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HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks.

Dai X, Li J, Liu T, Zhao PX.

Plant Cell Physiol. 2016 Jan;57(1):e12. doi: 10.1093/pcp/pcv200. Epub 2015 Dec 12.


LegumeIP 2.0-a platform for the study of gene function and genome evolution in legumes.

Li J, Dai X, Zhuang Z, Zhao PX.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1189-94. doi: 10.1093/nar/gkv1237. Epub 2015 Nov 17.


Chlorpyrifos Induces the Expression of the Epstein-Barr Virus Lytic Cycle Activator BZLF-1 via Reactive Oxygen Species.

Zhao L, Xie F, Wang TT, Liu MY, Li JL, Shang L, Deng ZX, Zhao PX, Ma XM.

Oxid Med Cell Longev. 2015;2015:309125. doi: 10.1155/2015/309125. Epub 2015 Jul 14.


MET-XAlign: a metabolite cross-alignment tool for LC/MS-based comparative metabolomics.

Zhang W, Lei Z, Huhman D, Sumner LW, Zhao PX.

Anal Chem. 2015 Sep 15;87(18):9114-9. doi: 10.1021/acs.analchem.5b01324. Epub 2015 Aug 31.


Hyperbaric oxygen preconditioning inhibits skin flap apoptosis in a rat ischemia-reperfusion model.

Xiao YD, Liu YQ, Li JL, Ma XM, Wang YB, Liu YF, Zhang MZ, Zhao PX, Xie F, Deng ZX.

J Surg Res. 2015 Dec;199(2):732-9. doi: 10.1016/j.jss.2015.06.038. Epub 2015 Jun 23.


The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies.

O'Rourke JA, Fu F, Bucciarelli B, Yang SS, Samac DA, Lamb JF, Monteros MJ, Graham MA, Gronwald JW, Krom N, Li J, Dai X, Zhao PX, Vance CP.

BMC Genomics. 2015 Jul 7;16:502. doi: 10.1186/s12864-015-1718-7.


Hydrogen-rich saline attenuates skin ischemia/reperfusion induced apoptosis via regulating Bax/Bcl-2 ratio and ASK-1/JNK pathway.

Liu YQ, Liu YF, Ma XM, Xiao YD, Wang YB, Zhang MZ, Cheng AX, Wang TT, Li JL, Zhao PX, Xie F, Zhang X.

J Plast Reconstr Aesthet Surg. 2015 Jul;68(7):e147-56. doi: 10.1016/j.bjps.2015.03.001. Epub 2015 Mar 19.


Bioinformatics tools for achieving better gene silencing in plants.

Ahmed F, Dai X, Zhao PX.

Methods Mol Biol. 2015;1287:43-60. doi: 10.1007/978-1-4939-2453-0_3. Review.


Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in Arabidopsis thaliana.

Ahmed F, Senthil-Kumar M, Lee S, Dai X, Mysore KS, Zhao PX.

RNA Biol. 2014;11(11):1414-29. doi: 10.1080/15476286.2014.996474.


Arabidopsis ERF109 mediates cross-talk between jasmonic acid and auxin biosynthesis during lateral root formation.

Cai XT, Xu P, Zhao PX, Liu R, Yu LH, Xiang CB.

Nat Commun. 2014 Dec 19;5:5833. doi: 10.1038/ncomms6833.


Quality evaluation of extracted ion chromatograms and chromatographic peaks in liquid chromatography/mass spectrometry-based metabolomics data.

Zhang W, Zhao PX.

BMC Bioinformatics. 2014;15 Suppl 11:S5. doi: 10.1186/1471-2105-15-S11-S5. Epub 2014 Oct 21.


An RNA-Seq based gene expression atlas of the common bean.

O'Rourke JA, Iniguez LP, Fu F, Bucciarelli B, Miller SS, Jackson SA, McClean PE, Li J, Dai X, Zhao PX, Hernandez G, Vance CP.

BMC Genomics. 2014 Oct 6;15:866. doi: 10.1186/1471-2164-15-866.


Prediction of membrane transport proteins and their substrate specificities using primary sequence information.

Mishra NK, Chang J, Zhao PX.

PLoS One. 2014 Jun 26;9(6):e100278. doi: 10.1371/journal.pone.0100278. eCollection 2014.


MET-COFEA: a liquid chromatography/mass spectrometry data processing platform for metabolite compound feature extraction and annotation.

Zhang W, Chang J, Lei Z, Huhman D, Sumner LW, Zhao PX.

Anal Chem. 2014 Jul 1;86(13):6245-53. doi: 10.1021/ac501162k. Epub 2014 Jun 9.


Systems and evolutionary characterization of microRNAs and their underlying regulatory networks in soybean cotyledons.

Goettel W, Liu Z, Xia J, Zhang W, Zhao PX, An YQ.

PLoS One. 2014 Jan 27;9(1):e86153. doi: 10.1371/journal.pone.0086153. eCollection 2014.


Global transcriptome sequencing using the Illumina platform and the development of EST-SSR markers in autotetraploid alfalfa.

Liu Z, Chen T, Ma L, Zhao Z, Zhao PX, Nan Z, Wang Y.

PLoS One. 2013 Dec 12;8(12):e83549. doi: 10.1371/journal.pone.0083549. eCollection 2013.


DeGNServer: deciphering genome-scale gene networks through high performance reverse engineering analysis.

Li J, Wei H, Zhao PX.

Biomed Res Int. 2013;2013:856325. doi: 10.1155/2013/856325. Epub 2013 Nov 17.


PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool.

Dai X, Sinharoy S, Udvardi M, Zhao PX.

BMC Bioinformatics. 2013 Nov 12;14:321. doi: 10.1186/1471-2105-14-321.


GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data.

Li J, Wei H, Liu T, Zhao PX.

Nucleic Acids Res. 2014 Mar;42(5):e32. doi: 10.1093/nar/gkt983. Epub 2013 Oct 30.


[Spatiotemporal variation of vegetation in northern Shaanxi of Northwest China based on SPOT-VGT NDVI].

Yang YZ, Zhao PX, Hao HK, Chang M.

Ying Yong Sheng Tai Xue Bao. 2012 Jul;23(7):1897-903. Chinese.

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