Identifying functional single nucleotide polymorphisms in the human CArGome

Serum Response Factor–Dependent MicroRNAs Regulate Gastrointestinal Smooth Muscle Cell Phenotypes

(2011) Chanjae Park et al.   GASTROENTEROLOGY

is-rSNP: a novel technique for in silico regulatory SNP detection

(2010) Geoff Macintyre et al.   BIOINFORMATICS

CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments

(2010) Lakshmi Kuttippurathu et al.   BIOINFORMATICS

Transcription factors Elk-1 and SRF are engaged in IL1-dependent regulation of ZC3H12A expression

(2010) Aneta Kasza et al.   BMC MOLECULAR BIOLOGY

Myocardin-related transcription factors regulate the Cdk5/Pctaire1 kinase cascade to control neurite outgrowth, neuronal migration and brain development

(2010) M. H. Mokalled et al.   DEVELOPMENT

Quantifying the effect of sequence variation on regulatory interactions

(2010) Thomas Manke et al.   HUMAN MUTATION

Role of serum response factor in the pathogenesis of disease

(2010) Joseph M Miano   LABORATORY INVESTIGATION

Myocardin-Related Transcription Factor A Is a Common Mediator of Mechanical Stress- and Neurohumoral Stimulation-Induced Cardiac Hypertrophic Signaling Leading to Activation of Brain Natriuretic Peptide Gene Expression

(2010) K. Kuwahara et al.   MOLECULAR AND CELLULAR BIOLOGY

Serum Response Factor Utilizes Distinct Promoter- and Enhancer-Based Mechanisms To Regulate Cytoskeletal Gene Expression in Macrophages

(2010) A. L. Sullivan et al.   MOLECULAR AND CELLULAR BIOLOGY

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

Comparative assessment of methods for aligning multiple genome sequences

(2010) Xiaoyu Chen et al.   NATURE BIOTECHNOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Genomewide Association Studies and Assessment of the Risk of Disease

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

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis

(2010) Valentina Boeva et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

ENCODE whole-genome data in the UCSC genome browser (2011 update)

(2010) Brian J. Raney et al.   NUCLEIC ACIDS RESEARCH

Coordinated Expression Domains in Mammalian Genomes

(2010) Yong H. Woo et al.   PLoS One

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Genome-wide prediction of transcription factor binding sites using an integrated model

(2010) Kyoung-Jae Won et al.   GENOME BIOLOGY

An Open Access Database of Genome-wide Association Results

(2009) Andrew D Johnson et al.   BMC Medical Genetics

Next generation tools for the annotation of human SNPs

(2009) Rachel Karchin   BRIEFINGS IN BIOINFORMATICS

The Smooth Muscle Cell-restrictedKCNMB1Ion Channel Subunit Is a Direct Transcriptional Target of Serum Response Factor and Myocardin

(2009) Xiaochun Long et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Human genetic variation and its contribution to complex traits

(2009) Kelly A. Frazer et al.   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Genomewide Association Studies and Human Disease

(2009) John Hardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

COTRASIF: conservation-aided transcription-factor-binding site finder

(2009) Bogdan Tokovenko et al.   NUCLEIC ACIDS RESEARCH

Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP

(2009) Adam Ameur 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

SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies

(2009) Zongli Xu et al.   NUCLEIC ACIDS RESEARCH

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SNPs in human miRNA genes affect biogenesis and function

(2009) G. Sun et al.   RNA

Eukaryotic transcription factor binding sites--modeling and integrative search methods

(2008) S. Hannenhalli   BIOINFORMATICS

Predicting functional regulatory polymorphisms

(2008) Ali Torkamani et al.   BIOINFORMATICS

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

(2008) Lucas D. Ward et al.   BIOINFORMATICS

SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms

(2008) C. Chelala et al.   BIOINFORMATICS

MotifMap: a human genome-wide map of candidate regulatory motif sites

(2008) Xiaohui Xie et al.   BIOINFORMATICS

Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: Current and developing technologies

(2008) B CHORLEY et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

Progress and challenges in genome-wide association studies in humans

(2008) Peter Donnelly   NATURE

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

(2008) Anton Valouev et al.   NATURE METHODS

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system

(2008) Alexander R. Pico et al.   NUCLEIC ACIDS RESEARCH

ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species

(2008) Bart Hooghe et al.   NUCLEIC ACIDS RESEARCH

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation

(2008) Malin C. Andersen et al.   PLoS Computational Biology

FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease

(2008) Rong Chen et al.   GENOME BIOLOGY