List of works - Holger Fröhlich

A Bayesian network view on nested effects models.

scientific article

A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions.

scientific article

A Machine Learning Approach to Automated Gait Analysis for the Noldus Catwalk (TM)System

scientific article published on 24 August 2017

A Simple 3-Parameter Model for Cancer Incidences

scientific article published on 21 February 2018

A systems pharmacology approach to improve drug therapy in NSCLC: establishing a CESAR network.

scientific article published on January 2014

Activation of AMP-activated protein kinase sensitizes lung cancer cells and H1299 xenografts to erlotinib

scientific article published on 10 September 2014

Automated classification of the behavior of rats in the forced swimming test with support vector machines

scientific article published on 29 November 2007

Benefits of a factorial design focusing on inclusion of female and male animals in one experiment

scientific article published on 13 April 2019

Bioinformatical evaluation of modified nucleosides as biomedical markers in diagnosis of breast cancer

scientific article published on 01 May 2008

Biomarker gene signature discovery integrating network knowledge

scientific article published on 27 February 2012

Boosting probabilistic graphical model inference by incorporating prior knowledge from multiple sources.

scientific article

CD4+ T cell counts reflect the immunosuppressive state of CD4 helper cells in patients after allogeneic stem cell transplantation

scientific article published on 15 August 2014

Changes in serum miRNAs following generalized convulsive seizures in human mesial temporal lobe epilepsy.

scientific article published on 7 November 2016

Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes

scientific article published on 20 October 2014

Classic bladder exstrophy and adenocarcinoma of the bladder: Methylome analysis provide no evidence for underlying disease-mechanisms of this association

scientific article published on 31 May 2019

Clustering of Alzheimer's and Parkinson's disease based on genetic burden of shared molecular mechanisms

scientific article published on 05 November 2020

Corrigendum: The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

scientific article published on 29 April 2020

Cross-talk between AMPK and EGFR dependent Signaling in Non-Small Cell Lung Cancer.

scientific article published on 09 June 2016

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

scientific article

DNA methylation signature in peripheral blood reveals distinct characteristics of human X chromosome numerical aberrations

scientific article published on 28 July 2015

Data and Graph Mining in Chemical Space for ADME and Activity Data Sets

Deep learning for clustering of multivariate clinical patient trajectories with missing values

scientific article published on 01 November 2019

Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions

scientific article published on 8 October 2009

Differences in cohort study data affect external validation of artificial intelligence models for predictive diagnostics of dementia - lessons for translation into clinical practice

scientific article published on 22 June 2020

Different microRNA profiles in chronic epilepsy versus acute seizure mouse models

scientific article

Dynamic Bayesian Network Modeling of the Interplay between EGFR and Hedgehog Signaling

scientific article published on 16 November 2015

Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data

scientific article

Epigenome-wide DNA methylation analysis in siblings and monozygotic twins discordant for sporadic Parkinson's disease revealed different epigenetic patterns in peripheral blood mononuclear cells

scientific article published on 6 October 2016

Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data

scientific article

Evaluating the Alzheimer's disease data landscape

scientific article published on 16 December 2020

Evidence for contribution of epigenetic mechanisms in the pathogenesis of systemic mast cell activation disease

article

Exosomal microRNA miR-92a concentration in serum reflects human brown fat activity

scientific article

Expectation propagation for large scale Bayesian inference of non-linear molecular networks from perturbation data.

scientific article

Fast and efficient dynamic nested effects models

scientific article

Feature selection for descriptor based classification models. 1. Theory and GA-SEC algorithm

scientific article published in May 2004

From hype to reality: data science enabling personalized medicine

scientific article published on 27 August 2018

GOSim--an R-package for computation of information theoretic GO similarities between terms and gene products

scientific article

Genome-wide CNV analysis in 221 unrelated patients and targeted high-throughput sequencing reveal novel causative candidate genes for colorectal adenomatous polyposis

scientific article published on 30 September 2014

GuiltyTargets: Prioritization of Novel Therapeutic Targets with Deep Network Representation Learning

preprint

GuiltyTargets: Prioritization of Novel Therapeutic Targets with Deep Network Representation Learning

scientific article published on 19 June 2020

Hsp90 inhibition differentially destabilises MAP kinase and TGF-beta signalling components in cancer cells revealed by kinase-targeted chemoproteomics

scientific article

Immune system modeling and related pathologies

scientific article published on 17 December 2012

Including network knowledge into Cox regression models for biomarker signature discovery

scientific article published on 15 January 2014

Increasing the sensitivity of reverse phase protein arrays by antibody-mediated signal amplification

scientific article published on 22 June 2010

Inferring modulators of genetic interactions with epistatic nested effects models

scientific article

Integrating digital gait data with metabolomics and clinical data to predict outcomes in Parkinson’s disease

scientific article published on 06 September 2024

Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients

scientific article

Inter-locus as well as intra-locus heterogeneity in LINE-1 promoter methylation in common human cancers suggests selective demethylation pressure at specific CpGs.

scientific article

Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data

scientific article

Kernel Functions for Attributed Molecular Graphs – A New Similarity-Based Approach to ADME Prediction in Classification and Regression

scientific article (publication date: April 2006)

Key Players of Cisplatin Resistance: Towards a Systems Pharmacology Approach

scientific article

Kit transduced signals counteract erythroid maturation by MAPK-dependent modulation of erythropoietin signaling and apoptosis induction in mouse fetal liver

scientific article published on 17 October 2014

Knowledge-based approach to identify key determinants of cisplatin sensitivity

scientific article published in August 2017

L-dopa increases α-synuclein DNA methylation in Parkinson's disease patients in vivo and in vitro

scientific article published on 14 July 2015

Learning (from) the errors of a systems biology model

scientific article published on 11 February 2016

Learning gene network structure from time laps cell imaging in RNAi Knock downs

scientific article

Linking metabolic network features to phenotypes using sparse group lasso.

scientific article published in November 2017

MC EMiNEM maps the interaction landscape of the Mediator

scientific article

Metabonomics in cancer diagnosis: mass spectrometry-based profiling of urinary nucleosides from breast cancer patients

scientific article published on 01 June 2008

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance

scientific article

NEMix: single-cell nested effects models for probabilistic pathway stimulation

scientific article

NSCLC cells adapted to EGFR inhibition accumulate EGFR interacting proteins and down-regulate microRNA related to epithelial-mesenchymal transition

scientific article published on January 2014

Nested effects models for learning signaling networks from perturbation data

scientific article

Network Based Consensus Gene Signatures for Biomarker Discovery in Breast Cancer ⬇️

scientific article published on October 25, 2011

Network and data integration for biomarker signature discovery via network smoothed T-statistics

scientific article

Optimal multiparametric set-up modelled for best survival outcomes in palliative treatment of liver malignancies: unsupervised machine learning and 3 PM recommendations

scientific article published on 10 August 2020

PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data

scientific article published on 16 April 2020

Patients' perception of Parkinson's disease-associated pain following initiation of rotigotine: a multicenter non-interventional study

scientific article

Predicting pathway membership via domain signatures.

scientific article published on August 2008

Predicting potent compounds via model-based global optimization.

scientific article published on 14 February 2013

Premenopausal breast cancer: potential clinical utility of a multi-omics based machine learning approach for patient stratification

scientific article published on 11 April 2018

Prognostic gene signatures for patient stratification in breast cancer: accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions.

scientific article

Realistic simulation of virtual multi-scale, multi-modal patient trajectories using Bayesian networks and sparse auto-encoders

scientific article published on 03 July 2020

SEEDS: Data driven inference of structural model errors and unknown inputs for dynamic systems biology

scientific article published on 15 September 2020

Skewed X-chromosome inactivation and XIST locus methylation levels do not contribute to the lower prevalence of Parkinson's disease in females.

scientific article

Steiner tree methods for optimal sub-network identification: an empirical study ⬇️

scientific article published on April 30, 2013

Stimulation of MMP-1 and CCL2 by NAMPT in PDL cells.

scientific article published on 22 August 2013

Susceptibility variants on chromosome 7p21.1 suggest HDAC9 as a new candidate gene for male-pattern baldness

scientific article published in December 2011

TGF-beta1 does not induce senescence of multipotent mesenchymal stromal cells and has similar effects in early and late passages

scientific article

TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level

scientific article

Ten quick tips for biomarker discovery and validation analyses using machine learning

scientific article published on 11 August 2022

The EMT transcription factor Zeb2 controls adult murine hematopoietic differentiation by regulating cytokine signaling

scientific article published on 28 September 2016

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

preprint

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

scientific article published on 22 November 2019

Towards Clinically More Relevant Dissection of Patient Heterogeneity via Survival based Bayesian Clustering

scientific article published on 26 July 2017

Towards a Central Role of in the Bladder Exstrophy⁻Epispadias Complex (BEEC): Computational Characterization of Genetic Variants and Structural Modelling

article

Towards a mechanism-based taxonomy of Alzheimer’s and Parkinson’s disease ⬇️

conference poster

Unsupervised automated high throughput phenotyping of RNAi time-lapse movies

scientific article

Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer's Disease and Reconstruction of Relevant Biological Mechanisms

scientific article published in Scientific Reports

Utilising the EGFR interactome to identify mechanisms of drug resistance in non-small cell lung cancer - Proof of concept towards a systems pharmacology approach

scientific article published on 22 April 2016

Variational Autoencoder Modular Bayesian Networks for Simulation of Heterogeneous Clinical Study Data

publication published on 28 May 2020

Voice perturbations under the stress overload in young individuals: phenotyping and suboptimal health as predictors for cascading pathologies

scientific article published on 12 November 2020

biRte: Bayesian inference of context-specific regulator activities and transcriptional networks

scientific article

miR-155 regulates differentiation of brown and beige adipocytes via a bistable circuit.

scientific article published on January 2013

netClass: an R-package for network based, integrative biomarker signature discovery

scientific article

pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery

scientific article published on 30 March 2011

List of works by Holger Fröhlich

A Bayesian network view on nested effects models.

A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions.

A Machine Learning Approach to Automated Gait Analysis for the Noldus Catwalk (TM)System

A Simple 3-Parameter Model for Cancer Incidences

A systems pharmacology approach to improve drug therapy in NSCLC: establishing a CESAR network.

Activation of AMP-activated protein kinase sensitizes lung cancer cells and H1299 xenografts to erlotinib

Automated classification of the behavior of rats in the forced swimming test with support vector machines

Benefits of a factorial design focusing on inclusion of female and male animals in one experiment

Bioinformatical evaluation of modified nucleosides as biomedical markers in diagnosis of breast cancer

Biomarker gene signature discovery integrating network knowledge

Boosting probabilistic graphical model inference by incorporating prior knowledge from multiple sources.

CD4+ T cell counts reflect the immunosuppressive state of CD4 helper cells in patients after allogeneic stem cell transplantation

Changes in serum miRNAs following generalized convulsive seizures in human mesial temporal lobe epilepsy.

Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes

Classic bladder exstrophy and adenocarcinoma of the bladder: Methylome analysis provide no evidence for underlying disease-mechanisms of this association

Clustering of Alzheimer's and Parkinson's disease based on genetic burden of shared molecular mechanisms

Corrigendum: The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling

Cross-talk between AMPK and EGFR dependent Signaling in Non-Small Cell Lung Cancer.

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

DNA methylation signature in peripheral blood reveals distinct characteristics of human X chromosome numerical aberrations

Data and Graph Mining in Chemical Space for ADME and Activity Data Sets

Deep learning for clustering of multivariate clinical patient trajectories with missing values

Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions

Differences in cohort study data affect external validation of artificial intelligence models for predictive diagnostics of dementia - lessons for translation into clinical practice

Different microRNA profiles in chronic epilepsy versus acute seizure mouse models

Dynamic Bayesian Network Modeling of the Interplay between EGFR and Hedgehog Signaling

Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data

Epigenome-wide DNA methylation analysis in siblings and monozygotic twins discordant for sporadic Parkinson's disease revealed different epigenetic patterns in peripheral blood mononuclear cells

Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data

Evaluating the Alzheimer's disease data landscape

Evidence for contribution of epigenetic mechanisms in the pathogenesis of systemic mast cell activation disease

Exosomal microRNA miR-92a concentration in serum reflects human brown fat activity

Expectation propagation for large scale Bayesian inference of non-linear molecular networks from perturbation data.

Fast and efficient dynamic nested effects models

Feature selection for descriptor based classification models. 1. Theory and GA-SEC algorithm

From hype to reality: data science enabling personalized medicine

GOSim--an R-package for computation of information theoretic GO similarities between terms and gene products

Genome-wide CNV analysis in 221 unrelated patients and targeted high-throughput sequencing reveal novel causative candidate genes for colorectal adenomatous polyposis

GuiltyTargets: Prioritization of Novel Therapeutic Targets with Deep Network Representation Learning

GuiltyTargets: Prioritization of Novel Therapeutic Targets with Deep Network Representation Learning

Hsp90 inhibition differentially destabilises MAP kinase and TGF-beta signalling components in cancer cells revealed by kinase-targeted chemoproteomics

Immune system modeling and related pathologies

Including network knowledge into Cox regression models for biomarker signature discovery

Increasing the sensitivity of reverse phase protein arrays by antibody-mediated signal amplification

Inferring modulators of genetic interactions with epistatic nested effects models

Integrating digital gait data with metabolomics and clinical data to predict outcomes in Parkinson’s disease

Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients

Inter-locus as well as intra-locus heterogeneity in LINE-1 promoter methylation in common human cancers suggests selective demethylation pressure at specific CpGs.

Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data

Kernel Functions for Attributed Molecular Graphs – A New Similarity-Based Approach to ADME Prediction in Classification and Regression

Key Players of Cisplatin Resistance: Towards a Systems Pharmacology Approach

Kit transduced signals counteract erythroid maturation by MAPK-dependent modulation of erythropoietin signaling and apoptosis induction in mouse fetal liver

Knowledge-based approach to identify key determinants of cisplatin sensitivity

L-dopa increases α-synuclein DNA methylation in Parkinson's disease patients in vivo and in vitro

Learning (from) the errors of a systems biology model

Learning gene network structure from time laps cell imaging in RNAi Knock downs

Linking metabolic network features to phenotypes using sparse group lasso.

MC EMiNEM maps the interaction landscape of the Mediator

Metabonomics in cancer diagnosis: mass spectrometry-based profiling of urinary nucleosides from breast cancer patients

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance

NEMix: single-cell nested effects models for probabilistic pathway stimulation

NSCLC cells adapted to EGFR inhibition accumulate EGFR interacting proteins and down-regulate microRNA related to epithelial-mesenchymal transition

Nested effects models for learning signaling networks from perturbation data

Network Based Consensus Gene Signatures for Biomarker Discovery in Breast Cancer ⬇️

Network and data integration for biomarker signature discovery via network smoothed T-statistics

Optimal multiparametric set-up modelled for best survival outcomes in palliative treatment of liver malignancies: unsupervised machine learning and 3 PM recommendations

PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data

Patients' perception of Parkinson's disease-associated pain following initiation of rotigotine: a multicenter non-interventional study

Predicting pathway membership via domain signatures.

Predicting potent compounds via model-based global optimization.

Premenopausal breast cancer: potential clinical utility of a multi-omics based machine learning approach for patient stratification

Prognostic gene signatures for patient stratification in breast cancer: accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions.

Realistic simulation of virtual multi-scale, multi-modal patient trajectories using Bayesian networks and sparse auto-encoders

SEEDS: Data driven inference of structural model errors and unknown inputs for dynamic systems biology

Skewed X-chromosome inactivation and XIST locus methylation levels do not contribute to the lower prevalence of Parkinson's disease in females.

Steiner tree methods for optimal sub-network identification: an empirical study ⬇️

Stimulation of MMP-1 and CCL2 by NAMPT in PDL cells.

Susceptibility variants on chromosome 7p21.1 suggest HDAC9 as a new candidate gene for male-pattern baldness

TGF-beta1 does not induce senescence of multipotent mesenchymal stromal cells and has similar effects in early and late passages