A novel multi-omics data analysis of dose-dependent and temporal changes in regulatory pathways due to chemical perturbation: a case study on caffeine

Using transcriptomics, proteomics and phosphoproteomics as new approach methodology (NAM) to define biological responses for chemical safety assessment

(2022) Yuan Li et al.   CHEMOSPHERE

Integrated multi-omics analysis reveals the underlying molecular mechanism for developmental neurotoxicity of perfluorooctanesulfonic acid in zebrafish

(2021) Hyojin Lee et al.   ENVIRONMENT INTERNATIONAL

Prospects and challenges of multi-omics data integration in toxicology

(2020) Sebastian Canzler et al.   ARCHIVES OF TOXICOLOGY

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis

(2020) Johannes Griss et al.   MOLECULAR & CELLULAR PROTEOMICS

Computational Analysis of Phosphoproteomics Data in Multi‐Omics Cancer Studies

(2020) Giulia Mantini et al.   PROTEOMICS

Network integration and modelling of dynamic drug responses at multi-omics levels

(2020) Nathalie Selevsek et al.   Communications Biology

The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

(2020) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Functional Translatome Proteomics Reveal Converging and Dose-Dependent Regulation by mTORC1 and eIF2α

(2019) Kevin Klann et al.   MOLECULAR CELL

Infer the in vivo point of departure with ToxCast in vitro assay data using a robust learning approach

(2018) Dong Wang   ARCHIVES OF TOXICOLOGY

Omics Advances in Ecotoxicology

(2018) Xiaowei Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data

(2018) Nadezhda T. Doncheva et al.   JOURNAL OF PROTEOME RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop

(2017) Roland Buesen et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Recent findings and technological advances in phosphoproteomics for cells and tissues

(2015) Louise von Stechow et al.   Expert Review of Proteomics

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data

(2015) Pengyi Yang et al.   PLoS Computational Biology

Proteomics for systems toxicology

(2014) Bjoern Titz et al.   Computational and Structural Biotechnology Journal

Improving the Human Hazard Characterization of Chemicals: A Tox21 Update

(2013) Raymond R. Tice et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Molecular Toxicity Identification Evaluation (mTIE) Approach Predicts Chemical Exposure in Daphnia magna

(2013) Philipp Antczak et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Down-weighting overlapping genes improves gene set analysis

(2012) Adi Tarca et al.   BMC BIOINFORMATICS

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE