8 Result(s)
within
John F. McDonald
Microarrays
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Article
Open AccessLeveraging TCGA gene expression data to build predictive models for cancer drug response
Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning mo...
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Open AccessDe novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance
Gene-fusion or chimeric transcripts have been implicated in the onset and progression of a variety of cancers. Massively parallel RNA sequencing (RNA-Seq) of the cellular transcriptome is a promising approach ...
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Article
Open AccessIntegrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation
Genomic rearrangements or structural variants (SVs) are one of the most common classes of mutations in cancer.
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Open AccessThe effects of MicroRNA transfections on global patterns of gene expression in ovarian cancer cells are functionally coordinated
MicroRNAs (miRNAs) are a class of small RNAs that have been linked to a number of diseases including cancer. The potential application of miRNAs in the diagnostics and therapeutics of ovarian and other cancers...
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Open AccessGene expression profiling supports the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as ovarian cancer initiating cells
Accumulating evidence suggests that somatic stem cells undergo mutagenic transformation into cancer initiating cells. The serous subtype of ovarian adenocarcinoma in humans has been hypothesized to arise from ...
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Open AccessOvarian cancer detection from metabolomic liquid chromatography/mass spectrometry data by support vector machines
The majority of ovarian cancer biomarker discovery efforts focus on the identification of proteins that can improve the predictive power of presently available diagnostic tests. We here show that metabolomics,...
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Open AccessEvolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA
The majority of human non-protein-coding DNA is made up of repetitive sequences, mainly transposable elements (TEs). It is becoming increasingly apparent that many of these repetitive DNA sequence elements enc...
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Open AccessEvolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences
LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to b...
