@article {1718091,
	title = {Epigenetics as a mediator of genetic risk in osteoarthritis: role during development, homeostasis, aging, and disease progression},
	journal = {Am J Physiol Cell Physiol},
	volume = {324},
	number = {5},
	year = {2023},
	month = {2023 May 01},
	pages = {C1078-C1088},
	abstract = {The identification of genomic loci that are associated with osteoarthritis (OA) has provided a starting point for understanding how genetic variation activates catabolic processes in the joint. However, genetic variants can only alter gene expression and cellular function when the epigenetic environment is permissive to these effects. In this review, we provide examples of how epigenetic shifts at distinct life stages can alter the risk for OA, which we posit is critical for the proper interpretation of genome-wide association studies (GWAS). During development, intensive work on the growth and differentiation factor 5 (GDF5) locus has revealed the importance of tissue-specific enhancer activity in controlling both joint development and the subsequent risk for OA. During homeostasis in adults, underlying genetic risk factors may help establish beneficial or catabolic "set points" that dictate tissue function, with a strong cumulative effect on OA risk. During aging, methylation changes and the reorganization of chromatin can "unmask" the effects of genetic variants. The destructive function of variants that alter aging would only mediate effects after reproductive competence and thus avoid any evolutionary selection pressure, as consistent with larger frameworks of biological aging and its relationship to disease. A similar "unmasking" may occur during OA progression, which is supported by the finding of distinct expression quantitative trait loci (eQTLs) in chondrocytes depending on the degree of tissue degradation. Finally, we propose that massively parallel reporter assays (MPRAs) will be a valuable tool to test the function of putative OA GWAS variants in chondrocytes from different life stages.},
	keywords = {Adult, Aging, Disease Progression, Epigenesis, Genetic, Genetic Predisposition to Disease, Genome-Wide Association Study, Homeostasis, Humans, Osteoarthritis, Risk Factors},
	issn = {1522-1563},
	doi = {10.1152/ajpcell.00574.2022},
	author = {Richard, Daniel and Capellini, Terence D and Diekman, Brian O}
}
@article {1718086,
	title = {The functional and evolutionary impacts of human-specific deletions in conserved elements},
	journal = {Science},
	volume = {380},
	number = {6643},
	year = {2023},
	month = {2023 Apr 28},
	pages = {eabn2253},
	abstract = {Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.},
	keywords = {Brain, Conserved Sequence, Evolution, Molecular, Gene Expression Regulation, Developmental, Genome, Genomics, Humans, RNA-Binding Proteins, Sequence Deletion},
	issn = {1095-9203},
	doi = {10.1126/science.abn2253},
	author = {Xue, James R and Mackay-Smith, Ava and Mouri, Kousuke and Garcia, Meilin Fernandez and Dong, Michael X and Akers, Jared F and Noble, Mark and Li, Xue and Lindblad-Toh, Kerstin and Karlsson, Elinor K and Noonan, James P and Capellini, Terence D and Brennand, Kristen J and Tewhey, Ryan and Sabeti, Pardis C and Reilly, Steven K}
}
@article {1718096,
	title = {Human and African ape myosin heavy chain content and the evolution of hominin skeletal muscle},
	journal = {Comp Biochem Physiol A Mol Integr Physiol},
	volume = {281},
	year = {2023},
	month = {2023 Jul},
	pages = {111415},
	abstract = {Humans are unique among terrestrial mammals in our manner of walking and running, reflecting 7 to 8~Ma of musculoskeletal evolution since diverging with the genus Pan. One component of this is a shift in our skeletal muscle biology towards a predominance of myosin heavy chain (MyHC) I isoforms (i.e. slow fibers) across our pelvis and lower limbs, which distinguishes us from chimpanzees. Here, new MyHC data from 35 pelvis and hind limb muscles of a Western gorilla (Gorilla gorilla) are presented. These data are combined with a similar chimpanzee dataset to assess the MyHC I content of humans in comparison to African apes (chimpanzees and gorillas) and other terrestrial mammals. The responsiveness of human skeletal muscle to behavioral interventions is also compared to the human-African ape differential. Humans are distinct from African apes and among a small group of terrestrial mammals whose pelvis and lower limb muscle is slow fiber dominant, on average. Behavioral interventions, including immobilization, bed rest, spaceflight and exercise, can induce modest decreases and increases in human MyHC I content (i.e. -9.3\% to 2.3\%, n~=~2033 subjects), but these shifts are much smaller than the mean human-African ape differential (i.e. 31\%). Taken together, these results indicate muscle fiber content is likely an evolvable trait under selection in the hominin lineage. As such, we highlight potential targets of selection in the genome (e.g. regions that regulate MyHC content) that may play an important role in hominin skeletal muscle evolution.},
	keywords = {Animals, Hominidae, Humans, Mammals, Muscle Fibers, Skeletal, Muscle, Skeletal, Myosin Heavy Chains, Pan troglodytes, Protein Isoforms},
	issn = {1531-4332},
	doi = {10.1016/j.cbpa.2023.111415},
	author = {Queeno, Samantha R and Reiser, Peter J and Orr, Caley M and Capellini, Terence D and Sterner, Kirstin N and O{\textquoteright}Neill, Matthew C}
}
@article {1718101,
	title = {Lineage-specific differences and regulatory networks governing human chondrocyte development},
	journal = {Elife},
	volume = {12},
	year = {2023},
	month = {2023 Mar 15},
	abstract = {To address large gaps in our understanding of the molecular regulation of articular and growth plate cartilage development in humans, we used our directed differentiation approach to generate these distinct cartilage tissues from human embryonic stem cells. The resulting transcriptomic profiles of hESC-derived articular and growth plate chondrocytes were similar to fetal epiphyseal and growth plate chondrocytes, with respect to genes both known and previously unknown to cartilage biology. With the goal to characterize the regulatory landscapes accompanying these respective transcriptomes, we mapped chromatin accessibility in hESC-derived chondrocyte lineages, and mouse embryonic chondrocytes, using ATAC-sequencing. Integration of the expression dataset with the differentially accessible genomic regions revealed lineage-specific gene regulatory networks. We validated functional interactions of two transcription factors (TFs) (RUNX2 in growth plate chondrocytes and RELA in articular chondrocytes) with their predicted genomic targets. The maps we provide thus represent a framework for probing regulatory interactions governing chondrocyte differentiation. This work constitutes a substantial step towards comprehensive and comparative molecular characterizations of distinct chondrogenic lineages and sheds new light on human cartilage development and biology.},
	keywords = {Animals, Cartilage, Cell Differentiation, Chondrocytes, Chondrogenesis, Growth Plate, Humans, Mice, Transcription Factors},
	issn = {2050-084X},
	doi = {10.7554/eLife.79925},
	author = {Richard, Daniel and Pregizer, Steven and Venkatasubramanian, Divya and Raftery, Rosanne M and Muthuirulan, Pushpanathan and Liu, Zun and Capellini, Terence D and Craft, April M}
}
@article {1718081,
	title = {Molecular mechanism of synovial joint site specification and induction in developing vertebrate limbs},
	journal = {Development},
	volume = {150},
	number = {13},
	year = {2023},
	month = {2023 Jul 01},
	abstract = {The vertebrate appendage comprises three primary segments, the stylopod, zeugopod and autopod, each separated by joints. The molecular mechanisms governing the specification of joint sites, which define segment lengths and thereby limb architecture, remain largely unknown. Existing literature suggests that reciprocal gradients of retinoic acid (RA) and fibroblast growth factor (FGF) signaling define the expression domains of the putative segment markers Meis1, Hoxa11 and Hoxa13. Barx1 is expressed in the presumptive joint sites. Our data demonstrate that RA-FGF signaling gradients define the expression domain of Barx1 in the first presumptive joint site. When misexpressed, Barx1 induces ectopic interzone-like structures, and its loss of function partially blocks interzone development. Simultaneous perturbations of RA-FGF signaling gradients result in predictable shifts of Barx1 expression domains along the proximo-distal axis and, consequently, in the formation of repositioned joints. Our data suggest that during early limb bud development in chick, Meis1 and Hoxa11 expression domains are overlapping, whereas the Barx1 expression domain resides within the Hoxa11 expression domain. However, once the interzone is formed, the expression domains are refined and the Barx1 expression domain becomes congruent with the border of these two putative segment markers.},
	keywords = {Animals, Extremities, Gene Expression Regulation, Developmental, Joints, Myeloid Ecotropic Viral Integration Site 1 Protein, Transcription Factors, Vertebrates},
	issn = {1477-9129},
	doi = {10.1242/dev.201335},
	author = {Yadav, Upendra S and Biswas, Tathagata and Singh, Pratik N and Gupta, Pankaj and Chakraborty, Soura and Delgado, Irene and Zafar, Hamim and Capellini, Terence D and Torres, Miguel and Bandyopadhyay, Amitabha}
}
@article {1718076,
	title = {The Notch-mediated circuitry in the evolution and generation of new cell lineages: the tooth model},
	journal = {Cell Mol Life Sci},
	volume = {80},
	number = {7},
	year = {2023},
	month = {2023 Jun 18},
	pages = {182},
	abstract = {The Notch pathway is an ancient, evolutionary conserved intercellular signaling mechanism that is involved in cell fate specification and proper embryonic development. The Jagged2 gene, which encodes a ligand for the Notch family of receptors, is expressed from the earliest stages of odontogenesis in epithelial cells that will later generate the enamel-producing ameloblasts. Homozygous Jagged2 mutant mice exhibit abnormal tooth morphology and impaired enamel deposition. Enamel composition and structure in mammals are tightly linked to the enamel organ that represents an evolutionary unit formed by distinct dental epithelial cell types. The physical cooperativity between Notch ligands and receptors suggests that Jagged2 deletion could alter the expression profile of Notch receptors, thus modifying the whole Notch signaling cascade in cells within the enamel organ. Indeed, both Notch1 and Notch2 expression are severely disturbed in the enamel organ of Jagged2 mutant teeth. It appears that the deregulation of the Notch signaling cascade reverts the evolutionary path generating dental structures more reminiscent of the enameloid of fishes rather than of mammalian enamel. Loss of interactions between Notch and Jagged proteins may initiate the suppression of complementary dental epithelial cell fates acquired during evolution. We propose that the increased number of Notch homologues in metazoa enabled incipient sister cell types to form and maintain distinctive cell fates within organs and tissues along evolution.},
	keywords = {Animals, Carrier Proteins, Cell Differentiation, Cell Lineage, Female, Mammals, Membrane Proteins, Mice, Pregnancy, Receptors, Notch, Serrate-Jagged Proteins},
	issn = {1420-9071},
	doi = {10.1007/s00018-023-04831-7},
	author = {Mitsiadis, Thimios A and Pagella, Pierfrancesco and Capellini, Terence D and Smith, Moya Meredith}
}
@article {1718106,
	title = {Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals},
	journal = {Elife},
	volume = {12},
	year = {2023},
	month = {2023 Feb 10},
	abstract = {Individuals infected with the SARS-CoV-2 virus present with a wide variety of symptoms ranging from asymptomatic to severe and even lethal outcomes. Past research has revealed a genetic haplotype on chromosome 3 that entered the human population via introgression from Neanderthals as the strongest genetic risk factor for the severe response to COVID-19. However, the specific variants along this introgressed haplotype that contribute to this risk and the biological mechanisms that are involved remain unclear. Here, we assess the variants present on the risk haplotype for their likelihood of driving the genetic predisposition to severe COVID-19 outcomes. We do this by first exploring their impact on the regulation of genes involved in COVID-19 infection using a variety of population genetics and functional genomics tools. We then perform a locus-specific massively parallel reporter assay to individually assess the regulatory potential of each allele on the haplotype in a multipotent immune-related cell line. We ultimately reduce the set of over 600 linked genetic variants to identify four introgressed alleles that are strong functional candidates for driving the association between this locus and severe COVID-19. Using reporter assays in the presence/absence of SARS-CoV-2, we find evidence that these variants respond to viral infection. These variants likely drive the locus{\textquoteright} impact on severity by modulating the regulation of two critical chemokine receptor genes: CCR1 and CCR5. These alleles are ideal targets for future functional investigations into the interaction between host genomics and COVID-19 outcomes.},
	keywords = {Animals, COVID-19, Genetics, Population, Humans, Neanderthals, SARS-CoV-2, Virus Diseases},
	issn = {2050-084X},
	doi = {10.7554/eLife.71235},
	author = {Jagoda, Evelyn and Marnetto, Davide and Senevirathne, Gayani and Gonzalez, Victoria and Baid, Kaushal and Montinaro, Francesco and Richard, Daniel and Falzarano, Darryl and LeBlanc, Emmanuelle V and Colpitts, Che C and Banerjee, Arinjay and Pagani, Luca and Capellini, Terence D}
}
@article {1718071,
	title = {A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2},
	journal = {Nat Commun},
	volume = {14},
	number = {1},
	year = {2023},
	month = {2023 Jul 06},
	pages = {3993},
	abstract = {A lingering question in developmental biology has centered on how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. Here, using the murine hindlimb as a model, we investigate the elusive mechanisms whereby PBX TALE homeoproteins, viewed primarily as HOX cofactors, attain context-specific developmental roles despite ubiquitous presence in the embryo. We first demonstrate that mesenchymal-specific loss of PBX1/2 or the transcriptional regulator HAND2 generates similar limb phenotypes. By combining tissue-specific and temporally controlled mutagenesis with multi-omics approaches, we reconstruct a gene regulatory network (GRN) at organismal-level resolution that is collaboratively directed by PBX1/2 and HAND2 interactions in subsets of posterior hindlimb mesenchymal cells. Genome-wide profiling of PBX1 binding across multiple embryonic tissues further reveals that HAND2 interacts with subsets of PBX-bound regions to regulate limb-specific GRNs. Our research elucidates fundamental principles by which promiscuous transcription factors cooperate with cofactors that display domain-restricted localization to instruct tissue-specific developmental programs.},
	keywords = {Animals, Gene Regulatory Networks, Homeodomain Proteins, Mice, Pre-B-Cell Leukemia Transcription Factor 1, Transcription Factors},
	issn = {2041-1723},
	doi = {10.1038/s41467-023-39443-z},
	author = {Losa, Marta and Barozzi, Iros and Osterwalder, Marco and Hermosilla-Aguayo, Viviana and Morabito, Angela and Chac{\'o}n, Brandon H and Zarrineh, Peyman and Girdziusaite, Ausra and Benazet, Jean Denis and Zhu, Jianjian and Mackem, Susan and Capellini, Terence D and Dickel, Diane and Bobola, Nicoletta and Zuniga, Aim{\'e}e and Visel, Axel and Zeller, Rolf and Selleri, Licia}
}
@article {1718121,
	title = {Author Correction: Joint disease-specificity at the regulatory base-pair level},
	journal = {Nat Commun},
	volume = {13},
	number = {1},
	year = {2022},
	month = {2022 Jan 27},
	pages = {631},
	issn = {2041-1723},
	doi = {10.1038/s41467-022-28073-6},
	author = {Muthuirulan, Pushpanathan and Zhao, Dewei and Young, Mariel and Richard, Daniel and Liu, Zun and Emami, Alireza and Portilla, Gabriela and Hosseinzadeh, Shayan and Cao, Jiaxue and Maridas, David and Sedlak, Mary and Menghini, Danilo and Cheng, Liangliang and Li, Lu and Ding, Xinjia and Ding, Yan and Rosen, Vicki and Kiapour, Ata M and Capellini, Terence D}
}
@article {1718131,
	title = {Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells},
	journal = {Mol Biol Evol},
	volume = {39},
	number = {1},
	year = {2022},
	month = {2022 Jan 07},
	abstract = {Although some variation introgressed from Neanderthals has undergone selective sweeps, little is known about its functional significance. We used a Massively Parallel Reporter Assay (MPRA) to assay 5,353 high-frequency introgressed variants for their ability to modulate the gene expression within 170 bp of endogenous sequence. We identified 2,548 variants in active putative cis-regulatory elements (CREs) and 292 expression-modulating variants (emVars). These emVars are predicted to alter the binding motifs of important immune transcription factors, are enriched for associations with neutrophil and white blood cell count, and are associated with the expression of genes that function in innate immune pathways including inflammatory response and antiviral defense. We combined the MPRA data with other data sets to identify strong candidates to be driver variants of positive selection including an emVar that may contribute to protection against severe COVID-19 response. We endogenously deleted two CREs containing expression-modulation variants linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2, respectively, three genes differentially expressed during influenza infection. Overall, we present the first database of experimentally identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans.},
	keywords = {Animals, Gene Expression, Genetic Variation, Genome, Human, Humans, Immunity, Innate, Inflammation, Neanderthals},
	issn = {1537-1719},
	doi = {10.1093/molbev/msab304},
	author = {Jagoda, Evelyn and Xue, James R and Reilly, Steven K and Dannemann, Michael and Racimo, Fernando and Huerta-Sanchez, Emilia and Sankararaman, Sriram and Kelso, Janet and Pagani, Luca and Sabeti, Pardis C and Capellini, Terence D}
}
@article {1718111,
	title = {The developmental impacts of natural selection on human pelvic morphology},
	journal = {Sci Adv},
	volume = {8},
	number = {33},
	year = {2022},
	month = {2022 Aug 19},
	pages = {eabq4884},
	abstract = {Evolutionary responses to selection for bipedalism and childbirth have shaped the human pelvis, a structure that differs substantially from that in apes. Morphology related to these factors is present by birth, yet the developmental-genetic mechanisms governing pelvic shape remain largely unknown. Here, we pinpoint and characterize a key gestational window when human-specific pelvic morphology becomes recognizable, as the ilium and the entire pelvis acquire traits essential for human walking and birth. We next use functional genomics to molecularly characterize chondrocytes from different pelvic subelements during this window to reveal their developmental-genetic architectures. We then find notable evidence of ancient selection and genetic constraint on regulatory sequences involved in ilium expansion and growth, findings complemented by our phenotypic analyses showing that variation in iliac traits is reduced in humans compared to African apes. Our datasets provide important resources for musculoskeletal biology and begin to elucidate developmental mechanisms that shape human-specific morphology.},
	keywords = {Animals, Biological Evolution, Female, Hominidae, Humans, Parturition, Pelvis, Pregnancy, Selection, Genetic},
	issn = {2375-2548},
	doi = {10.1126/sciadv.abq4884},
	author = {Young, Mariel and Richard, Daniel and Grabowski, Mark and Auerbach, Benjamin M and de Bakker, Bernadette S and Hagoort, Jaco and Muthuirulan, Pushpanathan and Kharkar, Vismaya and Kurki, Helen K and Betti, Lia and Birkenstock, Lyena and Lewton, Kristi L and Capellini, Terence D}
}
@article {1718126,
	title = {Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas},
	journal = {Curr Biol},
	volume = {32},
	number = {2},
	year = {2022},
	month = {2022 Jan 24},
	pages = {289-303.e6},
	abstract = {Despite the great diversity of vertebrate limb proportion and our deep understanding of the genetic mechanisms that drive skeletal elongation, little is known about how individual bones reach different lengths in any species. Here, we directly compare the transcriptomes of homologous growth cartilages of the mouse (Mus musculus) and bipedal jerboa (Jaculus jaculus), the latter of which has "mouse-like" arms but extremely long metatarsals of the feet. Intersecting gene-expression differences in metatarsals and forearms of the two species revealed that about 10\% of orthologous genes are associated with the disproportionately rapid elongation of neonatal jerboa feet. These include genes and enriched pathways not previously associated with endochondral elongation as well as those that might diversify skeletal proportion in addition to their known requirements for bone growth throughout the skeleton. We also identified transcription regulators that might act as "nodes" for sweeping differences in genome expression between species. Among these, Shox2, which is necessary for proximal limb elongation, has gained expression in jerboa metatarsals where it has not been detected in other vertebrates. We show that Shox2 is sufficient to increase mouse distal limb length, and a nearby putative cis-regulatory region is preferentially accessible in jerboa metatarsals. In addition to mechanisms that might directly promote growth, we found evidence that jerboa foot elongation may occur in part by de-repressing latent growth potential. The genes and pathways that we identified here provide a framework to understand the modular genetic control of skeletal growth and the remarkable malleability of vertebrate limb proportion.},
	keywords = {Animals, Extremities, Foot, Mice, Rodentia, Transcription Factors, Transcriptome},
	issn = {1879-0445},
	doi = {10.1016/j.cub.2021.10.063},
	author = {Saxena, Aditya and Sharma, Virag and Muthuirulan, Pushpanathan and Neufeld, Stanley J and Tran, Mai P and Gutierrez, Haydee L and Chen, Kevin D and Erberich, Joel M and Birmingham, Amanda and Capellini, Terence D and Cobb, John and Hiller, Michael and Cooper, Kimberly L}
}
@article {1718116,
	title = {Intronic regulation of SARS-CoV-2 receptor (ACE2) expression mediated by immune signaling and oxidative stress pathways},
	journal = {iScience},
	volume = {25},
	number = {7},
	year = {2022},
	month = {2022 Jul 15},
	pages = {104614},
