Genetic and Gene Expression Resources for Osteoporosis and Bone Biology Research

Application of Single-Cell and Spatial Omics in Musculoskeletal Disorder Research

(2023) Site Feng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Single-cell RNA sequencing identifies Fgf23-expressing osteocytes in response to 1,25-dihydroxyvitamin D3 treatment

(2023) Ayako Hanai et al.   Frontiers in Physiology

Single cell cortical bone transcriptomics define novel osteolineage gene sets altered in chronic kidney disease

(2023) Rafiou Agoro et al.   Frontiers in Endocrinology

Advances in spatial transcriptomics and related data analysis strategies

(2023) Jun Du et al.   Journal of Translational Medicine

An effector index to predict target genes at GWAS loci

(2022) Vincenzo Forgetta et al.   HUMAN GENETICS

Prioritization of genes relevant to bone fragility through the unbiased integration of aging mouse bone transcriptomics and human GWAS analyses

(2022) Serra Kaya et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Zebrafish Information Network, the knowledgebase for Danio rerio research

(2022) Yvonne M Bradford et al.   GENETICS

Functional Validation of Osteoporosis Genetic Findings Using Small Fish Models

(2022) Erika Kague et al.   Genes

An epigenome-wide view of osteoarthritis in primary tissues

(2022) Peter Kreitmaier et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Identifying Causes of Fracture Beyond Bone Mineral Density: Evidence From Human Genetics

(2022) Tianyuan Lu et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Single-Cell RNA Sequencing: Unravelling the Bone One Cell at a Time

(2022) Ryan C. Chai   Current Osteoporosis Reports

Molecular Identification of Spatially Distinct Anabolic Responses to Mechanical Loading in Murine Cortical Bone

(2022) Carolyn Chlebek et al.   JOURNAL OF BONE AND MINERAL RESEARCH

The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource

(2022) Elliot Sollis et al.   NUCLEIC ACIDS RESEARCH

Bone-cartilage crosstalk informed by aging mouse bone transcriptomics and human osteoarthritis genome-wide association studies

(2022) Serra Kaya et al.   Bone Reports

Skeletal biology and disease modeling in zebrafish

(2021) K Dietrich et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Investigating the genetic architecture of noncognitive skills using GWAS-by-subtraction

(2021) Perline A. Demange et al.   NATURE GENETICS

Osteoclasts recycle via osteomorphs during RANKL-stimulated bone resorption

(2021) Michelle M. McDonald et al.   CELL

A molecular quantitative trait locus map for osteoarthritis

(2021) Julia Steinberg et al.   Nature Communications

Calvaria Bone Transcriptome in Mouse Models of Osteogenesis Imperfecta

(2021) Pierre Moffatt et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Osteocyte transcriptome mapping identifies a molecular landscape controlling skeletal homeostasis and susceptibility to skeletal disease

(2021) Scott E. Youlten et al.   Nature Communications

Identifying therapeutic drug targets using bidirectional effect genes

(2021) Karol Estrada et al.   Nature Communications

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

(2021) Basel M. Al-Barghouthi et al.   Nature Communications

The developing mouse coronal suture at single-cell resolution

(2021) D’Juan T. Farmer et al.   Nature Communications

Bone Microarchitecture Phenotypes Identified in Older Adults Are Associated With Different Levels of Osteoporotic Fracture Risk

(2021) Danielle E Whittier et al.   JOURNAL OF BONE AND MINERAL RESEARCH

The Musculoskeletal Knowledge Portal: improving access to multi-omics data

(2021) Jennifer J. Westendorf et al.   Nature Reviews Rheumatology

RNAseq and RNA molecular barcoding reveal differential gene expression in cortical bone following hindlimb unloading in female mice

(2021) Jordan M. Spatz et al.   PLoS One

From bulk, single-cell to spatial RNA sequencing

(2021) Xinmin Li et al.   International Journal of Oral Science

Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin

(2021) Jialiang S. Wang et al.   Nature Communications

The Osteocyte Transcriptome: Discovering Messages Buried Within Bone

(2021) Natalie KY Wee et al.   Current Osteoporosis Reports

CYP11B1 variants influence skeletal maturation via alternative splicing

(2021) Olja Grgic et al.   Communications Biology

Identification of osteoclast-osteoblast coupling factors in humans reveals links between bone and energy metabolism

(2020) Megan M. Weivoda et al.   Nature Communications

SINGLE CELL RNA SEQUENCING OF CALVARIAL AND LONG BONE ENDOCORTICAL CELLS

(2020) Ugur M. Ayturk et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Old Mice Have Less Transcriptional Activation But Similar Periosteal Cell Proliferation Compared to Young‐Adult Mice in Response to in vivo Mechanical Loading

(2020) Christopher J Chermside‐Scabbo et al.   JOURNAL OF BONE AND MINERAL RESEARCH

The Musculoskeletal Knowledge Portal: Making Omics Data Useful to the Broader Scientific Community

(2020) Douglas P. Kiel et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics

(2020) Maya Ghoussaini et al.   NUCLEIC ACIDS RESEARCH

The mouse Gene Expression Database (GXD): 2021 update

(2020) Richard M Baldarelli et al.   NUCLEIC ACIDS RESEARCH

FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2021 update

(2020) Yanhui Hu et al.   NUCLEIC ACIDS RESEARCH

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Cross-Species RNA-Seq Study Comparing Transcriptomes of Enriched Osteocyte Populations in the Tibia and Skull

(2020) Ning Wang et al.   Frontiers in Endocrinology

Genetic basis of falling risk susceptibility in the UK Biobank Study

(2020) Katerina Trajanoska et al.   Communications Biology

Genetic regulatory mechanisms in human osteoclasts suggest a role for the STMP1 and DCSTAMP genes in Paget’s disease of bone

(2019) Benjamin H. Mullin et al.   Scientific Reports

Opportunities and challenges for transcriptome-wide association studies

(2019) Michael Wainberg et al.   NATURE GENETICS

Meta‐Analysis of Genomewide Association Studies Reveals Genetic Variants for Hip Bone Geometry

(2019) Yi‐Hsiang Hsu et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Using zebrafish to study skeletal genomics

(2019) Ronald Y. Kwon et al.   BONE

The Unmixing Problem: A Guide to Applying Single-Cell RNA Sequencing to Bone

(2019) Matthew B Greenblatt et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Priority index for human genetics and drug discovery

(2019) Robert M. Plenge   NATURE GENETICS

A genetics-led approach defines the drug target landscape of 30 immune-related traits

(2019) Hai Fang et al.   NATURE GENETICS

Increased autophagy in EphrinB2-deficient osteocytes is associated with elevated secondary mineralization and brittle bone

(2019) Christina Vrahnas et al.   Nature Communications

GWAS of bone size yields twelve loci that also affect height, BMD, osteoarthritis or fractures

(2019) Unnur Styrkarsdottir et al.   Nature Communications

The Post-GWAS Era: From Association to Function

(2018) Michael D. Gallagher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Life-Course Genome-wide Association Study Meta-analysis of Total Body BMD and Assessment of Age-Specific Effects

(2018) Carolina Medina-Gomez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Expression Quantitative Trait Locus Study of Bone Mineral Density GWAS Variants in Human Osteoclasts

(2018) Benjamin H Mullin et al.   JOURNAL OF BONE AND MINERAL RESEARCH

The MR-Base platform supports systematic causal inference across the human phenome

(2018) Gibran Hemani et al.   eLife

Assessment of the genetic and clinical determinants of fracture risk: genome wide association and mendelian randomisation study

(2018) Katerina Trajanoska et al.   BMJ-British Medical Journal

Identification of Novel Loci Associated With Hip Shape: A Meta-Analysis of Genomewide Association Studies

(2018) Denis A Baird et al.   JOURNAL OF BONE AND MINERAL RESEARCH

An atlas of genetic influences on osteoporosis in humans and mice

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

Cortical and trabecular bone microarchitecture as an independent predictor of incident fracture risk in older women and men in the Bone Microarchitecture International Consortium (BoMIC): a prospective study

(2018) Elizabeth J Samelson et al.   Lancet Diabetes & Endocrinology

Old age and the associated impairment of bones' adaptation to loading are associated with transcriptomic changes in cellular metabolism, cell-matrix interactions and the cell cycle

