Loic Royer

Publications

• Requirements and specification of bioinformatics use cases
• GoGene: gene annotation in the fast lane
• Querying Semantic Web Contents
• Bioinformatics Demonstrators
• Optical Aberration Correction via Phase Diversity and Deep Learning
• CLIJ: GPU-accelerated image processing for everyone
• Unraveling protein networks with power graph analysis
• Gopubmed: Exploring pubmed with ontological background knowledge
• Me and my friends: gene mention normalization with background knowledge
• A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation
• Gene mention normalization and interaction extraction with context models and sentence motifs
• Prova: Rule-based java scripting for distributed web applications: A case study in bioinformatics
• Improving text mining with controlled natural language: A case study for protein interactions
• Genome-wide expression profiling and functional network analysis upon neuroectodermal conversion of human mesenchymal stem cells suggest HIF-1 and miR-124a as important regulators
• Network compression as a quality measure for protein interaction networks
• Attempto Controlled English and the semantic web
• ClearVolume: open-source live 3D visualization for light-sheet microscopy
• Specification of a model, language and architecture for evolution and reactivity
• Whole blood genome-wide expression profiling and network analysis suggest MELAS master regulators
• Specification of a model, language and architecture for reactivity and evolution
• Whole-genome expression analysis of human mesenchymal stromal cells exposed to ultrasmooth tantalum vs. titanium oxide surfaces
• Visualization and Interactive Analysis for Complex Networks by means of Lossless Network Compression
• Identification of cancer and cell-cycle genes with protein interactions and literature mining
• Stem Cells Show Neuroectodermal Features Obtained From Mesenchymal Stem Cells
• Unraveling the structure and evaluating the quality of protein networks with power graph analysis
• Visualising protein interaction networks with power graphs
• Array-based identification of potential osteoarthritis key genes using mesenchymal stromal cells from osteoarthritic versus healthy donors
• Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms
• Array-based identification of potential osteoarthritis key genes using mesenchymal stromal cells from osteoarthritic versus healthy donors
• Isotropic Reconstruction of 3D Fluorescence Microscopy Images Using Convolutional Neural Networks
• Cellular aspect ratio and cell division mechanics underlie the patterning of cell progeny in diverse mammalian epithelia
• Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy
• Parallel hierarchies: A visualization for cross-tabulating hierarchical categories
• A practical guide to adaptive light-sheet microscopy
• In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level
• Querying Semantic Web Contents
• Unraveling the structure and assessing the quality of protein interaction networks with power graph analysis
• High-Resolution, Large Field-of-View, and Multi-View Single Objective Light-Sheet Microscopy
• Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms
• Elimination of nurse cell nuclei that shuttle into oocytes during oogenesis
• Self-supervised deep learning encodes high-resolution features of protein subcellular localization
• Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction
• Molecular Cross-Validation for Single-Cell RNA-seq
• Self-Supervised Deep Learning Encodes High-Resolution Features of Protein Subcellular Localization
• ZAF – The First Open Source Fully Automated Feeder for Aquatic Facilities
• Image Deconvolution via Noise-Tolerant Self-Supervised Inversion
• Noise2Self: Blind denoising by self-supervision
• Noise2Seif: Blind denoising by self-supervision
• Isotropic reconstruction of 3D fluorescence microscopy images using convolutional neural networks
• GoPubMed: Exploring PubMed with ontological background knowledge
• Querying semantic web contents a case study
• OpenCell: Endogenous tagging for the cartography of human cellular organization
• A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation
• DaXi—high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy
• Convexity shape constraints for image segmentation
• OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization
• ZeroCostDL4Mic: An open platform to use deep-learning in microscopy
• GoGene: Gene annotation in the fast lane
• Pycro-Manager: open-source software for customized and reproducible microscope control
• ZAF, The First Open Source Fully Automated Feeder for Aquatic Facilities
• Content-aware image restoration: pushing the limits of fluorescence microscopy
• Colocalization Analysis for Cryosectioned and Immunostained Tissue Samples with or without Label Retention Expansion Microscopy (LR-ExM) by JACoP
• ClearVolume: Open-source live 3D visualization for light-sheet microscopy
• Neuropilin-1 Mediates SARS-CoV-2 Infection of Astrocytes in Brain Organoids, Inducing Inflammation Leading to Dysfunction and Death of Neurons
• Democratising deep learning for microscopy with ZeroCostDL4Mic
• The future of bioimage analysis: a dialog between mind and machine
• Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps
• Zebrahub – Multimodal Zebrafish Developmental Atlas Reveals the State-Transition Dynamics of Late-Vertebrate Pluripotent Axial Progenitors
• Omega — harnessing the power of large language models for bioimage analysis
• PCM1 conveys centrosome asymmetry to polarized endosome dynamics in regulating daughter cell fate
• Challenges and Progress in RNA Velocity: Comparative Analysis Across Multiple Biological Contexts
• Repeated extrinsic and anisotropic mechanical inputs promote polarized adherens junction elongation