Publications
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2024
Journal Articles
Wang DD. , Katoch M. , Jabari S. , Blümcke I. , Blumenthal DB. Lu DH. , Coras R. , Wang YJ. , Shi J. , Zhou WJ. , Kobow K. , Piao YS. :Correction to: The specific DNA methylation landscape in focal cortical dysplasia ILAE type 3D (Acta Neuropathologica Communications, (2023), 11, 1, (129), 10.1186/s40478-023-01618-6) Acta Neuropathologica Communications 12 2024 ), Article No.: 49 ISSN: 2051-5960 10.1186/s40478-024-01752-9 Download Sarkar S. Wu T. , Harwood M. , Silva AC. :A Transfer Learning-Based Framework for Classifying Lymph Node Metastasis in Prostate Cancer Patients Biomedicines 12 2024 ), Article No.: 2345 ISSN: 2227-9059 10.3390/biomedicines12102345 Download Hoffmann M. , Poschenrieder JM. , Incudini M. , Baier S. , Fritz A. , Maier A. , Hartung M. , Hoffmann C. , Trummer N. , Adamowicz K. , Picciani M. , Scheibling E. , Harl MV. , Lesch I. , Frey H. , Kayser S. , Wissenberg P. , Schwartz L. , Hafner L. , Acharya A. , Hackl L. , Grabert G. , Lee SG. , Cho G. , Cloward ME. , Jankowski J. , Lee HK. , Tsoy O. , Wenke N. , Pedersen AG. , Bønnelykke K. , Mandarino A. , Melograna F. , Schulz L. , Climente-González H. , Wilhelm M. , Iapichino L. , Wienbrandt L. , Ellinghaus D. , Van Steen K. , Grossi M. , Furth PA. , Hennighausen L. , Di Pierro A. , Baumbach J. , Kacprowski T. , List M. , Blumenthal DB. Network medicine-based epistasis detection in complex diseases: Ready for quantum computing Nucleic Acids Research 52 2024 ), p. 10144-10160 ISSN: 0305-1048 10.1093/nar/gkae697 Download Bernett J. , Blumenthal DB. Grimm DG. , Haselbeck F. , Joeres R. , Kalinina OV. , List M. :Guiding questions to avoid data leakage in biological machine learning applications Nature Methods 21 2024 ), p. 1444-1453 ISSN: 1548-7091 10.1038/s41592-024-02362-y Download Maier A. , Hartung M. , Abovsky M. , Adamowicz K. , Bader GD. , Baier S. , Blumenthal DB. Chen J. , Elkjaer ML. , Garcia-Hernandez C. , Helmy M. , Hoffmann M. , Jurisica I. , Kotlyar M. , Lazareva O. , Levi H. , List M. , Lobentanzer S. , Loscalzo J. , Malod-Dognin N. , Manz Q. , Matschinske J. , Mee M. , Oubounyt M. , Pastrello C. , Pico AR. , Pillich RT. , Poschenrieder JM. , Pratt D. , Pržulj N. , Sadegh S. , Saez-Rodriguez J. , Sarkar S. Shaked G. , Shamir R. , Trummer N. , Turhan U. , Wang RS. , Zolotareva O. , Baumbach J. :Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing Nucleic Acids Research 52 2024 ), p. W481-W488 ISSN: 0305-1048 10.1093/nar/gkae388 Download Bernett J. , Blumenthal DB. List M. :Cracking the black box of deep sequence-based protein-protein interaction prediction Briefings in Bioinformatics 25 2024 ), Article No.: bbae076 ISSN: 1467-5463 10.1093/bib/bbae076 Download Kersting J. , Lazareva O. , Louadi Z. , Baumbach J. , Blumenthal DB. List M. :DysRegNet: Patient-specific and confounder-aware dysregulated network inference towards precision therapeutics British Journal of Pharmacology 2024 )ISSN: 0007-1188 10.1111/bph.17395 https://bpspubs.onlinelibrary.wiley.com/doi/10.1111/bph.17395 Download Khnaisser C. , Hamrouni H. , Blumenthal DB. Dignös A. , Gamper J. :Efficiently Labeling and Retrieving Temporal Anomalies in Relational Databases Information Systems Frontiers 2024 )ISSN: 1387-3326 10.1007/s10796-024-10495-w Download Hartebrodt A. Röttger R. , Blumenthal DB. Federated singular value decomposition for high-dimensional data Data Mining and Knowledge Discovery 38 2024 ), p. 938 - 975 ISSN: 1573-756X 10.1007/s10618-023-00983-z Download Galindez G. , List M. , Baumbach J. , Völker U. , Mäder U. , Blumenthal DB. Kacprowski T. :Inference of differential gene regulatory networks using boosted differential trees Bioinformatics Advances 4 2024 ), Article No.: vbae034 ISSN: 2635-0041 10.1093/bioadv/vbae034 Download Sarkar S. Möller A. Hartebrodt A. Erdmann M. , Ostalecki C. , Baur A. , Blumenthal DB. Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma npj Systems Biology and Applications 10 2024 ), Article No.: 143 ISSN: 2056-7189 10.1038/s41540-024-00474-x Download Menche C. , Schuhwerk H. , Armstark I. , Gupta P. , Fuchs K. , van Roey R. , Mosa MH. , Hartebrodt A. Hajjaj Y. , Clavel Ezquerra A. , Selvaraju MK. , Geppert CI. , Bärthel S. , Saur D. , Greten FR. , Brabletz S. , Blumenthal DB. Weigert A. , Brabletz T. , Farin HF. , Stemmler MP. :ZEB1-mediated fibroblast polarization controls inflammation and sensitivity to immunotherapy in colorectal cancer EMBO Reports 2024 )ISSN: 1469-221X 10.1038/s44319-024-00186-7 Download
Conference Contributions
Giurgiu M. , Wittstruck N. , Rodriguez-Fos E. , González RC. , Brückner L. , Krienelke-Szymansky A. , Helmsauer K. , Hartebrodt A. Euskirchen P. , Koche RP. , Haase K. , Reinert K. , Henssen AG. :Decoil: Reconstructing Extrachromosomal DNA Structural Heterogeneity from Long-Read Sequencing Data 28th International Conference on Research in Computational Molecular Biology, RECOMB 2024 (Cambridge, MA 29/04/2024 - 02/05/2024 )In: Jian Ma (ed.): Research in Computational Molecular Biology. 28th Annual International Conference, RECOMB 2024, Cambridge, MA, USA, April 29–May 2, 2024, Proceedings , Cham 2024 10.1007/978-1-0716-3989-4_41 Download
2023
Journal Articles
Gärttner S. , Frank F. , Woller F. Meier A. , Ray N. :Estimating relative diffusion from 3D micro-CT images using CNNs Artificial Intelligence in Geosciences 4 2023 ), p. 199-208 ISSN: 2666-5441 10.1016/j.aiig.2023.11.001 Download Sadegh S. , Skelton J. , Anastasi E. , Maier A. , Adamowicz K. , Möller A. Kriege NM. , Kronberg J. , Haller T. , Kacprowski T. , Wipat A. , Baumbach J. , Blumenthal DB. Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond Nature Communications 14 2023 ), Article No.: 1662 ISSN: 2041-1723 10.1038/s41467-023-37349-4 Download Wang DD. , Katoch M. , Jabari S. , Blümcke I. , Blumenthal DB. Lu DH. , Coras R. , Wang YJ. , Shi J. , Zhou WJ. , Kobow K. , Piao YS. :The specific DNA methylation landscape in focal cortical dysplasia ILAE type 3D Acta Neuropathologica Communications 11 2023 ), Article No.: 129 ISSN: 2051-5960 10.1186/s40478-023-01618-6 Download Sarkar S. Lucchetta M. , Maier A. , Abdrabbou MMM. , Baumbach J. , List M. , Schaefer MH. , Blumenthal DB. Online bias-aware disease module mining with ROBUST-Web Bioinformatics 35 2023 ), Article No.: btad345 ISSN: 1367-4803 10.1093/bioinformatics/btad345 Download Hoffmann M. , Trummer N. , Schwartz L. , Jankowski J. , Lee HK. , Willruth LL. , Lazareva O. , Yuan K. , Baumgarten N. , Schmidt F. , Baumbach J. , Schulz MH. , Blumenthal DB. Hennighausen L. , List M. :TF-Prioritizer: a Java pipeline to prioritize condition-specific transcription factors GigaScience 12 2023 ), Article No.: giad026 ISSN: 2047-217X 10.1093/gigascience/giad026 Download Sarkar S. Min K. , Ikram W. , Tatton RW. , Riaz IB. , Silva AC. , Bryce AH. , Moore C. , Ho TH. , Sonpavde G. , Abdul-Muhsin HM. , Singh P. , Wu T. :Performing Automatic Identification and Staging of Urothelial Carcinoma in Bladder Cancer Patients Using a Hybrid Deep-Machine Learning Approach Cancers 15 2023 ), Article No.: 1673 ISSN: 2072-6694 10.3390/cancers15061673 Download Ketteler A. , Blumenthal DB. Demographic confounders distort inference of gene regulatory and gene co-expression networks in cancer Briefings in Bioinformatics 24 2023 ), Article No.: bbad413 ISSN: 1467-5463 10.1093/bib/bbad413 Download Gerlach L. , Blumenthal DB. On the role of network topology in German-Jewish recommendation letter networks in the early twentieth century Applied Network Science 8 2023 ), Article No.: 24 ISSN: 2364-8228 10.1007/s41109-023-00550-x Download Hartebrodt A. Röttger R. :Privacy of Federated QR Decomposition Using Additive Secure Multiparty Computation IEEE Transactions on Information Forensics and Security 18 2023 ), p. 5122-5132 ISSN: 1556-6013 10.1109/TIFS.2023.3301710 Download Boria N. , Kiederle J. , Yger F. , Blumenthal DB. The edge-preservation similarity for comparing rooted, unordered, node-labeled trees Pattern Recognition Letters 167 2023 ), p. 189-195 ISSN: 0167-8655 10.1016/j.patrec.2023.02.017 Download
2022
Journal Articles
Adamowicz K. , Maier A. , Baumbach J. , Blumenthal DB. Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST Briefings in Bioinformatics 2022 )ISSN: 1467-5463 10.1093/bib/bbac247 https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac247/6618231?guestAccessKey=e1b9455f-ac28-4d46-af6d-c51b3b98cc8d Download Blumenthal DB. Bougleux S. , Dignoes A. , Gamper J. :Enumerating dissimilar minimum cost perfect and error-correcting bipartite matchings for robust data matching Information Sciences 596 2022 ), p. 202-221 ISSN: 0020-0255 10.1016/j.ins.2022.03.017 Download Torkzadehmahani R. , Nasirigerdeh R. , Blumenthal DB. Kacprowski T. , List M. , Matschinske J. , Spaeth J. , Wenke NK. , Baumbach J. :Privacy-Preserving Artificial Intelligence Techniques in Biomedicine Methods of Information in Medicine 2022 )ISSN: 0026-1270 10.1055/s-0041-1740630 Download 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 Bioinformatics 38 2022 ), p. 1600-1606 ISSN: 1367-4803 10.1093/bioinformatics/btab876 https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab876/6497106?guestAccessKey=27c2a19b-11b5-4c3c-88d5-f1131e3809a9 Download
Conference Contributions
2021
Journal Articles
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 Genome Biology 22 2021 ), Article No.: 338 ISSN: 1474-760X 10.1186/s13059-021-02553-2 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 Nature Communications 12 2021 ), Article No.: 6848 ISSN: 2041-1723 10.1038/s41467-021-27138-2 Download Lazareva O. , Baumbach J. , List M. , Blumenthal DB. On the limits of active module identification Briefings in Bioinformatics 22 2021 ), Article No.: bbab066 ISSN: 1467-5463 10.1093/bib/bbab066 https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab066/6189770?guestAccessKey=1be406a0-6b26-4e15-b32b-505c1ea2b279 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 Information Systems 100 2021 ), Article No.: 101766 ISSN: 0306-4379 10.1016/j.is.2021.101766 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 Nature Methods 18 2021 ), p. 1128 - 1131 ISSN: 1548-7091 10.1038/s41592-021-01241-0 https://rdcu.be/cv5H7 Download Blumenthal DB. Gamper J. , Bougleux S. , Brun L. :Upper Bounding Graph Edit Distance Based on Rings and Machine Learning International Journal of Pattern Recognition and Artificial Intelligence 2021 ), Article No.: 2151008 ISSN: 0218-0014 10.1142/S0218001421510083 Download
Conference Contributions
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 11/07/2021 - 15/07/2021 )In: Proceedings of the 44th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR '21) , New York, NY, USA 2021 10.1145/3404835.3462996 Download Hartebrodt A. Nasirigerdeh R. , Blumenthal DB. Röttger R. :Federated Principal Component Analysis for Genome-Wide Association Studies 21st IEEE International Conference on Data Mining (ICDM) (Auckland, New Zealand 07/12/2021 - 10/12/2021 )In: 21st IEEE International Conference on Data Mining (ICDM) 2021 10.1109/ICDM51629.2021.00127 Download 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 29/09/2021 - 01/10/2021 )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 10.1007/978-3-030-89657-7_24 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 29/09/2021 - 01/10/2021 )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 10.1007/978-3-030-89657-7_25 Download
2020
Journal Articles
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 Nature Communications 11 2020 ), Article No.: 3518 ISSN: 2041-1723 10.1038/s41467-020-17189-2 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 Assay and Drug Development Technologies 18 2020 ), p. 348-355 ISSN: 1540-658X 10.1089/adt.2020.1010 Download Blumenthal DB. Viola L. , List M. , Baumbach J. , Tieri P. , Kacprowski T. :EpiGEN: An epistasis simulation pipeline Bioinformatics 36 2020 ), p. 4957-4959 ISSN: 1367-4803 10.1093/bioinformatics/btaa245 https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa245/5820008?guestAccessKey=2385c5f1-6587-4065-b2f2-1039765fa5b6 Download Helmer S. , Blumenthal DB. Paschen K. :What is meaningful research and how should we measure it? Scientometrics 125 2020 ), p. 153-169 ISSN: 0138-9130 10.1007/s11192-020-03649-5 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 Bioinformatics 37 2020 ), p. 2398 - 2404 ISSN: 1367-4803 10.1093/bioinformatics/btaa1076 https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa1076/6050718?guestAccessKey=e2e9cb2b-ac3d-44a6-abc7-2b92ae15d34c Download Blumenthal DB. Baumbach J. , Hoffmann M. , Kacprowski T. , List M. :A framework for modeling epistatic interaction Bioinformatics 37 2020 ), p. 1708 - 1716 ISSN: 1367-4803 10.1093/bioinformatics/btaa990 https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa990/6012351?guestAccessKey=4683fb7f-7afc-4b9c-b0d5-3d0085904eb4 Download Bougleux S. , Gauzere B. , Blumenthal DB. Brun L. :Fast linear sum assignment with error-correction and no cost constraints Pattern Recognition Letters 134 2020 ), p. 37-45 ISSN: 0167-8655 10.1016/j.patrec.2018.03.032 Download Blumenthal DB. Gamper J. :On the exact computation of the graph edit distance Pattern Recognition Letters 134 2020 ), p. 46-57 ISSN: 0167-8655 10.1016/j.patrec.2018.05.002 Download Blumenthal DB. Boria N. , Gamper J. , Bougleux S. , Brun L. :Comparing heuristics for graph edit distance computation Vldb Journal 29 2020 ), p. 419-458 ISSN: 1066-8888 10.1007/s00778-019-00544-1 Download Chondrogiannis T. , Bouros P. , Gamper J. , Leser U. , Blumenthal DB. Finding k-shortest paths with limited overlap Vldb Journal 2020 )ISSN: 1066-8888 10.1007/s00778-020-00604-x Download Boria N. , Blumenthal DB. Bougleux S. , Brun L. :Improved local search for graph edit distance Pattern Recognition Letters 129 2020 ), p. 19-25 ISSN: 0167-8655 10.1016/j.patrec.2019.10.028 Download
2018
Journal Articles
Conference Contributions
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 20/08/2018 - 24/08/2018 )In: Proceedings - International Conference on Pattern Recognition 2018 10.1109/ICPR.2018.8546055 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 06/11/2018 - 09/11/2018 )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 10.1145/3274895.3274903 Download 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 17/08/2018 - 19/08/2018 )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 10.1007/978-3-319-97785-0_28 Download
2017
Conference Contributions
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 19/04/2017 - 22/04/2017 )In: Proceedings - International Conference on Data Engineering 2017 10.1109/ICDE.2017.57 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 16/05/2017 - 18/05/2017 )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 10.1007/978-3-319-58961-9_19 Download