TY - JOUR AU - Lovett, S. T. AU - Segall, A. M. PY - 2004 DA - 2004// TI - New views of the bacterial chromosome JO - EMBO Rep VL - 5 UR - https://doi.org/10.1038/sj.embor.7400232 DO - 10.1038/sj.embor.7400232 ID - Lovett2004 ER - TY - JOUR AU - Niki, H. AU - Yamaichi, Y. AU - Hiraga, S. PY - 2000 DA - 2000// TI - Dynamic organization of chromosomal DNA in Escherichia coli JO - Genes Dev VL - 14 ID - Niki2000 ER - TY - JOUR AU - Zimmerman, S. B. PY - 2003 DA - 2003// TI - Underlying regularity in the shapes of nucleoids of Escherichia coli: implications for nucleoid organization and partition JO - J Struct Biol VL - 142 UR - https://doi.org/10.1016/S1047-8477(02)00637-8 DO - 10.1016/S1047-8477(02)00637-8 ID - Zimmerman2003 ER - TY - JOUR AU - Cunha, S. AU - Woldringh, C. L. AU - Odijk, T. PY - 2001 DA - 2001// TI - Polymer-mediated compaction and internal dynamics of isolated Escherichia coli nucleoids JO - J Struct Biol VL - 136 UR - https://doi.org/10.1006/jsbi.2001.4420 DO - 10.1006/jsbi.2001.4420 ID - Cunha2001 ER - TY - JOUR AU - Valens, M. AU - Penaud, S. AU - Rossignol, M. AU - Cornet, F. AU - Boccard, F. PY - 2004 DA - 2004// TI - Macrodomain organization of the Escherichia coli chromosome JO - Embo J VL - 23 UR - https://doi.org/10.1038/sj.emboj.7600434 DO - 10.1038/sj.emboj.7600434 ID - Valens2004 ER - TY - JOUR AU - Audit, B. AU - Ouzounis, C. A. PY - 2003 DA - 2003// TI - From genes to genomes: universal scale-invariant properties of microbial chromosome organisation JO - J Mol Biol VL - 332 UR - https://doi.org/10.1016/S0022-2836(03)00811-8 DO - 10.1016/S0022-2836(03)00811-8 ID - Audit2003 ER - TY - JOUR AU - Nitschke, P. AU - Guerdoux-Jamet, P. AU - Chiapello, H. AU - Faroux, G. AU - Henaut, C. AU - Henaut, A. AU - Danchin, A. PY - 1998 DA - 1998// TI - Indigo: a World-Wide-Web review of genomes and gene functions JO - FEMS Microbiol Rev VL - 22 UR - https://doi.org/10.1111/j.1574-6976.1998.tb00368.x DO - 10.1111/j.1574-6976.1998.tb00368.x ID - Nitschke1998 ER - TY - JOUR AU - Danchin, A. AU - Guerdoux-Jamet, P. AU - Moszer, I. AU - Nitschke, P. PY - 2000 DA - 2000// TI - Mapping the bacterial cell architecture into the chromosome JO - Philos Trans R Soc Lond B Biol Sci VL - 355 UR - https://doi.org/10.1098/rstb.2000.0557 DO - 10.1098/rstb.2000.0557 ID - Danchin2000 ER - TY - JOUR AU - Jeong, K. S. AU - Ahn, J. AU - Khodursky, A. B. PY - 2004 DA - 2004// TI - Spatial patterns of transcriptional activity in the chromosome of Escherichia coli JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-11-r86 DO - 10.1186/gb-2004-5-11-r86 ID - Jeong2004 ER - TY - JOUR AU - Steinhauser, D. AU - Junker, B. H. AU - Luedemann, A. AU - Selbig, J. AU - Kopka, J. PY - 2004 DA - 2004// TI - Hypothesis-driven approach to predict transcriptional units from gene expression data JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth182 DO - 10.1093/bioinformatics/bth182 ID - Steinhauser2004 ER - TY - JOUR AU - Sabatti, C. AU - Rohlin, L. AU - Oh, M. K. AU - Liao, J. C. PY - 2002 DA - 2002// TI - Co-expression pattern from DNA microarray experiments as a tool for operon prediction JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/gkf388 DO - 10.1093/nar/gkf388 ID - Sabatti2002 ER - TY - CHAP AU - Pettijohn, D. E. ED - F.C., N. e. i. d. h. a. r. d. t. PY - 1999 DA - 1999// TI - The Nucleoid BT - Escherichia coli and Salmonella Cellular and Molecular Biology PB - ASM Press CY - Washington, DC ID - Pettijohn1999 ER - TY - JOUR AU - Lee, H. K. AU - Hsu, A. K. AU - Sajdak, J. AU - Qin, J. AU - Pavlidis, P. PY - 2004 DA - 2004// TI - Coexpression analysis of human genes across many microarray data sets JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1910904 DO - 10.1101/gr.1910904 ID - Lee2004 ER - TY - JOUR AU - Allocco, D. J. AU - Kohane, I. S. AU - Butte, A. J. PY - 2004 DA - 2004// TI - Quantifying the relationship between co-expression, co-regulation and gene function JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-18 DO - 10.1186/1471-2105-5-18 ID - Allocco2004 ER - TY - CHAP AU - Press, W. H. PY - 1992 DA - 1992// TI - Kendall's Tau BT - Numerical recipes in C : the art of scientific computing PB - Cambridge University Press CY - Cambridge ID - Press1992 ER - TY - CHAP AU - Kendall, M. G. AU - Ord, J. K. AU - Stuart, A. PY - 1983 DA - 1983// TI - Stationay time-series BT - The advanced theory of statistics 3 Design and analysis, and time series PB - London CY - Griffin ID - Kendall1983 ER - TY - JOUR AU - Rocha, E. P. AU - Sekowska, A. AU - Danchin, A. PY - 2000 DA - 2000// TI - Sulphur islands in the Escherichia coli genome: markers of the cell's architecture? JO - FEBS Lett VL - 476 UR - https://doi.org/10.1016/S0014-5793(00)01660-4 DO - 10.1016/S0014-5793(00)01660-4 ID - Rocha2000 ER - TY - JOUR AU - Kepes, F. PY - 2004 DA - 2004// TI - Periodic transcriptional organization of the E.coli genome JO - J Mol Biol VL - 340 UR - https://doi.org/10.1016/j.jmb.2004.05.039 DO - 10.1016/j.jmb.2004.05.039 ID - Kepes2004 ER - TY - JOUR AU - Willenbrock, H. AU - Ussery, D. W. PY - 2004 DA - 2004// TI - Chromatin architecture and gene expression in Escherichia coli JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-12-252 DO - 10.1186/gb-2004-5-12-252 ID - Willenbrock2004 ER - TY - JOUR AU - Donachie, W. AU - Begg, K. J. PY - 1989 DA - 1989// TI - Cell Length, Nucleoid Separation, and Cell Division of Rod-Shaped and Spherical Cells of Escherichia coli JO - J Bacteriology VL - 171 ID - Donachie1989 ER - TY - CHAP AU - Noller, H. F. AU - Nomua, M. ED - F.C., N. e. i. d. h. a. r. d. t. PY - 1999 DA - 1999// TI - Ribosomes BT - Escherichia coli and Salmonella Cellular and Molecular Biology PB - ASM Press CY - Washington, DC ID - Noller1999 ER - TY - JOUR AU - Murphy, L. D. AU - Zimmerman, S. B. PY - 2002 DA - 2002// TI - Hypothesis: the RNase-sensitive restraint to unfolding of spermidine nucleoids from Escherichia coli is composed of cotranslational insertion linkages JO - Biophys Chem VL - 101-102 UR - https://doi.org/10.1016/S0301-4622(02)00163-1 DO - 10.1016/S0301-4622(02)00163-1 ID - Murphy2002 ER - TY - JOUR AU - Krasilnikov, A. S. AU - Podtelezhnikov, A. AU - Vologodskii, A. AU - Mirkin, S. M. PY - 1999 DA - 1999// TI - Large-scale effects of transcriptional DNA supercoiling in vivo JO - J Mol Biol VL - 292 UR - https://doi.org/10.1006/jmbi.1999.3117 DO - 10.1006/jmbi.1999.3117 ID - Krasilnikov1999 ER - TY - JOUR AU - Helmann, J. D. AU - Wu, M. F. AU - Gaballa, A. AU - Kobel, P. A. AU - Morshedi, M. M. AU - Fawcett, P. AU - Paddon, C. PY - 2003 DA - 2003// TI - The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcription factors JO - J Bacteriol VL - 185 UR - https://doi.org/10.1128/JB.185.1.243-253.2003 DO - 10.1128/JB.185.1.243-253.2003 ID - Helmann2003 ER - TY - JOUR AU - Yoshida, K. AU - Kobayashi, K. AU - Miwa, Y. AU - Kang, C. M. AU - Matsunaga, M. AU - Yamaguchi, H. AU - Tojo, S. AU - Yamamoto, M. AU - Nishi, R. AU - Ogasawara, N. AU - Nakayama, T. AU - Fujita, Y. PY - 2001 DA - 2001// TI - Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.3.683 DO - 10.1093/nar/29.3.683 ID - Yoshida2001 ER - TY - JOUR AU - Yoshida, K. AU - Yamaguchi, H. AU - Kinehara, M. AU - Ohki, Y. H. AU - Nakaura, Y. AU - Fujita, Y. PY - 2003 DA - 2003// TI - Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box JO - Mol Microbiol VL - 49 UR - https://doi.org/10.1046/j.1365-2958.2003.03567.x DO - 10.1046/j.1365-2958.2003.03567.x ID - Yoshida2003 ER - TY - JOUR AU - Ogura, M. AU - Yamaguchi, H. AU - Yoshida, K. AU - Fujita, Y. AU - Tanaka, T. PY - 2001 DA - 2001// TI - DNA microarray analysis of Bacillus subtilis DegU, ComA and PhoP regulons: an approach to comprehensive analysis of B.subtilis two- component regulatory systems JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.18.3804 DO - 10.1093/nar/29.18.3804 ID - Ogura2001 ER - TY - JOUR AU - Ogura, M. AU - Yamaguchi, H. AU - Kobayashi, K. AU - Ogasawara, N. AU - Fujita, Y. AU - Tanaka, T. PY - 2002 DA - 2002// TI - Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK JO - J Bacteriol VL - 184 UR - https://doi.org/10.1128/JB.184.9.2344-2351.2002 DO - 10.1128/JB.184.9.2344-2351.2002 ID - Ogura2002 ER - TY - JOUR AU - Kobayashi, K. AU - Ogura, M. AU - Yamaguchi, H. AU - Yoshida, K. AU - Ogasawara, N. AU - Tanaka, T. AU - Fujita, Y. PY - 2001 DA - 2001// TI - Comprehensive DNA microarray analysis of Bacillus subtilis two- component regulatory systems JO - J Bacteriol VL - 183 UR - https://doi.org/10.1128/JB.183.24.7365-7370.2001 DO - 10.1128/JB.183.24.7365-7370.2001 ID - Kobayashi2001 ER - TY - JOUR AU - Asai, K. AU - Yamaguchi, H. AU - Kang, C. M. AU - Yoshida, K. AU - Fujita, Y. AU - Sadaie, Y. PY - 2003 DA - 2003// TI - DNA microarray analysis of Bacillus subtilis sigma factors of extracytoplasmic function family JO - FEMS Microbiol Lett VL - 220 UR - https://doi.org/10.1016/S0378-1097(03)00093-4 DO - 10.1016/S0378-1097(03)00093-4 ID - Asai2003 ER - TY - JOUR AU - Doan, T. AU - Servant, P. AU - Tojo, S. AU - Yamaguchi, H. AU - Lerondel, G. AU - Yoshida, K. AU - Fujita, Y. AU - Aymerich, S. PY - 2003 DA - 2003// TI - The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malate JO - Microbiology VL - 149 UR - https://doi.org/10.1099/mic.0.26256-0 DO - 10.1099/mic.0.26256-0 ID - Doan2003 ER - TY - JOUR AU - Molle, V. AU - Nakaura, Y. AU - Shivers, R. P. AU - Yamaguchi, H. AU - Losick, R. AU - Fujita, Y. AU - Sonenshein, A. L. PY - 2003 DA - 2003// TI - Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis JO - J Bacteriol VL - 185 UR - https://doi.org/10.1128/JB.185.6.1911-1922.2003 DO - 10.1128/JB.185.6.1911-1922.2003 ID - Molle2003 ER - TY - JOUR AU - Watanabe, S. AU - Hamano, M. AU - Kakeshita, H. AU - Bunai, K. AU - Tojo, S. AU - Yamaguchi, H. AU - Fujita, Y. AU - Wong, S. L. AU - Yamane, K. PY - 2003 DA - 2003// TI - Mannitol-1-phosphate dehydrogenase (MtlD) is required for mannitol and glucitol assimilation in Bacillus subtilis: possible cooperation of mtl and gut operons JO - J Bacteriol VL - 185 UR - https://doi.org/10.1128/JB.185.16.4816-4824.2003 DO - 10.1128/JB.185.16.4816-4824.2003 ID - Watanabe2003 ER - TY - JOUR AU - Jarmer, H. AU - Berka, R. AU - Knudsen, S. AU - Saxild, H. H. PY - 2002 DA - 2002// TI - Transcriptome analysis documents induced competence of Bacillus subtilis during nitrogen limiting conditions JO - FEMS Microbiol Lett VL - 206 UR - https://doi.org/10.1111/j.1574-6968.2002.tb11009.x DO - 10.1111/j.1574-6968.2002.tb11009.x ID - Jarmer2002 ER - TY - JOUR AU - Mori, H. AU - Horiuchi, T. AU - Isono, K. AU - Wada, C. AU - Kanaya, S. AU - Kitagawa, M. AU - Ara, T. AU - Ohshima, H. PY - 2001 DA - 2001// TI - [Post sequence genome analysis of Escherichia coli] JO - Tanpakushitsu Kakusan Koso VL - 46 ID - Mori2001 ER - TY - JOUR AU - Newton, M. A. AU - Kendziorski, C. M. AU - Richmond, C. S. AU - Blattner, F. R. AU - Tsui, K. W. PY - 2001 DA - 2001// TI - On differential variability of expression ratios: improving statistical inference about gene expression changes from microarray data JO - J Comput Biol VL - 8 UR - https://doi.org/10.1089/106652701300099074 DO - 10.1089/106652701300099074 ID - Newton2001 ER -