Digital Biology Lab - Publications List

Books

2008

Dong Xu, James Keller, Mihail Popescu, Rajkumar Bondugula (2008) Application of Fuzzy Logic in Bioinformatics Imperial College Press, London, UK

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Journal articles

2011

2010

Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry Nguyen, Dong Xu, Gary Stacey, Jianlin Cheng (2010) A Knowledge Database of Soybean Transcription Factors BMC: Plant Biology

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Jeremy Schmutz, Steven B Cannon, Jessica Schlueter, Jianxin Ma, Therese Mitros, William Nelson, David L Hyten, Qijian Song, Jay J Thelen, Jianlin Cheng, Dong Xu, Uffe Hellsten, Gregory D May, Yeisoo Yu, Tetsuya Sakurai, Taishi Umezawa, Madan K Bhattacharyya, Devinder Sandhu, Babu Valliyodan, Erika Lindquist, Myron Peto, David Grant, Shengqiang Shu, David Goodstein, Kerrie Barry, Montona Futrell-Griggs, Brian Abernathy, Jianchang Du, Zhixi Tian, Liucun Zhu, Navdeep Gill, Trupti Joshi, Marc Libault, Anand Sethuraman, Xue-Cheng Zhang, Kazuo Shinozaki, Henry T Nguyen, Rod A Wing, Perry Cregan, James Specht, Jane Grimwood, Dan Rokhsar, Gary Stacey, Randy C Shoemaker, Scott A Jackson (2010) Genome Sequence of the Palaeopolyploid Soybean Nature 463: 178-83

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2009

Zhao Song, Luonan Chen, Dong Xu (2009) Confidence Assessment for Protein Identification by Using Peptide-Mass Fingerprinting Data Proteomics 9(11): 3090-3099

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Dong Xu (2009) Computational Methods for Protein Sequence Comparison and Search. Current Protocols in Protein Science

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Mihail Popescu, Dong Xu (2009) Mapping Genes to Biological Pathways Using Ontological Fuzzy Rule Systems Artech House, Norwood, MA, USA

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2008

Lourdes Pena-Castillo, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kyu Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Ning Lin, Gabriel F Berriz, Francis D Gibbons, Gert Lanckriet, Jian Qiu, Charles Grant, Zafer Barutcuoglu, David P Hill, David Warde-Farley, Chris Grouios, Debajyoti Ray, Judith A Blake, Minghua Deng, Michael I Jordan, William S Noble, Quaid Morris, Judith Klein-Seetharaman, Ziv Bar-Joseph, Ting Chen, Fengzhu Sun, Olga G Troyanskaya, Edward M Marcotte, Dong Xu, Timothy R Hughes, Frederick P Roth (2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence Genome Biology 9:

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Qingguo Wang, Yi Shang, Dong Xu (2008) A New Clustering-Based Method for Protein Structure Selection Proceeding of the IEEE World Congress on Computational Intelligence 2891-2898

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Gyan P Srivastava, Jing Qiu, Dong Xu (2008) Functional Annotation from Meta-Analysis of Microarray Datasets Proceeding of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008) 367-271

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Jianjiong Gao, Ganesh Kumar Agrawal, Jay J Thelen, Dong Xu (2008) P3DB: a plant protein phosphorylation database Nucleic Acids Research 37: D960-962.

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Jianjiong Gao, Ganesh Kumar Agrawal, Jay J Thelen, Dong Xu (2008) P3DB: a plant protein phosphorylation database Nucleic Acids Research

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Shunfu Xu, Chao Zhang, Yi Miao, Jianjiong Gao, Dong Xu Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif. BMC Genomics

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Books

2008	Dong Xu, James Keller, Mihail Popescu, Rajkumar Bondugula (2008) Application of Fuzzy Logic in Bioinformatics Imperial College Press, London, UK Abstract: Notes:
Journal articles

2011	Yong Wang, Ruisheng Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen (2011) Inferring Gene Regulatory Networks from Genetical Genomics data Computational Methodologies in Gene Regulatory Networks Abstract: Notes:
	Jingfen Zhang, Qingguo Wang, Bogdan Barz, Zhiquan He, Ioan Kosztin, Yi Shang, Dong Xu (2011) MUFOLD: A New Solution for Protein 3D Structure Prediction Proteins: Structure, Function, and Bioinformatics Abstract: Notes:
	Gyan Prakash Srivastava, Garima Kushwaha, Huidong Shi, Dong Xu (2011) High-throughput Primer and Probe Design for Genome-Wide DNA Methylation Study Using PRIMEGENS A Practical Guide to Bioinformatics Analysis Abstract: Notes:
	Dongyu Zhao, Yan Wang, Di Luo, Xiaohu Shi, Liupu Wang, Dong Xu, Jun Yu, Yanchun Liang (2011) PMirP: A pre-microRNA prediction method based on structure-sequence hybrid features. Artificial Intelligence in Medicine Artificial Intelligence in Medicine. Abstract: Notes:
	Martin Hajduch, Ganesh Kumar Agrawal, Jill E Casteel, Trupti Joshi, Zhao Song, Mingyi Zhou, Huachun Wang, Dong Xu, Jay J Thelen (2011) Systems Analysis of Seed Filling in Arabidopsis: Using General Linear Modeling to Assess Concordance of Transcript and Protein Expression Plant Physiology Abstract: Notes:

	Liupu Wang, Juexin Wang, Michael Wang, Yanchun Liang, Dong Xu (2011) User experience evaluation of Google search for obtaining medical knowledge: a case study. International Journal of Data Mining and Bioinformatics Abstract: Notes:
	Gyan Prakash Srivastava, Ping Li, Jingdong Liu, Dong Xu (2011) Identification of Transcription Factor's Targets Using Tissue-specific Transcriptomic Data in Arabidopsis thaliana. BMC Systems Biology Abstract: Notes:
	Gyan Prakash Srivastava, Jing Qiu, Dong Xu (2011) Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis International Journal of Data Mining and Bioinformatics Abstract: Notes:
2010	Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan, Henry Nguyen, Dong Xu, Gary Stacey, Jianlin Cheng (2010) A Knowledge Database of Soybean Transcription Factors BMC: Plant Biology Abstract: Notes:
	Trupti Joshi, Zhe Yan, Marc Libault, Dong-Hoon Jeong, Sunhee Park, Pamela J Green, D Janine Sherrier, Andrew Farmer, Greg May, Blake C Meyers, Dong Xu, Gary Stacey (2010) Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics 11: Abstract: Notes:
	Jeremy Schmutz, Steven B Cannon, Jessica Schlueter, Jianxin Ma, Therese Mitros, William Nelson, David L Hyten, Qijian Song, Jay J Thelen, Jianlin Cheng, Dong Xu, Uffe Hellsten, Gregory D May, Yeisoo Yu, Tetsuya Sakurai, Taishi Umezawa, Madan K Bhattacharyya, Devinder Sandhu, Babu Valliyodan, Erika Lindquist, Myron Peto, David Grant, Shengqiang Shu, David Goodstein, Kerrie Barry, Montona Futrell-Griggs, Brian Abernathy, Jianchang Du, Zhixi Tian, Liucun Zhu, Navdeep Gill, Trupti Joshi, Marc Libault, Anand Sethuraman, Xue-Cheng Zhang, Kazuo Shinozaki, Henry T Nguyen, Rod A Wing, Perry Cregan, James Specht, Jane Grimwood, Dan Rokhsar, Gary Stacey, Randy C Shoemaker, Scott A Jackson (2010) Genome Sequence of the Palaeopolyploid Soybean Nature 463: 178-83 Abstract: Notes:
2009	Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, Dong Xu (2009) ComPhy: Prokaryotic Composite Distance Phylogenies Inferred from Whole-Genome Gene Sets. . BMC Bioinformatics Abstract: Notes:
	Dong Xu (2009) Mutual understanding between Traditional Chinese Medicine and systems biology: gaps, challenges and opportunities International Journal of Functional Informatics and Personalised Medicine 2: 248-260 Abstract: Notes:
	Mingjie Chen, Brian P Mooney, Martin Hajduch, Jill E Casteel, Trupti Joshi, Mingyi Zhou, Dong Xu, Jay J Thelen (2009) System Analysis of An Arabidopsis Mutant Altered in de novo Fatty Acid Synthesis Reveals Diverse Changes in Seed Composition and Metabolic Regulation Plant Physiology 150: 27-41 Abstract: Notes:
	Laurent Brechenmacher, Joohyun Lee, Sherri Sachdev, Zhao Song, Tran Hong Nha Nguyen, Joshi Trupti, Beverly Dague, Nathan Oehrle, Marc Libault, Brian Mooney, Dong Xu, Bret Cooper, Gary Stacey (2009) Establishment of a Protein Reference Map for Soybean Root Hair Cells Plant Physiology 149: 670-682 Abstract: Notes:

