Tim Beißbarth

50 papers B 1Journal 36Unranked 9

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	HIDE: hierarchical cell-type deconvolution. Bioinform. Dennis Völkl, Malte Mensching-Buhr, Thomas Sterr, Sarah Bolz, Andreas Schäfer, Nicole Seifert, Jana Tauschke, Austin Rayford, Oddbjørn Straume, Helena U. Zacharias, Sushma Nagaraja Grellscheid, Tim Beißbarth, Michael Altenbuchinger, Franziska Görtler
2025	J	`jnl`	Prediction of gene expression using histone modification patterns extracted by Particle Swarm Optimization. Bioinform. Niels Benjamin Paul, Jonas C. Wolber, Malte Lennart Sahrhage, Tim Beißbarth, Martin Haubrock
2024	J	`jnl`	Adaptive digital tissue deconvolution. Bioinform. Franziska Görtler, Malte Mensching-Buhr, Ørjan Skaar, Stefan Schrod, Thomas Sterr, Andreas Schäfer, Tim Beißbarth, Anagha Joshi, Helena U. Zacharias, Sushma Nagaraja Grellscheid, Michael Altenbuchinger
2024	J	`jnl`	CODEX: COunterfactual Deep learning for the Bioinform. Stefan Schrod, Helena U. Zacharias, Tim Beißbarth, Anne-Christin Hauschild, Michael Altenbuchinger
2024	B	`conf`	SpaCeNet: Spatial Cellular Networks from Omics Data. RECOMB 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
2024	J	`jnl`	Stable feature selection utilizing Graph Convolutional Neural Network and Layer-wise Relevance Propagation for biomarker discovery in breast cancer. Artif. Intell. Medicine Hryhorii Chereda, Andreas Leha, Tim Beißbarth
2023	J	`jnl`	Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification. Bioinform. Bastian Pfeifer, Hryhorii Chereda, Roman Martin, Anna Saranti, Sandra Clemens, Anne-Christin Hauschild, Tim Beißbarth, Andreas Holzinger, Dominik Heider
2023	—	`conf`	Onkopipe: A Snakemake Based DNA-Sequencing Pipeline for Clinical Variant Analysis in Precision Medicine. GMDS Jingyu Yang, Tim Beißbarth, Jürgen Dönitz
2022	J	`jnl`	BITES: Balanced Individual Treatment Effect for Survival data. CoRR Stefan Schrod, Andreas Schäfer, Stefan Solbrig, Robert Lohmayer, Wolfram Gronwald, Peter J. Oefner, Tim Beißbarth, Rainer Spang, Helena U. Zacharias, Michael Altenbuchinger
2022	J	`jnl`	BITES: balanced individual treatment effect for survival data. Bioinform. Stefan Schrod, Andreas Schäfer, Stefan Solbrig, Robert Lohmayer, Wolfram Gronwald, Peter J. Oefner, Tim Beißbarth, Rainer Spang, Helena U. Zacharias, Michael Altenbuchinger
2022	—	`conf`	Identifying Actionable Variants in Cancer - The Dual Web and Batch Processing Tool MTB-Report. GMDS Nadine S. Kurz, Júlia Perera-Bel, Charlotte Höltermann, Tim Tucholski, Jingyu Yang, Tim Beißbarth, Jürgen Dönitz
2021	—	`ed.`	German Medical Data Sciences 2021: Digital Medicine: Recognize - Understand - Heal - Proceedings of the Joint Conference of the 66th Annual Meeting of the German Association of Medical Informatics, Biometry, and Epidemiology e.V. (gmds) and the 13th Annual Meeting of the TMF - Technology, Methods, and Infrastructure for Networked Medical Research e.V. 2021 online in Kiel, Germany, September 26-30, 2021 GMDS Rainer Röhrig, Tim Beißbarth, Jochem König, Claudia Ose, Géraldine Rauch, Ulrich Sax, Björn Schreiweis, Martin Sedlmayr
2021	—	`ed.`	German Medical Data Sciences: Bringing Data to Life - Proceedings of the Joint Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology (gmds e.V.) and the Central European Network - International Biometric Society (CEN-IBS) 2020 in Berlin, Germany GMDS Rainer Röhrig, Tim Beißbarth, Werner Brannath, Hans-Ulrich Prokosch, Irene Schmidtmann, Susanne Stolpe, Antonia Zapf
2021	—	`conf`	Predicting the Effect of Variants of Unknown Significance in Molecular Tumor Boards with the VUS-Predict Pipeline. GMDS Vanessa Schlotzig, Kevin Kornrumpf, Alexander König, Tim Tucholski, Jonas Hügel, Tobias R. Overbeck, Tim Beißbarth, Raphael Koch, Jürgen Dönitz
2019	—	`conf`	Reconstruction of Different Modes of WNT Dependent Protein Networks from Time Series Protein Quantification. GMDS Maren Sitte, Kerstin Menck, Astrid Wachter, Eileen Reinz, Ulrike Korf, Stefan Wiemann, Annalen Bleckmann, Tim Beißbarth
2019	—	`conf`	Utilizing Molecular Network Information via Graph Convolutional Neural Networks to Predict Metastatic Event in Breast Cancer. GMDS Hryhorii Chereda, Annalen Bleckmann, Frank Kramer, Andreas Leha, Tim Beißbarth
2018	—	`ed.`	German Medical Data Sciences: A Learning Healthcare System - Proceedings of the 63rd Annual Meeting of the German Association of Medical Informatics, Biometry and Epidemiology (GMDS e.V.) 2018 in Osnabrück, Germany, 2-6 September 2018, GMDS 2018 GMDS Ursula Hübner, Ulrich Sax, Hans-Ulrich Prokosch, Bernhard Breil, Harald Binder, Antonia Zapf, Brigitte Strahwald, Tim Beißbarth, Niels Grabe, Anke Schöler
2018	—	`conf`	Using RNA-Seq Data for the Detection of a Panel of Clinically Relevant Mutations. GMDS Alexander Wolff, Júlia Perera-Bel, Hans-Ulrich Schildhaus, Kia Homayounfar, Bawarjan Schatlo, Annalen Bleckmann, Tim Beißbarth
2015	J	`jnl`	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. Kathrin Becker, Martin Stauber, Frank Schwarz, Tim Beißbarth
2015	J	`jnl`	Comparative study on gene set and pathway topology-based enrichment methods. BMC Bioinform. Michaela Bayerlová, Klaus Jung, Frank Kramer, Florian Klemm, Annalen Bleckmann, Tim Beißbarth
2015	J	`jnl`	pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge. Bioinform. Astrid Wachter, Tim Beißbarth
2014	J	`jnl`	Adaption of the global test idea to proteomics data with missing values. Bioinform. Klaus Jung, Hassan Dihazi, Asima Bibi, Gry H. Dihazi, Tim Beißbarth
2014	J	`jnl`	Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell lines. BMC Syst. Biol. Silvia von der Heyde, Christian Bender, Frauke Henjes, Johanna Sonntag, Ulrike Korf, Tim Beißbarth
2013	J	`jnl`	Connecting high-dimensional mRNA and miRNA expression data for binary medical classification problems. Comput. Methods Programs Biomed. Mathias Fuchs, Tim Beißbarth, Edgar Wingender, Klaus Jung
2013	—	`ed.`	German Conference on Bioinformatics 2013, GCB 2013, Göttingen, Germany, September 10-13, 2013 GCB Tim Beißbarth, Martin Kollmar, Andreas Leha, Burkhard Morgenstern, Anne-Kathrin Schultz, Stephan Waack, Edgar Wingender
2013	—	`conf`	Utilization of ordinal response structures in classification with high-dimensional expression data. GCB Andreas Leha, Klaus Jung, Tim Beißbarth
2013	J	`jnl`	rBiopaxParser - an R package to parse, modify and visualize BioPAX data. Bioinform. Frank Kramer, Michaela Bayerlová, Florian Klemm, Annalen Bleckmann, Tim Beißbarth
2011	J	`jnl`	Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes. Bioinform. Klaus Jung, Benjamin Becker, Edgar Brunner, Tim Beißbarth
2011	J	`jnl`	Graph based fusion of miRNA and mRNA expression data improves clinical outcome prediction in prostate cancer. BMC Bioinform. Stephan Gade, Christine Porzelius, Maria Fälth, Jan C. Brase, Daniela Wuttig, Ruprecht Kuner, Harald Binder, Holger Sültmann, Tim Beißbarth
2011	J	`jnl`	Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'. BMC Bioinform. Christian Bender, Silvia von der Heyde, Frauke Henjes, Stefan Wiemann, Ulrike Korf, Tim Beißbarth
2011	J	`jnl`	Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes. BMC Bioinform. Klaus Jung, Tim Friede, Tim Beißbarth
2011	J	`jnl`	Sequential Interim Analyses of Survival Data in DNA Microarray Experiments. BMC Bioinform. Andreas Leha, Tim Beißbarth, Klaus Jung
2011	J	`jnl`	pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery. Bioinform. Marc Johannes, Holger Fröhlich, Holger Sültmann, Tim Beißbarth
2010	J	`jnl`	A new sensitivity-preferred strategy to build prediction rules for therapy response of cancer patients using gene expression data. Comput. Methods Programs Biomed. Klaus Jung, Marian Grade, Jochen Gaedcke, Peter Jo, Lennart Opitz, Heinz Becker, B. Michael Ghadimi, Tim Beißbarth
2010	J	`jnl`	Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data. Bioinform. Christian Bender, Frauke Henjes, Holger Fröhlich, Stefan Wiemann, Ulrike Korf, Tim Beißbarth
2010	J	`jnl`	Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients. Bioinform. Marc Johannes, Jan C. Brase, Holger Fröhlich, Stephan Gade, Mathias C. Gehrmann, Maria Fälth, Holger Sültmann, Tim Beißbarth
2010	J	`jnl`	QuantProReloaded: quantitative analysis of microspot immunoassays. Bioinform. Anika Jöcker, Johanna Sonntag, Frauke Henjes, Frank Götschel, Achim Tresch, Tim Beißbarth, Stefan Wiemann, Ulrike Korf
2010	J	`jnl`	RPPanalyzer: Analysis of reverse-phase protein array data. Bioinform. Heiko A. Mannsperger, Stephan Gade, Frauke Henjes, Tim Beißbarth, Ulrike Korf
2009	J	`jnl`	Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions. BMC Bioinform. Holger Fröhlich, Özgür Sahin, Dorit Arlt, Christian Bender, Tim Beißbarth
2009	J	`jnl`	Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst. Biol. 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
2008	J	`jnl`	Analyzing gene perturbation screens with nested effects models in R and bioconductor. Bioinform. Holger Fröhlich, Tim Beißbarth, Achim Tresch, Dennis Kostka, Juby Jacob, Rainer Spang, Florian Markowetz
2008	J	`jnl`	Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data. Bioinform. Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth
2008	J	`jnl`	Extending pathways based on gene lists using InterPro domain signatures. BMC Bioinform. Florian Hahne, Alexander Mehrle, Dorit Arlt, Annemarie Poustka, Stefan Wiemann, Tim Beißbarth
2008	J	`jnl`	Predicting pathway membership via domain signatures. Bioinform. Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth
2007	J	`jnl`	Discrimination of Direct and Indirect Interactions in a Network of Regulatory Effects. J. Comput. Biol. Achim Tresch, Tim Beißbarth, Holger Sültmann, Ruprecht Kuner, Annemarie Poustka, Andreas Buness
2007	—	`conf`	Estimating Large Scale Scale Signaling Networks through Nested Effects Models from Intervention Effects in Microarray Data. German Conference on Bioinformatics Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth
2007	J	`jnl`	GOSim - an R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinform. Holger Fröhlich, Nora Speer, Annemarie Poustka, Tim Beißbarth
2007	J	`jnl`	Large scale statistical inference of signaling pathways from RNAi and microarray data. BMC Bioinform. Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth
2005	—	`conf`	A systematic approach for comprehensive T-cell epitope discovery using peptide libraries. ISMB (Supplement of Bioinformatics) Tim Beißbarth, Jason A. Tye-Din, Gordon K. Smyth, Terence P. Speed, Robert P. Anderson
2000	J	`jnl`	Processing and quality control of DNA array hybridization data. Bioinform. 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