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Missing value estimation methods for DNA microarrays
TLDR
It is shown that KNNimpute appears to provide a more robust and sensitive method for missing value estimation than SVDimpute, and both SVD Impute and KNN Impute surpass the commonly used row average method (as well as filling missing values with zeros).
The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes
TLDR
It is found that 97% of gene deletions exhibited a measurable growth phenotype, suggesting that nearly all genes are essential for optimal growth in at least one condition.
Diversity of gene expression in adenocarcinoma of the lung
TLDR
Gene expression analysis promises to extend and refine standard pathologic analysis and make possible the subclassification of adenocarcinoma into subgroups that correlated with the degree of tumor differentiation as well as patient survival.
Principal components analysis to summarize microarray experiments: application to sporulation time series.
TLDR
This work shows that application of PCA to expression data allows us to summarize the ways in which gene responses vary under different conditions, and suggests that much of the observed variability in the experiment can be summarized in just 2 components.
Estimation of the warfarin dose with clinical and pharmacogenetic data.
TLDR
The use of a pharmacogenetic algorithm for estimating the appropriate initial dose of warfarin produces recommendations that are significantly closer to the required stable therapeutic dose than those derived from a clinical algorithm or a fixed-dose approach.
Data-Driven Prediction of Drug Effects and Interactions
TLDR
Better than tarot cards or crystal balls, the authors show that intricate analyses of observational clinical data can improve physicians’ ability to predict the future—at least with respect to as yet uncharacterized adverse drug effects and interactions.
Guidelines for investigating causality of sequence variants in human disease
TLDR
The key challenges of assessing sequence variants in human disease are discussed, integrating both gene-level and variant-level support for causality and guidelines for summarizing confidence in variant pathogenicity are proposed.
Doxorubicin pathways: pharmacodynamics and adverse effects
The goal of this study is to give a brief background on the literature supporting the PharmGKB pathway about doxorubicin action, and provides a summary of this active area of research. The reader is
PharmGKB: the Pharmacogenetics Knowledge Base
TLDR
The Pharmacogenetics Knowledge Base (PharmGKB) contains genomic, phenotype and clinical information collected from ongoing pharmacogenetic studies, and its associated tools for processing that information are tailored for leading-edge pharmacogenetics research.
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