Creation and implications of a phenome-genome network

AJ Butte, IS Kohane - Nature biotechnology, 2006 - nature.com
Although gene and protein measurements are increasing in quantity and
comprehensiveness, they do not characterize a sample's entire phenotype in an …

Finding our way through phenotypes

AR Deans, SE Lewis, E Huala, SS Anzaldo… - PLoS …, 2015 - journals.plos.org
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data,
their current form inhibits productive data analysis. The lack of a community-wide …

From genotype to phenotype: systems biology meets natural variation

PN Benfey, T Mitchell-Olds - Science, 2008 - science.org
The promise that came with genome sequencing was that we would soon know what genes
do, particularly genes involved in human diseases and those of importance to agriculture …

The functional annotation of mammalian genomes: the challenge of phenotyping

SDM Brown, W Wurst, R Kühn… - Annual review of …, 2009 - annualreviews.org
The mouse is central to the goal of establishing a comprehensive functional annotation of
the mammalian genome that will help elucidate various human disease genes and …

An integrated systems genetics and omics toolkit to probe gene function

H Li, X Wang, D Rukina, Q Huang, T Lin, V Sorrentino… - Cell systems, 2018 - cell.com
Identifying genetic and environmental factors that impact complex traits and common
diseases is a high biomedical priority. Here, we developed, validated, and implemented a …

The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information

CL Smith, CAW Goldsmith, JT Eppig - Genome biology, 2005 - Springer
Abstract The Mammalian Phenotype (MP) Ontology enables robust annotation of
mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are …

PhenomeNET: a whole-phenome approach to disease gene discovery

R Hoehndorf, PN Schofield… - Nucleic acids research, 2011 - academic.oup.com
Phenotypes are investigated in model organisms to understand and reveal the molecular
mechanisms underlying disease. Phenotype ontologies were developed to capture and …

Comparing genomic expression patterns across species identifies shared transcriptional profile in aging

SA McCarroll, CT Murphy, S Zou, SD Pletcher… - Nature …, 2004 - nature.com
We developed a method for systematically comparing gene expression patterns across
organisms using genome-wide comparative analysis of DNA microarray experiments. We …

The 1,000genome,the 100,000 analysis?

ER Mardis - Genome medicine, 2010 - Springer
How well do we understand the functions encoded by our genome? Certainly,
comprehensive functional informa tion about proteins, including the impact of mutations, is …

Integrating phenotype ontologies across multiple species

CJ Mungall, GV Gkoutos, CL Smith, MA Haendel… - Genome biology, 2010 - Springer
Phenotype ontologies are typically constructed to serve the needs of a particular community,
such as annotation of genotype-phenotype associations in mouse or human. Here we …