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Publications
59. Thomas de Bang, Peter Knut Lundquist, Xinbin Dai, Clarissa Boschiero, Zhaohong Zhuang, Pooja Pant, Ivone Torres-Jerez, Sonali Roy, Joaquina Nogales, Vijaykumar Veerappan, Rebecca Dickstein, Michael K Udvardi, Patrick X. Zhao and Wolf Scheible, Genome-wide Identification of Medicago Peptides involved in Macronutrient Responses and Nodulation, Plant Physiology, 2017, doi: 10.1104/pp.17.01096. (Link)

58. Yi Zheng, Chen Jiao, Honghe Sun, Hernan G. Rosli, Marina A. Pombo, Peifen Zhang, Michael Banf, Xinbin Dai, Gregory B. Martin, James J. Giovannoni, Patrick X. Zhao, Seung Y. Rhee and Zhangjun Fei, iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases, Molecular Plant, 2016, doi: 10.1016/j.molp.2016.09.014. (Link)

57. Jun Li and Patrick X. Zhao, Mining Functional Modules in Heterogeneous Biological Networks using Multiplex PageRank Approach, Frontiers in Plant Science, 2016, 7:903, doi: 10.3389/fpls.2016.00903. (Link)

56. Wenchao Zhang, Xinbin Dai, Qishan Wang, Shizhong Xu and Patrick X. Zhao, PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies, PLOS Computational Biology, 2016, doi: 10.1371/journal.pcbi.1004925. (Link)

55. Jiading Yang, Eric Worley, Qin Ma, Jun Li, Ivone Torres-Jerez, Gaoyang Li, Patrick X. Zhao, Ying Xu, Yuhong Tang and Michael Udvardi, Nitrogen remobilization and conservation, and underlying senescence-associated gene expression in the perennial switchgrass Panicum virgatum, New Phytologist, 2016, doi: 10.1111/nph.13898. (Link)

54. Xinbin Dai, Jun Li, Tingsong Liu and Patrick X. Zhao, HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks, Plant Cell Physiology, 2016, doi: 10.1093/pcp/pcv200. (Link)

53. Jun Li, Xinbin Dai, Zhaohong Zhuang and Patrick X. Zhao, LegumeIP 2.0-a platform for the study of gene function and genome evolution in legumes, Nucleic Acids Research, 2016, doi: 10.1093/nar/gkv1237. (Link)

52. Wenchao Zhang, Zhentian Lei, David Huhman, Lloyd W. Sumner and Patrick X. Zhao, MET-XAlign: A Metabolite Cross-Alignment Tool for LC/MS-Based Comparative Metabolomics, Analytical Chemistry, 2015, doi: 10.1021/acs.analchem.5b01324. (Link)

51. Jamie A. O’Rourke, Fengli Fu, Bruna Bucciarelli, S. Sam Yang, Deborah A. Samac, JoAnn F. S. Lamb, Maria J. Monteros, Michelle A. Graham, John W. Gronwald, Nick Krom, Jun Li, Xinbin Dai, Patrick X. Zhao and Carroll P. Vance, The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies, BMC Genomics, 2015, 16:502, doi: 10.1186/s12864-015-1718-7. (Link)

50. Firoz Ahmed, Muthappa Senthil-Kumar, Seonghee Lee, Xinbin Dai, Kirankumar Mysore and Patrick X. Zhao, 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, 2015, 11(11), 1414-14295, doi: 10.1080/15476286.2014.996474. (Link)

49. Firoz Ahmed, Xinbin Dai, and Patrick X. Zhao, Bioinformatics Tools for Achieving Better Gene Silencing in Plants, in Kirankumar S. Mysore and Senthil-Kumar Muthappa (Editors), Plant Gene Silencing: Methods and Protocols (Methods in Molecular Biology), 2015, vol. 1287, p. 43-60, doi: 10.1007/978-1-4939-2453-0_3, ISBN-13: 978-1493924523, Springer, New York. (Link)

48. Jun Li, Hairong Wei, Tingsong Liu, Xinbin Dai and Patrick X. Zhao, LegumeIP: an integrative platform for comparative genomics and transcriptomics of model legumes, in Frans J. de Bruijn (Editor), Biological Nitrogen Fixation, 2015, ISBN-13: 978-1118637043, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030. (Link)

47. Wenchao Zhang and Patrick X. Zhao, Quality evaluation of extracted ion chromatograms and chromatographic peaks in liquid chromatography/mass spectrometry-based metabolomics data, BMC Bioinformatics, 2014, 15(Suppl 11):S5, doi: 10.1186/1471-2105-15-S11-S5. (Link)

46. Jamie A. O'Rourke, Luis P. Iniguez, Fengli Fu, Bruna Bucciarelli, Susan S. Miller, Scott A. Jackson, Philip E. McClean, Jun Li, Xinbin Dai, Patrick X. Zhao, Georgina Hernandez and Carroll P. Vance, An RNA-Seq based gene expression atlas of the common bean, BMC Genomics, 2014, 15:866, doi: 10.1186/1471-2164-15-866. (Link)

45. Wenchao Zhang , Junil Chang , Zhentian Lei , David Huhman , Lloyd W. Sumner and Patrick X. Zhao, MET-COFEA: A Liquid Chromatography/Mass Spectrometry Data Processing Platform for Metabolite Compound Feature Extraction and Annotation, analytical chemistry, 2014, doi: 10.1021/ac501162k. (Link)

44. Nitish K. Mishra, Junil Chang and Patrick X. Zhao, Prediction of membrane transport proteins and their substrate specificities using primary sequence information, PLoS ONE, 2014, doi: 10.1371/journal.pone.0100278. (Link)

43. Michael T. Parker, Yuan Zhong, Xinbin Dai, Shiliang Wang, Patrick X. Zhao, Comparative genomic and transcriptomic analysis of terpene synthases in Arabidopsis and Medicago, IET Systems Biology, 2014, doi: 10.1049/iet-syb.2013.0032. (Link)

42. Wolfgang Goettel, Zongrang Liu, Jing Xia, Weixiong Zhang, Patrick X. Zhao, Yong-Qiang Charles An, Systems and Evolutionary Characterization of MicroRNAs and Their Underlying Regulatory Networks in Soybean Cotyledons, PLoS ONE, 2014, 9(1):e86153, doi: 10.1371/journal.pone.0086153. (Link)

41. Zhipeng Liu, Tianlong Chen, Lichao Ma, Zhiguang Zhao, Patrick X. Zhao, Zhibiao Nan and Yanrong Wang, Global Transcriptome Sequencing Using the Illumina Platform and the Development of EST-SSR Markers in Autotetraploid Alfalfa, PLoS ONE, 2013, 8(12):e83549, doi: 10.1371/journal.pone.0083549. (Link)

40. Xinbin Dai, Senjuti Sinharoy, Michael K. Udvardi and Patrick X. Zhao, PlantTFcat: An Online Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool, BMC Bioinformatics, 2013, 14:321, doi:10.1186/1471-2105-14-321. (Link)

39. Jun Li, Hairong Wei, Tingsong Liu and Patrick X. Zhao, GPLEXUS: Enabling Genome-scale Gene Association Network Reconstruction and Analysis for Very Large-scale Expression Data, Nucleic Acids Research, 2013, doi: 10.1093/nar/gkt983. (Link)

38. Jun Li, Hairong Wei and Patrick X. Zhao, DeGNServer: Deciphering Genome-scale Gene Networks through High Performance Reverse Engineering Analysis, BioMed Research International, vol. 2013, Article ID 856325, 2013, doi:10.1155/2013/856325. (Link)

37. Dong-Man Khu, Rafael Reyno, Yuanhong Han, Patrick X. Zhao, Joseph H. Bouton, E. Charles Brummer, and Maria J. Monteros, Identification of Aluminum Tolerance QTLs in Tetraploid Alfalfa, Crop Science, 2012, doi: 10.2135/cropsci2012.03.0181. (Link)

36. Jagdeep Kaur, Mercy Thokala, Alexandre Robert-Seilaniantz, Patrick X. Zhao, Hadrien Peyret, Howard Berg, Sona Pandey, Jonathan Jones and Dilip Shah, Subcellular targeting of an evolutionarily conserved plant defensin MtDef4.2 determines the outcome of plant-pathogen interaction in transgenic Arabidopsis, Mol Plant Pathol, 2012 Jul 9, doi: 10.1111/j.1364-3703.2012.00813.x. (Link)

35. Zhentian Lei, Haiquan Li, Junil Chang, Patrick X. Zhao and Lloyd W. Sumner, MET-IDEA version 2.06: Improved Efficiency and Additional Functions for Mass Spectrometry-Based Metabolomics Data Processing, Metabolomics, Volume 8, Supplement 1 (2012), 105-110, doi: 10.1007/s11306-012-0397-5. (Link)

34. Jun Li, Xinbin Dai, Tingsong Liu and Patrick X. Zhao, LegumeIP: An Integrative Database for Comparative Genomics and Transcriptomics of Model Legumes, Nucleic Acids Research, 2012, 40 (D1): D1221-D1229, doi: 10.1093/nar/gkr939. (Link)

33. Michael Puckette, Niranjani J. Iyer, Yuhong Tang, Xin-Bin Dai, Patrick X. Zhao and Ramamurthy Mahalingam, Differential mRNA Translation in Medicago truncatula Accessions with Contrasting Responses to Ozone-Induced Oxidative Stress, Molecular Plant, 2012, 5 (1):187-204, doi:10.1093/mp/ssr069. (Link)

32. Nevin D. Young, Frédéric Debellé, Giles E. D. Oldroyd, Rene Geurts, Steven B. Cannon, Michael K. Udvardi, Vagner A. Benedito, Klaus F. X. Mayer, Jérôme Gouzy, Heiko Schoof, Yves Van de Peer,Sebastian Proost, Douglas R. Cook, Blake C. Meyers, Manuel Spannagl, Foo Cheung, Stéphane De Mita,Vivek Krishnakumar, Heidrun Gundlach, Shiguo Zhou, Joann Mudge, Arvind K. Bharti, Jeremy D. Murray,Marina A. Naoumkina, Benjamin Rosen, Kevin A. T. Silverstein, Haibao Tang, Stephane Rombauts, Patrick X. Zhao, Peng Zhou, Valérie Barbe, Philippe Bardou, Michael Bechner, Arnaud Bellec, Anne Berger, Hélène Bergès, Shelby Bidwell, Ton Bisseling, Nathalie Choisne, Arnaud Couloux, Roxanne Denny, Shweta Deshpande, Xinbin Dai, Jeff J. Doyle, Anne-Marie Dudez, Andrew D. Farmer, Stéphanie Fouteau, Carolien Franken, Chrystel Gibelin, John Gish, Steven Goldstein, Alvaro J. González, Pamela J. Green, Asis Hallab,Marijke Hartog, Axin Hua, Sean J. Humphray, Dong-Hoon Jeong, Yi Jing, Anika Jöcker, Steve M. Kenton,Dong-Jin Kim, Kathrin Klee, Hongshing Lai, Chunting Lang, Shaoping Lin, Simone L. Macmil, Ghislaine Magdelenat, Lucy Matthews, Jamison McCorrison, Erin L. Monaghan, Jeong-Hwan Mun, Fares Z. Najar,Christine Nicholson, Céline Noirot, Majesta O’Bleness, Charles R. Paule, Julie Poulain, Florent Prion,Baifang Qin, Chunmei Qu, Ernest F. Retzel, Claire Riddle, Erika Sallet, Sylvie Samain, Nicolas Samson,Iryna Sanders, Olivier Saurat, Claude Scarpelli, Thomas Schiex, Béatrice Segurens, Andrew J. Severin, D. Janine Sherrier, Ruihua Shi, Sarah Sims, Susan R. Singer, Senjuti Sinharoy, Lieven Sterck, Agnès Viollet,Bing-Bing Wang, Keqin Wang, Mingyi Wang, Xiaohong Wang, Jens Warfsmann, Jean Weissenbach, Doug D. White, Jim D. White, Graham B. Wiley, Patrick Wincker, Yanbo Xing, Limei Yang, Ziyun Yao, Fu Ying,Jixian Zhai, Liping Zhou, Antoine Zuber, Jean Dénarié, Richard A. Dixon, Gregory D. May, David C. Schwartz, Jane Rogers, Francis Quétier, Christopher D. Town and Bruce A. Roe, The Medicago genome provides insight into the evolution of rhizobial symbioses, Nature, 2011, doi:10.1038/nature10625. (Link)

31. Firoz Ahmed, Vagner A. Benedito and Patrick X. Zhao, Mining functional elements in messenger RNAs: overview, challenges, and perspectives, Frontiers in Plant Science, 2011, 2:84, doi: 10.3389/fpls.2011.00084. (Link)

30. Yuanhong Han, Yun Kang, Ivone Torres-Jerez, Foo Cheung, Christopher D. Town, Patrick X. Zhao, Michael K. Udvardi and Maria J. Monteros, Genome-wide SNP Discovery in Tetraploid Alfalfa Using 454 Sequencing and High Resolution Melting Analysis, BMC Genomics, 2011, 12:350, doi:10.1186/1471-2164-12-350. (Link)

29. Xinbin Dai and Patrick X. Zhao, psRNATarget: A Plant Small RNA Target Analysis Server, Nucleic Acids Research, 2011, doi: 10.1093/nar/gkr319. (Link)

28. Zhentian Lei, Bonnie Watson, Xinbin Dai, Patrick X. Zhao and Lloyd W. Sumner, A legume specific protein database (LegProt) improves the number of identified peptides, confidence scores and overall protein identification success rates for legume proteomics, Phytochemistry, 2011. (Link)

27. Xinbin Dai, Zhaohong Zhuang and Patrick X. Zhao, Computational analysis of miRNA targets in plants: current status and challenges, Briefings in Bioinformatics, 2010, doi: 10.1093/bib/bbq065. (Link).

26. Marina A. Naoumkina, Qiao Zhao, Lina Gallego-Giraldo, Xinbin Dai, Patrick X. Zhao and Richard A. Dixon, Genome-wide analysis of phenylpropanoid defence pathways, Molecular Plant Pathology, 2010, doi: 10.1111/j.1364-3703.2010.00648.x. (Link)

25. Rakesh Kaundal, Reena Saini and Patrick X. Zhao, Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis thaliana. Plant Physiology, 2010, doi:10.1104/pp.110.156851. (Link)

24. Mingyi Wang, Vagner Benedito, Patrick X. Zhao, and Michael K. Udvardi, Inferring Large-scale Gene Regulatory Networks using a Low-Order Constraint-based Algorithm. Molecular BioSystems, 2010, doi:10.1039/b917571g. (Link)

23. Ji He, Vagner A. Benedito, Mingyi Wang, Jeremy D Murray, Patrick X. Zhao, Yuhong Tang, and Michael Udvardi, The Medicago truncatula gene expression atlas web server. BMC Bioinformatics, 2009, 10: 441. (Link)

22. Vagner A. Benedito, Haiquan Li, Xinbin Dai, Ji He, Rakesh Kaundal, Ivone Torres-Jerez, Maria J. Harrison, Yuhong Tang, Patrick X. Zhao and Michael K. Udvardi, Genomic inventory and transcriptional analysis of Medicago truncatula transporters. Plant Physiology, 2009, doi: 10.1104/pp.109.148684. (Link)

21. Haiquan Li, Vagner A. Benedito, Michael K. Udvardi and Patrick X. Zhao, TransportTP: A two-phase classification approach for membrane transporter prediction and characterization, BMC Bioinformatics, 2009, 10:418. (Link)

20. Xinbin Dai, Guodong Wang, Dong Sik Yang, Yuhong Tang, Pierre Broun, M. David Marks, Lloyd W. Sumner, Richard A. Dixon and Patrick X. Zhao. TrichOME: A comparative omics database for plant trichomes. Plant Physiology, 2009, doi: 10.1104/pp.109.145813. (Link)

19. Li Tian , Gregory J Peel , Zhentian Lei , Naveed Aziz , Xinbin Dai , Ji He , Bonnie Watson , Patrick X. Zhao, Lloyd W Sumner and Richard A Dixon, Transcript and proteomic analysis of developing white lupin (Lupinus albus L.) roots. BMC Plant Biology, 2009, 9:1, doi:10.1186/1471-2229-9-1. (Link)

18. Haiquan Li, Jinyan Li and Patrick X. Zhao. Discovery of Protein Interaction Sites. In Bioinforamtics section, Encyclopedia of Data Warehousing and Mining, Second Edition, ISBN: 978-1-60566-010-3, edited by Dr. John Wang. August 2008 Published under the imprint Information Science Reference (formerly Idea Group Reference). (Link, PDF)

17. Guodong Wang, Li Tian, Naveed Aziz, Pierre Broun, Xinbin Dai, Ji He, Andrew King, Patrick X. Zhao and Richard A. Dixon, Terpene biosynthesis in glandular trichomes of hop (Humulus lupulus L.), Plant Physiology, 2008, 10.1104/pp.108.125187. (Link)

16. Yan Zhang, Ji He, Patrick X. Zhao, Joseph H Bouton and Maria J Monteros. Genome-wide Identification of Microsatellites in White Clover (Trifolium repens L.) using FIASCO and phpSSRMiner. Plant Methods 2008. (Link)

15. Xinbin Dai and Patrick X. Zhao. pssRNAMiner: A plant short small RNA regulatory cascade analysis server. Nucleic Acids Research, 2008, doi: 10.1093/nar/gkn297. (Link)

14. Vagner Benedito, Ivone Torez-Jerez, Jeremy Murray, Andry Andriankaja, Stacey Allen, Klementina Kakar, Maren Wandrey, Jerome Verdier, Helene Zuber, Thomas Ott, Sandra Moreau, Andreas Niebel, Tancred Frickey, Georg Weiller, Ji He, Xinbin Dai, Patrick X. Zhao, Yuhong Tang, and Michael Udvardi. A gene expression atlas of the model legume Medicago truncatula. The Plant Journal , 2008, doi:10.1111/j.1365-313X.2008.03519.x. (Link)

13. Haiquan Li, Xinbin Dai and Xuechun Zhao. A Nearest Neighbor Approach for Automated Transporter Prediction and Categorization from Protein Sequences. Bioinformatics, 2008, doi:10.1093/bioinformatics/btn099. (Link)

12. MA Rouf Mian, Yan Zhang, Zeng-Yu Wang, Ji-Yi Zhang, Xiaofei Cheng, Lei Chen, Konstantin Chekhovskiy, Xinbin Dai, Chunhong Mao, Foo Cheung, Xuechun Zhao, Ji He, Angela D Scott, Christopher D Town and Gregory D May. Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages. BMC Plant Biology, 2008, 8:27 doi:10.1186/1471-2229-8-27. (Link)

11. Million Tadege, Jiangqi Wen, Ji He, Haidi Tu, Younsig Kwak, Alexis Eschstruth, Anne Cayrel, Gabi Endre, Patrick X. Zhao, Mireille Chabaud, Pascal Ratet and Kirankumar Mysore. Large scale insertional mutagenesis using Tnt1 retrotransposon in the model legume Medicago truncatula. The Plant Journal, 2008, 54 (2), 335-347 doi:10.1111/j.1365-313X.2008.03418.x (Link)

10. Marina Naoumkina, Ivone Torres-Jerez, Stacy Allen, Ji He, Patrick X. Zhao, Richard A Dixon and Gregory D May, Analysis of cDNA libraries from developing seeds of guar (Cyamopsis tetragonoloba (L.) Taub). BMC Plant Biology, Nov. 23, 2007. 7 (1):62. (PDF)

9. Asuka Itaya, Ralf Bundschuh, Anthony Archual, Je-Gun Joung, Zhangjun Fei, Xinbin Dai, Patrick X. Zhao, Yuhong Tang,Richard S. Nelson and Biao Ding, Small RNAs in Tomato Fruit and Leaf Development, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2008, 1779(2): 99-107 (Link)

8. Saeed Irian, Ping Xu, Xinbin Dai, Patrick X. Zhao, and Marilyn J. Roossinck, Regulation of a Virus-Induced lethal disease in Tomato Revealed by Long SAGE analyses, Molecular Plant-Microbe Interactions, Dec. 2007, 20 (12):1477-88. (PDF)

7. Xinbin Dai, Ji He, and Xuechun Zhao. A New Systematic Computational approach to Predict Target Genes of Transcription Factors. Nucleic Acids Research. 2007;35(13):4433-40. NAR Online. (PDF)

6. Amanda K. Broz, Corey D. Broeckling, Ji He, Xinbin Dai, Patrick X. Zhao, and Jorge M. Vivanco. A first step in understanding an invasive weed through its genes: an EST analysis of invasive Centaurea maculosa. BMC Plant Biology. 7:25, 2007. (PDF)

5. Ji He, Xinbin Dai, and Xuechun Zhao. 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). April 2007. p17-24. (PDF)

4. Ji He, Xinbin Dai, and Xuechun Zhao. PLAN: A web platform for automating high-throughput BLAST searches and for managing and mining results. BMC Bioinformatics. 8:53, 2007. (PDF)

3. Vagner A. Benedito, Xinbin Dai, Ji He, Patrick X. Zhao, and Michael K. Udvardi. Functional Genomics of Plant Transporters in Legume Nodules. Functional Plant Biology. 33(8), p731–736, 2006. (PDF)

2. Ji He, Xinbin Dai, and Xuechun Zhao. A Systematic Computational Approach for Transcription Factor Target Gene Prediction. In IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). September 2006. p385-391. (PDF)

1. Corey D. Broeckling, Indira Reddy, Tony Duran, Xuechun Zhao, and Lloyd W. Sumner, MET-IDEA: data extraction tool for mass spectrometry-based metabolomics, Anal Chem. July 2006, 78(13):4334-41. (Link)

 

Copyright © 2007 by The Samuel Roberts Noble Foundation, Inc.