Comparison of quantitation methods in proteomics to define relevant toxicological information on AhR activation of HepG2 cells by BaP

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

The aryl hydrocarbon receptor as a target of environmental stressors – Implications for pollution mediated stress and inflammatory responses

(2020) Christoph F.A. Vogel et al.   Redox Biology

TMT labeling for the masses: A robust and cost-efficient, in-solution labeling approach

(2019) Jana Zecha et al.   MOLECULAR & CELLULAR PROTEOMICS

Benzo[a]pyrene (BaP) exposure generates persistent reactive oxygen species (ROS) to inhibit the NF-κB pathway in medaka (Oryzias melastigma)

(2019) Qian Cui et al.   ENVIRONMENTAL POLLUTION

A multi-omics approach reveals mechanisms of nanomaterial toxicity and structure–activity relationships in alveolar macrophages

(2019) Anne Bannuscher et al.   Nanotoxicology

An in-depth multi-omics analysis in RLE-6TN rat alveolar epithelial cells allows for nanomaterial categorization

(2019) Isabel Karkossa et al.   Particle and Fibre Toxicology

Systematic Comparison of Label-Free, SILAC, and TMT Techniques to Study Early Adaption toward Inhibition of EGFR Signaling in the Colorectal Cancer Cell Line DiFi

(2019) Markus Stepath et al.   JOURNAL OF PROTEOME RESEARCH

Proteome-Wide Evaluation of Two Common Protein Quantification Methods

(2018) Jeremy D. O’Connell et al.   JOURNAL OF PROTEOME RESEARCH

Proteome-wide identification of ubiquitin interactions using UbIA-MS

(2018) Xiaofei Zhang et al.   Nature Protocols

Single-pot, solid-phase-enhanced sample preparation for proteomics experiments

(2018) Christopher S. Hughes et al.   Nature Protocols

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Current trends in quantitative proteomics - an update

(2017) H. Li et al.   JOURNAL OF MASS SPECTROMETRY

Clinical effects of chemical exposures on mitochondrial function

(2017) Zarazuela Zolkipli-Cunningham et al.   TOXICOLOGY

Identification of essential transcription factors for adequate DNA damage response after benzo(a)pyrene and aflatoxin B1 exposure by combining transcriptomics with functional genomics

(2017) Evelyn Smit et al.   TOXICOLOGY

Air particulate matter induced oxidative stress and inflammation in cardiovascular disease and atherosclerosis: The role of Nrf2 and AhR-mediated pathways

(2017) Akeem O. Lawal   TOXICOLOGY LETTERS

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

Characterization of chemical-induced sterile inflammation in vitro: application of the model compound ketoconazole in a human hepatic co-culture system

(2016) Franziska Wewering et al.   ARCHIVES OF TOXICOLOGY

Fine particulate matter air pollution and atherosclerosis: Mechanistic insights

(2016) Yuntao Bai et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Toxicoproteomics in human health and disease: an update

(2016) Shankar Suman et al.   Expert Review of Proteomics

An in vitro alveolar macrophage assay for predicting the short-term inhalation toxicity of nanomaterials

(2016) Martin Wiemann et al.   JOURNAL OF NANOBIOTECHNOLOGY

New insights into BaP-induced toxicity: role of major metabolites in transcriptomics and contribution to hepatocarcinogenesis

(2015) Terezinha Souza et al.   ARCHIVES OF TOXICOLOGY

Polycyclic Aromatic Hydrocarbons in the Mainstream Smoke of Popular U.S. Cigarettes

(2015) An T. Vu et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Air pollution and public health: emerging hazards and improved understanding of risk

(2015) Frank J. Kelly et al.   ENVIRONMENTAL GEOCHEMISTRY AND HEALTH

Cytochrome P450 1 family and cancers

(2015) Ryeo-Eun Go et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

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

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

Aryl hydrocarbon receptor: Linking environment to immunity

(2015) Marina Cella et al.   SEMINARS IN IMMUNOLOGY

Pathway and Time-Resolved Benzo[a]pyrene Toxicity on Hepa1c1c7 Cells at Toxic and Subtoxic Exposure

(2014) Stefan Kalkhof et al.   JOURNAL OF PROTEOME RESEARCH

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomics for systems toxicology

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

Role of Nrf2 in Oxidative Stress and Toxicity

(2013) Qiang Ma   Annual Review of Pharmacology and Toxicology

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Stable isotope labeling of mammals (SILAM) for in vivo quantitative proteomic analysis

(2013) Navin Rauniyar et al.   METHODS

Tobacco Smoking

(2013) Jonathan M. Samet   Thoracic Surgery Clinics

Benchmarking stable isotope labeling based quantitative proteomics

(2012) A.F. Maarten Altelaar et al.   Journal of Proteomics

The aryl hydrocarbon receptor regulates focal adhesion sites through a non-genomic FAK/Src pathway

(2012) C Tomkiewicz et al.   ONCOGENE

Review on proteomic analyses of benzo[a]pyrene toxicity

(2012) Nisha Verma et al.   PROTEOMICS

Mass spectrometry based proteomics, background, status and future needs

(2012) Peter Roepstorff   Protein & Cell

Transcriptional signatures of regulatory and toxic responses to benzo-[a]-pyrene exposure

(2011) Jacob J Michaelson et al.   BMC GENOMICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Comparative proteomic analysis of cellular response of human airway epithelial cells (A549) to benzo(a)pyrene

(2011) Lingfeng Min et al.   TOXICOLOGY MECHANISMS AND METHODS

DIGE-Based Protein Expression Analysis of B[a]P-Exposed Hepatoma Cells Reveals a Complex Stress Response Including Alterations in Oxidative Stress, Cell Cycle Control, and Cytoskeleton Motility at Toxic and Subacute Concentrations

(2010) Franziska Dautel et al.   JOURNAL OF PROTEOME RESEARCH

Mass Spectrometry-Based Label-Free Quantitative Proteomics

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

iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”

(2009) Saw Yen Ow et al.   JOURNAL OF PROTEOME RESEARCH

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

(2009) Paul J Boersema et al.   Nature Protocols

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Quantitative proteomics using stable isotope labeling with amino acids in cell culture

(2008) H C Harsha et al.   Nature Protocols

Precision proteomics: The case for high resolution and high mass accuracy

(2008) M. Mann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA