List of works - Nils Blüthgen

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

scientific article published on 20 May 2022

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

scientific article

A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts

scientific article published on 12 January 2009

A transcriptome-based classifier to identify developmental toxicants by stem cell testing: design, validation and optimization for histone deacetylase inhibitors

scientific article

An immediate-late gene expression module decodes ERK signal duration

scientific article published on 3 May 2017

An immediate-late gene expression module decodes ERK signal duration

scientific article published on 25 September 2017

Analysis of impedance-based cellular growth assays

scientific article published on 21 April 2015

Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A. ⬇️

scientific article published on 29 December 2015

Assessment of stem cell differentiation based on genome-wide expression profiles

scientific article published on 01 July 2018

Bacterial computing with engineered populations

scientific article published on July 2015

Cell type-dependent differential activation of ERK by oncogenic KRAS in colon cancer and intestinal epithelium

scientific article published on 02 July 2019

Competing docking interactions can bring about bistability in the MAPK cascade

scientific article published on 25 May 2007

Computer-assisted curation of a human regulatory core network from the biological literature.

scientific article published on 29 November 2014

DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas and pancreatic neuroendocrine tumors

scientific article published on 01 March 2022

Discovering causal signaling pathways through gene-expression patterns

scientific article

Dissecting the action of an evolutionary conserved non-coding region on renin promoter activity

scientific article

Effects of RAF inhibitors on PI3K/AKT signalling depend on mutational status of the RAS/RAF signalling axis

scientific article

Effects of sequestration on signal transduction cascades

scientific article published in March 2006

Efficient translation initiation dictates codon usage at gene start

scientific article published on 18 June 2013

From Reaction Networks to Information Flow—Using Modular Response Analysis to Track Information in Signaling Networks ⬇️

scientific article published on January 1, 2011

Gene expression. MicroRNA control of protein expression noise

scientific article

Genome-wide profiling of the activity-dependent hippocampal transcriptome

scientific article

Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases

scientific article published on January 2006

Grouping of histone deacetylase inhibitors and other toxicants disturbing neural crest migration by transcriptional profiling

scientific article published on 31 July 2015

HOMGL-comparing genelists across species and with different accession numbers

scientific article published on January 2004

Handling and Interpreting Gene Groups

article

How robust are switches in intracellular signaling cascades?

scientific article published in December 2003

Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum.

scientific article

Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells

scientific article

Inferring combinatorial regulation of transcription in silico

scientific article

Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability

scientific article

Mathematical models in mammalian cell biology

scientific article published on 15 July 2008

Measuring specialization in species interaction networks

scientific article

Mechanisms Generating Ultrasensitivity, Bistability, and Oscillations in Signal Transduction

Multilevel regulation of HIF-1 signaling by TTP.

scientific article published on 23 August 2012

Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data

scientific article

Network quantification of EGFR signaling unveils potential for targeted combination therapy.

scientific article published on January 2013

Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance

scientific article published on 04 November 2021

Noise management by molecular networks

scientific article

Oncogenic β-catenin and PIK3CA instruct network states and cancer phenotypes in intestinal organoids.

scientific article

Personalized signaling models for personalized treatments

scientific article published on 01 January 2020

Perturbation-response genes reveal signaling footprints in cancer gene expression

scientific article published on 2 January 2018

Quantitative analysis of ultrasensitive responses

scientific article published on August 2005

RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway

scientific article published on 14 July 2015

RORγt⁺ innate lymphoid cells acquire a proinflammatory program upon engagement of the activating receptor NKp44.

scientific article published on 20 June 2013

Recurrent design patterns in the feedback regulation of the mammalian signalling network

scientific article published on 6 May 2008

Reduced replication origin licensing selectively kills KRAS-mutant colorectal cancer cells via mitotic catastrophe

scientific article published on 01 July 2020

Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS.

scientific article

Robustness of signal transduction pathways ⬇️

scientific article published on September 25, 2012

Seed-based systematic discovery of specific transcription factor target genes.

scientific article

Sequestration shapes the response of signal transduction cascades

scientific article published on November 2006

Signal integration by the CYP1A1 promoter--a quantitative study

scientific article published on May 2015

Signaling output: it's all about timing and feedbacks

scientific article published on 27 November 2015

Silence on the relevant literature and errors in implementation

scientific article published in April 2015

Spatial partitioning of the regulatory landscape of the X-inactivation centre ⬇️

scientific article (publication date: 11 April 2012)

Specialization, constraints, and conflicting interests in mutualistic networks

scientific article published in February 2007

Stem Cell-Derived Immature Human Dorsal Root Ganglia Neurons to Identify Peripheral Neurotoxicants

scientific article published on March 2016

Strong negative feedback from Erk to Raf confers robustness to MAPK signalling.

scientific article published on May 2011

SysBioMed report: advancing systems biology for medical applications.

scientific article published on May 2009

Systems biologists seek fuller integration of systems biology approaches in new cancer research programs

scientific article

Targetfinder.org: a resource for systematic discovery of transcription factor target genes

scientific article published on 11 May 2010

The cancer cell proteome and transcriptome predicts sensitivity to targeted and cytotoxic drugs

scientific article published on 28 June 2019

The gene regulatory network of mESC differentiation: a benchmark for reverse engineering methods

article

The two active X chromosomes in female ESCs block exit from the pluripotent state by modulating the ESC signaling network

scientific article

Tracking in vivo dynamics of NK cells transferred in patients undergoing stem cell transplantation

scientific article published on 30 June 2014

TransFind--predicting transcriptional regulators for gene sets

scientific article

Transcriptional feedbacks in mammalian signal transduction pathways facilitate rapid and reliable protein induction

scientific article published on 7 May 2010

Transcriptional profiling of Saccharomyces cerevisiae cells under adhesion-inducing conditions

scientific article

Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction

scientific article

List of works by Nils Blüthgen

A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts

A transcriptome-based classifier to identify developmental toxicants by stem cell testing: design, validation and optimization for histone deacetylase inhibitors

An immediate-late gene expression module decodes ERK signal duration

An immediate-late gene expression module decodes ERK signal duration

Analysis of impedance-based cellular growth assays

Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A. ⬇️

Assessment of stem cell differentiation based on genome-wide expression profiles

Bacterial computing with engineered populations

Cell type-dependent differential activation of ERK by oncogenic KRAS in colon cancer and intestinal epithelium

Competing docking interactions can bring about bistability in the MAPK cascade

Computer-assisted curation of a human regulatory core network from the biological literature.

DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas and pancreatic neuroendocrine tumors

Discovering causal signaling pathways through gene-expression patterns

Dissecting the action of an evolutionary conserved non-coding region on renin promoter activity

Effects of RAF inhibitors on PI3K/AKT signalling depend on mutational status of the RAS/RAF signalling axis

Effects of sequestration on signal transduction cascades

Efficient translation initiation dictates codon usage at gene start

From Reaction Networks to Information Flow—Using Modular Response Analysis to Track Information in Signaling Networks ⬇️

Gene expression. MicroRNA control of protein expression noise

Genome-wide profiling of the activity-dependent hippocampal transcriptome

Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases

Grouping of histone deacetylase inhibitors and other toxicants disturbing neural crest migration by transcriptional profiling

HOMGL-comparing genelists across species and with different accession numbers

Handling and Interpreting Gene Groups

How robust are switches in intracellular signaling cascades?

Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum.

Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells

Inferring combinatorial regulation of transcription in silico

Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability

Mathematical models in mammalian cell biology

Measuring specialization in species interaction networks

Mechanisms Generating Ultrasensitivity, Bistability, and Oscillations in Signal Transduction

Multilevel regulation of HIF-1 signaling by TTP.

Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data

Network quantification of EGFR signaling unveils potential for targeted combination therapy.

Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance

Noise management by molecular networks

Oncogenic β-catenin and PIK3CA instruct network states and cancer phenotypes in intestinal organoids.

Personalized signaling models for personalized treatments

Perturbation-response genes reveal signaling footprints in cancer gene expression

Quantitative analysis of ultrasensitive responses

RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway

RORγt⁺ innate lymphoid cells acquire a proinflammatory program upon engagement of the activating receptor NKp44.

Recurrent design patterns in the feedback regulation of the mammalian signalling network

Reduced replication origin licensing selectively kills KRAS-mutant colorectal cancer cells via mitotic catastrophe

Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS.

Robustness of signal transduction pathways ⬇️

Seed-based systematic discovery of specific transcription factor target genes.

Sequestration shapes the response of signal transduction cascades

Signal integration by the CYP1A1 promoter--a quantitative study

Signaling output: it's all about timing and feedbacks

Silence on the relevant literature and errors in implementation

Spatial partitioning of the regulatory landscape of the X-inactivation centre ⬇️

Specialization, constraints, and conflicting interests in mutualistic networks

Stem Cell-Derived Immature Human Dorsal Root Ganglia Neurons to Identify Peripheral Neurotoxicants

Strong negative feedback from Erk to Raf confers robustness to MAPK signalling.

SysBioMed report: advancing systems biology for medical applications.

Systems biologists seek fuller integration of systems biology approaches in new cancer research programs

Targetfinder.org: a resource for systematic discovery of transcription factor target genes

The cancer cell proteome and transcriptome predicts sensitivity to targeted and cytotoxic drugs

The gene regulatory network of mESC differentiation: a benchmark for reverse engineering methods

The two active X chromosomes in female ESCs block exit from the pluripotent state by modulating the ESC signaling network

Tracking in vivo dynamics of NK cells transferred in patients undergoing stem cell transplantation

TransFind--predicting transcriptional regulators for gene sets

Transcriptional feedbacks in mammalian signal transduction pathways facilitate rapid and reliable protein induction

Transcriptional profiling of Saccharomyces cerevisiae cells under adhesion-inducing conditions

Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction