Single-cell transcriptomics and epigenomics point to CD58-CD2 interaction in controlling primary melanoma growth and immunity. Cancer Communications, (n/a)n/aJohn Wiley & Sons, Ltd, January 2025. [PUMA: Yaff melanoma myown single-cell topic_lifescience transcriptomics] URL
Single-cell transcriptomics and epigenomics point to CD58-CD2 interaction in controlling primary melanoma growth and immunity. Cancer Communications, (n/a)n/aJohn Wiley & Sons, Ltd, January 2025. [PUMA: melanoma myown single-cell topic_lifescience transcriptomics] URL
Prediction of tissue and clinical thrombectomy outcome in acute ischaemic stroke using deep learning. In Masud Husain (Eds.), Brain, awaf013, January 2025. [PUMA: biomarker cdss cnn computer_vision deep_learning myown neuroimaging neurology topic_lifescience] URL
Utilizing transformers on OCT imagery and metadata for treatment response prediction in macular edema patients. Lecture Notes in Computer Science, 3--15, Springer Nature Switzerland, Cham, 2023. [PUMA: OCT Xack edema macular prediction response topic_lifescience transformers treatment]
Self-supervised learning in histopathology: New perspectives for prostate cancer grading. Lecture Notes in Computer Science, 348--360, Springer Nature Switzerland, Cham, 2024. [PUMA: Yaff cancer grading histopathology learning prostate self-supervised topic_lifescience]
A generalized and versatile framework to train and evaluate autoencoders for biological representation learning and beyond: AUTOENCODIX. bioRxiv, Cold Spring Harbor Laboratory, December 2024. [PUMA: topic_lifescience] URL
Neuromorphic hardware for sustainable AI data centers. Zenodo, 2024. [PUMA: area_responsibleai topic_lifescience] URL
A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors. Cell, (187)23:6742--6759, Elsevier, 2024. [PUMA: topic_lifescience]
Metrics reloaded: recommendations for image analysis validation. Nature methods, (21)2:195--212, Nature Publishing Group US New York, 2024. [PUMA: topic_lifescience]
Gut Analysis Toolbox--automating quantitative analysis of enteric neurons. Journal of Cell Science, (137)20The Company of Biologists, 2024. [PUMA: topic_lifescience]
Zebrahub--Multimodal zebrafish developmental atlas reveals the State-transition dynamics of late-vertebrate pluripotent axial progenitors. BioRxiv, 2023--03, Cold Spring Harbor Laboratory, 2023. [PUMA: topic_lifescience]
Slice2Volume: Fusion of multimodal medical imaging and light microscopy data of irradiation-injured brain tissue in 3D. Radiotherapy and Oncology, (182):109591, Elsevier, 2023. [PUMA: topic_lifescience]
Towards Transparency and Knowledge Exchange in AI- assisted Data Analysis Code Generation. Zenodo, October 2024. [PUMA: unit_transfer topic_language topic_lifescience] URL
A comparative patient-level prediction study in OMOP CDM: applicative potential and insights from synthetic data. Scientific reports, (14)1Nature Publishing Group, Jan 27, 2024. [PUMA: Databases, Electronic FIS_scads Factual, Health Humans, Informatics, Learning, Machine Medical Records topic_lifescience]
Automated quantification of photoreceptor outer segments in developing and degenerating retinas on microscopy images across scales. FRONTIERS IN MOLECULAR NEUROSCIENCE, (17 (2024))Frontiers Media S.A., May 24, 2024. [PUMA: unit_transfer topic_lifescience FIS_scads imported]
Efficient Raycasting of View-Dependent Piecewise Constant Representations of Volumetric Data. Jun 17, 2022. [PUMA: topic_visualcomputing topic_lifescience FIS_scads Human-centered Visualization Visualization, and computing, concepts paradigms, techniques theory,]
Content-adaptive generation and parallel compositing of volumetric depth images for responsive visualization of large volume data. Jun 29, 2022. [PUMA: topic_visualcomputing topic_lifescience FIS_scads Human-centered Visualization Visualization, and computing, concepts paradigms techniques theory,]
Streamlining intersectoral provision of real-world health data: a service platform for improved clinical research and patient care. Frontiers in medicine, (11):1377209, Frontiers Media S.A., 2024. [PUMA: topic_lifescience FIS_scads imported]
Towards Standardizing Ophthalmic Data for Seamless Interoperability in Eye Care. Studies in health technology and informatics, (317):139--145, IOS Press, Amsterdam u. a., Aug 30, 2024. [PUMA: topic_lifescience Diseases/therapy, Electronic Eye FIS_scads Germany, Health Humans, Information Interoperability/standards, Learning, Level Machine Ophthalmology Records/standards, Seven/standards,]
Leptin deficiency-caused behavioral change - A comparative analysis using EthoVision and DeepLabCut. Frontiers in neuroscience, (17)Frontiers Media S.A., Mar 24, 2023. [PUMA: topic_lifescience Behavioral Deep DeepLabCut, EthoVision, FIS_scads Obesity analysis, learning,]
CCR2 macrophage response determines the functional outcome following cardiomyocyte transplantation. Genome medicine, (15)1BioMed Central, London, Aug 10, 2023. [PUMA: topic_lifescience Animals, C57BL, Cardiac/metabolism, Cell FIS_scads Immunocompromised, Inbred Infarction, Machine Macrophages, Macrophages/metabolism, Mice, Monocytes/metabolism Myocardial Myocytes, Single-cell, infarction, learning, therapy,]
Ten Topics to Get Started in Medical Informatics Research. Journal of Medical Internet Research, (25)JMIR Publications Inc., Jul 24, 2023. [PUMA: topic_lifescience Algorithms, Clinical Curriculum, Digital FIS_scads Germany, Health Humans, Informatics, Interdisciplinary Medical Research clinical communication, data, digital health health, informatics informatics, interdisciplinary medical research]
Artificial Intelligence Reporting Guidelines' Adherence in Nephrology for Improved Research and Clinical Outcomes. Biomedicines, (12)3MDPI, Basel, Mar 7, 2024. [PUMA: topic_lifescience FIS_scads imported]
How to customize common data models for rare diseases: an OMOP-based implementation and lessons learned. Orphanet journal of rare diseases, (19)1BioMed Central, London, Aug 14, 2024. [PUMA: topic_lifescience Diseases FIS_scads Humans, Rare]
Methods Used in the Development of Common Data Models for Health Data: Scoping Review. JMIR medical informatics, (11)JMIR Publications Inc., Aug 3, 2023. [PUMA: topic_lifescience FIS_scads imported]
Synthetic Data Generation in Hematology - Paving the Way for OMOP and FHIR Integration. Studies in health technology and informatics, (316):1472--1476, IOS Press, Amsterdam u. a., Aug 22, 2024. [PUMA: topic_lifescience Acute, Assessment, Care Electronic FIS_scads Health Hematology, Humans, Information Interoperability, Leukemia, Myeloid, Outcome Records,]
Challenges and applications in generative AI for clinical tabular data in physiology. Pflügers Archiv : European journal of physiology, Springer, Berlin u. a., Oct 17, 2024. [PUMA: topic_lifescience FIS_scads imported]
Netrank: network-based approach for biomarker discovery. BMC bioinformatics, (24)1BioMed Central, London, Jul 29, 2023. [PUMA: topic_lifescience Algorithms, Area Biomedical Curve, Disease FIS_scads Gene Humans, Library Progression, Research, Under]
Word-based GWAS harnesses the rich potential of genomic data for E. coli quinolone resistance. Frontiers in microbiology, (14):1276332, Frontiers Media S.A., 2023. [PUMA: topic_lifescience FIS_scads imported]
Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation. New Phytologist, (240)2:770--783, Wiley-Blackwell, Oxford u. a., Aug 7, 2023. [PUMA: topic_lifescience Adhesives/metabolism, Bacteria Biofilms, Diatoms/metabolism, FIS_scads Gene Horizontal, Transfer,]
Is Protein BLAST a thing of the past?. Nature communications, (14)1Nature Publishing Group, Dec 11, 2023. [PUMA: topic_lifescience Databases, FIS_scads Protein, Proteins/genetics]
The Rad52 SSAP superfamily and new insight into homologous recombination. Communications biology, (6)1Springer Nature, Jan 23, 2023. [PUMA: topic_lifescience DNA FIS_scads Homologous Protein/genetics Rad52 Recombination Recombination, Repair and]
Spontaneous flow instabilities of active polar fluids in three dimensions. Physical Review Research, (5)2American Physical Society, College Park, April 2023. [PUMA: topic_lifescience FIS_scads imported]
Inverse Dirichlet weighting enables reliable training of physics informed neural networks. Machine learning: science and technology, (3)1IOP Publishing Ltd., Feb 15, 2022. [PUMA: topic_lifescience ALGORITHM FIS_scads active catastrophic flow forgetting, gradient modeling, multi-objective multi-scale networks, neural physics-informed regularization, training, turbulence,]
STENCIL-NET for equation-free forecasting from data. Scientific reports, (13)1Nature Publishing Group, December 2023. [PUMA: topic_lifescience FIS_scads imported]
A numerical solver for active hydrodynamics in three dimensions and its application to active turbulence. Physics of fluids, (35)10American Institute of Physics, Oct 1, 2023. [PUMA: topic_lifescience FIS_scads imported]
A Unifying Mathematical Definition of Particle Methods. IEEE open journal of the computer society : an open access publication of the IEEE Computer Society, (4):97--108, Institute of Electrical and Electronics Engineers Inc., 2023. [PUMA: topic_lifescience Algorithmics, FIS_scads algorithms, definition, engineering formal mesh-free methods, parallelization, particle simulation software]
Learning deterministic hydrodynamic equations from stochastic active particle dynamics. Jan 21, 2022. [PUMA: topic_lifescience FIS_scads cond-mat.soft, cs.LG, physics.data-an]
Parallel Discrete Convolutions on Adaptive Particle Representations of Images. IEEE Transactions on Image Processing, (31):4197--4212, Wiley-IEEE Press, Jan 1, 2022. [PUMA: topic_lifescience Convolution, Data FIS_scads Image Microscopy, Signal processing, reconstruction, resolution resolution, structures,]
A C++ Library for Memory Layout and Performance Portability of Scientific Applications. In Jeremy Singer, Yehia Elkhatib, Dora Blanco Heras, Patrick Diehl, Nick Brown, and Aleksandar Ilic (Eds.), Euro-Par 2022, 109--120, Springer Science and Business Media B.V., Germany, 2023. [PUMA: topic_lifescience C++ FIS_scads GPU, algorithms, generic layout, memory multi-core, performance portability tuples,]
Adaptive weighting of Bayesian physics informed neural networks for multitask and multiscale forward and inverse problems. Journal of computational physics, (491)Academic Press Inc., Oct 15, 2023. [PUMA: topic_lifescience Adaptive Artificial Bayesian Carlo, FIS_scads Hamiltonian Intelligence, Monte Multi-objective Quantification Uncertainty learning, networks, neural physics-informed training, weight]
Stability selection enables robust learning of differential equations from limited noisy data. Proceedings of the Royal Society of London : Series A, Mathematical, physical and engineering sciences, (478)2262Royal Society Publishing, June 2022. [PUMA: topic_lifescience FIS_scads PAR differential equations, learning learning, machine proteins, regression, selection, sparse stability statistical theory]
Genomic events stratifying prognosis of early gastric cancer. Gastric Cancer, 1--12, Springer, 2024. [PUMA: topic_lifescience area_bigdata ep imported]
Targeting adhesion G protein-coupled receptors. Current status and future perspectives. Structure, Elsevier, November 2024. [PUMA: topic_lifescience ADGRG1; ADGRG2; ADGRG3; ADGRG5; ADGRG6; ADGRG7; GPCRs; GPR114; GPR126; GPR128; GPR56; GPR64; GPR97; adhesion area_bigdata discovery; drug ep ligands; molecules; small structure]
Usefulness of voxel-wise Pearson correlation coefficient for reproducibility and repeatability measurements in PET. Nuklearmedizin, 2012. [PUMA: imported topic_lifescience]
Time to upgrade: A new OpenSPIM guide to build and operate advanced OpenSPIM configurations. Advanced biology, (6)4:2101182, 2022. [PUMA: imported topic_lifescience]
Bio-Image Informatics Index BIII: A unique database of image analysis tools and workflows for and by the bioimaging community. arXiv preprint arXiv:2312.11256, 2023. [PUMA: imported topic_lifescience]
Gliding motility of the diatom Craspedostauros australis correlates with the intracellular movement of raphid-specific myosins. bioRxiv, 2024--03, Cold Spring Harbor Laboratory, 2024. [PUMA: imported topic_lifescience]
Interactive design of GPU-accelerated image data flow graphs and cross-platform deployment using multi-lingual code generation. bioRxiv, 2020--11, Cold Spring Harbor Laboratory, 2020. [PUMA: imported topic_lifescience]
A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors. Cell, (187)23:6742--6759, Elsevier, 2024. [PUMA: imported topic_lifescience]
GPU-accelerating ImageJ Macro image processing workflows using CLIJ. Bioimage Data Analysis Workflows--Advanced Components and Methods, 89--114, Springer International Publishing Cham, 2022. [PUMA: imported topic_lifescience]
Slice2Volume: Fusion of multimodal medical imaging and light microscopy data of irradiation-injured brain tissue in 3D. Radiotherapy and Oncology, (182):109591, Elsevier, 2023. [PUMA: imported topic_lifescience]
Image processing filters for grids of cells analogous to filters processing grids of pixels. Frontiers in Computer Science, 105, Frontiers, 2021. [PUMA: imported topic_lifescience]
Dose--volume predictors of early esophageal toxicity in non-small cell lung cancer patients treated with accelerated-hyperfractionated radiotherapy. Radiotherapy and Oncology, (143):44--50, Elsevier, 2020. [PUMA: imported topic_lifescience]
Swarm intelligence allows automatic volume analysis basing on low contrast 18 F-fluoromisonidazole-PET of head and neck cancer patients. 2013. [PUMA: imported topic_lifescience]
Evaluation of a deformable registration algorithm for subsequent lung computed tomography imaging during radiochemotherapy. Medical Physics, (43)9:5028--5039, American Association of Physicists in Medicine, 2016. [PUMA: imported topic_lifescience]
Analysis of actomyosin dynamics at local cellular and tissue scales using time-lapse movies of cultured drosophila egg chambers. JoVE (Journal of Visualized Experiments), 148:e58587, 2019. [PUMA: imported topic_lifescience]
Optimisation and Validation of a Swarm Intelligence Based Segmentation Algorithm for Low Contrast Positron Emission Tomography. 2014. [PUMA: imported topic_lifescience]
Bat teeth illuminate the diversification of mammalian tooth classes. bioRxiv, 2021--12, Cold Spring Harbor Laboratory, 2021. [PUMA: imported topic_lifescience]
Bat teeth illuminate the diversification of mammalian tooth classes. Nature communications, (14)1:4687, Nature Publishing Group UK London, 2023. [PUMA: imported topic_lifescience]
Challenges and opportunities for bioimage analysis core-facilities. Journal of Microscopy, (294)3:338--349, 2024. [PUMA: imported topic_lifescience]
Benchmarking Large Language Models for Bio-Image Analysis Code Generation. bioRxiv, 2024--04, Cold Spring Harbor Laboratory, 2024. [PUMA: imported topic_language topic_lifescience]
Gliding motility of the diatom Craspedostauros australis coincides with the intracellular movement of raphid-specific myosins. Communications Biology, (7)1:1187, Nature Publishing Group UK London, 2024. [PUMA: imported topic_lifescience]
FDG uptake in normal tissues assessed by PET during treatment has prognostic value for treatment results in head and neck squamous cell carcinomas undergoing radiochemotherapy. Radiotherapy and Oncology, (122)3:437--444, Elsevier, 2017. [PUMA: imported topic_lifescience]
Image Guided orthotopic Tumor Models in Small Animals. STRAHLENTHERAPIE UND ONKOLOGIE, (191):S24--S25, 2015. [PUMA: imported topic_lifescience]
Open microscopy in the life sciences: quo vadis?. Nature methods, (19)9:1020--1025, Nature Publishing Group US New York, 2022. [PUMA: imported topic_lifescience]
Wie weit bewegen sich die Schwerpunkte hypoxischer Tumorsubvolumina von HNO-Tumoren unter kombinierter Radiochemotherapie.. Nuklearmedizin, 2010. [PUMA: imported topic_lifescience]
The Fiji Updater, My favorite image analysis tool, by Neubias members. Imaging and Microscopy, March 2021Wiley Analytical Science, 2021. [PUMA: imported topic_lifescience]
Exogenous ethanol induces a metabolic switch that prolongs the survival of Caenorhabditis elegans dauer larva and enhances its resistance to desiccation. Aging Cell, (19)10:e13214, 2020. [PUMA: imported topic_lifescience]
Meeting in the middle: towards successful multidisciplinary bioimage analysis collaboration. Frontiers in bioinformatics, (2):889755, Frontiers Media SA, 2022. [PUMA: imported topic_lifescience]
Spatial distribution of FMISO in head and neck squamous cell carcinomas during radio-chemotherapy and its correlation to pattern of failure. Acta Oncologica, (54)9:1355--1363, Taylor & Francis, 2015. [PUMA: imported topic_lifescience]
Stabilität des Hypoxietracers 18 F-FMISO während sequentieller PET-Untersuchungen bei Patienten mit radiochemotherapierten HNO-Tumoren und Korrelation von funktionellen Tumor-Subvolumina zur Rezidivlokalisation. Strahlentherapie und Onkologie, 2014. [PUMA: imported topic_lifescience]
On the Reliability of Automatic Volume Delineation in Low-Contrast 18 F FMISO-PET Imaging. Molecular Radio-Oncology, 175--187, Springer Berlin Heidelberg, 2016. [PUMA: imported topic_lifescience]
Fluor-18-Misonidazol-PET/CT unter kurativ intendierter Radiochemotherapie bei Patienten mit lokal fortgeschrittenen Kopf-Hals-Tumoren (KHT)--eine prospektive Explorationsstudie. Nuklearmedizin, 2013. [PUMA: imported topic_lifescience]
Prognostic value of baseline 18F-fluorodeoxyglucose positron emission tomography parameters MTV, TLG and asphericity in an international multicenter cohort of nasopharyngeal carcinoma patients. PloS one, (15)7:e0236841, Public Library of Science San Francisco, CA USA, 2020. [PUMA: imported topic_lifescience]
Self-reproduction versus transition rules in ant colonies for medical volume segmentation. International Conference on Swarm Intelligence, 316--323, 2012. [PUMA: imported topic_lifescience]
Physical correction model for automatic correction of intensity non-uniformity in magnetic resonance imaging. Physics and Imaging in Radiation Oncology, (4):32--38, Elsevier, 2017. [PUMA: imported topic_lifescience]
Towards Transparency and Knowledge Exchange in AI- assisted Data Analysis Code Generation. Zenodo, October 2024. [PUMA: imported topic_language topic_lifescience] URL
Gut Analysis Toolbox--automating quantitative analysis of enteric neurons. Journal of Cell Science, (137)20The Company of Biologists, 2024. [PUMA: imported topic_lifescience]
Influence of deformable Image Registration of PET/CT Data on Signal Values wihin a Contour: Deformation on Contours or Image Data?. STRAHLENTHERAPIE UND ONKOLOGIE, (190):59--59, 2014. [PUMA: imported topic_lifescience]
A new segmentation algorithm for low contrast positron emission tomography based on ant colony optimization. Crossing Borders within the ABC: Automation, Biomedical Engineering and Computer Science, (55):505--510, 2010. [PUMA: imported topic_lifescience]
Virtuelle Ameisen zur Segmentierung von Positronen-Emissions-Tomographie Daten: Auswirkungen auf die Receiver Operating Characteristic. RöFo-Fortschritte auf dem Gebiet der Röntgenstrahlen und der bildgebenden Verfahren, (183)S 01:WI\_PO2, 2011. [PUMA: imported topic_lifescience]
Two or four hour 18F FMISO-PET in HNSCC. Nuklearmedizin-NuclearMedicine, (50)01:22--27, Schattauer GmbH, 2011. [PUMA: imported topic_lifescience]
NanoPyx: super-fast bioimage analysis powered by adaptive machine learning. bioRxiv, 2023--08, Cold Spring Harbor Laboratory, 2023. [PUMA: imported topic_lifescience]
Swarm intelligence for medical volume segmentation: the contribution of self-reproduction. KI 2011: Advances in Artificial Intelligence: 34th Annual German Conference on AI, Berlin, Germany, October 4-7, 2011. Proceedings 34, 111--121, 2011. [PUMA: imported topic_lifescience]
Zebrahub--Multimodal zebrafish developmental atlas reveals the State-transition dynamics of late-vertebrate pluripotent axial progenitors. BioRxiv, 2023--03, Cold Spring Harbor Laboratory, 2023. [PUMA: imported topic_lifescience]
The crucial role of bioimage analysts in scientific research and publication. Journal of cell science, (137)20The Company of Biologists, 2024. [PUMA: imported topic_lifescience]
Two or four hour 18F FMISO-PET in HNSCC. Nuklearmedizin, (50)01:22--27, Georg Thieme Verlag KG, 2011. [PUMA: imported topic_lifescience]
High-precision image-guided proton irradiation of mouse brain sub-volumes. Radiotherapy and Oncology, (146):205--212, Elsevier, 2020. [PUMA: imported topic_lifescience]
FMISO-PET-based lymph node hypoxia adds to the prognostic value of tumor only hypoxia in HNSCC patients. Radiotherapy and Oncology, (130):97--103, Elsevier, 2019. [PUMA: imported topic_lifescience]
LABKIT: labeling and segmentation toolkit for big image data. Frontiers in computer science, (4):777728, Frontiers, 2022. [PUMA: imported topic_lifescience]
The prognostic value of FMISO-PET-based synchronous tumor and lymph node hypoxia outperforms that of tumor hypoxia only in patients with advanced stage HNSSC-secondary analysis of Dresden FMISO trail. ONCOLOGY RESEARCH AND TREATMENT, (41):186--186, 2018. [PUMA: imported topic_lifescience]
Timely neurogenesis enables increased nuclear packing order during neuronal lamination. bioRxiv, 2024--11, Cold Spring Harbor Laboratory, 2024. [PUMA: imported topic_lifescience]
Star-convex polyhedra for 3D object detection and segmentation in microscopy. Proceedings of the IEEE/CVF winter conference on applications of computer vision, 3666--3673, 2020. [PUMA: imported topic_lifescience]
Metrics reloaded: recommendations for image analysis validation. Nature methods, (21)2:195--212, Nature Publishing Group US New York, 2024. [PUMA: imported topic_lifescience]
Common limitations of image processing metrics: A picture story. arXiv preprint arXiv:2104.05642, 2021. [PUMA: imported topic_lifescience]
Automated Quantification of Photoreceptor Outer Segments in Developing and Degenerating Retinas on Microscopic Images across Scales. Investigative Ophthalmology & Visual Science, (65)7:5878--5878, The Association for Research in Vision and Ophthalmology, 2024. [PUMA: imported topic_lifescience]
A Call for FAIR and Open-Access Training Materials to advance Bioimage Analysis. 2024. [PUMA: imported topic_lifescience]
A hitchhiker's guide through the bio-image analysis software universe. Febs Letters, (596)19:2472--2485, 2022. [PUMA: imported topic_lifescience]
Stability of the Hypoxia Tracer 18F-FMISO during sequential PET-Studies in Patients with radio chemotherapy ENT-Tumors and Correlation of functional Tumor-Subvolumes for Recurrence Localization. Strahlentherapie und Onkologie, (190):52--52, Urban & Vogel, 2014. [PUMA: imported topic_lifescience]