(Q31039375)

16 September 2017

Network-Based Analysis of eQTL Data to Prioritize Driver Mutations (English)

1 reference

16 September 2017

1 reference

4

1 reference

16 September 2017

3

Luc De Raedt

1 reference

16 September 2017

Dries De Maeyer

1

1 reference

16 September 2017

Bram Weytjens

series ordinal

2

1 reference

16 September 2017

23 January 2016

1 reference

Genome Biology and Evolution

16 September 2017

1 reference

16 September 2017

8

1 reference

16 September 2017

3

1 reference

16 September 2017

481-494

1 reference

describes a project that uses

16 September 2017

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/4825419

based on heuristic

inferred from PubMed Central ID database lookup

cites work

First-Step Mutations during Adaptation Restore the Expression of Hundreds of Genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Pathway Relevance Ranking for Tumor Samples through Network-Based Data Integration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Prediction of antibiotic resistance by gene expression profiles.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

The spectrum of adaptive mutations in experimental evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Expanding the computational toolbox for mining cancer genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Data, information, knowledge and principle: back to metabolism in KEGG

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Genome dynamics during experimental evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

The Cancer Genome Atlas Pan-Cancer analysis project

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Network-based stratification of tumor mutations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Simultaneous identification of multiple driver pathways in cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Evolution after introduction of a novel metabolic pathway consistently leads to restoration of wild-type physiology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

PheNetic: network-based interpretation of unstructured gene lists in E. coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

The Escherichia coli Cpx envelope stress response regulates genes of diverse function that impact antibiotic resistance and membrane integrity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Parallel evolutionary dynamics of adaptive diversification in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

EnrichNet: network-based gene set enrichment analysis.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

A network-based approach for predicting missing pathway interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

21 June 2018

Experimental evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Fast gapped-read alignment with Bowtie 2

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Evolutionary insight from whole-genome sequencing of experimentally evolved microbes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

COLOMBOS: access port for cross-platform bacterial expression compendia

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

A systems biology approach sheds new light on Escherichia coli acid resistance

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

De novo discovery of mutated driver pathways in cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Diminishing returns epistasis among beneficial mutations decelerates adaptation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Metabolite-enabled eradication of bacterial persisters by aminoglycosides

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Second-order selection for evolvability in a large Escherichia coli population

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Discovering pathways by orienting edges in protein interaction networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Genome evolution and adaptation in a long-term experiment with Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Death and cannibalism in a seasonal environment facilitate bacterial coexistence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

STRING 8--a global view on proteins and their functional interactions in 630 organisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

The genomic landscapes of human breast and colorectal cancers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Genetic and phenotypic identification of fusidic acid-resistant mutants with the small-colony-variant phenotype in Staphylococcus aureus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Stress-induced mutagenesis in bacteria.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

A multidimensional analysis of genes mutated in breast and colorectal cancers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Cyclic AMP receptor protein-dependent activation of the Escherichia coli acsP2 promoter by a synergistic class III mechanism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Long-Term Experimental Evolution in Escherichia coli. VIII. Dynamics of a Balanced Polymorphism

21 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

21 June 2018

https://api.crossref.org/works/10.1093%2FGBE%2FEVW010

Comparison of growth, acetate production, and acetate inhibition of Escherichia coli strains in batch and fed-batch fermentations

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4825419

Negative epistasis between beneficial mutations in an evolving bacterial population

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW010

Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW010

Genomic buffering mitigates the effects of deleterious mutations in bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW010

SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW010

False discovery rate, sensitivity and sample size for microarray studies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW010

Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW010

The molecular diversity of adaptive convergence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW010

Algorithms for detecting significantly mutated pathways in cancer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW010

EPSILON: an eQTL prioritization framework using similarity measures derived from local networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FGBE%2FEVW010

RNA stability: Remember your driver

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26802430

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/GBE/EVW010

1 reference

16 September 2017

1 reference

16 September 2017

PubMed publication ID

26802430

1 reference