	Zhao Song, Luonan Chen, Dong Xu (2009) Confidence Assessment for Protein Identification by Using Peptide-Mass Fingerprinting Data Proteomics 9(11): 3090-3099 Abstract: Notes:
	Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, Dong Xu (2009) Using genome-scale-gene-based composite distance to infer prokaryotic phylogenies. Proceeding of 7th APBC (Asian Pacific Bioinformatics Conference), Beijing, China 40-52 Abstract: Notes:
	Sandra Thibivilliers, Trupti Joshi, Kimberly B Campbell, Brian Scheffler, Dong Xu, Bret Cooper, Henry T Nguyen, Gary Stacey (2009) Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection. BMC Plant Biology Abstract: Notes:
	Jianjiong Gao, Ganesh Kumar Agrawal, Jay J Thelen, Zoran Obradovic, A Keith Dunker, Dong Xu (2009) A New Machine Learning Approach for Protein Phosphorylation Site Prediction in Plants. Lecture Notes in Bioinformatics (LNBI 5462): Proceeding of the First International Conference on Bioinformatics and Computational Biology (BICoB) Abstract: Notes:
	Yi Shang, Qingguo Wang, Jingfen Zhang, Bogdan Barz, Rajkumar Bondugula, Ioan Kosztin, Dong Xu (2009) A New Computational Intelligent Approach to Protein Tertiary Structure Prediction Advance in Computational Intelligence Ed: Xin Yao. University of Science and Technology of China Press Abstract: Notes:
	Guan Ning Lin, Zheng Wang, Dong Xu, Jianlin Cheng (2009) Sequence-based prediction of protein folding rates using contacts, secondary structures and support vector machines. Proceeding of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2009) pp. 3-8. Abstract: Notes:
	Dong Xu (2009) Computational Methods for Protein Sequence Comparison and Search. Current Protocols in Protein Science Abstract: Notes:
	Marc Libault, Trupti Joshi, Vagner A Benedito, Dong Xu, Michael K Udvardi, Gary Stacey (2009) Legume transcription factor genes; what makes legumes so special? Plant Physiology Plant Physiology 151: 991-1001 Abstract: Notes:
	Marc Libault, Trupti Joshi, Kaori Takahashi, Andrea Hurley-Sommer, Kari Puricelli, Sean Blake, Richard E Finger, Christopher G Taylor, Dong Xu, Henry Nguyen, Gary Stacey (2009) Large scale analysis of soybean regulatory gene expression identifies a Myb gene involved in soybean nodule development. Plant Physiology 151: 1207-1220 Abstract: Notes:
	Mihail Popescu, Dong Xu (2009) Mapping Genes to Biological Pathways Using Ontological Fuzzy Rule Systems Artech House, Norwood, MA, USA Abstract: Notes:

	Gyan Prakash Srivastava, Trupti Joshi, Zhao Song, Chao Zhang, Guan Ning Lin, Ping Li, Andy Ross, Mihail Popescu, Jingdong Liu, Jing Qiu, Dong Xu (2009) GO-based Gene Function and Network Characterization", in, "Ontology-Based Data Mining in Biomedical Research . Mihail Popescu and Dong Xu eds. Artech House, Norwood, MA, USA 83-111 Abstract: Notes:
2008	Laurent Brechenmacher, Moon-Young Kim, Marisol Benitez, Min Li, Trupti Joshi, Bernarda Calla, Mei Phing Lee, Marc Libault, Lila O Vodkin, Dong Xu, Suk-Ha Lee, Steven J Clough, Gary Stacey (2008) Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Molecular Plant-Microbe Interactions.Molecular Plant-Microbe Interactions. 21: 5. 631-645 Abstract: Notes:
	Debjani Ghosh, Gyan P Srivastava, Dong Xu, R Michael Roberts (2008) The Interaction between Stress-Activated Protein Kinase Interacting Protein 1 (SIN1/MAKPAP1) and poly(RC) Binding Protein-2(PCBP2): Potential Involvement In Counteracting Environmental Stress. Proceedings of National Academy of Sciences 105 (33): 11673-11678 Abstract: Notes:
	Lourdes Pena-Castillo, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kyu Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Ning Lin, Gabriel F Berriz, Francis D Gibbons, Gert Lanckriet, Jian Qiu, Charles Grant, Zafer Barutcuoglu, David P Hill, David Warde-Farley, Chris Grouios, Debajyoti Ray, Judith A Blake, Minghua Deng, Michael I Jordan, William S Noble, Quaid Morris, Judith Klein-Seetharaman, Ziv Bar-Joseph, Ting Chen, Fengzhu Sun, Olga G Troyanskaya, Edward M Marcotte, Dong Xu, Timothy R Hughes, Frederick P Roth (2008) A critical assessment of Mus musculus gene function prediction using integrated genomic evidence Genome Biology 9: Abstract: Notes:
	Qingguo Wang, Yi Shang, Dong Xu (2008) A New Clustering-Based Method for Protein Structure Selection Proceeding of the IEEE World Congress on Computational Intelligence 2891-2898 Abstract: Notes:
	Gyan P Srivastava, Jing Qiu, Dong Xu (2008) Functional Annotation from Meta-Analysis of Microarray Datasets Proceeding of IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008) 367-271 Abstract: Notes:
	Sum Kim, Meng Li, Henry H Paik, Kenneth P Nephew, Huidong Shi, Robin Kramer, Dong Xu, Tim H -M Huang (2008) Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences. Pacific Symposium on Biocomputing, the Big Island of Hawaii, 13: 315-326 Abstract: Notes:
	Yu Chen, Dong Xu (2008) . Predicting Functional Modules Using Microarray and Protein Interaction Data. Analysis of Microarray Data, A Network-Based Approach 307-329 Abstract: Notes:
	Trupti Joshi, Chao Zhang, Guan Ning Lin, Zhao Song, Dong Xu (2008) GeneFAS: A tool for prediction of gene function using multiple sources of data. Genomics Protocols - Methods in Molecular Biology 439: 369-386 Abstract: Notes:
	Gyan P Srivastava, Juyuan Guo, Huidong Shi, Dong Xu (2008) PRIMEGENS-v2: Genome-wide primer design for analyzing DNA methylation patterns of CpG islands. Bioinformatics 24(17): 1837-42 Abstract: Notes:

	Chao Zhang, Trupti Joshi, Guan Ning Lin, Dong Xu (2008) An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data. International Journal of Computational Biology and Drug Design 1: 3. 254-274(21) Abstract: Notes:
	Jianjiong Gao, Ganesh Kumar Agrawal, Jay J Thelen, Dong Xu (2008) P3DB: a plant protein phosphorylation database Nucleic Acids Research 37: D960-962. Abstract: Notes:
	Rajkumar Bondugula, Dong Xu (2008) Combining Sequence and Structural Profiles for Protein Solvent Accessibility Prediction Proceeding of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB 2008) 195-200 Abstract: Notes:
	Christopher A Bottoms, Dong Xu (2008) Wanted: Unique Names for Unique Atom Positions. PDB-Wide Analysis of Diastereotopic Atom Names of Small Molecules Containing Diphosphate BMC Bioinformatics 9: 9. Abstract: Notes:
	Robin Kramer, Dong Xu (2008) Projecting Gene Expression Trajectories through Inducing Differential Equations from Microarray Time Series Experiments Journal of VLSI Signal Processing Systems. 50(3): 321-329 Abstract: Notes:
	Jianjiong Gao, Ganesh Kumar Agrawal, Jay J Thelen, Dong Xu (2008) P3DB: a plant protein phosphorylation database Nucleic Acids Research Abstract: Notes:
	Shunfu Xu, Chao Zhang, Yi Miao, Jianjiong Gao, Dong Xu Effector prediction in host-pathogen interaction based on a Markov model of a ubiquitous EPIYA motif. BMC Genomics Abstract: Notes: