(Q31724476)

29 July 2017

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

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29 July 2017

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1

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29 July 2017

7

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Department of Bioinformatics - BiGCaT

29 July 2017

3

Karolinska Institutet

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29 July 2017

4

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29 July 2017

5

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29 July 2017

6

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29 July 2017

Juuso A Parkkinen

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language of work or name

English

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publication date

3 July 2017

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29 July 2017

15

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published in

Nature Communications

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29 July 2017

8

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29 July 2017

15932

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29 July 2017

1

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Creative Commons Attribution 4.0 International

30 June 2019

copyright license

start time

3 July 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

1 reference

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=5500850

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/5500850

based on heuristic

inferred from PubMed Central ID database lookup

cites work

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

Toward the Replacement of Animal Experiments through the Bioinformatics-driven Analysis of 'Omics' Data from Human Cell Cultures

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

28 July 2018

Molecular Chemometrics

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

Key Challenges and Opportunities Associated with the Use of In Vitro Models to Detect Human DILI: Integrated Risk Assessment and Mitigation Plans

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Identification of selective cytotoxic and synthetic lethal drug responses in triple negative breast cancer cells.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Grouping 34 Chemicals Based on Mode of Action Using Connectivity Mapping

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Risk of acute and serious liver injury associated to nimesulide and other NSAIDs: data from drug-induced liver injury case-control study in Italy

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Integrating Publicly Available Data to Generate Computationally Predicted Adverse Outcome Pathways for Fatty Liver

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Lessons from Toxicology: Developing a 21st-Century Paradigm for Medical Research

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Setting Clinical Exposure Levels of Concern for Drug-Induced Liver Injury (DILI) Using Mechanistic in vitro Assays

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Adverse Outcome Pathways and Drug-Induced Liver Injury Testing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Probabilistic machine learning and artificial intelligence

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Developing tools for defining and establishing pathways of toxicity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Orchestrating high-throughput genomic analysis with Bioconductor

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

SEURAT: Safety Evaluation Ultimately Replacing Animal Testing--recommendations for future research in the field of predictive toxicology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Open TG-GATEs: a large-scale toxicogenomics database

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Genomic models of short-term exposure accurately predict long-term chemical carcinogenicity and identify putative mechanisms of action

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Drug-induced liver injury and drug development: industry perspective

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

A framework for the next generation of risk science

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Systems toxicology: from basic research to risk assessment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Causal analysis approaches in Ingenuity Pathway Analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

A correlation between the in vitro drug toxicity of drugs to cell lines that express human P450s and their propensity to cause liver injury in humans.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Idiosyncratic drug-induced liver injury: an update on the 2007 overview

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Incorporating new technologies into toxicity testing and risk assessment: moving from 21st century vision to a data-driven framework.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Systems pharmacology to predict drug toxicity: integration across levels of biological organization

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

The determination and interpretation of the therapeutic index in drug development

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

A decade of toxicogenomic research and its contribution to toxicological science

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

To test or not to test: Preliminary assessment of normality when comparing two independent samples

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

pROC: an open-source package for R and S+ to analyze and compare ROC curves

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Regularization Paths for Generalized Linear Models via Coordinate Descent

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Discovery of drug mode of action and drug repositioning from transcriptional responses

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

ROAST: rotation gene set tests for complex microarray experiments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

High-throughput cell-based screening of 4910 known drugs and drug-like small molecules identifies disulfiram as an inhibitor of prostate cancer cell growth

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Toxicology for the twenty-first century

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Network pharmacology: the next paradigm in drug discovery

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Dose response considerations in risk assessment--an overview of recent ILSI activities

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Data mining the NCI60 to predict generalized cytotoxicity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

The liver pharmacological and xenobiotic gene response repertoire

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Toxicology. Transforming environmental health protection

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

The NCI60 human tumour cell line anticancer drug screen

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

A new summarization method for Affymetrix probe level data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Concordance of the toxicity of pharmaceuticals in humans and in animals

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Foretelling toxicity: FDA researchers work to predict risk of liver injury from drugs.

28 July 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

Identification of small molecules enhancing autophagic function from drug network analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

Probabilistic drug connectivity mapping

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

The liver toxicity knowledge base: a systems approach to a complex end point

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

Cellular imaging predictions of clinical drug-induced liver injury.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

Use of micropatterned cocultures to detect compounds that cause drug-induced liver injury in humans

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

A high content screening assay to predict human drug-induced liver injury during drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

Probabilistic retrieval and visualization of biologically relevant microarray experiments

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

MADE4: an R package for multivariate analysis of gene expression data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

structSSI: Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

Statistical learning and selective inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

Developing structure-activity relationships for the prediction of hepatotoxicity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

Human drug-induced liver injury severity is highly associated with dual inhibition of liver mitochondrial function and bile salt export pump

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5500850

Advancing regulatory science

31 October 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

inferred from DOI database lookup

7 January 2021

based on heuristic

ggplot2: Elegant Graphics for Data Analysis

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS15932

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NCOMMS15932

1 reference

Dimensions Publication ID

29 July 2017

0 references

0 references

1 reference

29 July 2017

1 reference

PubMed ID

28671182