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Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
tl;dr
We discuss the evolution of knowledge base–driven pathway analysis over its first decade, distinctly divided into three generations based on the type of analysis they performed. Expand
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Systematic pan-cancer analysis of tumour purity
The tumour microenvironment is the non-cancerous cells present in and around a tumour, including mainly immune cells, but also fibroblasts and cells that comprise supporting blood vessels. TheseExpand
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Performance comparison of exome DNA sequencing technologies
Whole exome sequencing by high-throughput sequencing of target-enriched genomic DNA (exome-seq) has become common in basic and translational research as a means of interrogating the interpretableExpand
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xCell: digitally portraying the tissue cellular heterogeneity landscape
Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limitedExpand
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Exploiting drug-disease relationships for computational drug repositioning
tl;dr
In this review, we show that computational methods for drug repositioning can be classified in two axes: drug based, where discovery initiates from the chemical perspective, or disease based. Expand
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Quantifying the relationship between co-expression, co-regulation and gene function
tl;dr
We demonstrate how mRNA expression data and functional annotations can be used together to estimate the probability that genes with varying degrees of similarity in mRNA expression profile or function will be bound by a common transcription factor. Expand
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Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage
Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific subgroups inExpand
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Microarrays for an Integrative Genomics
From the Publisher: Functional genomics--the deconstruction of the genome to determine the biological function of genes and gene interactions--is one of the most fruitful new areas of biology. TheExpand
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Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets
tl;dr
We present the first quantitative framework to compare and contrast diseases by an integrated analysis of disease-related mRNA expression data and the human protein interaction network. Expand
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Systematic Evaluation of Drug–Disease Relationships to Identify Leads for Novel Drug Uses
Drug repositioning refers to the discovery of alternative uses for drugs—uses that are different from that for which the drugs were originally intended. One challenge in this effort lies in choosingExpand
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