A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions

A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury

(2017) Pekka Kohonen et al.   Nature Communications

Expert consensus on an in vitro approach to assess pulmonary fibrogenic potential of aerosolized nanomaterials

(2016) Amy J. Clippinger et al.   ARCHIVES OF TOXICOLOGY

Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database

(2016) Cynthia J. Grondin et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Multiwalled carbon nanotube-induced pulmonary inflammatory and fibrotic responses and genomic changes following aspiration exposure in mice: A 1-year postexposure study

(2016) Brandi N. Snyder-Talkington et al.   JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH-PART A-CURRENT ISSUES

Analyzing and interpreting genome data at the network level with ConsensusPathDB

(2016) Ralf Herwig et al.   Nature Protocols

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

The Comparative Toxicogenomics Database: update 2017

(2016) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

High throughput toxicity screening and intracellular detection of nanomaterials

(2016) Andrew R. Collins et al.   Wiley Interdisciplinary Reviews-Nanomedicine and Nanobiotechnology

Making big sense from big data in toxicology by read-across

(2016) Thomas Hartung   ALTEX-Alternatives to Animal Experimentation

Developing tools for defining and establishing pathways of toxicity

(2015) Melvin E. Andersen et al.   ARCHIVES OF TOXICOLOGY

Adverse Outcome Pathways can drive non-animal approaches for safety assessment

(2015) Natalie Burden et al.   JOURNAL OF APPLIED TOXICOLOGY

Advances in mechanisms and signaling pathways of carbon nanotube toxicity

(2015) Jie Dong et al.   Nanotoxicology

Fibrosis — A Common Pathway to Organ Injury and Failure

(2015) Don C. Rockey et al.   NEW ENGLAND JOURNAL OF MEDICINE

WikiPathways: capturing the full diversity of pathway knowledge

(2015) Martina Kutmon et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Nano-risk Science: application of toxicogenomics in an adverse outcome pathway framework for risk assessment of multi-walled carbon nanotubes

(2015) Sarah Labib et al.   Particle and Fibre Toxicology

Multi-walled carbon nanotube-induced gene expression in vitro : Concordance with in vivo studies

(2015) Brandi N. Snyder-Talkington et al.   TOXICOLOGY

The eNanoMapper database for nanomaterial safety information

(2015) Nina Jeliazkova et al.   Beilstein Journal of Nanotechnology

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

(2015) Stéphanie Boué et al.   Database-The Journal of Biological Databases and Curation

PathVisio 3: An Extendable Pathway Analysis Toolbox

(2015) Martina Kutmon et al.   PLoS Computational Biology

Hypoxia-sensitive pathways in inflammation-driven fibrosis

(2014) Mario C. Manresa et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Systems Toxicology: From Basic Research to Risk Assessment

(2014) Shana J. Sturla et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Anchoring molecular mechanisms to the adverse outcome pathway for skin sensitization: Analysis of existing data

(2014) Jochem W. van der Veen et al.   CRITICAL REVIEWS IN TOXICOLOGY

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

Applying Adverse Outcome Pathways (AOPs) to support Integrated Approaches to Testing and Assessment (IATA)

(2014) Knut Erik Tollefsen et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

mRNA and miRNA Regulatory Networks Reflective of Multi-Walled Carbon Nanotube-Induced Lung Inflammatory and Fibrotic Pathologies in Mice

(2014) Julian Dymacek et al.   TOXICOLOGICAL SCIENCES

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Hypoxia-inducible Factor 1 (HIF-1) Promotes Extracellular Matrix Remodeling under Hypoxic Conditions by InducingP4HA1, P4HA2,andPLOD2Expression in Fibroblasts

(2013) Daniele M. Gilkes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transcriptomic Analysis Reveals Novel Mechanistic Insight into Murine Biological Responses to Multi-Walled Carbon Nanotubes in Lungs and Cultured Lung Epithelial Cells

(2013) Sarah Søs Poulsen et al.   PLoS One

Incorporating New Technologies Into Toxicity Testing and Risk Assessment: Moving From 21st Century Vision to a Data-Driven Framework

(2013) Russell S. Thomas et al.   TOXICOLOGICAL SCIENCES

The adverse outcome pathway concept: A pragmatic tool in toxicology

(2013) Mathieu Vinken   TOXICOLOGY

System-based identification of toxicity pathways associated with multi-walled carbon nanotube-induced pathological responses

(2013) Brandi N. Snyder-Talkington et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

(2010) Martijn P van Iersel et al.   BMC BIOINFORMATICS

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Mouse pulmonary dose- and time course-responses induced by exposure to multi-walled carbon nanotubes

(2009) Dale W. Porter et al.   TOXICOLOGY

Presenting and exploring biological pathways with PathVisio

(2008) Martijn P van Iersel et al.   BMC BIOINFORMATICS