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Article
Open AccessCell-free DNA chromosome copy number variations predict outcomes in plasma cell myeloma
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Article
Open AccessCopy number variation of urine exfoliated cells by low-coverage whole genome sequencing for diagnosis of prostate adenocarcinoma: a prospective cohort study
Non-invasive, especially the urine-based diagnosis of prostate cancer (PCa) remains challenging. Although prostate cancer antigen (PSA) is widely used in prostate cancer screening, the false positives may resu...
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Article
Open AccessHigh chromosome instability identified by low-pass whole-genome sequencing assay is associated with TP53 copy loss and worse prognosis in BRCA1 germline mutation breast cancer
Though BRCA1 mutation is the most susceptible factor of breast cancer, its prognostic value is disputable. Here in this study, we use a novel method which based on whole-genome analysis to evaluate the chromosome...
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Article
Plasma cell-free DNA chromosomal instability analysis by low-pass whole-genome sequencing to monitor breast cancer relapse
Chromosomal instabilities (CIN) of plasma cell-free DNA (cfDNA) are common in breast cancer. We aimed to investigate the value of cfDNA CIN in monitoring the breast cancer relapse and additionally to compare i...
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Article
Recurrent amplification of MYC and TNFRSF11B in 8q24 is associated with poor survival in patients with gastric cancer
Gastric cancer (GC) is an aggressive malignancy whose mechanisms of development and progression are poorly understood. The identification of prognosis-related genomic loci and genes may suffer from the relativ...
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Article
Open AccessIdentification and validation of dysregulated MAPK7 (ERK5) as a novel oncogenic target in squamous cell lung and esophageal carcinoma
MAPK7/ERK5 (extracellular-signal-regulated kinase 5) functions within a canonical three-tiered MAPK (mitogen activated protein kinase) signaling cascade comprising MEK (MAPK/ERK kinase) 5, MEKK(MEK kinase) 2/3...
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Article
Open AccessOncogenic HER2 fusions in gastric cancer
Genetic amplification of HER2 drives tumorigenesis and cancer progression in a subset of patients with gastric cancer (GC), and treatment with trastuzumab, a humanized HER2-neutralizing antibody, improves the ove...
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Article
A knowledge-based method to predict the cooperative relationship between transcription factors
Identifying the cooperation between transcription factors is crucial and challenging to uncover the mystery behind the complex gene expression patterns. Computational methods aimed to infer transcription facto...
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Article
Predicting miRNA’s target from primary structure by the nearest neighbor algorithm
We used a machine learning method, the nearest neighbor algorithm (NNA), to learn the relationship between miRNAs and their target proteins, generating a predictor which can then judge whether a new miRNA-targ...
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Article
Open AccessUsing GeneReg to construct time delay gene regulatory networks
Understanding gene expression and regulation is essential for understanding biological mechanisms. Because gene expression profiling has been widely used in basic biological research, especially in transcripti...
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Article
Open AccessThe combination approach of SVM and ECOC for powerful identification and classification of transcription factor
Transcription factors (TFs) are core functional proteins which play important roles in gene expression control, and they are key factors for gene regulation network construction. Traditionally, they were ident...
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Article
Prediction of compounds’ biological function (metabolic pathways) based on functional group composition
Efficient in silico screening approaches may provide valuable hints on biological functions of the compound-candidates, which could help to screen functional compounds either in basic researches on metabolic p...
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Article
Open AccessThe use of global transcriptional analysis to reveal the biological and cellular events involved in distinct development phases of Trichophyton rubrum conidial germination
Conidia are considered to be the primary cause of infections by Trichophyton rubrum.
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Article
Open AccessGenomic characterization of ribitol teichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication
Staphylococcus aureus or MRSA (Methicillin Resistant S. aureus), is an acquired pathogen and the primary cause of nosocomial infections worldwide. In S. aureus, teichoic acid is an essential component of the cell...
