Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome

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