Publications @ RöttgerLab

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Publications

  1. Jacob Egebjerg, Maria Szomek, Katja Thaysen, Alice Dupont Juhl, Christoph Pratsch, Stephan Werner, Gerd Schneider, Richard Röttger and Daniel Wüstner. Automated quantification of vacuole fusion and lipophagy in Saccharomyces cerevisiae from fluorescence and cryo-soft X-ray microscopy data using deep learning. Autophagy 0(0): 1-21 (2023). Link.
  2. Anne Hartebrodt, Richard Röttger and David B Blumenthal. Federated singular value decomposition for high-dimensional data. Data Mining and Knowledge Discovery: 1–38 (2023). Link.
  3. David Schneeberger, Richard Röttger, Federico Cabitza, Andrea Campagner, Markus Plass, Heimo Müller and Andreas Holzinger. The tower of babel in explainable artificial intelligence (XAI). In International Cross-Domain Conference for Machine Learning and Knowledge Extraction. (2023): 65–81.
  4. Andreas Holzinger, Anna Saranti, Anne-Christin Hauschild, Jacqueline Beinecke, Dominik Heider, Richard Röttger, Heimo Mueller, Jan Baumbach and Bastian Pfeifer. Human-in-the-Loop Integration with Domain-Knowledge Graphs for Explainable Federated Deep Learning. In International Cross-Domain Conference for Machine Learning and Knowledge Extraction. (2023): 45–64.
  5. Anne Hartebrodt and Richard Röttger. Privacy of federated QR decomposition using additive secure multiparty computation. IEEE Transactions on Information Forensics and Security (2023). Link.
  6. Julian Matschinske, Julian Späth, Mohammad Bakhtiari, Niklas Probul, Kazemi Majdabadi MM, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Anne Hartebrodt, Balazs-Attila Orban, Sándor-József Fejér and others. The FeatureCloud Platform for Federated Learning in Biomedicine: Unified Approach. Journal of Medical Internet Research 25: e42621–e42621 (2023). Link.
  7. Dženan Mašić, Kristian Stengaard-Pedersen, Brian Bridal Løgstrup, Kim Hørslev-Petersen, Merete Lund Hetland, Peter Junker, Mikkel Østergaard, Claus Henrik Nielsen, Mogens Kruhøffer, Mathias Emil Bøgebjerg and others. Plasma levels of multiple cardiovascular-and inflammation-related proteins analysed for associations with disease activity and anti-cyclic citrullinated peptide status in active early rheumatoid arthritis. Clinical and experimental rheumatology (2023). Link.
  8. Jacob Egebjerg, Maria Szomek, Katja Thaysen, Alice Dupont Juhl, Christoph Pratsch, Stephan Werner, Gerd Schneider, Richard Röttger and Daniel Wüstner. Automated quantification of lipophagy in Saccharomyces cerevisiae from fluorescence and cryo-soft X-ray microscopy data using deep learning. bioRxiv: 2023–02 (2023). This paper has now been published with Autophagy.
  9. Tobias Greisager Rehfeldt, Konrad Krawczyk, Simon Gregersen Echers, Paolo Marcatili, Pawel Palczynski, Richard Röttger and Veit Schwaemmle. Variance Analysis of LC-MS Experimental Factors and Their Impact on Machine Learning. bioRxiv: 2023–05 (2023). Link.
  10. Eline Sandvig Andersen, Claus Østergaard, Richard Röttger, Anne Friesgaard Christensen, Ivan Brandslund and Claus Lohman Brasen. POCT urine dipstick versus central laboratory analyses: Diagnostic performance and logistics in the medical emergency department. Clinical Biochemistry 111: 17–25 (2023).
  11. Marcos V Conde, Radu Timofte, Yibin Huang, Jingyang Peng, Chang Chen, Cheng Li, Eduardo Pérez-Pellitero, Fenglong Song, Furui Bai, Shuai Liu and others. Reversed image signal processing and RAW reconstruction. AIM 2022 challenge report. In Computer Vision–ECCV 2022 Workshops: Tel Aviv, Israel, October 23–27, 2022, Proceedings, Part III. (2022): 3–26. Link.
  12. Maria L Elkjaer, Lukas Simon, Tobias Frisch, Lisa-Marie Bente, Tim Kacprowski, Mads Thomassen, Richard Reynolds, Jan Baumbach, Richard Röttger and Zsolt Illes. Hypothesis of a potential BrainBiota and its relation to CNS autoimmune inflammation. Frontiers in Immunology 13 (2022). Link.
  13. Marcos V Conde, Radu Timofte, Yibin Huang, Jingyang Peng, Chang Chen, Cheng Li, Eduardo Pérez-Pellitero, Fenglong Song, Furui Bai, Shuai Liu and others. Reversed image signal processing and raw reconstruction. aim 2022 challenge report. arXiv preprint arXiv:2210.11153 (2022). Link. This paper has now been published with the full proceedings with Springer.
  14. Anne Hartebrodt and Richard Röttger. Privacy of federated QR decomposition using additive secure multiparty computation. arXiv preprint arXiv:2210.06163 (2022). Link.
  15. Anne Hartebrodt, Reza Nasirigerdeh, Jan Bamubach, David Benjamin Blumenthal, Tim Kacprowski and Richard Röttger. Medical data safety via federated machine learning. In RExPO22 Conference. (2022). Link.
  16. Juan Marı́n-Vega, Michael Sloth, Peter Schneider-Kamp and Richard Röttger. DRHDR: A dual branch residual network for multi-bracket high dynamic range imaging. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. (2022): 844–852. Link.
  17. Eduardo Pérez-Pellitero, Sibi Catley-Chandar, Richard Shaw, Aleš Leonardis, Radu Timofte, Zexin Zhang, Cen Liu, Yunbo Peng, Yue Lin, Gaocheng Yu and others. NTIRE 2022 challenge on high dynamic range imaging: Methods and results. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. (2022): 1009–1023. Link.
  18. Anne Hartebrodt, Richard Röttger and David B Blumenthal. Federated singular value decomposition for high dimensional data. arXiv preprint arXiv:2205.12109 (2022). Link.
  19. Anne Hartebrodt and Richard Röttger. Federated Horizontally Partitioned Principal Component Analysis for Biomedical Applications. Bioinformatics Advances (2022). Link.
  20. Tim Daniel Rose, Thibault Bechtler, Octavia-Andreea Ciora, Kim Anh Lilian Le, Florian Molnar, Nikolai Koehler, Jan Baumbach, Richard Röttger and Josch Konstantin Pauling. MoSBi: Automated signature mining for molecular stratification and subtyping. Proceedings of the National Academy of Sciences 119(16): e2118210119 (2022). Link.
  21. Maria Louise Elkjær, Richard Röttger, Jan Baumbach and Zsolt Illes. A systematic review of tissue and single cell transcriptome/proteome studies of the brain in multiple sclerosis. Frontiers in Immunology 13: 524 (2022). Link.
  22. Tobias Greisager Rehfeldt, Konrad Krawczyk, Mathias Bøgebjerg, Veit Schwämmle and Richard Röttger. MS2AI: Automated repurposing of public peptide LC-MS data for machine learning applications. Bioinformatics 38(3): 875–877 (2022). Link.
  23. Anne Hartebrodt, Reza Nasirigerdeh, David B Blumenthal and Richard Röttger. Federated Principal Component Analysis for Genome-Wide Association Studies. In 2021 IEEE International Conference on Data Mining (ICDM). (2021): 1090–1095. Link.
  24. Julian Matschinske, Nicolas Alcaraz, Arriel Benis, Martin Golebiewski, Dominik G Grimm, Lukas Heumos, Tim Kacprowski, Olga Lazareva, Markus List, Zakaria Louadi, Josch K Pauling, Nico Pfeifer, Richard Röttger, Veit Schwämmle, Gregor Sturm, Alberto Traverso, Kristel Van Steen, Martiela Vaz Freitas, Gerda Cristal Villalba Silva, Leonard Wee, Nina K Wenke, Massimiliano Zanin, Olga Zolotareva, Jan Baumbach and David B Blumenthal. The AIMe registry for artificial intelligence in biomedical research. Nature methods 18(10): 1128–1131 (2021). Link.
  25. Maja Skov Kragsnaes, Jens Kjeldsen, Hans Christian Horn, Heidi Lausten Munk, Jens Kristian Pedersen, Søren Andreas Just, Palle Ahlquist, Jesper Rømhild Davidsen, Anna Christine Nilsson, Richard Röttger, Mogens Kruhøffer, Julian R Marchesi, Karsten Kristiansen, Robin Christensen and Torkell Ellingsen. Response to: ‘Correspondence on ‘Safety and efficacy of faecal microbiota transplantation for active peripheral psoriatic arthritis: an exploratory randomised placebo-controlled trial’ by McGonagle et al. Annals of the Rheumatic Diseases (2021). Link.
  26. Konrad Krawczyk, Tadeusz Chelkowski, Daniel J Laydon, Swapnil Mishra, Denise Xifara, Seth Flaxman, Thomas Mellan, Veit Schwämmle, Richard Röttger, Johannes T Hadsund and Samir Bhatt. Quantifying Online News Media Coverage of the COVID-19 Pandemic: Text Mining Study and Resource. Journal of medical Internet research 23(6): e28253 (2021). Link. A minor correction regarding the author names has been released.
  27. Julian Matschinske, Julian Späth, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Anne Hartebrodt, Balázs Orbán, Sándor Fejér, Olga Zolotareva, Mohammad Bakhtiari, Béla Bihari, Marcus Bloice, Nina C Donner, Walid Fdhila, Tobias Frisch, Anne-Christin Hauschild, Dominik Heider, Andreas Holzinger, Walter Hötzendorfer, Jan Hospes, Tim Kacprowski, Markus Kastelitz, Markus List, Rudolf Mayer, Mónika Moga, Heimo Müller, Anastasia Pustozerova, Richard Röttger, Anna Saranti, Harald HHW Schmidt, Christof Tschohl, Nina K Wenke and Jan Baumbach. The FeatureCloud AI Store for Federated Learning in Biomedicine and Beyond. arXiv preprint arXiv:2105.05734 (2021). Link.
  28. Alexander GB Grønning, Mhaned Oubounyt, Kristiyan Kanev, Jesper Lund, Tim Kacprowski, Dietmar Zehn, Richard Röttger and Jan Baumbach. Enabling single-cell trajectory network enrichment. Nature Computational Science 1(2): 153–163 (2021). Link.
  29. Tobias Greisager Rehfeldt, Konrad Krawczyk, Mathias Bøgebjerg, Veit Schwämmle and Richard Röttger. MS2AI: Automated repurposing of public peptide LC-MS data for machine learning applications. bioRxiv (2021). Link. This paper has now beed published with Bioinformatics.
  30. Maria L Elkjaer, Tobias Frisch, Arianna Tonazzolli, Richard Röttger, Richard Reynolds, Jan Baumbach and Zsolt Illes. Unbiased examination of genome-wide human endogenous retrovirus transcripts in MS brain lesions. Multiple Sclerosis Journal: 1352458520987269 (2021). Link.
  31. Tim Daniel Rose, Thibault Bechtler, Octavia-Andreea Ciora, Kim Anh Lilian Le, Florian Molnar, Nikolai Koehler, Jan Baumbach, Richard Röttger and Josch Konstantin Pauling. MoSBi: Automated signature mining for molecular stratification and subtyping. bioRxiv (2021). Link.
  32. Reihaneh Torkzadehmahani, Reza Nasirigerdeh, David B Blumenthal, Tim Kacprowski, Markus List, Julian Matschinske, Julian Späth, Nina Kerstin Wenke, Béla Bihari, Tobias Frisch, Anne Hartebrodt, Anne-Christin Hausschild, Dominik Heider, Andreas Holzinger, Walter Hötzendorfer, Markus Kastelitz, Rudolf Mayer, Cristian Nogales, Anastasia Pustozerova, Richard Röttger, Harald H.H.W. Schmidt, Ameli Schwalber, Christof Tschohl, Andrea Wohner and Jan Baumbach. Privacy-preserving Artificial Intelligence Techniques in Biomedicine. arXiv preprint arXiv:2007.11621 (2020). Link.
  33. Alexander GB Grønning, Mhaned Oubounyt, Kristiyan Kanev, Jesper Lund, Tim Kacprowski, Dietmar Zehn, Richard Röttger and Jan Baumbach. Comparative single-cell trajectory network enrichment identifies pseudo-temporal systems biology patterns in hematopoiesis and CD8 T-cell development. bioRxiv (2020). Link. An extended version of the manuscript is now published in Nature Computational Science.
  34. Konrad Krawczyk, Tadeusz Chelkowski, Daniel J Laydon, Swapnil Mishra, Denise Xifara, Seth Flaxman, Thomas Mellan, Veit Schwämmle, Richard Röttger, Johannes T Hadsund and Samir Bhatt. Quantifying the online news media coverage of the COVID-19 pandemic. medRxiv (2020). Link. An extended version of the manuscript is now published in Journal of medical Internet research.
  35. Christian Wiwie, Richard Röttger and Jan Baumbach. TiCoNE 2: A Composite Clustering Model for Robust Cluster Analyses on Noisy Data. arXiv preprint arXiv:1904.12353 (2019). Link.
  36. Alexander Rauch, Anders K Haakonsson, Jesper GS Madsen, Mette Larsen, Isabel Forss, Martin R Madsen, Elvira L Van Hauwaert, Christian Wiwie, Naja Z Jespersen, Michaela Tencerova, Ronni Nielsen, Bjørk D Larsen, Richard Röttger, Jan Baumbach, Camilla Scheele, Moustapha Kassem and Susanne Mandrup. Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis. Nature genetics 51(4): 716–727 (2019). Link. A minor correction regarding incorrect colors in a figure has been released.
  37. Christian Wiwie, Irina Kuznetsova, Ahmed Mostafa, Alexander Rauch, Anders Haakonsson, Inigo Barrio-Hernandez, Blagoy Blagoev, Susanne Mandrup, Harald HHW Schmidt, Stephan Pleschka, Richard Röttger and Jan Baumbach. Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets. Systems Medicine 2(1): 1–9 (2019). Link.
  38. Simon J Larsen, Richard Röttger, Harald H H W Schmidt and Jan Baumbach. E. coli gene regulatory networks are inconsistent with gene expression data. Nucleic acids research 47(1): 85–92 (2019). Link.
  39. Christian Wiwie, Jan Baumbach and Richard Röttger. Guiding biomedical clustering with ClustEval. Nature protocols 13(6): 1429–1444 (2018). Link.
  40. Syed S Hassan, Syed B Jamal, Leandro G Radusky, Sandeep Tiwari, Asad Ullah, Javed Ali, Paulo VSD Carvalho, Rida Shams, Sabir Khan, Henrique CP Figueiredo, Debmalya Barh, Preetam Ghosh, Artur Silva, Jan Baumbach, Richard Röttger, Adrián G Turjanski and Vasco AC Azevedo. The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets. Frontiers in genetics 9: 44 (2018). Link.
  41. Tobias Frisch, Jonatan Gøttcke, Richard Röttger, Qihua Tan and Jan Baumbach. DiMmer: Discovery of Differentially Methylated Regions in Epigenome-Wide Association Study (EWAS) Data. In Data Mining for Systems Biology. Humana Press, New York, NY. (2018): 51–62. Link.
  42. Christian Wiwie, Alexander Rauch, Anders Haakonsson, Inigo Barrio-Hernandez, Blagoy Blagoev, Susanne Mandrup, Richard Röttger and Jan Baumbach. Elucidation of time-dependent systems biology cell response patterns with time course network enrichment. arXiv preprint arXiv:1710.10262 (2017). Link. An extended version of the manuscript is now published in Systems Medicine.
  43. Syed Babar Jamal, Syed Shah Hassan, Sandeep Tiwari, Marcus V Viana, Leandro de Jesus Benevides, Asad Ullah, Adrián G Turjanski, Debmalya Barh, Preetam Ghosh, Daniela Arruda Costa, Artur Silva, Richard Röttger, Jan Baumbach and Vasco AC Azevedo. An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PLoS One 12(10): e0186401 (2017). Link.
  44. Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Siomar Castro Soares, Sebastian Böcker, Vasco Azevedo and Jan Baumbach. LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. Journal of integrative bioinformatics 14(2) (2017). Link.
  45. Diogo Almeida, Ida Skov, Artur Silva, Fabio Vandin, Qihua Tan, Richard Röttger and Jan Baumbach. Efficient detection of differentially methylated regions using DiMmeR. Bioinformatics 33(4): 549–551 (2017). Link.
  46. Christian Wiwie and Richard Röttger. On the Power and Limits of Sequence Similarity Based Clustering of Proteins Into Families. In Pacific Symposium on Biocomputing 2017. (2017): 39–50. Link.
  47. Edson Luiz Folador, Paulo Vinícius Sanches Daltro Carvalho, Wanderson Marques Silva, Rafaela Salgado Ferreira, Artur Silva, Michael Gromiha, Preetam Ghosh, Debmalya Barh, Vasco Azevedo and Richard Röttger. In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks. BMC systems biology 10(1): 1–9 (2016). Link.
  48. Diogo Almeida, Ida Skov, Jesper Lund, Afsaneh Mohammadnejad, Artur Silva, Fabio Vandin, Qihua Tan, Jan Baumbach and Richard Röttger. Jllumina-A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing. Journal of integrative bioinformatics 13(4): 24–32 (2016). Link.
  49. Richard Röttger. Clustering of biological datasets in the era of big data. Journal of integrative bioinformatics 13(1): 52–81 (2016). Link.
  50. Mubo Chen, Jan Baumbach, Fabio Vandin, Richard Röttger, Eudes Barbosa, Mingchui Dong, Morten Frost, Lene Christiansen and Qihua Tan. Differentially methylated genomic regions in birth-weight discordant twin pairs. Annals of human genetics 80(2): 81–87 (2016). Link.
