DQBM Publications
2022
Bernd Bodenmiller
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Publications
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Vaccination with designed neopeptides induces intratumoral, cross-reactive CD4+ T cell responses in glioblastoma. Clinical Cancer Research, 28(24):5368-5382.
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Single-cell genomic variation induced by mutational processes in cancer. Nature, 612(7938):106-115.
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scQUEST: Quantifying tumor ecosystem heterogeneity from mass or flow cytometry data. STAR Protocols, 3(3):101578.
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T-cell recovery and evidence of persistent immune activation 12 months after severe COVID-19. Allergy, 77(8):2468-2481.
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A shared disease-associated oligodendrocyte signature among multiple CNS pathologies. Nature Neuroscience, 25(7):876-886.
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Breast tumor microenvironment structures are associated with genomic features and clinical outcome. Nature Genetics, 54(5):660-669.
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Single-cell proteomics defines the cellular heterogeneity of localized prostate cancer. Cell Reports Medicine, 3(4):100604.
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Acquired resistance to anti-PD1 therapy in patients with NSCLC reveals changes in T cell phenotypes and MET amplification. bioRxiv 487590v1, Cold Spring Harbor Laboratory.
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Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. Science Immunology, 7(70):eabk1692.
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Optimizing multiplexed imaging experimental design through tissue spatial segregation estimation. bioRxiv 470262, Cold Spring Harbor Laboratory.
Nicole Joller
ZORA Publication List
Publications
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Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity. Genes and immunity:183-195.
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Nematode microRNAs can Individually Regulate Interferon Regulatory Factor 4 and mTOR in Differentiating T Helper 2 Lymphocytes and Modulate Cytokine Production in Macrophages. Frontiers in Molecular Biosciences, 9:909312.
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Alkali therapy protects renal function, suppresses inflammation, and improves cellular metabolism in kidney disease. Clinical Science, 136(8):557-577.
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Moving to the Outskirts: Interplay Between Regulatory T Cells and Peripheral Tissues. Frontiers in Immunology, 13:864628.
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Dampening antiviral immunity can protect the host. FEBS Journal, 289(3):634-646.
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Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity. bioRxiv 479381, Cold Spring Harbor Laboratory.
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Microbiota colonization tunes the antigen threshold of microbiota-specific T cell activation in the gut. bioRxiv 501979, Cold Spring Harbor Laboratory.
Michael Krauthammer
ZORA Publication List
Publications
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Live slow-frozen human tumor tissues viable for 2D, 3D, ex vivo cultures and single-cell RNAseq. Communications Biology, 5:1144.
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ROS induction as a strategy to target persister cancer cells with low metabolic activity in NRAS mutated melanoma. bioRxiv 512839, Cold Spring Harbor Laboratory.
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Drug prescription clusters in the UK Biobank: An assessment of drug-drug interactions and patient outcomes in a large patient cohort. ArXiv.org 2207.08665, Cornell University.
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A versatile computational pipeline for the preprocessing of cell-free DNA fragmentation data. Cancer Research 82, University of Zurich.
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Abstract 1912: A versatile computational pipeline for the preprocessing of cell-free DNA fragmentation data. Cancer Research, 82(12_Supplem):1912.
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An empirical study of the effect of background data size on the stability of SHapley Additive exPlanations (SHAP) for deep learning models. ArXiv.org 2204.11351, Cornell University.
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AI support for ethical decision-making around resuscitation: proceed with care. Journal of Medical Ethics, 48(3):175-183.
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The Use and Ethics of Digital Twins in Medicine. Journal of Law, Medicine & Ethics, 50(3):583-596.
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Neue Lernziele für das Medizinstudium erarbeitet. In: Neue Lernziele für das Medizinstudium erarbeitet, 2022, 98-101.
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DDoS: A Graph Neural Network based Drug Synergy Prediction Algorithm. ArXiv.org 2210.00802, Cornell University.
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Approach for Named Entity Recognition and Case Identification Implemented by ZuKyo-JA Sub-team at the NTCIR-16 Real-MedNLP Task. In: NTCIR 16 Conference: Proceedings of the 16th NTCIR Conference on Evaluation of Information Access Technologies, Tokyo, Japan, 14 Juni 2022 - 17 Juni 2022, 322-329.
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Leveraging Token-Based Concept Information and Data Augmentation in Few-Resource NER: ZuKyo-EN at the NTCIR-16 Real-MedNLP task. In: NTCIR 16 Conference: Proceedings of the 16th NTCIR Conference on Evaluation of Information Access Technologies, Tokyo, Japan, 14 Juni 2022 - 17 Juni 2022, NTCIR.
Rolf Kümmerli
ZORA Publication List
Publications
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Collective decision-making in Pseudomonas aeruginosa involves transient segregation of quorum-sensing activities across cells. Current Biology, 32(24):5250-5261.e6.
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Coordination of siderophore gene expression among clonal cells of the bacterium Pseudomonas aeruginosa. Communications Biology, 5(1):545.
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Enforced specialization fosters mutual cheating and not division of labour in the bacterium Pseudomonas aeruginosa. Journal of Evolutionary Biology, 35(5):719-730.
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Evolution of the quorum sensing systems in Pseudomonas aeruginosa can involve both loss of regulon function and network modulation. bioRxiv 489656, Cold Spring Harbor Laboratory.
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A comprehensive method to elucidate pyoverdines produced by fluorescent Pseudomonas spp. by UHPLC-HR-MS/MS. Analytical and Bioanalytical Chemistry, 414(8):2671-2685.
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Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad. Ecology Letters, 25(1):138-150.
Bjoern Menze
ZORA Publication List
Publications
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ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset. Scientific Data, 9(1):762.
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Spatial proteomics in three-dimensional intact specimens. Cell, 185(26):5040-5058.e19.
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Face Restoration via Plug-and-Play 3D Facial Priors. IEEE Transactions on Pattern Analysis and Machine Intelligence, 44(12):8910-8926.
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The federated tumor segmentation (FeTS) tool: an open-source solution to further solid tumor research. Physics in Medicine and Biology, 67(20):204002.
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Application of machine learning to pretherapeutically estimate dosimetry in men with advanced prostate cancer treated with 177Lu-PSMA I&T therapy. European Journal of Nuclear Medicine and Molecular Imaging, 49(12):4064-4072.
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Efficient Claustrum Segmentation in T2-weighted Neonatal Brain MRI Using Transfer Learning from Adult Scans. Clinical Neuroradiology, 32(3):665-676.
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QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results. ArXiv.org 2112.1007, Cornell University.
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Focused Decoding Enables 3D Anatomical Detection by Transformers. ArXiv.org 2207.10774, Cornell University.
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Where is VALDO? VAscular Lesions Detection and segmentatiOn challenge at MICCAI 2021. ArXiv.org 2208.07167, Cornell University.
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SRflow: Deep learning based super-resolution of 4D-flow MRI data. Frontiers in Artificial Intelligence, 5:928181.
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A for-loop is all you need. For solving the inverse problem in the case of personalized tumor growth modeling. ArXiv.org 2205.04550, Cornell University.
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Physiology-based simulation of the retinal vasculature enables annotation-free segmentation of OCT angiographs. ArXiv.org 2207.11102, Cornell University.
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The Medical Segmentation Decathlon. Nature Communications, 13(1):4128.
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blob loss: instance imbalance aware loss functions for semantic segmentation. ArXiv.org 2205.08209, Cornell University.
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A Unified 3D Framework for Organs-at-Risk Localization and Segmentation for Radiation Therapy Planning. In: 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Glasgow, Scotland, United Kingdom, 11 July 2022 - 15 July 2022. Institute of Electrical and Electronics Engineers, 1544-1547.
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Self-Supervised Pretext Tasks in Model Robustness & Generalizability: A Revisit from Medical Imaging Perspective. In: 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Glasgow, Scotland, United Kingdom, 11 July 2022 - 15 July 2022. Institute of Electrical and Electronics Engineers, 5074-5079.
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A Dempster-Shafer approach to trustworthy AI with application to fetal brain MRI segmentation. ArXiv.org 2204.02779, Cornell University.
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Metrics reloaded: Pitfalls and recommendations for image analysis validation. ArXiv.org 2206.01653, Cornell University.
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Learning Shape Reconstruction from Sparse Measurements with Neural Implicit Functions. In: MIDL 2022, Zurich Switzerland, 6 July 2022. MLResearch Press, 1-13.
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Automated Opportunistic Osteoporosis Screening in Routine Computed Tomography of the Spine: Comparison With Dedicated Quantitative CT. Journal of Bone and Mineral Research, 37(7):1287-1296.
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Detecting CTP Truncation Artifacts in Acute Stroke Imaging from the Arterial Input and the Vascular Output Functions. medRxiv 22276371, Cold Spring Harbor Laboratory.
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ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset. ArXiv.org 2206.06694, Cornell University.
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Influence of Auditory Cues on the Neuronal Response to Naturalistic Visual Stimuli in a Virtual Reality Setting. Frontiers in Human Neuroscience, 16:809293.
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Level-Specific Volumetric BMD Threshold Values for the Prediction of Incident Vertebral Fractures Using Opportunistic QCT: A Case-Control Study. Frontiers in Endocrinology, 13:882163.
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Deep Quality Estimation: Creating Surrogate Models for Human Quality Ratings. ArXiv.org 2205.10355, Cornell University.
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Geometry-aware neural solver for fast Bayesian calibration of brain tumor models. IEEE Transactions on Medical Imaging, 41(5):1269-1278.
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Proof-of-concept Study to Estimate Individual Post-Therapy Dosimetry in Men with Advanced Prostate Cancer Treated with 177Lu-PSMA I&T Therapy. Research Square 1588151/v1, University of Zurich.
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Uncertainty-Aware and Lesion-Specific Image Synthesis in Multiple Sclerosis Magnetic Resonance Imaging: A Multicentric Validation Study. Frontiers in Neuroscience, 16:889808.
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Learning residual motion correction for fast and robust 3D multiparametric MRI. Medical Image Analysis, 77:102387.
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Detection and analysis of cerebral aneurysms based on X-ray rotational angiography - the CADA 2020 challenge. Medical Image Analysis, 77:102333.
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Region of Interest focused MRI to Synthetic CT Translation using Regression and Classification Multi-task Network. ArXiv.org 2203.16288, Cornell University.
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Relationformer: A Unified Framework for Image-to-Graph Generation. ArXiv.org 10202, Cornell University.
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A unified 3D framework for Organs at Risk Localization and Segmentation for Radiation Therapy Planning. ArXiv.org 00624, Cornell University.
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Modelling glioma progression, mass effect and intracranial pressure in patient anatomy. Journal of the Royal Society Interface, 19(188):20210922.
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Anatomy-Aware Inference of the 3D Standing Spine Posture from 2D Radiographs. Tomography, 8(1):479-496.
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Whole Brain Vessel Graphs: A Dataset and Benchmark for Graph Learning and Neuroscience (VesselGraph). ArXiv.org 2108.13233, Cornell University.
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Tumor Sink Effect in 68Ga-PSMA-11 PET: Myth or Reality?. Journal of Nuclear Medicine, 63(2):226-232.
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Landmark-Free Statistical Shape Modeling Via Neural Flow Deformations. In: Wang, Linwei; Dou, Qi; Fletcher, Thomas P; Speidel, Stefanie; Liu, Shuo. Medical Image Computing and Computer Assisted Intervention : MICCAI 2022. Cham: Springer, 453-463.
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FedCostWAvg: A New Averaging for Better Federated Learning. In: Crimi, Alessandro; Bakas, Spyridon. Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries. Cham: Springer, 383-391.
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Preoperative Prediction of Lymph Node Metastasis in Colorectal Cancer with Deep Learning. BME Frontiers, 2022:9860179.
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Beyond Medical Imaging - A Review of Multimodal Deep Learning in Radiology. TechRxiv 19103432, University of Zurich.
Magdalini Polymenidou
ZORA Publication List
Publications
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Comprehensive evaluation of human-derived anti-poly-GA antibodies in cellular and animal models of C9orf72 disease. Proceedings of the National Academy of Sciences of the United States of America, 119(49):e2123487119.
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An arrayed genome‐wide perturbation screen identifies the ribonucleoprotein Hnrnpk as rate‐limiting for prion propagation. The EMBO Journal, 41(23):e112338.
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Tau: a phase in the crowd. The EMBO Journal, 41:e111425.
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An Arrayed Genome-Wide Perturbation Screen Identifies the Ribonucleoprotein hnRNP K As Rate-Limiting for Prion Propagation. bioRxiv 482765, Cold Spring Harbor Laboratory.
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Identification of RNA–RBP Interactions in Subcellular Compartments by CLIP-Seq. In: Matějů, Daniel; Chao, Jeffrey A. The Integrated Stress Response - Methods and Protocols. New York: Springer, 305-323.
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Comprehensive preclinical evaluation of human-derived anti-poly-GA antibodies in cellular and animal models of C9ORF72 disease. bioRxiv 475329, Cold Spring Harbor Laboratory.
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TDP-43 oligomerization and RNA binding are codependent but their loss elicits distinct pathologies. bioRxiv PPR49, Cold Spring Harbor Laboratory.
2021
Bernd Bodenmiller
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An end-to-end workflow for multiplexed image processing and analysis. bioRxiv 468357, Cold Spring Harbor Laboratory.
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Cell‐to‐cell and type‐to‐type heterogeneity of signaling networks: insights from the crowd. Molecular Systems Biology, 17(10):e10402.
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Profound dysregulation of T cell homeostasis and function in patients with severe COVID‐19. Allergy, 76(9):2866-2881.
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Monogenic Diabetes and Integrated Stress Response Genes Display Altered Gene Expression in Type 1 Diabetes. Diabetes, 70(8):1885-1897.
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Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy. bioRxiv 454093, Cold Spring Harbor Laboratory.
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Exploration and analysis of molecularly annotated, 3D models of breast cancer at single-cell resolution using virtual reality. bioRxiv 448342, Cold Spring Harbor Laboratory.
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Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell Systems, 12(5):401-418.e12.
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Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data. Bioinformatics, 36(24):5706-5708.
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The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support. Cancer Cell, 39(3):288-293.
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Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Science, 371(6528):eaax2656.
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Single-Cell Proteomics Defines the Cellular Heterogeneity of Localized Prostate Cancer. bioRxiv 428046, Cold Spring Harbor Laboratory.
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A distinct innate immune signature marks progression from mild to severe COVID-19. Cell Reports Medicine, 2(1):100166.
Nicole Joller
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Asymmetric cell division shapes naive and virtual memory T-cell immunity during ageing. Nature Communications, 12:2715.
Michael Krauthammer
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Analyzing Patient Trajectories With Artificial Intelligence. Journal of Medical Internet Research, 23(12):e29812.
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Künstliche Intelligenz in der Medizin : Chancen und Risiken der KI. Hausarzt Praxis, 16(11):6-10.
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Positionspapier: Ein Rechtsrahmen für Künstliche Intelligenz. In: Workshop of the DSI (Digital Society Initiative) Strategy Lab, Balsthal, 26 August 2021 - 28 August 2021. Digital Society Initiative, 1-7.
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Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors. Cell Host & Microbe, 29(10):1573-1588.e7.
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Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis. STAR Protocols, 2(2):100581.
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Oncolytic virotherapy-mediated anti-tumor response: a single-cell perspective. Cancer Cell, 39(3):394-406.e4.
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Differential immunomodulatory effect of PARP inhibition in BRCA1 deficient and competent tumor cells. Biochemical Pharmacology, 184:114359.
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AttentionDDI: Siamese attention‑based deep learning method for drug–drug interaction predictions. BMC Bioinformatics, 22(1):412.
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Progressive Transformer-Based Generation of Radiology Reports. In: Empirical Methods in Natural Language Processing (EMNLP), Punta Cana, 7 November 2021 - 11 November 2021. ACL Anthology, 2824-2832.
Rolf Kümmerli
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Losing out to improve group fitness. eLife, 10:e75243.
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Ecology drives the evolution of diverse social strategies in Pseudomonas aeruginosa. Molecular Ecology, 30(20):5214-5228.
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Single-Cell Imaging Reveals That Staphylococcus aureus Is Highly Competitive Against Pseudomonas aeruginosa on Surfaces. Frontiers in Cellular and Infection Microbiology, 11:733991.
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Rapid and strain-specific resistance evolution of Staphylococcus aureus against inhibitory molecules secreted by Pseudomonas aeruginosa. bioRxiv 455797, Cold Spring Harbor Laboratory.
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Local adaptation, geographical distance and phylogenetic relatedness: Assessing the drivers of siderophore‐mediated social interactions in natural bacterial communities. Journal of Evolutionary Biology, 34(8):1266-1278.
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Loss of a pyoverdine secondary receptor in Pseudomonas aeruginosa results in a fitter strain suitable for population invasion. The ISME journal, 15(5):1330-1343.
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Pseudomonas aeruginosa reaches collective decisions via transient segregation of quorum sensing activities across cells. bioRxiv 436499, Cold Spring Harbor Laboratory.
Bjoern Menze
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Robust, Primitive, and Unsupervised Quality Estimation for Segmentation Ensembles. Frontiers in Neuroscience, 15:752780.
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Unmixing tissue compartments via deep learning T1-T2-relaxation correlation imaging. In: Seventeenth International Symposium on Medical Information Processing and Analysis, Campinas, Brazil, 17 November 2021 - 19 November 2021. SPIE, 120880P.
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The Brain Tumor Sequence Registration Challenge: Establishing Correspondence between Pre-Operative and Follow-up MRI scans of diffuse glioma patients. ArXiv.org 2112.06979, Cornell University.
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Multi-Centre, Multi-Vendor and Multi-Disease Cardiac Segmentation: The M&Ms Challenge. IEEE Transactions on Medical Imaging, 40(12):3543-3554.
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AIFNet: Automatic vascular function estimation for perfusion analysis using deep learning. Medical Image Analysis, 74:102211.
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Proteomics of spatially identified tissues in whole organs. bioRxiv 466753, Cold Spring Harbor Laboratory.
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Accelerated 3D whole-brain T1, T2, and proton density mapping: feasibility for clinical glioma MR imaging. Neuroradiology, 63(11):1831-1851.
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A Deep Learning Approach to Predicting Collateral Flow in Stroke Patients Using Radiomic Features from Perfusion Images. ArXiv.org 2110.12508, Cornell University.
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Pyramid Architecture Search for Real-Time Image Deblurring. In: 2021 IEEE/CVF International Conference on Computer Vision (ICCV), Montreal, QC, Canada, 10 October 2021 - 17 October 2021, IEEE.
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Semi-Implicit Neural Solver for Time-dependent Partial Differential Equations. ArXiv.org 2109.01467, Cornell University.
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GaNDLF: A Generally Nuanced Deep Learning Framework for Scalable End-to-End Clinical Workflows in Medical Imaging. ArXiv.org 2103.01006, Cornell University.
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Weakly supervised deep learning for determining the prognostic value of 18F-FDG PET/CT in extranodal natural killer/T cell lymphoma, nasal type. European Journal of Nuclear Medicine and Molecular Imaging, 48(10):3151-3161.
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An automatic multi-tissue human fetal brain segmentation benchmark using the Fetal Tissue Annotation Dataset. Scientific Data, 8(1):167-181.
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Evaluating the Robustness of Self-Supervised Learning in Medical Imaging. ArXiv.org 2105.06986, Cornell University.
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METGAN: Generative Tumour Inpainting and Modality Synthesis in Light Sheet Microscopy. ArXiv.org 10993, Cornell University.
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Micro-Ct Synthesis and Inner Ear Super Resolution via Generative Adversarial Networks and Bayesian Inference. In: 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), Nice, France, 13 April 2021 - 16 April 2021. Institute of Electrical and Electronics Engineers, online.
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Magdalini Polymenidou
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FTLD‐TDP assemblies seed neoaggregates with subtype‐specific features via a prion‐like cascade. EMBO Reports, 22(12):e53877.
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Cytoplasmic FUS triggers early behavioral alterations linked to cortical neuronal hyperactivity and inhibitory synaptic defects. Nature Communications, 12:3028.
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Synaptic FUS accumulation triggers early misregulation of synaptic RNAs in a mouse model of ALS. Nature Communications, 12(1):3027.
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Sharing is caring: The benefits of distributing protein aggregates among microglial networks. Neuron, 109(20):3228-3230.
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LAG3 is not expressed in human and murine neurons and does not modulate α‐synucleinopathies. EMBO Molecular Medicine:e 14745.
2020
Bernd Bodenmiller
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A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids. Molecular Systems Biology, 16:e9798.
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Multidimensional single-cell modeling of cellular signaling. bioRxiv 383711, Cold Spring Harbor Laboratory.
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Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data. bioRxiv 287516, Cold Spring Harbor Laboratory.
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A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids. bioRxiv 219659, Cold Spring Harbor Laboratory.
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Profiling Cell Signaling Networks at Single-cell Resolution. Molecular & Cellular Proteomics, 19(5):744-756.
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Uncovering axes of variation among single-cell cancer specimens. Nature Methods, 17(3):302-310.
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Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data. Scientific Reports, 10:1233.
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Deciphering the Signaling Network Landscape of Breast Cancer Improves Drug Sensitivity Prediction. bioRxiv 907691, Cold Spring Harbor Laboratory.
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The single-cell pathology landscape of breast cancer. Nature, 578(7796):615-620.
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An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. F1000Research, 9:1263.
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Highly multiplexed molecular and cellular mapping of breast cancer tissue in three dimensions using mass tomography. bioRxiv 113571, Cold Spring Harbor Laboratory.
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Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition. Frontiers in Physiology, 11:579117.
Michael Krauthammer
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AutoDiscern: rating the quality of online health information with hierarchical encoder attention-based neural networks. BMC Medical Informatics and Decision Making, 20:104.
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The association of MUC16 mutation with tumor mutation burden and its prognostic implications in cutaneous melanoma. Cancer Epidemiology Biomarkers & Prevention, 29(9):1792-1799.
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Iterations for Propensity Score Matching in MonetDB. In: 24thvEuropean Conference on Advances in Databases and Information Systems, ADBIS 2020, Lyon, 25 August 2020 - 27 August 2020. Springer, 189-203.
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AI support for ethical decision-making around resuscitation: proceed with care. medRxiv 20171769, Cold Spring Harbor Laboratory.
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Lost in anonymization — A data anonymization reference classification merging legal and technical considerations. Journal of Law, Medicine & Ethics, 48(1):228-231.
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Predicting base editing outcomes with an attention-based deep learning algorithm trained on high-throughput target library screens. bioRxiv 186544, Cold Spring Harbor Laboratory.
Rolf Kümmerli
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Microbial Mutualism: Will You Still Need Me, Will You Still Feed Me?. Current Biology, 30(18):R1041-R1043.
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Competition for iron drives phytopathogen control by natural rhizosphere microbiomes. Nature Microbiology, 5(8):1002-1010.
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Strain Background, Species Frequency, and Environmental Conditions Are Important in Determining Pseudomonas aeruginosa and Staphylococcus aureus Population Dynamics and Species Coexistence. Applied and Environmental Microbiology, 86(18):e00962-20.
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Antagonistic interactions subdue inter‐species green‐beard cooperation in bacteria. Journal of Evolutionary Biology, 33:1245-1255.
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Bacterial siderophores in community and host interactions. Nature Reviews. Microbiology, 18(3):152-163.
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Harnessing bacterial interactions to manage infections: a review on the opportunistic pathogen Pseudomonas aeruginosa as a case example. Journal of Medical Microbiology, 69(2):147-161.
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Positive linkage between bacterial social traits reveals that homogeneous rather than specialised behavioral repertoires prevail in natural Pseudomonas communities. FEMS Microbiology Ecology, 96(1):fiz185.
Bjoern Menze
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Deep learning for medical image analysis: a brief introduction. Neuro-Oncology Advances, 2(Supplement):iv35-iv41.
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DeepVesselNet: Vessel Segmentation, Centerline Prediction, and Bifurcation Detection in 3-D Angiographic Volumes. Frontiers in Neuroscience, 14:592352.
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CXCR4-Targeted PET Imaging of Central Nervous System B-Cell Lymphoma. Journal of Nuclear Medicine, 61(12):1765-1771.
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Rapid three-dimensional multiparametric MRI with quantitative transient-state imaging. Scientific Reports, 10:13769.
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Deep learning-enabled multi-organ segmentation in whole-body mouse scans. Nature Communications, 11:5626.
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Silent 3D MR sequence for quantitative and multicontrast T1 and proton density imaging. Physics in Medicine and Biology, 65(18):185010.
Magdalini Polymenidou
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Phase separation and neurodegenerative diseases: a disturbance in the force. Developmental Cell, 55(1):45-68.
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A Gut Feeling about C9ORF72. Trends in Immunology, 41(9):755-757.
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Cytoplasmic accumulation of FUS triggers early behavioral alterations linked to cortical neuronal hyperactivity and defects in inhibitory synapses. ArXiv.org 141556, Cornell University.
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Synaptic accumulation of FUS triggers age-dependent misregulation of inhibitory synapses in ALS-FUS mice. ArXiv.org 136010, Cornell University.
2019
Bernd Bodenmiller
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Hair eruption initiates and commensal skin microbiota aggravate adverse events of anti-EGFR therapy. Science Translational Medicine, 11(522):eaax2693.
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In-Depth Characterization of Monocyte-Derived Macrophages using a Mass Cytometry-Based Phagocytosis Assay. Scientific Reports, 9:1925.
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Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis. Cell Reports, 29(1):202-211.e6.
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IL-8 and CXCR1 expression is associated with cancer stem cell-like properties of clear cell renal cancer. Journal of Pathology, 248(3):377-389.
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Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling. Molecular Cell, 74(5):1086-1102.e5.
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A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer. Cell, 177(5):1330-1345.
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A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry. Cell Metabolism, 29(3):755-768.e5.
Michael Krauthammer
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Neural networks versus Logistic regression for 30 days all-cause readmission prediction. Scientific Reports, 9(1):9277.
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Mobile Health – Eine Technologie wird erwachsen. In: readme : Das Bulletin derUZH Alumni Informatik, 41, 1 September 2019, 3-5.
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A novel anti-melanoma SRC-family kinase inhibitor. OncoTarget, 10(23):2237-2251.
Rolf Kümmerli
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Genetic architecture constrains exploitation of siderophore cooperation in the bacterium Burkholderia cenocepacia. Evolution Letters, 3(6):610-622.
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Transposable temperate phages promote the evolution of divergent social strategies in Pseudomonas aeruginosa populations. Proceedings of the Royal Society of London, Series B: Biological Sciences, 286(1912):20191794.
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In-vivo microscopy reveals the impact of Pseudomonas aeruginosa social interactions on host colonization. The ISME journal, 13(10):2403-2414.
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Understanding policing as a mechanism of cheater control in cooperating bacteria. Journal of Evolutionary Biology, 32(5):412-424.
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Individual‐ versus group‐optimality in the production of secreted bacterial compounds. Evolution, 73(4):675-688.
Magdalini Polymenidou
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Structural Transition, Function and Dysfunction of TDP-43 in Neurodegenerative Diseases. CHIMIA International Journal for Chemistry, 73(5):380-390.
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Memory decline and its reversal in aging and neurodegeneration involve miR-183/96/182 biogenesis. Molecular Neurobiology, 56(5):3451-3462.
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The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity. Molecular Cell, 73(3):490-504.e6.