TY - JOUR AU - Segal, E. AU - Shapira, M. AU - Regev, A. AU - Pe'er, D. AU - Botstein, D. AU - Koller, D. AU - Friedman, N. PY - 2003 DA - 2003// TI - Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. JO - Nat Genet VL - 34 UR - https://doi.org/10.1038/ng1165 DO - 10.1038/ng1165 ID - Segal2003 ER - TY - JOUR AU - Bussemaker, H. J. AU - Li, H. AU - Siggia, E. D. PY - 2001 DA - 2001// TI - Regulatory element detection using correlation with expression. JO - Nat Genet VL - 27 UR - https://doi.org/10.1038/84792 DO - 10.1038/84792 ID - Bussemaker2001 ER - TY - JOUR AU - Tompa, M. AU - Li, N. AU - Bailey, T. L. AU - Church, G. M. AU - De Moor, B. AU - Eskin, E. AU - Favorov, A. V. AU - Frith, M. C. AU - Fu, Y. AU - Kent, W. J. PY - 2005 DA - 2005// TI - Assessing computational tools for the discovery of transcription factor binding sites. JO - Nat Biotechnol VL - 23 UR - https://doi.org/10.1038/nbt1053 DO - 10.1038/nbt1053 ID - Tompa2005 ER - TY - JOUR AU - Brazma, A. AU - Jonassen, I. AU - Vilo, J. AU - Ukkonen, E. PY - 1998 DA - 1998// TI - Predicting gene regulatory elements in silico on a genomic scale. JO - Genome Res VL - 8 ID - Brazma1998 ER - TY - JOUR AU - Tavazoie, S. AU - Hughes, J. D. AU - Campbell, M. J. AU - Cho, R. J. AU - Church, G. M. PY - 1999 DA - 1999// TI - Systematic determination of genetic network architecture. JO - Nat Genet VL - 22 UR - https://doi.org/10.1038/10343 DO - 10.1038/10343 ID - Tavazoie1999 ER - TY - JOUR AU - Mannhaupt, G. AU - Schnall, R. AU - Karpov, V. AU - Vetter, I. AU - Feldmann, H. PY - 1999 DA - 1999// TI - Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal, other genes in yeast. JO - FEBS Lett VL - 450 UR - https://doi.org/10.1016/S0014-5793(99)00467-6 DO - 10.1016/S0014-5793(99)00467-6 ID - Mannhaupt1999 ER - TY - JOUR AU - Bulyk, M. L. AU - McGuire, A. M. AU - Masuda, N. AU - Church, G. M. PY - 2004 DA - 2004// TI - A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1448004 DO - 10.1101/gr.1448004 ID - Bulyk2004 ER - TY - JOUR AU - Zubiaga, A. M. AU - Belasco, J. G. AU - Greenberg, M. E. PY - 1995 DA - 1995// TI - The nonamer UUAUUUAUU is the key AU-rich sequence motif that mediates mRNA degradation. JO - Mol Cell Biol VL - 15 UR - https://doi.org/10.1128/MCB.15.4.2219 DO - 10.1128/MCB.15.4.2219 ID - Zubiaga1995 ER - TY - JOUR AU - Wilusz, C. J. AU - Wilusz, J. PY - 2004 DA - 2004// TI - Bringing the role of mRNA decay in the control of gene expression into focus. JO - Trends Genet VL - 20 UR - https://doi.org/10.1016/j.tig.2004.07.011 DO - 10.1016/j.tig.2004.07.011 ID - Wilusz2004 ER - TY - JOUR AU - Yang, E. AU - van Nimwegen, E. AU - Zavolan, M. AU - Rajewsky, N. AU - Schroeder, M. AU - Magnasco, M. AU - Darnell, J. E. PY - 2003 DA - 2003// TI - Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.997703 DO - 10.1101/gr.997703 ID - Yang2003 ER - TY - JOUR AU - Xie, X. AU - Lu, J. AU - Kulbokas, E. J. AU - Golub, T. R. AU - Mootha, V. AU - Lindblad-Toh, K. AU - Lander, E. S. AU - Kellis, M. PY - 2005 DA - 2005// TI - Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. JO - Nature VL - 434 UR - https://doi.org/10.1038/nature03441 DO - 10.1038/nature03441 ID - Xie2005 ER - TY - JOUR AU - Lim, L. P. AU - Lau, N. C. AU - Garrett-Engele, P. AU - Grimson, A. AU - Schelter, J. M. AU - Castle, J. AU - Bartel, D. P. AU - Linsley, P. S. AU - Johnson, J. M. PY - 2005 DA - 2005// TI - Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. JO - Nature VL - 433 UR - https://doi.org/10.1038/nature03315 DO - 10.1038/nature03315 ID - Lim2005 ER - TY - JOUR AU - Beer, M. A. AU - Tavazoie, S. PY - 2004 DA - 2004// TI - Predicting gene expression from sequence. JO - Cell VL - 117 UR - https://doi.org/10.1016/S0092-8674(04)00304-6 DO - 10.1016/S0092-8674(04)00304-6 ID - Beer2004 ER - TY - JOUR AU - Wang, Y. AU - Liu, C. L. AU - Storey, J. D. AU - Tibshirani, R. J. AU - Herschlag, D. AU - Brown, P. O. PY - 2002 DA - 2002// TI - Precision and functional specificity in mRNA decay. JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.092538799 DO - 10.1073/pnas.092538799 ID - Wang2002 ER - TY - JOUR AU - Hurowitz, E. H. AU - Brown, P. O. PY - 2003 DA - 2003// TI - Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2003-5-1-r2 DO - 10.1186/gb-2003-5-1-r2 ID - Hurowitz2003 ER - TY - STD TI - A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs: Supplementary Material & Methods. [http://longitude.weizmann.ac.il/3UTRMotifs/] UR - http://longitude.weizmann.ac.il/3UTRMotifs/ ID - ref16 ER - TY - JOUR AU - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the false discovery rate: a practical and powerful approach to multiple testing. JO - J Roy Stat Soc VL - B ID - Benjamini1995 ER - TY - JOUR AU - Pilpel, Y. AU - Sudarsanam, P. AU - Church, G. M. PY - 2001 DA - 2001// TI - Identifying regulatory networks by combinatorial analysis of promoter elements. JO - Nat Genet VL - 29 UR - https://doi.org/10.1038/ng724 DO - 10.1038/ng724 ID - Pilpel2001 ER - TY - JOUR AU - Thompson, J. D. AU - Higgins, D. G. AU - Gibson, T. J. PY - 1994 DA - 1994// TI - CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.22.4673 DO - 10.1093/nar/22.22.4673 ID - Thompson1994 ER - TY - JOUR AU - Russo, P. AU - Li, W. Z. AU - Guo, Z. AU - Sherman, F. PY - 1993 DA - 1993// TI - Signals that produce 3' termini in CYC1 mRNA of the yeast Saccharomyces cerevisiae. JO - Mol Cell Biol VL - 13 UR - https://doi.org/10.1128/MCB.13.12.7836 DO - 10.1128/MCB.13.12.7836 ID - Russo1993 ER - TY - JOUR AU - Hughes, J. D. AU - Estep, P. W. AU - Tavazoie, S. AU - Church, G. M. PY - 2000 DA - 2000// TI - Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. JO - J Mol Biol VL - 296 UR - https://doi.org/10.1006/jmbi.2000.3519 DO - 10.1006/jmbi.2000.3519 ID - Hughes2000 ER - TY - JOUR AU - Graber, J. H. PY - 2003 DA - 2003// TI - Variations in yeast 3'-processing cis-elements correlate with transcript stability. JO - Trends Genet VL - 19 UR - https://doi.org/10.1016/S0168-9525(03)00196-3 DO - 10.1016/S0168-9525(03)00196-3 ID - Graber2003 ER - TY - JOUR AU - Kellis, M. AU - Patterson, N. AU - Endrizzi, M. AU - Birren, B. AU - Lander, E. S. PY - 2003 DA - 2003// TI - Sequencing and comparison of yeast species to identify genes and regulatory elements. JO - Nature VL - 423 UR - https://doi.org/10.1038/nature01644 DO - 10.1038/nature01644 ID - Kellis2003 ER - TY - JOUR AU - Doniger, S. W. AU - Huh, J. AU - Fay, J. C. PY - 2005 DA - 2005// TI - Identification of functional transcription factor binding sites using closely related Saccharomycesspecies. JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3578205 DO - 10.1101/gr.3578205 ID - Doniger2005 ER - TY - JOUR AU - Harbison, C. T. AU - Gordon, D. B. AU - Lee, T. I. AU - Rinaldi, N. J. AU - Macisaac, K. D. AU - Danford, T. W. AU - Hannett, N. M. AU - Tagne, J. B. AU - Reynolds, D. B. AU - Yoo, J. PY - 2004 DA - 2004// TI - Transcriptional regulatory code of a eukaryotic genome. JO - Nature VL - 431 UR - https://doi.org/10.1038/nature02800 DO - 10.1038/nature02800 ID - Harbison2004 ER - TY - JOUR AU - Harris, M. A. AU - Clark, J. AU - Ireland, A. AU - Lomax, J. AU - Ashburner, M. AU - Foulger, R. AU - Eilbeck, K. AU - Lewis, S. AU - Marshall, B. AU - Mungall, C. PY - 2004 DA - 2004// TI - The Gene Ontology (GO) database and informatics resource. JO - Nucleic Acids Res VL - 32 (Database issue) ID - Harris2004 ER - TY - JOUR AU - Gerber, A. P. AU - Herschlag, D. AU - Brown, P. O. PY - 2004 DA - 2004// TI - Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. JO - PLoS Biol VL - 2 UR - https://doi.org/10.1371/journal.pbio.0020079 DO - 10.1371/journal.pbio.0020079 ID - Gerber2004 ER - TY - JOUR AU - Lieb, J. D. AU - Liu, X. AU - Botstein, D. AU - Brown, P. O. PY - 2001 DA - 2001// TI - Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. JO - Nat Genet VL - 28 UR - https://doi.org/10.1038/ng569 DO - 10.1038/ng569 ID - Lieb2001 ER - TY - JOUR AU - Kafri, R. AU - Bar-Even, A. AU - Pilpel, Y. PY - 2005 DA - 2005// TI - Transcription control reprogramming in genetic backup circuits. JO - Nat Genet VL - 37 UR - https://doi.org/10.1038/ng1523 DO - 10.1038/ng1523 ID - Kafri2005 ER - TY - JOUR AU - Aach, J. AU - Rindone, W. AU - Church, G. M. PY - 2000 DA - 2000// TI - Systematic management and analysis of yeast gene expression data. JO - Genome Res VL - 10 UR - https://doi.org/10.1101/gr.10.4.431 DO - 10.1101/gr.10.4.431 ID - Aach2000 ER - TY - JOUR AU - Lapidot, M. AU - Pilpel, Y. PY - 2003 DA - 2003// TI - Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription. JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg593 DO - 10.1093/nar/gkg593 ID - Lapidot2003 ER - TY - JOUR AU - Cherry, J. M. AU - Adler, C. AU - Ball, C. AU - Chervitz, S. A. AU - Dwight, S. S. AU - Hester, E. T. AU - Jia, Y. AU - Juvik, G. AU - Roe, T. AU - Schroeder, M. PY - 1998 DA - 1998// TI - SGD: SaccharomycesGenome Database. JO - Nucleic Acids Res VL - 26 UR - https://doi.org/10.1093/nar/26.1.73 DO - 10.1093/nar/26.1.73 ID - Cherry1998 ER - TY - JOUR AU - Sylvestre, J. AU - Vialette, S. AU - Corral Debrinski, M. AU - Jacq, C. PY - 2003 DA - 2003// TI - Long mRNAs coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria. JO - Genome Biol VL - 4 UR - https://doi.org/10.1186/gb-2003-4-7-r44 DO - 10.1186/gb-2003-4-7-r44 ID - Sylvestre2003 ER - TY - JOUR AU - Jacobs Anderson, J. S. AU - Parker, R. PY - 2000 DA - 2000// TI - Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae. JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.7.1604 DO - 10.1093/nar/28.7.1604 ID - Jacobs Anderson2000 ER - TY - JOUR AU - Takano, A. AU - Endo, T. AU - Yoshihisa, T. PY - 2005 DA - 2005// TI - tRNA actively shuttles between the nucleus and cytosol in yeast. JO - Science VL - 309 UR - https://doi.org/10.1126/science.1113346 DO - 10.1126/science.1113346 ID - Takano2005 ER - TY - JOUR AU - Chartrand, P. AU - Meng, X. H. AU - Singer, R. H. AU - Long, R. M. PY - 1999 DA - 1999// TI - Structural elements required for the localization of ASH1 mRNA and of a green fluorescent protein reporter particle in vivo. JO - Curr Biol VL - 9 UR - https://doi.org/10.1016/S0960-9822(99)80144-4 DO - 10.1016/S0960-9822(99)80144-4 ID - Chartrand1999 ER - TY - JOUR AU - Tadauchi, T. AU - Matsumoto, K. AU - Herskowitz, I. AU - Irie, K. PY - 2001 DA - 2001// TI - Post-transcriptional regulation through the HO 3'-UTR by Mpt5, a yeast homolog of Pumilio and FBF. JO - EMBO J VL - 20 UR - https://doi.org/10.1093/emboj/20.3.552 DO - 10.1093/emboj/20.3.552 ID - Tadauchi2001 ER - TY - JOUR AU - Wilusz, C. J. AU - Wormington, M. AU - Peltz, S. W. PY - 2001 DA - 2001// TI - The cap-to-tail guide to mRNA turnover. JO - Nat Rev Mol Cell Biol VL - 2 UR - https://doi.org/10.1038/35067025 DO - 10.1038/35067025 ID - Wilusz2001 ER - TY - JOUR AU - Jansen, R. P. PY - 2001 DA - 2001// TI - mRNA localization: message on the move. JO - Nat Rev Mol Cell Biol VL - 2 UR - https://doi.org/10.1038/35067016 DO - 10.1038/35067016 ID - Jansen2001 ER - TY - JOUR AU - Gonsalvez, G. B. AU - Urbinati, C. R. AU - Long, R. M. PY - 2005 DA - 2005// TI - RNA localization in yeast: moving towards a mechanism. JO - Biol Cell VL - 97 UR - https://doi.org/10.1042/BC20040066 DO - 10.1042/BC20040066 ID - Gonsalvez2005 ER - TY - JOUR AU - Hazelrigg, T. PY - 1998 DA - 1998// TI - The destinies and destinations of RNAs. JO - Cell VL - 95 UR - https://doi.org/10.1016/S0092-8674(00)81613-X DO - 10.1016/S0092-8674(00)81613-X ID - Hazelrigg1998 ER - TY - JOUR AU - Kloc, M. AU - Zearfoss, N. R. AU - Etkin, L. D. PY - 2002 DA - 2002// TI - Mechanisms of subcellular mRNA localization. JO - Cell VL - 108 UR - https://doi.org/10.1016/S0092-8674(02)00651-7 DO - 10.1016/S0092-8674(02)00651-7 ID - Kloc2002 ER - TY - JOUR AU - Kuersten, S. AU - Goodwin, E. B. PY - 2003 DA - 2003// TI - The power of the 3' UTR: translational control and development. JO - Nat Rev Genet VL - 4 UR - https://doi.org/10.1038/nrg1125 DO - 10.1038/nrg1125 ID - Kuersten2003 ER - TY - JOUR AU - Elkon, R. AU - Linhart, C. AU - Sharan, R. AU - Shamir, R. AU - Shiloh, Y. PY - 2003 DA - 2003// TI - Genome-wide in silicoidentification of transcriptional regulators controlling the cell cycle in human cells. JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.947203 DO - 10.1101/gr.947203 ID - Elkon2003 ER - TY - JOUR AU - Eskin, E. AU - Pevzner, P. A. PY - 2002 DA - 2002// TI - Finding composite regulatory patterns in DNA sequences. JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.suppl_1.S354 DO - 10.1093/bioinformatics/18.suppl_1.S354 ID - Eskin2002 ER - TY - JOUR AU - Sinha, S. AU - Tompa, M. PY - 2003 DA - 2003// TI - YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation. JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg618 DO - 10.1093/nar/gkg618 ID - Sinha2003 ER - TY - JOUR AU - Ihmels, J. AU - Friedlander, G. AU - Bergmann, S. AU - Sarig, O. AU - Ziv, Y. AU - Barkai, N. PY - 2002 DA - 2002// TI - Revealing modular organization in the yeast transcriptional network. JO - Nat Genet VL - 31 ID - Ihmels2002 ER - TY - JOUR AU - Pavesi, G. AU - Mereghetti, P. AU - Mauri, G. AU - Pesole, G. PY - 2004 DA - 2004// TI - Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. JO - Nucleic Acids Res VL - 32 (Web Server issue) UR - https://doi.org/10.1093/nar/gkh465 DO - 10.1093/nar/gkh465 ID - Pavesi2004 ER - TY - JOUR AU - Emanuelsson, O. AU - Nielsen, H. AU - Brunak, S. AU - von Heijne, G. PY - 2000 DA - 2000// TI - Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. JO - J Mol Biol VL - 300 UR - https://doi.org/10.1006/jmbi.2000.3903 DO - 10.1006/jmbi.2000.3903 ID - Emanuelsson2000 ER - TY - JOUR AU - Kellems, R. E. AU - Butow, R. A. PY - 1972 DA - 1972// TI - Cytoplasmic-type 80 S ribosomes associated with yeast mitochondria. I. Evidence for ribosome binding sites on yeast mitochondria. JO - J Biol Chem VL - 247 ID - Kellems1972 ER - TY - JOUR AU - Kellems, R. E. AU - Allison, V. F. AU - Butow, R. A. PY - 1975 DA - 1975// TI - Cytoplasmic type 80S ribosomes associated with yeast mitochondria. IV. Attachment of ribosomes to the outer membrane of isolated mitochondria. JO - J Cell Biol VL - 65 UR - https://doi.org/10.1083/jcb.65.1.1 DO - 10.1083/jcb.65.1.1 ID - Kellems1975 ER - TY - JOUR AU - Marc, P. AU - Margeot, A. AU - Devaux, F. AU - Blugeon, C. AU - Corral-Debrinski, M. AU - Jacq, C. PY - 2002 DA - 2002// TI - Genome-wide analysis of mRNAs targeted to yeast mitochondria. JO - EMBO Rep VL - 3 UR - https://doi.org/10.1093/embo-reports/kvf025 DO - 10.1093/embo-reports/kvf025 ID - Marc2002 ER - TY - JOUR AU - Verner, K. PY - 1993 DA - 1993// TI - Co-translational protein import into mitochondria: an alternative view. JO - Trends Biochem Sci VL - 18 UR - https://doi.org/10.1016/0968-0004(93)90090-A DO - 10.1016/0968-0004(93)90090-A ID - Verner1993 ER - TY - JOUR AU - Szyrach, G. AU - Ott, M. AU - Bonnefoy, N. AU - Neupert, W. AU - Herrmann, J. M. PY - 2003 DA - 2003// TI - Ribosome binding to the Oxa1 complex facilitates co-translational protein insertion in mitochondria. JO - EMBO J VL - 22 UR - https://doi.org/10.1093/emboj/cdg623 DO - 10.1093/emboj/cdg623 ID - Szyrach2003 ER - TY - JOUR AU - Fujiki, M. AU - Verner, K. PY - 1993 DA - 1993// TI - Coupling of cytosolic protein synthesis and mitochondrial protein import in yeast. Evidence for cotranslational import in vivo. JO - J Biol Chem VL - 268 ID - Fujiki1993 ER - TY - JOUR AU - Huh, W. K. AU - Falvo, J. V. AU - Gerke, L. C. AU - Carroll, A. S. AU - Howson, R. W. AU - Weissman, J. S. AU - O'Shea, E. K. PY - 2003 DA - 2003// TI - Global analysis of protein localization in budding yeast. JO - Nature VL - 425 UR - https://doi.org/10.1038/nature02026 DO - 10.1038/nature02026 ID - Huh2003 ER - TY - JOUR AU - Rosenfeld, N. AU - Elowitz, M. B. AU - Alon, U. PY - 2002 DA - 2002// TI - Negative autoregulation speeds the response times of transcription networks. JO - J Mol Biol VL - 323 UR - https://doi.org/10.1016/S0022-2836(02)00994-4 DO - 10.1016/S0022-2836(02)00994-4 ID - Rosenfeld2002 ER - TY - JOUR AU - Bartel, D. P. AU - Chen, C. Z. PY - 2004 DA - 2004// TI - Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1328 DO - 10.1038/nrg1328 ID - Bartel2004 ER - TY - JOUR AU - Graber, J. H. AU - Cantor, C. R. AU - Mohr, S. C. AU - Smith, T. F. PY - 1999 DA - 1999// TI - Genomic detection of new yeast pre-mRNA 3'-end-processing signals. JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.3.888 DO - 10.1093/nar/27.3.888 ID - Graber1999 ER - TY - JOUR AU - Lord, P. W. AU - Stevens, R. D. AU - Brass, A. AU - Goble, C. A. PY - 2003 DA - 2003// TI - Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg153 DO - 10.1093/bioinformatics/btg153 ID - Lord2003 ER - TY - JOUR AU - Causton, H. C. AU - Ren, B. AU - Koh, S. S. AU - Harbison, C. T. AU - Kanin, E. AU - Jennings, E. G. AU - Lee, T. I. AU - True, H. L. AU - Lander, E. S. AU - Young, R. A. PY - 2001 DA - 2001// TI - Remodeling of yeast genome expression in response to environmental changes. JO - Mol Biol Cell VL - 12 UR - https://doi.org/10.1091/mbc.12.2.323 DO - 10.1091/mbc.12.2.323 ID - Causton2001 ER -