Ming Chen

University of Alaska Southeast, Juneau, Alaska, United States

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Publications (214)451.02 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Small RNA sequencing and degradome sequencing [also known as PARE (parallel analysis of RNA ends)] have provided rich information on the microRNA (miRNA) and its cleaved mRNA targets on a genome-wide scale in plants, but no computational tools have been developed to effectively and conveniently deconvolute the miRNA-target interaction (MTI).
    Bioinformatics (Oxford, England). 09/2014;
  • Lili Liu, Li Jiang, Ming Chen
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    ABSTRACT: Protein subcellular localization has been a long-standing key problem in investigating proteins' function, which provides important clues for revealing their functions and aids in understanding their interactions with other biomolecules at the cellular level. Here, we systematically defined the organelle-focused proteome and interactome in Oryza sativa. A total of 83.42% of the whole rice proteome obtained their subcellular localizations based on manual annotation, manual adjustment and predictors' cross validation. The final organelle-focused interactome were located in nine organelles. Furthermore, we discussed the cross talk bias between different organelles and the function organization accounting for nine organelles. Motif analysis illustrated the protein interaction bias in different organelles to implement certain biology functions. We exemplified the connection between functions and the overrepresented motifs in the organelle-focused interactomes and exemplified how to infer the functions of unknown proteins via expanding the over represented motifs.
    Current Protein and Peptide Science 07/2014; · 2.33 Impact Factor
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    ABSTRACT: A recent highlight of genomics research has been the discovery of many families of transcripts which have function but do not code for proteins. An important group is long noncoding RNAs (lncRNAs), which are typically longer than 200 nt, and whose members originate from thousands of loci across genomes. We review progress in understanding the biogenesis and regulatory mechanisms of lncRNAs. We describe diverse computational and high throughput technologies for identifying and studying lncRNAs. We discuss the current knowledge of functional elements embedded in lncRNAs as well as insights into the lncRNA-based regulatory network in animals. We also describe genome-wide studies of large amount of lncRNAs in plants, as well as knowledge of selected plant lncRNAs with a focus on biotic/abiotic stress-responsive lncRNAs.
    Briefings in functional genomics. 06/2014;
  • Source
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    ABSTRACT: A label-free and high-sensitive sensing technology for tumor cell recognition and detection was developed based on a novel 2×3 model of leaky surface acoustic wave (LSAW) aptasensor array. In this methodology, every resonator crystal unit of the LSAW aptasensor array had an individual oscillator circuit to work without mutual interference, and could oscillate independently with the phase shift stability of ±0.15° in air phase and ±0.3° in liquid phase. The aptamer was firstly assembled to the gold electrode surface of 100MHz LiTaO3 piezoelectric crystal, which could effectively captured target cells (MCF-7 cells) based on the specific interaction between aptamer and the overexpression of MUC1 protein on tumor cell surface. The aptamer-cell complexes increased the mass loading of LSAW aptasensor and led to phase shifts of LSAW. The plot of phase shift against the logarithm of concentration of MCF-7 cells was linear over the range from 1×10(2)cellsmL(-1) to 1×10(7)cellsmL(-1) with a correlation coefficient of 0.994. The detection limit as low as 32cellsmL(-1) was achieved for MCF-7 cells. The LSAW aptasensor also exhibited excellent specificity and stability. In addition, this aptasensor could be regenerated for ten times without irreversible loss of activity. Therefore, the LSAW aptasensor may offer a promising approach for tumor cell detection and have great potential in clinical applications.
