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

Caffeine increases maximal fat oxidation during a graded exercise test: is there a diurnal variation?

(2021) Mauricio Ramírez-Maldonado et al.   Journal of the International Society of Sports Nutrition

High-Throughput Transcriptomics Platform for Screening Environmental Chemicals

(2021) Joshua A Harrill et al.   TOXICOLOGICAL SCIENCES

Global Proteomics to Study Silica Nanoparticle-Induced Cytotoxicity and Its Mechanisms in HepG2 Cells

(2021) Sun Young Lee et al.   Biomolecules

High-Throughput Transcriptomic Analysis of Human Primary Hepatocyte Spheroids Exposed to Per- and Polyfluoroalkyl Substances as a Platform for Relative Potency Characterization

(2021) Andrea Rowan-Carroll et al.   TOXICOLOGICAL SCIENCES

Transcriptomic, proteomic, and metabolomic analyses identify candidate pathways linking maternal cadmium exposure to altered neurodevelopment and behavior

(2021) Kathleen M. Hudson et al.   Scientific Reports

The reactome pathway knowledgebase 2022

(2021) Marc Gillespie et al.   NUCLEIC ACIDS RESEARCH

Prospects and challenges of multi-omics data integration in toxicology

(2020) Sebastian Canzler et al.   ARCHIVES OF TOXICOLOGY

Quantitative phosphoproteomics to unravel the cellular response to chemical stressors with different modes of action

(2020) Bharath Sampadi et al.   ARCHIVES OF TOXICOLOGY

Unambiguous Phosphosite Localization through the Combination of Trypsin and LysargiNase Mirror Spectra in a Large-Scale Phosphoproteome Study

(2020) Feng Xu et al.   JOURNAL OF PROTEOME RESEARCH

A next generation risk assessment case study for coumarin in cosmetic products

(2020) M T Baltazar et al.   TOXICOLOGICAL SCIENCES

Identifying and Characterizing Stress Pathways of Concern for Consumer Safety in Next-Generation Risk Assessment

(2020) Sarah Hatherell et al.   TOXICOLOGICAL SCIENCES

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

(2020) Nathalie Selevsek et al.   Communications Biology

The forkhead-box family of transcription factors: key molecular players in colorectal cancer pathogenesis

(2019) Paul Laissue   Molecular Cancer

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)

(2019) Huaiyu Mi et al.   Nature Protocols

ChEA3: transcription factor enrichment analysis by orthogonal omics integration

(2019) Alexandra B Keenan et al.   NUCLEIC ACIDS RESEARCH

Use of Connectivity Mapping to Support Read Across: A Deeper Dive Using Data from 186 Chemicals, 19 Cell lines and 2 Case Studies

(2019) K. Nadira De Abrew et al.   TOXICOLOGY

Utility of In Vitro Bioactivity as a Lower Bound Estimate of In Vivo Adverse Effect Levels and in Risk-Based Prioritization

(2019) Katie Paul Friedman et al.   TOXICOLOGICAL SCIENCES

Caffeine modulates voluntary alcohol intake in mice depending on the access conditions: Involvement of adenosine receptors and the role of individual differences

(2019) N. SanMiguel et al.   PHARMACOLOGY BIOCHEMISTRY AND BEHAVIOR

A Web-Based System for Bayesian Benchmark Dose Estimation

(2018) Kan Shao et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

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

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Interindividual Differences in Caffeine Metabolism and Factors Driving Caffeine Consumption

(2018) Astrid Nehlig   PHARMACOLOGICAL REVIEWS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Functional abnormalities in induced Pluripotent Stem Cell-derived cardiomyocytes generated from titin-mutated patients with dilated cardiomyopathy

(2018) Revital Schick et al.   PLoS One

Identification of Missing Proteins in the Phosphoproteome of Kidney Cancer

(2017) Xuehui Peng et al.   JOURNAL OF PROTEOME RESEARCH

TiO2 with Tandem Fractionation (TAFT): An Approach for Rapid, Deep, Reproducible, and High-Throughput Phosphoproteome Analysis

(2017) Liangliang Ren et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative proteomics: challenges and opportunities in basic and applied research

(2017) Olga T Schubert et al.   Nature Protocols

Caffeine and Adenosine

(2017) Joaquim A. Ribeiro et al.   JOURNAL OF ALZHEIMERS DISEASE

A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling

(2017) Joanne M. Yeakley et al.   PLoS One

Recommended approaches in the application of toxicogenomics to derive points of departure for chemical risk assessment

(2016) Reza Farmahin et al.   ARCHIVES OF TOXICOLOGY

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Recombinant acetylated trypsin demonstrates superior stability and higher activity than commercial products in quantitative proteomics studies

(2016) Feilin Wu et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Erratum: How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

(2016) Nicholas J. Schurch et al.   RNA

Grouping 34 Chemicals Based on Mode of Action Using Connectivity Mapping

(2016) K. Nadira De Abrew et al.   TOXICOLOGICAL SCIENCES

The Impact of Protein Phosphorylation on Chlamydial Physiology

(2016) Ja E. Claywell et al.   Frontiers in Cellular and Infection Microbiology

Dark chemical matter as a promising starting point for drug lead discovery

(2015) Anne Mai Wassermann et al.   Nature Chemical Biology

Development of a rapid high-efficiency scalable process for acetylated Sus scrofa cationic trypsin production from Escherichia coli inclusion bodies

(2015) Mingzhi Zhao et al.   PROTEIN EXPRESSION AND PURIFICATION

Adaptive Posttranslational Control in Cellular Stress Response Pathways and Its Relationship to Toxicity Testing and Safety Assessment

(2015) Qiang Zhang et al.   TOXICOLOGICAL SCIENCES

Mechanism of cisplatin proximal tubule toxicity revealed by integrating transcriptomics, proteomics, metabolomics and biokinetics

(2015) Anja Wilmes et al.   TOXICOLOGY IN VITRO

Systematic Analysis of the Phosphoproteome and Kinase-substrate Networks in the Mouse Testis

(2014) Lin Qi et al.   MOLECULAR & CELLULAR PROTEOMICS

Caffeine attenuates lipid accumulation via activation of AMP-activated protein kinase signaling pathway in HepG2 cells

(2013) Hai Yan Quan et al.   BMB Reports

Caffeine relaxes smooth muscle through actin depolymerization

(2012) Tracy Tazzeo et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Application of integrated transcriptomic, proteomic and metabolomic profiling for the delineation of mechanisms of drug induced cell stress

(2012) Anja Wilmes et al.   Journal of Proteomics

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data

(2012) Chunxia Song et al.   MOLECULAR & CELLULAR PROTEOMICS

A tale with a Twist: a developmental gene with potential relevance for metabolic dysfunction and inflammation in adipose tissue

(2012) Anca D. Dobrian   Frontiers in Endocrinology

Genome-wide Correlation between mRNA and Protein in a Single Cell

(2011) Edward S. Yeung   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

Green tea catechins, caffeine and body-weight regulation

(2010) M.S. Westerterp-Plantenga   PHYSIOLOGY & BEHAVIOR

Mass Spectrometry-Based Label-Free Quantitative Proteomics

(2009) Wenhong Zhu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Cellular Stress Response Pathway System as a Sentinel Ensemble in Toxicological Screening

(2009) Steven O. Simmons et al.   TOXICOLOGICAL SCIENCES

Correlation of mRNA and protein levels: Cell type-specific gene expression of cluster designation antigens in the prostate

(2008) Laura E Pascal et al.   BMC GENOMICS