Towards quantitative biology: integration of biological information to elucidate disease pathways and to guide drug discovery (Q36282643)

13 August 2017

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title

Towards quantitative biology: integration of biological information to elucidate disease pathways and to guide drug discovery (English)

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13 August 2017

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Hans Peter Fischer

1

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13 August 2017

1 January 2005

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Biotechnology Annual Review

13 August 2017

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13 August 2017

11

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13 August 2017

1-68

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13 August 2017

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7 January 2021

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Translating basic cancer research into new cancer therapeutics

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Prediction of clinical drug efficacy by classification of drug-induced genomic expression profiles in vitro

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Toxicogenomics and drug discovery: will new technologies help us produce better drugs?

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The impact of pharmacogenetics and pharmacogenomics on drug discovery

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High-throughput screening: new technology for the 21st century

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Functional genomics: from genes to new therapies

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7 January 2021

Protein kinases--the major drug targets of the twenty-first century?

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7 January 2021

Regulation of mitogen-activated protein kinase signaling networks by G protein-coupled receptors.

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7 January 2021

The use of constitutively active GPCRs in drug discovery and functional genomics

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7 January 2021

G-protein-coupled receptor oligomerization and its potential for drug discovery

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7 January 2021

Potential histamine H2-receptor antagonists. 2. N.alpha.-Guanylhistamine

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The protein kinase complement of the human genome

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7 January 2021

Targeting protein kinases for tumor therapy

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7 January 2021

The impact of genomic and proteomic technologies on the development of new cancer drugs

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7 January 2021

Bioinformatics. Gene counters struggle to get the right answer

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7 January 2021

STI571 (Gleevec) as a paradigm for cancer therapy

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7 January 2021

Biomedical informatics for proteomics

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7 January 2021

A strategy for constructing large protein interaction maps using the yeast two-hybrid system: regulated expression arrays and two-phase mating

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7 January 2021

Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase

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7 January 2021

Protein microarray technology

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7 January 2021

Quality analysis and integration of large-scale molecular data sets

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7 January 2021

The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest

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7 January 2021

A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae

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7 January 2021

Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins

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7 January 2021

Functional organization of the yeast proteome by systematic analysis of protein complexes

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7 January 2021

The protein-protein interaction map of Helicobacter pylori

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7 January 2021

A protein interaction map of Drosophila melanogaster

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7 January 2021

Global transposon mutagenesis and a minimal Mycoplasma genome

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7 January 2021

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis

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7 January 2021

The Sequence of the Human Genome

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7 January 2021

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

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7 January 2021

Protein function in the post-genomic era.

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7 January 2021

Navigating gene expression using microarrays--a technology review

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7 January 2021

Tech.Sight. Biochips for gene spotting

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7 January 2021

Protein microarrays: challenges and promises

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7 January 2021

Metabolomics – the link between genotypes and phenotypes

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7 January 2021

Advances in proteomic technologies.

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7 January 2021

Metabolite profiling for plant functional genomics

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7 January 2021

Genomics. Defining genes in the genomics era.

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7 January 2021

Finding the genes in genomic DNA.

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7 January 2021

A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA.

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7 January 2021

Computational prediction of eukaryotic protein-coding genes

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7 January 2021

RNA expression analysis using a 30 base pair resolution Escherichia coli genome array

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7 January 2021

Large-scale transcriptional activity in chromosomes 21 and 22

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7 January 2021

A genomic view of alternative splicing

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7 January 2021

Initial sequencing and analysis of the human genome

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7 January 2021

A mammalian gene with introns instead of exons generating stable RNA products

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7 January 2021

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7 January 2021

Sequences, sequences, and sequences

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7 January 2021

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

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7 January 2021

Localizing proteins in the cell from their phylogenetic profiles.

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7 January 2021

A genomic perspective on protein families

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7 January 2021

The COG database: new developments in phylogenetic classification of proteins from complete genomes

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7 January 2021

Protein interaction maps for complete genomes based on gene fusion events

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7 January 2021

Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes

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7 January 2021

Structure and mechanism of DNA topoisomerase II

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7 January 2021

Comparative DNA sequence analysis of mouse and human protocadherin gene clusters

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7 January 2021

A striking organization of a large family of human neural cadherin-like cell adhesion genes

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7 January 2021

The use of gene clusters to infer functional coupling

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7 January 2021

Computational identification of operons in microbial genomes

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7 January 2021

Prediction of operons in microbial genomes

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7 January 2021

Operons in Escherichia coli: genomic analyses and predictions

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7 January 2021

Tandem clusters of membrane proteins in complete genome sequences.

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7 January 2021

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

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7 January 2021

Guilt by association: contextual information in genome analysis

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7 January 2021

A combined algorithm for genome-wide prediction of protein function

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7 January 2021

Detecting protein function and protein-protein interactions from genome sequences

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7 January 2021

Surviving the blockbuster syndrome

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7 January 2021

Genome-wide identification of tissue-specific enhancers in the Ciona tadpole

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7 January 2021

Transcription regulation and animal diversity

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7 January 2021

Scaling laws in the functional content of genomes

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7 January 2021

Location of enhancers is essential for the imprinting of H19 and Igf2 genes

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7 January 2021

An enhancer deletion affects both H19 and Igf2 expression

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7 January 2021

Discovery and modeling of transcriptional regulatory regions

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7 January 2021

Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome

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7 January 2021

Specificity, free energy and information content in protein-DNA interactions

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7 January 2021

Identification of regulatory regions which confer muscle-specific gene expression.

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7 January 2021

Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints.

1 reference

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7 January 2021

Cross-species characterization of the promoter region of the cystic fibrosis transmembrane conductance regulator gene reveals multiple levels of regulation.

1 reference

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7 January 2021

Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons

1 reference

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7 January 2021

Searching for regulatory elements in human noncoding sequences.

1 reference

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7 January 2021

Discovery of regulatory elements by a computational method for phylogenetic footprinting

1 reference

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7 January 2021

Conservation of DNA Regulatory Motifs and Discovery of New Motifs in Microbial Genomes

1 reference

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7 January 2021

Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Identifying functional elements by comparative DNA sequence analysis

1 reference

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7 January 2021

Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

MATCH: A tool for searching transcription factor binding sites in DNA sequences

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

1 reference

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7 January 2021

Who's your neighbor? New computational approaches for functional genomics

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Definition of the Bacillus subtilis PurR operator using genetic and bioinformatic tools and expansion of the PurR regulon with glyA, guaC, pbuG, xpt-pbuX, yqhZ-folD, and pbuO.

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Co-expression pattern from DNA microarray experiments as a tool for operon prediction

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12.

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

A predictive model for regulatory sequences directing liver-specific transcription.

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

TRANSFAC: transcriptional regulation, from patterns to profiles

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Identification of conserved regulatory elements by comparative genome analysis

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Transcriptional regulation of the stem cell leukemia gene (SCL)--comparative analysis of five vertebrate SCL loci

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Human-mouse genome comparisons to locate regulatory sites

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Integrating regulatory motif discovery and genome-wide expression analysis

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Systematic determination of genetic network architecture

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Identification of antibiotic stress-inducible promoters: a systematic approach to novel pathway-specific reporter assays for antibacterial drug discovery

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Microarray-based identification of a novel Streptococcus pneumoniae regulon controlled by an autoinduced peptide

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Large-scale analysis of the human and mouse transcriptomes

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

HLA class I heavy-chain gene promoter elements mediating synergy between tumor necrosis factor and interferons

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Predicting transcription factor synergism

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Information content of individual genetic sequences.

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter.

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Comparing expression profiles of genes with similar promoter regions.

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Chemosensitivity prediction by transcriptional profiling

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Basic local alignment search tool

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

The Pfam protein families database

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Multiclass cancer diagnosis using tumor gene expression signatures

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Integrated classification of lung tumors and cell lines by expression profiling

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Identifying regulatory networks by combinatorial analysis of promoter elements

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Concordance analysis of microbial genomes

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Searching for drug targets in microbial genomes

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

A genome-based approach for the identification of essential bacterial genes.

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Drug target validation and identification of secondary drug target effects using DNA microarrays

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

The impact of genomics and related technologies on the search for new antibiotics

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Bacterial targets and antibiotics: genome-based drug discovery

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Panel of Bacillus subtilis reporter strains indicative of various modes of action

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Gene expression changes triggered by exposure of Haemophilus influenzae to novobiocin or ciprofloxacin: combined transcription and translation analysis

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Exploring drug-induced alterations in gene expression in Mycobacterium tuberculosis by microarray hybridization

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Identification of putative gene based markers of renal toxicity

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Overview on the application of transcription profiling using selected nephrotoxicants for toxicology assessment

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Gene expression analysis reveals chemical-specific profiles

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Identification of toxicologically predictive gene sets using cDNA microarrays

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Bioengineering models of cell signaling

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Intrinsic noise in gene regulatory networks

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods

1 reference

https://api.crossref.org/works/10.1016%2FS1387-2656%2805%2911001-1

7 January 2021

10.1016/S1387-2656(05)11001-1

Identifiers

DOI

1 reference

13 August 2017

1 reference

PubMed ID

16216773