    Biosensors & bioelectronics 04/2014; 60C:318-324. · 5.43 Impact Factor
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    ABSTRACT: This research describes a new amplification signals system of the leaky surface acoustic wave (LSAW) bis-peptide nucleic acid (bis-PNA) biosensor for the simple, sensitive and rapid detection of the target double-stranded DNA (dsDNA). The system consists of a RecA protein-coated complementary single-stranded DNA (cssDNA) probe complex that amplifies the biological signal to improve the sensitivity of the biosensor. The bis-PNA probe for detecting HPV was first immobilized on a gold surface membrane of the detection channel. After the probe was completely hybridized with the corresponding target DNA, different concentrations of the "RecA protein-complementary single strand DNA probe" were added to react with the bis-PNA/dsDNA complex. The phase shift of the LSAW biosensors, which was measured and found to be most significant when the RecA protein was 45μg/mL and the ATPγS was 2.5mmol/L. Compared with other concentrations (P<0.01) of RecA and ATPγS, the value of the phase shift was (11.74±1.03) degrees and the ratio of the phase shift and hybridization time clearly outperformed that of the other concentrations. Compared to the direct hybridization of the bis-PNA probe and the target DNA sequence, the sensitivity was effectively improved and the detection time was significantly shortened. PNA binding adjacent to the area of the target sequence homologous to the probe significantly increased the yield of the hybridization reaction between the PNA/dsDNA complex and the RecA protein-coated cssDNA probe. In this condition, the phase shift was significantly obvious and the detection time was significantly shortened. In conclusion, the combination of the RecA protein-coated cssDNA probe and the LSAW bis-PNA biosensor provides sensitivity and simple and rapid detection of clinical trace pathogenic microorganisms.
    Biosensors & bioelectronics 04/2014; 60C:259-264. · 5.43 Impact Factor
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    ABSTRACT: This paper focuses on the capacity-approaching, nonuniform signaling for the pulse amplitude modulated (PAM) visible light communications under the non-negativity, peak power, and dimmable average power constraints. The input distribution is characterized by three parameters, i.e., the intensities, the probabilities, and the number of mass points in the PAM constellation. In the open literature, no analytical expression can be used to obtain the capacity-achieving input distribution. In this paper, a computationally simple but capacity-approaching input distribution is alternatively derived by determining the three aforementioned parameters. The resulting input distribution can serve as a useful tool not to approach the channel capacity but to guide the practical system design. Numerical results substantiate that the derived input distribution is a capacity-approaching distribution and can offer a better performance gain in comparison with the commonly employed uniform input distribution.
    Journal of the Optical Society of America A 03/2014; 31(3):561-8. · 1.67 Impact Factor
  • Nan Wang, Ming Chen, Xia Wu, Jianxin Dai
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    ABSTRACT: This paper investigates the precoder design problem in a two-hop amplify-and-forward multiple-input-multiple-output relay system. Many previous works on this problem are based on the minimum mean-square error criterion and the presence of a direct link between the source and the destination is ignored. In this paper, we propose a new method for joint source and relay precoder design based on maximizing the mutual information between the source and the destination, taking both the relay link and the direct link into account. In contrast to previous works, which consider the transmit power constraints of the source and the relay independently, we assume a total power constraint on the sum transmit power of the source and the relay instead to study also the optimal power distribution over the two nodes. A constrained optimization problem with respect to the unknown source precoder matrix and relay precoder matrix is then formulated, which is nonconvex and very difficult to solve directly. We propose a structural constraint on the precoders by analyzing the structure of the problem and referring to related works. With the proposed precoders' structure and by applying the Hadamard's inequality, the original problem is simplified from a matrix-valued problem to a scalar-valued one. However, the new scalar-valued problem is still nonconvex and we manage to convert it into two subproblems and solve it in an iterative fashion. By using the Karash---Kuhn---Tucker (KKT) conditions, we give out the closed-form solutions to the subprobelms. Simulation results demonstrate that the proposed design method converges rapidly and significantly outperforms the existing methods.
    Wireless Personal Communications 03/2014; 75(1):511-530. · 0.43 Impact Factor
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    ABSTRACT: This paper studies regional planning issues of coordinated multi-point (CoMP) transmission with perfect feedback under single-user scenario. To determine a reasonable regional planning based on semi-dynamic cooperation idea, the net ergodic capacity optimization problem is derived when given the downlink received signal expression and the definition of penalty factor. The variables that should be optimized are the number of coordinated base stations (BSs) and the dividing-area radius. In order to solve this joint optimization problem, the capacity of non-CoMP and CoMP is analyzed and simplified with knowledge of index random distribution. Again on the basis of the above simplified expression, approximate results of two plans that determine a certain relationship between the number of cooperative BSs and the cell radius are given by using the method of fixed variable and calculus formula. Simulation results show that the two approximate curves are consistent with the results obtained by Monte Carlo simulation.
    Wireless Personal Communications 02/2014; · 0.43 Impact Factor
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    ABSTRACT: Drug-resistant mutations of hepatitis B virus (HBV) are the major obstacles to successful therapy for chronic hepatitis B infection. Although there are many methods for detecting the antiviral drug-resistant mutations of HBV, their applications are restricted because of their shortcomings, such as low sensitivity, the time required, and the high cost. For this study, a multiplex ligation-dependent probe real-time PCR (MLP-RT-PCR) method was developed to simultaneously detect lamivudine (LAM)- and adefovir (ADV)-resistant HBV mutants (those with the mutations rtM204V/I, rtA181V/T, and rtN236T). The new method combined the high-throughput nature of multiplex ligation-dependent probe amplification (MLPA) with the rapid and sensitive detection of real-time PCR. In this report, MLP-RT-PCR was evaluated by detecting drug-resistant mutants in 116 patients with chronic hepatitis B infection. By MLP-RT-PCR analysis, LAM-resistant mutations were detected in 41 patients (35.3%), ADV-resistant mutations were detected in 17 patients (14.7%), and LAM- and-ADV-resistant mutations were detected in 5 patients (4.3%). Based on the results of MLP-RT-PCR, the mutations rtM204V, rtM204I, rtA181T, rtA181V, and rtN236T were 95.7% (111/116 patients), 98.3% (114/116 patients), 99.1% (115/116 patients), 98.3% (114/116 patients), and 99.1% (115/116 patients) concordant, respectively, with those of direct sequencing. The MLP-RT-PCR assay was more sensitive than direct sequencing for detecting mutations with low frequencies. Four samples containing the low-frequency (<10%) mutants were identified by MLP-RT-PCR and further confirmed by clonal sequencing. MLP-RT-PCR is a rapid and sensitive method that enables the detection of multidrug-resistant HBV mutations in clinical practice.
    Journal of clinical microbiology 02/2014; 52(2):460-6. · 4.16 Impact Factor
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    ABSTRACT: This research describes a new amplification signals system of the leaky surface acoustic wave (LSAW) bis-peptide nucleic acid (bis-PNA) biosensor for the simple, sensitive and rapid detection of the target double-stranded DNA (dsDNA). The system consists of a RecA protein-coated complementary single-stranded DNA (cssDNA) probe complex that amplifies the biological signal to improve the sensitivity of the biosensor. The bis-PNA probe for detecting HPV was first immobilized on a gold surface membrane of the detection channel. After the probe was completely hybridized with the corresponding target DNA, different concentrations of the “RecA protein-complementary single strand DNA probe” were added to react with the bis-PNA/dsDNA complex. The phase shift of the LSAW biosensors, which was measured and found to be most significant when the RecA protein was 45 μg/mL and the ATPγS was 2.5 mmol/L. Compared with other concentrations (P<0.01) of RecA and ATPγS, the value of the phase shift was (11.74±1.03) degrees and the ratio of the phase shift and hybridization time clearly outperformed that of the other concentrations. Compared to the direct hybridization of the bis-PNA probe and the target DNA sequence, the sensitivity was effectively improved and the detection time was significantly shortened. PNA binding adjacent to the area of the target sequence homologous to the probe significantly increased the yield of the hybridization reaction between the PNA/dsDNA complex and the RecA protein-coated cssDNA probe. In this condition, the phase shift was significantly obvious and the detection time was significantly shortened. In conclusion, the combination of the RecA protein-coated cssDNA probe and the LSAW bis-PNA biosensor provides sensitivity and simple and rapid detection of clinical trace pathogenic microorganisms.
    Biosensors & bioelectronics 01/2014; 60:259–264. · 5.43 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: A label-free and high-sensitive sensing technology for tumor cell recognition and detection was developed based on a novel 2×3 model of leaky surface acoustic wave (LSAW) aptasensor array. In this methodology, every resonator crystal unit of the LSAW aptasensor array had an individual oscillator circuit to work without mutual interference, and could oscillate independently with the phase shift stability of ±0.15° in air phase and ±0.3° in liquid phase. The aptamer was firstly assembled to the gold electrode surface of 100 MHz LiTaO3 piezoelectric crystal, which could effectively captured target cells (MCF-7 cells) based on the specific interaction between aptamer and the overexpression of MUC1 protein on tumor cell surface. The aptamer-cell complexes increased the mass loading of LSAW aptasensor and led to phase shifts of LSAW. The plot of phase shift against the logarithm of concentration of MCF-7 cells was linear over the range from 1×102 cells mL−1 to 1×107 cells mL−1 with a correlation coefficient of 0.994. The detection limit as low as 32 cells mL−1 was achieved for MCF-7 cells. The LSAW aptasensor also exhibited excellent specificity and stability. In addition, this aptasensor could be regenerated for ten times without irreversible loss of activity. Therefore, the LSAW aptasensor may offer a promising approach for tumor cell detection and have great potential in clinical applications.
    Biosensors & bioelectronics 01/2014; 60:318–324. · 5.43 Impact Factor
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    ABSTRACT: A strained-SiGe p-channel metal-oxide-semiconductor-field-effect transistors (p-MOSFETS) with higher-κ LaLuO3 gate dielectric was fabricated and electrically characterized. The novel higher-κ (κ~30) gate dielectric, LaLuO3, was deposited by molecular-beam deposition and shows good quality for integration into the transistor. The transistor features good output and transfer characteristics. The hole mobility was extracted by the splitting C—V method and a value of 200cm2/V·s was obtained for strong inversion conditions, which indicates that the hole mobility is well enhanced by SiGe channel and that the LaLuO3 layer does not induce additional significant carrier scattering. Gate induced drain leakage is measured and analyzed by using an analytical model. Band-to-band tunneling efficiencies under high and low fields are found to be different, and the tunneling mechanism is discussed.
    12/2013; 31(1).
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    ABSTRACT: Our knowledge of the role of higher-order chromatin structures in transcription of microRNA genes (MIRs) is evolving rapidly. Here we investigate the effect of 3D architecture of chromatin on the transcriptional regulation of MIRs. We demonstrate that MIRs have transcriptional features that are similar to protein-coding genes. RNA polymerase II-associated ChIA-PET data reveal that many groups of MIRs and protein-coding genes are organized into functionally compartmentalized chromatin communities and undergo coordinated expression when their genomic loci are spatially colocated. We observe that MIRs display widespread communication in those transcriptionally active communities. Moreover, miRNA-target interactions are significantly enriched among communities with functional homogeneity while depleted from the same community from which they originated, suggesting MIRs coordinating function-related pathways at posttranscriptional level. Further investigation demonstrates the existence of spatial MIR-MIR chromatin interacting networks. We show that groups of spatially coordinated MIRs are frequently from the same family and involved in the same disease category. The spatial interaction network possesses both common and cell-specific subnetwork modules that result from the spatial organization of chromatin within different cell types. Together, our study unveils an entirely unexplored layer of MIR regulation throughout the human genome that links the spatial coordination of MIRs to their co-expression and function.
    Nucleic Acids Research 12/2013; · 8.81 Impact Factor
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    ABSTRACT: In plants, Dicer-like 1 (DCL1)-mediated two-step cleavages are essential for the processing of microRNA (miRNA) gene products. Interestingly, DCL1 has been indicated to be involved in the production of many small RNAs (sRNAs) that cannot be classified as canonical miRNAs. However, genomic and functional information on the non-miRNA, DCL1-dependent sRNAs is still limited. Here, we propose a secondary structure-based approach for identification of the precursors containing novel DCL1-dependent sRNA loci. To demonstrate the utility of the workflow: first, 5898 DCL1-dependent sRNAs of 20-24 nucleotides were identified from the sRNA high-throughput sequencing data sets prepared from rice DCL1 RNA interference transgenic lines. Those perfectly mapped to the rice pre-miRNAs (precursor microRNAs) were removed. The remaining 5795 sRNAs were then mapped onto the rice genome, obtaining 30 902 perfectly matched loci belonging to 2310 sRNAs. A total of 4631 clusters of sRNA loci were defined for secondary structure prediction by using RNAfold. The prediction results generated by two algorithms, namely MFE (minimum free energy) and centroid, were manually compared to identify the conserved long-stem structures containing DCL1-dependent sRNA loci. For the purpose of a case study, a portion of the prediction results was screened manually. As a result, 60 clusters displayed great potential for forming featured long-stem structures for the generation of DCL1-dependent sRNAs. Together, the results indicate that the proposed workflow is applicable for the identification of novel DCL1-dependent sRNA loci on plant genomes.
    Journal of Experimental Botany 12/2013; · 5.79 Impact Factor
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    ABSTRACT: An improvement is introduced of the modified successive-cancellation (MSC) decoding for polar codes, in which local decoders at rate-other nodes are simplified. This improvement reduces the decoding latency and complexity of the MSC decoding with no sacrifice in error performance. Furthermore, in our method, the decoding latency decreases rapidly with increasing signal-to-noise ratio. Significant latency and complexity reductions are shown by simulation results.
    IEEE Communications Letters 12/2013; 17(12):2360-2363. · 1.16 Impact Factor
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    ABSTRACT: This manuscript described a novel 2×3 model of leaky surface acoustic wave (LSAW) immunosensor array for label-free and high-sensitive detection of Cyclosporin A (CsA) in whole-blood samples. In this technique, every resonator crystal unit of the LSAW immunosensor array had an individual oscillator circuit to work without mutual interference. The LSAW immunosensor was first immobilized with protein A from Staphylococcus aureus and monoclonal anti-CsA antibody on the gold electrode surface of 100MHz LiTaO3 piezoelectric crystals, which then captured the CsA. The CsA increased the mass loading of LSAW immunosensor and leaded to phase shifts of LSAW. Consequently, under optimal conditions, the designed LSAW immunosensor exhibited a detection limit of 0.89ng/mL, quantification limit of 2.96ng/mL, and wide dynamic linear range from 1ng/mL to 1000ng/mL for CsA detection. Application of the LSAW immunosensor array to clinical sample revealed that consistency and comparability between LSAW immunosensor and the enzyme multiplied immunoassay method were good. Moreover, the immunosensor could be regenerated for ten times without appreciable loss of activity. Therefore, the self-designed LSAW immunosensor array provided a rapid, accurate, label-free, easy handling, and dynamic real-time method for the detection of immunosuppressive drugs in clinical laboratory.
    Biosensors & bioelectronics 11/2013; 54C:151-157. · 5.43 Impact Factor
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    ABSTRACT: Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this work has mostly been limited to model organisms. Recently, the development of deep sequencing, especial RNA-Seq, has made it possible to carry out studies in non-model species.Result: RNA-Seq data of Chinese bayberry was analyzed to investigate the bias of codon usage and codon pairs. High frequency codons (AGG, GCU, AAG and GAU), as well as low frequency ones (NCG and NUA codons) were identified, and 397 high frequency codon pairs were observed. Meanwhile, 26 preferred and 141 avoided neighboring codon pairs were also identified, which showed more significant bias than the same pairs with one or more intervening codons. Codon patterns were also analyzed at the plant kingdom, organism and gene levels. Changes during plant evolution were evident using RSCU (relative synonymous codon usage), which was even more significant than GC3s (GC content of 3rd synonymous codons). Nine GO categories were differentially and independently influenced by CAI (codon adaptation index) or GC3s, especially in 'Molecular function' category. Within a gene, the average CAI increased from 0.720 to 0.785 in the first 50 codons, and then more slowly thereafter. Furthermore, the preferred as well as avoided codons at the position just following the start codon AUG were identified and discussed in relation to the key positions in Kozak sequences. A comprehensive codon usage Table and number of high-frequency codon pairs were established. Bias in codon usage as well as in neighboring codon pairs was observed, and the significance of this in avoiding DNA mutation, increasing protein production and regulating protein synthesis rate was proposed. Codon usage patterns at three levels were revealed and the significance in plant evolution analysis, gene function classification, and protein translation start site predication were discussed. This work promotes the study of codon biology, and provides some reference for analysis and comprehensive application of RNA-Seq data from other non-model species.
    BMC Genomics 10/2013; 14(1):732. · 4.40 Impact Factor
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    ABSTRACT: Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary model of gene regulations for seasonal pistillate flowering in hickory (Carya cathayensis) was proposed. The genome-wide dynamic transcriptome was characterized via the joint-approach of RNA sequencing and microarray analysis. Differential transcript abundance analysis uncovered the dynamic transcript abundance patterns of flowering correlated genes and their major functions based on Gene Ontology (GO) analysis. To explore pistillate flowering mechanism in hickory, a comprehensive flowering gene regulatory network based on Arabidopsis thaliana was constructed by additional literature mining. A total of 114 putative flowering or floral genes including 31 with differential transcript abundance were identified in hickory. The locations, functions and dynamic transcript abundances were analyzed in the gene regulatory networks. A genome-wide co-expression network for the putative flowering or floral genes shows three flowering regulatory modules corresponding to response to light abiotic stimulus, cold stress, and reproductive development process, respectively. Totally 27 potential flowering or floral genes were recruited which are meaningful to understand the hickory specific seasonal flowering mechanism better. Flowering event of pistillate flower bud in hickory is triggered by several pathways synchronously including the photoperiod, autonomous, vernalization, gibberellin, and sucrose pathway. Totally 21 potential flowering or floral genes were recruited from the genome-wide co-expression network function module analysis. Moreover, the analysis provides a potential FLC-like gene based vernalization pathway and an 'AC' model for pistillate flower development in hickory. This work provides an available framework for pistillate flower development in hickory, which is significant for insight into regulation of flowering and floral development of woody plants.
    BMC Genomics 10/2013; 14(1):691. · 4.40 Impact Factor
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    ABSTRACT: Short-channel high-mobility Si/Si0.5Ge0.5/silicon-on-insulator (SOI) quantum-well p-type metal-oxide-semiconductor field effect transistors (p-MOSFETs) were fabricated and electrically characterized. The transistors show good transfer and output characteristics with Ion/Ioff ratio up to 105 and sub-threshold slope down to 100mV/dec. HfO2/TiN gate stack is employed and the equivalent oxide thickness of 1.1 nm is achieved. The effective hole mobility of the transistors reaches 200cm2/V·s, which is 2.12 times the Si universal hole mobility.
    Chinese Physics Letters 10/2013; 30(10):8502-. · 0.92 Impact Factor
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    ABSTRACT: Abstract
    Applied Surface Science 09/2013; 280:212-218. · 2.54 Impact Factor

Publication Stats

1k Citations
451.02 Total Impact Points

Institutions

  • 2010–2014
    • University of Alaska Southeast
      Juneau, Alaska, United States
    • University of Jinan (Jinan, China)
      Chi-nan-shih, Shandong Sheng, China
    • Harbin Medical University
      • College of Bioinformatics Science and Technology
      Harbin, Heilongjiang Sheng, China
    • Huzhou University
      Wuhing, Zhejiang Sheng, China
  • 2008–2014
    • Southeast University (China)
      Nan-ching-hsü, Jiangxi Sheng, China
    • The University of Calgary
      • Department of Biochemistry and Molecular Biology
      Calgary, Alberta, Canada
  • 2002–2014
    • Third Military Medical University
      • Institute of Burn Research
      Ch’ung-ch’ing-shih, Chongqing Shi, China
  • 2005–2013
    • Zhejiang University
      • • College of Life Sciences
      • • College of Animal Sciences
      Hangzhou, Zhejiang Sheng, China
  • 2012
    • Southwest Hospital
      Nan-ching-hsü, Jiangxi Sheng, China
    • Zhejiang University of Technology
      Hang-hsien, Zhejiang Sheng, China
  • 2011–2012
    • Hangzhou Normal University
      • College of Life and Environmental Sciences
      Hangzhou, Zhejiang Sheng, China
  • 2008–2010
    • Shandong University
      • Department of Physics
      Chi-nan-shih, Shandong Sheng, China
  • 2002–2010
    • Bielefeld University
      • • Faculty of Technology
      • • Bioinformatics and Medical Informatics
      Bielefeld, North Rhine-Westphalia, Germany
  • 2009
    • PLA University of Science and Technology
      Peping, Beijing, China
    • Nanjing University of Aeronautics & Astronautics
      • College of Electronic and Information Engineering
      Nan-ching, Jiangsu Sheng, China