In silico approaches to mechanistic and predictive toxicology: an introduction to bioinformatics for toxicologists (Q34599613)

3 August 2017

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title

In silico approaches to mechanistic and predictive toxicology: an introduction to bioinformatics for toxicologists (English)

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3 August 2017

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Mark R Fielden

1

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3 August 2017

Jason B Matthews

2

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3 August 2017

Kirsten C Fertuck

3

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3 August 2017

Robert G Halgren

4

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3 August 2017

Tim R Zacharewski

5

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3 August 2017

language of work or name

English

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publication date

1 March 2002

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Critical Reviews in Toxicology

3 August 2017

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3 August 2017

32

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3 August 2017

2

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3 August 2017

67-112

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Bioinformatics--principles and potential of a new multidisciplinary tool

3 August 2017

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https://api.crossref.org/works/10.1080%2F20024091064183

Chemoinformatics - predicting the physicochemical properties of 'drug-like' molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Complementary DNA sequencing: expressed sequence tags and human genome project

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Identification and cloning of differentially expressed genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Construction of a normalized cDNA library for the Trypanosoma cruzi genome project

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Normalization and subtraction: two approaches to facilitate gene discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

dbEST--database for "expressed sequence tags"

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The TIGR gene indices: reconstruction and representation of expressed gene sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Database resources of the National Center for Biotechnology Information.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

An optimized protocol for analysis of EST sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Serial analysis of gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

GXD: a gene expression database for the laboratory mouse. The Gene Expression Database Group.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Discovery of three genes specifically expressed in human prostate by expressed sequence tag database analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The significance of digital gene expression profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

SAGEmap: a public gene expression resource

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

IMAGE cDNA clones, UniGene clustering, and ACeDB: an integrated resource for expressed sequence information

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Towards detection of orthologues in sequence databases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

A general method applicable to the search for similarities in the amino acid sequence of two proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Identification of common molecular subsequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Improved tools for biological sequence comparison

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Basic local alignment search tool

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Homology-based fold predictions for Mycoplasma genitalium proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Analysis of compositionally biased regions in sequence databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Amino acid substitution matrices from protein blocks

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Amino acid substitution matrices from an information theoretic perspective

21 January 2018

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https://api.crossref.org/works/10.1080%2F20024091064183

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Local alignment statistics

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Characterization of a subset of the basic-helix-loop-helix-PAS superfamily that interacts with components of the dioxin signaling pathway

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The PAS superfamily: sensors of environmental and developmental signals

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Control of cell lineage-specific development and transcription by bHLH-PAS proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The basic-helix-loop-helix-PAS orphan MOP3 forms transcriptionally active complexes with circadian and hypoxia factors

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Identification and mapping of human cDNAs homologous to Drosophila mutant genes through EST database searching.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Screening human EST database for identification of candidate genes in respiratory chain deficiency.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. The Mouse Genome Database Group

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Drug discovery: a historical perspective

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

DIALIGN: finding local similarities by multiple sequence alignment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Pattern-induced multi-sequence alignment (PUMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Comparative protein structure modeling of genes and genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

A comprehensive comparison of multiple sequence alignment programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Profile analysis: detection of distantly related proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

A flexible motif search technique based on generalized profiles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Pfam: a comprehensive database of protein domain families based on seed alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The PRINTS protein fingerprint database in its fifth year.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The Blocks database--a system for protein classification

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

SMART, a simple modular architecture research tool: identification of signaling domains

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Recent improvements of the ProDom database of protein domain families

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Protein sequence databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The Protein Data Bank: a computer-based archival file for macromolecular structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Twilight zone of protein sequence alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Accurate modeling of protein conformation by automatic segment matching

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Predicting protein three-dimensional structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Molecular modeling of mammalian cytochromes P450: application to study enzyme function

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

RASMOL: biomolecular graphics for all

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

A geometric approach to macromolecule-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Development and validation of a genetic algorithm for flexible docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Ligand docking to proteins with discrete side-chain flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Structure-based inhibitors of HIV-1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Structure-based discovery of inhibitors of thymidylate synthase

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Differential binding affinities of PCBs, HO-PCBs, and aroclors with recombinant human, rainbow trout (Onchorhynkiss mykiss), and green anole (Anolis carolinensis) estrogen receptors, using a semi-high throughput competitive binding assay

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

High-resolution crystal structure of cytochrome P450cam

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The practice of structure activity relationships (SAR) in toxicology

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Using three-dimensional quantitative structure-activity relationships to examine estrogen receptor binding affinities of polychlorinated hydroxybiphenyls

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Ligand-based identification of environmental estrogens.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Induction of the estrogen specific mitogenic response of MCF-7 cells by selected analogues of estradiol-17 beta: a 3D QSAR study

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Three-dimensional quantitative structure-activity relationships of dioxins and dioxin-like compounds: model validation and Ah receptor characterization

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Going the distance: a current view of enhancer action

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Differences and similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

TRANSFAC: an integrated system for gene expression regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Comparison of the consensus sequence flanking translational start sites in Drosophila and vertebrates

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The eukaryotic promoter database (EPD).

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The density of transcriptional elements in promoter and non-promoter sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Detecting patterns of protein distribution and gene expression in silico

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

trans-Activation of PPARalpha and PPARgamma by structurally diverse environmental chemicals

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The nuclear receptor CAR mediates specific xenobiotic induction of drug metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Humanized xenobiotic response in mice expressing nuclear receptor SXR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Activity of benzo[a]pyrene and its hydroxylated metabolites in an estrogen receptor-alpha reporter gene assay

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Regulatory mechanisms of cellular response to oxidative stress

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Transcription factor Nrf2 coordinately regulates a group of oxidative stress-inducible genes in macrophages

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Consensus patterns in DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

A consensus sequence for binding of Lrp to DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Specificity of the Mnt protein. Independent effects of mutations at different positions in the operator.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Characterization of single-nucleotide polymorphisms in coding regions of human genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Pharmacogenetics and pharmacogenomics: why is this relevant to the clinical geneticist?

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Single nucleotide polymorphism hunting in cyberspace.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Single nucleotide polymorphisms as tools in human genetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

dbSNP: a database of single nucleotide polymorphisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Use of molecular variation in the NCBI dbSNP database

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

An SNP map of the human genome generated by reduced representation shotgun sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Microchip electrophoresis: a method for high-speed SNP detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Pharmacogenetics and adverse drug reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Drug-metabolizing enzymes, polymorphisms and interindividual response to environmental toxicants

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Identification and functional characterization of human soluble epoxide hydrolase genetic polymorphisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Mammalian class theta GST and differential susceptibility to carcinogens: a review

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The genomic era: a crucial role for the public health sciences

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The environmental genome project: ethical, legal, and social implications

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Quantitative monitoring of gene expression patterns with a complementary DNA microarray

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Microarrays and toxicology: the advent of toxicogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The principles and practice of toxigenomics: applications and opportunities

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Proteomics: applications in basic and applied biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Parallel human genome analysis: microarray-based expression monitoring of 1000 genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Use of a cDNA microarray to analyse gene expression patterns in human cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Exploring the metabolic and genetic control of gene expression on a genomic scale

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Concise review: gene expression applied to toxicology

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Functional discovery via a compendium of expression profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Cluster analysis and display of genome-wide expression patterns

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Analysis of large-scale gene expression data

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Toxicogenomics-based discrimination of toxic mechanism in HepG2 human hepatoma cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

A Review Of Monte Carlo Tests Of Cluster Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Systematic determination of genetic network architecture

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Genomic expression programs in the response of yeast cells to environmental changes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

A pulmonary rat gene array for screening altered expression profiles in air pollutant-induced lung injury

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Development of a toxicological gene array and quantitative assessment of this technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The transcriptional signature of dioxin in human hepatoma HepG2 cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F20024091064183

21 January 2018

Identifiers

DOI

10.1080/20024091064183

1 reference

3 August 2017

1 reference