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Conference proceedings

  1. Pustozerova A, Baumbach J, Mayer R (2023) Differentially Private Federated Learning: Privacy and Utility Analysis of Output Perturbation and DP-SGD. In 2023 IEEE International Conference on Big Data, Big Data, December, 2023, Sorrento, Italy.

  2. Pustozerova A, Baumbach J, Mayer R (2023) Analysing Utility Loss in Federated Learning with Differential Privacy. In International Conference on Trust, Security and Privacy in Computing and Communications, TrustCom, November 2023, Exeter, UK.

  3. Holzinger A, Saranti A, Hauschild AC, Beinecke J, Heider D, Roettger R, Mueller H, Baumbach J, Pfeifer B (2023) Human-in-the-Loop Integration with Domain-Knowledge Graphs for Explainable Federated Deep Learning. CD-MAKE 2023, Aug 22. (pp. 45-64). Springer Lecture Notes in Computer Science, vol 14065.

  4. Wolff J, Matschinske J, Baumgart D, Pytlik A, Keck A, Natarajan A, von Schacky CE, Pauling JK, Baumbach J (2022) Federated machine learning for a facilitated implementation of Artificial Intelligence in healthcare – a proof of concept study for the prediction of Coronary Artery Calcification Scores. J Integr Bioinform. 2022 Sep 05, 2022;pp. 20220032. (download from De Gruyter)

  5. Nasirigerdeh R, Torkzadehmahani R, Baumbach J, Blumenthal DB (2021) On the Privacy of Federated Pipelines. In Proceedings of the 44th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR ’21), July 11–15, 2021, Virtual Event, Canada. ACM, New York, NY, USA. https://doi.org/10.1145/3404835.3462996

  6. Sanchez CS, Wieder A, Sottovia P, Bortoli S, Baumbach J, Axenie C. (2020) GANNSTER: Graph-Augmented Neural Network Spatio-Temporal Reasoner for Traffic Forecasting. Proceedings of of the Joint European Conference on Machine Learning and Knowledge Discovery in Databases, ECML/PKDD, Sep. 14-18 2020, Ghent, Belgium (accepted)

  7. List M, Amirabad AD, Kostka D, Schulz MH. (2019) Large-scale inference of competing endogenous RNA network with sparse partial correlation ISMB/ECCB, Bioinformatics, 2019 Jul 15;35(14):i596-i604. (download from Oxford Academic)

  8. Sturm G, Finotello F, Petitprez F, Zhang JD, Baumbach J, Fridman WH, List M, Aneichyk T (2019) Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. Proceedings of the Intelligent Systems for Molecular Biology, ISMB, Bioinformatics 2019 2019 Jul 15;35(14):i436-i445. (download from Oxford Academic)

  9. Schmidt F*, List M*, Cukuroglu E, Köhler S, Göke J, Schulz MH. (2018) An ontology-based method for assessing batch effect adjustment approaches in heterogeneous data sets. Proceedings of the European Conference on Computational Biology, ECCB, Sept. 9-12, 2018, Athens (Greece) Bioinformatics 2018, (download from Oxford Academic) (*joint first authors)

  10. Barbosa E, Röttger R, Hauschild AC, Castro Soares S, Böcker S, Azevedo V, Baumbach J. (2017) LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. J Integr Bioinform. 2017 Jul 5;14(2). (download from DeGruyter)

  11. Larsen SJ, Baumbach J. (2017) CytoMCS: a multiple maximum common subgraph detection tool for Cytoscape. J Integr Bioinform. 2017 Jul 21;14(2). (download from DeGruyter)

  12. Larsen SJ, Alkaersig FG, Ditzel HJ, Jurisica I, Alcaraz N, Baumbach J. (2016) A Simulated Annealing Algorithm for Maximum Common Edge Subgraph Detection in Biological Networks. Proceedings of the Genetic and Evolutionary Computation Conference 2016, GECCO, July 20-24, 2016, Denver, USA. 2016: 341-348. (download from ACM).

  13. List M, Franz M, Thomassen M, Kruse TA, Tan Q, Mollenhauer J, Baumbach J. (2015) OpenLabNotes - An Eletronic Laboratory Notebook Extension for OpenLabFramework. J Integr Bioinform. 2015 Oct 6;12(3):274. (download from JIB)

  14. List M, Block I, Pedersen ML, Christiansen H, Schmidt S, Thomassen M, Tan Q, Baumbach J, Mollenhauer J. (2014) Microarray R-based Analysis of Complex Lysate Experiments with MIRACLE. Proceedings of the European Conference on Computational Biology, ECCB, Sept 7-10 2014, Strassbourg (France). Bioinformatics 2014, 30 (17): i631-i638. (download from Oxford Academic)

  15. Baumbach J, Guo J, Sun P. (2014) Complexity of Dense Bicluster Editing Problems. Proceedings of the International Computing and Combinatorics Conference 2014, COCOON, August 2014, Atlanta, USA. Lecture Notes in Computer Science, Vol. 8591, 2014, pp 154-165. (download from Springer)

  16. List M, Hauschild AC, Tan Q, Kruse TA, Mollenhauer J, Batra R*, Baumbach J*. (2014) Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data. J Integr Bioinform. 11(2):236, 2014. (download from JIB) (* joint last author)

