Global Quantitative Modeling of Chromatin Factor Interactions

A Network Model of the Molecular Organization of Chromatin in Drosophila

(2013) Joke G. van Bemmel et al.   MOLECULAR CELL

Identification and Characterization of SMARCAL1 Protein Complexes

(2013) Rémy Bétous et al.   PLoS One

Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks

(2013) Julia Lasserre et al.   PLoS Computational Biology

Histone Monoubiquitylation Position Determines Specificity and Direction of Enzymatic Cross-talk with Histone Methyltransferases Dot1L and PRC2

(2012) Sarah J. Whitcomb et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

Dosage compensation in Drosophila melanogaster: epigenetic fine-tuning of chromosome-wide transcription

(2012) Thomas Conrad et al.   NATURE REVIEWS GENETICS

Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease

(2012) Omar Haq et al.   PLoS Computational Biology

Modeling gene expression using chromatin features in various cellular contexts

(2012) Xianjun Dong et al.   GENOME BIOLOGY

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

(2011) D. Hebenstreit et al.   Molecular Systems Biology

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

(2011) Chao Cheng et al.   GENOME BIOLOGY

High-dimensional Ising model selection using ℓ 1 -regularized logistic regression

(2010) Pradeep Ravikumar et al.   ANNALS OF STATISTICS

rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments

(2010) Arnaud Droit et al.   BIOINFORMATICS

The Language of Histone Crosstalk

(2010) Jung-Shin Lee et al.   CELL

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

(2010) Guillaume J. Filion et al.   CELL

The transcriptional diversity of 25 Drosophila cell lines

(2010) L. Cherbas et al.   GENOME RESEARCH

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt

(2009) Clemens Grimm et al.   EMBO JOURNAL

Bayesian network analysis of targeting interactions in chromatin

(2009) B. van Steensel et al.   GENOME RESEARCH

Using continuous features in the maximum entropy model

(2009) Dong Yu et al.   PATTERN RECOGNITION LETTERS

A Sequence Motif within Chromatin Entry Sites Directs MSL Establishment on the Drosophila X Chromosome

(2008) Artyom A. Alekseyenko et al.   CELL

Inferring causal relationships among different histone modifications and gene expression

(2008) H. Yu et al.   GENOME RESEARCH

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA