Publications

Iris Divé, Jasmin a Schäfer, Katharina J Weber, Ali Yavuz Çakır, Nikita a Verheyden, Nadja I Lorenz, Seon-Ah Chong, Pia S Zeiner, Carmen Franiczek, Benedikt Sauer, Others (2026). Tumor-associated epilepsy and high expression of xCT shape the proteome of IDH-wildtype glioblastoma. Cell Death Discovery.

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Achim Hekler, Florian Buettner (2026). Toward trustworthy healthcare AI: designing academic research for translation readiness. Molecular Systems Biology.

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Julius C Enssle, Björn Häupl, Arber Qoku, Boya Wang, George W Wright, Sharon Barrans, Yulai Zhou, Matthew a Care, Cathy Burton, Caitlin Gribbin, Others (2026). Pathogenesis of diffuse large B cell lymphoma proteogenotypes. Cancer Cell.

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Arber Qoku, Tyra Stickel, Sareh AmeriFar, Thomas Oellerich, Sebastian Wolf, Florian Buettner (2026). PACMON: Pathway-guided Multi-Omics data integration for interpreting large-scale perturbation screens. bioRxiv.

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Lukas Kuhn, Giuseppe Serra, Florian Buettner (2026). Non-Contrastive Vision-Language Learning with Predictive Embedding Alignment. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Workshops.

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Alexander Koebler, Lukas Kuhn, Ingo Thon, Florian Buettner (2026). LVLM-Aided Alignment of Task-Specific Vision Models. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition.

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Kevin De Azevedo, Yusuf Berk Oruc, Florian Buettner (2026). Interpretable multi-omics integration across mixed-order tensors with MANTRA. Molecular Systems Biology.

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Thomas Decker, Volker Tresp, Florian Buettner (2026). Improving perturbation-based explanations by understanding the role of uncertainty calibration. Advances in Neural Information Processing Systems.

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Azza Jenane, Nassim Walha, Lukas Kuhn, Florian Buettner (2026). From Entropy to Calibrated Uncertainty: Training Language Models to Reason About Uncertainty. Proceedings of the AISTATS 2026 Workshop: Towards Trustworthy Predictions: Theory and Applications of Calibration for Modern AI.

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Nassim Walha, Sebastian G Gruber, Thomas Decker, Yinchong Yang, Alireza Javanmardi, Eyke Hüllermeier, Florian Buettner (2026). Fine-grained uncertainty decomposition in large language models: A spectral approach. Proceedings of the AAAI Conference on Artificial Intelligence.

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Giuseppe Serra, Ben Werner, Florian Buettner (2026). FedAgree: Label-Free Performance Estimation under Distribution Shift for Federated Medical Analysis. The 29th International Conference on Medical Image Computing and Computer Assisted Intervention.

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Sebastian G. Gruber, Nassim Walha, Francis Bach, Florian Buettner (2026). Eigenvalue Calibration for Semantic Embeddings of Large Language Models. arXiv.

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Zahra Moslehi, Sareh AmeriFar, Kevin De Azevedo, Florian Buettner (2025). Learning interpretable representations of single-cell multi-omics data with multi-output Gaussian processes. Nucleic Acids Research.

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Alexander Koebler, Thomas Decker, Ingo Thon, Volker Tresp, Florian Buettner (2025). Incremental Uncertainty-aware Performance Monitoring with Active Labeling Intervention. Proceedings of The 28th International Conference on Artificial Intelligence and Statistics.

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Arber Qoku, Martin Rohbeck, Florin C Walter, Ilia Kats, Oliver Stegle, Florian Buettner (2025). MOFA-FLEX: A Factor Model Framework for Integrating Omics Data with Prior Knowledge. bioRxiv.

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Sarmad Ahmad Khan, Simon Bernatz, Zahra Moslehi, Florian Buettner (2025). Machine Learning based Analysis for Radiomics Features Robustness in Real-World Deployment Scenarios. arXiv.

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Giuseppe Serra, Ben Werner, Florian Buettner (2025). How to Leverage Predictive Uncertainty Estimates for Reducing Catastrophic Forgetting in Online Continual Learning. Transactions on Machine Learning Research.

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Giuseppe Serra, Florian Buettner (2025). Federated Continual Learning Goes Online: Uncertainty-Aware Memory Management for Vision Tasks and Beyond. The Thirteenth International Conference on Learning Representations.

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Lukas Kuhn, Sari Sadiya, J"org Schl"otterer, Florian Buettner, Christin Seifert, Gemma Roig (2025). Efficient Unsupervised Shortcut Learning Detection and Mitigation in Transformers. Proceedings of the IEEE/CVF International Conference on Computer Vision.

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Alexandra Geßner, Akanksha Jolly, Tessa P Sijmonsma, Yannick Matthess, Manuel Kaulich, Stephan G"unther, Florian Buettner, Others (2025). Differentiation hierarchy in adult B cell acute lymphoblastic leukemia at clonal resolution. bioRxiv.

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Mariano Ruz Jurado, David Rodriguez Morales, Elijah Genetzakis, Fatemeh Behjati Ardakani, Lukas Zanders, Ariane Fischer, Florian Buettner, Marcel H Schulz, Stefanie Dimmeler, David John (2025). Decoding heart failure subtypes with neural networks via differential explanation analysis. Briefings in Bioinformatics.

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Giuseppe Serra, Florian Buettner (2025). DATS: Distance-Aware Temperature Scaling for Calibrated Class-Incremental Learning. arXiv.

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Sarmad Ahmad Khan, Dominik Faerber, Danielle Kirkey, Simon Raffel, Brian Hadland, Michael Deininger, Florian Buettner, Others (2025). Cross-Species Morphology Learning Enables Nucleic Acid-Independent Detection of Live Mutant Blood Cells. bioRxiv.

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Achim Hekler, Lukas Kuhn, Florian Buettner (2025). Beyond Overconfidence: Foundation Models Redefine Calibration in Deep Neural Networks. arXiv.

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Tim J Adler, Jan-Hinrich Nölke, Annika Reinke, Minu Dietlinde Tizabi, Sebastian Gruber, Dasha Trofimova, Lynton Ardizzone, Paul F Jaeger, Florian Buettner, Ullrich Köthe, Others (2025). Application-driven validation of posteriors in inverse problems. Medical Image Analysis.

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Lukas Kuhn, Florian Buettner (2025). An autonomous agent for auditing and improving the reliability of clinical AI models. arXiv.

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Kevin De Azevedo, Florian Buettner (2024). Unified Analysis of Multi-order Tensors for Integrative Molecular Profiling. bioRxiv.

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Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Acion, Michela Antonelli, Others (2024). Understanding metric-related pitfalls in image analysis validation. Nature methods.

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Alexander Koebler, Christian Greisinger, Jan Paulus, Ingo Thon, Florian Buettner (2024). Through the Eyes of the Expert: Aligning Human and Machine Attention for Industrial AI. International Conference on Human-Computer Interaction.

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Thomas Decker, Ananta R Bhattarai, Jindong Gu, Volker Tresp, Florian Buettner (2024). Provably Better Explanations with Optimized Aggregation of Feature Attributions. International Conference on Machine Learning.

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Alexander Koebler, Ingo Thon, Florian Buettner (2024). MoRE-LLM: Mixture of Rule Experts Guided by a Large Language Model. 2024 IEEE International Conference on Data Mining (ICDM).

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Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Others (2024). Metrics reloaded: recommendations for image analysis validation. Nature methods.

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Edwin Alvarez-Mamani, Florian Buettner, Cesar a Beltran-Castanon, Alfredo J Ibanez (2024). Exploratory analysis of metabolic changes using mass spectrometry data and graph embeddings. Scientific reports.

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Thomas Decker, Alexander Koebler, Michael Lebacher, Ingo Thon, Volker Tresp, Florian Buettner (2024). Explanatory Model Monitoring to Understand the Effects of Feature Shifts on Performance. Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining.

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Xudong Sun, Christian Feistner, Alexander Gossmann, Gabriele Schwarz, Raja Muhammad Umer, Lukas Beer, Florian Buettner, Others (2024). DomainLab: A modular Python package for domain generalization in deep learning. arXiv.

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Sebastian G Gruber, Pascal Tobias Ziegler, Florian Buettner (2024). Disentangling Mean Embeddings for Better Diagnostics of Image Generators. arXiv preprint arXiv:2409.01314.

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Teodora Popordanoska, Sebastian Gregor Gruber, Aleksei Tiulpin, Florian Buettner, Matthew B Blaschko (2024). Consistent and Asymptotically Unbiased Estimation of Proper Calibration Errors. International Conference on Artificial Intelligence and Statistics.

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Sebastian Gregor Gruber, Florian Buettner (2024). A Bias-Variance-Covariance Decomposition of Kernel Scores for Generative Models. International Conference on Machine Learning.

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Sebastian Gruber, Florian Buettner (2023). Uncertainty Estimates of Predictions via a General Bias-Variance Decomposition. International Conference on Artificial Intelligence and Statistics.

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Achim Hekler, Titus J Brinker, Florian Buettner (2023). Test Time Augmentation Meets Post-hoc Calibration: Uncertainty Quantification under Real-World Conditions. Proceedings of the AAAI Conference on Artificial Intelligence.

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Arber Qoku, Nikoletta Katsaouni, Nadine Flinner, Florian Buettner, Marcel H Schulz (2023). Multimodal analysis methods in predictive biomedicine. Computational and structural biotechnology journal.

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Arber Qoku, Florian Buettner (2023). Encoding domain knowledge in multi-view latent variable models: A bayesian approach with structured sparsity. International Conference on Artificial Intelligence and Statistics.

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Maria Destito, Paolo Zaffino, J Sabatino, C Critelli, Arber Qoku, Florian Buettner, Salvatore De Rosa, Others (2023). Deep Learning Model for Video-Classification of Echocardiography Images. 2023 IEEE International Conference on Metrology for eXtended Reality, Artificial Intelligence and Neural Engineering (MetroXRAINE).

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Ashok Kumar Jayavelu, Sebastian Wolf, Florian Buettner, Gabriela Alexe, Björn Häupl, Federico Comoglio, Constanze Schneider, Carmen Doebele, Dominik C Fuhrmann, Sebastian Wagner, Others (2022). The proteogenomic subtypes of acute myeloid leukemia. Cancer Cell.

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Fernando Anjos-Afonso, Florian Buettner, Syed a Mian, Hefin Rhys, Jimena Perez-Lloret, Manuel Garcia-Albornoz, Namrata Rastogi, Linda Ariza-McNaughton, Dominique Bonnet (2022). Single cell analyses identify a highly regenerative and homogenous human CD34+ hematopoietic stem cell population. Nature communications.

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Adele M Nicolas, Marina Pesic, Esther Engel, Paul K Ziegler, Markus Diefenhardt, Kilian B Kennel, Florian Buettner, Claire Conche, Valentina Petrocelli, Eiman Elwakeel, Others (2022). Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer. Cancer Cell.

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Sebastian Gruber, Florian Buettner (2022). Better uncertainty calibration via proper scores for classification and beyond. Advances in Neural Information Processing Systems.

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Christian Tomani, Florian Buettner (2021). Towards trustworthy predictions from deep neural networks with fast adversarial calibration. Thirty-Fifth AAAI Conference on Artificial Intelligence.

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Christian Tomani, Daniel Cremers, Florian Buettner (2021). Parameterized Temperature Scaling for Boosting the Expressive Power in Post-Hoc Uncertainty Calibration. arXiv preprint arXiv:2102.12182.

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Yinchong Yang, Florian Buettner (2021). Multi-output Gaussian Processes for uncertainty-aware recommender systems. Uncertainty in Artificial Intelligence.

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Xudong Sun, Florian Buettner (2021). Hierarchical Domain Invariant Variational Auto-Encoding with weak domain supervision. arXiv preprint arXiv:2101.09436.

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Yushan Liu, Markus M. Geipel, Christoph Tietz, Florian Buettner (2020). TIMELY: Improving Labeling Consistency in Medical Imaging for Cell Type Classification. arXiv preprint arXiv:2007.05307.

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Anna SE Cuomo, Daniel D. Seaton, Davis J. McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner (2020). Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression. Nature communications.

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Christian Tomani, Sebastian Gruber, Muhammed Ebrar Erdem, Daniel Cremers, Florian Buettner (2020). Post-hoc Uncertainty Calibration for Domain Drift Scenarios. arXiv preprint arXiv:2012.10988.

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Ricard Argelaguet, Hisham Mohammed, Stephen J. Clark, L. Carine Stapel, Christel Krueger, Chantriolnt-Andreas Kapourani, Yunlong Xiang, Courtney Hanna, Sebastien Smallwood, Ximena Ibarra-Soria (2019). Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification. BioRxiv.

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Julia Tischler, Wolfram H. Gruhn, John Reid, Edward Allgeyer, Florian Buettner, Carsten Marr, Fabian Theis, Ben D. Simons, Lorenz Wernisch, M. Azim Surani (2019). Metabolic regulation of pluripotency and germ cell fate through α-ketoglutarate. The EMBO journal.

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Pankaj Gupta, Yatin Chaudhary, Florian Buettner, Hinrich Schütze (2019). Document informed neural autoregressive topic models with distributional prior. Proceedings of the AAAI Conference on Artificial Intelligence.

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Ben GL Vanneste, Florian Buettner, Michael Pinkawa, Philippe Lambin, Aswin L. Hoffmann (2019). Ano-rectal wall dose-surface maps localize the dosimetric benefit of hydrogel rectum spacers in prostate cancer radiotherapy. Clinical and translational radiation oncology.

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Pankaj Gupta, Yatin Chaudhary, Florian Buettner, Hinrich Schütze (2018). Texttovec: Deep contextualized neural autoregressive topic models of language with distributed compositional prior. arXiv preprint arXiv:1810.03947.

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Pankaj Gupta, Yatin Chaudhary, Florian Buettner, Hinrich Schütze (2018). texttovec: Deep contextualized neural autoregressive models of language with distributed compositional prior. Preprint arxiv.

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Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C. Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle (2018). Multi-Omics Factor Analysis—a framework for unsupervised integration of multi-omics data sets. Molecular systems biology.

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Pankaj Gupta, Florian Buettner, Hinrich Schütze (2018). Document informed neural autoregressive topic models. arXiv preprint arXiv:1808.03793.

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Hubert S. Gabryś, Florian Buettner, Florian Sterzing, Henrik Hauswald, Mark Bangert (2018). Design and selection of machine learning methods using radiomics and dosiomics for normal tissue complication probability modeling of xerostomia. Frontiers in oncology.

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Nina Cabezas-Wallscheid, Florian Buettner, Pia Sommerkamp, Daniel Klimmeck, Luisa Ladel, Frederic B. Thalheimer, Daniel Pastor-Flores, Leticia P. Roma, Simon Renders, Petra Zeisberger (2017). Vitamin A-retinoic acid signaling regulates hematopoietic stem cell dormancy. Cell.

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Felix Buggenthin, Florian Buettner, Philipp S. Hoppe, Max Endele, Manuel Kroiss, Michael Strasser, Michael Schwarzfischer, Dirk Loeffler, Konstantinos D. Kokkaliaris, Oliver Hilsenbeck (2017). Prospective identification of hematopoietic lineage choice by deep learning. Nature methods.

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Hubert Szymon Gabryś, Florian Buettner, Florian Sterzing, Henrik Hauswald, Mark Bangert (2017). Parotid gland mean dose as a xerostomia predictor in low-dose domains. Acta Oncologica.

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Florian Buettner, Kyle Jay, Harry Wischnewski, Thomas Stadelmann, Shady Saad, Konstantins Jefimovs, Madina Mansurova, Juan Gerez, Claus M. Azzalin, Reinhard Dechant (2017). Non-targeted metabolomic approach reveals two distinct types of metabolic responses to telomerase dysfunction in S. cerevisiae. Metabolomics.

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Florian Buettner, Naruemon Pratanwanich, Davis J. McCarthy, John C. Marioni, Oliver Stegle (2017). f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq. Genome biology.

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Thomas Blasi, Florian Buettner, Michael K. Strasser, Carsten Marr, Fabian J. Theis (2017). cgcorrect: a method to correct for confounding cell–cell variation due to cell growth in single-cell transcriptomics. Physical biology.

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Anne-Kristin Heninger, Anne Eugster, Denise Kuehn, Florian Buettner, Matthias Kuhn, Annett Lindner, Sevina Dietz, Sibille Jergens, Carmen Wilhelm, Andreas Beyerlein (2017). A divergent population of autoantigen-responsive CD4+ T cells in infants prior to β cell autoimmunity. Science translational medicine.

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Michael Laimighofer, J. A. N. Krumsiek, Florian Buettner, Fabian J. Theis (2016). Unbiased prediction and feature selection in high-dimensional survival regression. Journal of Computational Biology.

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Philipp Angerer, Laleh Haghverdi, Maren Büttner, Fabian J. Theis, Carsten Marr, Florian Buettner (2016). destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics.

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Jason CH Tsang, Yong Yu, Shannon Burke, Florian Buettner, Cui Wang, Aleksandra A. Kolodziejczyk, Sarah A. Teichmann, Liming Lu, Pentao Liu (2015). Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells. Genome biology.

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Steffen Sass, Florian Buettner, Nikola S. Mueller, Fabian J. Theis (2015). RAMONA: a Web application for gene set analysis on multilevel omics data. Bioinformatics.

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Ezio Bonifacio, Anette-G. Ziegler, Georgeanna Klingensmith, Edith Schober, Polly J. Bingley, Marietta Rottenkolber, Anke Theil, Anne Eugster, Ramona Puff, Claudia Peplow (2015). Effects of high-dose oral insulin on immune responses in children at high risk for type 1 diabetes: the Pre-POINT randomized clinical trial. Jama.

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Laleh Haghverdi, Florian Buettner, Fabian J. Theis (2015). Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics.

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Victoria Moignard, Steven Woodhouse, Laleh Haghverdi, Andrew J. Lilly, Yosuke Tanaka, Adam C. Wilkinson, Florian Buettner, Iain C. Macaulay, Wajid Jawaid, Evangelia Diamanti (2015). Decoding the regulatory network of early blood development from single-cell gene expression measurements. Nature biotechnology.

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Antonio Scialdone, Kedar N. Natarajan, Luis R. Saraiva, Valentina Proserpio, Sarah A. Teichmann, Oliver Stegle, John C. Marioni, Florian Buettner (2015). Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods.

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Florian Buettner, Kedar N. Natarajan, F. Paolo Casale, Valentina Proserpio, Antonio Scialdone, Fabian J. Theis, Sarah A. Teichmann, John C. Marioni, Oliver Stegle (2015). Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nature biotechnology.

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Nicola K. Wilson, David G. Kent, Florian Buettner, Mona Shehata, Iain C. Macaulay, Fernando J. Calero-Nieto, Manuel Sánchez Castillo, Caroline A. Oedekoven, Evangelia Diamanti, Reiner Schulte (2015). Combined single-cell functional and gene expression analysis resolves heterogeneity within stem cell populations. Cell stem cell.

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M. A. Ebert, S. L. Gulliford, F. Buettner, Kerwyn Foo, A. Haworth, A. Kennedy, D. J. Joseph, J. W. Denham (2014). Two non-parametric methods for derivation of constraints from radiotherapy dose–histogram data. Physics in Medicine & Biology.

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Florian Buettner, Victoria Moignard, Berthold Göttgens, Fabian J. Theis (2014). Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data. Bioinformatics.

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A. Mareike Schmidt, Stephan R. Fagerer, Konstantins Jefimovs, Florian Buettner, Christian Marro, Erdem C. Siringil, Karl L. Boehlen, Martin Pabst, Alfredo J. Ibáñez (2014). Molecular phenotypic profiling of a Saccharomyces cerevisiae strain at the single-cell level. Analyst.

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Christiane Winkler, Jan Krumsiek, Florian Buettner, Christof Angermüller, Eleni Z. Giannopoulou, Fabian J. Theis, Anette-Gabriele Ziegler, Ezio Bonifacio (2014). Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes. Diabetologia.

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Victoria Moignard, Iain C. Macaulay, Gemma Swiers, Florian Buettner, Judith Schütte, Fernando J. Calero-Nieto, Sarah Kinston, Anagha Joshi, Rebecca Hannah, Fabian J. Theis (2013). Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. Nature cell biology.

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Steffen Sass, Florian Buettner, Nikola S. Mueller, Fabian J. Theis (2013). A modular framework for gene set analysis integrating multilevel omics data. Nucleic acids research.

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Florian Buettner, Sarah L. Gulliford, Steve Webb, Matthew R. Sydes, David P. Dearnaley, Mike Partridge (2012). The dose–response of the anal sphincter region–an analysis of data from the MRC RT01 trial. Radiotherapy and Oncology.

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Florian Buettner, Aisha B. Miah, Sarah L. Gulliford, Emma Hall, Kevin J. Harrington, Steve Webb, Mike Partridge, Christopher M. Nutting (2012). Novel approaches to improve the therapeutic index of head and neck radiotherapy: an analysis of data from the PARSPORT randomised phase III trial. Radiotherapy and Oncology.

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Florian Buettner, Fabian J. Theis (2012). A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst. Bioinformatics.

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Florian Buettner, Sarah L. Gulliford, Steve Webb, Mike Partridge (2011). Modeling late rectal toxicities based on a parameterized representation of the 3D dose distribution. Physics in Medicine & Biology.

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F. Buettner, S. L. Gulliford, S. Webb, M. Partridge (2010). Using Bayesian logistic regression to evaluate a new type of dosimetric constraint for prostate radiotherapy treatment planning. Medical physics.

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Florian Buettner, Sarah L. Gulliford, Steve Webb, Mike Partridge (2009). Using dose-surface maps to predict radiation-induced rectal bleeding: a neural network approach. Physics in Medicine & Biology.

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Florian Buettner, Sarah L. Gulliford, Steve Webb, Matthew R. Sydes, David P. Dearnaley, Mike Partridge (2009). Assessing correlations between the spatial distribution of the dose to the rectal wall and late rectal toxicity after prostate radiotherapy: an analysis of data from the MRC RT01 trial (ISRCTN 47772397). Physics in Medicine & Biology.

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Joao Seco, Greg C. Sharp, Ziji Wu, David Gierga, Florian Buettner, Harald Paganetti (2008). Dosimetric impact of motion in free-breathing and gated lung radiotherapy: A 4D Monte Carlo study of intrafraction and interfraction effects. Medical physics.

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Giovanni Volpe, Gajendra P. Singh, Florian Buettner, Anna M. Drets, Dmitri v. Petrov (2006). Optical trapping dynamics for cell identification. Optical Trapping and Optical Micromanipulation III.

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