Caterina Strambio De Castillia

Publications

• MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text
• QUAREP-LiMi WGs 2 & 7 Joint endeavor: joining forces with manufacturers to build a shared community camera glossary and metadata model
• Microscopy reproducibility for the real world: building interactive tools to document light microscopy experiments based on community specifications
• QUAREP - WG7 - MetadataOpen microscopy documentation for the real world: interactive tools for quality, reproducibility and sharing value of imaging experiments based on community specifications
• QUAREP-WG7: Open microscopy documentation for the real world: interactive tools for quality, reproducibility and sharing value of imaging experiments based on community specifications
• Open microscopy documentation for the real world: interactive tools for quality, reproducibility and sharing value of imaging experiments based on community specifications
• Community Guidelines and Tools for the Collection and Reporting of Microscopy Metadata
• Results of community surveys organized by the members of the BioImaging North America – Quality Control and Data Management Working Group to understand the microscopy reporting and reprodubility needs of the bioimaging community
• Research Data Management Community Guidelines and Tools for Reporting and Reproducibility in Light Microscopy
• Community-driven fair data management and reproducibility for the whole image-data life cycle
• Reporting of Microscopy Metadata - How to Improve Quality and Reproducibility in Bio-Imaging
• IWG Abstract 3 - Capture of Microscopy Metadata associated with FISH Omics Chromatin Tracing Experiments on the 4DN-Data Portal
• IWG Abstract 2: FAIR exchange of Chromatin Tracing datasets from the 4 DN Data Portal using the newly developed 4 DN FOF CT data exchange format
• Reporting and reproducibility in microscopy through rigorous image publication and community-driven tools for research data management
• Reporting & Reproducibility in Microscopy
• WU-BIMAC/NBOMicroscopyMetadataSpecs: 4DN-BINA-OME (NBO) Microscopy Metadata Specifications - v2.01
• Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications
• Getting started with Micro-Meta App Tutorial
• WU-BIMAC/MicroMetaApp-Electron: 1.6.19-b1-1 stable beta
• Getting started with Micro-Meta App Tutorial
• Community-developed checklists for publishing images and image analysis
• Towards a common standard for data and specimen provenance in life sciences
• Micro-Meta App - React
• Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
• Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model
• Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications
• Getting started with Micro-Meta App Tutorial
• A perspective on Microscopy Metadata: data provenance and quality control
• Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model
• 4DN-BINA-OME (NBO) Tiered Microscopy Metadata Specifications - v2.01 - XSD schema
• 4DN-BINA-OME (NBO) Tiered Microscopy Metadata Specifications - v2.01 - XLS Spreadsheet and Entity Relationship schemas
• Micro-Meta App - Electron
• Micro-Meta App - OMERO plug-in
• 4DN Metadata Schema XSD to JSON Converter
• 4DN Microscopy Metadata Reader
• ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen And Data
• Towards a Common Standard for Data and Specimen Provenance in Life Sciences
• MethodsJ2: A Software Tool to Improve Microscopy Methods Reporting
• WU-BIMAC/MicroMetaApp-Electron: 1.3.3-b1-1 stable beta
• WU-BIMAC/MicroMetaApp-React: 4DN v5 Integration - XVI
• OmegaProject/Omega: Omega public beta release 0.47
• WU-BIMAC/MicroMetaApp-Omero: 1.2.2-b1-1 stable beta
• Example Microscopy Metadata JSON files produced using Micro-Meta App to document the acquisition of example images using the custom-built TIRF Epifluorescence Structured Illumination Microscope
• QUAREP‐LiMi: A community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
• SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data
• Example Microscopy Metadata JSON files produced using Micro-Meta App to document example microscopy experiments performed at individual core facilities
• Microscopy metadata: more important and less boring than you think
• REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.
• QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy.
• MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community
• Micro-Meta App documentation and tutorials
• QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
• The DHODH Inhibitor PTC299 Arrests SARS-CoV-2 Replication and Suppresses Induction of Inflammatory Cytokines
• The DHODH inhibitor PTC299 arrests SARS-CoV-2 replication and suppresses induction of inflammatory cytokines.
