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Evaluating feature attribution methods in the image domain.
- Published in:
- Machine Learning, 2024, v. 113, n. 9, p. 6019, doi. 10.1007/s10994-024-06550-x
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- Publication type:
- Article
An innate immune signature induced by AS01- or AS03-adjuvanted vaccines predicts the antibody response magnitude and quality consistently over time.
- Published in:
- Frontiers in Immunology, 2024, p. 1, doi. 10.3389/fimmu.2024.1412732
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- Publication type:
- Article
Spotless, a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics.
- Published in:
- eLife, 2024, p. 1, doi. 10.7554/eLife.88431
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- Publication type:
- Article
Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools.
- Published in:
- Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae179
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- Publication type:
- Article
Uncertainty-aware single-cell annotation with a hierarchical reject option.
- Published in:
- Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae128
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- Publication type:
- Article
Machine Learning Pipeline for Predicting Bone Marrow Edema Along the Sacroiliac Joints on Magnetic Resonance Imaging.
- Published in:
- Arthritis & Rheumatology, 2023, v. 75, n. 12, p. 2169, doi. 10.1002/art.42650
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- Publication type:
- Article
A bispecific Clec9A-PD-L1 targeted type I interferon profoundly reshapes the tumor microenvironment towards an antitumor state.
- Published in:
- Molecular Cancer, 2023, v. 22, n. 1, p. 1, doi. 10.1186/s12943-023-01908-6
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- Publication type:
- Article
Gut Inflammation in Axial Spondyloarthritis Patients is Characterized by a Marked Type 17 Skewed Mucosal Innate‐like T Cell Signature.
- Published in:
- Arthritis & Rheumatology, 2023, v. 75, n. 11, p. 1969, doi. 10.1002/art.42627
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- Publication type:
- Article
Functions of the RIP kinase family members in the skin.
- Published in:
- Cellular & Molecular Life Sciences, 2023, v. 80, n. 10, p. 1, doi. 10.1007/s00018-023-04917-2
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- Publication type:
- Article
Single-cell molecular profiling using ex vivo functional readouts fuels precision oncology in glioblastoma.
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- Cellular & Molecular Life Sciences, 2023, v. 80, n. 6, p. 1, doi. 10.1007/s00018-023-04772-1
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- Article
Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.
- Published in:
- 2023
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- Publication type:
- Letter
Single-cell RNA and protein profiling of immune cells from the mouse brain and its border tissues.
- Published in:
- Nature Protocols, 2022, v. 17, n. 10, p. 2354, doi. 10.1038/s41596-022-00716-4
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- Publication type:
- Article
The Euroflow PID Orientation Tube in the diagnostic workup of primary immunodeficiency: Daily practice performance in a tertiary university hospital.
- Published in:
- Frontiers in Immunology, 2022, v. 13, p. 1, doi. 10.3389/fimmu.2022.937738
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- Publication type:
- Article
Challenges in translational machine learning.
- Published in:
- Human Genetics, 2022, v. 141, n. 9, p. 1451, doi. 10.1007/s00439-022-02439-8
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- Publication type:
- Article
CARD14 Signalling Ensures Cell Survival and Cancer Associated Gene Expression in Prostate Cancer Cells.
- Published in:
- Biomedicines, 2022, v. 10, n. 8, p. N.PAG, doi. 10.3390/biomedicines10082008
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- Publication type:
- Article
PeacoQC: Peak‐based selection of high quality cytometry data.
- Published in:
- Cytometry. Part A, 2022, v. 101, n. 4, p. 325, doi. 10.1002/cyto.a.24501
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- Publication type:
- Article
Targeting ferroptosis protects against experimental (multi)organ dysfunction and death.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28718-6
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- Publication type:
- Article
Operational tolerance after hematopoietic stem cell transplantation is characterized by distinct transcriptional, phenotypic, and metabolic signatures.
- Published in:
- Science Translational Medicine, 2022, v. 14, n. 633, p. 1, doi. 10.1126/scitranslmed.abg3083
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- Publication type:
- Article
Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq.
- Published in:
- Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02628-8
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- Publication type:
- Article
SCMFTS: Scalable and Distributed Complexity Measures and Features for Univariate and Multivariate Time Series in Big Data Environments.
- Published in:
- International Journal of Computational Intelligence Systems, 2021, v. 14, n. 1, p. 1, doi. 10.1007/s44196-021-00036-7
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- Publication type:
- Article
OTULIN maintains skin homeostasis by controlling keratinocyte death and stem cell identity.
- Published in:
- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25944-2
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- Publication type:
- Article
Computational flow cytometry as a diagnostic tool in suspected‐myelodysplastic syndromes.
- Published in:
- Cytometry. Part A, 2021, v. 99, n. 8, p. 814, doi. 10.1002/cyto.a.24360
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- Publication type:
- Article
Analyzing high-dimensional cytometry data using FlowSOM.
- Published in:
- Nature Protocols, 2021, v. 16, n. 8, p. 3775, doi. 10.1038/s41596-021-00550-0
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- Publication type:
- Article
Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells.
- Published in:
- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-24152-2
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- Publication type:
- Article
Immune Monitoring in Melanoma and Urothelial Cancer Patients Treated with Anti-PD-1 Immunotherapy and SBRT Discloses Tumor Specific Immune Signatures.
- Published in:
- Cancers, 2021, v. 13, n. 11, p. 2630, doi. 10.3390/cancers13112630
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- Publication type:
- Article
Fibrotic enzymes modulate wound‐induced skin tumorigenesis.
- Published in:
- EMBO Reports, 2021, v. 22, n. 5, p. 1, doi. 10.15252/embr.202051573
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- Publication type:
- Article
Stabilization of Human Whole Blood Samples for Multicenter and Retrospective Immunophenotyping Studies.
- Published in:
- Cytometry. Part A, 2021, v. 99, n. 5, p. 524, doi. 10.1002/cyto.a.24241
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- Publication type:
- Article
Mining Topological Structure in Graphs through Forest Representations.
- Published in:
- Journal of Machine Learning Research, 2020, v. 21, n. 189-216, p. 1
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- Publication type:
- Article
TinGa: fast and flexible trajectory inference with Growing Neural Gas.
- Published in:
- Bioinformatics, 2020, v. 36, p. i66, doi. 10.1093/bioinformatics/btaa463
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- Publication type:
- Article
A scalable SCENIC workflow for single-cell gene regulatory network analysis.
- Published in:
- Nature Protocols, 2020, v. 15, n. 7, p. 2247, doi. 10.1038/s41596-020-0336-2
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- Publication type:
- Article
Trajectory-based differential expression analysis for single-cell sequencing data.
- Published in:
- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-14766-3
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- Publication type:
- Article
Special Issue on Machine Learning for Single Cell Data.
- Published in:
- Cytometry. Part A, 2020, v. 97, n. 3, p. 217, doi. 10.1002/cyto.a.23986
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- Publication type:
- Article
CytoNorm: A Normalization Algorithm for Cytometry Data.
- Published in:
- Cytometry. Part A, 2020, v. 97, n. 3, p. 268, doi. 10.1002/cyto.a.23904
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- Publication type:
- Article
Classification of Human White Blood Cells Using Machine Learning for Stain‐Free Imaging Flow Cytometry.
- Published in:
- Cytometry. Part A, 2020, v. 97, n. 3, p. 308, doi. 10.1002/cyto.a.23920
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- Publication type:
- Article
An interactive ImageJ plugin for semi-automated image denoising in electron microscopy.
- Published in:
- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-14529-0
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- Publication type:
- Article
A Computational Pipeline for the Diagnosis of CVID Patients.
- Published in:
- Frontiers in Immunology, 2019, p. 1, doi. 10.3389/fimmu.2019.02009
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- Publication type:
- Article
Essential guidelines for computational method benchmarking.
- Published in:
- Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1738-8
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- Publication type:
- Article
A comparison of single-cell trajectory inference methods.
- Published in:
- Nature Biotechnology, 2019, v. 37, n. 5, p. 547, doi. 10.1038/s41587-019-0071-9
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- Publication type:
- Article
Nlrp3 inflammasome activation and Gasdermin D-driven pyroptosis are immunopathogenic upon gastrointestinal norovirus infection.
- Published in:
- PLoS Pathogens, 2019, v. 15, n. 4, p. 1, doi. 10.1371/journal.ppat.1007709
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- Publication type:
- Article
Computational approaches for high‐throughput single‐cell data analysis.
- Published in:
- FEBS Journal, 2019, v. 286, n. 8, p. 1451, doi. 10.1111/febs.14613
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- Publication type:
- Article
Stabilization of cytokine mRNAs in iNKT cells requires the serine-threonine kinase IRE1alpha.
- Published in:
- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-07758-x
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- Publication type:
- Article
SpliceRover: interpretable convolutional neural networks for improved splice site prediction.
- Published in:
- Bioinformatics, 2018, v. 34, n. 24, p. 4180, doi. 10.1093/bioinformatics/bty497
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- Publication type:
- Article
Myocarditis Elicits Dendritic Cell and Monocyte Infiltration in the Heart and Self-Antigen Presentation by Conventional Type 2 Dendritic Cells.
- Published in:
- Frontiers in Immunology, 2018, p. N.PAG, doi. 10.3389/fimmu.2018.02714
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- Publication type:
- Article
Mechanical strain determines the site-specific localization of inflammation and tissue damage in arthritis.
- Published in:
- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-06933-4
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- Publication type:
- Article
Dynamic affinity-based classification of multi-class imbalanced data with one-versus-one decomposition: a fuzzy rough set approach.
- Published in:
- Knowledge & Information Systems, 2018, v. 56, n. 1, p. 55, doi. 10.1007/s10115-017-1126-1
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- Publication type:
- Article
<italic>Nanos</italic> genes and their role in development and beyond.
- Published in:
- Cellular & Molecular Life Sciences, 2018, v. 75, n. 11, p. 1929, doi. 10.1007/s00018-018-2766-3
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- Publication type:
- Article
Ancient Origin of the CARD–Coiled Coil/Bcl10/MALT1-Like Paracaspase Signaling Complex Indicates Unknown Critical Functions.
- Published in:
- Frontiers in Immunology, 2018, p. 1, doi. 10.3389/fimmu.2018.01136
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- Publication type:
- Article
IncGraph: Incremental graphlet counting for topology optimisation.
- Published in:
- PLoS ONE, 2018, v. 13, n. 4, p. 1, doi. 10.1371/journal.pone.0195997
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- Publication type:
- Article
A comprehensive evaluation of module detection methods for gene expression data.
- Published in:
- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03424-4
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- Publication type:
- Article
GC Content of Early Metazoan Genes and Its Impact on Gene Expression Levels in Mammalian Cell Lines.
- Published in:
- Genome Biology & Evolution, 2018, v. 10, n. 3, p. 909, doi. 10.1093/gbe/evy040
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- Publication type:
- Article