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Jiang, Peng

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Jiang, Peng
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    MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes
    (BioMed Central, 2014) Zheng, Xiaoqi; Zhao, Qian; Wu, Hua-Jun; Li, Wei; Wang, Haiyun; Meyer, Clifford; Qin, Qian Alvin; Xu, Han; Zang, Chongzhi; Jiang, Peng; Li, Fuqiang; Hou, Yong; He, Jianxing; Wang, Jun; Zhang, Peng; Zhang, Yong; Liu, Xiaole
    We propose a statistical algorithm MethylPurify that uses regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples alone. MethylPurify can identify differentially methylated regions (DMRs) from individual tumor methylome samples, without genomic variation information or prior knowledge from other datasets. In simulations with mixed bisulfite reads from cancer and normal cell lines, MethylPurify correctly inferred tumor purity and identified over 96% of the DMRs. From patient data, MethylPurify gave satisfactory DMR calls from tumor methylome samples alone, and revealed potential missed DMRs by tumor to normal comparison due to tumor heterogeneity. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0419-x) contains supplementary material, which is available to authorized users.
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    Inference of transcriptional regulation in cancers
    (Proceedings of the National Academy of Sciences, 2015) Jiang, Peng; Freedman, Matthew; Liu, Jun; Liu, Xiaole
    We developed an efficient and accurate computational framework, RABIT (regression analysis with background integration), and comprehensively integrated public transcription factor (TF)-binding profiles with TCGA tumor-profiling datasets in 18 cancer types. To systematically search for cancer-associated TFs, RABIT controls the effect of tumor-confounding factors on transcriptional regulation, such as copy number alteration, DNA methylation, and TF somatic mutation. Our predicted TF regulatory activity in tumors is highly consistent with the knowledge from cancer gene databases and reveals many previously unidentified cancer-associated TFs. We also analyzed RNA-binding protein regulation in cancer and demonstrated that RABIT is a general platform for predicting oncogenic gene expression regulators.
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    Exploring genetic associations with ceRNA regulation in the human genome
    (Oxford University Press, 2017) Li, Mulin Jun; Zhang, Jian; Liang, Qian; Xuan, Chenghao; Wu, Jiexing; Jiang, Peng; Li, Wei; Zhu, Yun; Wang, Panwen; Fernandez, Daniel; Shen, Yujun; Chen, Yiwen; Kocher, Jean-Pierre A.; Yu, Ying; Sham, Pak Chung; Wang, Junwen; Liu, Jun; Liu, X. Shirley
    Abstract Competing endogenous RNAs (ceRNAs) are RNA molecules that sequester shared microRNAs (miRNAs) thereby affecting the expression of other targets of the miRNAs. Whether genetic variants in ceRNA can affect its biological function and disease development is still an open question. Here we identified a large number of genetic variants that are associated with ceRNA's function using Geuvaids RNA-seq data for 462 individuals from the 1000 Genomes Project. We call these loci competing endogenous RNA expression quantitative trait loci or ‘cerQTL’, and found that a large number of them were unexplored in conventional eQTL mapping. We identified many cerQTLs that have undergone recent positive selection in different human populations, and showed that single nucleotide polymorphisms in gene 3΄UTRs at the miRNA seed binding regions can simultaneously regulate gene expression changes in both cis and trans by the ceRNA mechanism. We also discovered that cerQTLs are significantly enriched in traits/diseases associated variants reported from genome-wide association studies in the miRNA binding sites, suggesting that disease susceptibilities could be attributed to ceRNA regulation. Further in vitro functional experiments demonstrated that a cerQTL rs11540855 can regulate ceRNA function. These results provide a comprehensive catalog of functional non-coding regulatory variants that may be responsible for ceRNA crosstalk at the post-transcriptional level.
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    Precipitation Extremes Influence Patterns and Partitioning of Evapotranspiration and Transpiration in a Deciduous Boreal Larch Forest
    (Elsevier BV, 2020-06) Liu, Jialin; Cheng, FangYan; Munger, William; Jiang, Peng; Chen, Siyue; Ji, Weiwen; Man, XiuLing; Whitby, Timothy
    High latitude boreal forests are experiencing dramatic changes in climate and hydrology. It is not clear how boreal forests will adapt to hydrological change or how stable they will be to extreme climate fluctuations and shifts in ecosystem water availability (EWA; residuals between precipitation and evapotranspiration). Although there have been numerous studies in North American and European boreal forests, the Siberian boreal region is underrepresented. Moreover, Siberia is dominated by deciduous conifers (larch) that may have different response to shifting hydrology than boreal evergreens do. We observed evapotranspiration (ET) by eddy covariance technique and transpiration (T) by sap-flow probes on a subsample of trees within the flux-tower footprint through two growing seasons in a larch forest in northernmost China. Ecosystems at the margins of their zone could be amongst the first to experience significant shifts in structure and function. At this site there have already been signs of permafrost degradation and more frequent temperature and precipitation anomalies. The canopy-dominant larch accounted for half the total T fluxes. The remaining 50% was distributed evenly among intermediate and suppressed trees. T is the dominant subcomponent in ET, where overall T/ET varies of 66%–84% depending on precipitation patterns. In dormant and early growing seasons, T still constitutes a majority of ET even though the canopy foliage is not fully developed because cold soil creates a negative soil to air vapor pressure gradient that impedes evaporation. However, in the peak growing season, excess precipitation reduces T while providing sufficient wetness for surface evaporation. ET from standard data product based on MODIS satellite reflectance underestimates tower ET by 17%–29%. Solar-induced chlorophyll fluorescence measured by satellite is well correlated with tower ET (r2 = 0.69–0.73) and could provide a better basis for regional ET extrapolations. A global comparison of data for 2000–2018 period reveals that boreal forests not only have the smallest annual MODIS ET but also the least EWA compared to temperate and tropical forests. Also, even though boreal deciduous and evergreens have comparable annual ET, their T/ET and EWA are distinct. This work highlights how short-term precipitation extremes may shift ecosystem function and structure by changing EWA through exported runoff. Sites along boreal ecotones are critical to observe for signs of shifts in their structure, function, and response to climate anomalies.