Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations

Gene annotation bias impedes biomedical research

(2018) Winston A. Haynes et al.   Scientific Reports

Impact of outdated gene annotations on pathway enrichment analysis

(2016) Lina Wadi et al.   NATURE METHODS

Using predictive specificity to determine when gene set analysis is biologically meaningful

(2016) Sara Ballouz et al.   NUCLEIC ACIDS RESEARCH

Methods to increase reproducibility in differential gene expression via meta-analysis

(2016) Timothy E. Sweeney et al.   NUCLEIC ACIDS RESEARCH

Robust classification of bacterial and viral infections via integrated host gene expression diagnostics

(2016) Timothy E. Sweeney et al.   Science Translational Medicine

Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis

(2016) Timothy E Sweeney et al.   Lancet Respiratory Medicine

Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses

(2015) Marta Andres-Terre et al.   IMMUNITY

PANTHER version 10: expanded protein families and functions, and analysis tools

(2015) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

A comprehensive time-course–based multicohort analysis of sepsis and sterile inflammation reveals a robust diagnostic gene set

(2015) Timothy E. Sweeney et al.   Science Translational Medicine

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective

(2014) Yuxiang Jiang et al.   BIOINFORMATICS

A Meta-analysis of Lung Cancer Gene Expression Identifies PTK7 as a Survival Gene in Lung Adenocarcinoma

(2014) R. Chen et al.   CANCER RESEARCH

Bias tradeoffs in the creation and analysis of protein–protein interaction networks

(2014) Jesse Gillis et al.   Journal of Proteomics

SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer

(2014) Pawel K. Mazur et al.   NATURE

The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies

(2013) S. Harispe et al.   BIOINFORMATICS

Assessing identity, redundancy and confounds in Gene Ontology annotations over time

(2013) Jesse Gillis et al.   BIOINFORMATICS

A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation

(2013) Purvesh Khatri et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Ten Quick Tips for Using the Gene Ontology

(2013) Judith A. Blake   PLoS Computational Biology

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

(2013) Alexandra M. Schnoes et al.   PLoS Computational Biology

A task-based approach for Gene Ontology evaluation

(2013) Erik L Clarke et al.   Journal of Biomedical Semantics

Impact of ontology evolution on functional analyses

(2012) Anika Groß et al.   BIOINFORMATICS

Raise standards for preclinical cancer research

(2012) C. Glenn Begley et al.   NATURE

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

(2012) Jesse Gillis et al.   PLoS Computational Biology

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

The Impact of Multifunctional Genes on "Guilt by Association" Analysis

(2011) Jesse Gillis et al.   PLoS One

An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis

(2010) Matthew P. R. Berry et al.   NATURE

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS