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Spatial patterns of transcriptional activity in the chromosome of Escherichia coli
Kyeong Soo Jeong, Jaeyong Ahn, Arkady B Khodursky
Genome Biol. 2004; 5(11): R86. Published online 2004 October 27. doi: 10.1186/gb-2004-5-11-r86
PMCID:
PMC545777
Abstract Full Text PDF–2.1M Supplementary Material
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 Is Cited by the Following 37 Articles in this Archive:
Genomic Arrangement of Regulons in Bacterial Genomes
Han Zhang, Yanbin Yin, Victor Olman, Ying Xu
PLoS One. 2012; 7(1): e29496. Published online 2012 January 3. doi: 10.1371/journal.pone.0029496
PMCID:
PMC3250446
Abstract Full Text PDF–943K Supplementary Material
Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle
Patrick Sobetzko, Andrew Travers, Georgi Muskhelishvili
Proc Natl Acad Sci U S A. 2012 January 10; 109(2): E42–E50. Published online 2011 December 19. doi: 10.1073/pnas.1108229109
Includes additional comments & authors
PMCID:
PMC3258614
Abstract Full Text PDF–1.7M Supplementary Material
CAGO: A Software Tool for Dynamic Visual Comparison and Correlation Measurement of Genome Organization
Yi-Feng Chang, Chuan-Hsiung Chang
PLoS One. 2011; 6(11): e27080. Published online 2011 November 17. doi: 10.1371/journal.pone.0027080
PMCID:
PMC3219657
Abstract Full Text PDF–1.5M Supplementary Material
A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation
Miriam Fritsche, Songling Li, Dieter W. Heermann, Paul A. Wiggins
Nucleic Acids Res. 2012 February; 40(3): 972–980. Published online 2011 October 5. doi: 10.1093/nar/gkr779
PMCID:
PMC3273793
Abstract Full Text PDF–2.3M Supplementary Material
Structural Coupling between RNA Polymerase Composition and DNA Supercoiling in Coordinating Transcription: a Global Role for the Omega Subunit?
Marcel Geertz, Andrew Travers, Sanja Mehandziska, Patrick Sobetzko, Sarath Chandra Janga, Nobuo Shimamoto, Georgi Muskhelishvili
mBio. 2011 Jul-Aug; 2(4): e00034-11. Published online 2011 August 2. doi: 10.1128/mBio.00034-11
PMCID:
PMC3147163
Abstract Full Text PDF–1.0M Supplementary Material
Analog regulation of metabolic demand
Nikolaus Sonnenschein, Marcel Geertz, Georgi Muskhelishvili, Marc-Thorsten Hütt
BMC Syst Biol. 2011; 5: 40. Published online 2011 March 15. doi: 10.1186/1752-0509-5-40
PMCID:
PMC3068955
Abstract Full Text PDF–4.3M Supplementary Material
Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data
Guanghua Xiao, Xinlei Wang, Arkady B. Khodursky
J Am Stat Assoc. Author manuscript; available in PMC 2011 July 12.
Published in final edited form as: J Am Stat Assoc. 2011 March; 106(493): 61–72. doi: 10.1198/jasa.2010.ap0950
PMCID:
PMC3134274
Abstract Full Text PDF–6.1M
Phenotypic Landscape of a Bacterial Cell
Robert J. Nichols, Saunak Sen, Yoe Jin Choo, Pedro Beltrao, Matylda Zietek, Rachna Chaba, Sueyoung Lee, Krystyna M. Kazmierczak, Karis J. Lee, Angela Wong, Michael Shales, Susan Lovett, Malcolm E. Winkler, Nevan J. Krogan, Athanasios Typas, Carol A. Gross
Cell. Author manuscript; available in PMC 2012 January 7.
Published in final edited form as: Cell. 2011 January 7; 144(1): 143–156. Published online 2010 December 23. doi: 10.1016/j.cell.2010.11.052
PMCID:
PMC3060659
Abstract Full Text PDF–1.9M Supplementary Material
Chromosomal Rearrangements Formed by rrn Recombination Do Not Improve Replichore Balance in Host-Specific Salmonella enterica Serovars
T. David Matthews, Robert Edwards, Stanley Maloy
PLoS One. 2010; 5(10): e13503. Published online 2010 October 19. doi: 10.1371/journal.pone.0013503
PMCID:
PMC2957434
Abstract Full Text PDF–487K Supplementary Material
Replication-biased genome organisation in the crenarchaeon Sulfolobus
Anders F Andersson, Erik A Pelve, Stefan Lindeberg, Magnus Lundgren, Peter Nilsson, Rolf Bernander
BMC Genomics. 2010; 11: 454. Published online 2010 July 28. doi: 10.1186/1471-2164-11-454
PMCID:
PMC3091651
Abstract Full Text PDF–513K Supplementary Material
Chromosomal periodicity and positional networks of genes in Escherichia coli
Anthony Mathelier, Alessandra Carbone
Mol Syst Biol. 2010; 6: 366. Published online 2010 May 11. doi: 10.1038/msb.2010.21
PMCID:
PMC2890325
Abstract Full Text PDF–944K Supplementary Material
Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome
Yanbin Yin, Han Zhang, Victor Olman, Ying Xu
Proc Natl Acad Sci U S A. 2010 April 6; 107(14): 6310–6315. Published online 2010 March 22. doi: 10.1073/pnas.0911237107
PMCID:
PMC2851940
Abstract Full Text PDF–255K Supplementary Material
Twisting of the DNA-binding surface by a β-strand-bearing proline modulates DNA gyrase activity
Tung-Ju Hsieh, Tien-Jui Yen, Te-Sheng Lin, Hsun-Tang Chang, Shu-Yun Huang, Chun-Hua Hsu, Lynn Farh, Nei-Li Chan
Nucleic Acids Res. 2010 July; 38(12): 4173–4181. Published online 2010 March 9. doi: 10.1093/nar/gkq153
PMCID:
PMC2896533
Abstract Full Text PDF–7.5M Supplementary Material
Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU
Michael Berger, Anca Farcas, Marcel Geertz, Petya Zhelyazkova, Klaudia Brix, Andrew Travers, Georgi Muskhelishvili
EMBO Rep. 2010 January; 11(1): 59–64. Published online 2009 November 13. doi: 10.1038/embor.2009.232
PMCID:
PMC2816637
Abstract Full Text PDF–692K Supplementary Material
Role of Translational Coupling in Robustness of Bacterial Chemotaxis Pathway
Linda Løvdok, Kajetan Bentele, Nikita Vladimirov, Anette Müller, Ferencz S. Pop, Dirk Lebiedz, Markus Kollmann, Victor Sourjik
PLoS Biol. 2009 August; 7(8): e1000171. Published online 2009 August 18. doi: 10.1371/journal.pbio.1000171
PMCID:
PMC2716512
Abstract Full Text PDF–523K Supplementary Material
Differential replication dynamics for large and small Vibrio chromosomes affect gene dosage, expression and location
Rikard Dryselius, Kaori Izutsu, Takeshi Honda, Tetsuya Iida
BMC Genomics. 2008; 9: 559. Published online 2008 November 26. doi: 10.1186/1471-2164-9-559
PMCID:
PMC2612033
Abstract Full Text PDF–1.4M Supplementary Material
Bacteria as computers making computers
Antoine Danchin
FEMS Microbiol Rev. 2009 January; 33(1): 3–26. Published online 2008 November 11. doi: 10.1111/j.1574-6976.2008.00137.x
PMCID:
PMC2704931
Abstract Full Text PDF–553K
Analyzing stochastic transcription to elucidate the nucleoid's organization
Alessandra Riva, Anne-Sophie Carpentier, Frédérique Barloy-Hubler, Angélique Chéron, Alain Hénaut
BMC Genomics. 2008; 9: 125. Published online 2008 March 10. doi: 10.1186/1471-2164-9-125
PMCID:
PMC2270832
Abstract Full Text PDF–367K Supplementary Material
Dissecting the logical types of network control in gene expression profiles
Carsten Marr, Marcel Geertz, Marc-Thorsten Hütt, Georgi Muskhelishvili
BMC Syst Biol. 2008; 2: 18. Published online 2008 February 19. doi: 10.1186/1752-0509-2-18
PMCID:
PMC2263018
