50 |
Liu, X., Li, Y. I. & Pritchard, J. K. Trans effects on gene expression can drive omnigenic inheritance. Cell 177, 1022–1034 e1026 (2019). |
5 |
Muerdter, F. et al. Resolving systematic errors in widely used enhancer activity assays in human cells. Nat. Methods 15, 141–149 (2018). |
6 |
Wang, X. et al. High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human. Nat. Commun. 9, 5380 (2018). |
15 |
Yona, A. H., Alm, E. J. & Gore, J. Random sequences rapidly evolve into de novo promoters. Nat. Commun. 9, 1530 (2018). |
4 |
van Arensbergen, J. et al. Genome-wide mapping of autonomous promoter activity in human cells. Nat. Biotechnol. 35, 145–153 (2017). |
14 |
Cuperus, J. T. et al. Deep learning of the regulatory grammar of yeast 5’ untranslated regions from 500,000 random sequences. Genome Res. 27, 2015–2024 (2017). |
31 |
Levo, M. et al. Systematic investigation of transcription factor activity in the context of chromatin using massively parallel binding and expression assays. Mol. Cell 65, 604–617 e606 (2017). |
49 |
Boyle, E. A., Li, Y. I. & Pritchard, J. K. An expanded view of complex traits: from polygenic to omnigenic. Cell 169, 1177–1186 (2017). |
54 |
de Boer, C. High-efficiency S. cerevisiae lithium acetate transformation. protocols.io https://doi.org/10.17504/protocols.io.j4tcqwn (2017). |
59 |
Abadi, M. et al. TensorFlow: large-scale machine learning on heterogeneous systems. arXiv 1603.04467 (2016). |
20 |
Shalem, O. et al. Systematic dissection of the sequence determinants of gene 3’ end mediated expression control. PLoS Genet. 11, e1005147 (2015). |
55 |
Deng, C., Daley, T. & Smith, A. D. Applications of species accumulation curves in large-scale biological data analysis. Quant. Biol. 3, 135–144 (2015). |
9 |
Hughes, T. R. & de Boer, C. G. Mapping yeast transcriptional networks. Genetics 195, 9–36 (2013). |
10 |
Jolma, A. et al. DNA-binding specificities of human transcription factors. Cell 152, 327–339 (2013). |
19 |
Kosuri, S. et al. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc. Natl Acad. Sci. USA 110, 14024–14029 (2013). |
7 |
Sharon, E. et al. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat. Biotechnol. 30, 521–530 (2012). |
18 |
de Boer, C. G. & Hughes, T. R. YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res. 40, D169–D179 (2012). |
56 |
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012). |
61 |
Cherry, J. M. et al. Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. 40, D700–D705 (2012). |
11 |
Nutiu, R. et al. Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat. Biotechnol. 29, 659–664 (2011). |
26 |
Zhang, Z. et al. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332, 977–980 (2011). |
30 |
Ganapathi, M. et al. Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast. Nucleic Acids Res. 39, 2032–2044 (2011). |
52 |
Erb, I. & van Nimwegen, E. Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters. PloS One 6, e24279 (2011). |
3 |
Kinney, J. B., Murugan, A., Callan, C. G. Jr. & Cox, E. C. Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc. Natl Acad. Sci. USA107, 9158–9163 (2010). |
8 |
Gertz, J., Siggia, E. D. & Cohen, B. A. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457, 215–218 (2009). |
16 |
Wunderlich, Z. & Mirny, L. A. Different gene regulation strategies revealed by analysis of binding motifs. Trends Genet. 25, 434–440 (2009). |
27 |
Hesselberth, J. R. et al. Global mapping of protein–DNA interactions in vivo by digital genomic footprinting. Nat. Methods 6, 283–289 (2009). |
29 |
Hartley, P. D. & Madhani, H. D. Mechanisms that specify promoter nucleosome location and identity. Cell 137, 445–458 (2009). |
51 |
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009). |
58 |
Segal, E. & Widom, J. From DNA sequence to transcriptional behaviour: a quantitative approach. Nat. Rev. Genet. 10, 443–456 (2009). |
2 |
Yuan, Y., Guo, L., Shen, L. & Liu, J. S. Predicting gene expression from sequence: a reexamination. PLoS Comput. Biol. 3, e243 (2007). |
46 |
Hibbs, M. A. et al. Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics 23, 2692–2699 (2007). |
25 |
Liu, X., Lee, C. K., Granek, J. A., Clarke, N. D. & Lieb, J. D. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res. 16, 1517–1528 (2006). |
34 |
