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Mining the Selective Remodeling of DNA Methylation in Promoter Regions to Identify Robust Gene-Level Associations With Phenotype

Yuan Quan, Fengji Liang, Si-Min Deng, Yuexing Zhu, Ying Chen, Jianghui Xiong,

Epigenetics is an essential biological frontier linking genetics to the environment, where DNA methylation is one of the most studied epigenetic events. In recent years, through the epigenome-wide association study (EWAS), researchers have identified thousands of phenotype-related methylation sites. However, the overlaps of identified phenotype-related DNA methylation sites between various ... Read more >>

Front Mol Biosci (Frontiers in molecular biosciences)
[2021, 8:]

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Mining the Selective Remodeling of DNA Methylation in Promoter Regions to Identify Robust Gene-Level Associations With Phenotype.

Yuan Quan, Fengji Liang, Si-Min Deng, Yuexing Zhu, Ying Chen, Jianghui Xiong,

Epigenetics is an essential biological frontier linking genetics to the environment, where DNA methylation is one of the most studied epigenetic events. In recent years, through the epigenome-wide association study (EWAS), researchers have identified thousands of phenotype-related methylation sites. However, the overlaps of identified phenotype-related DNA methylation sites between various ... Read more >>

Front Mol Biosci (Frontiers in molecular biosciences)
[2021, 8:597513]

Cited: 2 times

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Blood Cell DNA Methylation of Aging-Related Ubiquitination Gene DZIP3 Can Predict the Onset of Early Stage Colorectal Cancer.

Yuan Quan, Fengji Liang, Deqing Wu, Xueqing Yao, Zhihuang Hu, Yuexing Zhu, Ying Chen, Andong Wu, Danian Tang, Bingyang Huang, Ruifeng Xu, Zejian Lyu, Qian Yan, Lang Luo, Zhengzhi Ning, Yong Li, Jianghui Xiong,

There is a body of evidence that the aging immune system is linked to cancer. In this study, with aging- and immune-related DNA methylation data, we investigated the DNA methylation regulation changes in promoters with other regions of genes during aging and their association with the immune-cell proportion in the ... Read more >>

Front Oncol (Frontiers in oncology)
[2020, 10:544330]

Cited: 2 times

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Ten days of complete fasting affected subjective sensations but not cognitive abilities in healthy adults.

Chao Yang, Qianying Ma, Hongyu Zhang, Feng Wu, Manrui Wu, Chengjia Yang, Ying Chen, Jianghui Xiong, Wenjuan Liu, Hailong Wang, Ruilin Wu, Zhongquan Dai, Yinghui Li,

<h4>Purpose</h4>People may be unable to obtain anything edible for days under some circumstances, but they must maintain their calmness and cognition to navigate solutions. Our aim was to study changes in subjective sensations and cognition in healthy adults during a 10-day complete fasting experiment.<h4>Methods</h4>Thirteen healthy male volunteers voluntarily participated in ... Read more >>

Eur J Nutr (European journal of nutrition)
[2021, 60(5):2747-2758]

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Time series analysis of microbiome and metabolome at multiple body sites in steady long-term isolation confinement.

Qiang Feng, Xiang Lan, Xiaoli Ji, Meihui Li, Shili Liu, Jianghui Xiong, Yanbo Yu, Zhipeng Liu, Zi Xu, Li He, Ying Chen, Haisheng Dong, Pu Chen, Bin Chen, Kunlun He, Yinghui Li,

Gut (Gut)
[2021, 70(7):1409-1412]

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Mining the Selective Remodeling of DNA Methylation in Promoter Regions to Identify Robust Gene-Level Associations with Phenotype

Yuan Quan, Fengji Liang, Yuexing Zhu, Ying Chen, Ruifeng Xu, Jianghui Xiong,

Epigenetics is an essential biological frontier linking genetics to the environment, where DNA methylation is one of the most studied epigenetic events. In recent years, through the epigenome-wide association study (EWAS), researchers have identified thousands of phenotype-related methylation sites. However, the overlap between identified phenotype-related DNA methylation sites are often ... Read more >>

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Physiological Acclimatization of the Liver to 180-Day Isolation and the Mars Solar Day.

