Publications
-
Hans Chetan, Sharma Neekun, Sen Sidharth, Zeng Shuai, Dev Rishabh, Jiang Yuexu, Mahajan Advitiya, Joshi Trupti. Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization. Scientific Reports. 2019 May 29; 9(1):7999. doi: 10.1038/s41598-019-44266-4.
-
Fei He, Rui Wang, Yanxin Gao, Duolin Wang, Yang Yu, Dong Xu, and Xiaowei Zhao. Protein Ubiquitylation and Sumoylation Site Prediction Based on Ensemble and Transfer Learning. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2019), in press.
-
Han Wang, Yuning Yang, Jiawen Yu, Xi Wang, Pingping Sun, Dawei Zhao, and Dong Xu. DMCTOP: Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2019), in press.
-
Sai Swathi Sivarathri, Prasad Calyam, Yuanxun Zhang, Ashish Pandey, Cong Chen, Dong Xu, Trupti Joshi and Satish Nair. Chatbot Guided Domain-science Knowledge Discovery in a Science Gateway Application. Gateways 2019, San Diego, California. In press.
-
Fei He, Duolin Wang, Yulia Innokenteva, Olha Kholod, Dmitriy Shin and Dong Xu. 2019. Extracting Molecular Entity and Their Interactions from Pathway Figures Based on Deep Learning. In Proceedings of ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB’19). Niagara Falls, NY, USA, In press.
-
Xiaosong Han, Haiyan Zhao, Hao Xu, Yun Yang, Yanchun Liang, Dong Xu. Molecular Basis of Food Classification in Traditional Chinese Medicine. ICSA Springer Book Series in Biostatistics and Bioinformatics. In press.
-
Duolin Wang, Juexin Wang, Yu Chen, Sean Yang, Qin Zeng, Jingdong Liu and Dong Xu. Improving Maize Trait through Modifying Combination of Genes. ICSA Springer Book Series in Biostatistics and Bioinformatics. In press.
-
Renchu Guan, Xiaojing Wen, Yanchun Liang, Dong Xu, Baorun He, Xiaoyue Feng. Trends in Alzheimer's Disease Research Based upon Machine Learning Analysis of PubMed Abstracts. International Journal of Biological Sciences. In press.
-
Beverly J. Agtuca, Sylwia A. Stopka, Thalita R. Tuleski, Fernanda P. do Amaral, Sterling Evans, Yang Liu, Dong Xu, Rose Adele Monteiro, David W. Koppenaal, Ljiljana Paša-Tolić, Christopher R. Anderton, Akos Vertes, and Gary Stacey. In situ metabolomic analysis of Setaria viridis roots colonized by beneficial endophytic bacteria. Molecular Plant-Microbe Interactions. In press.
-
Chao Fang, Zhaoyu Li, Dong Xu1, and Yi Shang. MUFold-SSW: A new webserver for predicting protein secondary structures, torsion angles, and turns. Bioinformatics. In press.
-
Lingtao Su, Guixia Liu, Juexin Wang, Dong Xu. A rectified factor network based biclustering method for detecting cancer-related coding genes and miRNAs, and their interactions. Methods. In press.
-
Yuexu Jiang, Yanchun Liang, Duolin Wang, Dong Xu, Trupti Joshi. A Dynamic Programming Approach to Integrate Gene Expression Data and Network Information for Pathway Model Generation. Bioinformatics. In press.
-
Yuexu Jiang, Duolin Wang, Dong Xu, Trupti Joshi. IMPRes-Pro: A High Dimensional Multiomics Integration Method for In Silico Hypothesis Generation. Methods. In press.
-
Wenbo Wang, Zhaoyu Li, Junlin Wang, Dong Xu, and Yi Shang. PSICA: a fast and accurate web service for protein model quality analysis. Nucleic Acids Research. In press.
-
Wenbo Wang, Junlin Wang, Dong Xu, Yi Shang. Two New Heuristic Methods for Protein Model Quality Assessment. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press.
-
Kefu Cai, Jie Wang, Jaclyn Eissman, Juexin Wang, Gerald Nwosu, Wangzhen Shen, Hui-Ci Liang, Xiao-Jing Li, Hai-Xia Zhu, Yong-Hong Yi, Jeffrey Song, Dong Xu, Eric Delpire, Wei-Ping Liao, Yi-Wu Shi, Jing-Qiong Kang. A missense mutation in SLC6A1 associated with Lennox-Gastaut syndrome impairs GABA transporter 1 protein trafficking and function. Experimental Neurology. 320:112973, 2019.
-
Sadia Akter, Dong Xu, Susan Carol Nagel, John J Bromfield, Katherine Pelch, Gilbert B Wilshire, Trupti Joshi. Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data. Frontiers in Genetics, https://doi.org/10.3389/fgene.2019.00766, 2019.
-
Xiaoyue Feng, Hao Zhang, Yijie Ren, Penghui Shang, Yi Zhu, Yanchun Liang, Renchu Guan, and Dong Xu. Pubmender: Deep Learning Based Recommender System for Biomedical Publication Venue. Journal of Medical Internet Research. 21:e12957, 2019.
-
Tuyen D. Do, Tri D. Vuong, David Dunn, Michael Clubb, Babu Valliyodan, Gunvant Patil, Pengyin Chen. Identification of new loci for salt tolerance in soybean by high-resolution genome-wide association mapping. BMC Genomics. 20:318, 2019.
-
Hans Chetan, Sharma Neekun, Sen Sidharth, Zeng Shuai, Dev Rishabh, Jiang Yuexu, Mahajan Advitiya, Joshi Trupti. Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization. Scientific Reports. 2019. In Press.
-
Ming Liu, Zhiqian Zhou, Penghui Shang, and Dong Xu. Fuzzified Image Enhancement for Deep Learning in Iris Recognition. IEEE Transactions on Fuzzy Systems. In press.
-
Matthew Dickinson, Saptarshi Debroy, Prasad Calyam, Samaikya Valluripally, Yuanxun Zhang, Ronny Bazan Antequera, Trupti Joshi, Tommi White and Dong Xu. Multi-cloud Performance and Security Driven Federated Workflow Management. IEEE Transactions on Cloud Computing. doi:10.1109/TCC.2018.2849699, in press.
-
Duolin Wang, Yanchun Liang, Dong Xu. Capsule Network for Protein Post-Translational Modification Site Prediction. Bioinformatics. 35: 2386–2394, 2019.
-
Wenbo Wang, Junlin Wang, Dong Xu, Yi Shang. Two New Heuristic Methods for Protein Model Quality Assessment. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press.
-
Thang La, Edward Large, Earl Taliercio, Thomas E. Carter Jr., Randall Nelson, Qijian Song, Jason Gillman, Dong Xu, Henry T. Nguyen, Grover Shannon, and Andrew Scaboo. Characterization of a USDA Collection of Wild Soybean (Glycine soja Siebold & Zucc.) Accessions for Seed Composition and Agronomic Traits. Crop Science. 59 (1), 233-251, 2019.
-
Silvas J Prince, Babu Valliyodan, Heng Ye, Ming Yang, Shuaishuai Tai, Wushu Hu, Mackensie Murphy, Lorellin A Durnell, Li Song, Trupti Joshi, Yan Liu, Jan Van de Velde, Klaas Vandepoele, J. Grover Shannon, Henry T Nguyen. Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number. 2019. Plant Cell and Environment 42 (1): 212–229.
-
Miranda Carrie, Culp Carolyn, Skrabisova Maria, Joshi Trupti, Belzile François, Grant David, Bilyeu Kristin. Molecular Tools for Detecting Pdh1 Can Improve Soybean Breeding Efficiency by Reducing Yield Losses Due to Pod Shatter. Mol Breeding (2019) 39: 27. https://doi.org/10.1007/s11032-019-0935-1
-
Dan Li, William Yang, Yifan Zhang, Jack Y Yang, Renchu Guan, Dong Xu and Mary Qu Yang. Genomic analyses based on pulmonary adenocarcinoma in situ reveal early lung cancer signature. BMC Medical Genomics 2018, 11(Suppl 5):106.
-
Yuanxun Zhang, Prasad Calyam, Trupti Joshi, Satish Nair, Dong Xu. Domain-specific Topic Model for Knowledge Discovery through Conversational Agents in Data Intensive Scientific Communities. 2018 IEEE International Conference on Big Data, 4886-4895, 2018.
-
Fang, Chao, Yi Shang, and Dong Xu. Improving Protein Gamma-Turn Prediction Using Inception Capsule Networks. Scientific Reports. 8:15741, DOI:10.1038/s41598-018-34114-2, 2018.
-
Chen Keasar, Liam J McGuffin, Björn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren Blake, Leandro Oliveira Bortot, Renzhi Cao, BK Dhanasekaran, Itzhel Dimas, Rodrigo Antonio Faccioli, Eshel Faraggi, Robert Ganzynkowicz, Sambit Ghosh, Soma Ghosh, Artur Giełdoń, Lukasz Golon, Yi He, Lim Heo, Jie Hou, Main Khan, Firas Khatib, George A Khoury, Chris Kieslich, David E Kim, Pawel Krupa, Gyu Rie Lee, Hongbo Li, Jilong Li, Agnieszka Lipska, Adam Liwo, Ali Hassan A Maghrabi, Milot Mirdita, Shokoufeh Mirzaei, Magdalena A Mozolewska, Melis Onel, Sergey Ovchinnikov, Anand Shah, Utkarsh Shah, Tomer Sidi, Adam K Sieradzan, Magdalena Ślusarz, Rafal Ślusarz, James Smadbeck, Phanourios Tamamis, Nicholas Trieber, Tomasz Wirecki, Yanping Yin, Yang Zhang, Jaume Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Brian Koepnick, Zoran Popović, Bartlomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Alexandre Cláudio Botazzo Delbem, Christodoulos Floudas, Andrzej Kloczkowski, Stanislaw Ołdziej, Michael Levitt, Harold Scheraga, Chaok Seok, Johannes Söding, Saraswathi Vishveshwara, Dong Xu, Silvia N Crivelli. Scientific reports. 8:9939, 2018.
-
Ye Liu, Zhengfei Yu, Jingxuan Zhu, Song Wang, Dong Xu, Weiwei Han. Why Is a High Temperature Needed by Thermus thermophilus Argonaute During mRNA Silencing: A Theoretical Study. Frontiers in Chemistry, 6: 223, 2018. DOI:10.3389/fchem.2018.00223
-
Qi Zhao, Yuanning Liu, Ning Zhang, Menghan Hu, Hao Zhang, Trupti Joshi and Dong Xu. Evidence for plant-derived xenomiRs based on a large-scale analysis of public small RNA sequencing data from human samples. PLOS One. 13(6):e0187519, 2018.
-
Ning Zhang, R. Shyama Prasad Rao, Fernanda Salvato, Jesper Havelund, Ian Møller, Jay Thelen, Dong Xu. MU-LOC: A Machine-Learning Method for Predicting Mitochondrially Localized Proteins in Plants. Front. Plant Sci. 9:634, 2018. DOI:10.3389/fpls.2018.00634.
-
Donghui Wang, Yanchun Liang, Dong Xu, Xiaoyue Feng, and Renchu Guan. A Content-Based Recommender System for Computer Science Publications. Knowledge-Based Systems. 157:1-9, 2018.
-
Yun Wu, Zhiquan He, Hao Lin, Yufei Zheng, Jingfen Zhang, Dong Xu. A fast projection-based algorithm for clustering big data, Interdisciplinary Sciences: Computational Life Sciences.1-7, 2018.
-
Chao Fang, Yi Shang, and Dong Xu. Prediction of Protein Backbone Torsion Angles Using Deep Residual Inception Neural Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In press. DOI:10.1109/TCBB.2018.2814586.
-
Chao Fang, Yi Shang, and Dong Xu. MUFOLD-SS: New Deep Inception-Inside-Inception Networks for Protein Secondary Structure Prediction. PROTEINS: Structure, Function, and Bioinformatics. 86:592-598, 2018.
-
R. Shyama Prasad Rao, Ning Zhang, Dong Xu, Ian Max Møller. CarbonylDB: A curated data-resource of protein carbonylation sites. Bioinformatics. 34:2518–2520, 2018.
-
Saad M Khan, Jason E. Denney, Michael X. Wang, and Dong Xu. Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway’s involvement in juvenile myelomonocytic leukemia. Quantitative Biology. 6:85-97. 2018.
-
“Application of Deep Learning in Bioinformatics”, keynote talk, International Conference on Genome Informatics (GIW), Kunming, China, December 4, 2018.
-
Khan Mather A, Castro-Guerrero Norma A, McInturf Samuel A, Nguyen Nga T, Dame Ashley N, Wang Jiaojiao, Rebecca K, Joshi Trupti, Jurisson Silvia S, Nusinow, Dmitri A, Mendoza-Cozatl David G. Changes in iron availability in Arabidopsis are rapidly sensed in the leaf vasculature and impaired sensing leads to opposite transcriptional programs in leaves and roots. Plant, Cell and Environment. 2018. Oct;41(10):2263-2276. doi: 10.1111/pce.13192. Epub 2018 Jun 19.
-
Boerman Erika, Sen Sidharth, Shaw Rebecca, Joshi Trupti, Segal Steven. Expression and Bioinformatics Analysis of Ion Channel and Receptor Genes in Mouse Resistance Arteries: Effects of Cell Type, Vessel Type and Biological Age. Microcirculation. 2018 May;25(4):e12452. doi: 10.1111/micc.12452.
-
Mariel C. Isidra-Arellano, María del Rocio Reyero-Saavedra, Maria del Socorro Sánchez-Correa, Lise Pingault, Sidharth Sen, Trupti Joshi, Lourdes Girard, Norma A. Castro-Guerrero, David G. Mendoza-Cozatl, Marc Libault, Oswaldo Valdés-López. Phosphate deficiency negatively affects early steps of the symbiosis between common bean and rhizobia. Genes (Basel). 2018 Oct 15;9(10). pii: E498. doi: 10.3390/genes9100498.
-
Mary Galli, Arjun Khakhar, Zefu Lu, Zongliang Chen, Sidharth Sen, Trupti Joshi, Jennifer L. Nemhauser, Robert J. Schmitz, and Andrea Gallavotti. The DNA binding landscape of the maize auxin response factor family. Nature Communications. Nature Communications. 2018. Volume 9, Article number: 4526 (2018).
-
Majumder K, Wang J, Boftsi M, Fuller MS, Rede JE, Joshi T, Pintel DJ. Parvovirus minute virus of mice interacts with sites of cellular DNA damage to establish and amplify its lytic infection. eLife. 2018;7:e37750.
-
Yuexu Jiang, Duolin Wang, Dong Xu. DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectional LSTM. Proceedings of the Pacific Symposium on Biocomputing, 2018.
-
Yuanxun Zhang, Calyam Prasad, Trupti Joshi, Satish Nair, Dong Xu. Domain-specific Topic Model for Knowledge Discovery in Computational and Data Intensive Scientific Communities. 2018. BigData’18. 4886-4895. 10.1109/BigData.2018.8622309
-
S. Akter, D. Xu, S. C. Nagel, and T. Joshi. A Data Mining Approach for Biomarker Discovery Using Transcriptomics in Endometriosis. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 969-972. doi:10.1109/BIBM.2018.8621150
-
S. Zeng, Z. Lyu, S. R. Narisetti, D. Xu and T. Joshi. Knowledge Base Commons (KBCommons) v1.0: A multi OMICS' web-based data integration framework for biological discoveries. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 589-594. doi:10.1109/BIBM.2018.8621369.
-
Y. Jiang, D. Wang, D. Xu and T. Joshi. Integrating Gene Expression Data and Pathway Knowledge for In Silico Hypothesis Generation with IMPRes. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 102-107. doi:10.1109/BIBM.2018.8621465.
-
Weiwei Han, Jingxuan Zhu, Song Wang, Dong Xu. Understanding the Phosphorylation Mechanism by Using Quantum Chemical Calculations and Molecular Dynamics Simulations. Journal of Physical Chemistry B. DOI: 10.1021/acs.jpcb.6b09421, 2016.
-
Duolin Wang, Juexin Wang, Yuexu Jiang, Yanchun Liang, Dong Xu. BFDCA: A Comprehensive Tool of Using Bayes Factor for Differential Co-expression Analysis. Journal of Molecular Biology. 429:446–453, 2017.
-
Md Shakhawat Hossain, Taiji Kawakatsu, Kyung Do Kim, Ning Zhang, Cuong Nguyen, Saad Khan, Josef Batek, Trupti Joshi, Jeremy Schmutz, Jane Grimwood, Robert Schmitz, Dong Xu, Scott A Jackson, Joseph Ecker, Gary Stacey. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. New Phytologist. DOI: 10.1111/nph.14421, 2017.
-
Dan Meng, Guitao Cao, Ye Duan, Minghua Zhu, Liping Tu, Dong Xu, and Jiatuo Xu. Tongue Images Classification Based on Constrained High Dispersal Network, Evidence-Based Complementary and Alternative Medicine, doi:10.1155/2017/7452427, 2017.
-
Dong Xu, May D. Wang, Fengfeng Zhou, and Yunpeng Cai eds. “Health Informatics Data Analysis - Methods and Examples”, Springer. 2017.
-
Jianchao Du, Zhu Liang, Jiantao Xu, Yan Zhao, Xiaoyun Li, Yanli Zhang, Dandan Zhao, Ruxuan Chen, Yang Liu, Trupti Joshi, Jiahui Chang, Zhiqing Wang, Yanxu Zhang, Jindong Zhu, Qiang Liu, Dong Xu, Chengyu Jiang. Plant-derived phosphocholine facilitates cellular uptake of anti-pulmonary fibrotic HJT-sRNA-m7. Science China Life Sciences, 62: 309-320, 2019.
-
Xiaoyue Feng, Yanchun Liang, Xiaohu Shi, Dong Xu, Xu Wang, Renchu Guan. Overfitting Reduction of Text Classification Based on AdaBELM. Entropy. 9(7), 330, 2017.
-
Chao Fang, Yi Shang, and Dong Xu. MUFold-SS: Protein Secondary Structure Prediction Using Deep Inception-Inside-Inception Networks. arXiv preprint arXiv:1709.06165, 2017.
-
Saad M Khan, Jason E. Denney, Michael X. Wang, and Dong Xu. Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway’s involvement in juvenile myelomonocytic leukemia. Quantitative Biology. 33, 3909–3916, 2017.
-
Duolin Wang, Shuai Zeng, Chunhui Xu, Wangren Qiu, Yanchun Liang, Trupti Joshi, Dong Xu. MusiteDeep: A Deep-learning Framework for General and Kinase-specific Phosphorylation Site Prediction. Bioinformatics. 33(24):3909-3916, 2017.
-
Jingxuan Zhu, Yishuo Lv, Xiaosong Han, Dong Xu and Weiwei Han. Understanding the differences of the ligand binding/unbinding pathways between phosphorylated and non-phosphorylated ARH1 using molecular dynamics simulations. Scientific Reports. 7, 12439, doi:10.1038/s41598-017-12031-0, 2017.
-
Juexin Wang, Robert Sheridan, S. Onur Sumer, Nikolaus Schultz, Dong Xu, and Jianjiong Gao. G2S: A web-service for annotating genomic variants on 3D protein structures. Bioinformatics.
-
Son Phong Nguyen, Zhaoyu Li, Dong Xu, and Yi Shang. New Deep Learning Methods for Protein Loop Modeling. IEEE/ACM Transactions on Computational Biology and Bioinformatics.
-
Dong Xu, May D. Wang, Fengfeng Zhou, and Yunpeng Cai eds. “Health Informatics Data Analysis - Methods and Examples”, Springer. 2017.
-
Juexin Wang, Joseph Luttrell IV, Ning Zhang, Saad Khan, NianQing Shi, Michael X. Wang, Jing-Qiong Kang, Zheng Wang, and Dong Xu. Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling. In: Translational Biomedical Informatics: A Precision Medicine Perspective, edited by Bairong Shen, Haixu Tang and Xiaoqian Jiang, pages 39-61, 2017.
-
Ratchadaporn Kanawong, Tayo Obafemi-Ajayi, Dahai Liu, Meng Zhang, Dong Xu, Ye Duan. Tongue Image Analysis and Its Mobile App Development for Health Diagnosis. In: Translational Biomedical Informatics: A Precision Medicine Perspective, Translational Informatics in Smart Healthcare. Advances in Experimental Medicine and Biology, edited by Bairong Shen, Springer Singapore, Vol. 1005, pages 99-121, 2017.
-
Qiuming Yao and Dong Xu. Bioinformatics Analysis of Protein Phosphorylation in Plant Systems Biology Using P3DB. In: Protein Bioinformatics: From Protein Modifications and Networks to Proteomics, edited by Aalt D. J. van Dijk, Springer New York, pages 127-138, 2017.
-
Trupti Joshi, Jiaojiao Wang, Hongxin Zhang, Shiyuan Chen, Shuai Zeng, Bowei Xu and Dong Xu. The Evolution of Soybean Knowledge Base (SoyKB). In: Plant Genomics Databases: Methods and Protocols, edited by Cathy H. Wu, Cecilia N. Arighi and, Karen E. Ross, Springer New York, pages 149-159, 2017.
-
Zheng Wang, Tong Liu, Juexin Wang, Xiu-Feng Wan and Dong Xu. Remote homolog identification for protein structure prediction and function study. Handbook of Computational Molecular Biology, CRC Press, Chapman & Hall-CRC Mathematical and Computational Biology, edited by Srinivas Aluru and Mona Singh, In press.
-
Nattapon Thanintorn, Juexin Wang, Ilker Ersoy, Zainab Al-Taie, Yuexu Jiang, Duolin Wang, Megha Verma, Trupti Joshi, Richard Hammer, Dong Xu, and Dmitriy Shin. RDF Sketch Maps - Knowledge Complexity Reduction for Precision Medicine Analytics. Pac Symp Biocomput. 21:417-28. 2016.
-
Matthew Dickinson, Saptarshi Debroy, Prasad Calyam, Samaikya Valluripally, Yuanxun Zhang, Trupti Joshi, Dong Xu, End-to-End Security Formalization and Alignment for Federated Workflow Management, IEEE Cloud – Research Track, 2016.
-
Chao Fang, Yi Shang, and Dong Xu. A New Deep Neighbor-Residual Neural Network for Protein Secondary Structure Prediction. 29th IEEE International Conference on Tools with Artificial Intelligence (ICTAI2017), Nov. 6-8, 2017.
-
Zhaoyu Li, Son P. Nguyen, Dong Xu, and Yi Shang. Protein Loop Modeling Using Deep Generative Adversarial Network. 29th IEEE International Conference on Tools with Artificial Intelligence (ICTAI2017), Nov. 6-8, 2017.
-
Ronny Bazan Antequera, Prasad Calyam, Saptarshi Debroy, Longhai Cui, Sripriya Seetharam, Matthew Dickinson, Trupti Joshi, Dong Xu, Tsegereda Beyene.
ADON: Application-Driven Overlay Network-as-a-Service for Data-Intensive Science,
IEEE Transactions on Cloud Computing. pp(1):5555, doi:10.1109/TCC.2015.2511753, 2016
-
Yang Liu, Saad M. Khan, Juexin Wang, Mats Rynge, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, Joao V. Maldonado dos Santos, Babu Valliyodan, Prasad P. Calyam, Nirav Merchant, Henry T. Nguyen, Dong Xu, Trupti Joshi.
PGen: Large-Scale Genomic Variations Analysis Workflow and Browser in SoyKB.
BMC Bioinformatics. 201617(Suppl 13):337 DOI: 10.1186/s12859-016-1227-y
-
Weizhong Lin and Dong Xu.
Imbalanced Multi-label Learning for Identifying Antimicrobial Peptides and Their Functional Types.
Bioinformatics. Bioinformatics (2016) doi: 10.1093/bioinformatics/btw560
-
Li Zhang, Han Wang, Lun Yan, Lingtao Su, Dong Xu.
OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method.
Journal of Computational Biology. August 2016. doi:10.1089/cmb.2015.0236.
-
Matthew J. Salie, Ning Zhang, Veronika Lancikova, Dong Xu, Jay J. Thelen.
A Family of Negative Regulators Targets the Committed Step of De novo Fatty Acid Biosynthesis.
The Plant Cell August 24, 2016 tpc.00317.2016
-
Oswaldo Valdes-Lopez, Josef Batek, Nicolas Gomez-Hernandez, Coung T Nguyen, Mariel Carolina Isidra-Arellano, Ning Zhang, Trupti Joshi, Dong Xu, Kim K Hixson, Karl K Weitz, Joshua T Aldrisch, Ljiljana Paša-Tolic, Gary Stacey.
Soybean roots grown under heat stress show global changes in their transcriptional and proteomic profiles.
Frontiers in Plant Science, Section Plant Physiology.
-
Yiheng Wang, Tong Liu, Dong Xu, Huidong Shi, Chaoyang Zhang, Yin-Yuan Mo & Zheng Wang.
Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks.
Scientific Report. 22;6:19598, 2016.
-
Hao Zhang, Yanpu Li, Yuanning Liu, Haiming Liu, Hongyu Wang, Wen Jin, Yanmei Zhang, Chao Zhang and Dong Xu.
Role of plant MicroRNA in cross-species regulatory networks of humans.
BMC Systems Biology 2016, 10:60, DOI: 10.1186/s12918-016-0292-1, 2016.
-
Cuong The Nguyen, Kiwamu Tanaka, Yangrong Cao, Sung-Hwan Cho, Dong Xu, Gary Stacey.
Computational Analysis of the Ligand Binding Site of the Extracellular ATP Receptor, DORN1.
PLoS ONE 11(9): e0161894. doi:10.1371/journal.pone.0161894, 2016.
-
Garima Kushwaha, Mikhail Dozmorov, Jing Qiu, Huidong Shi, Dong Xu.
Hypomethylation Coordinates Antagonistically with Hypermethylation in Cancer Development: A Case Study of Leukemia.
Human Genomics. 10:18. doi: 10.1186/s40246-016-0071-5, 2016.
-
Wang-Ren Qiu, Bi-Qian Sun, Xuan Xiao, Dong Xu, Kuo-Chen Chou
iPhos-PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory,
Molecular Informatics. 35:1 – 10, DOI: 10.1002/minf.201600010, 2016.
-
Chao Wang, Haicang Zhang, Wei-Mou Zheng, Dong Xu, Jianwei Zhu, Bing Wang, Kang Ning, Shiwei Sun, Shuai Cheng Li, and Dongbo Bu.
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.
Bioinformatics, 32(3):462-464. doi: 10.1093/bioinformatics/btv581, 2016.
-
Chuanchao Zhang, Wang Jiguang, Zhang chao, Juan Liu, Dong Xu and Luonan Chen.
Network Stratification Analysis for Identifying Function-specific Network Layers.
Molecular BioSystems, DOI:10.1039/C5MB00782H, 2016.
-
Henan Wang, Chong He, Garima Kushwaha, Dong Xu and Jing Qiu.
A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data.
BMC Bioinformatics, 17(1):7, doi:10.1186/s12859-015-0850-3, 2016.
-
Hongbo Li, Yanchun Liang, Ning Zhang, Jinsong Guo, Dong Xu, Zhanshan Li.
Improving degree-based variable ordering heuristics for solving constraint satisfaction problems.
Journal of Heuristics, 22:125–145, DOI:10.1007/s10732-015-9305-2, 2016.
-
Li Song, Silvas Prince, Babu Valliyodan, Trupti Joshi, Joao V. Maldonado dos Santos, Jiaojiao Wang,
Li Lin, Jinrong Wan, Yongqin Wang, Dong Xu and Henry T. Nguyen
Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions. BMC Genomics.
2016 Jan 15;17(1):57. doi: 10.1186/s12864-016-2378-y.
-
João Vitor Maldonado dos Santos, Babu Valliyodan, Trupti Joshi, Saad M. Khan, Yang Liu, Juexin Wang, Tri D. Vuong, Marcelo Fernandes de Oliveira, Francismar Corrêa Marcelino-Guimarães,corresponding author Dong Xu, Henry T. Nguyen, and Ricardo Vilela Abdelnoor.
Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing
BMC Genomics. 2016 Feb 13. doi: 10.1186/s12864-016-2431-x
-
Babu Valliyodan, Dan Qiu, Gunvant Patil, Peng Zeng, Jiaying Huang, Lu Dai, Chengxuan Chen, Yanjun Li, Trupti Joshi, Li Song, Tri D. Vuong, Theresa A. Musket, Dong Xu, J. Grover Shannon, Cheng Shifeng, Xin Liu, and Henry T. Nguyenb.
Landscape of genomic diversity and trait discovery in soybean
BMC Genomics. 2016 Feb 13. doi: 10.1186/s12864-016-2431-x
-
Oswaldo Valdés-López, Josef Batek, Nicolas Gomez-Hernandez, Cuong T. Nguyen, Mariel C. Isidra-Arellano, Ning Zhang, Trupti Joshi3, Dong Xu, Kim K. Hixson, Karl K. Weitz, Joshua T. Aldrich, Ljiljana Paša-Tolić and Gary Stacey.
Soybean roots grown under heat stress show global changes in their transcriptional and proteomic profiles
Front. Plant Sci. 7:517. doi: 10.3389/fpls.2016.00517
-
Juexin Wang, Trupti Joshi, Babu Valliyodan, Haiying Shi, Yanchun Liang, Henry T. Nguyen, Jing Zhang and Dong Xu.
A Bayesian model for detection of high-order interactions among genetic variants
in genome-wide association studies. BMC Genomics. 2015 Nov 25;16(1):1011.
doi: 10.1186/s12864-015-2217-6.
-
Silvas J Prince, Li Song, Dan Qiu, Joao V Maldonado dos Santos, Chenglin Chai,
Trupti Joshi, Gunvant Patil, Babu Valliyodan, Tri D Vuong, Mackensie Murphy,
Konstantinos Krampis, Dominic M Tucker, Ruslan Biyashev, Anne E Dorrance, MA Saghai Maroof,
Dong Xu, J Grover Shannon and Henry T Nguyen.
Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean.
BMC Genomics. 2015 Feb 25;16:132. doi: 10.1186/s12864-015-1334-6.
-
Sripriya Seetharam, Prasad Calyam, Tsegereda Beyene.
ADON: Application-Driven Overlay Network-as-a-Service for Data-Intensive Science
IEEE Transactions on Cloud Computing. 2015. Volume:PP Issue:99. DOI: 10.1109/TCC.2015.2511753
-
Kiwamu Tanaka, Sung-Hwan Cho, Hyeyoung Lee, An Q. Pham, Josef M. Batek, Shiqi Cui,
Jing Qiu, Saad M. Khan, Trupti Joshi, Zhanyuan J. Zhang, Dong Xu, and Gary Stacey.
Effect of lipo-chitooligosaccharide on early growth of C4 grass seedlings.
J Exp Bot. 2015 Sep; 66(19): 5727–5738. doi: 10.1093/jxb/erv260
-
Md Shakhawat Hossain, Trupti Joshi, and Gary Stacey.
System approaches to study root hairs as a single cell plant model: current status and future perspectives.
Front Plant Sci. 2015 May 19;6:363. doi: 10.3389/fpls.2015.00363. eCollection 2015.
-
Syed NH, Prince SJ, Mutava RN, Patil G, Li S, Chen W,
Babu V, Joshi T, Khan S and Nguyen HT. Core clock, SUB1,
and ABAR genes mediate flooding and drought responses via
alternative splicing in soybean. Journal of Experimental
Botany. 2015. doi:10.1093/jxb/erv407.
-
Truyen N Quach, Hanh TM Nguyen, Babu Valliyodan, Trupti Joshi, Dong Xu, Henry T Nguyen
Genome-wide expression analysis of soybean NF-Y genes reveals potential function in development and drought response
June 2015, Volume 290, Issue 3, pp 1095-1115
DOI: 10.1007/s00438-014-0978-2
-
Yongqing Jiao, Tri D Vuong, Yan Liu, Clinton Meinhardt, Yang Liu, Trupti Joshi, Perry B Cregan, Dong Xu, J Grover Shannon, Henry T Nguyen
Identification and evaluation of quantitative trait loci underlying resistance to multiple HG types of soybean cyst nematode in soybean PI 437655
January 2015, Volume 128, Issue 1, pp 15-23
DOI: 10.1007/s00122-014-2409-5
-
Jing-Qiong Kang, Wangzhen Shen, Chengwen Zhou, Dong Xu, Robert L Macdonald
The human epilepsy mutation GABRG2 (Q390X) causes chronic subunit accumulation and neurodegeneration
Nature Neuroscience 18, 988–996 (2015)
doi:10.1038/nn.4024
-
Sha Lu, Xiaoyan Yin, William Spollen, Ning Zhang, Dong Xu, James Schoelz, Kristin Bilyeu, Zhanyuan J Zhang
Analysis of the siRNA-mediated gene silencing process targeting three homologous genes controlling soybean seed oil quality
Published: June 10, 2015
DOI: 10.1371/journal.pone.0129010
-
Daiyong Deng, Ning Zhang, Dong Xu, Mary Reed, Fengjing Liu, Guolu Zheng.
Polymorphism of the glucosyltransferase gene (ycjM) in Escherichia coli and its use for tracking human fecal pollution in water
Science of The Total Environment. Volume 537, 15 December 2015, Pages 260–267
doi:10.1016/j.scitotenv.2015.08.019
- Chengli Xu, Xiangwu Ju, Dandan Song, Fengming Huang, Depei Tang, Zhen Zou,
Chao Zhang, Trupti Joshi, Lijuan Jia, Weihai Xu, Kai-Feng Xu, Qian Wang, Yanlei Xiong,
Zhenmin Guo, Xiangmei Chen, Fumin Huang, Jiantao Xu, Ying Zhong, Yi Zhu, Yi Peng, Li Wang,
Xinyu Zhang, Rui Jiang, Dangsheng Li, Tao Jiang, Dong Xu, Chengyu Jiang.
An association analysis between psychophysical characteristics and genome-wide gene
expression changes in human adaptation to the extreme climate at the Antarctic Dome Argus.
Molecular Psychiatry, 20:536–544; doi:10.1038/mp.2014.72, 2015.
- Silvas J Prince, Li Song, Dan Qiu, Joao V Maldonado dos
Santos, Chenglin Chai, Trupti Joshi, Gunvant Patil, Babu
Valliyodan, Tri D Vuong, Mackensie Murphy, Konstantinos Krampis,
Dominic M Tucker, Ruslan Biyashev, Anne E Dorrance, MA Saghai
Maroof, Dong Xu, J Grover Shannon and Henry T Nguyen. Genetic
variants in root architecture-related genes in a Glycine soja
accession, a potential resource to improve cultivated soybean. BMC
Genomics 2015, 16:132 doi:10.1186/s12864-015-1334-6. 2015.
- Qiuming Yao, Waltraud X. Schulze, and Dong Xu.
Phosphorylation Site Prediction in Plants. In: Plant
Phosphoproteomics, edited by Waltraud X. Schulze. Humana
Press/Springer, New York, Heidelberg, Dordrecht, London. Chapter
17, 217-228, 2015.
- Waltraud X. Schulze, Qiuming Yao, and Dong Xu. Databases
for Plant Phosphoproteomics. In: Plant Phosphoproteomics, edited
by Waltraud X. Schulze. Humana Press/Springer, New York,
Heidelberg, Dordrecht, London. Chapter 16, 207-216, 2015.
- Garima Kushwaha, Gyan Prakash Srivastava, and Dong Xu.
PRIMEGENSw3: A Web-Based Tool for High-Throughput Primer and Probe
Design. 1275:181-99. doi: 10.1007/978-1-4939-2365-6_14. 2015.
- Silvas J. Prince, Trupti Joshi, Raymond N. Mutava, Naeem Syed, Maldonado
dos Santos Joao Vitor, Gunvant Patil, Li Song, JiaoJiao Wang, Li Lin, Wei Chen,
J. Grover Shannon, Babu Valliyodan, Dong Xu, Henry T. Nguyen. Comparative analysis
of the drought-responsive transcriptome in soybean lines contrasting for canopy wilting.
Plant Science, Volume 240, Pages 65–78. doi:10.1016/j.plantsci.2015.08.017.
November 2015.
- Chenglin Chai, Yongqin Wang, Trupti Joshi, Babu
Valliyodan, Silvas Prince, Lydia Michel, Dong Xu, Henry T
Nguyen.Soybean transcription factor ORFeome associated with
drought resistance: a valuable resource to accelerate research on
abiotic stress resistance. BMC genomics 2015, 16:596
- Patil G, Valliyodan B, Deshmukh R, Prince S, Nicander B,
Zhao M, Sonah H, Song L, Lin L, Chaudhary J, Liu Y, Joshi T, Xu D
and Nguyen HT. Soybean (Glycine max) SWEET gene family: insights
through comparative genomics, transcriptome profiling and whole
genome re-sequence analysis. BMC Genomics 2015, 16:520.
- Jiao Y, Vuong TD, Liu Y, Li Z, Noe J, Robbins RT, Joshi T,
Xu D, Shannon JG, Nguyen HT. Identification of quantitative trait
loci underlying resistance to southern root-knot and reniform
nematodes in soybean accession PI 567516C. Mol Breed.
2015;35(6):131. Epub 2015 May 23.
- Tanaka K, Cho SH, Lee H, Pham AQ, Batek JM, Cui S, Qiu J,
Khan SM, Joshi T, Zhang ZJ, Xu D, Stacey G. Effect of
lipo-chitooligosaccharide on early growth of C4 grass seedlings. J
Exp Bot. 2015 Jun 6. pii: erv260. [Epub ahead of print]
- Hossain Md Shakhawat, Joshi Trupti, Stacey Gary. System
approaches to study root hairs as a single cell plant model:
current status and future perspectives. Front. Plant Sci. 2015.
Vol 6. doi: 10.3389/fpls.2015.00363
- Yan Zhe, Hossain Md Shakhawat, Valdés-López Oswaldo, Hoang
Nhung T, Zhai Jixian, Wang Jun, Libault Marc, Brechenmacher
Laurent, Findley Seth, Joshi Trupti, Qi, Lijuan, Sherrier D.
Janine, Ji Tieming, Meyers Blake, Xu Dong, Stacey Gary.
Identification and functional characterization of soybean root
hair microRNAs expressed in response to Bradyrhizobium japonicum
infection. Journal of Plant Biotechnology. 2015. Plant
Biotechnology Journal (2015), pp. 1–10.
- Wan J, Vuong T, Jiao Y, Joshi T, Zhang H, Cui S, Qiu J, Xu
D, and Nguyen HT. Whole-genome gene expression profiling revealed
genes and pathways potentially involved in regulating the
interactions of soybean with cyst nematode (Heterodera glycines
Ichinohe). BMC Genomics 2015, 16:148.
doi:10.1186/s12864-015-1316-8.
-
Zhiquan He, Chao Zhang, Yang Xu, Shuai Zeng, Jingfen Zhang, Dong Xu
MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis
BMC Genomics 2014, 15(Suppl 11):S2
doi:10.1186/1471-2164-15-S11-S2
-
A new Hidden Markov Model for protein Quality Assessment using compatibility between protein sequence and structure
Zhiquan He, Wenji Ma, Jingfen Zhang, Dong Xu
Tsinghua Science and Technology (Volume:19 , Issue: 6 )
DOI:10.1109/TST.2014.6961026
-
DongMei Yu, Chao Zhang, PeiWu Qin, Peter V Cornish, Dong Xu
RNA-protein distance patterns in ribosomes reveal the mechanism of translational attenuation
November 2014, Volume 57, Issue 11, pp 1131-1139
DOI 10.1007/s11427-014-4753-8
-
Daiyong Deng, Ning Zhang, Azlin Mustapha, Dong Xu, Tumen Wuliji, Mary Farley, John Yang, Bin Hua, Fengjing Liu, Guolu Zheng
Differentiating enteric Escherichia coli from environmental bacteria through the putative glucosyltransferase gene (ycjM)
Water Research Volume 61, 15 September 2014, Pages 224–231
doi:10.1016/j.watres.2014.05.015
-
Ryan McGreevy, Abhishek Singharoy, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo Perozo, Klaus Schulten
xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures
Acta Cryst. (2014). D70, 2344-2355
doi:10.1107/S1399004714013856
-
Zhou Li, Yingfeng Wang, Qiuming Yao, Nicholas B Justice, Tae-Hyuk Ahn, Dong Xu, Robert L Hettich, Jillian F Banfield, Chongle Pan
Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community
Nature Communications 5, Article number: 4405
doi:10.1038/ncomms5405
-
Yan Chen, Yi Shang, Dong Xu
Multi-dimensional scaling and MODELLER-based evolutionary algorithms for protein model refinement
Evolutionary Computation (CEC), 2014 IEEE Congress on
DOI:10.1109/CEC.2014.6900443
-
Son P Nguyen, Yi Shang, Dong Xu
DL-PRO: A novel deep learning method for protein model quality assessment
Neural Networks (IJCNN), 2014 International Joint Conference on Page(s): 2071 - 2078.
Date of Conference:6-11 July 2014
DOI:10.1109/IJCNN.2014.6889891
-
Sooyoung Franck, William L Franck, Sean R Birke, Woo-Suk Chang, Dipen P Sangurdekar, Eddie Cytryn, Trupti Joshi, Michael Sadowsky, Gary Stacey, Dong Xu, David W Emerich
Comparative transcriptomic analysis of symbiotic Bradyrhizobium japonicum
Springer Science Business Media Dordrecht, 2014
DOI 10.1007/s13199-014-0294-y
-
Rui Liu, Xiangtian Yu, Xiaoping Liu, Dong Xu, Kazuyuki Aihara, Luonan Chen
Identifying critical transitions of complex diseases based on a single sample
Bioinformatics (2014) 30 (11): 1579-1586.
doi: 10.1093/bioinformatics/btu084 First published online: February 10, 2014
-
Jianjiong Gao, Dong Xu, Grzegorz Sabat, Hector Valdivia, Wei Xu, Nian-Qing Shi
Disrupting KATP channels diminishes the estrogen-mediated protection in female mutant mice during ischemia-reperfusion
BioMed Central
DOI 10.1186/1559-0275-11-19
-
Tiffany Langewisch, Hongxin Zhang, Ryan Vincent, Trupti Joshi, Dong Xu, Kristin Bilyeu
Major Soybean Maturity Gene Haplotypes Revealed by SNPViz Analysis of 72 Sequenced Soybean Genomes
Public Library of Science Volume9 Issue4 Pages e94150
Published: April 11, 2014DOI: 10.1371/journal.pone.0094150
-
Jianjiong Gao, Chao Zhang, Martijn van Iersel, Li Zhang, Dong Xu, Nikolaus Schultz, Alexander R Pico
BridgeDb app: unifying identifier mapping services for Cytoscape
Version 1. F1000Res. 2014; 3: 148.
doi: 10.12688/f1000research.4521.1
- Oswaldo Valdes-Lopez, Saad M Khan, Robert J. Schmitz,
Shiqi Cui, Jing Qiu, Trupti Joshi, Dong Xu, Brian Diers, Joseph R.
Ecker, and Gary Stacey. Genotypic variation of gene expression
during the soybean innate immunity response. Plant Genetic
Resources: Characterization and Utilization (2014) 12(S1);
S27–S30. doi:10.1017/S1479262114000197.
- Tiffany Langewisch, Hongxin Zhang, Ryan Vincent, Trupti
Joshi, Dong Xu, Kristin Bilyeu. Major soybean maturity gene
haplotypes revealed by SNPViz analysis of 72 sequenced soybean
genomes. PLoS One. 2014 Apr 11;9(4):e94150. doi:
10.1371/journal.pone.0094150. eCollection 2014.
- Trupti Joshi, Robert Williamson, Kapil Patil, Suwit
Viyanon, Xiangge Li, Yufu Zhang, Wenchuan Qi, Dong Li, Jeremy
Zimmer, Uday Illindala, Shawn Foley, Robert Campbell, Ye Duan,
Dong Xu. Virtual physical examination (VPE): a multimedia system
for education in medicine. Volume 4, Issue 3-4. DOI:
10.1504/IJFIPM.2014.068176. 2014
- Appel, Heidi M., Fescemyer, H., Ehlting, J., Weston, D.,
Rehrig, E., Joshi, T., Xu, D., Bohlmann, J., and Schultz, Jack.
Transcriptional responses of Arabidopsis thaliana to chewing and
sucking insect herbivores. Front Plant Sci. 2014 Nov 14;5:565.
doi: 10.3389/fpls.2014.00565. eCollection 2014.
- Qiuming Yao, Huangyi Ge, Shangquan Wu, Ning Zhang, Wei
Chen, Chunhui Xu, Jianjiong Gao, Jay J. Thelen, and Dong Xu. P3DB
3.0: From plant phosphorylation sites to protein networks. Nucleic
Acids Research. 1;42(1):D1206-D1213, 2014.
- Trupti Joshi, Michael R. Fitzpatrick, Shiyuan Chen, Yang
Liu, Hongxin Zhang, Ryan Z. Endacott, Eric C. Gaudiello, Gary
Stacey, Henry T. Nguyen, Dong Xu. Soybean Knowledge Base (SoyKB):
A web resource for integration of soybean translational genomics
and molecular breeding. Nucleic Acids Research. 42(1):D1245-D1252,
2014.
-
Jianjiong Gao, Qiuming Yao, CURTIS HARRISON BOLLINGER, DONG XU
Analysis and Prediction of Protein Posttranslational Modification Sites
Publisher : Wiley-IEEE Press Edition : 1 Pages : 536 Copyright Year : 2014
ISBN : 9781118567869
-
R SP Rao, Dong Xu, Jay J Thelen, Ján A Miernyk
Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation
BMC Bioinformatics201314(Suppl 14):S14 DOI: 10.1186/1471-2105-14-S14-S14© Prasad Rao et al.; licensee BioMed Central Ltd. 2013 Published: 9 October 2013
- Qingguo Wang, Charles Shang, Dong Xu, Yi Shang. New MDS
and Clustering Based Algorithms for Protein Model Quality
Assessment and Selection. International Journal on Artificial
Intelligence Tools. 22:1360006 (19 pages), 2013.
- Han Wang, Zhiquan He, Chao Zhang, Li Zhang, Dong Xu.
Transmembrane Protein Alignment and Fold Recognition Based on
Predicted Topology. PLoS ONE 8(7): e69744.
doi:10.1371/journal.pone.0069744. 2013.
- Schmitz RJ1, He Y, Valdés-López O, Khan SM, Joshi T, Urich
MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR. Epigenome-wide
inheritance of cytosine methylation variants in a recombinant
inbred population. Genome Res. 2013 Oct;23(10):1663-74. doi:
10.1101/gr.152538.112. Epub 2013 Jun 5.
- Juexin Wang, Liang Chen, Yan Wang, Jingfen Zhang, Yanchun
Liang, Dong Xu. A Computational Systems Biology Study for
Understanding Salt Tolerance Mechanism in Rice. PLoS ONE 8(6):
e64929. doi:10.1371/journal.pone.0064929, 2013.
- Hao Zhang, Zhi Li, Yanpu Li, Yuanning Liu, Junxin Liu, Xin
Li, Tingjie Shen, Yunna Duan, Minggang Hu, Dong Xu. A
computational method for predicting regulation of human microRNAs
on the influenza virus genome. BMC Systems Biology. 7(Suppl 2):S3
doi:10.1186/1752-0509-7-S2-S3, 2013.
- Yuanning Liu, Yaping Chang, Chao Zhang, Qingkai Wei,
Jingbo Chen, Huiling Chen, Dong Xu. Influence of mRNA features on
siRNA interference efficacy. Journal of Bioinformatics and
Computational Biology. 11(3):1341004. doi:
10.1142/S0219720013410047, 2013.
- Yuanning Liu, Yaping Chang, Dong Xu, Zhi Li, Hao Zhang,
Jie Li, Mingyao Tian. Optimized Design of siRNA Based on
Multi-featured Comparison and Analysis of H1N1 Virus.
International Journal of Data Mining and Bioinformatics.
7(4):345-57, 2013.
- Zhiquan He, Meshari Alazmi, Jingfen Zhang, Dong Xu.
Protein structural model selection by combining consensus and
single scoring methods. PLoS One. 8(9):e74006. doi:
10.1371/journal.pone.0074006. 2013.
- Chao Zhang, Jiguang Wang, Kristina Hanspers, Dong Xu,
Luonan Chen, Alexander R. Pico. NOA: a cytoscape plugin for
network ontology analysis. Bioinformatics. 29(16):2066-2067, 2013.
- Jingfen Zhang, Dong Xu: Fast algorithm for
population-based protein structural model analysis. Proteomics,
13:221-229, 2013.
- Nagib Ahsan, Yadong Huang, Alejandro Tovar-Mendez, Kirby N
Swatek, Jingfen Zhang, Ján A. Miernyk, Dong Xu, and Jay J Thelen.
A versatile mass spectrometry-based method to both identify kinase
client-relationships and characterize signaling network topology.
Journal of Proteome Research. 12:937-948, 2013.
- Trupti Joshi, Babu Valliyodan, Jeng-Hung Wu, Suk-Ha Lee,
Dong Xu, Henry T. Nguyen. Genomic differences between cultivated
soybean, G. max and its wild relative G. soja. BMC Genomics. 14
Suppl 1:S5. doi: 10.1186/1471-2164-14-S1-S5. 2013.
- Trupti Joshi, Kapil Patil, Michael R
Fitzpatrick, Levi D Franklin, Qiuming Yao, Jeffrey R Cook, Zheng
Wang, Marc Libault, Laurent Brechenmacher, Babu Valliyodan,
Xiaolei Wu, Jianlin Cheng, Gary Stacey, Henry T Nguyen and Dong
Xu. Soybean Knowledge Base (SoyKB): a web resource for soybean
translational genomics. BMC Genomics, 13(Suppl 1):S15.
doi:10.1186/1471-2164-13-S1-S15, 2012.
- Chao Zhang, Guolu Zheng, Shun-Fu Xu, and Dong Xu.
Computational challenges in characterization of bacteria and
bacteria-host interactions based on genomic data. Journal of
Computer Science and Technology, 27(2): 225-239, 2012.
- Chao Zhang, Shun-Fu Xu, and Dong Xu. Risk Assessment of
Gastric Cancer Caused by Helicobacter pylori Using CagA Sequence
Markers. PLoS ONE. 7(5): e36844. doi:10.1371/journal.pone.0036844,
2012.
- Chao Zhang, Kristina Hanspers, Allan Kuchinsky, Nathan
Salomonis, Dong Xu, Alexander R Pico. Mosiac: Making Biological
Sense of Complex Networks. Bioinformatics. 28:1943–1944, 2012.
- Liupu Wang, Juexin Wang, Michael Wang, Yong Li, Yanchun
Liang, Dong Xu. Using internet search engines to obtain medical
information: a comparative study. J Med Internet Res 14(3):e74,
2012.
- Tran Hong Nha Nguyen, Laurent Brechenmacher, Joshua
Aldrich, Therese Clauss, Marina Gritsenko, Kim Hixson, Marc
Libault, Kiwamu Tanaka, Feng Yang, Qiuming Yao, Ljiljana
Pasa-Tolic, Dong Xu, Henry T. Nguyen, and Gary Stacey.
Quantitative Phosphoproteomic Analysis of Soybean Root Hairs
Inoculated with Bradyrhizobium japonicum. Mol Cell Proteomics,
10.1074/mcp.M112.018028, 2012.
- Qiuming Yao, Curtis Bollinger, Jianjiong Gao, Dong Xu, and
Jay J. Thelen. P3DB: an integrated database for plant protein
phosphorylation. Front. Plant Sci. 3:206. doi:
10.3389/fpls.2012.00206. 2012.
- Qiuming Yao, Jianjiong Gao, Curtis Bollinger, Jay J.
Thelen, and Dong Xu. Predicting and analyzing protein
phosphorylation sites in plants using Musite. Front. Plant Sci.
3:186. doi: 10.3389/fpls.2012.00186. 2012.
- Mingzhu Zhu, Xin Deng, Trupti Joshi, Dong Xu, Gary Stacey,
Jianlin Cheng. Reconstructing differentially co-expressed gene
modules and regulatory networks of soybean cells. BMC Genomics.
13:437. doi: 10.1186/1471-2164-13-437, 2012.
- David A. Roeseler, Shrikesh Sachdev, Desire M. Buckley,
Trupti Joshi, Doris K. Wu, Dong Xu, Mark Hannink and Samuel T.
Waters. Elongation Factor 1 alpha1 and genes associated with Usher
syndromes are down-stream targets of GBX2. Plos One. 7:e47366.
doi:10.1371/journal.pone.0047366, 2012.
- Allison N. Tegge, Charles W. Caldwell, Dong Xu. Pathway
correlation profile of gene-gene co-expression for identifying
pathway perturbation. PLoS One. 7:e52127. doi:
10.1371/journal.pone.0052127. 2012.
- Nagib Ahsan, Kirby N Swatek, Jingfen Zhang, Ján A.
Miernyk, Dong Xu, and Jay J Thelen. Scanning mutagenesis" of the
amino acid sequences flanking phosphorylation site 1 of the
mitochondrial pyruvate dehydrogenase complex. Front Plant Sci.
3:153. doi: 10.3389/fpls.2012.00153, 2012.
- Xue-Cheng Zhang, Zheng Wang, Xinyan Zhang, Mi Ha Le,
Jianguo Sun, Dong Xu, Jianlin Cheng, Gary Stacey. Evolutionary
dynamics of protein domain architecture in plants. BMC Evol Biol.
12:6. doi: 10.1186/1471-2148-12-6, 2012.
- Ratchadaporn Kanawong, Wentao Xu, Dong Xu, Shao Li, Tao
Ma, Ye Duan: An automatic tongue detection and segmentation
framework for computer-aided tongue image analysis. I. J.
Functional Informatics and Personalised Medicine. 4:56-68, 2012.
- Ratchadaporn Kanawong, Tayo Obafemi-Ajayi, Tao Ma, Dong
Xu, Shao Li, and Ye Duan. Automated Tongue Feature Extraction for
ZHENG Classification in Traditional Chinese Medicine.
Evidence-Based Complementary and Alternative Medicine,
doi:10.1155/2012/912852, 2012.
- Louis J. Meyer, Jianjiong Gao, Dong Xu, and Jay J. Thelen.
Phosphoproteomic analysis of seed maturation in arabidopsis,
rapeseed, and soybean. Plant Physiology. 159:517-528, 2012.
- Jingfen Zhang, Zhiquan He, Qingguo Wang, Bogdan Barz, Ioan
Kosztin, Yi Shang, and Dong Xu. Prediction of protein tertiary
structures using MUFOLD. Methods Mol Biol. 815:3-13, 2012.
- Dong Xu. Protein Databases on the Internet. In: Current
Protocols in Protein Science, edited by J. E. Coligan, B. M. Dunn,
H. L. Ploegh, D. W. Speicher, and P. T. Wingfield. John Wiley &
Sons, New York. Chapter 2:Unit2.6. doi:
10.1002/0471140864.ps0206s70, 2012.
- Jianjiong Gao, Dong Xu. Correlation between
posttranslational modification and intrinsic disorder in protein.
Pac Symp Biocomput. 94-103, 2012.
- Zhiquan He, Jingfen Zhang, Yang Xu, and Yi Shang, Dong Xu.
Protein structural model selection based on protein-dependent
scoring function. Statistics and its Interface. 5:109-115, 2012.
- Chao Zhang, Kristina Hanspers, Allan Kuchinsky, Nathan
Salomonis, Dong Xu and Alexander R. Pico. Mosaic: making
biological sense of complex networks. Bioinformatics. 28
(14):1943-1944, 2012.
- Louis J. Meyer, Jianjiong Gao, Dong Xu, and Jay J. Thelen.
Phosphoproteomic analysis of seed maturation in arabidopsis,
rapeseed, and soybean. Plant Physiology. 159:517-528, 2012.
- Zheng Wang, Xuecheng Zhang, Mi Ha Le, Dong Xu, Gary
Stacey, Jianlin Cheng. A protein domain co-occurrence network
approach for predicting protein function and inferring species
phylogeny. PLoS ONE. 6(3):e17906, 2011.
- Gyan Prakash Srivastava, Mamatha Hanumappa, Garima
Kushwaha, Henry T. Nguyen and Dong Xu. PRIMEGENS-v2:
Homolog-specific PCR primer design for profiling splice variants.
Nucleic Acid Research. 39(10):e69, 2011.
- Yanchun Liang, Fan Zhang, Juexin Wang, Trupti Joshi, Yan
Wang, Dong Xu. Prediction of drought-resistant genes in
Arabidopsis thaliana using SVM-RFE. PLoS ONE. 6(7):e21750.
doi:10.1371/journal.pone.0021750, 2011.
- Marc Libault, Manjula Govindarajulu, R. Howard Berg, Yee
Tsuey Ong, Kari Puricelli, Christopher G. Taylor, Dong Xu, and
Gary Stacey. A Dual-Targeted Soybean Protein Is Involved in
Bradyrhizobium japonicum Infection of Soybean Root Hair and
Cortical Cells. Mol Plant Microbe Interact. 24:1051- 1060, 2011.
- Jingfen Zhang, Qingguo Wang, Kittinun Vantasin, Jiong
Zhang, Zhiquan He, Ioan Kosztin, Yi Shang, and Dong Xu. A
multilayer evaluation approach for protein structure prediction
and model quality assessment. Proteins: Structure, Function, and
Bioinformatics, 79 (S10):172–184, 2011.
- Qingguo Wang, Kittinun Vantasin, Dong Xu, Yi Shang.
MUFOLD-WQA: A new selective consensus method for quality
assessment in protein structure prediction. Proteins: Structure,
Function, and Bioinformatics, 79 (S10):185-195, 2011.
- Liupu Wang, Juexin Wang, Michael Wang, Yanchun Liang, and
Dong Xu. User experience evaluation of Google search for obtaining
medical knowledge: a case study. International Journal of Data
Mining and Bioinformatics. 5:626 – 639, 2011.
- Xiaohu Shi, Jingfen Zhang, Zhiquan He, Yi Shang, and Dong
Xu. A sampling-based method for ranking protein structural models
by integrating multiple scores and features. Current Protein and
Peptide Science. 12(6):540-8, 2011.
- Qingguo Wang, Yi Shang, and Dong Xu. Improving Consensus
Approach for Protein Structure Selection by Removing Redundancy.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
8: 1708-1715, 2011.
- Eun-Joon Lee, Lirong Pei, Gyan Srivastava, Trupti Joshi,
Garima Kushwaha, Jeong-Hyeon Choi, Keith D. Robertson, Xinguo
Wang, John K. Colbourne, Lu Zhang, Gary P. Schroth, Dong Xu, Kun
Zhang, Huidong Shi. Targeted bisulfite sequencing by solution
hybrid selection and massively parallel sequencing. Nucleic Acids
Research. doi: 10.1093/nar/gkr598, 2011.
- Guan Ning Lin, Chao Zhang, Dong Xu. Polytomy
identification in microbial phylogenetic reconstruction. BMC
Genomics. 5(Suppl 3):S2 doi:10.1186/1752-0509-5-S3-S2, 2011.
- Juexin Wang, Fan Zhang, Yan Wang, Yuan Fu, Dong Xu, and
Yanchun Liang. Identification of salt tolerance genes in rice from
microarray data using SVM-RFE. Proceeding of the International
Conference on Bioinformatics and Computational Biology
(BICoB-2011), March 2011, New Orleans, USA, pp. 30-35.
- Wentao Xu, Ratchadaporn Kanawong, Dong Xu, Shao Li, Tao
Ma, Guixu Zhang, Ye Duan. An automatic tongue detection and
segmentation framework for computer-aided tongue image analysis.
13th IEEE International Conference on e-Health Networking
Applications and Services (Healthcom), 2011.
- Jingfen Zhang and Dong Xu. Fast Algorithm for Clustering a
Large Number of Protein Structural Decoys. Proceedings of IEEE
International Conference on Bioinformatics & Biomedicine (BIBM
2011), Atlanta, USA, pp 30-36, November 2011.
- Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ,
Franklin LD, He J, Xu D, May G, Stacey G. An integrated
transcriptome atlas of the crop model Glycine max, and its use in
comparative analyses in plants. Plant J. 2010 Jul 1;63(1):86-99.
- Trupti Joshi, Qiuming Yao, Levi D. Franklin, Laurent
Brechenmacher, Babu Valliyodan, Gary Stacey, Henry Nguyen, and
Dong Xu. SoyMetDB: The Soybean Metabolome Database. Proceedings of
IEEE International Conference on Bioinformatics & Biomedicine
(BIBM 2010), Hong Kong, pp 203-208, December 2010.
- Chao Zhang, Shunfu Xu, and Dong Xu. Detection and
application of CagA sequence markers for assessing risk factor of
gastric cancer caused by Helicobacter pylori. Proceedings of IEEE
International Conference on Bioinformatics & Biomedicine (BIBM
2010), Hong Kong, pp 485-488, December 2010.
- Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. SNP
discovery by high-throughput sequencing in soybean. BMC Genomics.
2010 Aug 11;11:469.
- Martin Hajduch, Ganesh Kumar Agrawal, Jill E. Casteel,
Trupti Joshi, Zhao Song, Mingyi Zhou, Huachun Wang, Dong Xu, Jay
J. Thelen. Systems Analysis of Seed Filling in Arabidopsis: Using
General Linear Modeling to Assess Concordance of Transcript and
Protein Expression. Plant Physiology, April 2010, Vol. 152, pp.
1-10.
- 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 and Gary Stacey. Prediction of
novel miRNAs and associated target genes in Glycine max. BMC
Bioinformatics, 11(Suppl 1):S14, 2010.
- Zheng Wang, Marc Libault, Trupti Joshi, Babu Valliyodan,
Henry Nguyen, Dong Xu, Gary Stacey, and Jianlin Cheng. SoyDB: A
Knowledge Database of Soybean Transcription Factors, BMC: Plant
Biology 2010, 10:14.
- 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 and Scott
A. Jackson. Genome Sequence of the Palaeopolyploid Soybean .
Nature. 463:178-83, 2010.
- Jingfen Zhang, Qingguo Wang, Bogdan Barz, Zhiquan He, Ioan
Kosztin, Yi Shang, and Dong Xu. MUFOLD: A New Solution for Protein
3D Structure Prediction. Proteins: Structure, Function, and
Bioinformatics, 78:1137-1152, 2010.
- Dongyu Zhao, Yan Wang, Di Luo, Xiaohu Shi, Liupu Wang,
Dong Xu, Jun Yu, Yanchun Liang. PMirP: A pre-microRNA prediction
method based on structure-sequence hybrid features. Artificial
Intelligence in Medicine. 49(2):127-132. 2010.
- Gyan Prakash Srivastava, Ping Li, Jingdong Liu, and Dong
Xu. Identification of Transcription Factor's Targets Using
Tissue-specific Transcriptomic Data in Arabidopsis thaliana. BMC
Systems Biology. 4(Suppl 2):S2. 2010.
- Guan Ning Lin, Zheng Wang, Dong Xu, and Jianlin Cheng.
SeqRate: sequence-based protein folding type classification and
rates prediction. BMC Bioinformatics. 11(S-3): 1. 2010.
- Gyan Prakash Srivastava, Jing Qiu, and Dong Xu.
Genome-wide functional annotation by integrating multiple
microarray datasets using meta-analysis. International Journal of
Data Mining and Bioinformatics. 4(4):357-376. 2010.
- 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. 11(Suppl 3):S1.
2010.
- Jianjiong Gao, Jay J. Thelen, A. Keith Dunker, and Dong
Xu. Musite: a Tool for Global Prediction of General and
Kinase-Specific Phosphorylation Sites. Molecular & Cellular
Proteomics. 9(12):2586-600. 2010.
- Jeong-Hyeon Choi, Yajun Li, Juyuan Guo, Lirong Pei, Tibor
Rauch, Robin S. Kramer, Simone Macmil, Graham Wiley, Lynda B.
Bennett, Jennifer L. Schnabel, Kristen H. Taylor, Sun Kim, Dong
Xu, Arun Sreekumar, Gerd P. Pfeifer, Bruce Roe, Charles W.
Caldwell, Kapil N. Bhalla and Huidong Shi. Genome-wide DNA
methylation maps in follicular lymphoma cells determined by
methylation-enriched bisulfite sequencing. PLoS ONE. 5:9. 2010.
- Satish K. Guttikonda, Trupti Joshi, Naveen Bisht, Hui
Chen, Charles An, Sona Pandey, Dong Xu and Oliver Yu. Whole Genome
Co-expression Analysis of Soybean Cytochrome P450 Genes Identifies
Nodulation-Specific P450 Monooxygenases. BMC Plant Biology.
10:243. 2010.
- Jianjiong Gao and Dong Xu. The Musite open-source
framework for phosphorylation-site prediction. BMC Bioinformatics.
11(Suppl 12):S9. 2010.
- Marc Libault, Laurent Brechenmacher, Jianlin Cheng, Dong
Xu and Gary Stacey. Root Hair Systems Biology. Trends in Plant
Science. 15:641-650, 2010.
- Chi-Ren Shyu, Bin Pang, Pin-Hao Chi, Nan Zhao, Dmitry
Korkin1, and Dong Xu. ProteinDBS v2.0: A web server for global and
local protein structure search. Nucleic Acids Research; 38(SUPPL.
2):W53-W58. 2010.
- Jack Y Yang, Andrzej Niemierko, Ruzena Bajcsy, Dong Xu,
Brian D Athey, Aidong Zhang, Okan K Ersoy, Guo-zheng Li, Mark
Borodovsky, Joe C Zhang, Hamid R Arabnia, Youping Deng, A Keith
Dunker, Yunlong Liu, and Arif Ghafoor. 2K09 and thereafter : the
coming era of integrative bioinformatics, systems biology and
intelligent computing for functional genomics and personalized
medicine research. BMC Genomics. 11 Suppl 3:I1, 2010.
- Gyan Prakash Srivastava, Garima Kushwaha, Huidong Shi, and
Dong Xu. High-throughput Primer and Probe Design for Genome-Wide
DNA Methylation Study Using PRIMEGENS. In "A Practical Guide to
Bioinformatics Analysis". iConcept Press Ltd. 151-171, 2010.
- Huan Yang, Yan Wang, Trupti Joshi, Dong Xu, Shoupeng Yu,
and Yanchun Liang. MicroRNA Precursor Prediction Using SVM with
RNA Pairing Continuity Feature. In "Interdisciplinary Research and
Applications in Bioinformatics, Computational Biology, and
Environmental Sciences". Limin Angela Liu, Dong-Qing Wei and Yixue
Li eds. Medical Information Science Reference, Hershey-New York.
Chapter 7, 73-82. 2010.
- Chao Zhang Shunfu Xu Dong Xu. Detection and application of
CagA sequence markers for assessing risk factor of gastric cancer
caused by Helicobacter pylori. Proceedings of IEEE International
Conference on Bioinformatics & Biomedicine (BIBM 2010), Hong Kong,
pp 485-488, December 2010.
- Jingfen Zhang, Dong Xu, Wen Gao, Guohui Lin,
Simin He. Isotope pattern vector based tandem mass spectral data
calibration for improved peptide and protein identification, Rapid
Communications in Mass Spectrometry, 23(21):3448-3456, 2009.
- Yi Shang, Qingguo Wang, Jingfen Zhang, Bogdan Barz,
Rajkumar Bondugula, Ioan Kosztin, and Dong Xu. A New Computational
Intelligent Approach to Protein Tertiary Structure Prediction, in
“Computational Intelligence and Its Applications”. Ed: Xin Yao,
Xuelong Li, Dacheng Tao. University of Science and Technology of
China Press, 2009. ISBN 978-7-312-02218-0.
- Yong Wang, Rui-Sheng Wang, Trupti Joshi, Dong Xu,
Xiang-Sun Zhang, Luonan Chen, Yu Xia. A Linear Programming
Framework for Inferring Gene Regulatory Networks by Integrating
Heterogeneous Data. In " Handbook of Research on Computational
Methodologies in Gene Regulatory Networks". Sanjoy Das, Doina
Caragea, Stephen M. Welch, William H. Hsu eds. Medical Information
Science Reference, Hershey-New York. Chapter 19, 450-474, 2009.
- Guan Ning Lin, Zheng Wang, Dong Xu, and Jianlin Cheng.
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), Washington DC, USA, pp. 3-8, 2009.
- Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, and
Dong Xu. P3DB: a plant protein phosphorylation database. Nucleic
Acids Research, 37 (Database issue):D960-962, Epub 2009.
- Marc Libault , Trupti Joshi , Vagner A. Benedito , Dong Xu
, Michael K. Udvardi , and Gary Stacey. Legume transcription
factor genes; what makes legumes so special?. Plant Physiology
151:991-1001, 2009.
- 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. Large
scale analysis of soybean regulatory gene expression identifies a
Myb gene involved in soybean nodule development. Plant Physiology
151:1207-1220, 2009.
- Gyan Prakash Srivastava, Trupti Joshi, Zhao Song, Chao
Zhang, Guan Ning Lin, Ping Li, Andy Ross, Mihail Popescu, Jingdong
Liu, Jing Qiu, and Dong Xu, "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, 2009.
- Mihail Popescu and Dong Xu, "Mapping Genes to Biological
Pathways Using Ontological Fuzzy Rule Systems", Mihail Popescu and
Dong Xu eds. Artech House, Norwood, MA, USA. 113-132, 2009.
- Dong Xu. Computational Methods for Protein Sequence
Comparison and Search. In: Current Protocols in Protein Science,
edited by J. E. Coligan, B. M. Dunn, H. L. Ploegh, D. W. Speicher,
and P. T. Wingfield. John Wiley & Sons, New York. 56:2.1.1-2.1.27,
UNIT 2.1, 2009.
- Zhao Song, Luonan Chen, and Dong Xu. Confidence Assessment
for Protein Identification by Using Peptide-Mass Fingerprinting
Data. Proteomics, 9(11):3090-3099, 2009.
- Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, Zoran
Obradovic, A. Keith Dunker, and Dong Xu. 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), April 2009, New Orleans, USA, pp. 18-29.
- Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak
Chakraborty, and Dong Xu, ComPhy: Prokaryotic Composite Distance
Phylogenies Inferred from Whole-Genome Gene Sets. BMC
Bioinformatics, 2009, 10(Suppl 1):S5.
- Mingjie Chen, Brian P. Mooney, Martin Hajduch, Jill E.
Casteel, Trupti Joshi, Mingyi Zhou, Dong Xu, Jay J. Thelen. 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, 2009.
- Sandra Thibivilliers, Trupti Joshi, Kimberly B. Campbell,
Brian Scheffler, Dong Xu, Bret Cooper, Henry T. Nguyen and Gary
Stacey. Generation of Phaseolus vulgaris ESTs and investigation of
their regulation upon Uromyces appendiculatus infection. BMC Plant
Biology 2009, 9:46 (27 Apr 2009)
- 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, and Gary
Stacey. Establishment of a Protein Reference Map for Soybean Root
Hair Cells.Plant Physiology, February 2009, Vol. 149, pp. 670-682.
- Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak
Chakraborty, and Dong Xu. Using genome-scale-gene-based composite
distance to infer prokaryotic phylogenies. Proceeding of 7th APBC
(Asian Pacific Bioinformatics Conference), Beijing, China, pp.
40-52, 2009.
- Dong Xu. Mutual understanding between Traditional Chinese
Medicine and systems biology: gaps, challenges and opportunities,
International Journal of Functional Informatics and Personalised
Medicine, 2:248-260, 2009.
- Chao Zhang, Trupti Joshi, Guan Ning Lin, Dong Xu. An
integrated probabilistic approach for gene function prediction
using multiple sources of high-throughput data. International
Journal of Computational Biology and Drug Design, Volume 1, Number
3, 26 November 2008 , pp. 254-274(21).
- Christopher A. Bottoms and Dong Xu "Wanted: Unique Names
for Unique Atom Positions. PDB-Wide Analysis of Diastereotopic
Atom Names of Small Molecules Containing Diphosphate", BMC
Bioinformatics, 9 Suppl 9:S16, 2008.
- Gyan P Srivastava, Juyuan Guo, Huidong Shi, and Dong Xu.
PRIMEGENS-v2: Genome-wide primer design for analyzing DNA
methylation patterns of CpG islands. Bioinformatics,
24(17):1837-42, 2008.
- Robin Kramer and Dong Xu. Projecting Gene Expression
Trajectories through Inducing Differential Equations from
Microarray Time Series Experiments. Journal of VLSI Signal
Processing Systems. 50(3):321-329, 2008.
- Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, and
Dong Xu. P3DB: a plant protein phosphorylation database. Nucleic
Acids Research, Advance Access published online on October 17,
2008.
- Rajkumar Bondugula and Dong Xu. Combining Sequence and
Structural Profiles for Protein Solvent Accessibility Prediction,
Proceeding of the 7th Annual International Conference on
Computational Systems Bioinformatics (CSB 2008), Stanford
University, California, USA, pp. 195-200, 2008.
- Gyan P. Srivastava, Jing Qiu, Dong Xu. Functional
Annotation from Meta-Analysis of Microarray Datasets, Proceeding
of IEEE International Conference on Bioinformatics and Biomedicine
(BIBM 2008), Philadelphia, Pennsylvania, USA, pp. 367-271,
November 2008.
- Debjani Ghosh, Gyan P Srivastava, Dong Xu, and R. Michael
Roberts. 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, 2008.
- Dong Xu, James Keller, Mihail Popescu, and Rajkumar
Bondugula. "Application of Fuzzy Logic in Bioinformatics",
Imperial College Press, London, UK. 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. A critical assessment of Mus musculus gene
function prediction using integrated genomic evidence, Genome
Biology. 9(Suppl 1):S2 (27 June 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, and Gary
Stacey. Transcription profiling of soybean nodulation by
Bradyrhizobium japonicum. Molecular Plant-Microbe Interactions.
Vol.21, No. 5, 631-645, 2008.
- Trupti Joshi, Chao Zhang, Guan Ning Lin, Zhao Song, Dong
Xu. GeneFAS: A tool for prediction of gene function using multiple
sources of data. In "Genomics Protocols" volume of "Methods in
Molecular Biology", the second edition, edited by Ramnath
Elaswarapu and Michael P. Starkey. Humana Press, Totowa, New
Jersey. Vol.439, 369-386, 2008.
- Yu Chen and Dong Xu. Predicting Functional Modules Using
Microarray and Protein Interaction Data. In: Analysis of
Microarray Data, A Network-Based Approach, edited by F.
Emmert-Streib and M. Dehmer. VILEY_VCH Verlag GmbH &Co. KGaA,
Weinheim. 307-329, 2008.
- Sum Kim, Meng Li, Henry H. Paik, Kenneth P. Nephew,
Huidong Shi, Robin Kramer, Dong Xu, Tim H.-M. Huang. Predicting
DNA Methylation Susceptibility Using CpG Flanking Sequences.
Pacific Symposium on Biocomputing, the Big Island of Hawaii,
13:315-326, January, 2008.
- Qingguo Wang, Yi Shang, Dong Xu. A New Clustering-Based
Method for Protein Structure Selection, Proceeding of the IEEE
World Congress on Computational Intelligence, pp. 2891-2898, June
2008.
- Trupti Joshi, Jinrong Wan, Curtis J. Palm, Kara
Juneau, Ron Davis, Audrey Southwick, Katrina M. Ramonell, Gary
Stacey, Dong Xu. Bioinformatics Analyses of Arabidopsis thaliana
Tiling Array Expression Data In "Knowledge Discovery in
Bioinformatics: Techniques, Methods and Application" edited by Yi
Pan and Xiaohua (Tony) Hu, John Wiley and Sons, New York. Pages
57-70, 2007.
- Kristen H. Taylor, Robin S. Kramer, J. Wade Davis, Dong
Xu, Charles W. Caldwell, and Huidong Shi. Ultra-Deep Bisulfite
Sequencing Analysis of DNA Methylation Patterns in Multiple Gene
Promoters by 454-Sequencing. Cancer Research. 67(18):8511-8518,
2007.
- James O. Allen, Christiane M. Fauron, Patrick Minx, Leah
Westgate, Swetha Oddiraju, Guan Ning Lin, Louis Meyer, Hui Sun,
Kyung Kim, Chunyan Wang, Feiyu Du, Dong Xu, Michael Gibson, Jill
Cifrese, Sandra W. Clifton and Kathleen J. Newton. Comparisons
Among Two Fertile and Three Male-Sterile Mitochondrial Genomes of
Maize. Genetics, Vol. 177, 1173-1192. 2007.
- Woo-Suk Chang, William L. Franck, Eddie Cytryn, Sooyoung
Jeong, Trupti Joshi, David W. Emerich, Michael J. Sadowsky, Dong
Xu, and Gary Stacey. An Oligonucleotide Microarray Resource for
Transcriptional Profiling of Bradyrhizobium japonicum. Molecular
Plant-Microbe Interactions Vol. 20, No. 10, 1298-1307. 2007.
- Trupti Joshi and Dong Xu. Quantitative assessment of
relationship between sequence similarity and function similarity.
BMC Genomics, Vol. 8(1):222, 2007.
- Mihail Popescu, Dong Xu, Erik Taylor. GoFuzzKegg: Mapping
Genes to KEGG Pathways Using an Ontological Fuzzy Rule System.
Proc. of the 2007 IEEE Symposium on Comp. Intell. in Bioinf. and
Comp. Biology (CIBCB 2007), Hawaii, USA, pp. 298-303, 2007.
- Rajesh Kumar, Jing Qiu, Trupti Joshi, Babu Valliyodan,
Dong Xu, Henry T. Nguyen. Single Feature Polymorphism Discovery in
Rice. PLoS ONE 2(3): e284. doi:10.1371/journal.pone.0000284, 2007.
- Predrag S Krstic, Jack C. Wells, Miguel Fuentes-Cabrera,
Dong Xu, and James W. Lee. Toward electronic conductance
characterization of DNA nucleotide bases. Solid State Phenomena.
Vols 121-123, pages 1387-1390, 2007.
- Zhao Song, Luonan Chen, Ashwin Ganapathy, Xiu-Feng Wan,
Laurent Brechenmacher, Nengbing Tao, David Emerich, Gary Stacey,
Dong Xu. Development and Assessment of Scoring Functions for
Protein Identification Using Peptide Mass Fingerprinting Data.
Electrophoresis. 28:864-870, 2007.
- Rajkumar Bondugula and Dong Xu. MUPRED: A Tool for
Bridging the Gap between Template Based Methods and Sequence
Profile Based Methods for Protein Secondary Structure Prediction.
Proteins. 66(3):664-670, 2007.
- Mihail Popescu, Dong Xu. Mapping Genes to Pathways Using
Ontological Fuzzy Rule Systems. Fuzzy Systems Conference,
FUZZIEEE2007, London, UK, July 23-26, pp. 1-6, 2007.
- Yi Shang, Rajkumar Bondugula, Dong Xu, and Qingguo Wang.
"A New Method for Protein Tertiary Structure Prediction," in Proc.
IASTED Int'l Conf. on Computational Intelligence, Banff, Canada,
July, 2007.
- Ying Xu, Dong Xu, and Jie Liang eds. "Computational
Methods for Protein Structure Prediction and Modeling", I, II,
Springer-Verlag. 2006.
- Dong Xu and Ying Xu. Protein Structure Prediction as a
Systems Problem. In “Computational Methods for Protein Structure
Prediction and Modeling”, edited by Ying Xu, Dong Xu, and Jie
Liang. Springer-Verlag. Vol. 2. Pages 177-206, 2006.
- Guohui Lin, Dong Xu, Ying Xu. Computer Science for
Structural Bioinformatics. In “Computational Methods for Protein
Structure Prediction and Modeling”, edited by Ying Xu, Dong Xu,
and Jie Liang. Springer-Verlag. Vol. 2. Pages 241-266, 2006.
- Gyan Prakash Srivastava and Dong Xu. Genome-Scale Probe
and Primer Design with PRIMEGENS. In “Methods in Molecular
Biology”, vol 402: PCR Primer Design”, edited by Anton Yuryev,
Humana Press, Totowa, New Jersey. Pages 159-175, 2006.
- Hui Lu, Ognjen Perisic, and Dong Xu. Physical and Chemical
Basis for Structural Bioinformatics. In “Computational Methods for
Protein Structure Prediction and Modeling”, edited by Ying Xu,
Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages 267-297,
2006.
- Ying Xu, Zhijie Liu, Liming Cai, Dong Xu. Protein
Structure Prediction by Protein Threading. In “Computational
Methods for Protein Structure Prediction and Modeling”, edited by
Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages
1-42, 2006.
- Dong Xu, Jie Liang, and Ying Xu. Resources and
Infrastructure for Structural Bioinformatics. In “Computational
Methods for Protein Structure Prediction and Modeling”, edited by
Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag. Vol. 2. Pages
207-227, 2006.
- Xiufeng Wan, Guohui Lin and Dong Xu. Rnall: An Efficient
Algorithm for Predicting RNA Local Secondary Structural Landscape
in Genomes. Journal of Bioinformatics and Computational Biology.
4:1015-1031, 2006.
- Andrew Nunberg, Joseph A. Bedell, Mohammad A. Budiman,
Robert W. Citek, Sandra W. Clifton, Lucinda Fulton, Deana Pape,
Zheng Cai, Trupti Joshi, Henry Nguyen, Dong Xu and Gary Stacey.
Survey sequencing of soybean elucidates the genome structure and
composition. Functional Plant Biology. Vol. 33(8) 765-773, 2006.
- Dong Xu, Rajkumar Bondugula, Mihail Popescu, James M
Keller. "Bioinformatics and Fuzzy Logic". Proceeding of Fuzz-IEEE
2006 (IEEE International Conference on Fuzzy Systems), Vancouver,
BC, Canada, July 2006.
- Rajkumar Bondugula, Dong Xu, and Yi Shang. "A Fast
Algorithm for Low-Resolution Protein Structure Prediction".
Proceeding of the 28th International Conference of the IEEE
Engineering in Medicine and Biology Society, New York. 2006.
- Zhao Song, Luonan Chen, Chao Zhang, Dong Xu. "Design and
Implementation of Probability-Based Scoring Function for Peptide
Mass Fingerprinting Protein Identification". Proceeding of the
28th International Conference of the IEEE Engineering in Medicine
and Biology Society, New York. 2006. In press.
- Yong Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, and
Luonan Chen. "Supervised Inference of Gene Regulatory Networks by
Linear Programming". Lecture Notes in Computer Science, 4115,
551-561, 2006. (Also in Proceeding of the 2006 International
Conference on Intelligent Computing (ICIC 2006), Kunming, China).
- Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan
Chen. Inferring Gene Regulatory Networks from Multiple Microarray
Datasets. Bioinformatics. 22:2413-2420, 2006.
- Pin-Hao Chi, Chi-Ren Shyu, Dong Xu. A fast SCOP fold
classification system using content-based E-Predict algorithm. BMC
Bioinformatics. 7:362, 2006.
- Robin Kramer, Victor Olman, Ying Xu, and Dong Xu,
DigitalTree: A Tool for Displaying Biological Data in Tree
Structure. Lecture Notes in Computer Science, 3992, 855-862. (Also
in Proceeding of International Conference on Computational Science
2006 (ICCS 2006), University of Reading, UK.
- Monir Shababi, Karuppaiah Palanichelvam, Anthony B. Cole,
Dong Xu, Xiu-Feng Wan, and James E. Schoelz. The ribosomal shunt
translation strategy of Cauliflower mosaic virus has evolved from
ancient long terminal repeats. Journal of Virology. 80:3811-3822,
2006.