  51. Vinicius AC Abreu, Sintia Almeida, Sandeep Tiwari, Syed Shah Hassan, Diego Mariano, Artur Silva, Jan Baumbach, Vasco Azevedo and Richard Röttger. CMRegNet – An interspecies reference database for corynebacterial and mycobacterial regulatory networks. BMC genomics 16(1): 1–10 (2015). Link.
  52. Christian Wiwie, Jan Baumbach and Richard Röttger. Comparing the performance of biomedical clustering methods. Nature methods 12(11): 1033–1038 (2015). Link.
  53. Jan Baumbach and Richard Röttger. Computational Integrative Biology–on the joint analysis of diverse biological data sets. Integrative Biology 6(11): 1008–1009 (2014). Link. Editorial.
  54. Duong Vu, Szániszló Szöke, Christian Wiwie, Jan Baumbach, Gianluigi Cardinali, Richard Röttger and Vincent Robert. Massive fungal biodiversity data re-annotation with multi-level clustering. Scientific Reports 4(1): 1–9 (2014). Link.
  55. Eudes Barbosa, Richard Röttger, Anne-Christin Hauschild, Vasco Azevedo and Jan Baumbach. On the limits of computational functional genomics for bacterial lifestyle prediction. Briefings in functional genomics 13(5): 398–408 (2014). Link.
  56. Goksel Misirli, Jennifer Hallinan, Richard Röttger, Jan Baumbach and Anil Wipat. BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. Journal of integrative bioinformatics 11(2): 106–119 (2014). Link.
  57. Peng Sun, Nora K Speicher, Richard Röttger, Jiong Guo and Jan Baumbach. Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering. Nucleic acids research 42(9): e78–e78 (2014). Link.
  58. Anderson R Santos, Vanessa Bastos Pereira, Eudes Barbosa, Jan Baumbach, Josch Pauling, Richard Röttger, Meritxell Zurita Turk, Artur Silva, Anderson Miyoshi and Vasco Azevedo. Mature Epitope Density-A strategy for target selection based on immunoinformatics and exported prokaryotic proteins. BMC genomics 14(6): 1–11 (2013). Link.
  59. Richard Röttger, Prabhav Kalaghatgi, Peng Sun, Siomar de Castro Soares, Vasco Azevedo, Tobias Wittkop and Jan Baumbach. Density parameter estimation for finding clusters of homologous proteins—tracing actinobacterial pathogenicity lifestyles. Bioinformatics 29(2): 215–222 (2013). Link.
  60. Josch Pauling, Richard Röttger, Andreas Neuner, Heladia Salgado, Julio Collado-Vides, Prabhav Kalaghatgi, Vasco Azevedo, Andreas Tauch, Alfred Pühler and Jan Baumbach. On the trail of EHEC/EAEC—unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. Integrative Biology 4(7): 728–733 (2012). Link.
  61. Richard Röttger, Ulrich Rückert, Jan Taubert and Jan Baumbach. How Little Do We Actually Know? – On the Size of Gene Regulatory Networks.. IEEE/ACM transactions on computational biology and bioinformatics/IEEE, ACM 9(5): 1293–1300 (2012). Link.
  62. Richard Röttger, Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop and Jan Baumbach. Online transitivity clustering of biological data with missing values. In German Conference on Bioinformatics 2012. (2012). Link.
  63. Josch Pauling, Richard Röttger, Andreas Tauch, Vasco Azevedo and Jan Baumbach. CoryneRegNet 6.0—Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Research 40(D1): D610–D614 (2012). Link.
  64. Tobias Wittkop, Sven Rahmann, Richard Röttger, Sebastian Böcker and Jan Baumbach. Extension and robustness of transitivity clustering for protein–protein interaction network analysis. Internet Mathematics 7(4): 255–273 (2011). Link.
  65. Fabian Kneißl, Richard Röttger, Uwe Sandner, Jan Marco Leimeister and Helmut Krcmar. All-i-touch as combination of nfc and lifestyle. In 2009 first international workshop on Near Field Communication. (2009): 51–55. Link.

Book Chapters

  1. Richard Röttger. Unsupervised Learning: Cluster Analysis. In Nataša Pržulj (eds): Analyzing Network Data in Biology and Medicine: An Interdisciplinary Textbook for Biological, Medical and Computational Scientists. Cambridge University Press. (2019).
  2. Lena Bernhofer, Tobias Neumaier, Richard Röttger and Siarhei Trushyn. Me Label - The online Fashion Boutique fo 2020. In Patrick Nepper, Nikolas Konrad (eds): The Future of Social Commerce. Center for Digital Technology & Management (CDTM). (2009).

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