Informatics resources for the Collaborative Cross and related mouse populations

PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination

(2015) Christopher L. Baker et al.   PLoS Genetics

Extending reference assembly models

(2015) Deanna M Church et al.   GENOME BIOLOGY

Integrative Genetic Analysis of Allergic Inflammation in the Murine Lung

(2014) Samir N. P. Kelada et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Merging of multi-string BWTs with applications

(2014) J. Holt et al.   BIOINFORMATICS

Sequencing the Mouse Y Chromosome Reveals Convergent Gene Acquisition and Amplification on Both Sex Chromosomes

(2014) Y.Q. Shirleen Soh et al.   CELL

High-Resolution Sex-Specific Linkage Maps of the Mouse Reveal Polarized Distribution of Crossovers in Male Germline

(2014) Eric Yi Liu et al.   GENETICS

Novel Distal eQTL Analysis Demonstrates Effect of Population Genetic Architecture on Detecting and Interpreting Associations

(2014) M. Weiser et al.   GENETICS

Bayesian Modeling of Haplotype Effects in Multiparent Populations

(2014) Zhaojun Zhang et al.   GENETICS

RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

(2014) Steven C. Munger et al.   GENETICS

Fine-mapping QTLs in advanced intercross lines and other outbred populations

(2014) Natalia M. Gonzales et al.   MAMMALIAN GENOME

The Collaborative Cross as a Resource for Modeling Human Disease: CC011/Unc, a New Mouse Model for Spontaneous Colitis

(2014) Allison R. Rogala et al.   MAMMALIAN GENOME

Heritability and coefficient of genetic variation analyses of phenotypic traits provide strong basis for high-resolution QTL mapping in the Collaborative Cross mouse genetic reference population

(2014) Fuad A. Iraqi et al.   MAMMALIAN GENOME

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

A novel multi-alignment pipeline for high-throughput sequencing data

(2014) S. Huang et al.   Database-The Journal of Biological Databases and Curation

Using the emerging Collaborative Cross to probe the immune system

(2013) J Phillippi et al.   GENES AND IMMUNITY

Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research

(2013) Elissa J. Chesler   MAMMALIAN GENOME

Mouse Phenome Database

(2013) Stephen C. Grubb et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Genetic Architecture of Skewed X Inactivation in the Laboratory Mouse

(2013) John D. Calaway et al.   PLoS Genetics

Modeling Host Genetic Regulation of Influenza Pathogenesis in the Collaborative Cross

(2013) Martin T. Ferris et al.   PLoS Pathogens

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

(2012) John P Didion et al.   BMC GENOMICS

Imputation of Single-Nucleotide Polymorphisms in Inbred Mice Using Local Phylogeny

(2012) Jeremy R. Wang et al.   GENETICS

High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population

(2012) Karen L. Svenson et al.   GENETICS

A General Bayesian Approach to Analyzing Diallel Crosses of Inbred Strains

(2012) Alan B. Lenarcic et al.   GENETICS

The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population

(2012)   GENETICS

Genomic Prediction in Animals and Plants: Simulation of Data, Validation, Reporting, and Benchmarking

(2012) H. D. Daetwyler et al.   GENETICS

Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse

(2012) John P. Didion et al.   MAMMALIAN GENOME

Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits

(2012) Anatole Ghazalpour et al.   MAMMALIAN GENOME

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Lightweight algorithms for constructing and inverting the BWT of string collections

(2012) Markus J. Bauer et al.   THEORETICAL COMPUTER SCIENCE

Genetic Analysis of Hematological Parameters in Incipient Lines of the Collaborative Cross

(2012) Samir N. P. Kelada et al.   G3-Genes Genomes Genetics

Genetic analysis of complex traits in the emerging Collaborative Cross

(2011) David L. Aylor et al.   GENOME RESEARCH

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Subspecific origin and haplotype diversity in the laboratory mouse

(2011) Hyuna Yang et al.   NATURE GENETICS

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

Efficient genome ancestry inference in complex pedigrees with inbreeding

(2010) E. Y. Liu et al.   BIOINFORMATICS

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

A high-resolution association mapping panel for the dissection of complex traits in mice

(2010) B. J. Bennett et al.   GENOME RESEARCH

Mapping in Structured Populations by Resample Model Averaging

(2009) William Valdar et al.   GENETICS

A customized and versatile high-density genotyping array for the mouse

(2009) Hyuna Yang et al.   NATURE METHODS

A Complex Genetic Basis to X-Linked Hybrid Male Sterility Between Two Species of House Mice

(2008) J. M. Good et al.   GENETICS

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes

(2008) ARMANDO GERALDES et al.   MOLECULAR ECOLOGY

Mouse segmental duplication and copy number variation

(2008) Xinwei She et al.   NATURE GENETICS

Short read fragment assembly of bacterial genomes

(2007) M. J. Chaisson et al.   GENOME RESEARCH