34 Result(s)
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Article
Yadong Wang
Computational Biology/Bioinformatics
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Article
Cardiac tissue engineering using perfusion bioreactor systems
This protocol describes tissue engineering of synchronously contractile cardiac constructs by culturing cardiac cell populations on porous scaffolds (in some cases with an array of channels) and bioreactors wi...
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Open AccessConstructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements
With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex dise...
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Open AccessPrioritization of disease microRNAs through a human phenome-microRNAome network
The identification of disease-related microRNAs is vital for understanding the pathogenesis of diseases at the molecular level, and is critical for designing specific molecular tools for diagnosis, treatment a...
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Open AccessA modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer
Estrogens regulate diverse physiological processes in various tissues through genomic and non-genomic mechanisms that result in activation or repression of gene expression. Transcription regulation upon estrog...
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Open AccessIdentifying cross-category relations in gene ontology and constructing genome-specific term association networks
Gene Ontology (GO) has been widely used in biological databases, annotation projects, and computational analyses. Although the three GO categories are structured as independent ontologies, the biological relat...
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Open AccessTranscriptional regulation prediction of antiestrogen resistance in breast cancer based on RNA polymerase II binding data
Although endocrine therapy impedes estrogen-ER signaling pathway and thus reduces breast cancer mortality, patients remain at continued risk of relapse after tamoxifen or other endocrine therapies. Understandi...
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Open AccessTowards integrative gene functional similarity measurement
In Gene Ontology, the "Molecular Function" (MF) categorization is a widely used knowledge framework for gene function comparison and prediction. Its structure and annotation provide a convenient way to compare...
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Open AccessAn integrative approach for measuring semantic similarities using gene ontology
Gene Ontology (GO) provides rich information and a convenient way to study gene functional similarity, which has been successfully used in various applications. However, the existing GO based similarity measur...
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Open AccessMeasuring semantic similarities by combining gene ontology annotations and gene co-function networks
Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based...
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Open AccessImproving multiple sequence alignment by using better guide trees
Progressive sequence alignment is one of the most commonly used method for multiple sequence alignment. Roughly speaking, the method first builds a guide tree, and then aligns the sequences progressively accor...
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Open AccessmisFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads
Because of the short read length of high throughput sequencing data, assembly errors are introduced in genome assembly, which may have adverse impact to the downstream data analysis. Several tools have been de...
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Open AccessA network-based pathway-expanding approach for pathway analysis
Pathway analysis combining multiple types of high-throughput data, such as genomics and proteomics, has become the first choice to gain insights into the pathogenesis of complex diseases. Currently, several pa...
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Open AccessDTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data
The development of single-cell RNA sequencing has enabled profound discoveries in biology, ranging from the dissection of the composition of complex tissues to the identification of novel cell types and dynami...
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Open AccessDisSetSim: an online system for calculating similarity between disease sets
Functional similarity between molecules results in similar phenotypes, such as diseases. Therefore, it is an effective way to reveal the function of molecules based on their induced diseases. However, the lack...
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Open AccessIdentifying term relations cross different gene ontology categories
The Gene Ontology (GO) is a community-based bioinformatics resource that employs ontologies to represent biological knowledge and describes information about gene and gene product function. GO includes three i...
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Open AccessA framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip
DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has be...
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Open AccessModeling and correct the GC bias of tumor and normal WGS data for SCNA based tumor subclonal population inferring
Somatic copy number alternations (SCNAs) can be utilized to infer tumor subclonal populations in whole genome seuqncing studies, where usually their read count ratios between tumor-normal paired samples serve ...
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Open AccessOptimizing gene set annotations combining GO structure and gene expression data
With the rapid accumulation of genomic data, it has become a challenge issue to annotate and interpret these data. As a representative, Gene set enrichment analysis has been widely used to interpret large mole...
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Open AccessIntegrated entropy-based approach for analyzing exons and introns in DNA sequences
Numerous essential algorithms and methods, including entropy-based quantitative methods, have been developed to analyze complex DNA sequences since the last decade. Exons and introns are the most notable compo...
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Open AccessExtracting a biologically latent space of lung cancer epigenetics with variational autoencoders
Lung cancer is one of the most malignant tumors, causing over 1,000,000 deaths each year worldwide. Deep learning has brought success in many domains in recent years. DNA methylation, an epigenetic factor, is ...
