An Empirical Bayes approach for the identification of long-range chromosomal interaction from Hi-C data

Landscape of enhancer-enhancer cooperative regulation during human cardiac commitment

(2019) Hong Chen et al.   Molecular Therapy-Nucleic Acids

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

(2018) Wenxiu Ma et al.   METHODS

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Comparison of computational methods for Hi-C data analysis

(2017) Mattia Forcato et al.   NATURE METHODS

An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data

(2017) Mark Carty et al.   Nature Communications

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data

(2017) Borbala Mifsud et al.   PLoS One

A random effect model for reconstruction of spatial chromatin structure

(2016) Jincheol Park et al.   BIOMETRICS

Empirical Bayes deconvolution estimates

(2016) Bradley Efron   BIOMETRIKA

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data

(2015) Zheng Xu et al.   BIOINFORMATICS

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

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

(2014) Suhas S.P. Rao et al.   CELL

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

(2014) F. Ay et al.   GENOME RESEARCH

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Higher-order chromatin domains link eQTLs with the expression of far-away genes

(2013) Geet Duggal et al.   NUCLEIC ACIDS RESEARCH

The Database of Genomic Variants: a curated collection of structural variation in the human genome

(2013) Jeffrey R. MacDonald et al.   NUCLEIC ACIDS RESEARCH

HiCNorm: removing biases in Hi-C data via Poisson regression

(2012) Ming Hu et al.   BIOINFORMATICS

Haploinsufficiency ofSOX5at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features

(2012) Allen N. Lamb et al.   HUMAN MUTATION

A fast algorithm for matrix balancing

(2012) P. A. Knight et al.   IMA JOURNAL OF NUMERICAL ANALYSIS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

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

(2012) Maxim Imakaev et al.   NATURE METHODS

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Empirical null and false discovery rate inference for exponential families

(2009) Armin Schwartzman   Annals of Applied Statistics

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

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