	abstract = {The angiotensin-converting enzyme 2 (ACE2) protein is a key catalytic regulator of the renin-angiotensin system (RAS), involved in fluid homeostasis and blood pressure modulation. ACE2 also serves as a cell-surface receptor for some coronaviruses such as SARS-CoV and SARS-CoV-2. Improved characterization of ACE2 regulation may help us understand the effects of pre-existing conditions on COVID-19 incidence, as well as pathogenic dysregulation following viral infection. Here, we perform bioinformatic analyses to hypothesize on ACE2 gene regulation in two different physiological contexts, identifying putative regulatory elements of ACE2 expression. We perform functional validation of our computational predictions via targeted CRISPR-Cas9 deletions of these elements in~vitro, finding them responsive to immune signaling and oxidative-stress pathways. This contributes to our understanding of ACE2 gene regulation at baseline and immune challenge. Our work supports pursuit of these putative mechanisms in our understanding of infection/disease caused by current, and future, SARS-related viruses such as SARS-CoV-2.},
	issn = {2589-0042},
	doi = {10.1016/j.isci.2022.104614},
	author = {Richard, Daniel and Muthuirulan, Pushpanathan and Aguiar, Jennifer and Doxey, Andrew C and Banerjee, Arinjay and Mossman, Karen and Hirota, Jeremy and Capellini, Terence D}
}
@article {1718136,
	title = {Identification of IGF2BP1-related lncRNA-miRNA-mRNA network in goat skeletal muscle satellite cells},
	journal = {Anim Sci J},
	volume = {92},
	number = {1},
	year = {2021},
	month = {2021 Jan-Dec},
	pages = {e13631},
	abstract = {Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) plays essential roles in the proliferation of skeletal muscle satellite cells (MuSCs). Increasing evidence has shown that IGF2BP1 regulates the expression of noncoding RNAs and mRNAs. However, the related molecular network remains to be fully understood. Therefore, we performed RNA sequencing and analyzed the microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and mRNAs differentially expressed in goat MuSCs treated with IGF2BP1 overexpressing and empty vectors. A total of 36 miRNAs, 59 lncRNAs, and 44 mRNAs were differentially expressed caused by IGF2BP1. Expectedly, they were enriched in muscle development-related Rap1, PI3K-AKT, and FoxO signaling pathways. Finally, we constructed a lncRNA-miRNA-mRNA interaction network containing 30 lncRNAs, 15 miRNAs, and 34 mRNAs, in which several miRNAs, including miR-133a-3p, miR-204-5p, miR-125a-3p, miR-145-3p, and miR-423-5p, relate with cell growth and participate in muscle development. Overall, we constructed an IGF2BP1-related network, which provides new insight into the myogenic proliferation of goat.},
	keywords = {Animals, Gene Regulatory Networks, Goats, MicroRNAs, Phosphatidylinositol 3-Kinases, RNA, Long Noncoding, RNA, Messenger, Satellite Cells, Skeletal Muscle},
	issn = {1740-0929},
	doi = {10.1111/asj.13631},
	author = {Xu, Xiaoli and Leng, Junchen and Zhang, Xiao and Capellini, Terence D and Chen, Yuan and Yang, Liu and Chen, Zitong and Zheng, Shuailong and Zhang, Xujia and Zhan, Siyuan and Wang, Linjie and Zhong, Tao and Guo, Jiazhong and Niu, Lili and Wang, Yan and Dai, Dinghui and Zhang, Hongping and Li, Li and Cao, Jiaxue}
}
@article {1599642,
	title = {Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors},
	journal = {Elife},
	volume = {10},
	year = {2021},
	month = {2021 Jan 15},
	abstract = {The mechanical challenge of attaching elastic tendons to stiff bones is solved by the formation of a unique transitional tissue. Here, we show that murine tendon-to-bone attachment cells are bi-fated, activating a mixture of chondrocyte and tenocyte transcriptomes, under regulation of shared regulatory elements and Kr{\"u}ppel-like factors (KLFs) transcription factors. High-throughput bulk and single-cell RNA sequencing of humeral attachment cells revealed expression of hundreds of chondrogenic and tenogenic genes, which was validated by in situ hybridization and single-molecule ISH. ATAC sequencing showed that attachment cells share accessible intergenic chromatin areas with either tenocytes or chondrocytes. Epigenomic analysis revealed enhancer signatures for most of these regions. Transgenic mouse enhancer reporter assays verified the shared activity of some of these enhancers. Finally, integrative chromatin and motif analyses and transcriptomic data implicated KLFs as regulators of attachment cells. Indeed, blocking expression of both Klf2 and Klf4 in developing limb mesenchyme impaired their differentiation.},
	issn = {2050-084X},
	doi = {10.7554/eLife.55361},
	author = {Kult, Shiri and Olender, Tsviya and Osterwalder, Marco and Markman, Svetalana and Leshkowitz, Dena and Krief, Sharon and Blecher-Gonen, Ronnie and Ben-Moshe, Shani and Farack, Lydia and Keren-Shaul, Hadas and Salame, Tomer-Meir and Capellini, Terence D and Itzkovitz, Shalev and Amit, Ido and Visel, Axel and Zelzer, Elazar}
}
@article {1599640,
	title = {Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses},
	journal = {iScience},
	volume = {24},
	number = {5},
	year = {2021},
	month = {2021 May 21},
	pages = {102477},
	abstract = {Type I interferons (IFNs) are our first line of defense against virus infection. Recent studies have suggested the ability of SARS-CoV-2 proteins to inhibit IFN responses. Emerging data also suggest that timing and extent of IFN production is associated with manifestation of COVID-19 severity. In spite of progress in understanding how SARS-CoV-2 activates antiviral responses, mechanistic studies into wild-type SARS-CoV-2-mediated induction and inhibition of human type I IFN responses are scarce. Here we demonstrate that SARS-CoV-2 infection induces a type I IFN response in~vitro and in moderate cases of COVID-19. In~vitro stimulation of type I IFN expression and signaling in human airway epithelial cells is associated with activation of canonical transcriptions factors, and SARS-CoV-2 is unable to inhibit exogenous induction of these responses. Furthermore, we show that physiological levels of IFNα detected in patients with moderate COVID-19 is sufficient to suppress SARS-CoV-2 replication in human airway cells.},
	issn = {2589-0042},
	doi = {10.1016/j.isci.2021.102477},
	author = {Banerjee, Arinjay and El-Sayes, Nader and Budylowski, Patrick and Jacob, Rajesh Abraham and Richard, Daniel and Maan, Hassaan and Aguiar, Jennifer A and Demian, Wael L and Baid, Kaushal and D{\textquoteright}Agostino, Michael R and Ang, Jann Catherine and Murdza, Tetyana and Tremblay, Benjamin J-M and Afkhami, Sam and Karimzadeh, Mehran and Irving, Aaron T and Yip, Lily and Ostrowski, Mario and Hirota, Jeremy A and Kozak, Robert and Capellini, Terence D and Miller, Matthew S and Wang, Bo and Mubareka, Samira and McGeer, Allison J and McArthur, Andrew G and Doxey, Andrew C and Mossman, Karen}
}
@article {1599637,
	title = {Joint disease-specificity at the regulatory base-pair level},
	journal = {Nat Commun},
	volume = {12},
	number = {1},
	year = {2021},
	month = {2021 Jul 06},
	pages = {4161},
	abstract = {Given the pleiotropic nature of coding sequences and that many loci exhibit multiple disease associations, it is within non-coding sequence that disease-specificity likely exists. Here, we focus on joint disorders, finding among replicated loci, that GDF5 exhibits over twenty distinct associations, and we identify causal variants for two of its strongest associations, hip dysplasia and knee osteoarthritis. By mapping regulatory regions in joint chondrocytes, we pinpoint two variants (rs4911178; rs6060369), on the same risk haplotype, which reside in anatomical site-specific enhancers. We show that both variants have clinical relevance, impacting disease by altering morphology. By modeling each variant in humanized mice, we observe joint-specific response, correlating with GDF5 expression. Thus, we uncouple separate regulatory variants on a common risk haplotype that cause joint-specific disease. By broadening our perspective, we finally find that patterns of modularity at GDF5 are also found at over three-quarters of loci with multiple GWAS disease associations.},
	issn = {2041-1723},
	doi = {10.1038/s41467-021-24345-9},
	author = {Muthuirulan, Pushpanathan and Zhao, Dewei and Young, Mariel and Richard, Daniel and Liu, Zun and Emami, Alireza and Portilla, Gabriela and Hosseinzadeh, Shayan and Cao, Jiaxue and Maridas, David and Sedlak, Mary and Menghini, Danilo and Cheng, Liangliang and Li, Lu and Ding, Xinjia and Ding, Yan and Rosen, Vicki and Kiapour, Ata M and Capellini, Terence D}
}
@article {1599638,
	title = {Shifting epigenetic contexts influence regulatory variation and disease risk},
	journal = {Aging (Albany NY)},
	volume = {13},
	number = {12},
	year = {2021},
	month = {2021 06 16},
	pages = {15699-15749},
	abstract = {Epigenetic shifts are a hallmark of aging that impact transcriptional networks at regulatory level. These shifts may modify the effects of genetic regulatory variants during aging and contribute to disease pathomechanism. However, these shifts occur on the backdrop of epigenetic changes experienced throughout an individual{\textquoteright}s development into adulthood; thus, the phenotypic, and ultimately fitness, effects of regulatory variants subject to developmental- versus aging-related epigenetic shifts may differ considerably. Natural selection therefore may act differently on variants depending on their changing epigenetic context, which we propose as a novel lens through which to consider regulatory sequence evolution and phenotypic effects. Here, we define genomic regions subjected to altered chromatin accessibility as tissues transition from their fetal to adult forms, and subsequently from early to late adulthood. Based on these epigenomic datasets, we examine patterns of evolutionary constraint and potential functional impacts of sequence variation (e.g., genetic disease risk associations). We find that while the signals observed with developmental epigenetic changes are consistent with stronger fitness consequences (i.e., negative selection pressures), they tend to have weaker effects on genetic risk associations for aging-related diseases. Conversely, we see stronger effects of variants with increased local accessibility in adult tissues, strongest in young adult when compared to old. We propose a model for how epigenetic status of a region may influence the effects of evolutionary relevant sequence variation, and suggest that such a perspective on gene regulatory networks may elucidate our understanding of aging biology.},
	issn = {1945-4589},
	doi = {10.18632/aging.203194},
	author = {Richard, Daniel and Capellini, Terence D}
}
@article {1599641,
	title = {Single Cell Omics for Musculoskeletal Research},
	journal = {Curr Osteoporos Rep},
	volume = {19},
	number = {2},
	year = {2021},
	month = {2021 Apr},
	pages = {131-140},
	abstract = {PURPOSE OF REVIEW: The ability to analyze the molecular events occurring within individual cells as opposed to populations of cells is revolutionizing our understanding of musculoskeletal tissue development and disease. Single cell studies have the great potential of identifying cellular subpopulations that work in a synchronized fashion to regenerate and repair damaged tissues during normal homeostasis. In addition, such studies can elucidate how these processes break down in disease as well as identify cellular subpopulations that drive the disease. This review highlights three emerging technologies: single cell RNA sequencing (scRNA-seq), Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), and Cytometry by Time-Of-Flight (CyTOF) mass cytometry.

RECENT FINDINGS: Technological and bioinformatic tools to analyze the transcriptome, epigenome, and proteome at the individual cell level have advanced rapidly making data collection relatively easy; however, understanding how to access and interpret the data remains a challenge for many scientists. It is, therefore, of paramount significance to educate the musculoskeletal community on how single cell technologies can be used to answer research questions and advance translation. This article summarizes talks given during a workshop on "Single Cell Omics" at the 2020 annual meeting of the Orthopedic Research Society. Studies that applied scRNA-seq, ATAC-seq, and CyTOF mass cytometry to cartilage development and osteoarthritis are reviewed. This body of work shows how these cutting-edge tools can advance our understanding of the cellular heterogeneity and trajectories of lineage specification during development and disease.},
	issn = {1544-2241},
	doi = {10.1007/s11914-021-00662-2},
	author = {Rai, Muhammad Farooq and Wu, Chia-Lung and Capellini, Terence D and Guilak, Farshid and Dicks, Amanda R and Muthuirulan, Pushpanathan and Grandi, Fiorella and Bhutani, Nidhi and Westendorf, Jennifer J}
}
@article {1599639,
	title = {Subchondral bone length in knee osteoarthritis: A deep learning derived imaging measure and its association with radiographic and clinical outcomes},
	journal = {Arthritis Rheumatol},
	year = {2021},
	month = {2021 May 11},
	abstract = {OBJECTIVE: Develop a bone shape measure that reflects the extent of cartilage loss and bone flattening in knee osteoarthritis (OA) and test it against estimates of disease severity.

METHODS: A fast region-based convolutional neural network was trained to crop the knee joints in sagittal dual-echo steady state MRI sequences obtained from the Osteoarthritis Initiative (OAI). Publicly available annotations of the cartilage and menisci were used as references to annotate the tibia and the femur in 61 knees. Another deep neural network (U-Net) was developed to learn these annotations. Model predictions were compared with radiologist-driven annotations on an independent test set (27 knees). The U-Net was applied to automatically extract the knee joint structures on the larger OAI dataset (9,434 knees). We defined subchondral bone length (SBL), a novel shape measure characterizing the extent of overlying cartilage and bone flattening, and examined its relationship with radiographic joint space narrowing (JSN), concurrent WOMAC pain and disability as well as subsequent partial or total knee replacement (KR). Odds ratios for each outcome were estimated using relative changes in SBL on the OAI dataset into quartiles.

RESULT: Mean SBL values for knees with JSN were consistently different from knees without JSN. Greater changes of SBL from baseline were associated with greater pain and disability. For knees with medial or lateral JSN, the odds ratios between lowest and highest quartiles corresponding to SBL changes for future KR were 5.68 (95\% CI:[3.90,8.27]) and 7.19 (95\% CI:[3.71,13.95]), respectively.

CONCLUSION: SBL quantified OA status based on JSN severity. It has promise as an imaging marker in predicting clinical and structural OA outcomes.},
	issn = {2326-5205},
	doi = {10.1002/art.41808},
	author = {Chang, Gary H and Park, Lisa K and Le, Nina A and Jhun, Ray S and Surendran, Tejus and Lai, Joseph and Seo, Hojoon and Promchotichai, Nuwapa and Yoon, Grace and Scalera, Jonathan and Capellini, Terence D and Felson, David T and Kolachalama, Vijaya B}
}
@article {1599643,
	title = {Genome-wide association of phenotypes based on clustering patterns of hand osteoarthritis identify  as novel osteoarthritis gene},
	journal = {Ann Rheum Dis},
	year = {2020},
	month = {2020 Oct 14},
	abstract = {BACKGROUND: Despite recent advances in the understanding of the genetic architecture of osteoarthritis (OA), only two genetic loci have been identified for OA of the hand, in part explained by the complexity of the different hand joints and heterogeneity of OA pathology.

METHODS: We used data from the Rotterdam Study (RSI, RSII and RSIII) to create three hand OA phenotypes based on clustering patterns of radiographic OA severity to increase power in our modest discovery genome-wide association studies in the RS (n=8700), and sought replication in an independent cohort, the Framingham Heart Study (n=1203). We used multiple approaches that leverage different levels of information and functional data to further investigate the underlying biological mechanisms and candidate genes for replicated loci. We also attempted to replicate known OA loci at other joint sites, including the hips and knees.

RESULTS: We found two novel genome-wide significant loci for OA in the thumb joints. We identified WNT9A as a possible novel causal gene involved in OA pathogenesis. Furthermore, several previously identified genetic loci for OA seem to confer risk for OA across multiple joints: TGFa, RUNX2, COL27A1, ASTN2, IL11 and GDF5 loci.

CONCLUSIONS: We identified a robust novel genetic locus for hand OA on chromosome 1, of which WNT9A is the most likely causal gene. In addition, multiple genetic loci were identified to be associated with OA across multiple joints. Our study confirms the potential for novel insight into the genetic architecture of OA by using biologically meaningful stratified phenotypes.},
	issn = {1468-2060},
	doi = {10.1136/annrheumdis-2020-217834},
	author = {Boer, Cindy Germaine and Yau, Michelle S and Rice, Sarah J and Coutinho de Almeida, Rodrigo and Cheung, Kathleen and Styrkarsdottir, Unnur and Southam, Lorraine and Broer, Linda and Wilkinson, Jeremy Mark and Uitterlinden, Andr{\'e} G and Zeggini, Eleftheria and Felson, David and Loughlin, John and Young, Mariel and Capellini, Terence Dante and Meulenbelt, Ingrid and van Meurs, Joyce B J}
}
@article {1521629,
	title = {Assessment of knee pain from MR imaging using a convolutional Siamese network},
	journal = {Eur Radiol},
	volume = {30},
	number = {6},
	year = {2020},
	month = {2020 Jun},
	pages = {3538-3548},
	abstract = {OBJECTIVES: It remains difficult to characterize the source of pain in knee joints either using radiographs or magnetic resonance imaging (MRI). We sought to determine if advanced machine learning methods such as deep neural networks could distinguish knees with pain from those without it and identify the structural features that are associated with knee pain.

METHODS: We constructed a convolutional Siamese network to associate MRI scans obtained on subjects from the Osteoarthritis Initiative (OAI) with frequent unilateral knee pain comparing the knee with frequent pain to the contralateral knee without pain. The Siamese network architecture enabled pairwise learning of information from two-dimensional (2D) sagittal intermediate-weighted turbo spin echo slices obtained from similar locations on both knees. Class activation mapping (CAM) was utilized to create saliency maps, which highlighted the regions most associated with knee pain. The MRI scans and the CAMs of each subject were reviewed by an expert radiologist to identify the presence of abnormalities within the model-predicted regions of high association.

RESULTS: Using 10-fold cross-validation, our model achieved an area under curve (AUC) value of 0.808. When individuals whose knee WOMAC pain scores were not discordant were excluded, model performance increased to 0.853. The radiologist review revealed that about 86\% of the cases that were predicted correctly had effusion-synovitis within the regions that were most associated with pain.

CONCLUSIONS: This study demonstrates a proof of principle that deep learning can be applied to assess knee pain from MRI scans.

