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Book
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Protocol
The Present State and Future Direction of Integrated Gene Function Analysis
The determination of the function of the protein products of genes has been a major focus of molecular biology since the founding of the discipline. The development of knock-in, knock-down, and transgenic meth...
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Chapter
Gene Expression in HNC
Head and Neck Cancer (HNC), which is most commonly Head and Neck Squamous Cell Carcinoma (HNSCC), shows substantial changes in gene transcription, as typical for other cancers. In contrast to many cancers, met...
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Chapter and Conference Paper
Outlier Gene Set Analysis Combined with Top Scoring Pair Provides Robust Biomarkers of Pathway Activity
Cancer is a disease driven by pathway activity, while useful biomarkers to predict outcome (prognostic markers) or determine treatment (treatment markers) rely on individual genes, proteins, or metabolites. We...
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Article
Open AccessGene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma
Aberrant activation of signaling pathways downstream of epidermal growth factor receptor (EGFR) has been hypothesized to be one of the mechanisms of cetuximab (a monoclonal antibody against EGFR) resistance in...
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Chapter
Cancer Systems Biology
Cancer is a complex disease, resulting from system-wide interactions of biological processes rather than from any single underlying cause. The processes that drive all cancer development and progression have b...
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Book
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Chapter
Biomedical Informatics for Cancer Research: Introduction
Biomedical informatics encompasses a set of disciplines focused on develo**, implementing, and perfecting the use of informatics and computational tools in biomedical research and clinical care. In this volu...
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Chapter
Genomics Data Analysis Pipelines
Data size and flow are rapidly increasing in cancer research, as high-throughput technologies are developed for each molecular type present in the cell, from DNA sequences through metabolite levels. In order t...
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Book
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Protocol
Incorporation of Gene Ontology Annotations to Enhance Microarray Data Analysis
Typical microarray or GeneChip™ experiments now provide genome-wide measurements on gene expression across many conditions. Analysis often focuses on only a few of the genes, looking for those that are “differ...
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Protocol
Estimating Gene Function With Least Squares Nonnegative Matrix Factorization
Nonnegative matrix factorization is a machine learning algorithm that has extracted information from data in a number of fields, including imaging and spectral analysis, text mining, and microarray data analys...
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Chapter
Linking Gene Expression Patterns and Transcriptional Regulation in Plasmodium falciparum
Elucidation of the genome sequence of P. falciparum, the primary causative agent of human malaria, has opened new avenues for exploring the biology of this important microorganism. The CAMDA 2004 dataset offers a...
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Article
Open AccessThree allele combinations associated with Multiple Sclerosis
Multiple sclerosis (MS) is an immune-mediated disease of polygenic etiology. Dissection of its genetic background is a complex problem, because of the combinatorial possibilities of gene-gene interactions. As ...
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Article
Open AccessLS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates
Non-negative matrix factorisation (NMF), a machine learning algorithm, has been applied to the analysis of microarray data. A key feature of NMF is the ability to identify patterns that together explain the da...
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Article
Open AccessDetermination of strongly overlap** signaling activity from microarray data
As numerous diseases involve errors in signal transduction, modern therapeutics often target proteins involved in cellular signaling. Interpretation of the activity of signaling pathways during disease develop...
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Chapter
Genes Associated with Prognosis in Adenocarcinoma Across Studies at Multiple Institutions
Cancer is a complex disease, comprising many different specific malfunctions within the body. Because many biological processes occur simultaneously within all cells, the gene expression related to tumor behav...
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Chapter
The Biology behind Gene Expression: A Basic Tutorial
Microarrays measure the relative levels of gene expression within a set of cells isolated through an experimental procedure. Analysis of microarray data requires an understanding of how the mRNA measured with ...
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Chapter
Bayesian Decomposition
Gene chips and gene expression microarrays offer the opportunity to study biological systems on a genome-wide basis, exploring the full transcriptional response in an experiment or therapy. Because of the comp...
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Chapter
Bayesian Decomposition Analysis of Gene Expression in Yeast Deletion Mutants
Many methods have been proposed for the analysis of microarray data. In general, these methods are borrowed from statistics and data mining, and they ignore the underlying biology that gives rise to the data. ...
