Systems genetics in diversity outbred mice inform BMD GWAS and identify determinants of bone strength

Inhibition of fibroblast secreted QSOX1 perturbs extracellular matrix in the tumor microenvironment and decreases tumor growth and metastasis in murine cancer models

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WNT Signaling and Bone: Lessons From Skeletal Dysplasias and Disorders

(2020) Yentl Huybrechts et al.   Frontiers in Endocrinology

The GTEx Consortium atlas of genetic regulatory effects across human tissues

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Identification of a Core Module for Bone Mineral Density through the Integration of a Co-expression Network and GWAS Data

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Cleaning Genotype Data from Diversity Outbred Mice

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Wnt16 attenuates osteoarthritis progression through a PCP/JNK-mTORC1-PTHrP cascade

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Mouse genome-wide association and systems genetics identifies Lhfp as a regulator of bone mass

(2019) Larry D. Mesner et al.   PLoS Genetics

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

In vitro osteoblastic differentiation of mesenchymal stem cells generates cell layers with distinct properties

(2018) Hanna Hanna et al.   Stem Cell Research & Therapy

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multi-parent Populations

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An atlas of genetic influences on osteoporosis in humans and mice

(2018) John A. Morris et al.   NATURE GENETICS

Dissecting the Genetics of Osteoporosis using Systems Approaches

(2018) Basel M. Al-Barghouthi et al.   TRENDS IN GENETICS

Quantitative trait mapping in Diversity Outbred mice identifies two genomic regions associated with heart size

(2017) John R. Shorter et al.   MAMMALIAN GENOME

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis

(2017) John P Kemp et al.   NATURE GENETICS

Using GWAS to identify novel therapeutic targets for osteoporosis

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Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions

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Integrating GWAS and Co-expression Network Data Identifies Bone Mineral Density Genes SPTBN1 and MARK3 and an Osteoblast Functional Module

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MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Collagens VI and XII form complexes mediating osteoblast interactions during osteogenesis

(2016) Yayoi Izu et al.   CELL AND TISSUE RESEARCH

Heritability and Genetic Correlations for Bone Microarchitecture: The Framingham Study Families

(2016) David Karasik et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Periostin action in bone

(2016) Nicolas Bonnet et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

High-throughput discovery of novel developmental phenotypes

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Postmenopausal Osteoporosis

(2016) Dennis M. Black et al.   NEW ENGLAND JOURNAL OF MEDICINE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Arginase 1 is a negative regulator of osteoclast differentiation

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PAPP-A2 expression by osteoblasts is required for normal postnatal growth in mice

(2015) Neilab Amiri et al.   GROWTH HORMONE & IGF RESEARCH

Mechanism of the effect of glycosyltransferase GLT8D2 on fatty liver

(2015) Yutao Zhan et al.   Lipids in Health and Disease

Integrative network analysis reveals molecular mechanisms of blood pressure regulation

(2015) T. Huan et al.   Molecular Systems Biology

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Ebselen inhibits QSOX1 enzymatic activity and suppresses invasion of pancreatic and renal cancer cell lines

(2015) Paul D. Hanavan et al.   Oncotarget

The Mouse Universal Genotyping Array: From Substrains to Subspecies

(2015) Andrew P. Morgan et al.   G3-Genes Genomes Genetics

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(2015) Andrew P. Morgan   G3-Genes Genomes Genetics

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

Learning Bayesian Networks with thebnlearnRPackage

(2015) Marco Scutari   Journal of Statistical Software

FastRFunctions for Robust Correlations and Hierarchical Clustering

(2015) Peter Langfelder et al.   Journal of Statistical Software

Disulfide bond generation in mammalian blood serum: detection and purification of quiescin-sulfhydryl oxidase

(2014) Benjamin A. Israel et al.   FREE RADICAL BIOLOGY AND MEDICINE

Osteoblast-derived WNT16 represses osteoclastogenesis and prevents cortical bone fragility fractures

(2014) Sofia Movérare-Skrtic et al.   NATURE MEDICINE

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease

(2014) Ville-Petteri Mäkinen et al.   PLoS Genetics

Functional integration of skeletal traits: An intraskeletal assessment of bone size, mineralization, and volume covariance

(2013) Stephen H. Schlecht et al.   BONE

High-precision genetic mapping of behavioral traits in the diversity outbred mouse population

(2013) R. W. Logan et al.   GENES BRAIN AND BEHAVIOR

Systems genetics approaches to understand complex traits

(2013) Mete Civelek et al.   NATURE REVIEWS GENETICS

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

(2013) Gautier Koscielny et al.   NUCLEIC ACIDS RESEARCH

A Secreted Disulfide Catalyst Controls Extracellular Matrix Composition and Function

(2013) T. Ilani et al.   SCIENCE

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population

(2012) Karen L. Svenson et al.   GENETICS

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(2012) Gary A. Churchill et al.   MAMMALIAN GENOME

Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers

(2012) I.-M. Wang et al.   Molecular Systems Biology

FTO genotype is associated with phenotypic variability of body mass index

(2012) Jian Yang et al.   NATURE

Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture

(2012) Karol Estrada et al.   NATURE GENETICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Genetics of osteoporosis from genome-wide association studies: advances and challenges

(2012) J. Brent Richards et al.   NATURE REVIEWS GENETICS

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Guidelines for assessment of bone microstructure in rodents using micro-computed tomography

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The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics

(2010) J. A. Blake et al.   NUCLEIC ACIDS RESEARCH

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(2008) Seth Carbon et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

HCO3-/Cl- anion exchanger SLC4A2 is required for proper osteoclast differentiation and function

(2008) J. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA