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

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

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

(2011) O. Hakim et al.   GENOME RESEARCH

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology

(2009) Marieke Simonis et al.   NATURE METHODS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Transcription factories are nuclear subcompartments that remain in the absence of transcription

(2008) J. A. Mitchell et al.   GENES & DEVELOPMENT

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics