Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

A critical assessment of topologically associating domain prediction tools

(2017) Rola Dali et al.   NUCLEIC ACIDS RESEARCH

How computer science can help in understanding the 3D genome architecture

(2015) Yoli Shavit et al.   BRIEFINGS IN BIOINFORMATICS

Restraint-based three-dimensional modeling of genomes and genomic domains

(2015) François Serra et al.   FEBS LETTERS

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

(2015) Marie Trussart et al.   NUCLEIC ACIDS RESEARCH

A statistical approach for inferring the 3D structure of the genome

(2014) N. Varoquaux et al.   BIOINFORMATICS

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

(2014) Takeshi Mizuguchi et al.   NATURE

3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

3D Chromosome Modeling with Semi-Definite Programming and Hi-C Data

(2013) ZhiZhuo Zhang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling

(2013) Cheng Peng et al.   NUCLEIC ACIDS RESEARCH

Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

(2013) S. C. R. Elgin et al.   Cold Spring Harbor Perspectives in Biology

Bayesian Inference of Spatial Organizations of Chromosomes

(2013) Ming Hu et al.   PLoS Computational Biology

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

(2012) Tom Sexton et al.   CELL

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

(2012) Davide Baù et al.   METHODS

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Recovering ensembles of chromatin conformations from contact probabilities

(2012) Dario Meluzzi et al.   NUCLEIC ACIDS RESEARCH

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling

(2011) Mathieu Rousseau et al.   BMC BIOINFORMATICS

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

(2011) Mark A. Umbarger et al.   MOLECULAR CELL

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

(2010) Davide Baù et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

The Meaning of Gene Positioning

(2008) Takumi Takizawa et al.   CELL