Processing and quality control of DNA array hybridization data. - Tim Beißbarth; Kurt Fellenberg; Benedikt Brors; Rosa Arribas-Prat; Judith M. Boer; Nicole C. Hauser; Marcel Scheideler; Jörg D. Hoheisel; Günther Schütz; Annemarie Poustka; Martin Vingron (Bioinform., 2000)

A systematic approach for comprehensive T-cell epitope discovery using peptide libraries. - Tim Beißbarth; Jason A. Tye-Din; Gordon K. Smyth; Terence P. Speed; Robert P. Anderson (ISMB (Supplement of Bioinformatics), 2005)

Estimating Large Scale Scale Signaling Networks through Nested Effects Models from Intervention Effects in Microarray Data. - Holger Fröhlich; Mark Fellmann; Holger Sültmann; Annemarie Poustka; Tim Beißbarth (German Conference on Bioinformatics, 2007)

Large scale statistical inference of signaling pathways from RNAi and microarray data. - Holger Fröhlich; Mark Fellmann; Holger Sültmann; Annemarie Poustka; Tim Beißbarth (BMC Bioinform., 2007)

GOSim - an R-package for computation of information theoretic GO similarities between terms and gene products. - Holger Fröhlich; Nora Speer; Annemarie Poustka; Tim Beißbarth (BMC Bioinform., 2007)

Discrimination of Direct and Indirect Interactions in a Network of Regulatory Effects. - Achim Tresch; Tim Beißbarth; Holger Sültmann; Ruprecht Kuner; Annemarie Poustka; Andreas Buness (J. Comput. Biol., 2007)

Analyzing gene perturbation screens with nested effects models in R and bioconductor. - Holger Fröhlich; Tim Beißbarth; Achim Tresch; Dennis Kostka; Juby Jacob; Rainer Spang; Florian Markowetz (Bioinform., 2008)

Predicting pathway membership via domain signatures. - Holger Fröhlich; Mark Fellmann; Holger Sültmann; Annemarie Poustka; Tim Beißbarth (Bioinform., 2008)

Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data. - Holger Fröhlich; Mark Fellmann; Holger Sültmann; Annemarie Poustka; Tim Beißbarth (Bioinform., 2008)

Extending pathways based on gene lists using InterPro domain signatures. - Florian Hahne; Alexander Mehrle; Dorit Arlt; Annemarie Poustka; Stefan Wiemann; Tim Beißbarth (BMC Bioinform., 2008)

Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions. - Holger Fröhlich; Özgür Sahin; Dorit Arlt; Christian Bender; Tim Beißbarth (BMC Bioinform., 2009)

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. - Özgür Sahin; Holger Fröhlich; Christian Löbke; Ulrike Korf; Sara Burmester; Meher Majety; Jens Mattern; Ingo Schupp; Claudine Chaouiya; Denis Thieffry; Annemarie Poustka; Stefan Wiemann; et al. (BMC Syst. Biol., 2009)

Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data. - Christian Bender; Frauke Henjes; Holger Fröhlich; Stefan Wiemann; Ulrike Korf; Tim Beißbarth (Bioinform., 2010)

QuantProReloaded: quantitative analysis of microspot immunoassays. - Anika Jöcker; Johanna Sonntag; Frauke Henjes; Frank Götschel; Achim Tresch; Tim Beißbarth; Stefan Wiemann; Ulrike Korf (Bioinform., 2010)

Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients. - Marc Johannes; Jan C. Brase; Holger Fröhlich; Stephan Gade; Mathias C. Gehrmann; Maria Fälth; Holger Sültmann; Tim Beißbarth (Bioinform., 2010)

RPPanalyzer: Analysis of reverse-phase protein array data. - Heiko A. Mannsperger; Stephan Gade; Frauke Henjes; Tim Beißbarth; Ulrike Korf (Bioinform., 2010)

A new sensitivity-preferred strategy to build prediction rules for therapy response of cancer patients using gene expression data. - Klaus Jung; Marian Grade; Jochen Gaedcke; Peter Jo; Lennart Opitz; Heinz Becker; B. Michael Ghadimi; Tim Beißbarth (Comput. Methods Programs Biomed., 2010)

pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery. - Marc Johannes; Holger Fröhlich; Holger Sültmann; Tim Beißbarth (Bioinform., 2011)

Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes. - Klaus Jung; Benjamin Becker; Edgar Brunner; Tim Beißbarth (Bioinform., 2011)

Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'. - Christian Bender; Silvia von der Heyde; Frauke Henjes; Stefan Wiemann; Ulrike Korf; Tim Beißbarth (BMC Bioinform., 2011)

Graph based fusion of miRNA and mRNA expression data improves clinical outcome prediction in prostate cancer. - Stephan Gade; Christine Porzelius; Maria Fälth; Jan C. Brase; Daniela Wuttig; Ruprecht Kuner; Harald Binder; Holger Sültmann; Tim Beißbarth (BMC Bioinform., 2011)

Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes. - Klaus Jung; Tim Friede; Tim Beißbarth (BMC Bioinform., 2011)

Sequential Interim Analyses of Survival Data in DNA Microarray Experiments. - Andreas Leha; Tim Beißbarth; Klaus Jung (BMC Bioinform., 2011)