  17. Misirli G, Hallinan J, Roettger R, Baumbach J, Wipat A. (2014) BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species. J Integr Bioinform. 11(2):244, 2014. (download from JIB)

  18. Baumbach J, Guo J, Ibragimov R. (2014) Multiple Graph Edit Distance - Simultaneous Topological Alignment of Multiple Protein-Protein Interaction Networks with an Evolutionary Algorithm. Proceedings of the Genetic and Evolutionary Computation Conference 2014, GECCO, July 2014, Vancouver, Canada. 277-284. (download from ACM)

  19. Baumbach J, Guo J, Ibragimov .R (2014) Compactness-Preserving Mapping on Trees. Proceedings of Annual Symposium on Combinatorial Pattern Matching, CPM, June 2014, Moscow, Russia. Lecture Notes in Computer Science. Volume 8486, 2014, pp 162-171. (download from Springer)

  20. Ibragimov R, Malek M, Guo J, Baumbach J. (2013) GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment. Proceedings of the German Conference on Bioinformatics, GCB, 2013, OpenAccess Series in Informatics, 34:68--79. (download from OASIC)​

  21. Ibragimov R, Guo J, Baumbach J. (2013) Neighborhood-Preserving Mapping between Trees. Proceedings of the Workshop on Algorithms and Data Structures, WASD, August 2013, Ontario, Canada. Lecture Notes in Computer Science. Volume 8037, 2013, pp 427-438. (download from Springer)

  22. Ibragimov R, Martens J, Guo J, Baumbach J. (2013) NABEECO: Biological Network Alignment with Bee Colony Optimization Algorithm. Proceedings of the Genetic and Evolutionary Computation Conference 2013, GECCO, July 2013, Amsterdam, Netherlands. GECCO (Companion) 2013: 43-44.  (download from ACM)

  23. ​Böcker S, Baumbach J. (2013) Cluster Editing. Proceedings of the Computability in Europe conference, CiE, July 2013, Milan, Italy. Lecture Notes in Computer Science. Volume 7921, 2013, pp 33-44. (download from Springer)

  24. Baumbach J, Guo J, Ibragimov R. (2013) Covering Tree with Stars. Proceedings of the International Computing and Combinatorics Conference 2013, COCOON, June 2013, Hangzhou, PR China. Lecture Notes in Computer Science. Vol. 7936, 2013, pp 373-384. (download from Springer)

  25. Sung P, Guo J, Baumbach J. (2013) BiCluE - Exact and Heuristic Algorithms for Weighted Bi-cluster Editing of Biomedical Data. Proceedings of the Great Lakes Bioinformatics Conferences 2013, GLBIO, May 2013, Pittsburg, USA. BMC Proc. 2013 Dec 20;7(Suppl 7):S9. (download from BMC)

  26. Schneider T, Hauschild AC, Baumbach JI, Baumbach J. (2013) An integrative clinical database and diagnostics platform for biomarker analysis in ion mobility spectra of human exhaled air. J Integr Bioinform. 2013 Apr 2;10(2):218. (download from JIB)

  27. Roettger R, Kreutzer C, Vu TD, Wittkop T, Baumbach J. (2012) Online Transitivity Clustering of Biological Data with Missing Values. Proceedings of the German Conference on Bioinformatics, GCB, 2012, OpenAccess Series in Informatics, 26:57-68. (download from OASIC)​

  28. ​​​​​Baumbach J, Friedrich T, Koetzing T, Kromer A, Mueller J, Pauling J. (2012) Efficient algorithms for extracting biological key pathways with global constraints. Proceedings of the Genetic and Evolutionary Computation Conference, GECCO 2012, 2012, 169-176. (download from ACM)

  29. ​Sun P, Guo J, Baumbach J. (2012) Integrated simultaneous analysis of different biomedical data types with exact weighted bi-cluster editing. J Integr Bioinform, 2012 Jul 17;9(2):197 (download from JIB).

  30. Roettger R, Rueckert R, Taubert J, Baumbach J. (2012) ​How Little Do We Actually Know? -- On the Size of Gene Regulatory Networks.​ Proceedings of the 10th Asian Pacific Bioinformatics Conference, APBC, Jan 2012, Melbourne, Australia (download from IEEE)

  31. ​Wittkop T, Rahmann S, Baumbach J. (2010) Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0. J Integr Bioinform, 2008 Aug 25;5 (2). (download from JIB)

  32. Baumbach J, Wittkop T, Weile J, Kohl T, Rahmann S. (2008) MoRAine - A web server for fast computational transcription factor binding motif re-annotation. J Integr Bioinform, 5 (2) : 91, 2008 (download from JIB)

  33. Baumbach J, Bunkowski A, Lange S, Oberwahrenbrock T, Kleinboelting N, Rahmann S, Baumbach JI. (2007) IMS2 - An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath. J Integr Bioinform, 4 (3) : 75, 2007 (download from JIB)

  34. ​Rahmann S, Wittkop T, Baumbach J, Martin M, Truss A, Boecker S. (2007) Exact and Heuristic Algorithms for Weighted Cluster Editing. In Proc. 6th CSB, volume 6 of Computational Systems Bioinformatics. Imperial College Press, 2007 (download from World Scientific)

  35. Baumbach J, Brinkrolf K, Wittkop T, Tauch A, Rahmann S. (2006) CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes. J Integr Bioinform, 3 (2) : 24, 2006. (download from JIB)

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