Abstract Full Text PDF–780K Supplementary Material
How gene order is influenced by the biophysics of transcription regulation
Grigory Kolesov, Zeba Wunderlich, Olga N. Laikova, Mikhail S. Gelfand, Leonid A. Mirny
Proc Natl Acad Sci U S A. 2007 August 28; 104(35): 13948–13953. Published online 2007 August 20. doi: 10.1073/pnas.0700672104
PMCID:
PMC1955771
Abstract Full Text PDF–695K Supplementary Material
Chromosomal periodicity of evolutionarily conserved gene pairs
Matthew A. Wright, Peter Kharchenko, George M. Church, Daniel Segrè
Proc Natl Acad Sci U S A. 2007 June 19; 104(25): 10559–10564. Published online 2007 June 11. doi: 10.1073/pnas.0610776104
PMCID:
PMC1890563
Abstract Full Text PDF–1.8M Supplementary Material
Conservation of the links between gene transcription and chromosomal organization in the highly reduced genome of Buchnera aphidicola
José Viñuelas, Federica Calevro, Didier Remond, Jacques Bernillon, Yvan Rahbé, Gérard Febvay, Jean-Michel Fayard, Hubert Charles
BMC Genomics. 2007; 8: 143. Published online 2007 June 4. doi: 10.1186/1471-2164-8-143
PMCID:
PMC1899503
Abstract Full Text PDF–887K Supplementary Material
Identification of higher-order functional domains in the human ENCODE regions
Robert E. Thurman, Nathan Day, William S. Noble, John A. Stamatoyannopoulos
Genome Res. 2007 June; 17(6): 917–927. doi: 10.1101/gr.6081407
PMCID:
PMC1891350
Abstract Full Text PDF–477K
Growth Rate Toxicity Phenotypes and Homeostatic Supercoil Control Differentiate Escherichia coli from Salmonella enterica Serovar Typhimurium
Keith Champion, N. Patrick Higgins
J Bacteriol. 2007 August; 189(16): 5839–5849. Published online 2007 March 30. doi: 10.1128/JB.00083-07
PMCID:
PMC1952050
Abstract Full Text PDF–396K Supplementary Material
Prediction of highly expressed genes in microbes based on chromatin accessibility
Hanni Willenbrock, David W Ussery
BMC Mol Biol. 2007; 8: 11. Published online 2007 February 13. doi: 10.1186/1471-2199-8-11
PMCID:
PMC1805505
Abstract Full Text PDF–549K Supplementary Material
RecA can stimulate the relaxation activity of topoisomerase I: Molecular basis of topoisomerase-mediated genome-wide transcriptional responses in Escherichia coli
Amy R. Reckinger, Kyeong Soo Jeong, Arkady B. Khodursky, Hiroshi Hiasa
Nucleic Acids Res. 2007 January; 35(1): 79–86. Published online 2006 December 6. doi: 10.1093/nar/gkl981
PMCID:
PMC1761438
Abstract Full Text PDF–2.2M
Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments
Srinka Ghosh, Heather A Hirsch, Edward Sekinger, Kevin Struhl, Thomas R Gingeras
BMC Bioinformatics. 2006; 7: 434. Published online 2006 October 5. doi: 10.1186/1471-2105-7-434
PMCID:
PMC1615882
Abstract Full Text PDF–1.7M
Analysis of Pleiotropic Transcriptional Profiles: A Case Study of DNA Gyrase Inhibition
Kyeong Soo Jeong, Yang Xie, Hiroshi Hiasa, Arkady B Khodursky
PLoS Genet. 2006 September; 2(9): e152. Prepublished online 2006 August 2. Published online 2006 September 29. doi: 10.1371/journal.pgen.0020152
PMCID:
PMC1584274
Abstract Full Text PDF–1.0M Supplementary Material
Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome
Nicolas Blot, Ramesh Mavathur, Marcel Geertz, Andrew Travers, Georgi Muskhelishvili
EMBO Rep. 2006 July; 7(7): 710–715. Published online 2006 June 16. doi: 10.1038/sj.embor.7400729
PMCID:
PMC1500834
Abstract Full Text PDF–148K Supplementary Material
Operon information improves gene expression estimation for cDNA microarrays
Guanghua Xiao, Betsy Martinez-Vaz, Wei Pan, Arkady B Khodursky
BMC Genomics. 2006; 7: 87. Published online 2006 April 21. doi: 10.1186/1471-2164-7-87
PMCID:
PMC1513396
Abstract Full Text PDF–358K Supplementary Material
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