman, J.S. (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
-
22
-
-
0034388021
-
The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast
-
Olivas, W. and Parker, R. (2000) The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast. EMBO J., 19, 6602-6611.
-
(2000)
EMBO J.
, vol.19
, pp. 6602-6611
-
-
Olivas, W.1
Parker, R.2
-
23
-
-
32244436130
-
Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p
-
DOI 10.1038/nsmb1053, PII NSMB1053
-
Aviv, T., Lin, Z., Ben-Ari, G., Smibert, C.A. and Sicheri, F. (2006) Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat. Struct. Mol. Biol., 13, 168-176. (Pubitemid 43214721)
-
(2006)
Nature Structural and Molecular Biology
, vol.13
, Issue.2
, pp. 168-176
-
-
Aviv, T.1
Lin, Z.2
Ben-Ari, G.3
Smibert, C.A.4
Sicheri, F.5
-
24
-
-
66249108559
-
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs
-
Foat, B.C. and Stormo, G.D. (2009) Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs. Mol. Syst. Biol., 5, 268.
-
(2009)
Mol. Syst. Biol.
, vol.5
, pp. 268
-
-
Foat, B.C.1
Stormo, G.D.2
-
25
-
-
57649137957
-
Whi3, a developmental regulator of budding yeast, binds a large set of mRNAs functionally related to the endoplasmic reticulum
-
Colomina, N., Ferrezuelo, F., Wang, H., Aldea, M. and Gari, E. (2008) Whi3, a developmental regulator of budding yeast, binds a large set of mRNAs functionally related to the endoplasmic reticulum. J. Biol. Chem., 283, 28670-28679.
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 28670-28679
-
-
Colomina, N.1
Ferrezuelo, F.2
Wang, H.3
Aldea, M.4
Gari, E.5
-
26
-
-
29144464175
-
Unbiased selection of localization elements reveals cis-acting determinants of mRNA bud localization in Saccharomyces cerevisiae
-
DOI 10.1073/pnas.0509229102
-
Jambhekar, A., McDermott, K., Sorber, K., Shepard, K.A., Vale, R.D., Takizawa, P.A. and DeRisi, J.L. (2005) Unbiased selection of localization elements reveals cis-acting determinants of mRNA bud localization in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 102, 18005-18010. (Pubitemid 41798492)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.50
, pp. 18005-18010
-
-
Jambhekar, A.1
McDermott, K.2
Sorber, K.3
Shepard, K.A.4
Vale, R.D.5
Takizawa, P.A.6
DeRisi, J.L.7
-
27
-
-
18944388902
-
Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud
-
DOI 10.1128/MCB.25.11.4752-4766.2005
-
Olivier, C., Poirier, G., Gendron, P., Boisgontier, A., Major, F. and Chartrand, P. (2005) Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud. Mol. Cell Biol., 25, 4752-4766. (Pubitemid 40705777)
-
(2005)
Molecular and Cellular Biology
, vol.25
, Issue.11
, pp. 4752-4766
-
-
Olivier, C.1
Poirier, G.2
Gendron, P.3
Boisgontier, A.4
Major, F.5
Chartrand, P.6
-
28
-
-
0032921853
-
Structure and functions of nucleolin
-
Ginisty, H., Sicard, H., Roger, B. and Bouvet, P. (1999) Structure and functions of nucleolin. J. Cell Sci., 112(Pt 6), 761-772. (Pubitemid 29179310)
-
(1999)
Journal of Cell Science
, vol.112
, Issue.6
, pp. 761-772
-
-
Ginisty, H.1
Sicard, H.2
Roger, B.3
Bouvet, P.4
-
29
-
-
1242319345
-
Cotranscriptional recruitment of the serine-arginine-rich (SR)-like proteins Gbp2 and Hrb1 to nascent mRNA via the TREX complex
-
DOI 10.1073/pnas.0308663100
-
Hurt, E., Luo, M.J., Rother, S., Reed, R. and Strasser, K. (2004) Cotranscriptional recruitment of the serine-arginine-rich (SR)-like proteins Gbp2 and Hrb1 to nascent mRNA via the TREX complex. Proc. Natl Acad. Sci. USA, 101, 1858-1862. (Pubitemid 38228981)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.7
, pp. 1858-1862
-
-
Hurt, E.1
Luo, M.-J.2
Rother, S.3
Reed, R.4
Strasser, K.5
-
30
-
-
0035261381
-
Genomic strategies to identify mammalian regulatory sequences
-
DOI 10.1038/35052548
-
Pennacchio, L.A. and Rubin, E.M. (2001) Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet., 2, 100-109. (Pubitemid 33674001)
-
(2001)
Nature Reviews Genetics
, vol.2
, Issue.2
, pp. 100-109
-
-
Pennacchio, L.A.1
Rubin, E.M.2
-
31
-
-
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, B.A. and 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
-
32
-
-
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. and Lander, E.S. (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
-
33
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch, A.P., Spellman, P.T., Kao, C.M., Carmel-Harel, O., Eisen, M.B., Storz, G., Botstein, D. and Brown, P.O. (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
-
34
-
-
23144463134
-
T-profiler: Scoring the activity of predefined groups of genes using gene expression data
-
DOI 10.1093/nar/gki484
-
Boorsma, A., Foat, B.C., Vis, D., Klis, F. and Bussemaker, H.J. (2005) T-profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res., 33, W592-W595. (Pubitemid 44529991)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Boorsma, A.1
Foat, B.C.2
Vis, D.3
Klis, F.4
Bussemaker, H.J.5
-
35
-
-
24744453533
-
The promise and peril of continuous in vitro evolution
-
DOI 10.1007/s00239-004-0307-1
-
Johns, G.C. and Joyce, G.F. (2005) The promise and peril of continuous in vitro evolution. J. Mol. Evol., 61, 253-263. (Pubitemid 41298109)
-
(2005)
Journal of Molecular Evolution
, vol.61
, Issue.2
, pp. 253-263
-
-
Johns, G.C.1
Joyce, G.F.2
-
36
-
-
0032514717
-
Functional requirements for specific ligand recognition by a biotin- binding rna pseudoknot
-
DOI 10.1021/bi981371j
-
Wilson, C., Nix, J. and Szostak, J. (1998) Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot. Biochemistry, 37, 14410-14419. (Pubitemid 28489047)
-
(1998)
Biochemistry
, vol.37
, Issue.41
, pp. 14410-14419
-
-
Wilson, C.1
Nix, J.2
Szostak, J.3
-
37
-
-
43349093418
-
RNA secondary structure analysis using the Vienna RNA package
-
Chapter 12, Unit
-
Hofacker, I.L. (2004) RNA secondary structure analysis using the Vienna RNA package. Curr. Protoc. Bioinformatics, Chapter 12, Unit 12, 12.
-
(2004)
Curr. Protoc. Bioinformatics
, vol.12
, pp. 12
-
-
Hofacker, I.L.1
-
38
-
-
67649854477
-
Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs
-
Granneman, S., Kudla, G., Petfalski, E. and Tollervey, D. (2009) Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs. Proc. Natl Acad. Sci. USA, 106, 9613-9618.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 9613-9618
-
-
Granneman, S.1
Kudla, G.2
Petfalski, E.3
Tollervey, D.4
-
39
-
-
56549105330
-
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
-
DOI 10.1038/nature07488, PII NATURE07488
-
Licatalosi, D.D., Mele, A., Fak, J.J., Ule, J., Kayikci, M., Chi, S.W., Clark, T.A., Schweitzer, A.C., Blume, J.E., Wang, X. et al. (2008) HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature, 456, 464-469. (Pubitemid 352759008)
-
(2008)
Nature
, vol.456
, Issue.7221
, pp. 464-469
-
-
Licatalosi, D.D.1
Mele, A.2
Fak, J.J.3
Ule, J.4
Kayikci, M.5
Chi, S.W.6
Clark, T.A.7
Schweitzer, A.C.8
Blume, J.E.9
Wang, X.10
Darnell, J.C.11
Darnell, R.B.12
-
40
-
-
67650484984
-
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
-
Ray, D., Kazan, H., Chan, E.T., Pena Castillo, L., Chaudhry, S., Talukder, S., Blencowe, B.J., Morris, Q. and Hughes, T.R. (2009) Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat. Biotechnol., 27, 667-670.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 667-670
-
-
Ray, D.1
Kazan, H.2
Chan, E.T.3
Pena Castillo, L.4
Chaudhry, S.5
Talukder, S.6
Blencowe, B.J.7
Morris, Q.8
Hughes, T.R.9
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