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List of works by Jörg Rahnenführer

A Comprehensive Analysis of Human Gene Expression Profiles Identifies Stromal Immunoglobulin C as a Compatible Prognostic Marker in Human Solid Tumors

article

A Multicriteria Approach to Find Predictive and Sparse Models with Stable Feature Selection for High-Dimensional Data

scientific article

A detailed comparison of analysis processes for MCC-IMS data in disease classification-Automated methods can replace manual peak annotations

scientific article

A new measure for functional similarity of gene products based on Gene Ontology

scientific article published on 15 June 2006

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

scientific article

Altered Stress-Induced Regulation of Genes in Monocytes in Adults with a History of Childhood Adversity

scientific article published on 19 April 2016

Analysis of compound synergy in high-throughput cellular screens by population-based lifetime modeling

scientific article

Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas.

scientific article

Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes

scientific article

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

scientific article published on 01 July 2018

Automated clustering of ensembles of alternative models in protein structure databases.

scientific article

Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation.

scientific article published on 2 October 2012

Calculating the statistical significance of changes in pathway activity from gene expression data

scientific article published on 22 June 2004

Cellular and molecular characterization of early and late retinal stem cells/progenitors: differential regulation of proliferation and context dependent role of Notch signaling.

scientific article published in December 2004

Changes in cortical cytoskeletal and extracellular matrix gene expression in prostate cancer are related to oncogenic ERG deregulation.

scientific article

Classification with high-dimensional genetic data: assigning patients and genetic features to known classes

scientific article

Clinical outcome of patients with lymph node-positive prostate cancer following radical prostatectomy and extended sentinel lymph node dissection

scientific article published on 20 August 2014

Clonal cytogenetic progression within intratumorally heterogeneous meningiomas predicts tumor recurrence

scientific article published on 12 September 2011

Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra.

scientific article

Comparison of a teratogenic transcriptome-based predictive test based on human embryonic versus inducible pluripotent stem cells.

scientific article published on 30 December 2016

Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes.

scientific article

Computational methods for the design of effective therapies against drug resistant HIV strains

scientific article

Confirmation of human protein interaction data by human expression data

scientific article

Conformational analysis of alternative protein structures

scientific article published on 12 October 2007

Correspondence of tumor localization with tumor recurrence and cytogenetic progression in meningiomas

scientific article published in January 2008

Corrigendum to Normalization of data for viability and relative cell function curves

scientific article published on 01 January 2019

Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms

scientific article published on 28 January 2020

Cumulative disease progression models for cross-sectional data: a review and comparison

scientific article

D-score: a search engine independent MD-score.

scientific article published on 15 February 2013

DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs

scientific article

Definition of transcriptome-based indices for quantitative characterization of chemically disturbed stem cell development: introduction of the STOP-Toxukn and STOP-Toxukk tests

scientific article

Design principles of concentration-dependent transcriptome deviations in drug-exposed differentiating stem cells.

scientific article published on 21 January 2014

Detection of patient subgroups with differential expression in omics data: a comprehensive comparison of univariate measures

scientific article (publication date: 2013)

Determination of benchmark concentrations and their statistical uncertainty for cytotoxicity test data and functional in vitro assays

scientific article published on 12 December 2019

Development of a neural rosette formation assay (RoFA) to identify neurodevelopmental toxicants and to characterize their transcriptome disturbances

scientific article published on 11 November 2019

EDI3 links choline metabolism to integrin expression, cell adhesion and spreading

scientific article

ERBB2 and TOP2A in breast cancer: a comprehensive analysis of gene amplification, RNA levels, and protein expression and their influence on prognosis and prediction.

scientific article published on 6 April 2010

ERBB2 induces an antiapoptotic expression pattern of Bcl-2 family members in node-negative breast cancer.

scientific article published on 12 January 2010

Ep-CAM RNA expression predicts metastasis-free survival in three cohorts of untreated node-negative breast cancer

scientific article published on 30 March 2010

Epsin Family Member 3 and Ribosome-Related Genes Are Associated with Late Metastasis in Estrogen Receptor-Positive Breast Cancer and Long-Term Survival in Non-Small Cell Lung Cancer Using a Genome-Wide Identification and Validation Strategy

scientific article

Estimating HIV evolutionary pathways and the genetic barrier to drug resistance

scientific article published on 28 April 2005

Estimating cancer survival and clinical outcome based on genetic tumor progression scores

scientific article published on 10 February 2005

Evaluation of Adjusted and Unadjusted Indirect Comparison Methods in Benefit Assessment. A Simulation Study for Time-to-event Endpoints

scientific article published on 31 March 2017

Expression of aurora kinase A is associated with metastasis-free survival in node-negative breast cancer patients

scientific article

Factor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer

scientific article published on 05 February 2007

From smoking guns to footprints: mining for critical events of toxicity pathways in transcriptome data

scientific article published on 8 April 2015

From transient transcriptome responses to disturbed neurodevelopment: role of histone acetylation and methylation as epigenetic switch between reversible and irreversible drug effects.

scientific article

GOTax: investigating biological processes and biochemical activities along the taxonomic tree.

scientific article published on January 2007

Gelsolin Is Associated with Longer Metastasis-free Survival and Reduced Cell Migration in Estrogen Receptor-positive Breast Cancer.

scientific article published on October 2015

Glycerol-3-phosphate Acyltransferase 1 Promotes Tumor Cell Migration and Poor Survival in Ovarian Carcinoma.

scientific article published on 26 June 2017

Glycerophospholipid profile in oncogene-induced senescence

scientific article

Going from where to why--interpretable prediction of protein subcellular localization

scientific article

Hepatotoxicity of piperazine designer drugs: up-regulation of key enzymes of cholesterol and lipid biosynthesis

scientific article published on 28 January 2016

Human Pluripotent Stem Cell Based Developmental Toxicity Assays for Chemical Safety Screening and Systems Biology Data Generation

scientific article

Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach

scientific article

Hybrid clustering for microarray image analysis combining intensity and shape features

scientific article

Hyperdiploidy defines a distinct cytogenetic entity of meningiomas

scientific article published on 17 January 2007

Identification of sample annotation errors in gene expression datasets

scientific article

Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration.

scientific article

Image analysis for cDNA microarrays

scientific article published in January 2005

Impact of intratumoral heterogeneity of breast cancer tissue on quantitative metabolomics using high-resolution magic angle spinning 1 H NMR spectroscopy

scientific article

Impairment of human neural crest cell migration by prolonged exposure to interferon-beta.

scientific article

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure

scientific article

In vitro - in vivo correlation of gene expression alterations induced by liver carcinogens.

scientific article published in January 2012

Indirect Comparisons in Benefit Assessment

scientific article published on 20 October 2015

Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer.

scientific article published on 7 November 2017

Interferon-inducible guanylate binding protein (GBP2) is associated with better prognosis in breast cancer and indicates an efficient T cell response

scientific article

LIPG-promoted lipid storage mediates adaptation to oxidative stress in breast cancer

scientific article published on 07 February 2019

Learning multiple evolutionary pathways from cross-sectional data

scientific article

Loss of circadian clock gene expression is associated with tumor progression in breast cancer.

scientific article

Mechanical strain mimicking breathing amplifies alterations in gene expression induced by SiO2 NPs in lung epithelial cells

scientific article published on 16 August 2019

Metabolic profiling of ob/ob mouse fatty liver using HR-MAS 1H-NMR combined with gene expression analysis reveals alterations in betaine metabolism and the transsulfuration pathway

scientific article

Model selection for mixtures of mutagenetic trees

scientific article published on 23 June 2006

Model-based optimization of subgroup weights for survival analysis

scientific article published on 01 July 2019

Modelling nonstationary gene regulatory processes

scientific article published on 20 July 2010

Molecular biological determinations of meningioma progression and recurrence

scientific article

Mtreemix: a software package for learning and using mixture models of mutagenetic trees

scientific article published on 18 January 2005

No longer confidential: estimating the confidence of individual regression predictions

scientific article

Normalization of data for viability and relative cell function curves

scientific article published on 01 January 2018

Optimal strategies for sequential validation of significant features from high-dimensional genomic data

scientific article

P06.06PROGNOSIS OF MENINGIOMAS IN THE 1970S AND TODAY.

