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2020 – today
- 2024
[j30]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: 102840 (2024)- [c10]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: 344-347 - 2023
- [j29]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) - [c9]Jingyu Yang, Tim Beißbarth, Jürgen Dönitz:
Onkopipe: A Snakemake Based DNA-Sequencing Pipeline for Clinical Variant Analysis in Precision Medicine. GMDS 2023: 60-68 - [d1]Bastian Pfeifer, Hryhorii Chereda, Roman Martin, Anna Saranti, Sandra Clemens, Anne-Christin Hauschild, Tim Beißbarth, Andreas Holzinger, Dominik Heider:
Ensemble-GNN: Source Code and Data. Zenodo, 2023
- 2022
- [c8]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: 73-80 - [i1]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 abs/2201.03448 (2022) - 2021
- [c7]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: 209-216 - [e4]Rainer Röhrig, Tim Beißbarth, Werner Brannath, Hans-Ulrich Prokosch, Irene Schmidtmann, Susanne Stolpe, Antonia Zapf:
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. Studies in Health Technology and Informatics 278, IOS Press 2021, ISBN 978-1-64368-176-4 [contents] - [e3]Rainer Röhrig, Tim Beißbarth, Jochem König, Claudia Ose, Géraldine Rauch, Ulrich Sax, Björn Schreiweis, Martin Sedlmayr:
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. Studies in Health Technology and Informatics 283, IOS Press 2021, ISBN 978-1-64368-206-8 [contents]
2010 – 2019
- 2019
- [c6]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: 175-180 - [c5]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: 181-186 - 2018
- [c4]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: 217-221 - [e2]Ursula Hübner, Ulrich Sax, Hans-Ulrich Prokosch, Bernhard Breil, Harald Binder, Antonia Zapf, Brigitte Strahwald, Tim Beißbarth, Niels Grabe, Anke Schöler:
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. Studies in Health Technology and Informatics 253, IOS Press 2018, ISBN 978-1-61499-895-2 [contents] - 2015
- [j28]Astrid Wachter, Tim Beißbarth:
pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge. Bioinform. 31(18): 3072-3074 (2015) - [j27]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: 334:1-334:15 (2015) - [j26]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: 62-68 (2015) - 2014
- [j25]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): 1424-1430 (2014) - [j24]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: 75 (2014) - 2013
- [j23]Frank Kramer, Michaela Bayerlová, Florian Klemm, Annalen Bleckmann, Tim Beißbarth:
rBiopaxParser - an R package to parse, modify and visualize BioPAX data. Bioinform. 29(4): 520-522 (2013) - [j22]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): 592-601 (2013) - [c3]Andreas Leha, Klaus Jung, Tim Beißbarth:
Utilization of ordinal response structures in classification with high-dimensional expression data. GCB 2013: 90-100 - [e1]Tim Beißbarth, Martin Kollmar, Andreas Leha, Burkhard Morgenstern, Anne-Kathrin Schultz, Stephan Waack, Edgar Wingender:
German Conference on Bioinformatics 2013, GCB 2013, September 10-13, 2013, Göttingen, Germany. OASIcs 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2013, ISBN 978-3-939897-59-0 [contents] - 2011
- [j21]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): 1377-1383 (2011) - [j20]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): 1442-1443 (2011) - [j19]Andreas Leha, Tim Beißbarth, Klaus Jung:
Sequential Interim Analyses of Survival Data in DNA Microarray Experiments. BMC Bioinform. 12: 127 (2011) - [j18]Klaus Jung, Tim Friede, Tim Beißbarth:
Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes. BMC Bioinform. 12: 288 (2011) - [j17]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: 291 (2011) - [j16]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: 488 (2011) - 2010
- [j15]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): 2136-2144 (2010) - [j14]Heiko A. Mannsperger, Stephan Gade, Frauke Henjes, Tim Beißbarth, Ulrike Korf:
RPPanalyzer: Analysis of reverse-phase protein array data. Bioinform. 26(17): 2202-2203 (2010) - [j13]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) - [j12]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): 2480-2481 (2010) - [j11]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): 132-139 (2010)
2000 – 2009
- 2009
- [j10]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: 322 (2009) - [j9]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: 1 (2009) - 2008
- [j8]Holger Fröhlich, Mark Fellmann, Holger Sültmann, Annemarie Poustka, Tim Beißbarth:
Predicting pathway membership via domain signatures. Bioinform. 24(19): 2137-2142 (2008) - [j7]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): 2549-2550 (2008) - [j6]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): 2650-2656 (2008) - [j5]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) - 2007
- [j4]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) - [j3]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) - [j2]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): 1217-1228 (2007) - [c2]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: 45-54 - 2005
- [c1]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: 29-37 - 2000
- [j1]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:
Processing and quality control of DNA array hybridization data. Bioinform. 16(11): 1014-1022 (2000)
Coauthor Index
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last updated on 2024-10-07 22:22 CEST by the dblp team
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