Utilization of ordinal response structures in classification with high-dimensional expression data. - Andreas Leha; Klaus Jung; Tim Beißbarth (GCB, 2013)

rBiopaxParser - an R package to parse, modify and visualize BioPAX data. - Frank Kramer 001; Michaela Bayerlová; Florian Klemm; Annalen Bleckmann; Tim Beißbarth (Bioinform., 2013)

Connecting high-dimensional mRNA and miRNA expression data for binary medical classification problems. - Mathias Fuchs; Tim Beißbarth; Edgar Wingender; Klaus Jung (Comput. Methods Programs Biomed., 2013)

Adaption of the global test idea to proteomics data with missing values. - Klaus Jung; Hassan Dihazi; Asima Bibi; Gry H. Dihazi; Tim Beißbarth (Bioinform., 2014)

Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell lines. - Silvia von der Heyde; Christian Bender; Frauke Henjes; Johanna Sonntag; Ulrike Korf; Tim Beißbarth (BMC Syst. Biol., 2014)

pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge. - Astrid Wachter; Tim Beißbarth (Bioinform., 2015)

Comparative study on gene set and pathway topology-based enrichment methods. - Michaela Bayerlová; Klaus Jung; Frank Kramer 001; Florian Klemm; Annalen Bleckmann; Tim Beißbarth (BMC Bioinform., 2015)

Automated 3D-2D registration of X-ray microcomputed tomography with histological sections for dental implants in bone using chamfer matching and simulated annealing. - Kathrin Becker; Martin Stauber; Frank Schwarz; Tim Beißbarth (Comput. Medical Imaging Graph., 2015)

Using RNA-Seq Data for the Detection of a Panel of Clinically Relevant Mutations. - Alexander Wolff 002; Júlia Perera-Bel; Hans-Ulrich Schildhaus; Kia Homayounfar; Bawarjan Schatlo; Annalen Bleckmann; Tim Beißbarth (GMDS, 2018)

Utilizing Molecular Network Information via Graph Convolutional Neural Networks to Predict Metastatic Event in Breast Cancer. - Hryhorii Chereda; Annalen Bleckmann; Frank Kramer 001; Andreas Leha; Tim Beißbarth (GMDS, 2019)

Reconstruction of Different Modes of WNT Dependent Protein Networks from Time Series Protein Quantification. - Maren Sitte; Kerstin Menck; Astrid Wachter; Eileen Reinz; Ulrike Korf; Stefan Wiemann; Annalen Bleckmann; Tim Beißbarth (GMDS, 2019)

Predicting the Effect of Variants of Unknown Significance in Molecular Tumor Boards with the VUS-Predict Pipeline. - Vanessa Schlotzig; Kevin Kornrumpf; Alexander König; Tim Tucholski; Jonas Hügel; Tobias R. Overbeck; Tim Beißbarth; Raphael Koch; Jürgen Dönitz (GMDS, 2021)

Identifying Actionable Variants in Cancer - The Dual Web and Batch Processing Tool MTB-Report. - Nadine S. Kurz; Júlia Perera-Bel; Charlotte Höltermann; Tim Tucholski; Jingyu Yang; Tim Beißbarth; Jürgen Dönitz (GMDS, 2022)

BITES: balanced individual treatment effect for survival data. - Stefan Schrod; Andreas Schäfer 005; Stefan Solbrig; Robert Lohmayer; Wolfram Gronwald; Peter J. Oefner; Tim Beißbarth; Rainer Spang; Helena U. Zacharias; Michael Altenbuchinger (Bioinform., 2022)

Onkopipe: A Snakemake Based DNA-Sequencing Pipeline for Clinical Variant Analysis in Precision Medicine. - Jingyu Yang; Tim Beißbarth; Jürgen Dönitz (GMDS, 2023)

Ensemble-GNN: Source Code and Data. - Bastian Pfeifer; Hryhorii Chereda; Roman Martin; Anna Saranti; Sandra Clemens; Anne-Christin Hauschild; Tim Beißbarth; Andreas Holzinger; Dominik Heider (Zenodo, 2023)

Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification. - Bastian Pfeifer; Hryhorii Chereda; Roman Martin; Anna Saranti; Sandra Clemens; Anne-Christin Hauschild; Tim Beißbarth; Andreas Holzinger; Dominik Heider (Bioinform., 2023)

SpaCeNet: Spatial Cellular Networks from Omics Data. - Stefan Schrod; Niklas Lück; Robert Lohmayer; Stefan Solbrig; Tina Wipfler; Katherine H. Shutta; Marouen Ben Guebila; Andreas Schäfer 005; Tim Beißbarth; Helena U. Zacharias; Peter J. Oefner; John Quackenbush; et al. (RECOMB, 2024)

Stable feature selection utilizing Graph Convolutional Neural Network and Layer-wise Relevance Propagation for biomarker discovery in breast cancer. - Hryhorii Chereda; Andreas Leha; Tim Beißbarth (Artif. Intell. Medicine, 2024)

Adaptive digital tissue deconvolution. - Franziska Görtler; Malte Mensching-Buhr; Ørjan Skaar; Stefan Schrod; Thomas Sterr; Andreas Schäfer 005; Tim Beißbarth; Anagha Joshi; Helena U. Zacharias; Sushma Nagaraja Grellscheid; Michael Altenbuchinger (Bioinform., 2024)

CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations. - Stefan Schrod; Helena U. Zacharias; Tim Beißbarth; Anne-Christin Hauschild; Michael Altenbuchinger (Bioinform., 2024)