1. Staff

Patrick Zhao, Ph.D. Publications

Publication List

Zhang, W., Dai, X., Xu, S. & Zhao, P. X. (2019). GPU empowered pipelines for calculating genome-wide kinship matrices with ultra-high dimensional genetic variants and facilitating 1D and 2D GWAS. NAR Genomics and Bioinformatics, 2 (1), March 2020, lqz009 doi: 10.1093/nargab/lqz009.

Boschiero, C., Lundquist, P. K., Roy, S., Dai, X., Zhao, P. X. & Scheible, W-R. (2019). Identification and functional investigation of genome-encoded, small, secreted peptides in plants. Current Protocols in Plant Biology, 4 (3), e20098 doi: 10.1002/cppb.20098.

Gill, U. S., Nandety, R. S., Krom, N., Dai, X., Zhuang, Z., Tang, Y., Zhao, P. X. & Mysore, K. S. (2019). Draft genome sequence resource of switchgrass rust pathogen, Puccinia novopanici isolate Ard-01. Phytopathology, (epub ahead of print), doi: 10.1094/PHYTO-04-19-0118-A.

Huang, J., Wang, R., Dai, X., Feng, J., Zhang, H. & Zhao, P. X. (2019). A microRNA biogenesis-like pathway for producing phased small interfering RNA from a long non-coding RNA in rice. Journal of Experimental Botany, 70 (6), 1767-1774 doi: 10.1093/jxb/erz056.

Kim, B., Dai, X., Zhang, W., Zhuang, Z., Sanchez, D. L., Lübberstedt, T., Kang, Y., Udvardi, M. K., Beavis, W. D., Xu, S. & Zhao, P. X. (2018). GWASpro: A high-performance genome-wide association analysis server. Bioinformatics, 35 (14), 2512–2514 doi: 10.1093/bioinformatics/bty989.

Zhang, W., Dai, X., Xu, S. & Zhao, P. X. (2018). 2D association and integrative omics analysis in rice provides systems biology view in trait analysis. Communications Biology, 1 (153), doi:10.1038/s42003-018-0159-7.

Deng, W., Zhang, K., Liu, S., Zhao, P. X., Xu, S. & Wei, H. (2018). JRmGRN: Joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions. Bioinformatics, 34 (20), 3470–3478 https://doi.org/10.1093/bioinformatics/bty354.

Dai, X., Zhuang, Z. & Zhao, P. X. (2018). psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Research, 46 (W1), W49-W54 https://doi.org/10.1093/nar/gky316.

de Bang, T. C., Lundquist, P. K., Dai, X., Boschiero, C., Zhuang, Z., Pandey-Pant, P., Torres-Jerez, I., Roy, S., Nogales, J., Veerappan, V., Dickstein, R., Udvardi, M. K., Zhao, P. X. & Scheible, W-R. (2017). Genome-wide identification of medicago peptides involved in macronutrient responses and nodulation. Plant Physiology, 175 (4), 1669-1689 doi:10.1104/pp.17.01096.

Dai, X., Li, J., Liu, T. & Zhao, P. X. (2016). HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks. Plant & Cell Physiology, 57 (1), e12 doi: 10.1093/pcp/pcv200.

Zheng, Y., Jiao, C., Sun, H., Rosli, H. G., Pombo, M. A., Zhang, P., Banf, M., Dai, X., Martin, G. B., Giovannoni, J., Zhao, P. X., Rhee, S. Y. & Fei, Z. (2016). iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular Plant, 9 (12), 1667-1670 doi:10.1016/j.molp.2016.09.014.

Zhang, W., Dai, X., Wang, Q., Xu, S. & Zhao, P. X. (2016). PEPIS: A pipeline for estimating epistatic effects in quantitative trait locus mapping and genome-wide association studies. PLoS Computational Biology, 12 (5), e1004925 doi: 10.1371/journal.pcbi.1004925.

Li, J. & Zhao, P. X. (2016). Mining functional modules in heterogeneous biological networks using multiplex pagerank approach. Frontiers in Plant Science, 7 (903), doi: 10.3389/fpls.2016.00903.

Zhao, P. X. (2016). Large-scale Gene Association Network Inference and Functional Module Discovery in Plants. In International Plant and Animal Genome Conference XXIV Jan 9-13, 2016 .San Diego, California: Plant & Animal Genome.

Zhao, P. X. (2016). HRGRN: Model and Decipher Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks using Graph Theory. In International Plant and Animal Genome Conference XXIV Jan 9-13, 2016 .San Diego, California: Plant & Animal Genome.

Li, J., Dai, X., Zhuang, Z. & Zhao, P. X. (2016). The LegumeIP (2016 Release)-a web-based comparative genomics and gene expression atlas platform for the study of gene function and genome evolution in …. In International Plant and Animal Genome ..

Li, J., Dai, X., Zhuang, Z. & Zhao, P. X. (2016). LegumeIP 2.0—a platform for the study of gene function and genome evolution in legumes. Nucleic Acids Research, 44 (D1), D1189–D1194 doi: 10.1093/nar/gkv1237.

Dai, X., Li, J., Liu, T. & Zhao, P. X. (2016). W057 HRGRN: enabling graph search and integrative analysis of Arabidopsis signaling transduction, metabolism and gene regulation networks. In International Plant and Animal Genome Conference XXIV Jan 9-13, 2016 .San Diego, California: Plant & Animal Genome.

Yang, J., Worley, E., Ma, Q., Li, J., Torres-Jerez, I., Li, G., Zhao, P. X., Xu, Y., Tang, Y. & Udvardi, M. K. (2016). Nitrogen remobilization and conservation, and underlying senescence-associated gene expression in the perennial switchgrass Panicum virgatum. New Phytologist, 211 (1), 75-89 doi: 10.1111/nph.13898.

Zhang, W., Lei, Z., Huhman, D. V., Sumner, L. W. & Zhao, P. X. (2015). MET-XAlign: A metabolite cross-alignment tool for LC/MS-based comparative metabolomics. Analytical Chemistry, 87 (18), 9114-9119 doi:10.1021/acs.analchem.5b01324.

Li, J., Wei, H., Liu, T., Dai, X. & Zhao, P. X. (2015). LegumeIP: an integrative platform for comparative genomics and transcriptomics of model legumes. In F. J. de Bruijn (ed.), Biological Nitrogen Fixation. Hoboken, NJ, USA: John Wiley & Sons, Inc.

O'Rourke, J. A., Fu, F., Bucciarelli, B., Yang, S. S., Samac, D. A., Lamb, J. F., Monteros, M. J., Graham, M. A., Gronwald, J. W., Krom, N., Li, J., Dai, X., Zhao, P. X. & Vance, C.P. (2015). The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies. BMC Bioinformatics, 16 (502), 1-17 doi: 10.1186/s12864-015-1718-7.

Ahmed, F., Dai, X. & Zhao, P. X. (2015). Bioinformatics tools for achieving better gene silencing in plants. In Mysore K., Senthil-Kumar M. (eds), Plant Gene Silencing. Methods in Molecular Biology. (pp. 43-60). New York, NY: Humana Press.

Ahmed, F., Senthil-Kumar, M., Lee, S., Dai, X., Mysore, K. S. & Zhao, P. X. (2015). Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in Arabidopsis. RNA Biology, 11 (11), 1414-1429 doi: 10.1080/15476286.2014.996474.

Parker, M. T., Zhong, Y., Dai, X., Wang, S. & Zhao, P. X. (2014). Comparative genomic and transcriptomic analysis of terpene synthases in Arabidopsis and Medicago. IET Systems Biology, 8 (4), 146-153 doi:10.1049/iet-syb.2013.0032.

Zhang, W. & Zhao, P. X. (2014). Quality evaluation of extracted ion chromatograms and chromatographic peaks in liquid chromatography/mass spectrometry-based metabolomics data. In Proceedings of the 11th Annual MCBIOS Conference (pp. S5). Stillwater, OK: BMC Bioinformatics.

