4.7 Article

Combining time-resolved transcriptomics and proteomics data for Adverse Outcome Pathway refinement in ecotoxicology

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Environmental Sciences

Impacts of Neonicotinoids on the Bumble Bees Bombus terrestris and Bombus impatiens Examined through the Lens of an Adverse Outcome Pathway Framework

Allison A. Camp et al.

Summary: This article examines the impact of neonicotinoids on bumble bee populations and highlights the urgent need for additional studies, especially those focusing on cellular and organ responses in bumble bees exposed to neonicotinoids. Through the AOP framework, existing literature on the adverse outcome pathways is summarized, emphasizing the importance of addressing data gaps in the bumble bee research community.

ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY (2021)

Article Environmental Sciences

Transcriptional response of springtail (Folsomia candida) exposed to decabromodiphenyl ether-contaminated soil

Qian-Qian Zhang et al.

SCIENCE OF THE TOTAL ENVIRONMENT (2020)

Review Toxicology

Prospects and challenges of multi-omics data integration in toxicology

Sebastian Canzler et al.

ARCHIVES OF TOXICOLOGY (2020)

Article Chemistry, Analytical

MSqRob Takes the Missing Hurdle: Uniting Intensity- and Count-Based Proteomics

Ludger J. E. Goeminne et al.

ANALYTICAL CHEMISTRY (2020)

Review Environmental Sciences

Literature Review: Global Neonicotinoid Insecticide Occurrence in Aquatic Environments

Josephus F. Borsuah et al.

Article Biochemistry & Molecular Biology

Ensembl 2019

Fiona Cunningham et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemical Research Methods

Enhanced Global Post-translational Modification Discovery with MetaMorpheus

Stefan K. Solntsev et al.

JOURNAL OF PROTEOME RESEARCH (2018)

Article Biochemical Research Methods

IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics

Lev I. Levitsky et al.

JOURNAL OF PROTEOME RESEARCH (2018)

Article Biochemical Research Methods

SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines

Harald Barsnes et al.

JOURNAL OF PROTEOME RESEARCH (2018)

Article Environmental Sciences

Joining the Dots Between Omics and Environmental Management

Kenneth M. Y. Leung

INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT (2018)

Article Environmental Sciences

Effects of imidacloprid on detoxifying enzyme glutathione S-transferase on Folsomia candida (Collembola)

Panwad Sillapawattana et al.

ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH (2017)

Article Biochemical Research Methods

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro et al.

NATURE METHODS (2017)

Article Biotechnology & Applied Microbiology

Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida

Anna Faddeeva-Vakhrusheva et al.

BMC GENOMICS (2017)

Article Biochemical Research Methods

MultiQC: summarize analysis results for multiple tools and samples in a single report

Philip Ewels et al.

BIOINFORMATICS (2016)

Article Biochemistry & Molecular Biology

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

Enis Afgan et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Environmental Sciences

Significance of adverse outcome pathways in biomarker-based environmental risk assessment in aquatic organisms

Jin Wuk Lee et al.

JOURNAL OF ENVIRONMENTAL SCIENCES (2015)

Letter Biotechnology & Applied Microbiology

PeptideShaker enables reanalysis of MS-derived proteomics data sets

Marc Vaudel et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemistry & Molecular Biology

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

Matthew E. Ritchie et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Environmental Sciences

Systemic insecticides (neonicotinoids and fipronil): trends, uses, mode of action and metabolites

N. Simon-Delso et al.

ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH (2015)

Article Multidisciplinary Sciences

MS-GF plus makes progress towards a universal database search tool for proteomics

Sangtae Kim et al.

NATURE COMMUNICATIONS (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Integrated Analysis of Transcriptomic and Proteomic Data

Saad Haider et al.

CURRENT GENOMICS (2013)

Article Biochemical Research Methods

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data

Dattatreya Mellacheruvu et al.

NATURE METHODS (2013)

Letter Biotechnology & Applied Microbiology

A cross-platform toolkit for mass spectrometry and proteomics

Matthew C. Chambers et al.

NATURE BIOTECHNOLOGY (2012)

Article Zoology

Soil ecotoxicology: state of the art and future directions

Cornelis A. M. van Gestel

ZOOKEYS (2012)

Article Biochemistry & Molecular Biology

High throughput nano-liter RT-qPCR to classify soil contamination using a soil arthropod

Muriel E. de Boer et al.

BMC MOLECULAR BIOLOGY (2011)

Article Environmental Sciences

SYSTEMS BIOLOGY: LEADING THE REVOLUTION IN ECOTOXICOLOGY

Natalia Garcia-Reyero et al.

ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY (2011)

Article Environmental Sciences

ADVERSE OUTCOME PATHWAYS: A CONCEPTUAL FRAMEWORK TO SUPPORT ECOTOXICOLOGY RESEARCH AND RISK ASSESSMENT

Gerald T. Ankley et al.

ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY (2010)

Article Entomology

The effect of soil pH and temperature on Folsomia candida transcriptional regulation

Tjalf E. de Boer et al.

JOURNAL OF INSECT PHYSIOLOGY (2010)

Article Biotechnology & Applied Microbiology

Gene ontology analysis for RNA-seq: accounting for selection bias

Matthew D. Young et al.

GENOME BIOLOGY (2010)

Article Biochemical Research Methods

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

Steffen Durinck et al.

NATURE PROTOCOLS (2009)

Article Biochemistry & Molecular Biology

KAAS: an automatic genome annotation and pathway reconstruction server

Yuki Moriya et al.

NUCLEIC ACIDS RESEARCH (2007)