A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs

(2020) Matteo Bianchi et al.   BMC GENOMICS

Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny

(2020) Julian Catchen et al.   G3-Genes Genomes Genetics

Association between polymorphisms in the SOX9 region and canine disorder of sex development (78,XX; SRY-negative) revisited in a multibreed case-control study

(2019) Joanna Nowacka-Woszuk et al.   PLoS One

Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software

(2019) Daniel L. Cameron et al.   Nature Communications

Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology

(2019) Jocelyn Plassais et al.   Nature Communications

BarkBase: Epigenomic Annotation of Canine Genomes

(2019) Kate Megquier et al.   Genes

Genetic dissection of complex behaviour traits in German Shepherd dogs

(2019) Juliane Friedrich et al.   HEREDITY

ATXN3 promotes breast cancer metastasis by deubiquitinating KLF4

(2019) Haojing Zou et al.   CANCER LETTERS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Circulating exosomes suppress the induction of regulatory T cells via let-7i in multiple sclerosis

(2018) Kimitoshi Kimura et al.   Nature Communications

Down-regulation of the let-7i facilitates gastric cancer invasion and metastasis by targeting COL1A1

(2018) Yue Shi et al.   Protein & Cell

Nonredundant, Highly Connected MicroRNAs Control Functionality in Breast Cancer Networks

(2018) Guillermo de Anda-Jáuregui et al.   International Journal of Genomics

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

(2018) Jingtao Lilue et al.   NATURE GENETICS

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

(2018) Adam Ameur et al.   Genes

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

(2017) Daniel L. Cameron et al.   GENOME RESEARCH

Rare germline variants in known melanoma susceptibility genes in familial melanoma

(2017) Alisa M Goldstein et al.   HUMAN MOLECULAR GENETICS

A non-coding function of TYRP1 mRNA promotes melanoma growth

(2017) David Gilot et al.   NATURE CELL BIOLOGY

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

XX Disorder of Sex Development is associated with an insertion on chromosome 9 and downregulation of RSPO1 in dogs (Canis lupus familiaris)

(2017) Vicki N. Meyers-Wallen et al.   PLoS One

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

Loss of cadherin related family member 5 (CDHR5) expression in clear cell renal cell carcinoma is a prognostic marker of disease progression

(2017) Felix Marius Bläsius et al.   Oncotarget

Absolute quantification reveals the stable transmission of a high copy number variant linked to autoinflammatory disease

(2016) M. Olsson et al.   BMC GENOMICS

SLC25A22 Promotes Proliferation and Survival of Colorectal Cancer Cells With KRAS Mutations and Xenograft Tumor Progression in Mice via Intracellular Synthesis of Aspartate

(2016) Chi Chun Wong et al.   GASTROENTEROLOGY

Genotype imputation in the domestic dog

(2016) S. G. Friedenberg et al.   MAMMALIAN GENOME

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

An Improved microRNA Annotation of the Canine Genome

(2016) Luca Penso-Dolfin et al.   PLoS One

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

(2015) René L. Warren et al.   GigaScience

Evaluation of genetic association of neurodevelopment and neuroimmunological genes with antipsychotic treatment response in schizophrenia in Indian populations

(2015) Ajay Jajodia et al.   Molecular Genetics & Genomic Medicine

Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array

(2014) Anna-Maja Molin et al.   BMC GENOMICS

An Improved Canine Genome and a Comprehensive Catalogue of Coding Genes and Non-Coding Transcripts

(2014) Marc P. Hoeppner et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Genome-wide association study reveals two new risk loci for bipolar disorder

(2014) Thomas W. Mühleisen et al.   Nature Communications

Genome Sequencing Highlights the Dynamic Early History of Dogs

(2014) Adam H. Freedman et al.   PLoS Genetics

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Canine Cytochrome P-450 Pharmacogenetics

(2013) Michael H. Court   VETERINARY CLINICS OF NORTH AMERICA-SMALL ANIMAL PRACTICE

Genome-Wide Analysis in German Shepherd Dogs Reveals Association of a Locus on CFA 27 with Atopic Dermatitis

(2013) Katarina Tengvall et al.   PLoS Genetics

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Composition and organization of active centromere sequences in complex genomes

(2012) Karen E Hayden et al.   BMC GENOMICS

Identification of gene pathways implicated in Alzheimer's disease using longitudinal imaging phenotypes with sparse regression

(2012) Matt Silver et al.   NEUROIMAGE

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Novel origins of copy number variation in the dog genome

(2012) Jonas Berglund et al.   GENOME BIOLOGY

Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome

(2011) E. Axelsson et al.   GENOME RESEARCH

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A Comprehensive Linkage Map of the Dog Genome

(2009) A. K. Wong et al.   GENETICS

The genomic architecture of segmental duplications and associated copy number variants in dogs

(2009) T. J. Nicholas et al.   GENOME RESEARCH

Genome-wide association analysis reveals aSOD1mutation in canine degenerative myelopathy that resembles amyotrophic lateral sclerosis

(2009) Tomoyuki Awano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of Substrate Specificity of Dog CYP1A2 Using CYP1A2-Deficient and Wild-Type Dog Liver Microsomes

(2008) M. Mise et al.   DRUG METABOLISM AND DISPOSITION