Analysis of variation at transcription factor binding sites in Drosophila and humans

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

(2012) Guillaume Junion et al.   CELL

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism

(2012) Matthew T. Maurano et al.   PLoS Genetics

Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy

(2011) Scott Barolo   BIOESSAYS

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules

(2011) Bin Z. He et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

CTCF shapes chromatin by multiple mechanisms: the impact of 20 years of CTCF research on understanding the workings of chromatin

(2010) Rolf Ohlsson et al.   CHROMOSOMA

Charting the genetic interaction map of a cell

(2010) Michael Costanzo et al.   CURRENT OPINION IN BIOTECHNOLOGY

Drosophila melanogaster recombination rate calculator

(2010) Anna-Sophie Fiston-Lavier et al.   GENE

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

Genetic analysis of variation in transcription factor binding in yeast

(2010) Wei Zheng et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Genomewide Association Studies and Assessment of the Risk of Disease

(2010) Teri A. Manolio   NEW ENGLAND JOURNAL OF MEDICINE

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

The strength of transcription-factor binding modulates co-variation in transcriptional networks

(2010) Sergey V. Nuzhdin et al.   TRENDS IN GENETICS

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

(2010) Matthew T. Weirauch et al.   TRENDS IN GENETICS

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

(2010) Jacek Majewski et al.   TRENDS IN GENETICS

Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers

(2010) Justin Crocker et al.   Nature Communications

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

(2010) Robert K. Bradley et al.   PLOS BIOLOGY

Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers

(2010) Richard W. Lusk et al.   PLoS Genetics

Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites

(2009) Alan M Moses   BMC EVOLUTIONARY BIOLOGY

Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions

(2009) A. M. Bushey et al.   GENES & DEVELOPMENT

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Impact of DNA-binding position variants on yeast gene expression

(2009) Krishna B. S. Swamy et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

(2009) S. H. Meijsing et al.   SCIENCE

Evolution of Regulatory Sequences in 12 Drosophila Species

(2009) Jaebum Kim et al.   PLoS Genetics

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

FlyBase: enhancing Drosophila Gene Ontology annotations

(2008) S. Tweedie et al.   NUCLEIC ACIDS RESEARCH

Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

(2008) Justin Crocker et al.   PLOS BIOLOGY

Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation

(2008) Emily E. Hare et al.   PLoS Genetics