Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes

Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data

(2016) Aleksander Jankowski et al.   BIOINFORMATICS

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data

(2015) Juhani Kähärä et al.   BIOINFORMATICS

Deconvolving the Recognition of DNA Shape from Sequence

(2015) Namiko Abe et al.   CELL

Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism

(2015) Charles Blatti et al.   NUCLEIC ACIDS RESEARCH

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast

(2014) Zheng Kuang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mapping Yeast Transcriptional Networks

(2013) T. R. Hughes et al.   GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

(2013) Jason Piper et al.   NUCLEIC ACIDS RESEARCH

Differential principal component analysis of ChIP-seq

(2013) H. Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

Clocks, Metabolism, and the Epigenome

(2012) Dan Feng et al.   MOLECULAR CELL

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

The Fermentation Stress Response Protein Aaf1p/Yml081Wp Regulates Acetate Production in Saccharomyces cerevisiae

(2012) Christopher J. Walkey et al.   PLoS One

Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

(2012) N. Koike et al.   SCIENCE

BayesPeak—an R package for analysing ChIP-seq data

(2011) Jonathan Cairns et al.   BIOINFORMATICS

Transcription network and cyclin/CDKs: The yin and yang of cell cycle oscillators

(2011) Laura A. Simmons Kovacs et al.   CELL CYCLE

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L

(2011) Alexandre Huber et al.   EMBO JOURNAL

Acetyl-CoA Induces Cell Growth and Proliferation by Promoting the Acetylation of Histones at Growth Genes

(2011) Ling Cai et al.   MOLECULAR CELL

Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors

(2011) Chao Cheng et al.   GENOME BIOLOGY

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

(2011) Naim U Rashid et al.   GENOME BIOLOGY

Genome-wide MyoD Binding in Skeletal Muscle Cells: A Potential for Broad Cellular Reprogramming

(2010) Yi Cao et al.   DEVELOPMENTAL CELL

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Epigenetic control of neural precursor cell fate during development

(2010) Yusuke Hirabayashi et al.   NATURE REVIEWS NEUROSCIENCE

Gis1 is required for transcriptional reprogramming of carbon metabolism and the stress response during transition into stationary phase in yeast

(2009) N. Zhang et al.   MICROBIOLOGY-SGM

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS