Dong Xu

Dong Xu

Center for Computational Medicine and Bioinformatics, University of Michigan

Affiliated withUniversity of Michigan Tongji UniversityTongji Zhejiang College

Research Area

BiologyMedicine

Biography

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JoVE Journal Publications

Article
Total : 2
Year
A Protocol for Computer-Based Protein Structure and Function Prediction
Publication title
2011
2024

Other Publications

Article
Year
MUFOLD-WQA: A new selective consensus method for quality assessment in protein structure prediction.

Proteins| PubMed ID: 21997748

2011
Rank-one projections with adaptive margins for face recognition.

IEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society| PubMed ID: 17926705

2007
Epidermal growth factor-like domain 7 protects endothelial cells from hyperoxia-induced cell death.

American journal of physiology. Lung cellular and molecular physiology| PubMed ID: 17934064

2008
Design and implementation of probability-based scoring function for peptide mass fingerprinting protein identification.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference| PubMed ID: 17946250

2006
A fast algorithm for low-resolution protein structure prediction.

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference| PubMed ID: 17946724

2006
Genome-scale probe and primer design with PRIMEGENS.

Methods in molecular biology (Clifton, N.J.)| PubMed ID: 17951795

2007
Marginal Fisher analysis and its variants for human gait recognition and content- based image retrieval.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society| PubMed ID: 17990757

2007
Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data.

International journal of bioinformatics research and applications| PubMed ID: 18048140

2005
Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method.

International journal of bioinformatics research and applications| PubMed ID: 18048163

2006
2007
2008
Protein databases on the internet.

Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.]| PubMed ID: 18265344

2004
2008
Proprioception of ankle and knee joints in obese boys and nonobese boys.

Medical science monitor : international medical journal of experimental and clinical research| PubMed ID: 18301356

2008
[Establishment of an I-SceI system and its application to introduce DNA double-strand break into human hepatoma cell line HepG2].

Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology| PubMed ID: 18304424

2008
2008
Discriminant locally linear embedding with high-order tensor data.

IEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society| PubMed ID: 18348919

2008
Effects of two novel nucleoside analogues on different hepatitis B virus promoters.

World journal of gastroenterology : WJG| PubMed ID: 18350620

2008
GeneFAS: A tool for prediction of gene function using multiple sources of data.

Methods in molecular biology (Clifton, N.J.)| PubMed ID: 18370116

2008
2008
Transcription profiling of soybean nodulation by Bradyrhizobium japonicum.

Molecular plant-microbe interactions : MPMI| PubMed ID: 18393623

2008
2009
2011
Protein databases on the internet.

Current protocols in protein science / editorial board, John E. Coligan ... [et al.]| PubMed ID: 18429255

2004
Bioinformatics analysis for interactive proteomics.

Current protocols in protein science / editorial board, John E. Coligan ... [et al.]| PubMed ID: 18429286

2005
2008
Tai Chi exercise and muscle strength and endurance in older people.

Medicine and sport science| PubMed ID: 18487883

2008
Tai Chi exercise and proprioception behavior in old people.

Medicine and sport science| PubMed ID: 18487888

2008
2008
2008
Targeted screening of SiRNA directed HBV polymerase gene for effective inhibition of HBV expression.

Journal of Huazhong University of Science and Technology. Medical sciences = Hua zhong ke ji da xue xue bao. Yi xue Ying De wen ban = Huazhong keji daxue xuebao. Yixue Yingdewen ban| PubMed ID: 18563320

2008
2008
2008
2008
2008
2008
[Studies on absorption mechanism of loganin in intestines of rats].

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica| PubMed ID: 18652356

2008
A link between SIN1 (MAPKAP1) and poly(rC) binding protein 2 (PCBP2) in counteracting environmental stress.

Proceedings of the National Academy of Sciences of the United States of America| PubMed ID: 18687895

2008
Video event recognition using kernel methods with multilevel temporal alignment.

IEEE transactions on pattern analysis and machine intelligence| PubMed ID: 18787246

2008
2008
2008
Face recognition using spatially constrained earth mover's distance.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society| PubMed ID: 18854252

2008
P3DB: a plant protein phosphorylation database.

Nucleic acids research| PubMed ID: 18931372

2009
[Construction and identification of the eukaryotic expression vector pIRES2-EGFP-IL-1ra-Fcepsilon].

