Annotation of the domestic dog genome sequence: finding the missing genes

LUPA: A European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs

(2011) Anne-Sophie Lequarré et al.   VETERINARY JOURNAL

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

LGI2 Truncation Causes a Remitting Focal Epilepsy in Dogs

(2011) Eija H. Seppälä et al.   PLoS Genetics

Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping

(2011) Amaury Vaysse et al.   PLoS Genetics

A Novel Unstable Duplication Upstream of HAS2 Predisposes to a Breed-Defining Skin Phenotype and a Periodic Fever Syndrome in Chinese Shar-Pei Dogs

(2011) Mia Olsson et al.   PLoS Genetics

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes

(2010) M. Muffato et al.   BIOINFORMATICS

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1

(2010) F. Mohammad et al.   DEVELOPMENT

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex

(2010) Maria Wilbe et al.   NATURE GENETICS

CCDC39 is required for assembly of inner dynein arms and the dynein regulatory complex and for normal ciliary motility in humans and dogs

(2010) Anne-Christine Merveille et al.   NATURE GENETICS

Ensembl 2011

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

Localization of Canine Brachycephaly Using an Across Breed Mapping Approach

(2010) Danika Bannasch et al.   PLoS One

A canine Arylsulfatase G (ARSG) mutation leading to a sulfatase deficiency is associated with neuronal ceroid lipofuscinosis

(2010) M. Abitbol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MTM1 mutation associated with X-linked myotubular myopathy in Labrador Retrievers

(2010) A. H. Beggs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking footprints of artificial selection in the dog genome

(2010) J. M. Akey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Simple Genetic Architecture Underlies Morphological Variation in Dogs

(2010) Adam R. Boyko et al.   PLOS BIOLOGY

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Human and Non-Human Primate Genomes Share Hotspots of Positive Selection

(2010) David Enard et al.   PLoS Genetics

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

(2009) Nicole Cloonan et al.   BIOINFORMATICS

Revisiting the missing protein-coding gene catalog of the domestic dog

(2009) Thomas Derrien et al.   BMC GENOMICS

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

H19 acts as a trans regulator of the imprinted gene network controlling growth in mice

(2009) A. Gabory et al.   DEVELOPMENT

Non-coding RNAs: regulators of disease

(2009) Ryan J Taft et al.   JOURNAL OF PATHOLOGY

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

An Expressed Fgf4 Retrogene Is Associated with Breed-Defining Chondrodysplasia in Domestic Dogs

(2009) H. G. Parker et al.   SCIENCE

Coat Variation in the Domestic Dog Is Governed by Variants in Three Genes

(2009) E. Cadieu et al.   SCIENCE

A global view of genomic information – moving beyond the gene and the master regulator

(2009) John S. Mattick et al.   TRENDS IN GENETICS

The Genetic Signatures of Noncoding RNAs

(2009) John S. Mattick   PLoS Genetics

RNA Gain-of-Function in Spinocerebellar Ataxia Type 8

(2009) Randy S. Daughters et al.   PLoS Genetics

The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

(2009) Hideya Kawaji et al.   GENOME BIOLOGY

Single-Nucleotide-Polymorphism-Based Association Mapping of Dog Stereotypes

(2008) Paul Jones et al.   GENETICS

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA

(2008) Wenqiang Yu et al.   NATURE

Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase

(2008) Mohammad Ali Faghihi et al.   NATURE MEDICINE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A Mutation in Hairless Dogs Implicates FOXI3 in Ectodermal Development

(2008) Cord Drögemüller et al.   SCIENCE

The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin

(2008) T. Nagano et al.   SCIENCE

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY