The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

(2013) J. Ernst et al.   GENOME RESEARCH

Binary Interval Search: a scalable algorithm for counting interval intersections

(2012) Ryan M. Layer et al.   BIOINFORMATICS

An effective statistical evaluation of ChIPseq dataset similarity

(2012) Maria D. Chikina et al.   BIOINFORMATICS

Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis

(2012) L. C. Dore et al.   BLOOD

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

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

COPS: Detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets

(2012) Nati Ha et al.   PLoS One

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

(2012) Alexander Favorov et al.   PLoS Computational Biology

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

(2012) Yoichiro Shibata et al.   PLoS Genetics

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Random-Effects Model Aimed at Discovering Associations in Meta-Analysis of Genome-wide Association Studies

(2011) Buhm Han et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Subsampling methods for genomic inference

(2011) Peter J. Bickel et al.   Annals of Applied Statistics

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

An integrated ChIP-seq analysis platform with customizable workflows

(2011) Eugenia G Giannopoulou et al.   BMC BIOINFORMATICS

A co-ordinated interaction between CTCF and ER in breast cancer cells

(2011) Caryn S Ross-Innes et al.   BMC GENOMICS

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes

(2011) Subhajyoti De et al.   NATURE BIOTECHNOLOGY

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

DNA secondary structures and epigenetic determinants of cancer genome evolution

(2011) Subhajyoti De et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches

(2011) Ghia M. Euskirchen et al.   PLoS Genetics

The Genomic HyperBrowser: inferential genomics at the sequence level

(2011) Geir K Sandve et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence

(2010) David S Huen et al.   BMC BIOINFORMATICS

Structure, location and interactions of G-quadruplexes

(2010) Julian L. Huppert   FEBS Journal

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Scoring overlapping and adjacent signals from genome-wide ChIP and DamID assays

(2009) Audrey Qiuyan Fu et al.   Molecular BioSystems

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Determining significance of pairwise co-occurrences of events in bursty sequences

(2008) Niina Haiminen et al.   BMC BIOINFORMATICS