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学者姓名:杨铁林

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Integrating regulatory features data for prediction of functional disease-associated SNPs SCIE PubMed
期刊论文 | 2019 , 20 (1) , 26-32 | BRIEFINGS IN BIOINFORMATICS
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Abstract :

Genome-wide association studies (GWASs) are an effective strategy to identify susceptibility loci for human complex diseases. However, missing heritability is still a big problem. Most GWASs single-nucleotide polymorphisms (SNPs) are located in noncoding regions, which has been considered to be the unexplored territory of the genome. Recently, data from the Encyclopedia of DNA Elements (ENCODE) and Roadmap Epigenomics projects have shown that many GWASs SNPs in the noncoding regions fall within regulatory elements. In this study, we developed a pipeline named functional disease-associated SNPs prediction (FDSP), to identify novel susceptibility loci for complex diseases based on the interpretation of the functional features for known disease-associated variants with machine learning. We applied our pipeline to predict novel susceptibility SNPs for type 2 diabetes (T2D) and hypertension. The predicted SNPs could explain heritability beyond that explained by GWAS-associated SNPs. Functional annotation by expression quantitative trait loci analyses showed that the target genes of the predicted SNPs were significantly enriched in T2D or hypertension-related pathways in multiple tissues. Our results suggest that combining GWASs and regulatory features data could identify additional functional susceptibility SNPs for complex diseases. We hope FDSP could help to identify novel susceptibility loci for complex diseases and solve the missing heritability problem.

Keyword :

FDSP SNPs regulatory feature data machine learning complex diseases missing heritability

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GB/T 7714 Dong, Shan-Shan , Guo, Yan , Yao, Shi et al. Integrating regulatory features data for prediction of functional disease-associated SNPs [J]. | BRIEFINGS IN BIOINFORMATICS , 2019 , 20 (1) : 26-32 .
MLA Dong, Shan-Shan et al. "Integrating regulatory features data for prediction of functional disease-associated SNPs" . | BRIEFINGS IN BIOINFORMATICS 20 . 1 (2019) : 26-32 .
APA Dong, Shan-Shan , Guo, Yan , Yao, Shi , Chen, Yi-Xiao , He, Mo-Nan , Zhang, Yu-Jie et al. Integrating regulatory features data for prediction of functional disease-associated SNPs . | BRIEFINGS IN BIOINFORMATICS , 2019 , 20 (1) , 26-32 .
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Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia. PubMed SCIE
期刊论文 | 2019 , 9 | Translational psychiatry
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Nearly 95% of susceptibility SNPs identified by genome-wide association studies (GWASs) are located in non-coding regions, which causes a lot of difficulty in deciphering their biological functions on disease pathogenesis. Here, we aimed to conduct a comprehensive functional annotation for all the schizophrenia susceptibility loci obtained from GWASs. Considering varieties of epigenomic regulatory elements, we annotated all 22,688 acquired susceptibility SNPs according to their genomic positions to obtain functional SNPs. The comprehensive annotation indicated that these functional SNPs are broadly involved in diverse biological processes. Histone modification enrichment showed that H3K27ac, H3K36me3, H3K4me1, and H3K4me3 were related to the development of schizophrenia. Transcription factors (TFs) prediction, methylation quantitative trait loci (meQTL) analyses, expression quantitative trait loci (eQTL) analyses, and proteomic quantitative trait loci analyses (pQTL) identified 447 target protein-coding genes. Subsequently, differential expression analyses between schizophrenia cases and controls, nervous system phenotypes from mouse models, and protein-protein interaction with known schizophrenia-related pathways and genes were carried out with our target genes. We finaly prioritized 10 target genes for schizophrenia (CACNA1C, CLU, CSNK2B, GABBR1, GRIN2A, MAPK3, NOTCH4, SRR, TNF, and SYNGAP1). Our results may serve as an encyclopedia of schizophrenia susceptibility SNPs and offer holistic guides for post-GWAS functional experiments.

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GB/T 7714 Niu Hui-Min , Yang Ping , Chen Huan-Huan et al. Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia. [J]. | Translational psychiatry , 2019 , 9 .
MLA Niu Hui-Min et al. "Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia." . | Translational psychiatry 9 (2019) .
APA Niu Hui-Min , Yang Ping , Chen Huan-Huan , Hao Ruo-Han , Dong Shan-Shan , Yao Shi et al. Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia. . | Translational psychiatry , 2019 , 9 .
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Genetic polymorphisms of estrogen receptor genes are associated with breast cancer susceptibility in Chinese women SCIE PubMed
期刊论文 | 2019 , 19 | CANCER CELL INTERNATIONAL
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BackgroundEstrogen exposure is a widely known risk factor for BC. And the interaction of estrogen with estrogen receptor (ER) plays an important role in breast cancer development. This case-control study aims to assess the association of genetic polymorphisms in the estrogen receptor genes with breast cancer (BC) susceptibility in Chinese Han women.MethodsFour polymorphisms (rs2881766, rs9383951, rs9340799 in ESR1 and rs3020449 in ESR2) were genotyped in 459 patients and 549 healthy controls using the Sequenom MassARRAY method. Odds ratio (OR) and 95% confidence intervals (95% CI) were calculated to evaluate the associations. False-positive report probability (FPRP) was utilized to examine the noteworthiness of significant findings.ResultsWe observed that rs2881766 was associated with a decreased BC risk (GG vs. TT: OR=0.63, 95% CI=0.44-0.91; GG vs. TT/GT: OR=0.68, 95% CI=0.49-0.95), while rs3020449 was associated with an increased risk of BC (CT vs. TT: OR=1.58, 95% CI=1.21-2.06; CT/CC vs. TT: OR=1.54, 95% CI=1.20-1.98; TT/CC vs. CT: OR=1.48, 95% CI=1.15-1.90). The other two polymorphisms have no relation with BC susceptibility. In addition, rs2881766 was correlated with lymph node metastasis and ER expression, and rs3020449 was related to tumor size, histological grade and ER expression. The values of false-positive report probability indicated that the significant associations of BC risk with both rs2881766 and rs3020449 were noteworthy.ConclusionsOur study suggests that polymorphisms rs2881766 and rs3020449 in estrogen receptor genes were associated with BC susceptibility as well as clinical features in Chinese women. These findings need further validation in a large population.

Keyword :

Polymorphism Breast cancer Estrogen receptor genes Susceptibility

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GB/T 7714 Dai, Zhijun , Tian, Tian , Wang, Meng et al. Genetic polymorphisms of estrogen receptor genes are associated with breast cancer susceptibility in Chinese women [J]. | CANCER CELL INTERNATIONAL , 2019 , 19 .
MLA Dai, Zhijun et al. "Genetic polymorphisms of estrogen receptor genes are associated with breast cancer susceptibility in Chinese women" . | CANCER CELL INTERNATIONAL 19 (2019) .
APA Dai, Zhijun , Tian, Tian , Wang, Meng , Yang, Tielin , Li, Hongtao , Lin, Shuai et al. Genetic polymorphisms of estrogen receptor genes are associated with breast cancer susceptibility in Chinese women . | CANCER CELL INTERNATIONAL , 2019 , 19 .
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PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. PubMed
期刊论文 | 2018 | Bioinformatics
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Abstract :

Linkage disequilibrium (LD) decay is of great interest in population genetic studies. However, no tool is available now to do LD decay analysis from variant call format (VCF) files directly. In addition, generation of pair-wise LD measurements for whole genome SNPs usually resulting in large storage wasting files.We developed PopLDdecay, an open source software, for LD decay analysis from VCF files. It is fast and is able to handle large number of variants from sequencing data. It is also storage saving by avoiding exporting pair-wise results of LD measurements. Subgroup analyses are also supported.PopLDdecay is freely available at https://github.com/BGI-shenzhen/PopLDdecay.

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GB/T 7714 Zhang Chi , Dong Shan-Shan , Xu Jun-Yang et al. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. [J]. | Bioinformatics , 2018 .
MLA Zhang Chi et al. "PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files." . | Bioinformatics (2018) .
APA Zhang Chi , Dong Shan-Shan , Xu Jun-Yang , He Wei-Ming , Yang Tie-Lin . PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. . | Bioinformatics , 2018 .
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Gene expression profiles indicate tissue-specific obesity regulation changes and strong obesity relevant tissues SCIE PubMed Scopus
期刊论文 | 2018 , 42 (3) , 363-369 | INTERNATIONAL JOURNAL OF OBESITY
WoS CC Cited Count: 1 SCOPUS Cited Count: 2
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BACKGROUND: With the growing evidence that other tissues, apart from adipose, could have strong relevance to obesity, it is necessary to comprehensively understand the relationship between obesity and other tissues, and to point out the most relevant tissues. METHODS: There were 549 participants with 20 different tissue types involved in this study. We firstly employed both Spearman's correlation test and WGCNA (weighted correlation network analysis) to identify body mass index (BMI)-related genes. Subsequently, we performed enrichment analyses with obesity genes and pathways to see the different regulation patterns among tissues. In addition, we compared obesity genes identified by genome-wide association studies (GWAS) with BMI-related genes to find the overlapping proportion in each tissue. Finally, we integrated preceding results to identify six strong obesity relevant tissues and indicate three categories to represent different obesity relevant tissues. RESULTS: Statistical analyses revealed diverse BMI-related genes and tissue-specific enrichment patterns among tissues. Comparison between BMI-related genes and GWAS findings showed tissue-specific expression changes of GWAS genes. Ultimately, six tissues that showed predominant performance in enrichment analyses and significantly embraced GWAS genes were referred to as strong obesity relevant tissues, including adipose, esophagus, nerve, pancreas, pituitary and skin. We also proposed three categories to represent different obesity relevant tissues. CONCLUSIONS: We performed the first study to investigate the BMI-related gene expression changes across 20 tissues at the same time. With valid data analyses and comparison with GWAS findings, our study provides a holistic view of how different tissues correlate with obesity, and proposes target tissues for obesity pathogenesis investigation.

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GB/T 7714 Hao, R-H , Yang, T-L , Rong, Y. et al. Gene expression profiles indicate tissue-specific obesity regulation changes and strong obesity relevant tissues [J]. | INTERNATIONAL JOURNAL OF OBESITY , 2018 , 42 (3) : 363-369 .
MLA Hao, R-H et al. "Gene expression profiles indicate tissue-specific obesity regulation changes and strong obesity relevant tissues" . | INTERNATIONAL JOURNAL OF OBESITY 42 . 3 (2018) : 363-369 .
APA Hao, R-H , Yang, T-L , Rong, Y. , Yao, S. , Dong, S-S , Chen, H. et al. Gene expression profiles indicate tissue-specific obesity regulation changes and strong obesity relevant tissues . | INTERNATIONAL JOURNAL OF OBESITY , 2018 , 42 (3) , 363-369 .
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An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation SCIE PubMed Scopus
期刊论文 | 2018 , 102 (5) , 776-793 | AMERICAN JOURNAL OF HUMAN GENETICS
WoS CC Cited Count: 1
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Genome-wide association studies (GWASs) have reproducibly associated variants within intergenic regions of 1p36.12 locus with osteoporosis, but the functional roles underlying these noncoding variants are unknown. Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/ Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339) (similar to 360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.

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GB/T 7714 Chen, Xiao-Feng , Zhu, Dong-Li , Yang, Man et al. An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation [J]. | AMERICAN JOURNAL OF HUMAN GENETICS , 2018 , 102 (5) : 776-793 .
MLA Chen, Xiao-Feng et al. "An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation" . | AMERICAN JOURNAL OF HUMAN GENETICS 102 . 5 (2018) : 776-793 .
APA Chen, Xiao-Feng , Zhu, Dong-Li , Yang, Man , Hu, Wei-Xin , Duan, Yuan-Yuan , Lu, Bing-Jie et al. An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation . | AMERICAN JOURNAL OF HUMAN GENETICS , 2018 , 102 (5) , 776-793 .
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Matrine suppresses cardiac fibrosis by inhibiting the TGF-/Smad pathway in experimental diabetic cardiomyopathy SCIE PubMed Scopus
期刊论文 | 2018 , 17 (1) , 1775-1781 | MOLECULAR MEDICINE REPORTS
WoS CC Cited Count: 5 SCOPUS Cited Count: 3
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Cardiac fibrosis is one of the pathological characteristics of diabetic cardiomyopathy (DbCM). Matrine treatment has proven to be effective in cases of organ fibrosis and cardiovascular diseases. In the present study, the anti-fibrosis-associated cardioprotective effects of matrine on DbCM were investigated. Rats with experimental DbCM were administered matrine orally. Cardiac functions were evaluated using invasive hemodynamic examinations. Cardiac compliance was assessed in isolated hearts. Using Sirius Red and fluorescence staining, the collagen in diabetic hearts was visualized. MTT assay was used to select non-cytotoxic concentrations of matrine, which were subsequently used to treat isolated cardiac fibroblasts incubated under various conditions. Western blotting was performed to assess activation of the transforming growth factor-1 (TGF-1)/Smad signaling pathway. Rats with DbCM exhibited impaired heart compliance and left ventricular (LV) functions. Excessive collagen deposition in cardiac tissue was also observed. Furthermore, TGF-1/R-Smad (Smad2/3) signaling was revealed to be markedly activated; however, the expression of inhibitory Smad (I-Smad, also termed Smad7) was reduced in DbCM. Matrine administration led to a marked recovery in LV function and heart compliance by exerting inhibitory effects on TGF-1/R-Smad signaling pathway-induced fibrosis without affecting I-Smad. Incubation with a high concentration of glucose triggered the TGF-1/R-Smad (Smad2/3) signaling pathway and suppressed I-Smad signaling transduction in cultured cardiac fibroblasts, which led to an increase in the synthesis of collagen. After cardiac fibroblasts had been treated with matrine at non-cytotoxic concentrations without affecting I-Smad, matrine blocked TGF-1/R-Smad signaling transduction to repress collagen production and deposition. In conclusion, the results of the present study demonstrated that TGF-1/Smad signaling-associated cardiac fibrosis is involved in the impairment of heart compliance and LV dysfunction in DbCM. By exerting therapeutic effects against cardiac fibrosis via its influence on TGF-1/Smad signaling, matrine exhibited cardioprotective effects in DbCM.

Keyword :

matrine transforming growth factor-1 diabetic cardiomyopathy Smads fibrosis cardiac fibroblasts

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GB/T 7714 Zhang, Yong , Cui, Lei , Guan, Gongchang et al. Matrine suppresses cardiac fibrosis by inhibiting the TGF-/Smad pathway in experimental diabetic cardiomyopathy [J]. | MOLECULAR MEDICINE REPORTS , 2018 , 17 (1) : 1775-1781 .
MLA Zhang, Yong et al. "Matrine suppresses cardiac fibrosis by inhibiting the TGF-/Smad pathway in experimental diabetic cardiomyopathy" . | MOLECULAR MEDICINE REPORTS 17 . 1 (2018) : 1775-1781 .
APA Zhang, Yong , Cui, Lei , Guan, Gongchang , Wang, Junkui , Qiu, Chuan , Yang, Tielin et al. Matrine suppresses cardiac fibrosis by inhibiting the TGF-/Smad pathway in experimental diabetic cardiomyopathy . | MOLECULAR MEDICINE REPORTS , 2018 , 17 (1) , 1775-1781 .
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Runs of homozygosity associate with decreased risks of lung cancer in never-smoking East Asian females Scopus SCIE PubMed
期刊论文 | 2018 , 9 (21) , 3858-3866 | Journal of Cancer
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© Ivyspring International Publisher. Although genome-wide association studies (GWASs) have identified some risk single-nucleotide polymorphisms in East Asian never-smoking females, the unexplained missing heritability is still required to be investigated. Runs of homozygosity (ROHs) are thought to be a type of genetic variation acting on human complex traits and diseases. We detected ROHs in 8,881 East Asian never-smoking women. The summed ROHs were used to fit a logistic regression model which noteworthily revealed a significant association between ROHs and the decreased risk of lung cancer (P < 0.05). We identified 4 common ROHs regions located at 2p22.1, which were significantly associated with decreased risk of lung cancer (P = 2.00 × 10-4 - 1.35 × 10-4). Functional annotation was conducted to investigate the regulatory function of ROHs. The common ROHs were overlapped with potential regulatory elements, such as active epigenome elements and chromatin states in lung-derived cell lines. SOS1 and ARHGEF33 were significantly up-regulated as the putative target genes of the identified ROHs in lung cancer samples according to the analysis of differently expressed genes. Our results suggest that ROHs could act as recessive contributing factors and regulatory elements to influence the risk of lung cancer in never-smoking East Asian females.