KEY POINTS: {\textbullet} Our article is the first to leverage a deep learning framework to associate MR images of the knee with knee pain. {\textbullet} We developed a convolutional Siamese network that had the ability to fuse information from multiple two-dimensional (2D) MRI slices from the knee with pain and the contralateral knee of the same individual without pain to predict unilateral knee pain. {\textbullet} Our model achieved an area under curve (AUC) value of 0.808. When individuals who had WOMAC pain scores that were not discordant for knees (pain discordance ,
	issn = {1432-1084},
	doi = {10.1007/s00330-020-06658-3},
	author = {Chang, Gary H and Felson, David T and Qiu, Shangran and Guermazi, Ali and Capellini, Terence D and Kolachalama, Vijaya B}
}
@article {1521631,
	title = {Biological clocks and incremental growth line formation in dentine},
	journal = {J Anat},
	volume = {237},
	number = {2},
	year = {2020},
	month = {2020 Aug},
	pages = {367-378},
	abstract = {Dentine- and enamel-forming cells secrete matrix in consistent rhythmic phases, resulting in the formation of successive microscopic growth lines inside tooth crowns and roots. Experimental studies of various mammals have proven that these lines are laid down in subdaily, daily (circadian), and multidaily rhythms, but it is less clear how these rhythms are initiated and maintained. In 2001, researchers reported that lesioning the so-called master biological clock, the suprachiasmatic nucleus (SCN), halted daily line formation in rat dentine, whereas subdaily lines persisted. More recently, a key clock gene (Bmal1) expressed in the SCN in a circadian manner was also found to be active in dentine- and enamel- secretory cells. To probe these potential neurological and local mechanisms for the production of rhythmic lines in teeth, we reexamined the role of the SCN in growth line formation in Wistar rats and investigated the presence of daily lines in Bmal1 knockout mice (Bmal1 ). In contrast to the results of the 2001 study, we found that both daily and subdaily growth lines persisted in rat dentine after complete or partial SCN lesion in the majority of individuals. In mice, after transfer into constant darkness, daily rhythms continued to manifest as incremental lines in the dentine of each Bmal1 genotype (wild-type, Bmal , and Bmal1 ). These results affirm that the manifestation of biological rhythms in teeth is a robust phenomenon, imply a more autonomous role of local biological clocks in tooth growth than previously suggested, and underscore the need further to elucidate tissue-specific circadian biology and its role in incremental line formation. Investigations of this nature will strengthen an invaluable system for determining growth rates and calendar ages from mammalian hard tissues, as well as documenting the early lives of fossil hominins and other primates.},
	issn = {1469-7580},
	doi = {10.1111/joa.13198},
	author = {Papakyrikos, Amanda M and Manish Arora and Christine Austin and Boughner, Julia C and Capellini, Terence D and Dingwall, Heather L and Greba, Quentin and Howland, John G and Kato, Akiko and Wang, Xiu-Ping and Smith, Tanya M}
}
@article {1521630,
	title = {Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk},
	journal = {Cell},
	volume = {181},
	number = {2},
	year = {2020},
	month = {2020 Apr 16},
	pages = {362-381.e28},
	abstract = {During human evolution, the knee adapted to the biomechanical demands of bipedalism by altering chondrocyte developmental programs. This adaptive process was likely not without deleterious consequences to health. Today, osteoarthritis occurs in 250 million people, with risk variants enriched in non-coding sequences near chondrocyte genes, loci that likely became optimized during knee evolution. We explore this relationship by epigenetically profiling joint chondrocytes, revealing ancient selection and recent constraint and drift on knee regulatory elements, which also overlap osteoarthritis variants that contribute to disease heritability by tending to modify constrained functional sequence. We propose a model whereby genetic violations to regulatory constraint, tolerated during knee development, lead to adult pathology. In support, we discover a causal enhancer variant (rs6060369) present in billions of people at a risk locus (GDF5-UQCC1), showing how it impacts mouse knee-shape and osteoarthritis. Overall, our methods link an evolutionarily novel aspect of human anatomy to its pathogenesis.},
	issn = {1097-4172},
	doi = {10.1016/j.cell.2020.02.057},
	author = {Richard, Daniel and Liu, Zun and Cao, Jiaxue and Kiapour, Ata M and Willen, Jessica and Yarlagadda, Siddharth and Jagoda, Evelyn and Kolachalama, Vijaya B and Sieker, Jakob T and Chang, Gary H and Muthuirulan, Pushpanathan and Young, Mariel and Masson, Anand and Konrad, Johannes and Hosseinzadeh, Shayan and Maridas, David E and Rosen, Vicki and Krawetz, Roman and Roach, Neil and Capellini, Terence D}
}
@article {1521627,
	title = {Regulation of Gdf5 expression in joint remodelling, repair and osteoarthritis},
	journal = {Sci Rep},
	volume = {10},
	number = {1},
	year = {2020},
	month = {2020 01 13},
	pages = {157},
	abstract = {Growth and Differentiation Factor 5 (GDF5) is a key risk locus for osteoarthritis (OA). However, little is known regarding regulation of Gdf5 expression following joint tissue damage. Here, we employed Gdf5-LacZ reporter mouse lines to assess the spatiotemporal activity of Gdf5 regulatory sequences in experimental OA following destabilisation of the medial meniscus (DMM) and after acute cartilage injury and repair. Gdf5 expression was upregulated in articular cartilage post-DMM, and was increased in human OA cartilage as determined by immunohistochemistry and microarray analysis. Gdf5 expression was also upregulated during cartilage repair in mice and was switched on in injured synovium in prospective areas of cartilage formation, where it inversely correlated with expression of the transcriptional co-factor Yes-associated protein (Yap). Indeed, overexpression of Yap suppressed Gdf5 expression in chondroprogenitors in vitro. Gdf5 expression in both mouse injury models required regulatory sequence downstream of Gdf5 coding exons. Our findings suggest that Gdf5 upregulation in articular cartilage and synovium is a generic response to knee injury that is dependent on downstream regulatory sequence and in progenitors is associated with chondrogenic specification. We propose a role for Gdf5 in tissue remodelling and repair after injury, which may partly underpin its association with OA risk.},
	issn = {2045-2322},
	doi = {10.1038/s41598-019-57011-8},
	author = {Kania, Karolina and Colella, Fabio and Riemen, Anna H K and Wang, Hui and Howard, Kenneth A and Aigner, Thomas and Dell{\textquoteright}Accio, Francesco and Capellini, Terence D and Roelofs, Anke J and De Bari, Cosimo}
}
@article {1521628,
	title = {Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features},
	journal = {J Exp Zool B Mol Dev Evol},
	volume = {334},
	number = {2},
	year = {2020},
	month = {2020 Mar},
	pages = {100-112},
	abstract = {Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act, is still an open question in evolutionary developmental biology. We use high-resolution quantitative trait locus (QTL) mapping in the F generation of an advanced intercross experiment (LG,SM-G ) to characterize the genetic architecture of the mouse pelvis. We test the prediction that genomic features linked to developmental patterning and differentiation of the hind limb and pelvis and the regulation of chondrogenesis are overrepresented in QTL. We find 31 single QTL trait associations at the genome- or chromosome-wise significance level coalescing to 27 pleiotropic loci. We recover further QTL at a more relaxed significance threshold replicating locations found in a previous experiment in an earlier generation of the same population. QTL were more likely than chance to harbor Pitx1 and Sox9 Class II chromatin immunoprecipitation-seq features active during development of skeletal features. There was weak or no support for the enrichment of seven more categories of developmental features drawn from the literature. Our results suggest that genotypic variation is channeled through a subset of developmental processes involved in the generation of phenotypic variation in the pelvis. This finding indicates that the evolvability of complex traits may be subject to biases not evident from patterns of covariance among morphological features or developmental patterning when either is considered in isolation.},
	issn = {1552-5015},
	doi = {10.1002/jez.b.22926},
	author = {Roseman, Charles C and Capellini, Terence D and Jagoda, Evelyn and Williams, Scott A and Grabowski, Mark and O{\textquoteright}Connor, Christine and Polk, John D and Cheverud, James M}
}
@article {1521626,
	title = {Complex Phenotypes: Mechanisms Underlying Variation in Human Stature},
	journal = {Curr Osteoporos Rep},
	volume = {17},
	number = {5},
	year = {2019},
	month = {2019 10},
	pages = {301-323},
	abstract = {PURPOSE OF REVIEW: The goal of the review is to provide a comprehensive overview of the current understanding of the mechanisms underlying variation in human stature.

RECENT FINDINGS: Human height is an anthropometric trait that varies considerably within human populations as well as across the globe. Historically, much research focus was placed on understanding the biology of growth plate chondrocytes and how modifications to core chondrocyte proliferation and differentiation pathways potentially shaped height attainment in normal as well as pathological contexts. Recently, much progress has been made to improve our understanding regarding the mechanisms underlying the normal and pathological range of height variation within as well as between human populations, and today, it is understood to reflect complex interactions among a myriad of genetic, environmental, and evolutionary factors. Indeed, recent improvements in genetics (e.g., GWAS) and breakthroughs in functional genomics (e.g., whole exome sequencing, DNA methylation analysis, ATAC-sequencing, and CRISPR) have shed light on previously unknown pathways/mechanisms governing pathological and common height variation. Additionally, the use of an evolutionary perspective has also revealed important mechanisms that have shaped height variation across the planet. This review provides an overview of the current knowledge of the biological mechanisms underlying height variation by highlighting new research findings on skeletal growth control with an emphasis on previously unknown pathways/mechanisms influencing pathological and common height variation. In this context, this review also discusses how evolutionary forces likely shaped the genomic architecture of height across the globe.},
	issn = {1544-2241},
	doi = {10.1007/s11914-019-00527-9},
	author = {Muthuirulan, Pushpanathan and Capellini, Terence D}
}
@article {1521625,
	title = {A distinct transition from cell growth to physiological homeostasis in the tendon},
	journal = {eLife},
	volume = {2019 Sep 19;8:e48689. doi: 10.7554/eLife.48689. },
	year = {2019},
