{"type": "FeatureCollection", "features": [{"id": "10.1016/j.apsoil.2017.05.029", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:15:43Z", "type": "Journal Article", "created": "2017-06-30", "title": "A large set of microsatellites for the highly invasive earthworm Amynthas corticis predicted from low coverage genomes", "description": "Invasive species can significantly affect local biodiversity and create important challenges for conservation. They usually present an outstanding plasticity that permits the adaptation to the new environments. Understanding their genetic background is fundamental to better comprehend invasion dynamics and elaborate proper management plans as well to infer population and evolutionary patterns. Here, we present a reasonable set of tools for the study of a highly invasive earthworm, the megascolecid Amynthas corticis. We designed in silico a large set of primers targeting microsatellite regions (ca. 9400) from two low coverage genomes presented here. This study provides 154 high quality primer pairs targeting polymorphic repeats conserved in two Amynthas corticis mitochondrial lineages. From this dataset, a set of primer pairs (15) was validated by polymerase chain reaction with 86% consistent amplification, confirming the accuracy of the in silico prediction. Nine of the primer pairs tested were selected for population genetics and presented polymorphism in the studied populations, thus showing promising potential for future studies of this global invasive species. The nuclear markers used in this study appear to recapitulate and complement the mitochondrial relationships found in a previous study. Interestingly, all genotyped individuals showed at least one triploid locus profile among the tested loci, which may be evidence of polyploidy associated to their life history, in particular to asexual reproduction by parthenogenesis.", "keywords": ["Ecolog\u00eda (Biolog\u00eda)", "Microsatellite markers", "Invasive species", "Invertebrados", "15. Life on land", "636.082.11", "Gen\u00e9tica", "2401.08 Gen\u00e9tica Animal", "3. Good health", "2401.91 Invertebrados no Insectos", "Bioinformatics prediction", "2401.06 Ecolog\u00eda Animal", "595.1", "Earthworms", "Mitochondrial lineages", "574.3"]}, "links": [{"href": "https://orca.cardiff.ac.uk/id/eprint/101404/1/Applied%20soil.pdf"}, {"href": "https://doi.org/10.1016/j.apsoil.2017.05.029"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Soil%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.apsoil.2017.05.029", "name": "item", "description": "10.1016/j.apsoil.2017.05.029", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2017.05.029"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-10-01T00:00:00Z"}}, {"id": "10.1111/1462-2920.13954", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:20Z", "type": "Journal Article", "created": "2022-10-18", "title": "Application of stable-isotope labelling techniques for the detection of active diazotrophs", "description": "Summary<p>Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free\uffe2\uff80\uff90living or symbionts. Free\uffe2\uff80\uff90living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15N\uffe2\uff80\uff90based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15N\uffe2\uff80\uff90RNA\uffe2\uff80\uff90SIP approach optimized for environmental samples and benchmarked to 15N\uffe2\uff80\uff90DNA\uffe2\uff80\uff90SIP. Lastly, we investigated the feasibility of using SIP\uffe2\uff80\uff90Raman microspectroscopy for detecting 15N\uffe2\uff80\uff90labelled cells. Taken together, these tools allow identifying and investigating active free\uffe2\uff80\uff90living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single\uffe2\uff80\uff90cell level.</p>", "keywords": ["Spectrum Analysis", " Raman", "BIOLOGICAL SOIL CRUSTS", "106005 Bioinformatik", "106023 Molekularbiologie", "Nitrogen Fixation", "REVEALS", "FLUORESCENCE", "Research Articles", "Soil Microbiology", "106022 Mikrobiologie", "SPECTROSCOPY", "Bacteria", "Nitrogen Isotopes", "106003 Biodiversity research", "106023 Molecular biology", "GENETIC-REGULATION", "Archaea", "6. Clean water", "SURFACE-ENHANCED RAMAN", "COMMUNITY", "106003 Biodiversit\u00e4tsforschung", "13. Climate action", "Isotope Labeling", "106022 Microbiology", "NITROGEN-FIXATION", "106005 Bioinformatics", "RIBOSOMAL-RNA", "N-2 FIXATION"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13954"}, {"href": "https://doi.org/10.1111/1462-2920.13954"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.13954", "name": "item", "description": "10.1111/1462-2920.13954", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.13954"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-12-15T00:00:00Z"}}, {"id": "10.1016/j.xgen.2024.100639", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:17:10Z", "type": "Journal Article", "created": "2024-08-30", "title": "ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers", "description": "The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.", "keywords": ["330", "Bioinformatics", "Genome", " Human", "610", "Genomics", "Medical Oncology", "Somatic variant calling", "Polymorphism", " Single Nucleotide", "Article", "Benchmarking", "Oncology", "INDEL Mutation", "\u00c0rees tem\u00e0tiques de la UPC::Inform\u00e0tica::Aplicacions de la inform\u00e0tica::Bioinform\u00e0tica", "Neoplasms", "Cancer genomics", "Humans", "Benchmarking data", "Precision Medicine", "Software"]}, "links": [{"href": "https://doi.org/10.1016/j.xgen.2024.100639"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Cell%20Genomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.xgen.2024.100639", "name": "item", "description": "10.1016/j.xgen.2024.100639", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.xgen.2024.100639"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-09-01T00:00:00Z"}}, {"id": "10.1038/s41598-018-27781-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:17:35Z", "type": "Journal Article", "created": "2018-06-15", "title": "Characterization of a community-acquired-MRSA USA300 isolate from a river sample in Austria and whole genome sequence based comparison to a diverse collection of USA300 isolates", "description": "Abstract<p>The increasing emergence of multi-resistant bacteria in healthcare settings, in the community and in the environment represents a major health threat worldwide. In 2016, we started a pilot project to investigate antimicrobial resistance in surface water. Bacteria were enriched, cultivated on selective chromogenic media and species identification was carried out by MALDI-TOF analysis. From a river in southern Austria a methicillin resistant Staphylococcus aureus (MRSA) was isolated. Whole genome sequence analysis identified the isolate as ST8, spa type t008, SCCmecIV, PVL and ACME positive, which are main features of CA-MRSA USA300. Whole genome based cgMLST of the water isolate and comparison to 18 clinical MRSA USA300 isolates from the Austrian national reference laboratory for coagulase positive staphylococci originating from 2004, 2005 and 2016 and sequences of 146 USA300 isolates arbitrarily retrieved from the Sequence Read Archive revealed a close relatedness to a clinical isolate from Austria. The presence of a CA-MRSA USA300 isolate in an aquatic environment might pose a public health risk by serving as a potential source of infection or a source for emergence of new pathogenic MRSA clones.