Roberts, G. G. & Hudson, A. P. Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling. Mol. Genet. Genomics 276, 170–186 (2006). |
48 |
Tanay, A. Extensive low-affinity transcriptional interactions in the yeast genome. Gen. Res. 16, 962–972 (2006). |
53 |
Tong, A. H. & Boone, C. Synthetic genetic array analysis in Saccharomyces cerevisiae. Methods Mol. Biol. 313, 171–192 (2006). |
57 |
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006). |
62 |
Chua, G. et al. Identifying transcription factor functions and targets by phenotypic activation. Proc. Natl Acad. Sci. USA 103, 12045–12050 (2006). |
17 |
Arnosti, D. N. & Kulkarni, M. M. Transcriptional enhancers: intelligent enhanceosomes or flexible billboards? J. Cell. Biochem. 94, 890–898 (2005). |
21 |
Granek, J. A. & Clarke, N. D. Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol. 6, R87 (2005). |
1 |
Beer, M. A. & Tavazoie, S. Predicting gene expression from sequence. Cell 117, 185–198 (2004). |
28 |
Bernstein, B. E., Liu, C. L., Humphrey, E. L., Perlstein, E. O. & Schreiber, S. L. Global nucleosome occupancy in yeast. Genome Biol. 5, R62 (2004). |
44 |
Kim, T. S., Kim, H. Y., Yoon, J. H. & Kang, H. S. Recruitment of the Swi/Snf complex by Ste12-Tec1 promotes Flo8-Mss11-mediated activation of STA1 expression. Mol. Cell. Biol. 24, 9542–9556 (2004). |
45 |
Harbison, C. T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99–104 (2004). |
60 |
Kent, N. A., Eibert, S. M. & Mellor, J. Cbf1p is required for chromatin remodeling at promoter-proximal CACGTG motifs in yeast. J. Biol. Chem. 279, 27116–27123 (2004). |
22 |
Kulkarni, M. M. & Arnosti, D. N. Information display by transcriptional enhancers. Development 130, 6569–6575 (2003). |
24 |
Conlon, E. M., Liu, X. S., Lieb, J. D. & Liu, J. S. Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl Acad. Sci. USA 100, 3339–3344 (2003). |
43 |
Neely, K. E., Hassan, A. H., Brown, C. E., Howe, L. & Workman, J. L. Transcription activator interactions with multiple SWI/SNF subunits. Mol. Cell. Biol. 22, 1615–1625 (2002). |
23 |
Bussemaker, H. J., Li, H. & Siggia, E. D. Regulatory element detection using correlation with expression. Nat. Genet. 27, 167–171 (2001). |
37 |
Haurie, V. et al. The transcriptional activator Cat8p provides a major contribution to the reprogramming of carbon metabolism during the diauxic shift in Saccharomyces cerevisiae. J. Biol. Chem. 276, 76–85 (2001). |
39 |
Grauslund, M. & Ronnow, B. Carbon source-dependent transcriptional regulation of the mitochondrial glycerol-3-phosphate dehydrogenase gene, GUT2, from Saccharomyces cerevisiae. Can. J. Microbiol. 46, 1096–1100 (2000). |
42 |
Cullen, P. J. & Sprague, G. F. Jr. Glucose depletion causes haploid invasive growth in yeast. Proc. Natl Acad. Sci. USA 97, 13619–13624 (2000). |
38 |
Sato, T. et al. TheE-box DNA binding protein Sgc1p suppresses the gcr2 mutation, which is involved in transcriptional activation of glycolytic genes in Saccharomyces cerevisiae. FEBS Lett. 463, 307–311 (1999). |
40 |
Madhani, H. D. & Fink, G. R. Combinatorial control required for the specificity of yeast MAPK signaling. Science 275, 1314–1317 (1997). |
41 |
Gavrias, V., Andrianopoulos, A., Gimeno, C. J. & Timberlake, W. E. Saccharomyces cerevisiae TEC1 is required for pseudohyphal growth. Mol. Microbiol. 19, 1255–1263 (1996). |
36 |
Hedges, D., Proft, M. & Entian, K. D. CAT8, a new zinc cluster-encoding gene necessary for derepression of gluconeogenic enzymes in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 15, 1915–1922 (1995). |
47 |
Bednar, J. et al. Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. J. Mol. Biol. 254, 579–594 (1995). |
32 |
Axelrod, J. D., Reagan, M. S. & Majors, J. GAL4 disrupts a repressing nucleosome during activation of GAL1 transcription in vivo. Genes Dev. 7, 857–869 (1993). |
33 |
Morse, R. H. Nucleosome disruption by transcription factor binding in yeast. Science 262, 1563–1566 (1993). |
12 |
Oliphant, A. R., Brandl, C. J. & Struhl, K. Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol. Cell. Biol. 9, 2944–2949 (1989). |
35 |
Forsburg, S. L. & Guarente, L. Identification and characterization of HAP4: a third component of the CCAAT-bound HAP2/HAP3 heteromer. Genes Dev. 3, 1166–1178 (1989). |
13 |
Horwitz, M. S. & Loeb, L. A. Promoters selected from random DNA sequences. Proc. Natl Acad. Sci. USA 83, 7405–7409 (1986). |