• The 4DN-OME ontology: an OME-OWL extension with emphasis on usability, minimum information guidelines, and quality control for super-resolution fluorescence microscopy
• Adaptable Community Standards and Intuitive Metadata Collection Tools for Quantitative Light Microscopy
• Adaptable Community Standards and Intuitive Metadata Collection Tools for Quantitative Microscopy
• Adaptable Community Standards and Intuitive Metadata Collection Tools for Quantitative Microscopy
• BINA Quality Control and Data Management Working Group: increasing reproducibility, in biomedical imaging through shared imaging standards
• OMERO: keeping track of your image data, imaging experiments and image analysis + producing figures
• Community driven Minimum Information Guidelines for light microscopy: increasing the value, quality, and reproducibility of image data
• Community driven Minimum Information Guidelines for light microscopy: increasing the value, quality, and reproducibility of image data
• Micro-Meta App: an interactive software tool to facilitate collection of 4DN-BINA-OME compliant Microscopy Metadata
• Micro-Meta App: an interactive software tool to facilitate collection of 4DN-BINA-OME compliant Microscopy Metadata
• Micro-Meta App: an interactive software to facilitate the collection of OME-compliant microscopy metadata based on community-driven specifications
• ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data
• Metadata and Performance Tracking for Fluorescent Microscopes - Lowering the Documentation Burden - Micro-Meta App, An Interactive Tool for the Collection of Microscopy Metadata Based on the 4DN-OME Tiered System of Guidelines
• Metadata and Performance Tracking for Fluorescent Microscopes - Towards a Shared Microscopy Ontology - The 4DN-OME ontology: an OME-OWL extension with emphasis on usability, minimum information guidelines and quality control for super-resolution fluorescence microscopy
• An algorithm-centric Monte Carlo method to empirically quantify motion type estimation uncertainty in single-particle tracking
• CancerAvatarOmeroImporter
• Increasing reproducibility, data quality and fidelity in biomedical imaging through data provenance, quality control and unified imaging pipelines
• Reproducibility and Fidelity in biomedical imaging through the capture of data provenance and the use of easy-to-use unified imaging pipelines
• Cyclophilin A protects HIV-1 from restriction by human TRIM5α.
• OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control
• OmegaProject/OmegaCommons
• OmegaProject/GenericTools
• OmegaProject/OmegaOmeroCommons
• OmegaProject/TrajectoryGenerator
• OmegaProject/ArtificialImageGenerator
• 4DNMicroscopyMetadataTool
• OmegaProject/ImageJPlugins
• CancerAvatarOmeroDataWriter
• From “Pretty Pictures” to Quantitative Datasets: catalyzing advanced open-source image data management and analysis solutions through local application delivery hubs
• Practical demonstration of the Micro-Meta App Java prototype: a tool to collect metadata for standardized imaging experiment annotation
• OmegaProject/Minimum Information About Particle Tracking Experiments (MIAPTE) guidelines
• From “Pretty Pictures” to Quantitative Datasets: shared infrastructure to promote throughput, quality-control, reproducibility and dissemination
• From “Pretty Pictures” to Quantitative Datasets: catalyzing advanced open-source image data management and analysis solutions through local application delivery hubs
• Increasing reproducibility, data quality and fidelity in biomedical imaging through data provenance, quality control and unified imaging pipelines
• Reproducibility in biomedical imaging: the importance of data life-cycle management and metadata standards
• Reproducibility in biomedical imaging: the importance of metadata standards to capture data provenance
• From “Pretty Pictures” to Quantitative Datasets: increasing reproducibility, in biomedical imaging through data management, shared standards and unified pipelines
• Reproducibility in biomedical imaging through the use of flexible and intuitive biomedical imaging pipelines facilitating all steps of the imaging workflow
• Capture, Management and Integration of Experimental information, Image-data, Analysis results, and Error propagation
• OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control
• Towards the establishment of a UMass Bio-Image data Management and Analysis Center
• Minimum Information guidelines for fluorescence microscopy: increasing the value, quality, and fidelity of image data
• Micro-Meta App website
• Microscopy Metadata 4DN Guidelines
• MDEmic in a use case for microscopy metadata harmonization: Facilitating FAIR principles in practical application with metadata annotation tools
• The 4DN-OME ontology: an OME-OWL extension with emphasis on usability, minimum information guidelines and quality control for super-resolution fluorescence microscopy
• OMEGA: viral particle tracking work- and data-flows for images stored in OMERO
• Mutational analysis of the major homology region of Mason-Pfizer monkey virus by use of saturation mutagenesis.
• OMEGA: a novel bioimage informatics tool for integrated image analysis
• The essential yeast nucleoporin NUP159 is located on the cytoplasmic side of the nuclear pore complex and serves in karyopherin-mediated binding of transport substrate.
• Minimum Information About Particle Tracking Experiments.
• Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS.
• The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome.
• OMEGA project website: OMEGA, an open-source tool to foster collaboration in particle tracking experiments
• The nuclear pore complex-associated protein, Mlp2p, binds to the yeast spindle pole body and promotes its efficient assembly.
• Rapid isolation of functionally intact nuclei from the yeast Saccharomyces
• Evidence for biphasic uncoating during HIV-1 infection from a novel imaging assay.
• Presence of Transcriptional Elements in Putative Human Replication Origins
• Jumping over the fence: RNA nuclear export revisited
• OMEGA prototype tool – wiki main page: OMEGA 2011-2012 prototype release
• Optimization of human dendritic cell sample preparation for mass spectrometry-based proteomic studies.
• The Use of Variable Q1 Isolation Windows Improves Selectivity in LC-SWATH-MS Acquisition.
• Processing strategies and software solutions for data-independent acquisition in mass spectrometry.
• Optimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry
• TAPping into transport
• The nuclear pore complex: bridging nuclear transport and gene regulation.
• Gli aggregati sintrofici di Thiodictyion syntrophicum CAD16 e Desulfocapsa thiozymogenes CAD626 del lago di Cadagno
• Proteins connecting the nuclear pore complex with the nuclear interior.
• Two yeast nuclear pore complex proteins involved in mRNA export form a cytoplasmically oriented subcomplex.
• Isolation and characterization of nuclear envelopes from the yeast Saccharomyces.
• Isolation of nuclear envelope from Saccharomyces cerevisiae.
• The structure and composition of the yeast NPC.
• Isolation of Yeast Nuclear Pore Complex and Nuclear Envelopes
• A method for the rapid and efficient elution of native affinity-purified protein A tagged complexes.
• Isolation of Yeast Nuclear Pore Complex and Nuclear Envelopes
• AntiVirX Project Wiki
• Identification and characterization of Mlp1p and Mlp2p: Molecular components of filaments localized at the interface between the nuclear pore complex and the nuclear interior
• Open Microscopy Environment inteGrated Analysis (OMEGA) - alpha prototype
• Open Microscopy Environment inteGrated Analysis (OMEGA)
• Capture, Management and Integration of Experimental information, Image-data, Analysis results, and Error propagation
• Bringing OME to the bench
• OMEGA: viral particle tracking work- and data-flows for images stored in OMERO
• OMEGA: an open source environment to facilitate the execution of motion analysis workflows, to estimate error and to share results
• OMEGA: an open source environment to facilitate the analysis of intra-cellular motion, the estimation of error and the reproducibility and dissemination of analysis results
• OMEGA: an open source environment to facilitate the execution of motion analysis workflows, to estimate error and to share results
• Testing the use of OMERO as a bioimage informatics platform for HIV viral particle tracking
• TRIM5 is an innate immune sensor for the retrovirus capsid lattice.
• Cyclosporine blocks incorporation of HIV-1 envelope glycoprotein into virions.
• Potent inhibition of HIV-1 by TRIM5-cyclophilin fusion proteins engineered from human components.
• An invariant surface patch on the TRIM5alpha PRYSPRY domain is required for retroviral restriction but dispensable for capsid binding.
• Proposal for minimum information guidelines to report and reproduce results of particle tracking and motion analysis
• QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy
• Micro-Meta App - Electron implementation
• Micro-Meta App-OMERO plug-in
• WU-BIMAC/MicroMetaApp-Electron
• Micro-Meta App - React implementation
• Community-developed checklists for publishing images and image analyses
• OMEGA Application
• Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data
• Promoting adoption for Research image Data Management through education, usability, customization, added value, and automation