(Q34494671)

English

The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes

scientific article

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scholarly article

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Europe PubMed Central

2 August 2017

The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes (English)

1 reference

Europe PubMed Central

2 August 2017

Reinhard Guthke

8

object named as

Reinhard Guthke

1 reference

Europe PubMed Central

2 August 2017

Wolfgang Schmidt-Heck

2

object named as

Wolfgang Schmidt-Heck

1 reference

Europe PubMed Central

2 August 2017

9

object named as

Rolf Gebhardt

1 reference

Europe PubMed Central

2 August 2017

5

object named as

Jörg Linde

1 reference

Europe PubMed Central

2 August 2017

Sebastian Vlaic

1

object named as

Sebastian Vlaic

1 reference

Europe PubMed Central

2 August 2017

author name string

Madlen Matz-Soja

3

1 reference

Europe PubMed Central

2 August 2017

Eugenia Marbach

4

1 reference

Europe PubMed Central

2 August 2017

Anke Meyer-Baese

6

1 reference

Europe PubMed Central

2 August 2017

Sebastian Zellmer

7

1 reference

Europe PubMed Central

2 August 2017

publication date

29 November 2012

1 reference

Europe PubMed Central

2 August 2017

BMC Systems Biology

1 reference

Europe PubMed Central

2 August 2017

6

1 reference

Europe PubMed Central

2 August 2017

147

1 reference

Europe PubMed Central

2 August 2017

describes a project that uses

object named as

affy package

1 reference

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

object named as

Cytoscape

1 reference

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

0 references

https://scigraph.springernature.com/pub.10.1186/1752-0509-6-147

0 references

An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Genome-Wide Scale-Free Network Inference for Candida albicans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Foxa1 reduces lipid accumulation in human hepatocytes and is down-regulated in nonalcoholic fatty liver

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

ATF3, an HTLV-1 bZip factor binding protein, promotes proliferation of adult T-cell leukemia cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Transcription factors ETF, E2F, and SP-1 are involved in cytokine-independent proliferation of murine hepatocytes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Activation of the farnesoid X receptor provides protection against acetaminophen-induced hepatic toxicity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Tgif1 represses apolipoprotein gene expression in liver

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

The Fox genes in the liver: from organogenesis to functional integration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Phosphorylation and acetylation of histone H3 and autoregulation by early growth response 1 mediate interleukin 1beta induction of early growth response 1 transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Integrative modeling of transcriptional regulation in response to antirheumatic therapy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Gene regulatory network inference: data integration in dynamic models-a review

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Parameter optimization in S-system models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Information-theoretic inference of large transcriptional regulatory networks.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Novel definition files for human GeneChips based on GeneAnnot

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Functional interaction of hepatic nuclear factor-4 and peroxisome proliferator-activated receptor-gamma coactivator 1alpha in CYP7A1 regulation is inhibited by a key lipogenic activator, sterol regulatory element-binding protein-1c

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Reverse engineering of gene regulatory networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

oPOSSUM: integrated tools for analysis of regulatory motif over-representation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

The mouse C/EBPdelta gene promoter is regulated by STAT3 and Sp1 transcriptional activators, chromatin remodeling and c-Myc repression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Using GOstats to test gene lists for GO term association

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Regulation of hepatic fatty acid elongase and desaturase expression in diabetes and obesity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Farnesoid X receptor is essential for normal glucose homeostasis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Activation of the nuclear receptor FXR improves hyperglycemia and hyperlipidemia in diabetic mice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Computational cluster validation in post-genomic data analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Targeted disruption of Tgif, the mouse ortholog of a human holoprosencephaly gene, does not result in holoprosencephaly in mice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

A role for E2F6 in distinguishing G1/S- and G2/M-specific transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

C/EBPdelta is a downstream mediator of IL-6 induced growth inhibition of prostate cancer cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Bioconductor: open software development for computational biology and bioinformatics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Hepatic CCAAT/enhancer binding protein alpha mediates induction of lipogenesis and regulation of glucose homeostasis in leptin-deficient mice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Bile acids lower triglyceride levels via a pathway involving FXR, SHP, and SREBP-1c

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

affy--analysis of Affymetrix GeneChip data at the probe level

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Network biology: understanding the cell's functional organization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

JASPAR: an open-access database for eukaryotic transcription factor binding profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

A comprehensive search for HNF-3α-regulated genes in mouse hepatoma cells by 60K cDNA microarray and chromatin immunoprecipitation/PCR analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

New hepatocyte in vitro systems for drug metabolism: metabolic capacity and recommendations for application in basic research and drug development, standard operation procedures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

A gene-coexpression network for global discovery of conserved genetic modules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

A self-enabling TGFbeta response coupled to stress signaling: Smad engages stress response factor ATF3 for Id1 repression in epithelial cells.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Summaries of Affymetrix GeneChip probe level data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

TRANSFAC: transcriptional regulation, from patterns to profiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

The farnesoid X-receptor is an essential regulator of cholesterol homeostasis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

ATF3 induction following DNA damage is regulated by distinct signaling pathways and over-expression of ATF3 protein suppresses cells growth

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Regulation of life and death by the zinc finger transcription factor Egr-1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Forkhead transcription factors: key players in development and metabolism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

CCAAT/enhancer-binding proteins: structure, function and regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Activities of IRF-1

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Sterol regulatory element-binding protein-1 as a dominant transcription factor for gene regulation of lipogenic enzymes in the liver

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

A hierarchical unsupervised growing neural network for clustering gene expression patterns

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Circadian expression of the steroid 15 alpha-hydroxylase (Cyp2a4) and coumarin 7-hydroxylase (Cyp2a5) genes in mouse liver is regulated by the PAR leucine zipper transcription factor DBP

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Endogenous bile acids are ligands for the nuclear receptor FXR/BAR

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Bile acids: natural ligands for an orphan nuclear receptor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Identification of a nuclear receptor for bile acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

A Smad transcriptional corepressor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Regulation of sterol regulatory element binding proteins in livers of fasted and refed mice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Isoform 1c of sterol regulatory element binding protein is less active than isoform 1a in livers of transgenic mice and in cultured cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Differential expression of exons 1a and 1c in mRNAs for sterol regulatory element binding protein-1 in human and mouse organs and cultured cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Multiple steps in the regulation of transcription-factor level and activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Impaired energy homeostasis in C/EBP alpha knockout mice

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Antisense RNA of proto-oncogene c-fos blocks renewed growth of quiescent 3T3 cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

6 July 2018

Reverse engineering of gene networks with LASSO and nonlinear basis functions

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-147

21 January 2018

On cooperative quasi-equilibrium models of transcriptional regulation

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-147

21 January 2018

Disruption of hepatic C/EBPalpha results in impaired glucose tolerance and age-dependent hepatosteatosis.

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-147

21 January 2018

Targeted disruption of the nuclear receptor FXR/BAR impairs bile acid and lipid homeostasis.

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-147

21 January 2018

The farnesoid X receptor modulates hepatic carbohydrate metabolism during the fasting-refeeding transition.

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-147

21 January 2018

Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3573979

27 October 2018

Phylogenetic Reconstruction Using an Unsupervised Growing Neural Network That Adopts the Topology of a Phylogenetic Tree

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-147

21 January 2018

Pathway studio—the analysis and navigation of molecular networks

1 reference

https://pubmed.ncbi.nlm.nih.gov/23190768

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Multiple modes of repression by the Smad transcriptional corepressor TGIF

1 reference

https://pubmed.ncbi.nlm.nih.gov/23190768

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1752-0509-6-147

1 reference

Europe PubMed Central

2 August 2017

DBLP publication ID

journals/bmcsb/VlaicSMMLMZGG12

1 reference

DBLP Dataset 2021-01-02

28 January 2021

Dimensions Publication ID

0 references

1 reference

Europe PubMed Central

2 August 2017

1 reference

Europe PubMed Central

2 August 2017

ResearchGate publication ID

0 references

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