Hailong Chen, Ke Lv, Guohua Ji, Yanhong Yuan, Liang Lu, Fengji Liang, Kai Li, Zi Xu, Jianghui Xiong, Lina Qu, Yinghui Li,

Physiological changes in humans are evident under environmental conditions similar to those on a Mars mission involving both a space factor (long-term isolation) and a time factor (the Mars solar day). However, very few studies have investigated the response of the liver to those conditions. Serum protein levels, bilirubin levels, ... Read more >>

Biomed Res Int (BioMed research international)
[2020, 2020:2796510]

Cited: 1 time

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Insulin-resistance and depression cohort data mining to identify nutraceutical related DNA methylation biomarker for type 2 diabetes.

Fengji Liang, Yuan Quan, Andong Wu, Ying Chen, Ruifeng Xu, Yuexing Zhu, Jianghui Xiong,

Insulin-resistance (IR) is one of the most important precursors of type 2 diabetes (T2D). Recent evidence suggests an association of depression with the onset of T2D. Accumulating evidence shows that depression and T2D share common biological origins, and DNA methylation examination might reveal the link between lifestyle, disease risk, and ... Read more >>

Genes Dis (Genes & diseases)
[2021, 8(5):669-676]

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Aging immune system-related blood cell DNA methylation can predict the onset of early stage colorectal cancer

Yuan Quan, Fengji Liang, Deqing Wu, Xueqing Yao, Yuexing Zhu, Ying Chen, Andong Wu, Danian Tang, Bingyang Huang, Ruifeng Xu, Zejian Lyu, Qian Yan, Zhengzhi Ning, Yong Li, Jianghui Xiong,

<h4>Objective</h4> There is a body of evidence that the aging immune system is linked to cancer. Here, we hypothesized that ubiquitination might play a key gatekeeper role in immune system aging and tumorigenesis in CRC. Therefore, we will systematically study the DNA methylation of ubiquitination genes and screen candidate CRC ... Read more >>

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Personalized Epigenome Remodeling Under Biochemical and Psychological Changes During Long-Term Isolation Environment.

Fengji Liang, Ke Lv, Yue Wang, Yanhong Yuan, Liang Lu, Qiang Feng, Xiaolu Jing, Honghui Wang, Changning Liu, Simon Rayner, Shukuan Ling, Hailong Chen, Yumin Wan, Wanlong Zhou, Li He, Bin Wu, Lina Qu, Shanguang Chen, Jianghui Xiong, Yinghui Li,

It has been reported that several aspects of human health could be disturbed during a long-term isolated environment (for instance, the Mars-500 mission), including psychiatric disorders, circadian disruption, temporal dynamics of gut microbiota, immune responses, and physical-activity-related neuromuscular performance. Nevertheless, the mechanisms underlying these disturbances and the interactions among different ... Read more >>

Front Physiol (Frontiers in physiology)
[2019, 10:932]

Cited: 3 times

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DNA Methylation Biomarkers Predict Objective Responses to PD-1/PD-L1 Inhibition Blockade.

Gang Xue, Ze-Jia Cui, Xiong-Hui Zhou, Yue-Xing Zhu, Ying Chen, Feng-Ji Liang, Da-Nian Tang, Bing-Yang Huang, Hong-Yu Zhang, Zhi-Huang Hu, Xi-Yu Yuan, Jianghui Xiong,

Immune checkpoint inhibitor (ICI) treatment could bring long-lasting clinical benefits to patients with metastatic cancer. However, only a small proportion of patients respond to PD-1/PD-L1 blockade, so predictive biomarkers are needed. Here, based on DNA methylation profiles and the objective response rates (ORRs) of PD-1/PD-L1 inhibition therapy, we identified 269 ... Read more >>

Front Genet (Frontiers in genetics)
[2019, 10:724]

Cited: 5 times

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Integrated Analysis of DNA Methylation and Biochemical/Metabolic Parameter During the Long-Term Isolation Environment.

Yuan Quan, Fengji Liang, Yuexing Zhu, Ying Chen, Zi Xu, Fang Du, Ke Lv, Hailong Chen, Lina Qu, Ruifeng Xu, Hong-Yu Zhang, Jianghui Xiong, Yinghui Li,

Numerous studies have shown that changes in the epigenome are an important cause of human biochemical or metabolic parameter changes. Biochemical/metabolic parameter disorders of the human body are usually closely related to the occurrence of disease. Therefore, constructing credible DNA methylation site-biochemical/metabolic parameter associations are key in interpreting the pathogenesis ... Read more >>

Front Physiol (Frontiers in physiology)
[2019, 10:917]

Cited: 1 time

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Circulating microRNAs Correlated with Bone Loss Induced by 45 Days of Bed Rest.

Shukuan Ling, Guohui Zhong, Weijia Sun, Fengji Liang, Feng Wu, Hongxing Li, Yuheng Li, Dingsheng Zhao, Jinping Song, Xiaoyan Jin, Xiaorui Wu, Hailin Song, Qi Li, Yinghui Li, Shanguang Chen, Jianghui Xiong, Yingxian Li,

The purpose of this study was to find the circulating microRNAs (miRNAs) co-related with bone loss induced by bed rest, and testify whether the selected miRNAs could reflect the bone mineral status of human after bed-rest. We analyzed plasma miRNA levels of 16 subjects after 45 days of -6° head-down ... Read more >>

Front Physiol (Frontiers in physiology)
[2017, 8:69]

Cited: 5 times

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Functional constraints on adaptive evolution of protein ubiquitination sites.

Liang Lu, Yang Li, Zhongyang Liu, Fengji Liang, Feifei Guo, Shuai Yang, Dan Wang, Yangzhige He, Jianghui Xiong, Dong Li, Fuchu He,

It is still unclear whether there exist functional constraints on the evolution of protein ubiquitination sites, because most previous studies regarded all protein ubiquitination sites as a whole or only focused on limited structural properties. We tried to clarify the relation between functional constraints and ubiquitination sites evolution. We investigated ... Read more >>

Sci Rep (Scientific reports)
[2017, 7:39949]

Cited: 2 times

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Activation of HIF-1α and its downstream targets in rat hippocampus after long-term simulated microgravity exposure.

Tingmei Wang, Hailong Chen, Ke Lv, Guohua Ji, Fengji Liang, Yongliang Zhang, Yanli Wang, Xinmin Liu, Hongqing Cao, Guanghan Kan, Jianghui Xiong, Yinghui Li, Lina Qu,

Microgravity has many detrimental impact on brain functions, however the underlying mechanism remain unclear. In present study, 28 days of tail-suspension (30°) was used to simulate microgravity in rats. We showed that oxidative stress in hippocampus was increased after 28 days of simulated microgravity in consideration of the decreased expression ... Read more >>

Biochem Biophys Res Commun (Biochemical and biophysical research communications)
[2017, 485(3):591-597]

Cited: 4 times

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Comparison of the Prognostic Utility of the Diverse Molecular Data among lncRNA, DNA Methylation, microRNA, and mRNA across Five Human Cancers.

Li Xu, Liang Fengji, Liu Changning, Zhang Liangcai, Li Yinghui, Li Yu, Chen Shanguang, Xiong Jianghui,

<h4>Introduction</h4>Advances in high-throughput technologies have generated diverse informative molecular markers for cancer outcome prediction. Long non-coding RNA (lncRNA) and DNA methylation as new classes of promising markers are emerging as key molecules in human cancers; however, the prognostic utility of such diverse molecular data remains to be explored.<h4>Materials and methods</h4>We ... Read more >>

PLoS One (PloS one)
[2015, 10(11):e0142433]

Cited: 7 times

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Correction: Comparison of the Prognostic Utility of Diverse Molecular Data among lncRNA, DNA Methylation, microRNA and mRNA across Five Human Cancers.

Li Xu, Liang Fengji, Liu Changning, Zhang Liangcai, Li Yinghui, Li Yu, Chen Shanguang, Xiong Jianghui,

PLoS One (PloS one)
[2016, 11(3):e0152631]

Cited: 0 times

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Predicting response to preoperative chemotherapy agents by identifying drug action on modeled microRNA regulation networks.

