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The challenges of research data management in cardiovascular science: a DGK and DZHK position paper—executive summary.
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- Clinical Research in Cardiology, 2024, v. 113, n. 5, p. 672, doi. 10.1007/s00392-023-02303-3
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Heterogenous nuclear ribonucleoprotein D-like controls endothelial cell functions.
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- Biological Chemistry, 2024, v. 405, n. 4, p. 229, doi. 10.1515/hsz-2023-0254
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- Article
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation.
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- Nucleic Acids Research, 2024, v. 52, n. 2, p. 769, doi. 10.1093/nar/gkad1097
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Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq.
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- Nucleic Acids Research, 2024, v. 52, n. 1, p. e1, doi. 10.1093/nar/gkad998
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- Article
Transformer-based tool recommendation system in Galaxy.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05573-w
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RNA interaction format: a general data format for RNA interactions.
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- Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad665
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Meta-Analysis of Mechano-Sensitive Ion Channels in Human Hearts: Chamber- and Disease-Preferential mRNA Expression.
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- International Journal of Molecular Sciences, 2023, v. 24, n. 13, p. 10961, doi. 10.3390/ijms241310961
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Tyrosine kinase inhibitors can activate the NLRP3 inflammasome in myeloid cells through lysosomal damage and cell lysis.
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- Science Signaling, 2023, v. 16, n. 768, p. 1, doi. 10.1126/scisignal.abh1083
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Distinct SARS-CoV-2 RNA fragments activate Toll-like receptors 7 and 8 and induce cytokine release from human macrophages and microglia.
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- Frontiers in Immunology, 2023, v. 13, p. 1, doi. 10.3389/fimmu.2022.1066456
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An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy.
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- GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad028
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Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry.
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- MicroLife, 2023, v. 4, p. 1, doi. 10.1093/femsml/uqad001
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Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics.
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- MicroLife, 2023, v. 4, p. 1, doi. 10.1093/femsml/uqad012
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Genome wide CRISPR screen for Pasteurella multocida toxin (PMT) binding proteins reveals LDL Receptor Related Protein 1 (LRP1) as crucial cellular receptor.
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- PLoS Pathogens, 2022, v. 18, n. 12, p. 1, doi. 10.1371/journal.ppat.1010781
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CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection.
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- Bioinformatics, 2022, v. 38, p. ii42, doi. 10.1093/bioinformatics/btac466
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Spectrum of Genetic Variants in a Cohort of 37 Laterality Defect Cases.
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- Frontiers in Genetics, 2022, v. 13, p. 1, doi. 10.3389/fgene.2022.861236
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Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease.
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- Journal of Cheminformatics, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13321-022-00588-6
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RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria.
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- Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbab549
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Peakhood: individual site context extraction for CLIP-seq peak regions.
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- Bioinformatics, 2022, v. 38, n. 4, p. 1139, doi. 10.1093/bioinformatics/btab755
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Loop detection using Hi-C data with HiCExplorer.
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- GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac061
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Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition.
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- Nucleic Acids Research, 2021, v. 49, n. 22, p. 13075, doi. 10.1093/nar/gkab1161
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MicroRNA-100-5p and microRNA-298-5p released from apoptotic cortical neurons are endogenous Toll-like receptor 7/8 ligands that contribute to neurodegeneration.
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- Molecular Neurodegeneration, 2021, v. 16, n. 1, p. 1, doi. 10.1186/s13024-021-00498-5
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temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts.
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- Journal of Experimental Botany, 2021, v. 72, n. 21, p. 7564, doi. 10.1093/jxb/erab416
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Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs.
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- Bioinformatics, 2021, v. 37, n. 22, p. 4006, doi. 10.1093/bioinformatics/btab394
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SARS-CoV-2 sequence submission tool for the European Nucleotide Archive.
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- Bioinformatics, 2021, v. 37, n. 21, p. 3983, doi. 10.1093/bioinformatics/btab421
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RNAProt: an efficient and feature-rich RNA binding protein binding site predictor.
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- GigaScience, 2021, v. 10, n. 8, p. 1, doi. 10.1093/gigascience/giab054
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Scool: a new data storage format for single-cell Hi-C data.
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- Bioinformatics, 2021, v. 37, n. 14/15, p. 2053, doi. 10.1093/bioinformatics/btaa924
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HRIBO: high-throughput analysis of bacterial ribosome profiling data.
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- Bioinformatics, 2021, v. 37, n. 14/15, p. 2061, doi. 10.1093/bioinformatics/btaa959
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- Article
CRISPRloci: comprehensive and accurate annotation of CRISPR–Cas systems.
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- Nucleic Acids Research, 2021, v. 49, n. W1, p. W125, doi. 10.1093/nar/gkab456
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- Article
An Integrated Database of Small RNAs and Their Interplay With Transcriptional Gene Regulatory Networks in Corynebacteria.
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- Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.656435
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StoatyDive: Evaluation and classification of peak profiles for sequencing data.
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- GigaScience, 2021, v. 10, n. 6, p. 1, doi. 10.1093/gigascience/giab045
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Casboundary: automated definition of integral Cas cassettes.
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- Bioinformatics, 2021, v. 37, n. 10, p. 1352, doi. 10.1093/bioinformatics/btaa984
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- Article
CRISPRidentify: identification of CRISPR arrays using machine learning approach.
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- Nucleic Acids Research, 2021, v. 49, n. 4, p. e20, doi. 10.1093/nar/gkaa1158
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pyGenomeTracks: reproducible plots for multivariate genomic datasets.
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- Bioinformatics, 2021, v. 37, n. 3, p. 422, doi. 10.1093/bioinformatics/btaa692
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ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data.
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- GigaScience, 2021, v. 10, n. 2, p. 1, doi. 10.1093/gigascience/giaa158
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Tool recommender system in Galaxy using deep learning.
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- GigaScience, 2021, v. 10, n. 1, p. 1, doi. 10.1093/gigascience/giaa152
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Improving CLIP-seq data analysis by incorporating transcript information.
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- BMC Genomics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12864-020-07297-0
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Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains.
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- Algorithms for Molecular Biology, 2020, v. 15, n. 1, p. 1, doi. 10.1186/s13015-020-00179-w
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Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis.
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- GigaScience, 2020, v. 9, n. 11, p. 1, doi. 10.1093/gigascience/giaa108
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NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy.
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- GigaScience, 2020, v. 9, n. 10, p. 1, doi. 10.1093/gigascience/giaa105
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Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules.
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- Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-72905-8
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Temporospatial distribution and transcriptional profile of retinal microglia in the oxygen‐induced retinopathy mouse model.
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- Glia, 2020, v. 68, n. 9, p. 1859, doi. 10.1002/glia.23810
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The locality dilemma of Sankoff-like RNA alignments.
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- Bioinformatics, 2020, v. 36, p. i242, doi. 10.1093/bioinformatics/btaa431
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Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.
- Published in:
- Nucleic Acids Research, 2020, v. 48, n. W1, p. W177, doi. 10.1093/nar/gkaa220
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MutaRNA: analysis and visualization of mutation-induced changes in RNA structure.
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- Nucleic Acids Research, 2020, v. 48, n. W1, p. W287, doi. 10.1093/nar/gkaa331
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A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence.
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- MicroLife, 2020, v. 1, n. 1, p. 1, doi. 10.1093/femsml/uqaa002
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CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments.
- Published in:
- International Journal of Molecular Sciences, 2020, v. 21, n. 11, p. 3852, doi. 10.3390/ijms21113852
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Heterogeneous networks integration for disease–gene prioritization with node kernels.
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- Bioinformatics, 2020, v. 36, n. 9, p. 2649, doi. 10.1093/bioinformatics/btaa008
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FLASH: ultra-fast protocol to identify RNA–protein interactions in cells.
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- Nucleic Acids Research, 2020, v. 48, n. 3, p. e15, doi. 10.1093/nar/gkz1141
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The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment.
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- BMC Bioinformatics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12859-019-3143-4
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GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering.
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- GigaScience, 2019, v. 8, n. 12, p. N.PAG, doi. 10.1093/gigascience/giz150
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