</p>", "keywords": ["Methicillin-Resistant Staphylococcus aureus", "0301 basic medicine", "METHICILLIN-RESISTANT", "GENES", "TRANSMISSION", "Article", "Applied microbiology", "EMERGENCE", "03 medical and health sciences", "106005 Bioinformatik", "SDG 3 - Good Health and Well-being", "Rivers", "Sequence Homology", " Nucleic Acid", "Infectious-disease epidemiology", "ENVIRONMENT", "0303 health sciences", "ANTIMICROBIAL RESISTANCE", "RESISTANT STAPHYLOCOCCUS-AUREUS", "ANTIBIOTIC-RESISTANCE", "EVOLUTION", "3. Good health", "Community-Acquired Infections", "SDG 3 \u2013 Gesundheit und Wohlergehen", "Austria", "VIRULENCE", "Bacterial infection", "106005 Bioinformatics", "Genome", " Bacterial"]}, "links": [{"href": "https://www.nature.com/articles/s41598-018-27781-8.pdf"}, {"href": "https://doi.org/10.1038/s41598-018-27781-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-018-27781-8", "name": "item", "description": "10.1038/s41598-018-27781-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-018-27781-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-06-21T00:00:00Z"}}, {"id": "10.1080/1040841x.2022.2132850", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:01Z", "type": "Journal Article", "created": "2022-10-26", "title": "Bioinformatic approaches for studying the microbiome of fermented food", "description": "High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.", "keywords": ["2. Zero hunger", "0301 basic medicine", "metatranscriptomics", "Microbiota", "0206 medical engineering", "high-throughput sequencing", "Computational Biology", "High-Throughput Nucleotide Sequencing", "bioinformatics", "02 engineering and technology", "fermented foods", "03 medical and health sciences", "Metagenome", "Metagenomics", "Fermented Foods"]}, "links": [{"href": "https://www.tandfonline.com/doi/pdf/10.1080/1040841X.2022.2132850"}, {"href": "https://doi.org/10.1080/1040841x.2022.2132850"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Critical%20Reviews%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1080/1040841x.2022.2132850", "name": "item", "description": "10.1080/1040841x.2022.2132850", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1080/1040841x.2022.2132850"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-10-26T00:00:00Z"}}, {"id": "10.1093/bioinformatics/btz584", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:07Z", "type": "Journal Article", "created": "2019-08-19", "title": "MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network", "description": "Abstract                                   Motivation                   <p>Analysis of differential expression of genes is often performed to understand how the metabolic activity of an organism is impacted by a perturbation. However, because the system of metabolic regulation is complex and all changes are not directly reflected in the expression levels, interpreting these data can be difficult.</p>                                                   Results                   <p>In this work, we present a new algorithm and computational tool that uses a genome-scale metabolic reconstruction to infer metabolic changes from differential expression data. Using the framework of constraint-based analysis, our method produces a qualitative hypothesis of a change in metabolic activity. In other words, each reaction of the network is inferred to have increased, decreased, or remained unchanged in flux. In contrast to similar previous approaches, our method does not require a biological objective function and does not assign on/off activity states to genes. An implementation is provided and it is available online. We apply the method to three published datasets to show that it successfully accomplishes its two main goals: confirming or rejecting metabolic changes suggested by differentially expressed genes based on how well they fit in as parts of a coordinated metabolic change, as well as inferring changes in reactions whose genes did not undergo differential expression.</p>                                                   Availability and implementation                   <p>github.com/htpusa/moomin.</p>                                                   Supplementary information                   <p>Supplementary data are available at Bioinformatics online.</p>", "keywords": ["0301 basic medicine", "570", "[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Metabolic networks; omics data", "Genome", "[INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS]", "0206 medical engineering", "610", "Computational Biology", "[INFO.INFO-DS] Computer Science [cs]/Data Structures and Algorithms [cs.DS]", "02 engineering and technology", "[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Original Papers", "Models", " Biological", "03 medical and health sciences", "[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]", "Algorithms", "Metabolic Networks and Pathways", "[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]"]}, "links": [{"href": "https://iris.uniroma1.it/bitstream/11573/1321358/5/Pusa_MOOMIN_2020.pdf"}, {"href": "https://academic.oup.com/bioinformatics/article-pdf/36/2/514/48991611/btz584.pdf"}, {"href": "https://doi.org/10.1093/bioinformatics/btz584"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/bioinformatics/btz584", "name": "item", "description": "10.1093/bioinformatics/btz584", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/bioinformatics/btz584"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-22T00:00:00Z"}}, {"id": "10.1111/1462-2920.16213", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:21Z", "type": "Journal Article", "created": "2022-10-18", "title": "Application of stable\u2010isotope labelling techniques for the detection of active diazotrophs", "description": "Summary<p>Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free\uffe2\uff80\uff90living or symbionts. Free\uffe2\uff80\uff90living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15N\uffe2\uff80\uff90based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15N\uffe2\uff80\uff90RNA\uffe2\uff80\uff90SIP approach optimized for environmental samples and benchmarked to 15N\uffe2\uff80\uff90DNA\uffe2\uff80\uff90SIP. Lastly, we investigated the feasibility of using SIP\uffe2\uff80\uff90Raman microspectroscopy for detecting 15N\uffe2\uff80\uff90labelled cells. Taken together, these tools allow identifying and investigating active free\uffe2\uff80\uff90living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single\uffe2\uff80\uff90cell level.</p", "keywords": ["Spectrum Analysis", " Raman", "BIOLOGICAL SOIL CRUSTS", "106005 Bioinformatik", "106023 Molekularbiologie", "Nitrogen Fixation", "REVEALS", "FLUORESCENCE", "Research Articles", "Soil Microbiology", "106022 Mikrobiologie", "SPECTROSCOPY", "Bacteria", "Nitrogen Isotopes", "106003 Biodiversity research", "106023 Molecular biology", "GENETIC-REGULATION", "Archaea", "6. Clean water", "SURFACE-ENHANCED RAMAN", "COMMUNITY", "106003 Biodiversit\u00e4tsforschung", "13. Climate action", "Isotope Labeling", "106022 Microbiology", "NITROGEN-FIXATION", "106005 Bioinformatics", "RIBOSOMAL-RNA", "N-2 FIXATION"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13954"}, {"href": "https://doi.org/10.1111/1462-2920.16213"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.16213", "name": "item", "description": "10.1111/1462-2920.16213", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.16213"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-12-15T00:00:00Z"}}, {"id": "10.1128/msystems.00859-24", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:18:53Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACT                                     <p>               Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s               V               = 0.857, and Theil\uffe2\uff80\uff99s               U               = 0.316). For species-level community profiling, we found strong correlations (               r                                s                              &gt; 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average               r                                s                              = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.             </p>                            IMPORTANCE               <p>A quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.</p>", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/10.1128/msystems.00859-24"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00859-24", "name": "item", "description": "10.1128/msystems.00859-24", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00859-24"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "10.1534/g3.119.400716", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:19:15Z", "type": "Journal Article", "created": "2020-01-10", "title": "Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors", "description": "Abstract                <p>Bacillus firmus nematicidal bacterial strains are used to control plant parasitic nematode infestation of crops in agricultural production. Proteases are presumed to be the primary nematode virulence factors in nematicidal B. firmus degrading the nematode cuticle and other organs. We determined and compared the whole genome sequences of two nematicidal strains. Comparative genomics with a particular focus on possible virulence determinants revealed a wider range of possible virulence factors in a B. firmus isolate from a commercial bionematicide and a wild type Bacillus sp. isolate with nematicidal activity. The resulting 4.6 Mb B. firmus I-1582 and 5.3 Mb Bacillus sp. ZZV12-4809 genome assemblies contain respectively 18 and 19 homologs to nematode-virulent proteases, two nematode-virulent chitinase homologs in ZZV12-4809 and 28 and 36 secondary metabolite biosynthetic clusters, projected to encode antibiotics, small peptides, toxins and siderophores. The results of this study point to the genetic capability of B. firmus and related species for nematode virulence through a range of direct and indirect mechanisms.</p", "keywords": ["2. Zero hunger", "Whole Genome Sequencing", "complete genomes", "Virulence Factors", "Antinematodal Agents", "virulence factors", "bacillus firmus", "biological control", "Bacillus", "bioinformatics", "Genomics", "QH426-470", "Genome Report", "3. Good health", "Bacterial Proteins", "Drug Resistance", " Bacterial", "Genetics", "BACILLUS FIRMUS", " COMPLETE GENOMES", " BIOINFORMATICS", " BIOLOGICAL CONTROL", " NEMATICIDAL ACTIVITY", " VIRULENCE FACTORS", "Bacillus firmus", "nematicidal activity", "Genome", " Bacterial"]}, "links": [{"href": "http://academic.oup.com/g3journal/article-pdf/10/3/881/38825647/g3journal0881.pdf"}, {"href": "https://doi.org/10.1534/g3.119.400716"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/G3%20Genes%7CGenomes%7CGenetics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1534/g3.119.400716", "name": "item", "description": "10.1534/g3.119.400716", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1534/g3.119.400716"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-01T00:00:00Z"}}, {"id": "10.25387/g3.11522544.v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:20:08Z", "type": "Dataset", "created": "2020-01-09", "title": "Supplemental Material for Susi\u010d et al., 2020", "description": "Supplemental data corresponding to the manuscript titled: Whole genome sequencing and comparative genomics of two nematicidal <i>Bacillus</i> strains reveals a wide range of possible virulence factors. The data include the morphological characteristics of the two studied strains; 16S analysis; detailed phylogenetic positioning of the two strains within the genus Bacillus; detailed ANI, Tetra and TCS scores; strain-specific homologous clusters and their GO-term affiliations; BLASTP hits for putative nematode-virulent proteases; putative chitinase sequences analysis; and predicted/putative secondary metabolite clusters (antiSMASH analysis).<br>", "keywords": ["FOS: Computer and information sciences", "60503 Microbial Genetics", "FOS: Biological sciences", "60408 Genomics", "Microbiology", "60501 Bacteriology", "60102 Bioinformatics"], "contacts": [{"organization": "Susi\u010d, Nik, Jane\u017ei\u010d, Sandra, Rupnik, Maja, Stare, Barbara Geri\u010d,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.25387/g3.11522544.v1"}, {"rel": "self", "type": "application/geo+json", "title": "10.25387/g3.11522544.v1", "name": "item", "description": "10.25387/g3.11522544.v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.25387/g3.11522544.v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}, {"id": "10.25387/g3.11522544", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:20:08Z", "type": "Dataset", "created": "2020-01-09", "title": "Supplemental Material for Susi\u010d et al., 2020", "description": "Supplemental data corresponding to the manuscript titled: Whole genome sequencing and comparative genomics of two nematicidal <i>Bacillus</i> strains reveals a wide range of possible virulence factors. The data include the morphological characteristics of the two studied strains; 16S analysis; detailed phylogenetic positioning of the two strains within the genus Bacillus; detailed ANI, Tetra and TCS scores; strain-specific homologous clusters and their GO-term affiliations; BLASTP hits for putative nematode-virulent proteases; putative chitinase sequences analysis; and predicted/putative secondary metabolite clusters (antiSMASH analysis).<br>", "keywords": ["FOS: Computer and information sciences", "60503 Microbial Genetics", "FOS: Biological sciences", "60408 Genomics", "Microbiology", "60501 Bacteriology", "60102 Bioinformatics"], "contacts": [{"organization": "Susi\u010d, Nik, Jane\u017ei\u010d, Sandra, Rupnik, Maja, Stare, Barbara Geri\u010d,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.25387/g3.11522544"}, {"rel": "self", "type": "application/geo+json", "title": "10.25387/g3.11522544", "name": "item", "description": "10.25387/g3.11522544", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.25387/g3.11522544"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-01-01T00:00:00Z"}}, {"id": "10.31219/osf.io/jfdb9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:20:11Z", "type": "Journal Article", "created": "2021-03-15", "title": "Overcoming the challenges to enhancing experimental plant biology with computational modeling", "description": "<p>The study of complex biological systems necessitates computational modeling approaches that are currently underutilized in plant biology. Many plant biologists have trouble identifying or adopting modeling methods to their research, particularly mechanistic mathematical modeling. Here we address challenges that limit the use of computational modeling methods, particularly mechanistic mathematical modeling. We divide computational modeling techniques into either pattern models (e.g., bioinformatics, machine learning, or morphology) or mechanistic mathematical models (e.g., biochemical reactions, biophysics, or population models), which both contribute to plant biology research at different scales to answer different research questions. We present arguments and recommendations for the increased adoption of modeling by plant biologists interested in incorporating more modeling into their research programs. As some researchers find math and quantitative methods to be an obstacle to modeling, we provide suggestions for easy-to-use tools for non-specialists and for collaboration with specialists. This may especially be the case for mechanistic mathematical modeling, and we spend some extra time discussing this. Through a more thorough appreciation and awareness of the power of different kinds of modeling in plant biology, we hope to facilitate interdisciplinary, transformative research.</p>", "keywords": ["Other Physical Sciences and Mathematics", "computational modeling", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "experimental design", "Systems Biology", "Plant Sciences", "Research Methods in Life Sciences", "mathematical modeling", "Life Sciences", "Plant culture", "bioinformatics", "Plant Science", "collaboration", "SB1-1110", "03 medical and health sciences", "Other Life Sciences", "Physical Sciences and Mathematics"]}, "links": [{"href": "https://doi.org/10.31219/osf.io/jfdb9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.31219/osf.io/jfdb9", "name": "item", "description": "10.31219/osf.io/jfdb9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.31219/osf.io/jfdb9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-15T00:00:00Z"}}, {"id": "10.3389/fams.2019.00018", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:20:13Z", "type": "Journal Article", "created": "2019-04-12", "title": "Metabolic Games", "description": "Metabolic networks have been used to successfully predict phenotypes based on optimization principles. However, a general framework that would extend to situations not governed by simple optimization, such as multispecies communities, is still lacking. Concepts from evolutionary game theory have been proposed to amend the situation. Alternative metabolic states can be seen as strategies in a \u201cmetabolic game,\u201d and phenotypes can be predicted based on the equilibria of this game. In this survey, we review the literature on applying game theory to the study of metabolism, present the general idea of a metabolic game, and discuss open questions and future challenges.", "keywords": ["T57-57.97", "[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Applied mathematics. Quantitative methods", "flux balance analysis", "microbial interactions", "01 natural sciences", "QA273-280", "metabolic modeling", "0103 physical sciences", "metabolic networks", "[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation", "evolutionary game theory", "Probabilities. Mathematical statistics", "[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]"]}, "links": [{"href": "https://doi.org/10.3389/fams.2019.00018"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Applied%20Mathematics%20and%20Statistics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fams.2019.00018", "name": "item", "description": "10.3389/fams.2019.00018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fams.2019.00018"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-12T00:00:00Z"}}, {"id": "10.3390/s24113556", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:20:35Z", "type": "Journal Article", "created": "2024-05-31", "title": "Prediction Accuracy of Soil Chemical Parameters by Field- and Laboratory-Obtained vis-NIR Spectra after External Parameter Orthogonalization", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>One challenge in predicting soil parameters using in situ visible and near infrared spectroscopy is the distortion of the spectra due to soil moisture. External parameter orthogonalization (EPO) is a mathematical method to remove unwanted variability from spectra. We created two different EPO correction matrices based on the difference between spectra collected in situ and, respectively, spectra collected from the same soil samples after drying and sieving and after drying, sieving and finely grinding. Spectra from 134 soil samples recorded with two different spectrometers were split into calibration and validation sets and the two EPO corrections were applied. Clay, organic carbon and total nitrogen content were predicted by partial least squares regression for uncorrected and EPO-corrected spectra using models based on the same type of spectra (\u201cwithin domain\u201d) as well as using laboratory-based models to predict in situ collected spectra (\u201ccross-domain\u201d). Our results show that the within-domain prediction of clay is improved with EPO corrections only for the research grade spectrometer, with no improvement for the other parameters. For the cross-domain predictions, there was a positive effect from both EPO corrections on all parameters. Overall, we also found that in situ collected spectra provided an equally successful prediction as laboratory-based spectra.</p></article>", "keywords": ["EJP Soil", "570", "ProbeField", "Medical Sciences", "Bioinformatics", "clay content", "in situ soil spectroscopy", "TP1-1185", "01 natural sciences", "630", "Article", "Biomedical Informatics", "PLSR", "Medical Specialties", "Medicine and Health Sciences", "Spectroscopy", "soil spectroscopy", "proximal sensing", "0105 earth and related environmental sciences", "spectrometers", "Chemical technology", "rdCV", "04 agricultural and veterinary sciences", "soil organic carbon", "total nitrogen", "Oncology", "0401 agriculture", " forestry", " and fisheries", "soil moisture", "EPO"]}, "links": [{"href": "https://doi.org/10.3390/s24113556"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Sensors", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/s24113556", "name": "item", "description": "10.3390/s24113556", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/s24113556"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-05-31T00:00:00Z"}}, {"id": "10.7717/peerj.7421", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-24T16:23:37Z", "type": "Journal Article", "created": "2019-10-04", "title": "Different expression pattern of flowering pathway genes contribute to male or female organ development during floral transition in the monoecious weedAmbrosia artemisiifoliaL. (Asteraceae)", "description": "<p>The highly allergenic and invasive weedAmbrosia artemisiifoliaL. is a monoecius plant with separated male and female flowers. The genetic regulation of floral morphogenesis is a less understood field in the reproduction biology of this species. Therefore the objective of this work was to investigate the genetic control of sex determination during floral organogenesis. To this end, we performed a genome-wide transcriptional profiling of vegetative and generative tissues during the plant development comparing wild-growing and in vitro cultivated plants. RNA-seq on Illumina NextSeq 500 platform with an integrative bioinformatics analysis indicated differences in 80 floral gene expressions depending on photoperiodic and endogenous initial signals. Sex specificity of genes was validated based on RT-qPCR experiments. We found 11 and 16 uniquely expressed genes in female and male transcriptomes that were responsible particularly to maintain fertility and against abiotic stress. High gene expression of homologous such as FD, FT, TFL1 and CAL, SOC1, AP1 were characteristic to male and female floral meristems during organogenesis. Homologues transcripts of LFY and FLC were not found in the investigated generative and vegetative tissues. The repression of AP1 by TFL1 homolog was demonstrated in male flowers resulting exclusive expression of AP2 and PI that controlled stamen and carpel formation in the generative phase. Alterations of male and female floral meristem differentiation were demonstrated under photoperiodic and hormonal condition changes by applying in vitro treatments.</p", "keywords": ["0301 basic medicine", "0303 health sciences", "QH301-705.5", "Bioinformatics", "R", "03 medical and health sciences", "Organ development", "Medicine", "Flowering pathway", "14. Life underwater", "Biology (General)", "Transcriptomics", "Ambrosia artemisiifolia", "Monoecious"]}, "links": [{"href": "https://doi.org/10.7717/peerj.7421"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PeerJ", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.7717/peerj.7421", "name": "item", "description": "10.7717/peerj.7421", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.7717/peerj.7421"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-10-04T00:00:00Z"}}, {"id": "2117/418477", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:24:39Z", "type": "Journal Article", "created": "2024-08-30", "title": "ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers", "description": "The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.", "keywords": ["330", "Bioinformatics", "Genome", " Human", "610", "Genomics", "Medical Oncology", "Somatic variant calling", "Polymorphism", " Single Nucleotide", "Article", "Benchmarking", "Oncology", "INDEL Mutation", "\u00c0rees tem\u00e0tiques de la UPC::Inform\u00e0tica::Aplicacions de la inform\u00e0tica::Bioinform\u00e0tica", "Neoplasms", "Cancer genomics", "Humans", "Benchmarking data", "Precision Medicine", "Software"]}, "links": [{"href": "https://doi.org/2117/418477"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Cell%20Genomics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2117/418477", "name": "item", "description": "2117/418477", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2117/418477"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-09-01T00:00:00Z"}}, {"id": "2764305888", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:24:50Z", "type": "Journal Article", "created": "2022-10-18", "title": "Application of stable\u2010isotope labelling techniques for the detection of active diazotrophs", "description": "Summary<p>Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free\uffe2\uff80\uff90living or symbionts. Free\uffe2\uff80\uff90living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15N\uffe2\uff80\uff90based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15N\uffe2\uff80\uff90RNA\uffe2\uff80\uff90SIP approach optimized for environmental samples and benchmarked to 15N\uffe2\uff80\uff90DNA\uffe2\uff80\uff90SIP. Lastly, we investigated the feasibility of using SIP\uffe2\uff80\uff90Raman microspectroscopy for detecting 15N\uffe2\uff80\uff90labelled cells. Taken together, these tools allow identifying and investigating active free\uffe2\uff80\uff90living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single\uffe2\uff80\uff90cell level.</p", "keywords": ["Spectrum Analysis", " Raman", "BIOLOGICAL SOIL CRUSTS", "106005 Bioinformatik", "106023 Molekularbiologie", "Nitrogen Fixation", "REVEALS", "FLUORESCENCE", "Research Articles", "Soil Microbiology", "106022 Mikrobiologie", "SPECTROSCOPY", "Bacteria", "Nitrogen Isotopes", "106003 Biodiversity research", "106023 Molecular biology", "GENETIC-REGULATION", "Archaea", "6. Clean water", "SURFACE-ENHANCED RAMAN", "COMMUNITY", "106003 Biodiversit\u00e4tsforschung", "13. Climate action", "Isotope Labeling", "106022 Microbiology", "NITROGEN-FIXATION", "106005 Bioinformatics", "RIBOSOMAL-RNA", "N-2 FIXATION"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13954"}, {"href": "https://doi.org/2764305888"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2764305888", "name": "item", "description": "2764305888", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2764305888"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-12-15T00:00:00Z"}}, {"id": "2977681695", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-24T16:24:58Z", "type": "Journal Article", "created": "2019-10-04", "title": "Different expression pattern of flowering pathway genes contribute to male or female organ development during floral transition in the monoecious weedAmbrosia artemisiifoliaL. (Asteraceae)", "description": "<p>The highly allergenic and invasive weedAmbrosia artemisiifoliaL. is a monoecius plant with separated male and female flowers. The genetic regulation of floral morphogenesis is a less understood field in the reproduction biology of this species. Therefore the objective of this work was to investigate the genetic control of sex determination during floral organogenesis. To this end, we performed a genome-wide transcriptional profiling of vegetative and generative tissues during the plant development comparing wild-growing and in vitro cultivated plants. RNA-seq on Illumina NextSeq 500 platform with an integrative bioinformatics analysis indicated differences in 80 floral gene expressions depending on photoperiodic and endogenous initial signals. Sex specificity of genes was validated based on RT-qPCR experiments. We found 11 and 16 uniquely expressed genes in female and male transcriptomes that were responsible particularly to maintain fertility and against abiotic stress. High gene expression of homologous such as FD, FT, TFL1 and CAL, SOC1, AP1 were characteristic to male and female floral meristems during organogenesis. Homologues transcripts of LFY and FLC were not found in the investigated generative and vegetative tissues. The repression of AP1 by TFL1 homolog was demonstrated in male flowers resulting exclusive expression of AP2 and PI that controlled stamen and carpel formation in the generative phase. Alterations of male and female floral meristem differentiation were demonstrated under photoperiodic and hormonal condition changes by applying in vitro treatments.</p", "keywords": ["0301 basic medicine", "0303 health sciences", "QH301-705.5", "Bioinformatics", "R", "03 medical and health sciences", "Organ development", "Medicine", "Flowering pathway", "14. Life underwater", "Biology (General)", "Transcriptomics", "Ambrosia artemisiifolia", "Monoecious"]}, "links": [{"href": "https://doi.org/2977681695"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PeerJ", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2977681695", "name": "item", "description": "2977681695", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2977681695"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-10-04T00:00:00Z"}}, {"id": "2999294732", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:24:59Z", "type": "Journal Article", "created": "2020-01-10", "title": "Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors", "description": "Abstract                <p>Bacillus firmus nematicidal bacterial strains are used to control plant parasitic nematode infestation of crops in agricultural production. Proteases are presumed to be the primary nematode virulence factors in nematicidal B. firmus degrading the nematode cuticle and other organs. We determined and compared the whole genome sequences of two nematicidal strains. Comparative genomics with a particular focus on possible virulence determinants revealed a wider range of possible virulence factors in a B. firmus isolate from a commercial bionematicide and a wild type Bacillus sp. isolate with nematicidal activity. The resulting 4.6 Mb B. firmus I-1582 and 5.3 Mb Bacillus sp. ZZV12-4809 genome assemblies contain respectively 18 and 19 homologs to nematode-virulent proteases, two nematode-virulent chitinase homologs in ZZV12-4809 and 28 and 36 secondary metabolite biosynthetic clusters, projected to encode antibiotics, small peptides, toxins and siderophores. The results of this study point to the genetic capability of B. firmus and related species for nematode virulence through a range of direct and indirect mechanisms.</p", "keywords": ["2. Zero hunger", "Whole Genome Sequencing", "complete genomes", "Virulence Factors", "Antinematodal Agents", "virulence factors", "bacillus firmus", "biological control", "Bacillus", "bioinformatics", "Genomics", "QH426-470", "Genome Report", "3. Good health", "Bacterial Proteins", "Drug Resistance", " Bacterial", "Genetics", "BACILLUS FIRMUS", " COMPLETE GENOMES", " BIOINFORMATICS", " BIOLOGICAL CONTROL", " NEMATICIDAL ACTIVITY", " VIRULENCE FACTORS", "Bacillus firmus", "nematicidal activity", "Genome", " Bacterial"]}, "links": [{"href": "http://academic.oup.com/g3journal/article-pdf/10/3/881/38825647/g3journal0881.pdf"}, {"href": "https://doi.org/2999294732"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/G3%20Genes%7CGenomes%7CGenetics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2999294732", "name": "item", "description": "2999294732", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2999294732"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-01T00:00:00Z"}}, {"id": "3186494073", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:25:16Z", "type": "Journal Article", "created": "2021-03-15", "title": "Overcoming the challenges to enhancing experimental plant biology with computational modeling", "description": "<p>The study of complex biological systems necessitates computational modeling approaches that are currently underutilized in plant biology. Many plant biologists have trouble identifying or adopting modeling methods to their research, particularly mechanistic mathematical modeling. Here we address challenges that limit the use of computational modeling methods, particularly mechanistic mathematical modeling. We divide computational modeling techniques into either pattern models (e.g., bioinformatics, machine learning, or morphology) or mechanistic mathematical models (e.g., biochemical reactions, biophysics, or population models), which both contribute to plant biology research at different scales to answer different research questions. We present arguments and recommendations for the increased adoption of modeling by plant biologists interested in incorporating more modeling into their research programs. As some researchers find math and quantitative methods to be an obstacle to modeling, we provide suggestions for easy-to-use tools for non-specialists and for collaboration with specialists. This may especially be the case for mechanistic mathematical modeling, and we spend some extra time discussing this. Through a more thorough appreciation and awareness of the power of different kinds of modeling in plant biology, we hope to facilitate interdisciplinary, transformative research.</p>", "keywords": ["Other Physical Sciences and Mathematics", "computational modeling", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "experimental design", "Systems Biology", "Plant Sciences", "Research Methods in Life Sciences", "mathematical modeling", "Life Sciences", "Plant culture", "bioinformatics", "Plant Science", "collaboration", "SB1-1110", "03 medical and health sciences", "Other Life Sciences", "Physical Sciences and Mathematics"]}, "links": [{"href": "https://doi.org/3186494073"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3186494073", "name": "item", "description": "3186494073", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3186494073"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-15T00:00:00Z"}}, {"id": "PMC11494973", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:27:07Z", "type": "Journal Article", "created": "2024-09-10", "title": "A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities", "description": "ABSTRACT                                                             <p>                       Due to recent improvements, Nanopore sequencing has become a promising method for experiments relying on amplicon sequencing. We describe a flexible workflow to generate and annotate high-quality, full-length 16S rDNA amplicons. We evaluated it for two applications, namely, (i) identification of bacterial isolates and (ii) species-level profiling of microbial communities. We assessed the identification of single bacterial isolates by sequencing, using a set of barcoded full-length 16S rRNA gene primer pairs (pair A), on 47 isolates encompassing multiple genera and compared those results with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based identification. Species-level community profiling was tested with two sets of barcoded full-length 16S primer pairs (A and B) and compared to the results obtained with shotgun Illumina sequencing using 27 stool samples. We developed a Nextflow pipeline to retain high-quality reads and taxonomically annotate them. We found high agreement between our workflow and MALDI-TOF data for isolate identification (positive predictive value = 0.90, Cram\uffc3\uffa9r\uffe2\uff80\uff99s                       V                       = 0.857, and Theil\uffe2\uff80\uff99s                       U                       = 0.316). For species-level community profiling, we found strong correlations (                       r                                                s                                              &gt; 0.6) of alpha diversity indices between the two primer sets and Illumina sequencing. At the community level, we found significant but small differences when comparing sequencing techniques. Finally, we found a moderate to strong correlation when comparing the relative abundances of individual species (average                       r                                                s                                              = 0.6 and 0.533 for primers A and B). Despite identified shortcomings, the proposed workflow enabled accurate identification of single bacterial isolates and prominent features in microbial communities, making it a worthwhile alternative to MALDI-TOF MS and Illumina sequencing.                     </p>                                            IMPORTANCE                       <p>A quick, robust, simple, and cost-effective method to identify bacterial isolates and communities in each sample is indispensable in the fields of microbiology and infection biology. Recent technological advances in Oxford Nanopore Technologies sequencing make this technique an attractive option considering the adaptability, portability, and cost-effectiveness of the platform, even with small sequencing batches. Here, we validated a flexible workflow to identify bacterial isolates and characterize bacterial communities using the Oxford Nanopore Technologies sequencing platform combined with the most recent v14 chemistry kits. For bacterial isolates, we compared our nanopore-based approach to matrix-assisted laser desorption ionization-time of flight mass spectrometry-based identification. For species-level profiling of complex bacterial communities, we compared our nanopore-based approach to Illumina shotgun sequencing. For reproducibility purposes, we wrapped the code used to process the sequencing data into a ready-to-use and self-contained Nextflow pipeline.</p>", "keywords": ["DNA", " Bacterial", "1303 Biochemistry", "gut microbiome", "610 Medicine & health", "Microbiology", "Workflow", "1311 Genetics", "RNA", " Ribosomal", " 16S", "1312 Molecular Biology", "1706 Computer Science Applications", "DNA Barcoding", " Taxonomic", "Humans", "DNA sequencing", "Bacteria", "10179 Institute of Medical Microbiology", "Microbiota", "2404 Microbiology", "1314 Physiology", "bioinformatics", "QR1-502", "Nanopore Sequencing", "1105 Ecology", " Evolution", " Behavior and Systematics", "Spectrometry", " Mass", " Matrix-Assisted Laser Desorption-Ionization", "570 Life sciences; biology", "2611 Modeling and Simulation", "Research Article"]}, "links": [{"href": "https://doi.org/PMC11494973"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC11494973", "name": "item", "description": "PMC11494973", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC11494973"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-04-11T00:00:00Z"}}, {"id": "PMC5814836", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:27:09Z", "type": "Journal Article", "created": "2022-10-18", "title": "Application of stable\u2010isotope labelling techniques for the detection of active diazotrophs", "description": "Summary                   <p>                     Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free\uffe2\uff80\uff90living or symbionts. Free\uffe2\uff80\uff90living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several                     15                     N\uffe2\uff80\uff90based methods for detecting N                     2                     fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the                     15                     N                     2                     tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing                     15                     N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a                     15                     N\uffe2\uff80\uff90RNA\uffe2\uff80\uff90SIP approach optimized for environmental samples and benchmarked to                     15                     N\uffe2\uff80\uff90DNA\uffe2\uff80\uff90SIP. Lastly, we investigated the feasibility of using SIP\uffe2\uff80\uff90Raman microspectroscopy for detecting                     15                     N\uffe2\uff80\uff90labelled cells. Taken together, these tools allow identifying and investigating active free\uffe2\uff80\uff90living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single\uffe2\uff80\uff90cell level.                   </p", "keywords": ["Spectrum Analysis", " Raman", "BIOLOGICAL SOIL CRUSTS", "106005 Bioinformatik", "106023 Molekularbiologie", "Nitrogen Fixation", "REVEALS", "FLUORESCENCE", "Research Articles", "Soil Microbiology", "106022 Mikrobiologie", "SPECTROSCOPY", "Bacteria", "Nitrogen Isotopes", "106003 Biodiversity research", "106023 Molecular biology", "GENETIC-REGULATION", "Archaea", "6. Clean water", "SURFACE-ENHANCED RAMAN", "COMMUNITY", "106003 Biodiversit\u00e4tsforschung", "13. Climate action", "Isotope Labeling", "106022 Microbiology", "NITROGEN-FIXATION", "106005 Bioinformatics", "RIBOSOMAL-RNA", "N-2 FIXATION"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13954"}, {"href": "https://doi.org/PMC5814836"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC5814836", "name": "item", "description": "PMC5814836", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC5814836"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-12-15T00:00:00Z"}}, {"id": "PMC6779118", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-24T16:27:09Z", "type": "Journal Article", "created": "2019-10-04", "title": "Different expression pattern of flowering pathway genes contribute to male or female organ development during floral transition in the monoecious weed                     Ambrosia artemisiifolia                     L. (                     Asteraceae                     )", "description": "<p>                     The highly allergenic and invasive weed                     Ambrosia artemisiifolia                     L. is a monoecius plant with separated male and female flowers. The genetic regulation of floral morphogenesis is a less understood field in the reproduction biology of this species. Therefore the objective of this work was to investigate the genetic control of sex determination during floral organogenesis. To this end, we performed a genome-wide transcriptional profiling of vegetative and generative tissues during the plant development comparing wild-growing and in vitro cultivated plants. RNA-seq on Illumina NextSeq 500 platform with an integrative bioinformatics analysis indicated differences in 80 floral gene expressions depending on photoperiodic and endogenous initial signals. Sex specificity of genes was validated based on RT-qPCR experiments. We found 11 and 16 uniquely expressed genes in female and male transcriptomes that were responsible particularly to maintain fertility and against abiotic stress. High gene expression of homologous such as FD, FT, TFL1 and CAL, SOC1, AP1 were characteristic to male and female floral meristems during organogenesis. Homologues transcripts of LFY and FLC were not found in the investigated generative and vegetative tissues. The repression of AP1 by TFL1 homolog was demonstrated in male flowers resulting exclusive expression of AP2 and PI that controlled stamen and carpel formation in the generative phase. Alterations of male and female floral meristem differentiation were demonstrated under photoperiodic and hormonal condition changes by applying in vitro treatments.                   </p", "keywords": ["0301 basic medicine", "0303 health sciences", "QH301-705.5", "Bioinformatics", "R", "03 medical and health sciences", "Organ development", "Medicine", "Flowering pathway", "14. Life underwater", "Biology (General)", "Transcriptomics", "Ambrosia artemisiifolia", "Monoecious"]}, "links": [{"href": "https://doi.org/PMC6779118"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PeerJ", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC6779118", "name": "item", "description": "PMC6779118", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC6779118"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-10-04T00:00:00Z"}}, {"id": "PMC7056983", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:27:10Z", "type": "Journal Article", "created": "2020-01-10", "title": "Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors", "description": "Abstract                <p>Bacillus firmus nematicidal bacterial strains are used to control plant parasitic nematode infestation of crops in agricultural production. Proteases are presumed to be the primary nematode virulence factors in nematicidal B. firmus degrading the nematode cuticle and other organs. We determined and compared the whole genome sequences of two nematicidal strains. Comparative genomics with a particular focus on possible virulence determinants revealed a wider range of possible virulence factors in a B. firmus isolate from a commercial bionematicide and a wild type Bacillus sp. isolate with nematicidal activity. The resulting 4.6 Mb B. firmus I-1582 and 5.3 Mb Bacillus sp. ZZV12-4809 genome assemblies contain respectively 18 and 19 homologs to nematode-virulent proteases, two nematode-virulent chitinase homologs in ZZV12-4809 and 28 and 36 secondary metabolite biosynthetic clusters, projected to encode antibiotics, small peptides, toxins and siderophores. The results of this study point to the genetic capability of B. firmus and related species for nematode virulence through a range of direct and indirect mechanisms.</p", "keywords": ["2. Zero hunger", "Whole Genome Sequencing", "complete genomes", "Virulence Factors", "Antinematodal Agents", "virulence factors", "bacillus firmus", "biological control", "Bacillus", "bioinformatics", "Genomics", "QH426-470", "Genome Report", "3. Good health", "Bacterial Proteins", "Drug Resistance", " Bacterial", "Genetics", "Bacillus firmus", "nematicidal activity", "Genome", " Bacterial"]}, "links": [{"href": "http://academic.oup.com/g3journal/article-pdf/10/3/881/38825647/g3journal0881.pdf"}, {"href": "https://doi.org/PMC7056983"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/G3%20Genes%7CGenomes%7CGenetics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC7056983", "name": "item", "description": "PMC7056983", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC7056983"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-01T00:00:00Z"}}, {"id": "PMC8329482", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:27:11Z", "type": "Journal Article", "created": "2021-03-15", "title": "Overcoming the challenges to enhancing experimental plant biology with computational modeling", "description": "<p>The study of complex biological systems necessitates computational modeling approaches that are currently underutilized in plant biology. Many plant biologists have trouble identifying or adopting modeling methods to their research, particularly mechanistic mathematical modeling. Here we address challenges that limit the use of computational modeling methods, particularly mechanistic mathematical modeling. We divide computational modeling techniques into either pattern models (e.g., bioinformatics, machine learning, or morphology) or mechanistic mathematical models (e.g., biochemical reactions, biophysics, or population models), which both contribute to plant biology research at different scales to answer different research questions. We present arguments and recommendations for the increased adoption of modeling by plant biologists interested in incorporating more modeling into their research programs. As some researchers find math and quantitative methods to be an obstacle to modeling, we provide suggestions for easy-to-use tools for non-specialists and for collaboration with specialists. This may especially be the case for mechanistic mathematical modeling, and we spend some extra time discussing this. Through a more thorough appreciation and awareness of the power of different kinds of modeling in plant biology, we hope to facilitate interdisciplinary, transformative research.</p>", "keywords": ["Other Physical Sciences and Mathematics", "computational modeling", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "experimental design", "Systems Biology", "Plant Sciences", "Research Methods in Life Sciences", "mathematical modeling", "Life Sciences", "Plant culture", "bioinformatics", "Plant Science", "collaboration", "SB1-1110", "03 medical and health sciences", "Other Life Sciences", "Physical Sciences and Mathematics"]}, "links": [{"href": "https://doi.org/PMC8329482"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC8329482", "name": "item", "description": "PMC8329482", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC8329482"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-15T00:00:00Z"}}, {"id": "PMC8960993", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:27:12Z", "type": "Journal Article", "created": "2022-03-10", "title": "Heat Shock Response of the Active Microbiome From Perennial Cave Ice", "description": "<?xml version='1.0' encoding='UTF-8'?><article><p>Ice caves constitute the newly investigated frozen and secluded model habitats for evaluating the resilience of ice-entrapped microbiomes in response to climate changes. This survey identified the total and active prokaryotic and eukaryotic communities from millennium-old ice accumulated in Scarisoara cave (Romania) using Illumina shotgun sequencing of the ribosomal RNA (rRNA) and messenger RNA (mRNA)-based functional analysis of the metatranscriptome. Also, the response of active microbiome to heat shock treatment mimicking the environmental shift during ice melting was evaluated at both the taxonomic and metabolic levels. The putatively active microbial community was dominated by bacterial taxa belonging to Proteobacteria and Bacteroidetes, which are highly resilient to thermal variations, while the scarcely present archaea belonging to Methanomicrobia was majorly affected by heat shock. Among eukaryotes, the fungal rRNA community was shared between the resilient Chytridiomycota and Blastocladiomycota, and the more sensitive Ascomycota and Basidiomycota taxa. A complex microeukaryotic community highly represented by Tardigrada and Rotifera (Metazoa), Ciliophora and Cercozoa (Protozoa), and Chlorophyta (Plantae) was evidenced for the first time in this habitat. This community showed a quick reaction to heat shock, followed by a partial recovery after prolonged incubation at 4\u00b0C due to possible predation processes on the prokaryotic cluster. Analysis of mRNA differential gene expression revealed the presence of an active microbiome in the perennial ice from the Scarisoara cave and associated molecular mechanisms for coping with temperature variations by the upregulation of genes involved in enzyme recovery, energy storage, carbon and nitrogen regulation, and cell motility. This first report on the active microbiome embedded in perennial ice from caves and its response to temperature stress provided a glimpse into the impact of glaciers melting and the resilience mechanisms in this habitat, contributing to the knowledge on the functional role of active microbes in frozen environments and their response to climatic changes.</p></article>", "keywords": ["0301 basic medicine", "active microbiome", "microbial resilience", "0303 health sciences", "03 medical and health sciences", "meta-omics", "ice caves", "13. Climate action", "metatranscriptome", "bioinformatics", "heat-shock response", "Microbiology", "QR1-502"]}, "links": [{"href": "https://doi.org/PMC8960993"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "PMC8960993", "name": "item", "description": "PMC8960993", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC8960993"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-10T00:00:00Z"}}, {"id": "a45418f134a1c5fe703a883421d78a84", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:27:42Z", "type": "Report", "title": "Computational analysis of chromatin accessibility during early human induced regulatory T cell development", "keywords": ["immunology", "epigenetics", "617", "bioinformatics", "Master's Programme in Biomedical Technology", "004"], "contacts": [{"organization": "H\u00e4m\u00e4l\u00e4inen, Emmi", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/a45418f134a1c5fe703a883421d78a84"}, {"rel": "self", "type": "application/geo+json", "title": "a45418f134a1c5fe703a883421d78a84", "name": "item", "description": "a45418f134a1c5fe703a883421d78a84", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/a45418f134a1c5fe703a883421d78a84"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "4b2b65c6-ff50-4669-99cc-ace343de3548", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[5.81, 47.26], [5.81, 54.76], [15.77, 54.76], [15.77, 47.26], [5.81, 47.26]]]}, "properties": {"themes": [{"concepts": [{"id": "farming"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Soil"}, {"id": "Bioinformatics"}, {"id": "Computer programming"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "opendata"}, {"id": "bioinformatics"}, {"id": "scaling with ranked subsampling"}, {"id": "SRS"}, {"id": "microbiome data normalisation"}], "scheme": "Individual"}, {"concepts": [{"id": "Boden"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}], "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - SIGNAL's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - SIGNAL and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - SIGNAL and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - SIGNAL and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2023-10-17", "type": "Dataset", "created": "2020-07-01", "language": "eng", "title": "Scaling with ranked subsampling (SRS) algorithm for the normalization of species count data.", "description": "Scaling with ranked subsampling (SRS) is an algorithm for the normalization of species count data in ecology. So far, SRS has successfully been applied to microbial community data.\n\"SRS is now available on CRAN: https://CRAN.R-project.org/package=SRS\" \nAn implementation of SRS in R is available for download: https://metadata.bonares.de/smartEditor/rest/upload/ID_7049_2020_05_13_SRS_function_v1_0_R.zip\n\nSRS consists of two steps. In the first step, the counts for all OTUs (operational taxonomic untis) are divided by a scaling factor chosen in such a way that the sum of the scaled counts (Cscaled with integer or non-integer values) equals Cmin. In the second step, the non-integer count values are converted into integers by an algorithm that we dub ranked subsampling. The scaled count Cscaled for each OTU is split into the integer-part Cint by truncating the digits after the decimal separator (Cint = floor(Cscaled)) and the fractional part Cfrac (Cfrac = Cscaled - Cint). Since \u03a3Cint \u2264 Cmin, additional \u2206C = Cmin - \u03a3Cint counts have to be added to the library to reach the total count of Cmin. This is achieved as follows. OTUs are ranked in the descending order of their Cfrac values. Beginning with the OTU of the highest rank, single count per OTU is added to the normalized library until the total number of added counts reaches \u2206C and the sum of all counts in the normalized library equals Cmin. When the lowest Cfrag involved in picking \u2206C counts is shared by several OTUs, the OTUs used for adding a single count to the library are selected in the order of their Cint values. This selection minimizes the effect of normalization on the relative frequencies of OTUs. OTUs with identical Cfrag as well as Cint are sampled randomly without replacement.", "formats": [{"name": "CSV"}, {"name": "WWW:DOWNLOAD"}], "keywords": ["Soil", "Bioinformatics", "Computer programming", "opendata", "bioinformatics", "scaling with ranked subsampling", "SRS", "microbiome data normalisation", "Boden"], "contacts": [{"name": "Lukas Beule", "organization": "University of Goettingen", "position": null, "roles": ["author"], "phones": [{"value": null}], "emails": [{"value": "lukas.beule@agr.uni-goettingen.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "Petr Karlovsky", "organization": "University of Goettingen", "position": null, "roles": ["projectLeader"], "phones": [{"value": null}], "emails": [{"value": "pkarlov@gwdg.de"}], "addresses": [{"deliveryPoint": [null], "city": null, "administrativeArea": null, "postalCode": null, "country": null}], "links": [{"href": null}]}, {"name": "BonaRes Data Centre", "organization": "Leibniz Centre for Agricultural Landscape Research (ZALF)", "position": "Research Platform 'Data Analysis & Simulation' - WG Geodata", "roles": ["publisher"], "phones": [{"value": "+49 33432 82 171"}], "emails": [{"value": "bonares-datenzentrum@zalf.de"}], "addresses": [{"deliveryPoint": ["Eberswalder Strasse 84"], "city": "M\u00fcncheberg", "administrativeArea": "Brandenburg", "postalCode": "15374", "country": "Germany"}], "links": [{"href": null}]}, {"organization": "University of Goettingen", "roles": ["contributor"]}]}, "links": [{"href": "https://maps.bonares.de/mapapps/resources/apps/bonares/index.html?lang=en&mid=4b2b65c6-ff50-4669-99cc-ace343de3548", "rel": "information"}, {"href": "https://metadata.bonares.de/smartEditor/rest/upload/ID_7049_2020_05_13_SRS_function_v1_0_R.zip", "protocol": "WWW:DOWNLOAD", "rel": "download"}, {"rel": "self", "type": "application/geo+json", "title": "4b2b65c6-ff50-4669-99cc-ace343de3548", "name": "item", "description": "4b2b65c6-ff50-4669-99cc-ace343de3548", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/4b2b65c6-ff50-4669-99cc-ace343de3548"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-17T00:00:00Z"}}, {"id": "9730f571-96c7-4490-b5c2-e99d4c63f572", "type": "Feature", "geometry": {"type": "Polygon", "coordinates": [[[5.81, 47.26], [5.81, 54.76], [15.77, 54.76], [15.77, 47.26], [5.81, 47.26]]]}, "properties": {"themes": [{"concepts": [{"id": "environment"}], "scheme": "https://standards.iso.org/iso/19139/resources/gmxCodelists.xml#MD_TopicCategoryCode"}, {"concepts": [{"id": "Bioinformatics"}, {"id": "statistics"}, {"id": "Statistical methods"}, {"id": "microbial ecology"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "scaling with ranked subsampling"}, {"id": "SRS"}, {"id": "species count data"}, {"id": "normalization"}, {"id": "next generation sequencing data"}, {"id": "microbial ecology"}, {"id": "opendata"}], "scheme": "Individual"}, {"concepts": [{"id": "Bioinformatics"}, {"id": "statistics"}], "scheme": "AGROVOC Multilingual agricultural thesaurus"}, {"concepts": [{"id": "Boden"}], "scheme": "GEMET - INSPIRE themes, version 1.0"}], "rights": "Restrictions applied to assure the protection of privacy or intellectual property, and any special restrictions or limitations or warnings on using the resource or metadata. Reports, articles, papers, scientific and non - scientific works of any form, including tables, maps, or any other kind of output, in printed or electronic form, based in whole or in part on the data supplied, must contain an acknowledgement of the form: \"Data reused from the BonaRes Data Centre www.bonares.de. This data were created as part of the BonaRes Module A-Project - SIGNAL's research activities.\" Although every care has been taken in preparing and testing the data, the BonaRes Module A-Project - SIGNAL and the BonaRes Data Centre cannot guarantee that the data are correct; neither does the BonaRes Module A-Project - SIGNAL and the BonaRes Data Centre accept any liability whatsoever for any error, missing data or omission in the data, or for any loss or damage arising from its use. The BonaRes Module A-Project - SIGNAL and BonaRes Data Centre will not be responsible for any direct or indirect use which might be made of the data.", "updated": "2023-10-12", "type": "Dataset", "created": "2020-02-27", "language": "eng", "title": "Scaling with ranked subsampling (SRS) algorithm for the normalization of species count data.", "description": "--This data has been withdrawn by the author.--\nThe corrected dataset can be found here: https://doi.org/10.20387/bonares-2657-1NP3\n\nThe data has been withdrawn for following reasons: \"The published R-script was revised in the course of an external review process.\u201d\nThe data is no longer available for free reuse and will only be released by the data centre if there is a reasonable interest.\n\nSummary\nScaling with ranked subsampling (SRS) is an algorithm for the normalization of species count data in ecology. So far, SRS has successfully been applied to microbial community data. The normalization by SRS reduces the number of reads in each sample in such a way that (i) the total count equals Cmin, (ii) each removed OTU is less or equally abundant that any preserved OTU, and (iii) the relative frequencies of OTUs remaining in the sample after normalization are as close as possible to the frequencies in the original sample. The algorithm consists of two steps. In the first step, the counts for all OTUs are divided by a scaling factor chosen in such a way that the sum of the scaled counts (Cscaled with integer or non-integer values) equals Cmin. The relative frequencies of all OTUs remain unchanged. In the second step, the non-integer count values are converted into integers by an algorithm that we dub ranked subsampling. The scaled count Cscaled for each OTU is split into the integer-part Cint by truncating the digits after the decimal separator (Cint = floor(Cscaled)) and the fractional part Cfrac (Cfrac = Cscaled - Cint). Since \u03a3Cint \u2264 Cmin, additional \u2206C = Cmin - \u03a3Cint reads have to be added to the library to reach the total count of Cmin. This is achieved as follows. OTUs are ranked in the descending order of their Cfrac values, which lie in the open interval (0, 1). Beginning with the OTU of the highest rank, single count per OTU is added to the normalized library until the total number of added counts reaches \u2206C and the sum of all counts in the normalized library equals Cmin. For example, if \u2206C = 5 and the seven top Cfrac values are 0.96, 0.96, 0.88, 0.55, 0.55, 0.55, and 0.55, the following counts are added: a single count for each OTU with Cfrac of 0.96; a single count for the OTU with Cfrac of 0.88; and a single count each for two OTUs among those with Cfrac of 0.55. When the lowest Cfrag involved in picking \u2206C counts is shared by several OTUs, the OTUs used for adding a single count to the library are selected in the order of their Cint values. This selection minimizes the effect of normalization on the relative frequencies of OTUs. 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