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Group Leader at the Chan Zuckerberg Biohub in San Francisco. Work at the interface between AI, Microscopy, and Biology.

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

Loic Royer's public data