Integrative analysis of histone ChIP-seq and transcription data using Bayesian mixture models

Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data

(2013) Yanchun Bao et al.   BMC BIOINFORMATICS

A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements

(2012) Stefan Enroth et al.   Algorithms for Molecular Biology

Integrative Model-based clustering of microarray methylation and expression data

(2012) Matthias Kormaksson et al.   Annals of Applied Statistics

Bayesian correlated clustering to integrate multiple datasets

(2012) Paul Kirk et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Normalization of ChIP-seq data with control

(2012) Kun Liang et al.   BMC BIOINFORMATICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Regional Activation of the Cancer Genome by Long-Range Epigenetic Remodeling

(2012) Saul A. Bert et al.   CANCER CELL

Cancer Epigenetics: From Mechanism to Therapy

(2012) Mark A. Dawson et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

(2012) Andrew V. Biankin et al.   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia

(2012) Tino Schenk et al.   NATURE MEDICINE

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

ChIPnorm: A Statistical Method for Normalizing and Identifying Differential Regions in Histone Modification ChIP-seq Libraries

(2012) Nishanth Ulhas Nair et al.   PLoS One

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

Modeling gene expression using chromatin features in various cellular contexts

(2012) Xianjun Dong et al.   GENOME BIOLOGY

Identifying dispersed epigenomic domains from ChIP-Seq data

(2011) Qiang Song et al.   BIOINFORMATICS

Asymptotic behaviour of the posterior distribution in overfitted mixture models

(2011) Judith Rousseau et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

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

(2011) Chao Cheng et al.   GENOME BIOLOGY

Discovering transcriptional modules by Bayesian data integration

(2010) Richard S. Savage et al.   BIOINFORMATICS

Combining Mixture Components for Clustering

(2010) Jean-Patrick Baudry et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

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

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

EpiChIP: gene-by-gene quantification of epigenetic modification levels

(2010) Daniel Hebenstreit et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities

(2009) Martin Schäfer et al.   BIOINFORMATICS

Comparative study on ChIP-seq data: normalization and binding pattern characterization

(2009) Cenny Taslim et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana

(2009) Xiaoyu Zhang et al.   GENOME BIOLOGY

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data

(2008) Han Xu et al.   BIOINFORMATICS

Nonparametric Testing for DNA Copy Number Induced Differential mRNA Gene Expression

(2008) Wessel N. van Wieringen et al.   BIOMETRICS

Model-based variance-stabilizing transformation for Illumina microarray data

(2008) Simon M. Lin et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY