338 results found
    1. Computational and Systems Biology

    Simplifying the development of portable, scalable, and reproducible workflows

    Stephen R Piccolo et al.
    Descriptions, examples, and tools to enable biologists to use the Common Workflow Language for data processing and to facilitate computational reproducibility.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    An open-source computational and data resource to analyze digital maps of immunopeptidomes

    Etienne Caron et al.
    A community-based international effort generates standardized HLA allele-specific peptide assay libraries and enables the analysis of the human immunopeptidome by SWATH mass spectrometry.
    1. Cancer Biology

    Replication Study: Biomechanical remodeling of the microenvironment by stromal caveolin-1 favors tumor invasion and metastasis

    Mee Rie Sheen et al.
    Editors' Summary: This Replication Study has reproduced some parts of the original paper but other parts could not be interpreted.
    1. Structural Biology and Molecular Biophysics

    Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

    Dari Kimanius et al.
    Using GPUs for the costly computations in cryo-EM enables structure determination in mere days on a single workstation.
    1. Computational and Systems Biology

    Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species

    Arnaud Belcour et al.
    Computational models and software connect metagenomics to metabolic network reconstruction, assess metabolic complementarity between species, and identify critical species associated to functions of interest.
    1. Cell Biology

    Automated cell-type classification in intact tissues by single-cell molecular profiling

    Monica Nagendran et al.
    The ability to rapidly stain for any combination of genes in intact tissue with automated quantification of transcripts in individual cells and spatial re-mapping affords new insights into lung biology, and will greatly accelerate progress in scientific and medical research.
    1. Neuroscience

    FluoEM, virtual labeling of axons in three-dimensional electron microscopy data for long-range connectomics

    Florian Drawitsch et al.
    Methodology to annotate the multiple origins of axonal projections in dense electron microscopy data of mammalian nervous tissue without the need of chemical label conversion is reported.
    1. Computational and Systems Biology
    2. Immunology and Inflammation

    ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data

    James W Opzoomer et al.
    ImmunoCluster permits nonspecialist users to interrogate liquid and imaging mass, and flow cytometry datasets, resolving novel layers of cellular heterogeneity and insight, as well as producing publishable outputs and figures.
    1. Neuroscience

    Accelerating with FlyBrainLab the discovery of the functional logic of the Drosophila brain in the connectomic and synaptomic era

    Aurel A Lazar et al.
    FlyBrainLab is an open-source computing platform that integrates 3D exploration and visualization of diverse Drosophila connectomic/synaptomic datasets with interactive exploration of the functional logic of modeled executable brain circuits.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Highly contiguous assemblies of 101 drosophilid genomes

    Bernard Y Kim et al.
    One hundred one high-quality drosophilid genomes are released, along with low-cost assembly workflows, as an open community resource for studying genetics, ecology, and evolution in this important model system.

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