Tim Beißbarth

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 10

Top Topics

Feature Selection

Convolutional Neural Networks

Top Venues

Artif. Intell. Medicine

Publications

Hryhorii Chereda, Andreas Leha, Tim Beißbarth
Stable feature selection utilizing Graph Convolutional Neural Network and Layer-wise Relevance Propagation for biomarker discovery in breast cancer. Artif. Intell. Medicine 151 (2024)
Stefan Schrod, Niklas Lück, Robert Lohmayer, Stefan Solbrig, Tina Wipfler, Katherine H. Shutta, Marouen Ben Guebila, Andreas Schäfer, Tim Beißbarth, Helena U. Zacharias, Peter J. Oefner, John Quackenbush, Michael Altenbuchinger
SpaCeNet: Spatial Cellular Networks from Omics Data. RECOMB (2024)
Bastian Pfeifer, Hryhorii Chereda, Roman Martin, Anna Saranti, Sandra Clemens, Anne-Christin Hauschild, Tim Beißbarth, Andreas Holzinger, Dominik Heider
Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification. Bioinform. 39 (10) (2023)
Jingyu Yang, Tim Beißbarth, Jürgen Dönitz
Onkopipe: A Snakemake Based DNA-Sequencing Pipeline for Clinical Variant Analysis in Precision Medicine. GMDS (2023)
Nadine S. Kurz, Júlia Perera-Bel, Charlotte Höltermann, Tim Tucholski, Jingyu Yang, Tim Beißbarth, Jürgen Dönitz
Identifying Actionable Variants in Cancer - The Dual Web and Batch Processing Tool MTB-Report. GMDS (2022)
Stefan Schrod, Andreas Schäfer, Stefan Solbrig, Robert Lohmayer, Wolfram Gronwald, Peter J. Oefner, Tim Beißbarth, Rainer Spang, Helena U. Zacharias, Michael Altenbuchinger
BITES: Balanced Individual Treatment Effect for Survival data. CoRR (2022)
Vanessa Schlotzig, Kevin Kornrumpf, Alexander König, Tim Tucholski, Jonas Hügel, Tobias R. Overbeck, Tim Beißbarth, Raphael Koch, Jürgen Dönitz
Predicting the Effect of Variants of Unknown Significance in Molecular Tumor Boards with the VUS-Predict Pipeline. GMDS (2021)
Hryhorii Chereda, Annalen Bleckmann, Frank Kramer, Andreas Leha, Tim Beißbarth
Utilizing Molecular Network Information via Graph Convolutional Neural Networks to Predict Metastatic Event in Breast Cancer. GMDS (2019)
Maren Sitte, Kerstin Menck, Astrid Wachter, Eileen Reinz, Ulrike Korf, Stefan Wiemann, Annalen Bleckmann, Tim Beißbarth
Reconstruction of Different Modes of WNT Dependent Protein Networks from Time Series Protein Quantification. GMDS (2019)
Alexander Wolff, Júlia Perera-Bel, Hans-Ulrich Schildhaus, Kia Homayounfar, Bawarjan Schatlo, Annalen Bleckmann, Tim Beißbarth
Using RNA-Seq Data for the Detection of a Panel of Clinically Relevant Mutations. GMDS (2018)
Astrid Wachter, Tim Beißbarth
pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge. Bioinform. 31 (18) (2015)
Michaela Bayerlová, Klaus Jung, Frank Kramer, Florian Klemm, Annalen Bleckmann, Tim Beißbarth
Comparative study on gene set and pathway topology-based enrichment methods. BMC Bioinform. 16 (2015)
Kathrin Becker, Martin Stauber, Frank Schwarz, Tim Beißbarth
Automated 3D-2D registration of X-ray microcomputed tomography with histological sections for dental implants in bone using chamfer matching and simulated annealing. Comput. Medical Imaging Graph. 44 (2015)
Klaus Jung, Hassan Dihazi, Asima Bibi, Gry H. Dihazi, Tim Beißbarth
Adaption of the global test idea to proteomics data with missing values. Bioinform. 30 (10) (2014)
Silvia von der Heyde, Christian Bender, Frauke Henjes, Johanna Sonntag, Ulrike Korf, Tim Beißbarth
Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell lines. BMC Syst. Biol. 8 (2014)
Andreas Leha, Klaus Jung, Tim Beißbarth
Utilization of ordinal response structures in classification with high-dimensional expression data. GCB (2013)
Frank Kramer, Michaela Bayerlová, Florian Klemm, Annalen Bleckmann, Tim Beißbarth
rBiopaxParser - an R package to parse, modify and visualize BioPAX data. Bioinform. 29 (4) (2013)
Mathias Fuchs, Tim Beißbarth, Edgar Wingender, Klaus Jung
Connecting high-dimensional mRNA and miRNA expression data for binary medical classification problems. Comput. Methods Programs Biomed. 111 (3) (2013)
Andreas Leha, Tim Beißbarth, Klaus Jung
Sequential Interim Analyses of Survival Data in DNA Microarray Experiments. BMC Bioinform. 12 (2011)
Klaus Jung, Benjamin Becker, Edgar Brunner, Tim Beißbarth
Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes. Bioinform. 27 (10) (2011)
Stephan Gade, Christine Porzelius, Maria Fälth, Jan C. Brase, Daniela Wuttig, Ruprecht Kuner, Harald Binder, Holger Sültmann, Tim Beißbarth
Graph based fusion of miRNA and mRNA expression data improves clinical outcome prediction in prostate cancer. BMC Bioinform. 12 (2011)
Marc Johannes, Holger Fröhlich, Holger Sültmann, Tim Beißbarth
pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery. Bioinform. 27 (10) (2011)
Christian Bender, Silvia von der Heyde, Frauke Henjes, Stefan Wiemann, Ulrike Korf, Tim Beißbarth
Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'. BMC Bioinform. 12 (2011)
Klaus Jung, Tim Friede, Tim Beißbarth
Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes. BMC Bioinform. 12 (2011)
Anika Jöcker, Johanna Sonntag, Frauke Henjes, Frank Götschel, Achim Tresch, Tim Beißbarth, Stefan Wiemann, Ulrike Korf
QuantProReloaded: quantitative analysis of microspot immunoassays. Bioinform. 26 (19) (2010)
Klaus Jung, Marian Grade, Jochen Gaedcke, Peter Jo, Lennart Opitz, Heinz Becker, B. Michael Ghadimi, Tim Beißbarth
A new sensitivity-preferred strategy to build prediction rules for therapy response of cancer patients using gene expression data. Comput. Methods Programs Biomed. 100 (2) (2010)
Marc Johannes, Jan C. Brase, Holger Fröhlich, Stephan Gade, Mathias C. Gehrmann, Maria Fälth, Holger Sültmann, Tim Beißbarth
Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients. Bioinform. 26 (17) (2010)
Christian Bender, Frauke Henjes, Holger Fröhlich, Stefan Wiemann, Ulrike Korf, Tim Beißbarth
Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data. Bioinform. 26 (18) (2010)
Heiko A. Mannsperger, Stephan Gade, Frauke Henjes, Tim Beißbarth, Ulrike Korf
RPPanalyzer: Analysis of reverse-phase protein array data. Bioinform. 26 (17) (2010)
Holger Fröhlich, Özgür Sahin, Dorit Arlt, Christian Bender, Tim Beißbarth
Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions. BMC Bioinform. 10 (2009)
Özgür Sahin, Holger Fröhlich, Christian Löbke, Ulrike Korf, Sara Burmester, Meher Majety, Jens Mattern, Ingo Schupp, Claudine Chaouiya, Denis Thieffry, Annemarie Poustka, Stefan Wiemann, Tim Beißbarth, Dorit Arlt
Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst. Biol. 3 (2009)
Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth
Predicting pathway membership via domain signatures. Bioinform. 24 (19) (2008)
Florian Hahne, Alexander Mehrle, Dorit Arlt, Annemarie Poustka, Stefan Wiemann, Tim Beißbarth
Extending pathways based on gene lists using InterPro domain signatures. BMC Bioinform. 9 (2008)
Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth
Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data. Bioinform. 24 (22) (2008)
Holger Fröhlich, Tim Beißbarth, Achim Tresch, Dennis Kostka, Juby Jacob, Rainer Spang, Florian Markowetz
Analyzing gene perturbation screens with nested effects models in R and bioconductor. Bioinform. 24 (21) (2008)
Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth
Estimating Large Scale Scale Signaling Networks through Nested Effects Models from Intervention Effects in Microarray Data. German Conference on Bioinformatics (2007)
Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth
Large scale statistical inference of signaling pathways from RNAi and microarray data. BMC Bioinform. 8 (2007)
Achim Tresch, Tim Beißbarth, Holger Sültmann, Ruprecht Kuner, Annemarie Poustka, Andreas Buness
Discrimination of Direct and Indirect Interactions in a Network of Regulatory Effects. J. Comput. Biol. 14 (9) (2007)
Holger Fröhlich, Nora Speer, Annemarie Poustka, Tim Beißbarth
GOSim - an R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinform. 8 (2007)
Tim Beißbarth, Jason A. Tye-Din, Gordon K. Smyth, Terence P. Speed, Robert P. Anderson
A systematic approach for comprehensive T-cell epitope discovery using peptide libraries. ISMB (Supplement of Bioinformatics) (2005)
Tim Beißbarth, Kurt Fellenberg, Benedikt Brors, R. Arribas-Prat, J. M. Boer, Nicole C. Hauser, Marcel Scheideler, Jörg D. Hoheisel, G. Schütz, Annemarie Poustka, Martin Vingron
Processing and quality control of DNA array hybridization data. Bioinform. 16 (11) (2000)