scientific article published in September 2014

Patients with high-grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment

scientific article

Peek a peak: a glance at statistics for quantitative label-free proteomics.

scientific article published on April 2010

Polymorphisms in the IGF1 signalling pathway including the myostatin gene are associated with left ventricular mass in male athletes

scientific article published on 9 January 2009

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions

scientific article published on 18 May 2009

Prediction of human drug-induced liver injury (DILI) in relation to oral doses and blood concentrations

scientific article published on 27 June 2019

Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification

Profiling cancer testis antigens in non-small-cell lung cancer

scientific article published on 07 July 2016

Prognostic Impact of Tumor Cell Programmed Death Ligand 1 Expression and Immune Cell Infiltration in NSCLC

scientific article published on 09 January 2019

Prognostic impact of COX-2 in non-small cell lung cancer: a comprehensive compartment-specific evaluation of tumor and stromal cell expression

scientific article published on 31 October 2014

Prognostic influence of pre-operative C-reactive protein in node-negative breast cancer patients

scientific article

Prognostic significance of interferon regulating factor 4 (IRF4) in node-negative breast cancer.

scientific article

Protein phosphatase and TRAIL receptor genes as new candidate tumor genes on chromosome 8p in prostate cancer.

scientific article published in March 2008

Reaching the limits of prognostication in non-small cell lung cancer: an optimized biomarker panel fails to outperform clinical parameters.

scientific article

Reef calcifiers are adapted to episodic heat stress but vulnerable to sustained warming.

scientific article

Relevance of the incubation period in cytotoxicity testing with primary human hepatocytes

article

Retention time alignment algorithms for LC/MS data must consider non-linear shifts

scientific article

Retinal properties and potential of the adult mammalian ciliary epithelium stem cells

scientific article published in June 2005

Robust selection of cancer survival signatures from high-throughput genomic data using two-fold subsampling

scientific article

Role of thioredoxin reductase 1 and thioredoxin interacting protein in prognosis of breast cancer

scientific article

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores

scientific article published on 20 August 2008

Stability analysis of mixtures of mutagenetic trees

scientific article

Statistical analysis of MCC-IMS data for two group comparisons-an exemplary study on two devices

scientific article published on 04 June 2019

Stem Cell Transcriptome Responses and Corresponding Biomarkers That Indicate the Transition from Adaptive Responses to Cytotoxicity.

scientific article published on 21 December 2016

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

scientific article published on March 2016

Subtype-specific prognostic impact of different immune signatures in node-negative breast cancer.

scientific article published on 05 June 2017

Survival models with preclustered gene groups as covariates

scientific article

Test systems of developmental toxicity: state-of-the art and future perspectives.

scientific article published in December 2013

The G Protein-Coupled Bile Acid Receptor TGR5 (Gpbar1) Modulates Endothelin-1 Signaling in Liver

scientific article published on 19 November 2019

The lung-specific proteome defined by integration of transcriptomics and antibody-based profiling.

scientific article

The prognostic relevance of tumour-infiltrating plasma cells and immunoglobulin kappa C indicates an important role of the humoral immune response in non-small cell lung cancer

scientific article

TiMEx: a waiting time model for mutually exclusive cancer alterations

scientific article published on 9 July 2015

Toxicogenomics directory of chemically exposed human hepatocytes

scientific article

Toxicogenomics directory of rat hepatotoxicants in vivo and in cultivated hepatocytes

scientific article published on 03 December 2018

Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering.

scientific article

Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV.

scientific article

YLoc--an interpretable web server for predicting subcellular localization

scientific article published on 27 May 2010

p15 promoter methylation - a novel prognostic marker in glioblastoma patients.

scientific article published in June 2009

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