Fen zi xi bao sheng wu xue bao = Journal of molecular cell biology / Zhongguo xi bao sheng wu xue xue hui zhu ban| PubMed ID: 18959005

2008
2003
IMP dehydrogenase type 1 associates with polyribosomes translating rhodopsin mRNA.

The Journal of biological chemistry| PubMed ID: 18974094

2008
2009
2009
2009
2009
2009
[A study on the registration method and precision in image guided surgery].

Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi| PubMed ID: 19166185

2008
2009
2009
2009
2009
2009
2009
2009
Trajectory tracking control of omnidirectional wheeled mobile manipulators: robust neural network-based sliding mode approach.

IEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society| PubMed ID: 19336336

2009
2009
2009
Computational methods for protein sequence comparison and search.

Current protocols in protein science / editorial board, John E. Coligan ... [et al.]| PubMed ID: 19365790

2009
2009
Knockdown of ERp57 increases BiP/GRP78 induction and protects against hyperoxia and tunicamycin-induced apoptosis.

American journal of physiology. Lung cellular and molecular physiology| PubMed ID: 19411306

2009
Semi-supervised bilinear subspace learning.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society| PubMed ID: 19447714

2009
Expression of toll-like receptor 9 in peripheral blood mononuclear cells from patients with different hepatitis B and C viral loads.

Journal of Huazhong University of Science and Technology. Medical sciences = Hua zhong ke ji da xue xue bao. Yi xue Ying De wen ban = Huazhong keji daxue xuebao. Yixue Yingdewen ban| PubMed ID: 19513613

2009
2009
2009
Programmed cell death protein 5 (PDCD5) is phosphorylated by CK2 in vitro and in 293T cells.

Biochemical and biophysical research communications| PubMed ID: 19616514

2009
2009
Textual query of personal photos facilitated by large-scale web data.

IEEE transactions on pattern analysis and machine intelligence| PubMed ID: 20714015

2011
Combining sequence and structural profiles for protein solvent accessibility prediction.

Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference| PubMed ID: 19642280

2008
2009
2009
2009
2008
2008
Enhancing bilinear subspace learning by element rearrangement.

IEEE transactions on pattern analysis and machine intelligence| PubMed ID: 19696459

2009
2009
2009
2009
2010
2009
2009
2010
Management of lung nodules detected by volume CT scanning.

The New England journal of medicine| PubMed ID: 19955524

2009
2009
2010
2009
Bioinformatics methods for protein identification using Peptide mass fingerprinting.

Methods in molecular biology (Clifton, N.J.)| PubMed ID: 20013361

2010
2010
2010
An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data.

International journal of computational biology and drug design| PubMed ID: 20054992

2008
[Nitrogen removal under the condition of carbon source supplement in integrated vertical-flow constructed wetland].

Huan jing ke xue= Huanjing kexue / [bian ji, Zhongguo ke xue yuan huan jing ke xue wei yuan hui "Huan jing ke xue" bian ji wei yuan hui.]| PubMed ID: 20063744

2009
2010
2010
2009
2010
2010
2010
Flexible manifold embedding: a framework for semi-supervised and unsupervised dimension reduction.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society| PubMed ID: 20215078

2010
Genome wide exploration of the origin and evolution of amino acids.

BMC evolutionary biology| PubMed ID: 20230639

2010
Investigating the mechanism of disease in the RP10 form of retinitis pigmentosa.

Advances in experimental medicine and biology| PubMed ID: 20238057

2010
2009
2010
Recombinant human PDCD5 sensitizes chondrosarcomas to cisplatin chemotherapy in vitro and in vivo.

Apoptosis : an international journal on programmed cell death| PubMed ID: 20349137

2010
Purification and biochemical characterisation of a novel glutamate decarboxylase from rice bran.

Journal of the science of food and agriculture| PubMed ID: 20355143

2010
2010
PMirP: a pre-microRNA prediction method based on structure-sequence hybrid features.

Artificial intelligence in medicine| PubMed ID: 20399081

2010
2010
User-assisted ink-bleed reduction.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society| PubMed ID: 20421185

2010
[Generation and characterization of monoclonal antibody against human PIK3IP1].

Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology| PubMed ID: 20423653

2010
Image clustering using local discriminant models and global integration.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society| PubMed ID: 20423802

2010
2010
2010
2010
2010
[Study on optimization gradation of substrates in vertical flow constructed wetlands].

Huan jing ke xue= Huanjing kexue / [bian ji, Zhongguo ke xue yuan huan jing ke xue wei yuan hui "Huan jing ke xue" bian ji wei yuan hui.]| PubMed ID: 20623856

2010
[The diagnostic value of anti-SSA antibody in primary Sjögren's syndrome].

Zhonghua nei ke za zhi [Chinese journal of internal medicine]| PubMed ID: 20646416

2010
Widespread losses of vomeronasal signal transduction in bats.

Molecular biology and evolution| PubMed ID: 20693241

2011
2010
2010
The relationship between three heat shock protein 70 gene polymorphisms and susceptibility to lung cancer.

Clinical chemistry and laboratory medicine : CCLM / FESCC| PubMed ID: 20704535

2010
2011
Genome-wide functional annotation by integrating multiple microarray datasets using meta-analysis.

International journal of data mining and bioinformatics| PubMed ID: 20815137

2010
2010
2010
Root hair systems biology.

Trends in plant science| PubMed ID: 20851035

2010
2010
2010
2010
2010
Semisupervised dimensionality reduction and classification through virtual label regression.

IEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society| PubMed ID: 21118781

2011
Contrast-enhanced whole-heart coronary MRA at 3.0T for the evaluation of cardiac venous anatomy.

The international journal of cardiovascular imaging| PubMed ID: 21120611

2011
2010
2010
Long-term treatment with entecavir induces reversal of advanced fibrosis or cirrhosis in patients with chronic hepatitis B.

Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association| PubMed ID: 21145419

2011
[Characterization and comparison of the doppler compensation acoustic wave in Hipposideros armiger].

Dong wu xue yan jiu = Zoological research / "Dong wu xue yan jiu" bian ji wei yuan hui bian ji| PubMed ID: 21174358

2010
2011
l-Lysinium trifluoro-acetate.

Acta crystallographica. Section E, Structure reports online| PubMed ID: 21201423

2008
2011
2010
2011
[Application of acupuncture-assisted anesthesia in prostate biopsy via the perineum].

Zhongguo zhen jiu = Chinese acupuncture & moxibustion| PubMed ID: 21290841

2010
[Spectrum analysis methods of protein adsorption and design of biomedical materials].

Guang pu xue yu guang pu fen xi = Guang pu| PubMed ID: 21322223

2010
[Comparison of rDNA internal transcribed spacer sequences in asparagus].

Zhong yao cai = Zhongyaocai = Journal of Chinese medicinal materials| PubMed ID: 21355188

2010
CT- and computer-based features of small hamartomas.

Clinical imaging| PubMed ID: 21377049

2011
2011
2011
2011
Improving a consensus approach for protein structure selection by removing redundancy.

IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM| PubMed ID: 21519117

2011
Using Pseudomonas putida xylE gene to teach molecular cloning techniques for undergraduates.

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology| PubMed ID: 21567768

2009
2011
2011
[Removal nitrogen of integrated vertical-flow constructed wetland under aeration condition].

Huan jing ke xue= Huanjing kexue / [bian ji, Zhongguo ke xue yuan huan jing ke xue wei yuan hui "Huan jing ke xue" bian ji wei yuan hui.]| PubMed ID: 21634169

2011
Domain Transfer Multiple Kernel Learning.

IEEE transactions on pattern analysis and machine intelligence| PubMed ID: 21646679

2011
Improving Web image search by bag-based reranking.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society| PubMed ID: 21659029

2011
2011
2011
Human gait recognition using patch distribution feature and locality-constrained group sparse representation.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society| PubMed ID: 21724511

2012
2011
2011
2011
2011
2011
Histogram contextualization.

IEEE transactions on image processing : a publication of the IEEE Signal Processing Society| PubMed ID: 21824847

2012
Gender differences in foot shape: a study of Chinese young adults.

Sports biomechanics / International Society of Biomechanics in Sports| PubMed ID: 21834393

2011
A Multimedia Retrieval Framework Based on Semi-Supervised Ranking and Relevance Feedback.

IEEE transactions on pattern analysis and machine intelligence| PubMed ID: 21844624

2011
2011
[Investigation and countermeasures analysis of catering waste in southern city in China].

Huan jing ke xue= Huanjing kexue / [bian ji, Zhongguo ke xue yuan huan jing ke xue wei yuan hui "Huan jing ke xue" bian ji wei yuan hui.]| PubMed ID: 21922847

2011
2011
Spectral embedded clustering: a framework for in-sample and out-of-sample spectral clustering.

IEEE transactions on neural networks / a publication of the IEEE Neural Networks Council| PubMed ID: 21965198

2011
2011
Sliding window and regression based cup detection in digital fundus images for glaucoma diagnosis.

Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention| PubMed ID: 22003677

2011
Phosphorus removal by laboratory-scale unvegetated vertical-flow constructed wetland systems using anthracite, steel slag and related blends as substrate.

Water science and technology : a journal of the International Association on Water Pollution Research| PubMed ID: 22049770

2011
2011
Initialization independent clustering with actively self-training method.

IEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society| PubMed ID: 22086542

2012
2011
2011
Genomic and genetic evidence for the loss of umami taste in bats.

Genome biology and evolution| PubMed ID: 22117084

2012
2012
2012
Prediction of protein tertiary structures using MUFOLD.

Methods in molecular biology (Clifton, N.J.)| PubMed ID: 22130979

2012
Detection of Sudden Pedestrian Crossings for Driving Assistance Systems.

IEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society| PubMed ID: 22147306

2011
2011
Correlation between posttranslational modification and intrinsic disorder in protein.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing| PubMed ID: 22174266

2012
[Impact of prior cerebral infarction on in-hospital mortality in patients with acute myocardial infarction].

Zhonghua nei ke za zhi [Chinese journal of internal medicine]| PubMed ID: 22176961

2011
Pro-oncogenic potential of NM23-H2 in hepatocellular carcinoma.

Experimental & molecular medicine| PubMed ID: 22192927

2011
2011
Visual Event Recognition in Videos by Learning from Web Data.

IEEE transactions on pattern analysis and machine intelligence| PubMed ID: 22201057

2011
2012
2012
Protein databases on the Internet.

Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.]| PubMed ID: 22237858

2012
The successful treatment of flat warts with auricular acupuncture.

International journal of dermatology| PubMed ID: 22250633

2012
Evolutionary dynamics of protein domain architecture in plants.

BMC evolutionary biology| PubMed ID: 22252370

2012
Use experience evaluation of Google search for obtaining medical knowledge: a case study.

International journal of data mining and bioinformatics| PubMed ID: 22295748

2011
2012
2017
2018
The NFκB signaling pathway serves an important regulatory role in liver abscesses.

Experimental and therapeutic medicine| PubMed ID: 29904423

2018
Hypoxic-stabilized EPAS1 proteins transactivate DNMT1 and cause promoter hypermethylation and transcription inhibition of EPAS1 in non-small cell lung cancer.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology| PubMed ID: 29920222

2018
2020
2020
2020
2022
High Diagnostic Accuracy of Epigenetic Imprinting Biomarkers in Thyroid Nodules.

Journal of clinical oncology : official journal of the American Society of Clinical Oncology| PubMed ID: 36378996

2023
2022
2023
US-guided percutaneous radiofrequency ablation of secondary hyperparathyroidism as a bridge to renal transplantation.

International journal of hyperthermia : the official journal of European Society for Hyperthermic Oncology, North American Hyperthermia Group| PubMed ID: 37344379

2023
2024
2023
2023
2024
2024