	author = {Grinstein M, Dingwall HL, and Dingwall, HL and O{\textquoteright}Connor LD and Zou K and Capellini TD and Galloway JL.}
}
@article {1446658,
	title = {Exercise-induced loading increases ilium cortical area in a selectively bred mouse model},
	journal = {Am J Phys Anthropol},
	volume = {168},
	number = {3},
	year = {2019},
	month = {2019 Mar},
	pages = {543-551},
	abstract = {OBJECTIVES: Little is known about how ilium cortical bone responds to loading. Using a mouse model, this study presents data testing the hypothesis that iliac cross-sectional properties are altered in response to increased activity. MATERIALS AND METHODS: The sample derives from lines of High Runner (HR) mice bred for increased wheel-running activity. Four treatment groups of female mice were tested: non-selected control lines housed without (N = 19) and with wheels (N = 20), and HR mice housed without (N = 17) and with wheels (N = 18) for 13 weeks beginning at weaning. Each pelvis was μCT-scanned, cross-sectional properties (cortical area-Ct.Ar, total area-Tt.Ar, polar moment of area, and polar section modulus) were determined from the ilium midshaft, and robusticity indices (ratio of the square root of Ct.Ar or Tt.Ar to caudal ilium length) were calculated. Mixed models were implemented with linetype, wheel access, and presence of the mini-muscle phenotype as fixed effects, replicate line nested within linetype as a random effect, and body mass as a covariate. RESULTS: Results demonstrate that the mouse ilium morphologically resembles a long bone in cross section. Body mass and the mini-muscle phenotype were significant predictors of iliac cross-sectional properties. Wheel access only had a statistically significant effect on Ct.Ar and its robusticity index, with greater values in mice with wheel access. DISCUSSION: These results suggest that voluntary exercise increases cortical area, but does not otherwise strengthen the ilium in these mice, corroborating previous studies on the effect of increased wheel-running activity on femoral and humeral cross-sectional properties in these mice.},
	issn = {1096-8644},
	doi = {10.1002/ajpa.23770},
	url = {https://onlinelibrary.wiley.com/doi/full/10.1002/ajpa.23770},
	author = {Lewton, Kristi L and Ritzman, Terrence and Copes, Lynn E and Garland, Theodore and Capellini, Terence D}
}
@article {1446659,
	title = {Genetics of scapula and pelvis development: An evolutionary perspective},
	journal = {Curr Top Dev Biol},
	volume = {132},
	year = {2019},
	month = {2019},
	pages = {311-349},
	abstract = {In tetrapods, the scapular and pelvic girdles perform the important function of anchoring the limbs to the trunk of the body and facilitating the movement of each appendage. This shared function, however, is one of relatively few similarities between the scapula and pelvis, which have significantly different morphologies, evolutionary histories, embryonic origins, and underlying genetic pathways. The scapula evolved in jawless fish prior to the pelvis, and its embryonic development is unique among bones in that it is derived from multiple progenitor cell populations, including the dermomyotome, somatopleure, and neural crest. Conversely, the pelvis evolved several million years later in jawed fish, and it develops from an embryonic somatopleuric cell population. The genetic networks controlling the formation of the pelvis and scapula also share similarities and differences, with a number of genes shaping only one or the other, while other gene products such as PBX transcription factors act as hierarchical developmental regulators of both girdle structures. Here, we provide a detailed review of the cellular processes and genetic networks underlying pelvis and scapula formation in tetrapods, while also highlighting unanswered questions about girdle evolution and development.},
	issn = {1557-8933},
	doi = {10.1016/bs.ctdb.2018.12.007},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6430119/},
	author = {Young, Mariel and Selleri, Licia and Capellini, Terence D}
}
@article {1446655,
	title = {Identification of Novel Loci Associated With Hip Shape: A Meta-Analysis of Genomewide Association Studies},
	journal = {J Bone Miner Res},
	volume = {34},
	number = {2},
	year = {2019},
	month = {2019 Feb},
	pages = {241-251},
	abstract = {We aimed to report the first genomewide association study (GWAS) meta-analysis of dual-energy X-ray absorptiometry (DXA)-derived hip shape, which is thought to be related to the risk of both hip osteoarthritis and hip fracture. Ten hip shape modes (HSMs) were derived by statistical shape modeling using SHAPE software, from hip DXA scans in the Avon Longitudinal Study of Parents and Children (ALSPAC; adult females), TwinsUK (mixed sex), Framingham Osteoporosis Study (FOS; mixed), Osteoporotic Fractures in Men study (MrOS), and Study of Osteoporotic Fractures (SOF; females) (total N = 15,934). Associations were adjusted for age, sex, and ancestry. Five genomewide significant (p \&lt; 5 {\texttimes} 10 , adjusted for 10 independent outcomes) single-nucleotide polymorphisms (SNPs) were associated with HSM1, and three SNPs with HSM2. One SNP, in high linkage disequilibrium with rs2158915 associated with HSM1, was associated with HSM5 at genomewide significance. In a look-up of previous GWASs, three of the identified SNPs were associated with hip osteoarthritis, one with hip fracture, and five with height. Seven SNPs were within 200 kb of genes involved in endochondral bone formation, namely SOX9, PTHrP, RUNX1, NKX3-2, FGFR4, DICER1, and HHIP. The SNP adjacent to DICER1 also showed osteoblast cis-regulatory activity of GSC, in which mutations have previously been reported to cause hip dysplasia. For three of the lead SNPs, SNPs in high LD (r  \&gt; 0.5) were identified, which intersected with open chromatin sites as detected by ATAC-seq performed on embryonic mouse proximal femora. In conclusion, we identified eight SNPs independently associated with hip shape, most of which were associated with height and/or mapped close to endochondral bone formation genes, consistent with a contribution of processes involved in limb growth to hip shape and pathological sequelae. These findings raise the possibility that genetic studies of hip shape might help in understanding potential pathways involved in hip osteoarthritis and hip fracture. {\textcopyright} 2018 The Authors. Journal of Bone and Mineral Research Published by Wiley Periodicals, Inc.},
	issn = {1523-4681},
	doi = {10.1002/jbmr.3605},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375741/},
	author = {Baird, Denis A and Evans, Daniel S and Kamanu, Frederick K and Gregory, Jennifer S and Saunders, Fiona R and Giuraniuc, Claudiu V and Barr, Rebecca J and Aspden, Richard M and Jenkins, Deborah and Kiel, Douglas P and Orwoll, Eric S and Cummings, Steven R and Lane, Nancy E and Mullin, Benjamin H and Williams, Frances Mk and Richards, J Brent and Wilson, Scott G and Spector, Tim D and Faber, Benjamin G and Lawlor, Deborah A and Grundberg, Elin and Ohlsson, Claes and Pettersson-Kymmer, Ulrika and Capellini, Terence D and Richard, Daniel and Beck, Thomas J and Evans, David M and Paternoster, Lavinia and Karasik, David and Tobias, Jonathan H}
}
@article {1446661,
	title = {Mendelian Randomization analysis reveals a causal influence of circulating sclerostin levels on bone mineral density and fractures},
	journal = {J Bone Miner Res},
	year = {2019},
	month = {2019 Jun 06},
	abstract = {In bone, sclerostin is mainly osteocyte-derived and plays an important local role in adaptive responses to mechanical loading. Whether circulating levels of sclerostin also play a functional role is currently unclear, which we aimed to examine by two sample Mendelian Randomisation (MR). A genetic instrument for circulating sclerostin, derived from a genome wide association study (GWAS) meta-analysis of serum sclerostin in 10,584 European-descent individuals, was examined in relation to femoral neck bone mineral density (BMD; n= 32,744) in GEFOS, and estimated BMD by heel ultrasound (eBMD; n=426,824), and fracture risk (n=426,795), in UK Biobank. Our GWAS identified two novel serum sclerostin loci, B4GALNT3 (standard deviation (SD)) change in sclerostin per A allele (β=0.20, P=4.6x10 ), and GALNT1 (β=0.11 per G allele, P=4.4x10 ). B4GALNT3 is an N-acetyl-galactosaminyltransferase, adding a terminal LacdiNAc disaccharide to target glycocoproteins, found to be predominantly expressed in kidney, whereas GALNT1 is an enzyme causing mucin-type O-linked glycosylation. Using these two SNPs as genetic instruments, MR revealed an inverse causal relationship between serum sclerostin and femoral neck BMD (β= -0.12, 95\%CI= -0.20 to -0.05) and eBMD (β= -0.12, 95\%CI= -0.14 to -0.10), and a positive relationship with fracture risk (β= 0.11,95\%CI= 0.01 to 0.21). Colocalization analysis demonstrated common genetic signals within the B4GALNT3 locus for higher sclerostin, lower eBMD, and greater B4GALNT3 expression in arterial tissue (Probability\&gt;99\%). Our findings suggest that higher sclerostin levels are causally related to lower BMD and greater fracture risk. Hence, strategies for reducing circulating sclerostin, for example by targeting glycosylation enzymes as suggested by our GWAS results, may prove valuable in treating osteoporosis. This article is protected by copyright. All rights reserved.},
	issn = {1523-4681},
	doi = {10.1002/jbmr.3803},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jbmr.3803},
	author = {Zheng, Jie and Maerz, Winfried and Gergei, Ingrid and Kleber, Marcus and Drechsler, Christiane and Wanner, Christoph and Brandenburg, Vincent and Reppe, Sjur and Gautvik, Kaare M and Medina-Gomez, Carolina and Shevroja, Enisa and Gilly, Arthur and Park, Young-Chan and Dedoussis, George and Zeggini, Eleftheria and Lorentzon, Mattias and Henning, Petra and Lerner, Ulf H and Nilsson, Karin and Mov{\'e}rare-Skrtic, Sofia and Baird, Denis and Elsworth, Benjamin and Falk, Louise and Groom, Alix and Capellini, Terence D and Grundberg, Elin and Nethander, Maria and Ohlsson, Claes and Smith, George Davey and Tobias, Jonathan H}
}
@article {1446660,
	title = {Meta-Analysis of Genomewide Association Studies Reveals Genetic Variants for Hip Bone Geometry},
	journal = {J Bone Miner Res},
	year = {2019},
	month = {2019 Mar 19},
	pages = {e3698},
