Spatial features for Escherichia coli genome organization

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

(2014) F. Ay et al.   GENOME RESEARCH

Use of the Operon Structure of theC. elegansGenome as a Tool to Identify Functionally Related Proteins

(2013) Silvia Dossena et al.   CELLULAR PHYSIOLOGY AND BIOCHEMISTRY

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription

(2013) Cedric Cagliero et al.   NUCLEIC ACIDS RESEARCH

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial-Nuclear DNA Interactions Contribute to the Regulation of Nuclear Transcript Levels as Part of the Inter-Organelle Communication System

(2012) Chris D. M. Rodley et al.   PLoS One

Genomic Arrangement of Regulons in Bacterial Genomes

(2012) Han Zhang et al.   PLoS One

Enhancer and promoter interactions—long distance calls

(2011) Ivan Krivega et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

(2011) O. Hakim et al.   GENOME RESEARCH

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

A computational pipeline for comparative ChIP-seq analyses

(2011) Anaïs F Bardet et al.   Nature Protocols

Conservation, Rearrangement, and Deletion of Gene Pairs During the Evolution of Four Grass Genomes

(2010) N. Krom et al.   DNA RESEARCH

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

A Model for all Genomes: The Role of Transcription Factories

(2009) Peter R. Cook   JOURNAL OF MOLECULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY