Publications
- Privacy of federated QR decomposition using additive secure multiparty computation. IEEE Transactions on Information Forensics and Security (2023). Link. and .
- Julian Matschinske, Julian Späth, Mohammad Bakhtiari, Niklas Probul, Kazemi Majdabadi MM, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, The FeatureCloud Platform for Federated Learning in Biomedicine: Unified Approach. Journal of Medical Internet Research 25: e42621–e42621 (2023). Link. , Balazs-Attila Orban, Sándor-József Fejér and others.
- Dženan Mašić, Kristian Stengaard-Pedersen, Brian Bridal Løgstrup, Kim Hørslev-Petersen, Merete Lund Hetland, Peter Junker, Mikkel Østergaard, Claus Henrik Nielsen, Mogens Kruhøffer, 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. and others.
- Variance Analysis of LC-MS Experimental Factors and Their Impact on Machine Learning. bioRxiv: 2023–05 (2023). Link. , Konrad Krawczyk, Simon Gregersen Echers, Paolo Marcatili, Pawel Palczynski, Richard Roettger and Veit Schwaemmle.
- Eline Sandvig Andersen, Claus Østergaard, POCT urine dipstick versus central laboratory analyses: Diagnostic performance and logistics in the medical emergency department. Clinical Biochemistry 111: 17–25 (2023). , Anne Friesgaard Christensen, Ivan Brandslund and Claus Lohman Brasen.
- 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.
- Maria L Elkjaer, Lukas Simon, Hypothesis of a potential BrainBiota and its relation to CNS autoimmune inflammation. Frontiers in Immunology 13 (2022). Link. , Lisa-Marie Bente, Tim Kacprowski, Mads Thomassen, Richard Reynolds, Jan Baumbach, and Zsolt Illes.
- 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 beed published with the full proceedings with Springer.
- Privacy of federated QR decomposition using additive secure multiparty computation. arXiv preprint arXiv:2210.06163 (2022). Link. and .
- Medical data safety via federated machine learning. In RExPO22 Conference. (2022). Link. , Reza Nasirigerdeh, Jan Bamubach, David Benjamin Blumenthal, Tim Kacprowski and .
- 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. , Michael Sloth, Peter Schneider-Kamp and .
- 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.
- Federated singular value decomposition for high dimensional data. arXiv preprint arXiv:2205.12109 (2022). Link. , and David B Blumenthal.
- Federated Horizontally Partitioned Principal Component Analysis for Biomedical Applications. Bioinformatics Advances (2022). Link. and .
- Tim Daniel Rose, Thibault Bechtler, Octavia-Andreea Ciora, Kim Anh Lilian Le, Florian Molnar, Nikolai Koehler, Jan Baumbach, MoSBi: Automated signature mining for molecular stratification and subtyping. Proceedings of the National Academy of Sciences 119(16): e2118210119 (2022). Link. and Josch Konstantin Pauling.
- Maria Louise Elkjær, A systematic review of tissue and single cell transcriptome/proteome studies of the brain in multiple sclerosis. Frontiers in Immunology 13: 524 (2022). Link. , Jan Baumbach and Zsolt Illes.
- MS2AI: Automated repurposing of public peptide LC-MS data for machine learning applications. Bioinformatics 38(3): 875–877 (2022). Link. , Konrad Krawczyk, , Veit Schwämmle and .
- Federated Principal Component Analysis for Genome-Wide Association Studies. In 2021 IEEE International Conference on Data Mining (ICDM). (2021): 1090–1095. Link. , Reza Nasirigerdeh, David B Blumenthal and .
- 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, The AIMe registry for artificial intelligence in biomedical research. Nature methods 18(10): 1128–1131 (2021). Link. , 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.
- 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, 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. , Mogens Kruhøffer, Julian R Marchesi, Karsten Kristiansen, Robin Christensen and Torkell Ellingsen.
- Konrad Krawczyk, Tadeusz Chelkowski, Daniel J Laydon, Swapnil Mishra, Denise Xifara, Seth Flaxman, Thomas Mellan, Veit Schwämmle, 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. , Johannes T Hadsund and Samir Bhatt.
- Julian Matschinske, Julian Späth, Reza Nasirigerdeh, Reihaneh Torkzadehmahani, The FeatureCloud AI Store for Federated Learning in Biomedicine and Beyond. arXiv preprint arXiv:2105.05734 (2021). Link. , Balázs Orbán, Sándor Fejér, Olga Zolotareva, Mohammad Bakhtiari, Béla Bihari, Marcus Bloice, Nina C Donner, Walid Fdhila, , 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, , Anna Saranti, Harald HHW Schmidt, Christof Tschohl, Nina K Wenke and Jan Baumbach.
- Enabling single-cell trajectory network enrichment. Nature Computational Science 1(2): 153–163 (2021). Link. , Mhaned Oubounyt, Kristiyan Kanev, Jesper Lund, Tim Kacprowski, Dietmar Zehn, and Jan Baumbach.
- MS2AI: Automated repurposing of public peptide LC-MS data for machine learning applications. bioRxiv (2021). Link. This paper has now beed published with Bioinformatics. , Konrad Krawczyk, , Veit Schwämmle and .
- Maria L Elkjaer, Unbiased examination of genome-wide human endogenous retrovirus transcripts in MS brain lesions. Multiple Sclerosis Journal: 1352458520987269 (2021). Link. , , , Richard Reynolds, Jan Baumbach and Zsolt Illes.
- Tim Daniel Rose, Thibault Bechtler, Octavia-Andreea Ciora, Kim Anh Lilian Le, Florian Molnar, Nikolai Koehler, Jan Baumbach, MoSBi: Automated signature mining for molecular stratification and subtyping. bioRxiv (2021). Link. and Josch Konstantin Pauling.
- Reihaneh Torkzadehmahani, Reza Nasirigerdeh, David B Blumenthal, Tim Kacprowski, Markus List, Julian Matschinske, Julian Späth, Nina Kerstin Wenke, Béla Bihari, Privacy-preserving Artificial Intelligence Techniques in Biomedicine. arXiv preprint arXiv:2007.11621 (2020). Link. , , Anne-Christin Hausschild, Dominik Heider, Andreas Holzinger, Walter Hötzendorfer, Markus Kastelitz, Rudolf Mayer, Cristian Nogales, Anastasia Pustozerova, , Harald H.H.W. Schmidt, Ameli Schwalber, Christof Tschohl, Andrea Wohner 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. , Mhaned Oubounyt, Kristiyan Kanev, Jesper Lund, Tim Kacprowski, Dietmar Zehn, and Jan Baumbach.
- Konrad Krawczyk, Tadeusz Chelkowski, Daniel J Laydon, Swapnil Mishra, Denise Xifara, Seth Flaxman, Thomas Mellan, Veit Schwämmle, 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. , Johannes T Hadsund and Samir Bhatt.
- TiCoNE 2: A Composite Clustering Model for Robust Cluster Analyses on Noisy Data. arXiv preprint arXiv:1904.12353 (2019). Link. , and Jan Baumbach.
- Alexander Rauch, Anders K Haakonsson, Jesper GS Madsen, Mette Larsen, Isabel Forss, Martin R Madsen, Elvira L Van Hauwaert, 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. , Naja Z Jespersen, Michaela Tencerova, Ronni Nielsen, Bjørk D Larsen, , Jan Baumbach, Camilla Scheele, Moustapha Kassem and Susanne Mandrup.
- Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets. Systems Medicine 2(1): 1–9 (2019). Link. , Irina Kuznetsova, Ahmed Mostafa, Alexander Rauch, Anders Haakonsson, Inigo Barrio-Hernandez, Blagoy Blagoev, Susanne Mandrup, Harald HHW Schmidt, Stephan Pleschka, and Jan Baumbach.
- Simon J Larsen, E. coli gene regulatory networks are inconsistent with gene expression data. Nucleic acids research 47(1): 85–92 (2019). Link. , Harald H H W Schmidt and Jan Baumbach.
- Guiding biomedical clustering with ClustEval. Nature protocols 13(6): 1429–1444 (2018). Link. , Jan Baumbach and .
- 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, The druggable pocketome of Corynebacterium diphtheriae: A new approach for in silico putative druggable targets. Frontiers in genetics 9: 44 (2018). Link. , Adrián G Turjanski and Vasco AC Azevedo.
- 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. , Jonatan Gøttcke, , Qihua Tan 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. , Alexander Rauch, Anders Haakonsson, Inigo Barrio-Hernandez, Blagoy Blagoev, Susanne Mandrup, and Jan Baumbach.
- 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, An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PLoS One 12(10): e0186401 (2017). Link. , Jan Baumbach and Vasco AC Azevedo.
- Eudes Barbosa, LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. Journal of integrative bioinformatics 14(2) (2017). Link. , Anne-Christin Hauschild, Siomar Castro Soares, Sebastian Böcker, Vasco Azevedo and Jan Baumbach.
- Diogo Almeida, Ida Skov, Artur Silva, Fabio Vandin, Qihua Tan, Efficient detection of differentially methylated regions using DiMmeR. Bioinformatics 33(4): 549–551 (2017). Link. and Jan Baumbach.
- On the Power and Limits of Sequence Similarity Based Clustering of Proteins Into Families. In Pacific Symposium on Biocomputing 2017. (2017): 39–50. Link. and .
- 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 In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks. BMC systems biology 10(1): 1–9 (2016). Link. .
- Diogo Almeida, Ida Skov, Jesper Lund, Afsaneh Mohammadnejad, Artur Silva, Fabio Vandin, Qihua Tan, Jan Baumbach and 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. .
- Clustering of biological datasets in the era of big data. Journal of integrative bioinformatics 13(1): 52–81 (2016). Link. .
- Mubo Chen, Jan Baumbach, Fabio Vandin, Differentially methylated genomic regions in birth-weight discordant twin pairs. Annals of human genetics 80(2): 81–87 (2016). Link. , Eudes Barbosa, Mingchui Dong, Morten Frost, Lene Christiansen and Qihua Tan.
- Vinicius AC Abreu, Sintia Almeida, Sandeep Tiwari, Syed Shah Hassan, Diego Mariano, Artur Silva, Jan Baumbach, Vasco Azevedo and CMRegNet – An interspecies reference database for corynebacterial and mycobacterial regulatory networks. BMC genomics 16(1): 1–10 (2015). Link. .
- Comparing the performance of biomedical clustering methods. Nature methods 12(11): 1033–1038 (2015). Link. , Jan Baumbach and .
- Jan Baumbach and Computational Integrative Biology–on the joint analysis of diverse biological data sets. Integrative Biology 6(11): 1008–1009 (2014). Link. Editorial. .
- Duong Vu, Szániszló Szöke, Massive fungal biodiversity data re-annotation with multi-level clustering. Scientific Reports 4(1): 1–9 (2014). Link. , Jan Baumbach, Gianluigi Cardinali, and Vincent Robert.
- Eudes Barbosa, On the limits of computational functional genomics for bacterial lifestyle prediction. Briefings in functional genomics 13(5): 398–408 (2014). Link. , Anne-Christin Hauschild, Vasco Azevedo and Jan Baumbach.
- Goksel Misirli, Jennifer Hallinan, BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species. Journal of integrative bioinformatics 11(2): 106–119 (2014). Link. , Jan Baumbach and Anil Wipat.
- Peng Sun, Nora K Speicher, Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering. Nucleic acids research 42(9): e78–e78 (2014). Link. , Jiong Guo and Jan Baumbach.
- Anderson R Santos, Vanessa Bastos Pereira, Eudes Barbosa, Jan Baumbach, Josch Pauling, Mature Epitope Density-A strategy for target selection based on immunoinformatics and exported prokaryotic proteins. BMC genomics 14(6): 1–11 (2013). Link. , Meritxell Zurita Turk, Artur Silva, Anderson Miyoshi and Vasco Azevedo.
- Density parameter estimation for finding clusters of homologous proteins—tracing actinobacterial pathogenicity lifestyles. Bioinformatics 29(2): 215–222 (2013). Link. , Prabhav Kalaghatgi, Peng Sun, Siomar de Castro Soares, Vasco Azevedo, Tobias Wittkop and Jan Baumbach.
- Josch Pauling, 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. , Andreas Neuner, Heladia Salgado, Julio Collado-Vides, Prabhav Kalaghatgi, Vasco Azevedo, Andreas Tauch, Alfred Pühler 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. , Ulrich Rückert, Jan Taubert and Jan Baumbach.
- Online transitivity clustering of biological data with missing values. In German Conference on Bioinformatics 2012. (2012). Link. , Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop and Jan Baumbach.
- Josch Pauling, 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. , Andreas Tauch, Vasco Azevedo and Jan Baumbach.
- Tobias Wittkop, Sven Rahmann, Extension and robustness of transitivity clustering for protein–protein interaction network analysis. Internet Mathematics 7(4): 255–273 (2011). Link. , Sebastian Böcker and Jan Baumbach.
- Fabian Kneißl, All-i-touch as combination of nfc and lifestyle. In 2009 first international workshop on Near Field Communication. (2009): 51–55. Link. , Uwe Sandner, Jan Marco Leimeister and Helmut Krcmar.