(2017) Gabriel L. Galea et al.   GENE

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

Bivariate genome-wide association meta-analysis of pediatric musculoskeletal traits reveals pleiotropic effects at the SREBF1/TOM1L2 locus

(2017) Carolina Medina-Gomez et al.   Nature Communications

Osteocyte-Intrinsic TGF-β Signaling Regulates Bone Quality through Perilacunar/Canalicular Remodeling

(2017) Neha S. Dole et al.   Cell Reports

Osteocyte Mechanobiology

(2017) Yuhei Uda et al.   Current Osteoporosis Reports

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

(2017) Gina M. Calabrese et al.   Cell Systems

Evolving New Skeletal Traits by cis -Regulatory Changes in Bone Morphogenetic Proteins

(2016) Vahan B. Indjeian et al.   CELL

A reference panel of 64,976 haplotypes for genotype imputation

(2016)   NATURE GENETICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Whole‐genome sequencing identifies EN1 as a determinant of bone density and fracture

(2015) Hou‐Feng Zheng et al.   NATURE

The support of human genetic evidence for approved drug indications

(2015) Matthew R Nelson et al.   NATURE GENETICS

An atlas of genetic correlations across human diseases and traits

(2015) Brendan Bulik-Sullivan et al.   NATURE GENETICS

A gene-based association method for mapping traits using reference transcriptome data

(2015) Eric R Gamazon et al.   NATURE GENETICS

MAGMA: Generalized Gene-Set Analysis of GWAS Data

(2015) Christiaan A. de Leeuw et al.   PLoS Computational Biology

Effects of Age and Estrogen on Skeletal Gene Expression in Humans as Assessed by RNA Sequencing

(2015) Joshua N. Farr et al.   PLoS One

Osteocytes: Master Orchestrators of Bone

(2013) Mitchell B. Schaffler et al.   CALCIFIED TISSUE INTERNATIONAL

An RNA-seq protocol to identify mRNA expression changes in mouse diaphyseal bone: Applications in mice with bone property alteringLrp5mutations

(2013) Ugur M Ayturk et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Public Health Impact of Osteoporosis

(2013) J. A. Cauley   JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES

Validating therapeutic targets through human genetics

(2013) Robert M. Plenge et al.   NATURE REVIEWS DRUG DISCOVERY

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Demonstration of osteocytic perilacunar/canalicular remodeling in mice during lactation

(2012) Hai Qing et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Matrix metalloproteinase-13 is required for osteocytic perilacunar remodeling and maintains bone fracture resistance

(2012) Simon Y Tang et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Use of genome-wide association studies for drug repositioning

(2012) Philippe Sanseau et al.   NATURE BIOTECHNOLOGY

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

Osteocyte Signaling in Bone

(2012) Mitchell B. Schaffler et al.   Current Osteoporosis Reports

The False-positive to False-negative Ratio in Epidemiologic Studies

(2011) John P. A. Ioannidis et al.   EPIDEMIOLOGY

Molecular disease map of bone characterizing the postmenopausal osteoporosis phenotype

(2011) Rune Jemtland et al.   JOURNAL OF BONE AND MINERAL RESEARCH

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Gene expression patterns in bone following mechanical loading

(2010) Sara M Mantila Roosa et al.   JOURNAL OF BONE AND MINERAL RESEARCH

Genome-Wide Association Meta-Analysis of Cortical Bone Mineral Density Unravels Allelic Heterogeneity at the RANKL Locus and Potential Pleiotropic Effects on Bone

(2010) Lavinia Paternoster et al.   PLoS Genetics

An Integration of Genome-Wide Association Study and Gene Expression Profiling to Prioritize the Discovery of Novel Susceptibility Loci for Osteoporosis-Related Traits

(2010) Yi-Hsiang Hsu et al.   PLoS Genetics

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

Eight genes are highly associated with BMD variation in postmenopausal Caucasian women

(2009) Sjur Reppe et al.   BONE

Population genomics in a disease targeted primary cell model

(2009) E. Grundberg et al.   GENOME RESEARCH

Do osteocytes contribute to bone mineral homeostasis? Osteocytic osteolysis revisited

(2008) Anna Teti et al.   BONE

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE