(Q34897211)

5 August 2017

title

A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks (English)

1 reference

5 August 2017

0 references

Antonina Iagovitina

6

0 references

Alina Isakova

Alina Isakova

3

0 references

Sebastian M Waszak

Sebastian M Waszak

2

0 references

Korneel Hens

Korneel Hens

5

0 references

Bart Deplancke

Bart Deplancke

10

0 references

author name string

Carine Gubelmann

1

1 reference

5 August 2017

Wiebke Holcombe

4

1 reference

5 August 2017

Jean-Daniel Feuz

7

1 reference

5 August 2017

Sunil K Raghav

8

1 reference

5 August 2017

Jovan Simicevic

9

1 reference

5 August 2017

publication date

6 August 2013

1 reference

Molecular Systems Biology

5 August 2017

published in

1 reference

5 August 2017

volume

9

1 reference

5 August 2017

page(s)

682

1 reference

describes a project that uses

5 August 2017

Cytoscape

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Evaluation of methods for modeling transcription factor sequence specificity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

DNA-binding specificities of human transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Systematic localization of common disease-associated variation in regulatory DNA

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Analysis of variation at transcription factor binding sites in Drosophila and humans

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

An encyclopedia of mouse DNA elements (Mouse ENCODE).

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

A map of the cis-regulatory sequences in the mouse genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Integrative genomics identifies the corepressor SMRT as a gatekeeper of adipogenesis through the transcription factors C/EBPβ and KAISO.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Automated protein-DNA interaction screening of Drosophila regulatory elements

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Yeast one-hybrid assays for gene-centered human gene regulatory network mapping.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

The interferon-gamma-induced GTPase, mGBP-2, inhibits tumor necrosis factor alpha (TNF-alpha) induction of matrix metalloproteinase-9 (MMP-9) by inhibiting NF-kappaB and Rac protein

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

FIMO: scanning for occurrences of a given motif

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the Olig1 and Olig2 locus

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Cytoscape 2.8: new features for data integration and network visualization

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Sumoylation activates the transcriptional activity of Pax-6, an important transcription factor for eye and brain development

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

The mouse Gene Expression Database (GXD): 2011 update

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Sp1 acetylation is associated with loss of DNA binding at promoters associated with cell cycle arrest and cell death in a colon cell line.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Theoretical and empirical quality assessment of transcription factor-binding motifs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Determining the specificity of protein-DNA interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Onecut-2 knockout mice fail to thrive during early postnatal period and have altered patterns of gene expression in small intestine

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

RSK-mediated phosphorylation in the C/EBP{beta} leucine zipper regulates DNA binding, dimerization, and growth arrest activity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Functional cis-regulatory genomics for systems biology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

RFX2 is a candidate downstream amplifier of A-MYB regulation in mouse spermatogenesis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Experimental determination of the evolvability of a transcription factor

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

EMAGE mouse embryo spatial gene expression database: 2010 update

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Insights from genomic profiling of transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Ets1 and Ets2 are required for endothelial cell survival during embryonic angiogenesis.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

MicroRNAs are involved in erythroid differentiation control

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Experimental advances in the characterization of metazoan gene regulatory networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Histone modifications at human enhancers reflect global cell-type-specific gene expression

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Acetylation of Nrf2 by p300/CBP augments promoter-specific DNA binding of Nrf2 during the antioxidant response

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

ChIP-seq accurately predicts tissue-specific activity of enhancers

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

The DNA-encoded nucleosome organization of a eukaryotic genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

An experimentally derived confidence score for binary protein-protein interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Improving yeast two-hybrid screening systems

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

DBD--taxonomically broad transcription factor predictions: new content and functionality

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Small ubiquitin-like modifier modification regulates the DNA binding activity of glial cell missing Drosophila homolog a.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Genome-wide mapping of in vivo protein-DNA interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Sumoylation of Oct4 enhances its stability, DNA binding, and transactivation.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Role of the Onecut transcription factors in pancreas morphogenesis and in pancreatic and enteric endocrine differentiation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

A systems approach to measuring the binding energy landscapes of transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

TRED: a transcriptional regulatory element database, new entries and other development

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

VISTA Enhancer Browser--a database of tissue-specific human enhancers

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Cdx4 dysregulates Hox gene expression and generates acute myeloid leukemia alone and in cooperation with Meis1a in a murine model

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Acetylation of GATA-1 is required for chromatin occupancy

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Genome-wide analysis of mammalian promoter architecture and evolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

DBD: a transcription factor prediction database

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Embryonic stem cell-derived hematopoietic stem cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

The transcriptional landscape of the mammalian genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

A gateway-compatible yeast one-hybrid system.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Applied bioinformatics for the identification of regulatory elements

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Functional regulation of GATA-2 by acetylation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Id proteins in development, cell cycle and cancer

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Sp1- and Krüppel-like transcription factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

One hundred years of mouse genetics: an intellectual history. I. The classical period (1902-1980).

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Identification of a BMP-responsive element in Id1, the gene for inhibition of myogenesis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Phosphorylation represses Ets-1 DNA binding by reinforcing autoinhibition

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Expression patterns of Id1, Id2, and Id3 are highly related but distinct from that of Id4 during mouse embryogenesis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

A growth factor-induced kinase phosphorylates the serum response factor at a site that regulates its DNA-binding activity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

Different activation domains of Sp1 govern formation of multimers and mediate transcriptional synergism

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3779800

A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes.

8 July 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.38

Exhaustive benchmarking of the yeast two-hybrid system.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.38

A gene-centered C. elegans protein-DNA interaction network

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.38

PReMod: a database of genome-wide mammalian cis-regulatory module predictions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.38

The cdx-hox pathway in hematopoietic stem cell formation from embryonic stem cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.38

NMR structure of transcription factor Sp1 DNA binding domain

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23917988

12 December 2020

inferred from PubMed ID database lookup

Mouse brain organization revealed through direct genome-scale TF expression analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23917988

12 December 2020

inferred from PubMed ID database lookup

Lentiviral Vector Mediated Transgenesis

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.38

7 January 2021

inferred from DOI database lookup

Gateway-compatible yeast one-hybrid screens

1 reference

https://api.crossref.org/works/10.1038%2FMSB.2013.38

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1038/MSB.2013.38

1 reference

5 August 2017

1 reference

5 August 2017

1 reference