Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering. - Daniel Bozinov; Jörg Rahnenführer (Bioinform., 2002)

Multivariate permutation tests for the k-sample problem with clustered data. - Jörg Rahnenführer (Comput. Stat., 2002)

Predicting protein structure classes from function predictions. - Ingolf Sommer; Jörg Rahnenführer; Francisco S. Domingues; Ulrik de Lichtenberg; Thomas Lengauer (Bioinform., 2004)

Hybrid clustering for microarray image analysis combining intensity and shape features. - Jörg Rahnenführer; Daniel Bozinov (BMC Bioinform., 2004)

Mtreemix: a software package for learning and using mixture models of mutagenetic trees. - Niko Beerenwinkel; Jörg Rahnenführer; Rolf Kaiser; Daniel Hoffmann; Joachim Selbig; Thomas Lengauer (Bioinform., 2005)

Computational methods for the design of effective therapies against drug resistant HIV strains. - Niko Beerenwinkel; Tobias Sing; Thomas Lengauer; Jörg Rahnenführer; Kirsten Roomp; Igor Savenkov; Roman Fischer; Daniel Hoffmann; Joachim Selbig; Klaus Korn; Hauke Walter; Thomas Berg; et al. (Bioinform., 2005)

Estimating cancer survival and clinical outcome based on genetic tumor progression scores. - Jörg Rahnenführer; Niko Beerenwinkel; Wolfgang A. Schulz; Christian Hartmann 006; Andreas von Deimling; Bernd Wullich; Thomas Lengauer (Bioinform., 2005)

Confirmation of human protein interaction data by human expression data. - Andreas Hahn; Jörg Rahnenführer; Priti Talwar; Thomas Lengauer (BMC Bioinform., 2005)

Learning Multiple Evolutionary Pathways from Cross-Sectional Data. - Niko Beerenwinkel; Jörg Rahnenführer; Martin Däumer; Daniel Hoffmann; Rolf Kaiser; Joachim Selbig; Thomas Lengauer (J. Comput. Biol., 2005)

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. - Adrian Alexa; Jörg Rahnenführer; Thomas Lengauer (Bioinform., 2006)

A new measure for functional similarity of gene products based on Gene Ontology. - Andreas Schlicker; Francisco S. Domingues; Jörg Rahnenführer; Thomas Lengauer (BMC Bioinform., 2006)

Conformational analysis of alternative protein structures. - Francisco S. Domingues; Jörg Rahnenführer; Thomas Lengauer (Bioinform., 2007)

Applications of semantic similarity measures. - Andreas Schlicker; Fidel Ramírez; Jörg Rahnenführer; Carola Huthmacher; Alejandro Pironti; Francisco S. Domingues; Thomas Lengauer; Mario Albrecht (Ontologies and Text Mining for Life Sciences, 2008)

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. - Jasmina Bogojeska; Adrian Alexa; André Altmann; Thomas Lengauer; Jörg Rahnenführer (Bioinform., 2008)

Stability analysis of mixtures of mutagenetic trees. - Jasmina Bogojeska; Thomas Lengauer; Jörg Rahnenführer (BMC Bioinform., 2008)

Retention time alignment algorithms for LC/MS data must consider non-linear shifts. - Katharina Podwojski; Arno Fritsch; Daniel C. Chamrad; Wolfgang Paul 001; Barbara Sitek; Kai Stühler; Petra Mutzel; Christian Stephan; Helmut E. Meyer; Wolfgang Urfer; Katja Ickstadt; Jörg Rahnenführer (Bioinform., 2009)

Modelling Nonstationary Gene Regulatory Processes. - Marco Grzegorczyk; Dirk Husmeier; Jörg Rahnenführer (Adv. Bioinformatics, 2010)

Going from where to why - interpretable prediction of protein subcellular localization. - Sebastian Briesemeister; Jörg Rahnenführer; Oliver Kohlbacher (Bioinform., 2010)

Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes. - Birte Hellwig; Jan G. Hengstler; Marcus Schmidt; Mathias C. Gehrmann; Wiebke Schormann; Jörg Rahnenführer (BMC Bioinform., 2010)

YLoc - an interpretable web server for predicting subcellular localization. - Sebastian Briesemeister; Jörg Rahnenführer; Oliver Kohlbacher (Nucleic Acids Res., 2010)

Survival models with preclustered gene groups as covariates. - Kai Kammers; Michel Lang; Jan G. Hengstler; Marcus Schmidt; Jörg Rahnenführer (BMC Bioinform., 2011)

Modelling non-stationary dynamic gene regulatory processes with the BGM model. - Marco Grzegorczyk; Dirk Husmeier; Jörg Rahnenführer (Comput. Stat., 2011)

Poster abstracts of GCB 2015. - Martin Eisenacher; Jörg Rahnenführer; Axel Mosig; Sven Rahmann (PeerJ Prepr., 2015)

Invited presentations, junior research groups and research highlights at GCB 2015. - Axel Mosig; Jörg Rahnenführer; Martin Eisenacher; Sven Rahmann (PeerJ Prepr., 2015)

Faster Model-Based Optimization Through Resource-Aware Scheduling Strategies. - Jakob Richter; Helena Kotthaus; Bernd Bischl; Peter Marwedel; Jörg Rahnenführer; Michel Lang (LION, 2016)

TiMEx: a waiting time model for mutually exclusive cancer alterations. - Simona Constantinescu; Ewa Szczurek; Pejman Mohammadi 001; Jörg Rahnenführer; Niko Beerenwinkel (Bioinform., 2016)

Machine Learning meets Data-Driven Journalism: Boosting International Understanding and Transparency in News Coverage. - Elena Erdmann; Karin Boczek; Lars Koppers; Gerret von Nordheim; Christian Pölitz; Alejandro Molina 001; Katharina Morik; Henrik Müller; Jörg Rahnenführer; Kristian Kersting (CoRR, 2016)

RAMBO: Resource-Aware Model-Based Optimization with Scheduling for Heterogeneous Runtimes and a Comparison with Asynchronous Model-Based Optimization. - Helena Kotthaus; Jakob Richter; Andreas Lang 002; Janek Thomas; Bernd Bischl; Peter Marwedel; Jörg Rahnenführer; Michel Lang (LION, 2017)

Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV. - Katrin Hainke; Sebastian Szugat; Roland Fried; Jörg Rahnenführer (BMC Bioinform., 2017)

DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs. - Vera Rieder; Bernhard Blank-Landeshammer; Marleen Stuhr; Tilman Schell; Karsten Biß; Laxmikanth Kollipara; Achim Meyer; Markus Pfenninger; Hildegard Westphal; Albert Sickmann; Jörg Rahnenführer (BMC Bioinform., 2017)

A Multicriteria Approach to Find Predictive and Sparse Models with Stable Feature Selection for High-Dimensional Data. - Andrea Bommert; Jörg Rahnenführer; Michel Lang (Comput. Math. Methods Medicine, 2017)

High Dimensional Restrictive Federated Model Selection with Multi-objective Bayesian Optimization over Shifted Distributions. - Xudong Sun 002; Andrea Bommert; Florian Pfisterer; Jörg Rahnenführer; Michel Lang; Bernd Bischl (IntelliSys (1), 2019)

Model-based optimization of subgroup weights for survival analysis. - Jakob Richter; Katrin Madjar; Jörg Rahnenführer (Bioinform., 2019)

Model-based optimization with concept drifts. - Jakob Richter; Junjie Shi; Jian-Jia Chen; Jörg Rahnenführer; Michel Lang (GECCO, 2020)

Adjusted Measures for Feature Selection Stability for Data Sets with Similar Features. - Andrea Bommert; Jörg Rahnenführer (LOD (1), 2020)

Improving Latent Dirichlet Allocation: On Reliability of the Novel Method LDAPrototype. - Jonas Rieger; Jörg Rahnenführer; Carsten Jentsch (NLDB, 2020)

Assessing the Uncertainty of the Text Generating Process Using Topic Models. - Jonas Rieger; Carsten Jentsch; Jörg Rahnenführer (PKDD/ECML Workshops, 2020)

Cost-Constrained feature selection in binary classification: adaptations for greedy forward selection and genetic algorithms. - Rudolf Jagdhuber; Michel Lang; Arnulf Stenzl; Jochen Neuhaus; Jörg Rahnenführer (BMC Bioinform., 2020)

Improving Reliability of Latent Dirichlet Allocation by Assessing Its Stability Using Clustering Techniques on Replicated Runs. - Jonas Rieger; Lars Koppers; Carsten Jentsch; Jörg Rahnenführer (CoRR, 2020)

Feature Selection Methods for Cost-Constrained Classification in Random Forests. - Rudolf Jagdhuber; Michel Lang; Jörg Rahnenführer (CoRR, 2020)

Benchmark for filter methods for feature selection in high-dimensional classification data. - Andrea Bommert; Xudong Sun 002; Bernd Bischl; Jörg Rahnenführer; Michel Lang (Comput. Stat. Data Anal., 2020)

RollingLDA: An Update Algorithm of Latent Dirichlet Allocation to Construct Consistent Time Series from Textual Data. - Jonas Rieger; Carsten Jentsch; Jörg Rahnenführer (EMNLP (Findings), 2021)

Employing an Adjusted Stability Measure for Multi-criteria Model Fitting on Data Sets with Similar Features. - Andrea Bommert; Jörg Rahnenführer; Michel Lang (LOD, 2021)

Combining heterogeneous subgroups with graph-structured variable selection priors for Cox regression. - Katrin Madjar; Manuela Zucknick; Katja Ickstadt; Jörg Rahnenführer (BMC Bioinform., 2021)

Weighted Cox regression for the prediction of heterogeneous patient subgroups. - Katrin Madjar; Jörg Rahnenführer (BMC Medical Informatics Decis. Mak., 2021)

MODES: model-based optimization on distributed embedded systems. - Junjie Shi; Jiang Bian 003; Jakob Richter; Kuan-Hsun Chen; Jörg Rahnenführer; Haoyi Xiong; Jian-Jia Chen (Mach. Learn., 2021)

Implications on Feature Detection When Using the Benefit-Cost Ratio. - Rudolf Jagdhuber; Jörg Rahnenführer (SN Comput. Sci., 2021)

Editorial. - Katharina Morik; Jörg Rahnenführer; Christian Wietfeld (Mach. Learn. under Resour. Constraints Vol. 3 (3), 2022)

Survival Prediction and Model Selection. - Jörg Rahnenführer; Michel Lang; Jakob Richter (Mach. Learn. under Resour. Constraints Vol. 3 (3), 2022)

Benchmark of filter methods for feature selection in high-dimensional gene expression survival data. - Andrea Bommert; Thomas Welchowski; Matthias Schmid; Jörg Rahnenführer (Briefings Bioinform., 2022)

Correction to: Combining heterogeneous subgroups with graph-structured variable selection priors for Cox regression. - Katrin Madjar; Manuela Zucknick; Katja Ickstadt; Jörg Rahnenführer (BMC Bioinform., 2022)

Debunking Disinformation with GADMO: A Topic Modeling Analysis of a Comprehensive Corpus of German-language Fact-Checks. - Jonas Rieger; Nico Hornig; Jonathan Flossdorf; Henrik Müller; Stephan Mündges; Carsten Jentsch; Jörg Rahnenführer; Christina Elmer (LDK, 2023)

Designs for the simultaneous inference of concentration-response curves. - Leonie Schürmeyer; Kirsten Schorning; Jörg Rahnenführer (BMC Bioinform., 2023)

LDAPrototype: a model selection algorithm to improve reliability of latent Dirichlet allocation. - Jonas Rieger; Carsten Jentsch; Jörg Rahnenführer (PeerJ Comput. Sci., 2024)