Lida Zhu, Juan Liu, Fengji Liang, Simon Rayner, Jianghui Xiong,

Identifying patients most responsive to specific chemotherapy agents in neoadjuvant settings can help to maximize the benefits of treatment and minimize unnecessary side effects. Metagene approaches that predict response based on gene expression signatures derived from an associative analysis of clinical data can identify chance associations caused by the heterogeneity ... Read more >>

PLoS One (PloS one)
[2014, 9(5):e98140]

Cited: 2 times

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Ensemble classifier based on context specific miRNA regulation modules: a new method for cancer outcome prediction.

Xionghui Zhou, Juan Liu, Xinghuo Ye, Wei Wang, Jianghui Xiong,

<h4>Background</h4>Many classifiers which are constructed with chosen gene markers have been proposed to forecast the prognosis of patients who suffer from breast cancer. However, few of them has been applied in clinical practice because of the bad generalization, which results from the situation that markers selected by one method are ... Read more >>

BMC Bioinformatics (BMC bioinformatics)
[2013, 14 Suppl 12:S6]

Cited: 3 times

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Pre-clinical drug prioritization via prognosis-guided genetic interaction networks.

Jianghui Xiong, Juan Liu, Simon Rayner, Ze Tian, Yinghui Li, Shanguang Chen,

The high rates of failure in oncology drug clinical trials highlight the problems of using pre-clinical data to predict the clinical effects of drugs. Patient population heterogeneity and unpredictable physiology complicate pre-clinical cancer modeling efforts. We hypothesize that gene networks associated with cancer outcome in heterogeneous patient populations could serve ... Read more >>

PLoS One (PloS one)
[2010, 5(11):e13937]

Cited: 6 times

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Protective effects of flavonoids against oxidative stress induced by simulated microgravity in SH-SY5Y cells.

Lina Qu, Hailong Chen, Xinmin Liu, Lei Bi, Jianghui Xiong, Zebin Mao, Yinghui Li,

Many lines of evidence suggest that microgravity results in increased oxidative stress in the nervous system. In order to protect neuronal cells from oxidative damage induced by microgravity, we selected some flavonoids that might prevent oxidative stress because of their antioxidant activities. Among the 20 flavonoids we examined, we found ... Read more >>

Neurochem Res (Neurochemical research)
[2010, 35(9):1445-1454]

Cited: 19 times

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Protein-protein interaction reveals synergistic discrimination of cancer phenotype.

Jianghui Xiong, Juan Liu, Simon Rayner, Yinghui Li, Shanguang Chen,

Cancer is a disease associated with the deregulation of multiple gene networks. Microarray data has permitted researchers to identify gene panel markers for diagnosis or prognosis of cancer but these are not sufficient to make specific mechanistic assertions about phenotype switches. We propose a strategy to identify putative mechanisms of ... Read more >>

Cancer Inform (Cancer informatics)
[2010, 9:61-66]

Cited: 6 times

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Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration.

Jianghui Xiong, Simon Rayner, Kunyi Luo, Yinghui Li, Shanguang Chen,

<h4>Background</h4>The automation of many common molecular biology techniques has resulted in the accumulation of vast quantities of experimental data. One of the major challenges now facing researchers is how to process this data to yield useful information about a biological system (e.g. knowledge of genes and their products, and the ... Read more >>

BMC Bioinformatics (BMC bioinformatics)
[2006, 7:268]

Cited: 12 times

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Effects of simulated microgravity on nitric oxide level in cardiac myocytes and its mechanism.

Jianghui Xiong, Yinghui Li, Jielin Nie,

The depression of cardiac contractility induced by space microgravity is an important issue of aerospace medicine research, while its precise mechanism is still unknown. In the present study, we explored effects of simulated microgravity on nitric oxide (NO) level, inducible nitric oxide synthase (iNOS) expression and related regulative mechanism using ... Read more >>

Sci China C Life Sci (Science in China. Series C, Life sciences)
[2003, 46(3):302-309]

Cited: 4 times

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