Keyword :

Genetic risk factors GWASs Lung cancer Regulatory elements Runs of homozygosity

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GB/T 7714 Chen, Yi-Xiao , Guo, Yan , Dong, Shan-Shan et al. Runs of homozygosity associate with decreased risks of lung cancer in never-smoking East Asian females [J]. | Journal of Cancer , 2018 , 9 (21) : 3858-3866 .
MLA Chen, Yi-Xiao et al. "Runs of homozygosity associate with decreased risks of lung cancer in never-smoking East Asian females" . | Journal of Cancer 9 . 21 (2018) : 3858-3866 .
APA Chen, Yi-Xiao , Guo, Yan , Dong, Shan-Shan , Chen, Xiao-Feng , Chen, Jia-Bin , Zhang, Yu-Jie et al. Runs of homozygosity associate with decreased risks of lung cancer in never-smoking East Asian females . | Journal of Cancer , 2018 , 9 (21) , 3858-3866 .
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ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma SCIE PubMed Scopus
期刊论文 | 2018 , 9 | NATURE COMMUNICATIONS
WoS CC Cited Count: 6 SCOPUS Cited Count: 6
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In human mutant BRAF melanoma cells, the stemness transcription factor FOXD3 is rapidly induced by inhibition of ERK1/2 signaling and mediates adaptive resistance to RAF inhibitors. However, the mechanism underlying ERK signaling control of FOXD3 expression remains unknown. Here we show that SOX10 is both necessary and sufficient for RAF inhibitor-induced expression of FOXD3 in mutant BRAF melanoma cells. SOX10 activates the transcription of FOXD3 by binding to a regulatory element in FOXD3 promoter. Phosphorylation of SOX10 by ERK inhibits its transcription activity toward multiple target genes by interfering with the sumoylation of SOX10 at K55, which is essential for its transcription activity. Finally, depletion of SOX10 sensitizes mutant BRAF melanoma cells to RAF inhibitors in vitro and in vivo. Thus, our work discovers a novel phosphorylation-dependent regulatory mechanism of SOX10 transcription activity and completes an ERK1/2/SOX10/FOXD3/ERBB3 axis that mediates adaptive resistance to RAF inhibitors in mutant BRAF melanoma cells.

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GB/T 7714 Han, Shujun , Ren, Yibo , He, Wangxiao et al. ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma [J]. | NATURE COMMUNICATIONS , 2018 , 9 .
MLA Han, Shujun et al. "ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma" . | NATURE COMMUNICATIONS 9 (2018) .
APA Han, Shujun , Ren, Yibo , He, Wangxiao , Liu, Huadong , Zhi, Zhe , Zhu, Xinliang et al. ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma . | NATURE COMMUNICATIONS , 2018 , 9 .
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V-ATPases and osteoclasts: ambiguous future of V-ATPases inhibitors in osteoporosis SCIE PubMed
期刊论文 | 2018 , 8 (19) , 5379-5399 | THERANOSTICS
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Vacuolar ATPases (V-ATPases) play a critical role in regulating extracellular acidification of osteoclasts and bone resorption. The deficiencies of subunit a3 and d2 of V-ATPases result in increased bone density in humans and mice. One of the traditional drug design strategies in treating osteoporosis is the use of subunit a3 inhibitor. Recent findings connect subunits H and G1 with decreased bone density. Given the controversial effects of ATPase subunits on bone density, there is a critical need to review the subunits of V-ATPase in osteoclasts and their functions in regulating osteoclasts and bone remodeling. In this review, we comprehensively address the following areas: information about all V-ATPase subunits and their isoforms; summary of V-ATPase subunits associated with human genetic diseases; V-ATPase subunits and osteopetrosis/osteoporosis; screening of all V-ATPase subunits variants in GEFOS data and in-house data; spectrum of V-ATPase subunits during osteoclastogenesis; direct and indirect roles of subunits of V-ATPases in osteoclasts; V-ATPase-associated signaling pathways in osteoclasts; interactions among V-ATPase subunits in osteoclasts; osteoclast-specific V-ATPase inhibitors; perspective of future inhibitors or activators targeting V-ATPase subunits in the treatment of osteoporosis.

Keyword :

osteoclasts osteopetrosis signaling pathways pH inhibitor V-ATPase osteoporosis

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GB/T 7714 Duan, Xiaohong , Yang, Shaoqing , Zhang, Lei et al. V-ATPases and osteoclasts: ambiguous future of V-ATPases inhibitors in osteoporosis [J]. | THERANOSTICS , 2018 , 8 (19) : 5379-5399 .
MLA Duan, Xiaohong et al. "V-ATPases and osteoclasts: ambiguous future of V-ATPases inhibitors in osteoporosis" . | THERANOSTICS 8 . 19 (2018) : 5379-5399 .
APA Duan, Xiaohong , Yang, Shaoqing , Zhang, Lei , Yang, Tielin . V-ATPases and osteoclasts: ambiguous future of V-ATPases inhibitors in osteoporosis . | THERANOSTICS , 2018 , 8 (19) , 5379-5399 .
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