	abstract = {Hip geometry is an important predictor of fracture. We performed a meta-analysis of GWAS studies in adults to identify genetic variants that are associated with proximal femur geometry phenotypes. We analyzed four phenotypes: (i) femoral neck length; (ii) neck-shaft angle; (iii) femoral neck width, and (iv) femoral neck section modulus, estimated from DXA scans using algorithms of hip structure analysis. In the Discovery stage, 10 cohort studies were included in the fixed-effect meta-analysis, with up to 18,719 men and women ages 16 to 93 years. Association analyses were performed with \~{}2.5 million polymorphisms under an additive model adjusted for age, body mass index, and height. Replication analyses of meta-GWAS significant loci (at adjusted genomewide significance [GWS], threshold p <= 2.6 {\texttimes} 10 ) were performed in seven additional cohorts in silico. We looked up SNPs associated in our analysis, for association with height, bone mineral density (BMD), and fracture. In meta-analysis (combined Discovery and Replication stages), GWS associations were found at 5p15 (IRX1 and ADAMTS16); 5q35 near FGFR4; at 12p11 (in CCDC91); 11q13 (near LRP5 and PPP6R3 (rs7102273)). Several hip geometry signals overlapped with BMD, including LRP5 (chr. 11). Chr. 11 SNP rs7102273 was associated with any-type fracture (p = 7.5 {\texttimes} 10 ). We used bone transcriptome data and discovered several significant eQTLs, including rs7102273 and PPP6R3 expression (p = 0.0007), and rs6556301 (intergenic, chr.5 near FGFR4) and PDLIM7 expression (p = 0.005). In conclusion, we found associations between several genes and hip geometry measures that explained 12\% to 22\% of heritability at different sites. The results provide a defined set of genes related to biological pathways relevant to BMD and etiology of bone fragility. {\textcopyright} 2019 American Society for Bone and Mineral Research.},
	issn = {1523-4681},
	doi = {10.1002/jbmr.3698},
	url = {https://onlinelibrary.wiley.com/doi/full/10.1002/jbmr.3698},
	author = {Hsu, Yi-Hsiang and Estrada, Karol and Evangelou, Evangelos and Ackert-Bicknell, Cheryl and Akesson, Kristina and Beck, Thomas and Brown, Suzanne J and Capellini, Terence and Carbone, Laura and Cauley, Jane and Cheung, Ching-Lung and Cummings, Steven R and Czerwinski, Stefan and Demissie, Serkalem and Econs, Michael and Evans, Daniel and Farber, Charles and Gautvik, Kaare and Harris, Tamara and Kammerer, Candace and Kemp, John and Koller, Daniel L and Kung, Annie and Lawlor, Debbie and Lee, Miryoung and Lorentzon, Mattias and McGuigan, Fiona and Medina-Gomez, Carolina and Mitchell, Braxton and Newman, Anne and Nielson, Carrie and Ohlsson, Claes and Peacock, Munro and Reppe, Sjur and Richards, J Brent and Robbins, John and Sigurdsson, Gunnar and Spector, Timothy D and Stefansson, Kari and Streeten, Elizabeth and Styrkarsdottir, Unnur and Tobias, Jonathan and Trajanoska, Katerina and Uitterlinden, Andr{\'e} and Vandenput, Liesbeth and Wilson, Scott G and Yerges-Armstrong, Laura and Young, Mariel and Zillikens, Carola and Rivadeneira, Fernando and Kiel, Douglas P and Karasik, David}
}
@article {1446663,
	title = {Impact of broad regulatory regions on Gdf5 expression and function in knee development and susceptibility to osteoarthritis},
	journal = {Ann Rheum Dis},
	volume = {77},
	number = {3},
	year = {2018},
	month = {2018 03},
	pages = {450},
	abstract = {OBJECTIVES: Given the role of growth and differentiation factor 5 () in knee development and osteoarthritis risk, we sought to characterise knee defects resulting from loss of function and how its regulatory regions control knee formation and morphology. METHODS: The () mouse line, which harbours an inactivating mutation in , was used to survey how loss of function impacts knee morphology, while two transgenic reporter bacterial artificial chromosome mouse lines were used to assess the spatiotemporal activity and function of regulatory sequences in the context of clinically relevant knee anatomical features. RESULTS: Knees from homozygous mice () exhibit underdeveloped femoral condyles and tibial plateaus, no cruciate ligaments, and poorly developed menisci. Secondary ossification is also delayed in the distal femur and proximal tibia. mice have significantly narrower femoral condyles, femoral notches and tibial plateaus, and curvier medial femoral condyles, shallower trochlea, steeper lateral tibial slopes and smaller tibial spines. Regulatory sequences upstream from were weakly active in the prenatal knee, while downstream regulatory sequences were active throughout life. Importantly, downstream but not upstream regulatory sequences fully restored all the key morphological features disrupted in the mice. CONCLUSIONS: Knee morphology is profoundly affected by absence, and downstream regulatory sequences mediate its effects by controlling expression in knee tissues. This downstream region contains numerous enhancers harbouring human variants that span the osteoarthritis association interval. We posit that subtle alterations to morphology driven by changes in downstream regulatory sequence underlie this locus{\textquoteright} role in osteoarthritis risk.},
	keywords = {Animals, Genetic Predisposition to Disease, Growth Differentiation Factor 5, Knee Joint, Mice, Mice, Inbred BALB C, Mice, Transgenic, Mutation, Osteoarthritis, Knee, Regulatory Sequences, Nucleic Acid, Spatio-Temporal Analysis, X-Ray Microtomography},
	issn = {1468-2060},
	doi = {10.1136/annrheumdis-2017-212475},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338229/},
	author = {Pregizer, Steven K and Kiapour, Ata M and Young, Mariel and Chen, Hao and Schoor, Michael and Liu, Zun and Cao, Jiaxue and Rosen, Vicki and Capellini, Terence D}
}
@article {1446657,
	title = {A novel enhancer near the gene influences development and evolution of pelvic appendages in vertebrates},
	journal = {Elife},
	volume = {7},
	year = {2018},
	month = {2018 11 30},
	abstract = {Vertebrate pelvic reduction is a classic example of repeated evolution. Recurrent loss of pelvic appendages in sticklebacks has previously been linked to natural mutations in a pelvic enhancer that maps upstream of . The sequence of this upstream enhancer is not conserved to mammals, so we have surveyed a large region surrounding the mouse gene for other possible hind limb control sequences. Here we identify a new pelvic enhancer, , that maps downstream rather than upstream of drives expression in the posterior portion of the developing hind limb, and deleting the sequence from mice alters the size of several hind limb structures. sequences are broadly conserved from fish to mammals. A wild stickleback population lacking the pelvis has an insertion/deletion mutation that disrupts the structure and function of , suggesting that changes in this ancient enhancer contribute to evolutionary modification of pelvic appendages in nature.},
	keywords = {Animals, Base Sequence, Biological Evolution, Chromosomes, Artificial, Bacterial, Conserved Sequence, Enhancer Elements, Genetic, Fishes, Gene Expression Regulation, Developmental, Genetic Loci, Genome, Hindlimb, Lizards, Mice, Paired Box Transcription Factors, Pelvis, Sequence Deletion, Vertebrates},
	issn = {2050-084X},
	doi = {10.7554/eLife.38555},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/30499775/},
	author = {Thompson, Abbey C and Capellini, Terence D and Guenther, Catherine A and Chan, Yingguang Frank and Infante, Carlos R and Menke, Douglas B and Kingsley, David M}
}
@article {1446654,
	title = {A robust method for RNA extraction and purification from a single adult mouse tendon},
	journal = {PeerJ},
	volume = {6},
	year = {2018},
	month = {2018},
	pages = {e4664},
	abstract = {Background: Mechanistic understanding of tendon molecular and cellular biology is crucial toward furthering our abilities to design new therapies for tendon and ligament injuries and disease. Recent transcriptomic and epigenomic studies in the field have harnessed the power of mouse genetics to reveal new insights into tendon biology. However, many mouse studies pool tendon tissues or use amplification methods to perform RNA analysis, which can significantly increase the experimental costs and limit the ability to detect changes in expression of low copy transcripts. Methods: Single Achilles tendons were harvested from uninjured, contralateral injured, and wild type mice between three and five months of age, and RNA was extracted. RNA Integrity Number (RIN) and concentration were determined, and RT-qPCR gene expression analysis was performed. Results: After testing several RNA extraction approaches on single adult mouse Achilles tendons, we developed a protocol that was successful at obtaining high RIN and sufficient concentrations suitable for RNA analysis. We found that the RNA quality was sensitive to the time between tendon harvest and homogenization, and the RNA quality and concentration was dependent on the duration of homogenization. Using this method, we demonstrate that analysis of gene expression in single mouse tendons reduces the biological variation caused by pooling tendons from multiple mice. We also show successful use of this approach to analyze and gene expression changes in injured compared with uninjured control tendons. Discussion: Our work presents a robust, cost-effective, and straightforward method to extract high quality RNA from a single adult mouse Achilles tendon at sufficient amounts for RT-qPCR as well as RNA-seq. We show this can reduce variation and decrease the overall costs associated with experiments. This approach can also be applied to other skeletal tissues, as well as precious human samples.},
	issn = {2167-8359},
	doi = {10.7717/peerj.4664},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5922231/},
	author = {Grinstein, Mor and Dingwall, Heather L and Shah, Rishita R and Capellini, Terence D and Galloway, Jenna L}
}
@article {1446656,
	title = {The role of Gdf5 regulatory regions in development of hip morphology},
	journal = {PLoS One},
	volume = {13},
	number = {11},
	year = {2018},
	month = {2018},
	pages = {e0202785},
	abstract = {Given GDF5 involvement in hip development, and osteoarthritis (OA) and developmental hip dysplasia (DDH) risk, here we sought to assess the role(s) of GDF5 and its regulatory sequence on the development of hip morphology linked to injury risk. The brachypodism (bp) mouse, which harbors a Gdf5 inactivating mutation, was used to survey how Gdf5 loss of function impacts the development of hip morphology. Two transgenic Gdf5 reporter BAC lines were used to assess the spatiotemporal expression of Gdf5 regulatory sequences. Each BAC line was also used to assess the functional roles of upstream and downstream sequence on hip morphology. bp/bp mice had shorter femora with smaller femoral heads and necks as well as larger alpha angles, smaller anterior offsets, and smaller acetabula, compared to bp/+ mice (p\&lt;0.04). Regulatory sequences downstream of Gdf5 drove strong prenatal (E17) expression and low postnatal (6 months) expression across regions of femoral head and acetabulum. Conversely, upstream regulatory sequences drove very low expression at E17 and no detectable expression at 6 months. Importantly, downstream, but not upstream Gdf5 regulatory sequences fully restored all the key morphologic features disrupted in bp/bp mice. Hip morphology is profoundly affected by Gdf5 absence, and downstream regulatory sequences mediate its effects by controlling Gdf5 expression during development. This downstream region contains numerous enhancers harboring risk variants related to hip OA, DDH, and dislocation. We posit that subtle alterations to morphology driven by changes in downstream regulatory sequence underlie this locus{\textquoteright} role in hip injury risk.},
	keywords = {Animals, Gene Deletion, Gene Expression Regulation, Developmental, Growth Differentiation Factor 5, Hip, Male, Mice, Inbred BALB C, Mutation, Regulatory Sequences, Nucleic Acid},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0202785},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214493/},
	author = {Kiapour, Ata M and Cao, Jiaxue and Young, Mariel and Capellini, Terence D}
}
@article {1264656,
	title = {Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans},
	journal = {Molecular Biology and Evolution},
	volume = {Dec 6. doi: 10.1093/molbev/msx314.},
	year = {2017},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850494/},
	author = {Jagoda, Evelyn and Lawson, Daniel J and Wall, Jeffrey D and Lambert, David and Muller, Craig and Westaway, Michael and Leavesley, Matthew and Capellini, Terence D and Lahr, Marta Mirazon and Gerbault, Pascale and Thomas, Mark G and Migliano, Andrea Bamberg and Willerslev, Eske and Metspalu, Mait and Pagani, Luca}
}
@article {1264651,
	title = {Epigenetic profiling of growth plate chondrocytes sheds insight into regulatory genetic variation influencing height},
	journal = {eLife},
	volume = {Dec 5;6. pii: e29329. doi: 10.7554/eLife.29329.},
	year = {2017},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716665/},
	author = {Guo, Michael and Liu, Zun and Willen, Jessie and Shaw, Cameron P and Richard, Daniel and Jagoda, Evelyn and Doxey, Andrew C and Hirschhorn, Joel N and Capellini, Terence D}
}
@article {1107191,
	title = {Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk},
	journal = {Nature Genetics},
	volume = {49},
	number = {8},
	year = {2017},
	pages = {1202-1210},
	url = {https://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3911.html},
	author = {Capellini, TD and Chen, H and Cao, J and AC Doxey and A Kiapour and Schoor, M and Kingsley, DM}
}
@inbook {522541,
	title = {Combining genetic and developmental methods to study musculoskeletal evolution in primates},
	booktitle = {Building Bones},
	year = {2017},
	publisher = {Cambridge University Press},
	organization = {Cambridge University Press},
	author = {Capellini, TD and Dingwall, H}
}
@article {1107221,
	title = {Screening of reproduction-related single-nucleotide variations from MeDIP-seq data in sheep},
	journal = {Mol Reprod Dev},
	volume = {Nov;83},
	number = {11},
	year = {2016},
	pages = {958-967},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/27627189},
	author = {Cao, J and Wei, C and Zhang, S. and Capellini, TD and al et}
}
@article {1107216,
	title = {Dietary Variation and Evolution of Gene Copy Number among Dog Breeds},
	journal = {Plos One},
	volume = {Feb 10;11},
	number = {2},
	year = {2016},
	pages = {e0148899},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26863414},
	author = {Reiter, T and Jagoda, E and Capellini, TD}
}
@article {1107211,
	title = {Reply to Alm{\'e}cija: A new direction for reconstructing our last common ancestor with chimpanzees},
	journal = {Proc Natl Acad Sci U S A.},
	volume = {Feb 23;113},
	number = {8},
	year = {2016},
	pages = {E945},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26862164},
	author = {Young, NM and Capellini, TD and Roach, NT and Alemseged, Z.}
}
@article {1107206,
	title = {Reply to Alm{\'e}cija: A new direction for reconstructing our last common ancestor with chimpanzees},
	journal = {Proc Natl Acad Sci U S A.},
	volume = {Feb 23;113},
	number = {8},
	year = {2016},
	pages = {E945},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26862164},
	author = {Young, NM and Capellini, TD and Roach, NT and Alemseged, Z.}
}
@article {80551,
	title = {Heads, Shoulders, Elbows, Knees, and Toes: Modular Gdf5 Enhancers Control Different Joints in the Vertebrate Skeleton},
	journal = {Plos Genetics},
	volume = {Nov 30;12},
	number = {11},
	year = {2016},
	pages = {:e1006454},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/27902701},
	author = {Chen, H and Capellini, TD and Schoor, M and Mortlock, D. and Reddi, H and Kingsley, DM}
}
@inbook {80546,
	title = {Out on a limb: development and the evolution of the human appendages.},
	booktitle = {Evolutionary Developmental Anthropology},
	year = {2016},
	month = {2015},
	publisher = {Wiley Press},
	organization = {Wiley Press},
	author = {Young, N and Capellini, TD}
}
@article {1107201,
	title = {Reply to Melillo: Woranso-Mille is consistent with an australopithecine shoulder intermediate between African apes and Homo},
	journal = {Proc Natl Acad Sci U S A.},
	volume = {Dec 29;112},
	number = {52},
	year = {2015},
	pages = {E7160},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26676585},
	author = {Young, NM and Capellini, TD and Roach, NT and Alemseged, Z.}
}
@article {1107196,
	title = {DNA methylation Landscape of body size variation in sheep.},
	journal = {Scientific Reports},
	volume = {Oct 16; 5},
	year = {2015},
	pages = {13950},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26472088},
	author = {Cao, J and al et}
}
@article {522536,
	title = {Evidence from Fossil Hominin Shoulders Supports an African Ape Morphotype of the Last Common Ancestor.},
	journal = {Proc Natl Acad Sci U S A.},
	volume = {Sep 22;112},
	number = {38},
	year = {2015},
	month = {2015},
	pages = {11829-34},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26351685},
	author = {Young, N and Capellini, TD and N Roach and Alemseged, Z.}
}
@article {522531,
	title = {On the serial homology of the pectoral and pelvic girdles of tetrapods},
	journal = {Evolution.},
	volume = {Oct;69},
	number = {10},
	year = {2015},
	month = {2015},
	pages = {2543-55},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26374500},
	author = {KE Sears and Capellini, TD and R Diogo}
}
@article {522526,
	title = {A penile spine/vibrissa enhancer sequence in missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae.},
	journal = {PLoS ONE },
	volume = {8},
	number = {12},
	year = {2013},
	pages = {e84258},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/24367647},
	author = {Reno, PL and McLean, CY and Hines, JE and Capellini, TD and G Bejerano and Kingsley, DM}
}
@article {80536,
	title = {(2012) Congenital Asplenia in Mice and Humans with Mutations in a Pbx/Nkx2-5/p15 Module.},
	journal = {Developmental Cell},
	volume = {22},
	year = {2012},
	pages = {913-26},
	author = {Koss, M and Bolze, A and Brendolan, A and Saggese, M and Capellini, TD and Bojilova, E and Boisson, B and Prall, OW and Elliott, DA and Solloway, M and LentI, E and Hidaka, C and Chang, CP and Mahlaoui, N and Harvey, RP and Casanova, JL and Selleri, L}
}
@article {80531,
	title = {(2011) Pbx homeodomain proteins: TALEnted regulators of limb patterning and outgrowth. },
	journal = {Developmental Dynamics },
	volume = {240},
	year = {2011},
	pages = {1063-86},
	author = {Capellini, TD and Zappavigna, V and Selleri, L}
}
@article {80526,
	title = { (2011) Control of pelvic girdle development by genes of the Pbx family and Emx2. },
	journal = {Developmental Dynamics},
	volume = {240},
	year = {2011},
	pages = {1173-89},
	author = {Capellini, TD and Handschuh, K and Quintana, L and Ferretti, E and Di Giacomo, G and Fantini, S and Vaccari, G and Clarke, SL and Wenger, AM and Berjano, G and Sharpe, J and Zappavigna, V and Selleri, L}
}
@article {80521,
	title = {(2010) Human-specific loss of regulatory DNA and the evolution of human-specific traits. },
	journal = {Nature},
	volume = {471},
	year = {2010},
	pages = {216-9},
	author = {McLean, CY and Reno, PL and Pollen, AA and Bassan, AI and Capellini, TD and Guenther, C and Indjeian, VB and Lim, X and Menke, DB and Schaar, BT and Wenger, AM and Berjerano, G and Kingsley, DM}
}
@article {80516,
	title = {(2010) Scapula development is governed by genetic interactions of Pbx1 with its family members and with Emx2 via their cooperative control of Alx1.},
	journal = {Development},
	volume = {137},
	year = {2010},
	pages = {2259-69},
	author = {Capellini, TD and Vaccari, G and Ferretti, E and Fantini, S and He, M and Pellegrini, M and Quintana, L and Di Giacomo, G and Sharpe, J and Selleri, L and Zappavigna, V}
}
@article {80511,
	title = {(2008) Conservation of notochord gene expression across chordates: insights from the Leprecan gene family.},
	journal = {Genesis},
	volume = {46},
	year = {2008},
	pages = {683-96},
	author = {Capellini, TD and Dunn, MP and Passamaneck, YJ and Selleri, L and Di Gregorio, A}
}
@article {80506,
	title = {(2008) Pbx1/Pbx2 govern axial skeletal development by controlling Polycomb and Hox in mesoderm and Pax1/Pax9 in sclerotome.},
	journal = {Developmental Biology},
	volume = {321},
	number = {(2)},
	year = {2008},
	pages = {500-14},
	author = {Capellini, TD and Zewdu, R and Di Giacomo, G and Asciutti, S and Kugler, J and Di Gregorio, A and Selleri, L}
}
@article {80501,
	title = {(2007) Cooperation between p27 and p107 during endochondral ossification suggest a genetic pathway redundantly controlled by p27 and p130.},
	journal = {Molecular and Cellular Biology},
	volume = {27},
	number = {(14)},
	year = {2007},
	pages = {5167-71},
	author = {Yeh, N and Miller, JP and Gaur, T and Capellini, TD and Nikolich-Zugich, J and de la Hoz, C and Selleri, L and Bromage, TG and van Wijnen, AJ and Stein, GS and Lian, JB and Vidal, A and Koff, A}
}
@article {80491,
	title = {(2006) Pbx1/Pbx2 requirement for distal limb patterning is mediated by the hierarchical control of Hox spatial distribution and Shh expression.},
	journal = {Development},
	volume = {133},
	year = {2006},
	pages = {2263-73},
	author = {Capellini, TD and Di Giacomo, G and Salsi, V and Brendolan, A and Ferretti, E and Srivastava, D and Zappavigna, V and Selleri, L}
}
@article {80481,
	title = {(2006) Development and cancer: two sides of the same coin.},
	journal = {Integrative Approaches to Human Health and Evolution. Proceedings of the International Symposium {\textquotedblleft}Integrative Approaches to Human Health and Evolution{\textquotedblright} held in Madrid, Spain, between 18 and 20 April 2005},
	volume = {1296},
	year = {2006},
	pages = {147-59},
	author = {Vidal, A and Capellini, TD and Yeh, N and Selleri, L and Koff, A and Bromage, TG},
	editor = {Bromage, TG and Vidal, A and Aguirre, E and Perez-Ochoa, A}
}
@article {80476,
	title = {(2006) Spatio-temporal expression of Pbx3 during mouse organogenesis.},
	journal = {Gene Expression Patterns},
	volume = {6},
	year = {2006},
	pages = {747-57},
	author = {Di Giacomo, G and Koss, M and <strong>Capellini, TD</strong> and Brendolan, A and Popperl, H and Selleri, L}
}
@article {80471,
	title = {(2004) The TALE homeodomain protein Pbx2 is not essential for development and long-term survival.},
	journal = {Molecular and Cellular Biology },
	volume = {24},
	number = {(12)},
	year = {2004},
	pages = {5324-31},
	author = {Selleri, L and DiMartino, J and van Deursen, J and Brendolan, A and Sanyal, M and Boon, E and Capellini, TD and Smith, KS and Rhee, J and Popperl, H and Grosveld, G and Cleary, ML}
}
@article {80466,
	title = {(1997) Reconstructing the chronology of White Rocks cave using fluorine dating: a methodological overview.},
	journal = {Proceedings of the 12th Annual International Congress of speleology},
	volume = {3: Archaeology and Paleontology},
	year = {1997},
	pages = {145-49},
	author = {Capellini, TD}
}
@report {80461,
	title = { (1996) Native American human remains and mortuary artifacts. Submitted as a report for Kent State University following NAGPRA requirements and guidelines. (FEDERAL REPORT)},
	year = {1996},
	author = {Capellini, TD and Pedde, S and Ho, C and Picklesimer, J and Seeman, M}
}