O'Rourke, J. A., Iniguez, L. P., Fu, F., Bucciarelli, B., Miller, S. S., Jackson, S. A., McClean, P. E., Li, J., Dai, X., Zhao, P. X., Hernandez, G. & Vance, C. P. (2014). An RNA-Seq based gene expression atlas of the common bean. BMC Genetics, 15 (866), doi: 10.1186/1471-2164-15-866.

Mishra, N. K., Chang, J. & Zhao, P. X. (2014). Prediction of membrane transport proteins and their substrate specificities using primary sequence information. PLoS ONE, 9 (6), e100278 doi:10.1371/journal.pone.0100278.

Zhang, W., Chang, J., Lei, Z., Huhman, D. V., Sumner, L. W. & Zhao, P. X. (2014). MET-COFEA: A liquid chromatography/mass spectrometry data processing platform for metabolite compound feature extraction and annotation. Analytical Chemistry, 86 (13), 6245-6253 doi: 10.1021/ac501162k.

Goettel, W., Liu, Z., Xia, J., Zhang, W., Zhao, P. X. & An, Y-Q (2014). Systems and evolutionary characterization of microRNAs and their underlying regulatory networks in soybean cotyledons. PLoS ONE, 9 (1), e86153 doi: 10.1371/journal.pone.0086153.

Li, J., Wei, H. & Zhao, P. X. (2014). DeGNServer: deciphering genome-scale gene networks through high performance reverse engineering analysis. BioMed Research International, 2013, Article ID 856325 doi:10.1155/2013/856325.

Liu, Z., Chen, T., Ma, L., Zhao, Z., Zhao, P. X., Nan, Z. & Wang, Y. (2013). Global transcriptome sequencing using the illumina platform and the development of EST-SSR markers in autotetraploid alfalfa. PLoS ONE, 8 (12), e835491 doi:10.1371/journal.pone.0083549.

Dai, X., Sinharoy, S., Udvardi, M. K. & Zhao, P. X. (2013). PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool. BMC Bioinformatics, 14 (321), doi: 10.1186/1471-2105-14-321.

Li, J., Wei, H., Liu, T. & Zhao, P. X. (2013). GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data. Nucleic Acids Research, 42 (5), e32 doi:10.1093/nar/gkt983.

Li, J., Liu, T. & Zhao, P. X. (2013). GRNCASE: A high performance gene regulatory network construction and functional module discovery and analysis web server. In International Plant & Animal Genome Proceedings XXI January 12-16, 2013 .San Diego, California: Plant & Animal Genome.

Dai, X., Sinharoy, S., Udvardi, M. K. & Zhao, P. X. (2013). PlantTFcat: An online plant transcription factor and transcriptional regulator categorization and analysis tool . In International Plant & Animal Genome Conference Proceedings XXI January 12-16, 2013 .San Deigo, California: Plant & Animal Genome.

Khu, D. M., Reyno, R., Han, Y., Zhao, P. X., Bouton, J. H., Brummer, E. C. & Monteros, M. J. (2013). Identification of aluminum tolerance quantitative trait loci in tetraploid alfalfa. Crop Science, 53 (1), 148-163 doi:10.2135/cropsci2012.03.0181.

Li, J., Dai, X., Liu, T. & Zhao, P. X. (2012). LegumeIP: An integrative platform for comparative genomics and transcriptomics of model legumes . In International Plant & Animal Genome Proceedings XX January 14-18, 2012 .San Diego, California: Plant & Animal Genome.

Kaur, J., Thokala, M., Robert-Seilaniantz, A., Zhao, P. X., Peyret, H., Pandey, S. & Shah, D. (2012). Subcellular targeting of an evolutionarily conserved plant defensin MtDef4.2 determines the outcome of plant-pathogen interaction in transgenic Arabidopsis. Molecular Plant Pathology, 13 (9), 1032-1046 doi:10.1111/J.1364-3703.2012.00813.X.

Lei, Z., Li, H., Chang, J., Zhao, P. X. & Sumner, L. W. (2012). MET-IDEA version 2.06; improved efficiency and additional functions for mass spectrometry-based metabolomics data processing. Metabolomics, 8, S105–S110 doi:10.1007/s11306-012-0397-5.

Li, J., Dai, X., Liu, T., & Zhao, P. X. (2012). LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes. Nucleic Acids Research, 40 (D1), D1221–D1229 doi:10.1093/nar/gkr939.

Ahmed, F., Benedito, V. A., & Zhao, P. X. (2011). Mining functional elements in messenger RNAs: overview, challenges, and perspectives. Frontiers in Technical Advances in Plant Science, 2, 84 doi:10.3389/fpls.2011.00084.

Young, N. D., Debellé, F., Oldroyd, G., Geurts, R., Cannon, S. B., Udvardi, M. K., Benedito, V. A., Mayer, K.F.X., Gouzy, J., Schoof, H., Van de Peer, Y., Proost, S., Cook, D. R., Meyers, B.C., Spannagl, M., Cheung, F., De Mita, S., Krishnakumar, V., Gundlach, H., Zhou, S., Mudge, J., Bharti, A.K., Murray, J., Naoumkina, M., Rosen, B., Silverstein, K.A.T., Tang, H., Rombauts, S., Zhao, P. X., Zhou, P., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Bergès, H., Bidwell, T. G., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Dai, X., Doyle, J.J., Dudez, A-M., Farmer, A. D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Goldstein, S., González, A.J., Green, P.J., Hallab, A., Hartog, M., Hua, A., Humphray, S.J., Jeong, D-H., Jing, Y., Jöcker, A., Kenton, S. M., Kim, D-J., Klee, K., Lai, H., Lang, C., Lin, S., Macmil, S.L., Magdelenat, G., Matthews, L., McCorrison, J., Monaghan, E.L., Mun, J-H., Najar, F.Z., Nicholson, C., Noirot, C., O’Bleness, M., Paule, C.R., Poulain, J., Prion, F., Qin, B., Qu, C., Retzel, E. F., Riddle, C., Sallet, E., Samain, S., Samson, N., Sanders, I., Saurat, O., Scarpelli, C., Schiex, T., Segurens, B., Severin, A.J., Sherrier, D. J., Shi, R., Sims, S., Singer, S.R., Sinharoy, S., Sterck, L., Viollet, A., Wang, B-B., Wang, K., Wang, M., Wang, X-H., Warfsmann, J., Weissenbach, J., White, D.D., White, J. D., Wiley, G. B., Wincker, P., Xing, Y., Yang, L., Yao, Z., Ying, F., Zhai, J., Zhou, L., Zuber, A., Dénarié, J., Dixon, R. A., May, G. D., Schwartz, D.C., Rogers, J., Quétier, F., Town, C. D. & Roe, B. A. (2011). The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 480 (7378), 520-524 doi:10.1038/nature10625.

Puckette, M., Iyer, N. J., Tang, Y., Dai, X., Zhao, P. X. & Mahalingam, R. (2011). Differential mRNA translation in Medicago truncatula accessions with contrasting responses to ozone-induced oxidative stress. Molecular Plant, 5 (1), 187-204 doi:10.1093/mp/ssr069.

Han, Y., Kang, Y., Torres-Jerez, I., Cheung, F., Town, C. D., Zhao, P. X., Udvardi, M. K. & Monteros, M. J. (2011). Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis. BMC Genomics, 12 (350), doi:10.1186/1471-2164-12-350.

Dai, X., & Zhao, P. X. (2011). psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research, 39, W155–W159 doi:10.1093/nar/gkr319.

Lei, Z., Dai, X., Watson, B. S., Zhao, P. X. & Sumner, L. W. (2011). A legume specific protein database (LegProt) improves the number of identified peptides, confidence scores and overall protein identification success rates for legume proteomics. Phytochemistry, 72 (10), 1020-1027 doi:10.1016/j.phytochem.2011.01.026 .

Udvardi, M. K., Pislariu, C., Valentine, A. J. , Kryvoruchko, I., Sinharoy, S. , Wang, M., Duvvuru Muni , R. R., Torres-Jerez, I., Taylor, M. , Zhang, S. , Cheng, X., Wen, J. Q., He, J., Dai, X., Zhao, P. X., Tang, Y., Chen, R., Mysore, K. S., Ratet, P., Benedito, V. A., Oldroyd, G., & Murray, J. (2011). Functional genomics of medicago nodule development and differentiation (abstract). In International Plant & Animal Genomes XIX Conference .Town & Country Convention Center San Diego, CA: Plant & Animal Genomes.

Dai, X., Zhuang, Z., & Zhao, P. X. (2011). Computational analysis of miRNA targets in plants: current status and challenges. Briefings in Bioinformatics, 12 (2), 115-121 doi:10.1093/bib/bbq065.

Naoumkina, M., Zhao, Q., Gallego-Giraldo, L., Dai, X., Zhao, P. X. & Dixon, R. A. (2010). Genome-wide analysis of phenylpropanoid defence pathways. Molecular Plant Pathology, 11 (6), 829-846 doi:10.1111/j.1364-3703.2010.00648.x.

Kaundal, R., Saina, R., & Zhao, P. X. (2010). Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis . Plant Physiology, 154 (1), 36-54 DOI:10.1104/pp.110.156851.

Wang, M., Benedito, V. A., Zhao, P. X. & Udvardi, M. K. (2010). Inferring large-scale gene regulatory networks using a low-order constraint-based algorithm. Molecular Biosystems, 6 (6), 988-998 doi: 10.1039/b917571g.

Benedito, V. A., Li, H., Dai, X., Wandrey, M., He, J., Kaundal, R., Torres-Jerez, I., Gomez, S. K., Harrison, M. J., Tang, Y., Zhao, P. X. & Udvardi, M. K. (2010). Genomic inventory and transcriptional analysis of Medicago truncatula transporters. Plant Physiology, 152, 1716-1730 doi: 10.1104/pp.109.148684.

Dai, X., Wang, G., Yang, D - S., Tang, Y., Broun, P., Marks, M. D., Sumner, L. W., Dixon, R. A. & Zhao, P. X. (2010). TrichOME: A comparative omics database for plant trichomes. Plant Physiology, 152 (1), 44-54 doi: 10.1104/pp.109.145813.

He, J., Benedito, V. A., Wang, M., Murray, J., Zhao, P. X., Tang, Y. & Udvardi, M. K. (2009). The Medicago truncatula gene expression atlas web server. BMC Bioinformatics, 10 (441), doi:10.1186/1471-2105-10-441.

Li, H., Benedito, V. A., Udvardi, M. K. & Zhao, P. X. (2009). TransportTP: A two-phase classification approach for membrane transporter prediction and characterization. BMC Bioinformatics, 10 (418), doi:10.1186/1471-2105-10-418.

Tian, L., Peel, G. J., Lei, Z., Aziz, N., Dai, X., He, J., Watson, B. S., Zhao, P. X., Sumner, L. W., & Dixon, R. A. (2009). Transcript and proteomic analysis of developing white lupin (Lupinus albus L.) roots. BMC Plant Biology, 9 (1), DOI:10.1186/1471-2229-9-1.

Zhang, Y., He, J., Zhao, P. X., Bouton, J. H., & Monteros, M. J. (2008). Genome-wide identification of microsatellites in white clover (Trifolium repens L.) using FIASCO and phpSSRMiner. Plant Methods, 4 (19), DOI:10.1186/1746-4811-4-19.

Wang, G., Tian, L., Aziz, N., Broun, P., Dai, X., He, J., King, A, Zhao, P. X., & Dixon, R. A. (2008). Terpene biosynthesis in glandular trichomes of hop (Humulus lupulus L.). Plant Physiology, 148 (3), 1254-1266 DOI:10.1104/pp.108.125187.

Li, H., Li, J. & Zhao, P. X. (2008). Discovery of protein interaction sites. In Wang J. (eds), Encyclopedia of Data Warehousing and Mining (2nd ed.). (pp. 1-6). .

Benedito, V. A., Torres-Jerez, I., Murray, J., Andriankaja, A., Allen, N. S., Kakar, K., Wandrey, M., Verdier, J., Zuber, H., Ott, T., Moreau, S., Niebel, A., Frickey, T., Weiller, G., He, J., Dai, X., Zhao, P. X., Tang, Y. & Udvardi, M. K. (2008). A gene expression atlas of the model legume Medicago truncatula. Plant Journal, 55 (3), 504-513 DOI:10.111/j.1365-313X.2008.03519.x.

Tadege, M., Wen, J. Q., He, J., Tu, H., Kwak, Y., Eschstruth, A., Cayrel, A., Endre, G., Zhao, P. X., Chabaud, M., Ratet, P. & Mysore, K. S. (2008). Large-scale insertional mutagenesis using the Tnt1retrotransposon in the model legume Medicago truncatula. Plant Journal, 54 (2), 335-347 doi: 10.1111/j.1365-313X.2008.03418.x.

Dai, X., & Zhao, P. X. (2008). pssRNAMiner: A plant short small RNA regulatory cascade analysis server. Nucleic Acids Research, 36 (Suppl. 2), W114-W118 DOI:10.1093/nar/gkn297.

Itaya, A., Bundschuh, R., Archual, A. J., Joung, J. G., Fei, Z., Dai, X., Zhao, P. X., Tang, Y., Nelson, R. S. & Ding, B. (2008). Small RNAs in tomato fruit and leaf development. BBA-Biochimica et Biophysica Acta-gene Regulatory Mechanisms, 1779 (2), 99-107 DOI:10.1016/j.bbagrm.2007.09.003.

Dai, X., He, J., & Zhao, P. X. (2007). A new systematic computational approach to predicting target genes of transcription factors. Nucleic Acids Research, 35 (13), 4433-4440 DOI:10.1093/nar/gkm454.

Naoumkina, M., Torres-Jerez, I., Allen, S. N., He, J., Zhao, P. X., Dixon, R. A., & May, G. D. (2007). Analysis of cDNA libraries from developing seeds of guar (Cyamopsis tetragonoloba (L.) Taub). BMC Plant Biology, 7 (1), 62 DOI:10.1186/1471-2229-7-62/.

Irian, S, Xu, P., Dai, X., Zhao, P. X., & Roossinck, M. J. (2007). Regulation of a virus-induced lethal disease in tomato revealed by LongSAGE analysis. Molecular Plant-Microbe Interactions, 20 (12), 1477-1488 DOI:10.1094 /MPMI -20-12-1477..

Broz, A. K., Broeckling, C. D., He, J., Dai, X., Zhao, P. X., & Vivanco, J. M. (2007). A first step in understanding an invasive weed through its genes: an EST analysis of invasive Centaurea maculosa. BMC Plant Biology, 7 (25), DOI:10.1186/1471-2229-7-25.

He, J., Dai, X. & Zhao, P. X. (2007). Associative artificial neural network for discovery of highly correlated gene groups based on gene ontology and gene expression. In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (pp. 17-24). .

Benedito, V. A., Dai, X., He, J., Zhao, P. X. & Udvardi, M. K. (2006). Functional genomics of plant transporters in legume nodules. Functional Plant Biology, 33 (8), 731-736 doi: 10.1071/FP06085.

He, J., Dai, X., & Zhao, P. X. (2006). A systematic computational approach for transcription factor target gene prediction. In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (pp. 385-391). .

Broeckling, C. D., Reddy, I. R., Duran, A. L., Zhao, P. X., & Sumner, L. W. (2006). MET-IDEA: Data extraction tool for mass spectrometry-based metabolomics. Analytical Chemistry, 78 (13), 4334-4341 doi: 10.1021/ac0521596.