- Seung Yon Rhee, Julie Dickerson, and Dong Xu.
Bioinformatics and Its Applications in Plant Biology. Annual
Review of Plant Biology. 57:335-360. 2006.
- Xiaomeng Wu, Xiu-Feng Wan, Gang Wu, Dong Xu, and Guohui
Lin. Phylogenetic Analysis Using Complete Signature Information of
Whole Genomes and Clustered Neighbor-Joining Method. Journal of
Bioinformatics Research and Applications. 2:219-248, 2006.
- Xiu-Feng Wan, Jizhong Zhou, and Dong Xu. CodonO: A new
informatics method measuring synonymous codon usage bias.
International Journal of General Systems. 35:109-125, 2006
- Dong Xu, Ognen Duzlevski, and Xiu-Feng Wan. In search of
remote homolog. In Handbook of Computational Molecular Biology,
edited by Srinivas Aluru, CRC Press. 33:1-33:27, 2006.
- Yu Chen and Dong Xu. Bioinformatics Analysis for
Interactive Proteomics. In Current Protocols in Protein Science,
edited by J. E. Coligan, B. M. Dunn, H. L. Ploegh, D. W. Speicher,
and P. T. Wingfield. John Wiley & Sons, New York. 25.1.1-25.1.14,
2005.
- Xiu-Feng Wan and Dong Xu. Computational Methods for Remote
Homlog Identification. Current Protein and Peptide Science. Vol
6:527-546, 2005.
- Jinrong Wan, Michael Torres, Ashwin Ganapathy, Jay Thelen,
Beverly B. DaGue, Brian Mooney, Dong Xu, and Gary Stacey.
Proteomic analysis of soybean root hairs after infection by
Bradyrhizobium japonicum. Mol. Plant-Microbe Int. 18:458-467,
2005.
- Trupti Joshi, Yu Chen, Nickolai Alexandrov, Dong Xu.
Cellular Function Prediction and Biological Pathway Discovery in
Arabidopsis thaliana Using Microarray Data. International Journal
of Bioinformatics Research and Applications. Vol 1:335-350, 2005.
- Zhi-Zhong Chen, Guohui Lin, Romeo Rizzi, Jianjun Wen, Dong
Xu, Ying Xu, Tao Jiang: More Reliable Protein NMR Peak Assignment
via Improved 2-Interval Scheduling. Journal of Computational
Biology. 12 (2): 129-146, 2005.
- Xiu-Feng Wan, Tao Ren, Kai-Jian Luo, Ming Liao, Gui-Hong
Zhang, Jin-Ding Chen, Wei-Sheng Cao, Ye Li, Ning-Yi Jin, Dong Xu
and Chao-An Xin. Genetic characterization of H5N1 Avian Influenza
Viruses isolated in Southern China during the 2003-04 avian
influenza breakouts. Archives of Virology. 150 (6):1257-1266,
2005.
- Xiu-Feng Wan, Demet Ataman, Dong Xu.Application of
computational biology in understanding emerging infectious
diseases: inferring the biological function for S-M complex of
SARS-CoV. In "Bioinformatics:New Research", Edited by Nova Science
Publishers, Inc. New York. Pages 55-80. 2005.
- Xiu-Feng Wan and Dong Xu. Intrinsic terminator prediction
and its application in Synechococcus sp. WH8102. Journal of
Computer and Science Technology. 20:465-482, 2005.
- Yu Chen and Dong Xu. Genome-Scale Understanding Protein
Dispensability through Machine-Learning Analysis of
High-Throughput Data. Bioinformatics. 21:575-581, 2005.
- Rajkumar Bondugula, Ognen Duzlevski, Dong Xu. Profiles and
fuzzy K-nearest neighbor algorithm for protein secondary structure
prediction. Pages 85-94. Yi-Ping Phoebe Chen and Limsoon Wong,
editors. Proceedings of 3rd Asia-Pacific Bioinformatics
Conference, 17-21 January 2005, Singapore. Imperial College Press,
London.
- Yu Chen and Dong Xu. Genome-Scale Protein Function
Prediction in Yeast Saccharomyces Cerevisiae Through Integrating
Multiple Sources Of High-Throughput Data. Proceedings of the 2005
Pacific Symposium on Biocomputing (PSB), 471-482.
- Trupti Joshi, Yu Chen, Jeffrey M. Becker, Nickolai
Alexandrov, Dong Xu. Genome-Scale Gene Function Prediction Using
Multiple Sources of High-Throughput Data in Yeast Saccharomyces
cerevisiae. OMICS: A Journal of Integrative Biology Dec 2004, Vol.
8, No. 4: 322-333.
- Yu Chen and Dong Xu. Global Protein Function Annotation
through Mining Genome-Scale Data in Yeast Saccharomyces
cerevisiae. Nucleic Acid Research. 32:6414-6424, 2004.
- Wes G. Smith, Satish S. Nair, Dong Xu, Jyotsna Nair, and
Bernard D. Beitman. “Framework for Developing a Hierarchical Model
for Reward Focusing on the Nucleus Accumbens,” 26th International
Conference of the IEEE Engineering in Medicine and Biology
Society, Sept 2004, San Francisco, CA, USA. September 1-5,
2004.133-136
- Cline, C. H., Satish S. Nair, Dong Xu, Jyotsna Nair, and
Bernard D. Beitman. “Modeling Obsessive Compulsive Disorder,” 26th
International Conference of the IEEE Engineering in Medicine and
Biology Society, Sept 2004, San Francisco, CA, USA. September 1-5,
2004.890-893.
- Iyoho, A., Satish S. Nair, Dong Xu, Jyotsna Nair, and
Bernard D. Beitman. “Computational Modeling of Hysterical
Paralysis,” 26th International Conference of the IEEE Engineering
in Medicine and Biology Society, Sept 2004, San Francisco, CA,
USA. September 1-5, 2004.894-897
- Trupti Joshi, Yu Chen, Nickolai Alexandrov, Dong Xu.
Cellular Function Prediction and Biological Pathway Discovery in
Arabidopsis thaliana Using Microarray Data. Proceedings of the
26th Annual International Conference of the IEEE EMBS San
Francisco, CA, USA. September 1-5, 2004. 2881-2884.
- Ashwin Ganapathy, Xiu-Feng Wan, Jinrong Wan, Jay Thelen,
David W. Emerich, Gary Stacey, and Dong Xu. "Statistical
Assessment for Mass-spec Protein Identification Using Peptide
Fingerprinting Approach". Preceedings of the 26th International
Conference of the IEEE Engineering in Medicine and Biology
Society, pp. 3051-3054. Sept 1-5, 2004, San Francisco, CA.
- Xiu-Feng Wan, Dong Xu, Andris Kleinhofs, and Jizhong Zhou.
Quantitative relationship between codon usage bias and GC
composition across the unicellular genomes. BMC Evolutionary
Biology. BMC Evolutionary Biology 2004, 4:19, 2004.
- Yu Chen and Dong Xu. Prediction of Protein dispensability
through integrated analysis of multi-source high-throughput data.
In Proceeding of the 5th International Conference on Software
Engineering, Artificial Intelligence, Networking and
Parallel/Distributed Computing (SNPD 2004), pp 158-166. June 30 -
July 2, 2004. Beijing, China.
- Chi-Ren Shyu, Pin-Hao Chi, Grant Scott, Dong Xu.
ProteinDBS: A real-time retrieval system for protein structure
comparison. Nucleic Acid Research. 32 (Web Server issue): W572 -
CW575, 2004.
- Jun-tao Guo, Kyle Ellrott, Won Jae Chung, Dong Xu, Serguei
Passovets, Ying Xu. PROSPECT-PSPP: An Automatic Computational
Pipeline for Protein Structure Prediction. Nucleic Acid Research.
32 (Web Server issue): W522 - CW525, 2004.
- Joshi, Trupti; Chen, Yu; Becker, Jeffrey; Alexandrov,
Nickolai; Xu, Dong. Function Prediction for Hypothetical Proteins
in Yeast Saccharomyces cerevisiae Using Multiple Sources of
High-Throughput Data. Proceeding of the 8th World Multi-Conference
on Systemics, Cybernetics and Informatics (2004). Vol. IX, 17-20.
- Kunbin Qu, Yanmei Lu, Nan Lin, Rajinder Singh, Donald G.
Payan, Dong Xu. Computational and Experimental Studies on Human
Misshapen/NIK-Related Kinase MINK-1. Current Medicinal Chemistry.
11:569-582, 2004.
- Jane Razumovskaya, Victor Olman, Dong Xu, Ed Uberbacher,
Nathan C. VerBerkmoes, Robert L. Hettich, and Ying Xu, A
Computational Method for Assessing Peptide-Identification
Reliability in Tandem Mass Spectrometry Analysis with SEQUEST,
Proteomics. 4:961-969, 2004.
- Sonia M. Tiquia, Liyou Wu, Song C. Chong, Sergei
Passovets, Dong Xu, Ying Xu, and Jizhong Zhou. Evaluation of
50-mer oligonucleotide arrays for detecting microbial populations
in environmental samples. BioTechniques. 36:664-670, 2004.
- Xiufeng Wan, Dong Xu, and Jizhong Zhou. A new
informatics method measuring synonymous codon usage bias. In
Intelligent engineering systems through artificial neural
networks, vol 13, eds. Dagli et al., 1101-1018. New York, NY: ASME
Press.
- Victor Olman, Dong Xu, and Ying Xu. Solving data
clustering problem as a string search problem. Proceedings of
Conference on Statistical Data Mining and Knowledge Discovery (ed
by Hamparsum Bozdogan), Chapman & Hall/CRC, 417-434, 2003.
- Zhi-Zhong Chen, Tao Jiang, Guohui Lin, Jianjun Wen, Dong
Xu, Jinbo Xu, and Ying Xu. Approximation algorithms for NMR
spectral peak assignment. Theoretical Computer Science,
1-3(299):211-229. 2003.
- Victor Olman, Dong Xu, and Ying Xu. Identifications of
Regulatory Binding Sites Using Minimum Spanning Trees. In
Proceedings of the 2003 Pacific Symposium on Biocomputing (PSB).
Pages 327-338. 2003.
- Yu Chen, Trupti Joshi, Ying Xu, and Dong Xu. Towards
Automated Derivation of Biological Pathways Using High-Throughput
Biological Data. Proceeding of the 3rd IEEE Symposium on
Bioinformatics and Bioengineering (2003). 18-25, IEEE/CS Press.
- Manesh Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott,
Li Wang, Inna Vokler, Philip LoCascio, Dong Xu, and Ying Xu. A
Computational Pipeline for Protein Structure Prediction and
Analysis at Genome Scale. Proceeding of the 3rd IEEE Symposium on
Bioinformatics and Bioengineering (2003). 3-10, IEEE/CS Press.
- Guohui Lin, Dong Xu, Zhi-zhong Chen, Tao Jiang, Jianjun
Wen, and Ying Xu, Computational assignments of protein backbone
NMR peaks by efficient bounding and filtering, Journal of
Bioinformatics and Computational Biology. 31:944-52. 2003.
- Yu Chen and Dong Xu. Computational Analyses of
High-Throughput Protein-Protein Interaction Data. Current Protein
and Peptide Science. 4:159-181. 2003.
- Dong Xu, Dongsup Kim, Phuongan Dam, Manesh Shah, Edward C.
Uberbacher, and Ying Xu. Characterization of Protein Structure and
Function at Genome Scale Using a Computational Prediction
Pipeline. In "Genetic Engineering, Principles and Methods", edited
by Jane K. Setlow. Kluwer Academic / Plenum Publishers, New York.
269-293. 2003.
- Yongqing Liu, Jizhong Zhou, Marina V. Omelchenko, Alex S.
Beliaev, Amudhan Venkateswaran, Julia Stair, Liyou Wu, Dorothea K.
Thompson, Dong Xu, Igor B. Rogozin, Elena K. Gaidamakova, Min
Zhai, Kira S. Makarova, Eugene V. Koonin, and Michael J. Daly.
Transcriptome dynamics of Deinococcus radiodurans recovering from
ionizing radiation. Proceedings of National Academy of Sciences.
100: 4191-4196. 2003.
- Christal Yost, Loren Hauser, Frank Larimer, Dorothea
Thompson, Alexander Beliaev, Jizhong Zhou, Ying Xu, and Dong Xu. A
computational study of Shewanella oneidensis MR-1: Structural
prediction and functional inference of hypothetical proteins.
OMICS. 7:177-192. 2003.
- Victor Olman, Dong Xu, and Ying Xu. CUBIC: Identifications
of Regulatory Binding Sites through Data Clustering. Journal of
Bioinformatics and Computational Biology. 1:21-40. 2003.
- Yu Chen, Yutao Liu, Keith M. Goldstein, Jeffrey M. Becker,
Ying Xu, and Dong Xu. A Computational Study on the Signal
Transduction Pathway for Amino Acid and Peptide Transport in
Yeast: Bridging the Gap between High-Throughput Data and
Traditional Biology. Applied Genomics and Proteomics. 2:43-50.
2003.
- Dong Xu, Victor Olman, Li Wang, and Ying Xu. EXCAVATOR: a
computer program for gene expression data analysis. Nucleic Acid
Research. 31: 5582-5589. 2003.
- Manesh Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott,
Li Wang, Inna Vokler, Philip LoCascio, Dong Xu, and Ying Xu. A
Computational Pipeline for Protein Structure Prediction and
Analysis at Genome Scale. Bioinformatics. 19:1985-1996. 2003.
- Zhi-Zhong Chen, Tao Jiang, Guohui Lin, Romeo Rizzi,
Jianjun Wen, Dong Xu, Ying Xu. More reliable protein NMR peak
assignment via improved 2-interval scheduling. Proceedings of 11th
European Symposium on Algorithms (ESA2003). 580-592, 2003.
- Xiang Wan, Dong Xu, Carolyn M. Slupsky, Guohui Lin.
Automated Protein NMR Resonance Assignments. In Computational
Systems Bioinformatics (CSB2003). IEEE Computer Society, Los
Alamitos, California. Pages 197-207. 2003.
