Regulatory analysis of the C. elegans genome with spatiotemporal resolution

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Dynamic trans-Acting Factor Colocalization in Human Cells

(2013) Dan Xie et al.   CELL

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

(2013) L. Teytelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A High-Fidelity Cell Lineage Tracing Method for Obtaining Systematic Spatiotemporal Gene Expression Patterns in Caenorhabditis elegans

(2013) Daniel L Mace et al.   G3-Genes Genomes Genetics

Roles of the Developmental Regulator unc-62/Homothorax in Limiting Longevity in Caenorhabditis elegans

(2013) Eric L. Van Nostrand et al.   PLoS Genetics

An effective statistical evaluation of ChIPseq dataset similarity

(2012) Maria D. Chikina et al.   BIOINFORMATICS

CapSeq and CIP-TAP Identify Pol II Start Sites and Reveal Capped Small RNAs as C. elegans piRNA Precursors

(2012) Weifeng Gu et al.   CELL

A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans

(2012) Mihail Sarov et al.   CELL

Multidimensional regulation of gene expression in the C. elegans embryo

(2012) J. I. Murray et al.   GENOME RESEARCH

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS 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

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Endoderm development in Caenorhabditis elegans: The synergistic action of ELT-2 and -7 mediates the specification→differentiation transition

(2010) Erica M. Sommermann et al.   DEVELOPMENTAL BIOLOGY

A global analysis of C. elegans trans-splicing

(2010) M. A. Allen et al.   GENOME RESEARCH

PRDM1/Blimp-1 Controls Effector Cytokine Production in Human NK Cells

(2010) M. A. Smith et al.   JOURNAL OF IMMUNOLOGY

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Six and Eya promote apoptosis through direct transcriptional activation of the proapoptotic BH3-only gene egl-1 in Caenorhabditis elegans

(2010) T. Hirose et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response

(2010) Mei Zhong et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

(2009) Philippe Lefrançois et al.   BMC GENOMICS

Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans

(2009) Xiao Liu et al.   CELL

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

RNA Pol II Accumulates at Promoters of Growth Genes During Developmental Arrest

(2009) L. Ryan Baugh et al.   SCIENCE

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Automated analysis of embryonic gene expression with cellular resolution in C. elegans

(2008) John Isaac Murray et al.   NATURE METHODS

Regulatory logic of neuronal diversity: Terminal selector genes and selector motifs

(2008) O. Hobert   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA