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Robust enumeration of cell subsets from tissue expression profiles
We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures fromExpand
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Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
BackgroundRepbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of theExpand
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The prognostic landscape of genes and infiltrating immune cells across human cancers
Molecular profiles of tumors and tumor-associated cells hold great promise as biomarkers of clinical outcomes. However, existing data sets are fragmented and difficult to analyze systematically. HereExpand
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The Immune Landscape of Cancer
SUMMARY We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified sixExpand
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Calreticulin Is the Dominant Pro-Phagocytic Signal on Multiple Human Cancers and Is Counterbalanced by CD47
Calreticulin-induced phagocytosis of cancer cells can be counterbalanced by CD47 expression. Eat Up! Immune cells constantly patrol the body on a search and destroy campaign against foreign invaders.Expand
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The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors
CD47, a “don't eat me” signal for phagocytic cells, is expressed on the surface of all human solid tumor cells. Analysis of patient tumor and matched adjacent normal (nontumor) tissue revealed thatExpand
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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian (‘marsupial’) species to be sequenced, the opossum provides aExpand
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A Simple Method for Estimating Interactions Between a Treatment and a Large Number of Covariates
We consider a setting in which we have a treatment and a potentially large number of covariates for a set of observations, and wish to model their relationship with an outcome of interest. We proposeExpand
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Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia.
CONTEXT In many cancers, specific subpopulations of cells appear to be uniquely capable of initiating and maintaining tumors. The strongest support for this cancer stem cell model comes fromExpand
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Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation
Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degreeExpand
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