David B. Blumenthal

2022

• Bernett J., Krupke D., Sadegh S., Baumbach J., Fekete SP., Kacprowski T., List M., Blumenthal DB.:
  Robust disease module mining via enumeration of diverse prize-collecting Steiner trees
  In: Bioinformatics (2022)
  ISSN: 1367-4803
  DOI: 10.1093/bioinformatics/btab876
  URL: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab876/6497106?guestAccessKey=27c2a19b-11b5-4c3c-88d5-f1131e3809a9
  BibTeX: Download

2021

• Bause F., Blumenthal DB., Schubert E., Kriege NM.:
  Metric Indexing for Graph Similarity Search
  14th International Conference on Similarity Search and Applications (SISAP 2021) (Dortmund, 29. September 2021 - 1. October 2021)
  In: Reyes N, Connor R, Kriege N, Kazempour D, Bartolini I, Schubert E, Chen J (ed.): Proceedings of the 14th International Conference on Similarity Search and Applications (SISAP 2021), Cham: 2021
  DOI: 10.1007/978-3-030-89657-7_24
  BibTeX: Download
• Blumenthal DB., Boria N., Bougleux S., Brun L., Gamper J., Gaüzère B.:
  Scalable generalized median graph estimation and its manifold use in bioinformatics, clustering, classification, and indexing
  In: Information Systems 100 (2021), Article No.: 101766
  ISSN: 0306-4379
  DOI: 10.1016/j.is.2021.101766
  BibTeX: Download
• Blumenthal DB., Gamper J., Bougleux S., Brun L.:
  Upper Bounding Graph Edit Distance Based on Rings and Machine Learning
  In: International Journal of Pattern Recognition and Artificial Intelligence (2021), Article No.: 2151008
  ISSN: 0218-0014
  DOI: 10.1142/S0218001421510083
  BibTeX: Download
• Gnecco L., Boria N., Bougleux S., Yger F., Blumenthal DB.:
  The Minimum Edit Arborescence Problem and Its Use in Compressing Graph Collections
  14th International Conference on Similarity Search and Applications (SISAP 2021) (Dortmund, 29. September 2021 - 1. October 2021)
  In: Reyes N, Connor R, Kriege N, Kazempour D, Bartolini I, Schubert E, Chen J (ed.): Proceedings of the 14th International Conference on Similarity Search and Applications (SISAP 2021), Cham: 2021
  DOI: 10.1007/978-3-030-89657-7_25
  BibTeX: Download
• Lazareva O., Baumbach J., List M., Blumenthal DB.:
  On the limits of active module identification
  In: Briefings in Bioinformatics 22 (2021), Article No.: bbab066
  ISSN: 1467-5463
  DOI: 10.1093/bib/bbab066
  URL: https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab066/6189770?guestAccessKey=1be406a0-6b26-4e15-b32b-505c1ea2b279
  BibTeX: Download
• Matschinske J., Benis A., Alcaraz N., Golebiewski M., Grimm DG., Heumos L., Kacprowski T., Lazareva O., List M., Louadi Z., Pauling JK., Pfeifer N., Röttger R., Schwämmle V., Sturm G., Traverso A., Van Steen K., de Freitas MV., Villalba Silva GC., Wee L., Wenke NK., Zanin M., Zolotareva O., Baumbach J., Blumenthal DB.:
  The AIMe registry for artificial intelligence in biomedical research
  In: Nature Methods 18 (2021), p. 1128 - 1131
  ISSN: 1548-7091
  DOI: 10.1038/s41592-021-01241-0
  URL: https://rdcu.be/cv5H7
  BibTeX: Download
• Nasirigerdeh R., Torkzadehmahani R., Baumbach J., Blumenthal DB.:
  On the Privacy of Federated Pipelines
  The 44th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR '21) (Virtual Event, 11. July 2021 - 15. July 2021)
  In: Proceedings of the 44th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR '21), New York, NY, USA: 2021
  DOI: 10.1145/3404835.3462996
  BibTeX: Download
• Sadegh S., Skelton J., Anastasi E., Bernett J., Blumenthal DB., Galindez G., Salgado-Albarran M., Lazareva O., Flanagan K., Cockell S., Nogales C., Casas AI., Schmidt HHHW., Baumbach J., Wipat A., Kacprowski T.:
  Network medicine for disease module identification and drug repurposing with the NeDRex platform
  In: Nature Communications 12 (2021), Article No.: 6848
  ISSN: 2041-1723
  DOI: 10.1038/s41467-021-27138-2
  BibTeX: Download
• Zolotareva O., Nasirigerdeh R., Matschinske J., Torkzadehmahani R., Bakhtiari M., Frisch T., Spaeth J., Blumenthal DB., Abbasinejad A., Tieri P., Kaissis G., Rueckert D., Wenke NK., List M., Baumbach J.:
  Flimma: a federated and privacy-aware tool for differential gene expression analysis
  In: Genome Biology 22 (2021), Article No.: 338
  ISSN: 1474-760X
  DOI: 10.1186/s13059-021-02553-2
  BibTeX: Download

2020

• Blumenthal DB., Baumbach J., Hoffmann M., Kacprowski T., List M.:
  A framework for modeling epistatic interaction
  In: Bioinformatics 37 (2020), p. 1708 - 1716
  ISSN: 1367-4803
  DOI: 10.1093/bioinformatics/btaa990
  URL: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa990/6012351?guestAccessKey=4683fb7f-7afc-4b9c-b0d5-3d0085904eb4
  BibTeX: Download
• Blumenthal DB., Boria N., Gamper J., Bougleux S., Brun L.:
  Comparing heuristics for graph edit distance computation
  In: Vldb Journal 29 (2020), p. 419-458
  ISSN: 1066-8888
  DOI: 10.1007/s00778-019-00544-1
  BibTeX: Download
• Blumenthal DB., Gamper J.:
  On the exact computation of the graph edit distance
  In: Pattern Recognition Letters 134 (2020), p. 46-57
  ISSN: 0167-8655
  DOI: 10.1016/j.patrec.2018.05.002
  BibTeX: Download
• Blumenthal DB., Viola L., List M., Baumbach J., Tieri P., Kacprowski T.:
  EpiGEN: An epistasis simulation pipeline
  In: Bioinformatics 36 (2020), p. 4957-4959
  ISSN: 1367-4803
  DOI: 10.1093/bioinformatics/btaa245
  URL: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa245/5820008?guestAccessKey=2385c5f1-6587-4065-b2f2-1039765fa5b6
  BibTeX: Download
• Boria N., Blumenthal DB., Bougleux S., Brun L.:
  Improved local search for graph edit distance
  In: Pattern Recognition Letters 129 (2020), p. 19-25
  ISSN: 0167-8655
  DOI: 10.1016/j.patrec.2019.10.028
  BibTeX: Download
• Bougleux S., Gauzere B., Blumenthal DB., Brun L.:
  Fast linear sum assignment with error-correction and no cost constraints
  In: Pattern Recognition Letters 134 (2020), p. 37-45
  ISSN: 0167-8655
  DOI: 10.1016/j.patrec.2018.03.032
  BibTeX: Download
• Chondrogiannis T., Bouros P., Gamper J., Leser U., Blumenthal DB.:
  Finding k-shortest paths with limited overlap
  In: Vldb Journal (2020)
  ISSN: 1066-8888
  DOI: 10.1007/s00778-020-00604-x
  BibTeX: Download
• Helmer S., Blumenthal DB., Paschen K.:
  What is meaningful research and how should we measure it?
  In: Scientometrics 125 (2020), p. 153-169
  ISSN: 0138-9130
  DOI: 10.1007/s11192-020-03649-5
  BibTeX: Download
• Lazareva O., Canzar S., Yuan K., Baumbach J., Blumenthal DB., Tieri P., Kacprowski T., List M.:
  BiCoN: Network-constrained biclustering of patients and omics data
  In: Bioinformatics 37 (2020), p. 2398 - 2404
  ISSN: 1367-4803
  DOI: 10.1093/bioinformatics/btaa1076
  URL: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa1076/6050718?guestAccessKey=e2e9cb2b-ac3d-44a6-abc7-2b92ae15d34c
  BibTeX: Download
• Matschinske J., Salgado-Albarran M., Sadegh S., Bongiovanni D., Baumbach J., Blumenthal DB.:
  Individuating Possibly Repurposable Drugs and Drug Targets for COVID-19 Treatment through Hypothesis-Driven Systems Medicine Using CoVex
  In: Assay and Drug Development Technologies 18 (2020), p. 348-355
  ISSN: 1540-658X
  DOI: 10.1089/adt.2020.1010
  BibTeX: Download
• Sadegh S., Matschinske J., Blumenthal DB., Galindez G., Kacprowski T., List M., Nasirigerdeh R., Oubounyt M., Pichlmair A., Rose TD., Salgado-Albarran M., Spaeth J., Stukalov A., Wenke NK., Yuan K., Pauling JK., Baumbach J.:
  Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing
  In: Nature Communications 11 (2020), Article No.: 3518
  ISSN: 2041-1723
  DOI: 10.1038/s41467-020-17189-2
  BibTeX: Download

2019

• Blumenthal DB., Bougleux S., Gamper J., Brun L.:
  GEDLIB: A C++ Library for Graph Edit Distance Computation
  12th IAPR-TC15 Workshop on Graph-Based Representations in Pattern Recognition, GbRPR 2019 (Tours, 19. June 2019 - 21. June 2019)
  In: Donatello Conte, Jean-Yves Ramel, Pasquale Foggia (ed.): Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2019
  DOI: 10.1007/978-3-030-20081-7_2
  BibTeX: Download

2018

• Blumenthal DB., Bougleux S., Gamper J., Brun L.:
  Ring based approximation of graph edit distance
  Joint IAPR International Workshops on Structural and Syntactic Pattern Recognition, SSPR 2018 and Statistical Techniques in Pattern Recognition, SPR 2018 (Beijing, 17. August 2018 - 19. August 2018)
  In: Edwin R. Hancock, Tin Kam Ho, Battista Biggio, Richard C. Wilson, Antonio Robles-Kelly, Xiao Bai (ed.): Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2018
  DOI: 10.1007/978-3-319-97785-0_28
  BibTeX: Download
• Blumenthal DB., Daller E., Bougleux S., Brun L., Gamper J.:
  Quasimetric Graph Edit Distance as a Compact Quadratic Assignment Problem
  24th International Conference on Pattern Recognition, ICPR 2018 (Beijing, 20. August 2018 - 24. August 2018)
  In: Proceedings - International Conference on Pattern Recognition 2018
  DOI: 10.1109/ICPR.2018.8546055
  BibTeX: Download
• Blumenthal DB., Gamper J.:
  Improved lower bounds for graph edit distance
  In: IEEE Transactions on Knowledge and Data Engineering 30 (2018), p. 503-516
  ISSN: 1041-4347
  DOI: 10.1109/TKDE.2017.2772243
  BibTeX: Download
• Chondrogiannis T., Bouros P., Gamper J., Leser U., Blumenthal DB.:
  Finding k-dissimilar paths with minimum collective length
  26th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, ACM SIGSPATIAL GIS 2018 (Seattle, WA, 6. November 2018 - 9. November 2018)
  In: Li Xiong, Roberto Tamassia, Kashani Farnoush Banaei, Ralf Hartmut Guting, Erik Hoel (ed.): GIS: Proceedings of the ACM International Symposium on Advances in Geographic Information Systems 2018
  DOI: 10.1145/3274895.3274903
  BibTeX: Download

2017

• Blumenthal DB., Gamper J.:
  Correcting and speeding-up bounds for non-uniform graph edit distance
  33rd IEEE International Conference on Data Engineering, ICDE 2017 (San Diego, CA, 19. April 2017 - 22. April 2017)
  In: Proceedings - International Conference on Data Engineering 2017
  DOI: 10.1109/ICDE.2017.57
  BibTeX: Download
• Blumenthal DB., Gamper J.:
  Exact computation of graph edit distance for uniform and non-uniform metric edit costs
  11th IAPR-TC-15 International Workshop on Graph-Based Representations in Pattern Recognition, GbRPR 2017 (Anacapri, ITA, 16. May 2017 - 18. May 2017)
  In: Pasquale Foggia, Mario Vento, Cheng-Lin Liu (ed.): Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2017
  DOI: 10.1007/978-3-319-58961-9_19
  BibTeX: Download

Experts for reviewing scientific journals

• Bioinformatics (Oxford, England)
  since 5. November 2021
• Frontiers in Medicine
  since 3. September 2021
• Assay and Drug Development Technologies
  since 1. January 2021
• Heliyon
  since 1. January 2021
• Nature Communications
  since 1. January 2021
• Pattern Analysis and Applications
  since 1. January 2020
• BioData Mining
  since 1. January 2020
• Information Sciences
  since 1. January 2020
• European Journal of Operational Research
  since 1. January 2020
• Information Systems Frontiers
  since 1. January 2019
• Pattern Recognition Letters
  since 1. January 2019

Experts for funding organisations

• Ministerium für Kultur und Wissenschaft des Landes Nordrhein-Westfalen
  since 1. October 2021
• TUM Global Postdoc Fellowship
  since 1. January 2021
• The Research Council of Norway
  since 1. January 2021

• 2021: Best PhD Student Award (Faculty of Computer Science, Free University of Bozen-Bolzano)
• 2021: Best Talk Award (29th Conference on Intelligent Systems for Molecular Biology, Network Biology Community of Special Interest)
• 2017: Best Paper Award (11th IAPR-TC-15 International Workshop on Graph-Based Representations in Pattern Recognition)
• 2015: PhD Grant (Faculty of Computer Science, Free University of Bozen-Bolzano)
• 2015: MSc Award (Institute of Mathematics, Technical University of Berlin)
• 2007: Student Scholarship (German Academic Scholarship Foundation)