Identification of cis-regulatory sequence variations in individual genome sequences

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

In the loop: long range chromatin interactions and gene regulation

(2011) A. Dean   Briefings in Functional Genomics

cis-regulatory mutations are a genetic cause of human limb malformations

(2011) Julia E. VanderMeer et al.   DEVELOPMENTAL DYNAMICS

FA2H-related disorders: a novel c.270+3A>T splice-site mutation leads to a complex neurodegenerative phenotype

(2011) CATERINA GARONE et al.   DEVELOPMENTAL MEDICINE AND CHILD NEUROLOGY

A founder mutation in the Ashkenazi Jewish population affecting messenger RNA splicing of the CCM2 gene causes cerebral cavernous malformations

(2011) Carol J Gallione et al.   GENETICS IN MEDICINE

A novel mutation in the nerve-specific 5′UTR of the GJB1 gene causes X-linked Charcot-Marie-Tooth disease

(2011) Sinéad M. Murphy et al.   JOURNAL OF THE PERIPHERAL NERVOUS SYSTEM

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

(2011) Olivier Harismendy et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

A Functional Variant in MicroRNA-146a Promoter Modulates Its Expression and Confers Disease Risk for Systemic Lupus Erythematosus

(2011) Xiaobing Luo et al.   PLoS Genetics

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

(2010) Geoff Macintyre et al.   BIOINFORMATICS

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites

(2010) Stephen A. Ramsey et al.   BIOINFORMATICS

A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements

(2010) Alexander Churbanov et al.   BMC BIOINFORMATICS

TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation

(2010) Virginie Bernard et al.   BMC GENOMICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

Regulatory polymorphism in transcription factor KLF5 at the MEF2 element alters the response to angiotensin II and is associated with human hypertension

(2010) Yumiko Oishi et al.   FASEB JOURNAL

An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer

(2010) N. F. Wasserman et al.   GENOME RESEARCH

Massively parallel sequencing and rare disease

(2010) S. B. Ng et al.   HUMAN MOLECULAR GENETICS

MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets

(2010) Maxim Barenboim et al.   HUMAN MUTATION

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

A paired-end sequencing strategy to map the complex landscape of transcription initiation

(2010) Ting Ni et al.   NATURE METHODS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

(2010) K. Robasky et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2011

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

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

(2010) D. Schmidt et al.   SCIENCE

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Management of Gene Promoter Mutations in Molecular Diagnostics

(2009) K. M. K. de Vooght et al.   CLINICAL CHEMISTRY

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Long-range regulation at the SOX9 locus in development and disease

(2009) C T Gordon et al.   JOURNAL OF MEDICAL GENETICS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

(2009) Xianjun Dong et al.   NUCLEIC ACIDS RESEARCH

BioMart Central Portal—unified access to biological data

(2009) Syed Haider 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

Exome Sequencing of a Multigenerational Human Pedigree

(2009) Dale Hedges et al.   PLoS One

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

MetWAMer: eukaryotic translation initiation site prediction

(2008) Michael E Sparks et al.   BMC BIOINFORMATICS

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS

First evidence for an association of a functional variant in the microRNA-510 target site of the serotonin receptor-type 3E gene with diarrhea predominant irritable bowel syndrome

(2008) Johannes Kapeller et al.   HUMAN MOLECULAR GENETICS

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

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

De novo DNA synthesis using single molecule PCR

(2008) Tuval Ben Yehezkel et al.   NUCLEIC ACIDS RESEARCH

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites

(2008) Tom Whitington et al.   NUCLEIC ACIDS RESEARCH

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

(2008) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

RSAT: regulatory sequence analysis tools

(2008) M. Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation

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

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

(2008) Z. Wang et al.   RNA

Human-Specific Gain of Function in a Developmental Enhancer

(2008) S. Prabhakar et al.   SCIENCE