- Tema Fridman, Robert Day, Jane Razumovskaya, Dong Xu,
Andrey Gorin. Probability Profiles - Novel Approach in Tendem Mass
Spectrometry De Novo Sequencing. In Computational Systems
Bioinformatics (CSB2003). IEEE Computer Society, Los Alamitos,
California. Pages 415-418. 2003.
- Dongsup Kim, Dong Xu, Juntao Guo, Kyle Ellrott, Ying Xu,
PROSPECT II: protein structure prediction program for genome-scale
application. Protein Engineering, 16(9), 641-650, 2003.
- Ying Xu and Dong Xu. Protein Structure Prediction by
Protein Threading and Partial Experimental Data. In: Current
topics in computational biology, edited by Tao Jiang, Ying Xu, and
Michael Q. Zhang. The MIT press. Cambridge, Massachusetts. Pages
467-502. 2002.
- Ying Xu, Dong Xu, and Victor Olman. A Practical Method for
Interpretation of Threading Scores: An Application of Neural
Network. Statistica Sinica (special issue in bioinformatics).
12:159-177. 2002.
- Dong Xu and Ying Xu. Computational Studies of Protein
Structure and Function Using Threading Program PROSPECT. In
Protein Structure Prediction: Bioinformatic Approach, edited by
Igor Tsigelny. International University Line publishers (IUL), La
Jolla, CA. Pages 5-41. 2002.
- Ying Xu, Victor Olman, and Dong Xu. Clustering Gene
Expression Data Using a Graph-Theoretic Approach: An Application
of Minimum Spanning Trees. Bioinformatics. 18:526-535, 2002.
- Ying Xu, Dong Xu, Dongsup Kim, Victor Olman, Jane
Razumovskaya, and Tao Jiang Automated Assignment of Backbone NMR
Peaks Using Constrained Bipartite Matching. Computing in Science
and Engineering. Jan/Feb: 50-62. 2002.
- Dong Xu, Guangshan Li, Liyou Wu, Jizhong Zhou, and Ying
Xu. PRIMEGENS: A Computer Program for Robust and Efficient Design
of Gene-Specific Probes for Microarray Analysis. Bioinformatics.
18:1432-1437. 2002.
- Katrina M. Ramonell, Bing Zhang, Rob M. Ewing, Yu Chen,
Dong Xu, Gary Stacey, and Shauna Somerville. Microarray analysis
of chitin elicitation in Arabidopsis thaliana. Molecular Plant
Pathology. 3:301-311. 2002.
- Guohui Lin, Dong Xu, Zhi-Zhong Chen, Tao Jiang, and Ying
Xu. An Efficient Branch-and-Bound Algorithm for the Assignment of
Protein Backbone NMR Peaks. In Proceedings of the IEEE Computer
Society Bioinformatics Conference (CSB2002). IEEE Computer
Society, Los Alamitos, California. Pages 165-174. 2002.
- Ayca Akal-Strader, Sanjay Khare, Dong Xu, Fred Naider,
Jeff M. Becker. Residues in the first extracellular loop of a G
protein-coupled receptor play a role in signal transduction.
Journal of Biological Chemistry. 277:30581-30590. 2002.
- Zhi-Zhong Chen, Tao Jiang, Guohui Lin, Jianjun Wen, Dong
Xu, Ying Xu. Improved Approximation algorithms for NMR spectral
peak assignment In Proceedings of the 2002 Workshop on Algorithms
in BioInformatics (WABI 2002). 82-96. 2002.
- Grant S. Heffelfinger, Anthony Martino, Andrey Gorin, Ying
Xu, Mark D. Rintoul III, Al Geist, Hashimi M. Al-Hashimi, George
S. Davidson, Jean Loup Faulon, Laurie J. Frink, David M. Haaland,
William E. Hart, Erik Jakobsson, Todd Lane, Ming Li, Phil
Locascio, Frank Olken, Victor Olman,Brian Palenik, Steven J.
Plimpton, Diana C. Roe, Nagiza F. Samatova, Manesh Shah, Arie
Shoshoni, Charlie E. M. Strauss, Edward V.Thomas, Jerilyn A.
Timlin, and Dong Xu. Carbon Sequestration in Synechococcus Sp.:
From Molecular Machines to Hierarchical Modeling. OMICS. 6:
305-329. 2002.
- Juntao Guo, Dongsup Kim, Dong Xu, and Ying Xu, Improving
the Performance of DomainParser for Structural Domain Partition
using Neural Network, Nucleic Acids Research. 31:1-9, 2002.
- Dong Xu, Kunnumal Baburaj, Cynthia B. Peterson,
and Ying Xu. A Model for the Three-Dimensional Structure of
Vitronectin: Predictions for the Multi-Domain Protein from
Threading and Docking. Proteins: Structure, Function, and
Genetics. 44:312-320. 2001.
- Dong Xu, Oakley H. Crawford, Philip F. LoCascio, and Ying
Xu. Application of PROSPECT in CASP4: Characterizing Protein
Structures with New Folds.Proteins: Structure, Function, and
Genetics (CASP4 Special Issue). 46:140-148. 2001.
- Ying Xu, Victor Olman, and Dong Xu. Minimum Spanning Trees
for Gene Expression Data Clustering. In Proceedings of the 12th
International Conference on Genome Informatics (GIW), edited by S.
Miyano, R. Shamir and T. Takagi. Universal Academy Press, Tokyo.
Pages 24-33. 2001.
- Dong Xu, Michael A. Unseren, Ying Xu, and Edward C.
Uberbacher. Sequence-structure specificity of a knowledge based
energy function at the secondary structure level. Bioinformatics.
16:257-68, 2000.
- Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein,
and Engin Serpersu. Protein structure determination using protein
threading and sparse NMR data. In: The Fourth Annual International
Conference on Computational Molecular Biology, edited by R.
Shamir, S. Miyano, S. Istrail, P. Pevzner, and M. Waterman. Pages
299-307, ACM, Tokyo, Japan. 2000.
- Dong Xu and Ying Xu. Protein Databases on the Internet.
In: Current Protocols in Protein Science, edited by J. E. Coligan,
B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T. Wingfield.
John Wiley & Sons, New York. Volume 1, pages 2.6.1-2.6.15. 2000.
- Dong Xu and Ying Xu. Protein tertiary structure
prediction. In: Current Protocols in Protein Science, edited by J.
E. Coligan, B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T.
Wingfield. John Wiley & Sons, New York. Volume 1, pages
2.7.1-2.7.17. 2000.
- Dong Xu, Ying Xu, and Edward C. Uberbacher. Computational
tools for protein modeling. Current Protein and Peptide Science.
1:1-21. 2000.
- Dong Xu, Ying Xu, Gary Li, and Jizhong Zhou. A Computer
Program for Generating Gene-Specific Fragments for Microarrays. In
Currents in Computational Molecular Biology, edited by S. Miyano,
R. Shamir and T. Takagi. Universal Academy Press, Inc. Tokyo,
Japan. Pages 3-4. 2000.
- Ying Xu and Dong Xu. Protein threading using PROSPECT:
Design and evaluation.Proteins: Structure, Function, and Genetics.
40:343-354. 2000.
- Ying Xu, Dong Xu. Oakley H. Crawford, and J. Ralph
Einstein. "A computational method for NMR-constrained protein
threading." Journal of Computational Biology. 7:449-467. 2000.
- Ying Xu, Dong Xu, and Harold N. Gabow. Protein Domain
Decomposition using a Graph-Theoretic Approach. Bioinformatics.
16:1091-1104. 2000.
- Zhirong Sun, Xiaofeng Xia, Qing Guo, and Dong
Xu. Protein structure prediction in a 210-type lattice model:
parameter optimization in the genetic algorithm using orthogonal
array. Journal of Protein Chemistry. 18:39-46, 1999.
- Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein,
Frank Larimer, Edward C. Uberbacher, Michael A. Unseren, and Ge
Zhang. Protein threading by PROSPECT: a prediction experiment in
CASP3. Protein Engineering. 12:899-907, 1999.
- Dong Xu, Chung-Jung Tsai, and Ruth Nussinov. Mechanism and
Evolution of Protein Dimerization Protein Science. 7:533-544, 1998
(with a picture selected on the cover of the issue).
- Raquel Norel, Shuo L. Lin, Dong Xu, Haim J. Wolfson, and
Ruth Nussinov. Molecular surface variability and induced
conformational changes upon protein-protein associations. In:
Structure, Motion, Interaction and Expression of Biological
Macromolecules (Sarma, R. H. and Sarma, M. H. Eds.), Vol. 2, pp.
33-52, 1998, (also in The Proceedings of the 10th Conversation)
Adenine Press, Albany, NY.
- Shuo L. Lin, Dong Xu, Aijun Li, Maria Roiterst, Haim J.
Wolfson, and Ruth Nussinov. Electrostatics, allostericity and
activity of the yeast chorismate mutate. Proteins: Structure,
Function, and Genetics. 31:445-452, 1998.
- Chung-Jung Tsai, Dong Xu, and Ruth Nussinov. Protein
folding via binding, and vice versa (Review). Folding & Design,
3:R71-R80, 1998.
- Ying Xu, Dong Xu, and Edward C. Uberbacher. A new method
for modeling and solving the protein fold recognition problem. In:
The Second Annual International Conference on Computational
Molecular Biology, (Istrail, S, Pevzner, P, Waterman, M, eds) pp.
285-292. ACM New York, 1998.
- Ying Xu, Dong Xu, and Edward C. Uberbacher. An efficient
computational method for globally optimal threading. Journal of
Computational Biology. 5:597-614, 1998.
- Dong Xu, Shuo L. Lin, and Ruth Nussinov.
Protein Binding versus Protein Folding: The Role of Hydrophilic
Bridges in Protein Associations. Journal of Molecular Biology,
265:68-84, 1997.
- Zhirong Sun, Xiaoqian Rao, Liwei Peng, and Dong Xu.
Prediction of protein supersecondary structures based on the
artificial neural network method. Protein Engineering, 10:763-769,
1997.
- Shuo L. Lin, Dong Xu, Aijun Li, Maria Rosen, Haim J.
Wolfson, and Ruth Nussinov. Investigation of the enzymatic
mechanism of the yeast chorismate mutase by docking a transition
state analog. Journal of Molecular Biology, 271:838-845 1997.
- Chung-Jung Tsai, Dong Xu, and Ruth Nussinov. Structural
motifs at protein-protein interfaces: Protein cores versus
two-state and three-state model complexes. Protein Science,
6:1793-1805, 1997.
- Dong Xu, Chung-Jung Tsai, and Ruth Nussinov. Hydrogen
bonds and salt bridges across protein-protein interfaces. Protein
Engineering, 10:999-1012, 1997.
- Dong Xu and Ruth Nussinov. Favorable Domain Size in
Proteins. Folding & Design, 3:11-17, 1997.
- Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Jurgen
Kopke, and Hartmut Michel. Knowledge based structure prediction of
the light-harvesting complex II of rhodospirillum molischianum. In
P.M. Pardalos, D. Shalloway, and G. Xue, editors, Global
Minimization of Nonconvex Energy Functions: Molecular Conformation
and Protein Folding. American Mathematical Society. 97-122, 1996.
- Dong Xu, Charles Martin, and Klaus Schulten. Molecular
dynamics study of early picosecond events in the bacteriorhodopsin
photocycle: Dielectric response, vibrational cooling and the J, K
intermediates. Biophysical Journal, 70:453-460, 1996.
- Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Jurgen
Kopke, and Hartmut Michel. Prediction of the structure of an
integral membrane protein-the light-harvesting complex II of
rhodospirillum molischianum. In K.M. Merz and B. Roux, editors,
Biological Membranes: A Molecular Perspective from Computation and
Experiment, pages 503-533. Birkhauser, Cambridge, MA. 1996.
- Dong Xu, James Christopher Phillips, and Klaus Schulten.
Protein response to external electric fields: Relaxation,
hysteresis, echo. Journal of Physical Chemistry, 100:12108-12121,
1996.
- Dong Xu, Klaus Schulten, Oren M. Becker, and Martin
Karplus. Temperature quench echoes in proteins. Journal of
Chemical Physics, 103:3112-3123, 1995.
- Dong Xu and Klaus Schulten. Velocity reassignment echoes
in proteins. Journal of Chemical Physics, 103:3124-3139, 1995.
- Dong Xu, Mordechai Sheves, and Klaus Schulten. Molecular
dynamics study of the M412 intermediate of bacteriorhodopsin.
Biophysical Journal, 69:2745-2760, 1995.
- Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Jurgen
Kopke, and Hartmut Michel. Predicting the structure of the
light-harvesting complex II of rhodospirillum molischianum.
Protein Science, 4:1670-1682, 1995.
- William Humphrey, Dong Xu, Klaus Schulten, and Mordechai
Sheves. Molecular dynamics study of the early intermediates in the
bacteriorhodopsin photocycle. Journal of Physical Chemistry,
99:14549-14560, 1995.
- Klaus Schulten, William Humphrey, Ilya Logunov, Mordechai
Sheves, and Dong Xu. Molecular dynamics and quantum chemistry
studies of bacteriorhodopsin. Israel Journal of Chemistry,
99:14549-14560, 1995.
- Dong Xu and Klaus Schulten. Coupling of protein motion to
electron transfer in a photosynthetic reaction center:
Investigating the low temperature behaviour in the framework of
the spin-boson model. Chemical Physics, 182:91-117, 1994.
- Wensheng Zhou and Dong Xu. Microwave magnetic resonance in
reentrant spin glass spinel CoxZn1-xFe 2yCr1-2y O4 , Acta Physica
Sinica, 41(12):2043-2048, 1992.
- Dong Xu and Klaus Schulten. Multi-mode coupling of protein
motion to electron transfer in the photosynthetic reaction center:
Spin-boson theory based on a classical molecular dynamics
simulation. In The Photosynthetic Bacterial Reaction Center: II.
Structure, Spectroscopy and Dynamics, NATO ASI Series A: Life
Sciences (J. Breton and A. Vermeglio, editors), pages 301-312.
Plenum Press, New York, 1992.