TY - JOUR AU - Ren, B. AU - Robert, F. AU - Wyrick, J. J. AU - Aparicio, O. AU - Jennings, E. G. AU - Simon, I. AU - Zeitlinger, J. AU - Schreiber, J. AU - Hannett, N. AU - Kanin, E. PY - 2000 DA - 2000// TI - Genome-wide location and function of DNA binding proteins JO - Science VL - 290 UR - https://doi.org/10.1126/science.290.5500.2306 DO - 10.1126/science.290.5500.2306 ID - Ren2000 ER - TY - JOUR AU - Buck, M. J. AU - Lieb, J. D. PY - 2004 DA - 2004// TI - ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments JO - Genomics VL - 83 UR - https://doi.org/10.1016/j.ygeno.2003.11.004 DO - 10.1016/j.ygeno.2003.11.004 ID - Buck2004 ER - TY - JOUR AU - Grainger, D. C. AU - Overton, T. W. AU - Reppas, N. AU - Wade, J. T. AU - Tamai, E. AU - Hobman, J. L. AU - Constantinidou, C. AU - Struhl, K. AU - Church, G. AU - Busby, S. J. PY - 2004 DA - 2004// TI - Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays JO - J Bacteriol VL - 186 UR - https://doi.org/10.1128/JB.186.20.6938-6943.2004 DO - 10.1128/JB.186.20.6938-6943.2004 ID - Grainger2004 ER - TY - JOUR AU - Lee, T. I. AU - Johnstone, S. E. AU - Young, R. A. PY - 2006 DA - 2006// TI - Chromatin immunoprecipitation and microarray-based analysis of protein location JO - Nat Protoc VL - 1 UR - https://doi.org/10.1038/nprot.2006.98 DO - 10.1038/nprot.2006.98 ID - Lee2006 ER - TY - JOUR AU - Sandmann, T. AU - Jakobsen, J. S. AU - Furlong, E. E. PY - 2006 DA - 2006// TI - ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos JO - Nat Protoc VL - 1 UR - https://doi.org/10.1038/nprot.2006.383 DO - 10.1038/nprot.2006.383 ID - Sandmann2006 ER - TY - JOUR AU - Waldminghaus, T. AU - Skarstad, K. PY - 2009 DA - 2009// TI - The Escherichia coli SeqA protein JO - Plasmid VL - 61 UR - https://doi.org/10.1016/j.plasmid.2009.02.004 DO - 10.1016/j.plasmid.2009.02.004 ID - Waldminghaus2009 ER - TY - JOUR AU - Slater, S. AU - Wold, S. AU - Lu, M. AU - Boye, E. AU - Skarstad, K. AU - Kleckner, N. PY - 1995 DA - 1995// TI - E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration JO - Cell VL - 82 UR - https://doi.org/10.1016/0092-8674(95)90272-4 DO - 10.1016/0092-8674(95)90272-4 ID - Slater1995 ER - TY - JOUR AU - Campbell, J. L. AU - Kleckner, N. PY - 1990 DA - 1990// TI - E. coli oriC and the dnaA gene promoter are sequestered from dam methyltransferase following the passage of the chromosomal replication fork JO - Cell VL - 62 UR - https://doi.org/10.1016/0092-8674(90)90271-F DO - 10.1016/0092-8674(90)90271-F ID - Campbell1990 ER - TY - JOUR AU - Nagy, P. L. AU - Cleary, M. L. AU - Brown, P. O. AU - Lieb, J. D. PY - 2003 DA - 2003// TI - Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin JO - P Natl Acad Sci USA VL - 100 UR - https://doi.org/10.1073/pnas.1131966100 DO - 10.1073/pnas.1131966100 ID - Nagy2003 ER - TY - JOUR AU - Wade, J. T. AU - Roa, D. C. AU - Grainger, D. C. AU - Hurd, D. AU - Busby, S. J. AU - Struhl, K. AU - Nudler, E. PY - 2006 DA - 2006// TI - Extensive functional overlap between sigma factors in Escherichia coli JO - Nat Struct Biol VL - 13 UR - https://doi.org/10.1038/nsmb1130 DO - 10.1038/nsmb1130 ID - Wade2006 ER - TY - JOUR AU - Nonaka, G. AU - Blankschien, M. AU - Herman, C. AU - Gross, C. A. AU - Rhodius, V. A. PY - 2006 DA - 2006// TI - Regulon and promoter analysis of the E. coli heat-shock factor, σ32, reveals a multifaceted cellular response to heat stress JO - Genes Dev VL - 20 UR - https://doi.org/10.1101/gad.1428206 DO - 10.1101/gad.1428206 ID - Nonaka2006 ER - TY - JOUR AU - Johnson, D. S. AU - Li, W. AU - Gordon, D. B. AU - Bhattacharjee, A. AU - Curry, B. AU - Ghosh, J. AU - Brizuela, L. AU - Carroll, J. S. AU - Brown, M. AU - Flicek, P. PY - 2008 DA - 2008// TI - Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.7080508 DO - 10.1101/gr.7080508 ID - Johnson2008 ER - TY - JOUR AU - Vora, T. AU - Hottes, A. K. AU - Tavazoie, S. PY - 2009 DA - 2009// TI - Protein occupancy landscape of a bacterial genome JO - Mol Cell VL - 35 UR - https://doi.org/10.1016/j.molcel.2009.06.035 DO - 10.1016/j.molcel.2009.06.035 ID - Vora2009 ER - TY - JOUR AU - Bucca, G. AU - Laing, E. AU - Mersinias, V. AU - Allenby, N. AU - Hurd, D. AU - Holdstock, J. AU - Brenner, V. AU - Harrison, M. AU - Smith, C. P. PY - 2009 DA - 2009// TI - Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-1-r5 DO - 10.1186/gb-2009-10-1-r5 ID - Bucca2009 ER - TY - JOUR AU - Gruber, S. AU - Errington, J. PY - 2009 DA - 2009// TI - Recruitment of condensin to replication origin regions by ParB/SpoOJ promotes chromosome segregation in B. subtilis JO - Cell VL - 137 UR - https://doi.org/10.1016/j.cell.2009.02.035 DO - 10.1016/j.cell.2009.02.035 ID - Gruber2009 ER - TY - JOUR AU - D'Ambrosio, C. AU - Schmidt, C. K. AU - Katou, Y. AU - Kelly, G. AU - Itoh, T. AU - Shirahige, K. AU - Uhlmann, F. PY - 2008 DA - 2008// TI - Identification of cis-acting sites for condensin loading onto budding yeast chromosomes JO - Genes Dev VL - 22 UR - https://doi.org/10.1101/gad.1675708 DO - 10.1101/gad.1675708 ID - D'Ambrosio2008 ER - TY - JOUR AU - Schmidt, C. K. AU - Brookes, N. AU - Uhlmann, F. PY - 2009 DA - 2009// TI - Conserved features of cohesin binding along fission yeast chromosomes JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-5-r52 DO - 10.1186/gb-2009-10-5-r52 ID - Schmidt2009 ER - TY - JOUR AU - Peng, S. AU - Alekseyenko, A. A. AU - Larschan, E. AU - Kuroda, M. I. AU - Park, P. J. PY - 2007 DA - 2007// TI - Normalization and experimental design for ChIP-chip data JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-219 DO - 10.1186/1471-2105-8-219 ID - Peng2007 ER - TY - JOUR AU - Zhao, K. AU - Liu, M. AU - Burgess, R. R. PY - 2005 DA - 2005// TI - The global transcriptional response of Escherichia coli to induced σ32 protein involves σ32 regulon activation followed by inactivation and degradation of σ32in vivo JO - J Biol Chem VL - 280 UR - https://doi.org/10.1074/jbc.M500393200 DO - 10.1074/jbc.M500393200 ID - Zhao2005 ER - TY - JOUR AU - Grainger, D. C. AU - Hurd, D. AU - Goldberg, M. D. AU - Busby, S. J. PY - 2006 DA - 2006// TI - Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl542 DO - 10.1093/nar/gkl542 ID - Grainger2006 ER - TY - JOUR AU - Cho, B. K. AU - Knight, E. M. AU - Barrett, C. L. AU - Palsson, B. O. PY - 2008 DA - 2008// TI - Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.070276.107 DO - 10.1101/gr.070276.107 ID - Cho2008 ER - TY - JOUR AU - Carroll, J. S. AU - Meyer, C. A. AU - Song, J. AU - Li, W. AU - Geistlinger, T. R. AU - Eeckhoute, J. AU - Brodsky, A. S. AU - Keeton, E. K. AU - Fertuck, K. C. AU - Hall, G. F. PY - 2006 DA - 2006// TI - Genome-wide analysis of estrogen receptor binding sites JO - Nat Gen VL - 38 UR - https://doi.org/10.1038/ng1901 DO - 10.1038/ng1901 ID - Carroll2006 ER - TY - JOUR AU - Gevry, N. AU - Hardy, S. AU - Jacques, P. E. AU - Laflamme, L. AU - Svotelis, A. AU - Robert, F. AU - Gaudreau, L. PY - 2009 DA - 2009// TI - Histone H2A.Z is essential for estrogen receptor signaling JO - Genes Dev VL - 23 UR - https://doi.org/10.1101/gad.1787109 DO - 10.1101/gad.1787109 ID - Gevry2009 ER - TY - JOUR AU - Andrau, J. C. AU - van de Pasch, L. AU - Lijnzaad, P. AU - Bijma, T. AU - Koerkamp, M. G. AU - van de Peppel, J. AU - Werner, M. AU - Holstege, F. C. PY - 2006 DA - 2006// TI - Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA JO - Mol Cell VL - 22 UR - https://doi.org/10.1016/j.molcel.2006.03.023 DO - 10.1016/j.molcel.2006.03.023 ID - Andrau2006 ER - TY - JOUR AU - Fan, X. AU - Chou, D. M. AU - Struhl, K. PY - 2006 DA - 2006// TI - Activator-specific recruitment of Mediator in vivo JO - Nat Struct Mol Biol VL - 13 UR - https://doi.org/10.1038/nsmb1049 DO - 10.1038/nsmb1049 ID - Fan2006 ER - TY - JOUR AU - Zhu, X. AU - Wiren, M. AU - Sinha, I. AU - Rasmussen, N. N. AU - Linder, T. AU - Holmberg, S. AU - Ekwall, K. AU - Gustafsson, C. M. PY - 2006 DA - 2006// TI - Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions JO - Mol Cell VL - 22 UR - https://doi.org/10.1016/j.molcel.2006.03.032 DO - 10.1016/j.molcel.2006.03.032 ID - Zhu2006 ER - TY - JOUR AU - Fan, X. AU - Struhl, K. PY - 2009 DA - 2009// TI - Where does mediator bind in vivo? JO - PLoS ONE VL - 4 UR - https://doi.org/10.1371/journal.pone.0005029 DO - 10.1371/journal.pone.0005029 ID - Fan2009 ER - TY - JOUR AU - Gordan, R. AU - Hartemink, A. J. AU - Bulyk, M. L. PY - 2009 DA - 2009// TI - Distinguishing direct versus indirect transcription factor-DNA interactions JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.094144.109 DO - 10.1101/gr.094144.109 ID - Gordan2009 ER - TY - JOUR AU - Partridge, J. D. AU - Bodenmiller, D. M. AU - Humphrys, M. S. AU - Spiro, S. PY - 2009 DA - 2009// TI - NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility JO - Mol Microbiol VL - 73 UR - https://doi.org/10.1111/j.1365-2958.2009.06799.x DO - 10.1111/j.1365-2958.2009.06799.x ID - Partridge2009 ER - TY - JOUR AU - Efromovich, S. AU - Grainger, D. AU - Bodenmiller, D. AU - Spiro, S. PY - 2008 DA - 2008// TI - Genome-wide identification of binding sites for the nitric oxide-sensitive transcriptional regulator NsrR JO - Methods Enzymol VL - 437 UR - https://doi.org/10.1016/S0076-6879(07)37012-2 DO - 10.1016/S0076-6879(07)37012-2 ID - Efromovich2008 ER - TY - JOUR AU - Auerbach, R. K. AU - Euskirchen, G. AU - Rozowsky, J. AU - Lamarre-Vincent, N. AU - Moqtaderi, Z. AU - Lefrancois, P. AU - Struhl, K. AU - Gerstein, M. AU - Snyder, M. PY - 2009 DA - 2009// TI - Mapping accessible chromatin regions using Sono-Seq JO - Proc Natl Acad Sci USA VL - 106 UR - https://doi.org/10.1073/pnas.0905443106 DO - 10.1073/pnas.0905443106 ID - Auerbach2009 ER - TY - JOUR AU - Lefrancois, P. AU - Euskirchen, G. M. AU - Auerbach, R. K. AU - Rozowsky, J. AU - Gibson, T. AU - Yellman, C. M. AU - Gerstein, M. AU - Snyder, M. PY - 2009 DA - 2009// TI - Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing JO - BMC Genomics VL - 10 UR - https://doi.org/10.1186/1471-2164-10-37 DO - 10.1186/1471-2164-10-37 ID - Lefrancois2009 ER - TY - JOUR AU - Lu, M. AU - Campbell, J. L. AU - Boye, E. AU - Kleckner, N. PY - 1994 DA - 1994// TI - SeqA: a negative modulator of replication initiation in E. coli JO - Cell VL - 77 UR - https://doi.org/10.1016/0092-8674(94)90156-2 DO - 10.1016/0092-8674(94)90156-2 ID - Lu1994 ER - TY - JOUR AU - Brendler, T. AU - Sawitzke, J. AU - Sergueev, K. AU - Austin, S. PY - 2000 DA - 2000// TI - A case for sliding SeqA tracts at anchored replication forks during Escherichia coli chromosome replication and segregation JO - EMBO J VL - 19 UR - https://doi.org/10.1093/emboj/19.22.6249 DO - 10.1093/emboj/19.22.6249 ID - Brendler2000 ER - TY - JOUR AU - Yamazoe, M. AU - Adachi, S. AU - Kanaya, S. AU - Ohsumi, K. AU - Hiraga, S. PY - 2005 DA - 2005// TI - Sequential binding of SeqA protein to nascent DNA segments at replication forks in synchronized cultures of Escherichia coli JO - Mol Microbiol VL - 55 UR - https://doi.org/10.1111/j.1365-2958.2004.04389.x DO - 10.1111/j.1365-2958.2004.04389.x ID - Yamazoe2005 ER - TY - JOUR AU - Gentleman, R. C. AU - Carey, V. J. AU - Bates, D. M. AU - Bolstad, B. AU - Dettling, M. AU - Dudoit, S. AU - Ellis, B. AU - Gautier, L. AU - Ge, Y. AU - Gentry, J. PY - 2004 DA - 2004// TI - Bioconductor: open software development for computational biology and bioinformatics JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-10-r80 DO - 10.1186/gb-2004-5-10-r80 ID - Gentleman2004 ER - TY - JOUR AU - Smyth, G. K. AU - Speed, T. PY - 2003 DA - 2003// TI - Normalization of cDNA microarray data JO - Methods VL - 31 UR - https://doi.org/10.1016/S1046-2023(03)00155-5 DO - 10.1016/S1046-2023(03)00155-5 ID - Smyth2003 ER - TY - JOUR AU - Ghai, R. AU - Hain, T. AU - Chakraborty, T. PY - 2004 DA - 2004// TI - GenomeViz: visualizing microbial genomes JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-198 DO - 10.1186/1471-2105-5-198 ID - Ghai2004 ER -