Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome
出版年份 2017 全文链接
标题
Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome
作者
关键词
-
出版物
NUCLEIC ACIDS RESEARCH
Volume 45, Issue 13, Pages 7541-7554
出版商
Oxford University Press (OUP)
发表日期
2017-06-14
DOI
10.1093/nar/gkx541
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae
- (2017) Marie Trussart et al. Nature Communications
- Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation
- (2016) Brad A. Krajina et al. BIOPHYSICAL JOURNAL
- Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries
- (2016) Tung BK Le et al. EMBO JOURNAL
- Colocalization of distant chromosomal loci in space in E. coli : a bacterial nucleolus
- (2016) Tamas Gaal et al. GENES & DEVELOPMENT
- Chromosomal location of the DnaA-reactivating sequenceDARS2is important to regulate timely initiation of DNA replication inEscherichia coli
- (2016) Yukie Inoue et al. GENES TO CELLS
- Spatial features for Escherichia coli genome organization
- (2015) Ting Xie et al. BMC GENOMICS
- Comparison of Molecular Contours for Measuring Writhe in Atomistic Supercoiled DNA
- (2015) Thana Sutthibutpong et al. Journal of Chemical Theory and Computation
- Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology
- (2015) Michael Feig et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling
- (2015) Fabrizio Benedetti et al. NUCLEIC ACIDS RESEARCH
- RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
- (2015) Socorro Gama-Castro et al. NUCLEIC ACIDS RESEARCH
- Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid
- (2015) Mathew Stracy et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Effects of topological constraints on globular polymers
- (2015) Maxim V. Imakaev et al. Soft Matter
- Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid
- (2015) Vittore F. Scolari et al. Soft Matter
- Diffusion within the Cytoplasm: A Mesoscale Model of Interacting Macromolecules
- (2014) Fabio Trovato et al. BIOPHYSICAL JOURNAL
- The bacterial nucleoid: nature, dynamics and sister segregation
- (2014) Nancy Kleckner et al. CURRENT OPINION IN MICROBIOLOGY
- RNA polymerase: chromosome domain boundary maker and regulator of supercoil density
- (2014) N Patrick Higgins CURRENT OPINION IN MICROBIOLOGY
- Time-dependent effects of transcription- and translation-halting drugs on the spatial distributions of theEscherichia colichromosome and ribosomes
- (2014) Somenath Bakshi et al. MOLECULAR MICROBIOLOGY
- Effects of supercoiling on enhancer–promoter contacts
- (2014) Fabrizio Benedetti et al. NUCLEIC ACIDS RESEARCH
- DNA topology confers sequence specificity to nonspecific architectural proteins
- (2014) Juan Wei et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Single-particle tracking reveals that free ribosomal subunits are not excluded from the Escherichia coli nucleoid
- (2014) A. Sanamrad et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- New Mechanistic and Functional Insights into DNA Topoisomerases
- (2013) Stefanie Hartman Chen et al. Annual Review of Biochemistry
- A Model of H-NS Mediated Compaction of Bacterial DNA
- (2013) Marc Joyeux et al. BIOPHYSICAL JOURNAL
- Four-Dimensional Imaging of E. coli Nucleoid Organization and Dynamics in Living Cells
- (2013) Jay K. Fisher et al. CELL
- Polymer modeling of the E. coli genome reveals the involvement of locus positioning and macrodomain structuring for the control of chromosome conformation and segregation
- (2013) Ivan Junier et al. NUCLEIC ACIDS RESEARCH
- DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale
- (2013) Tianyin Zhou et al. NUCLEIC ACIDS RESEARCH
- Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription
- (2013) Cedric Cagliero et al. NUCLEIC ACIDS RESEARCH
- Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and repressors
- (2013) D. G. Priest et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization
- (2013) C. A. Brackley et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement
- (2013) S.-H. Hong et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome
- (2013) T. B. K. Le et al. SCIENCE
- Architectural organization in E. coli nucleoid
- (2012) Mirjana Macvanin et al. Biochimica et Biophysica Acta-Gene Regulatory Mechanisms
- A Whole-Cell Computational Model Predicts Phenotype from Genotype
- (2012) Jonathan R. Karr et al. CELL
- Characterization of the Geometry and Topology of DNA Pictured As a Discrete Collection of Atoms
- (2012) Nicolas Clauvelin et al. Journal of Chemical Theory and Computation
- Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation
- (2012) Elijah Roberts et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Membrane protein expression triggers chromosomal locus repositioning in bacteria
- (2012) E. A. Libby et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Entropy-Based Mechanism of Ribosome-Nucleoid Segregation in E. coli Cells
- (2011) Jagannath Mondal et al. BIOPHYSICAL JOURNAL
- The fractal globule as a model of chromatin architecture in the cell
- (2011) Leonid A. Mirny CHROMOSOME RESEARCH
- The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation
- (2011) Mark A. Umbarger et al. MOLECULAR CELL
- A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation
- (2011) Miriam Fritsche et al. NUCLEIC ACIDS RESEARCH
- Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle
- (2011) P. Sobetzko et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria
- (2011) W. Wang et al. SCIENCE
- DNA condensation in bacteria: Interplay between macromolecular crowding and nucleoid proteins
- (2010) Renko de Vries BIOCHIMIE
- Twist-writhe partitioning in a coarse-grained DNA minicircle model
- (2010) Mehmet Sayar et al. PHYSICAL REVIEW E
- Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm
- (2010) Stephanie C. Weber et al. PHYSICAL REVIEW LETTERS
- A Geometrical Model for DNA Organization in Bacteria
- (2010) Mathias Buenemann et al. PLoS One
- Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion
- (2010) T. Ando et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome
- (2010) Y. Yin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament
- (2010) P. A. Wiggins et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization
- (2010) Ivan Junier et al. PLoS Computational Biology
- Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm
- (2010) Sean R. McGuffee et al. PLoS Computational Biology
- Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA
- (2009) K. Fujimitsu et al. GENES & DEVELOPMENT
- Active Transcription of rRNA Operons Condenses the Nucleoid in Escherichia coli: Examining the Effect of Transcription on Nucleoid Structure in the Absence of Transertion
- (2009) J. E. Cabrera et al. JOURNAL OF BACTERIOLOGY
- Searching DNA via a “Monkey Bar” Mechanism: The Significance of Disordered Tails
- (2009) Dana Vuzman et al. JOURNAL OF MOLECULAR BIOLOGY
- Protein Occupancy Landscape of a Bacterial Genome
- (2009) Tiffany Vora et al. MOLECULAR CELL
- The role of DNA shape in protein–DNA recognition
- (2009) Remo Rohs et al. NATURE
- Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
- (2009) E. Lieberman-Aiden et al. SCIENCE
- DNA dynamics vary according to macrodomain topography in theE. colichromosome
- (2008) Olivier Espeli et al. MOLECULAR MICROBIOLOGY
- Visualizing one-dimensional diffusion of proteins along DNA
- (2008) Jason Gorman et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Towards a molecular dynamics consensus view of B-DNA flexibility
- (2008) Alberto Pérez et al. NUCLEIC ACIDS RESEARCH
- Supercoiling and Denaturation of DNA Loops
- (2008) T. B. Liverpool et al. PHYSICAL REVIEW LETTERS
- Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces
- (2008) Rex A. Kerr et al. SIAM JOURNAL ON SCIENTIFIC COMPUTING
- Structure and Dynamics of Interphase Chromosomes
- (2008) Angelo Rosa et al. PLoS Computational Biology
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now