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View article: A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants
A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants Open
The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other t…
View article: A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants
A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants Open
The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other t…
View article: A framework for identifying factors controlling cyanobacterium <i>Microcystis flos‐aquae</i> blooms by coupled <scp>CCM</scp>–<scp>ECCM</scp> Bayesian networks
A framework for identifying factors controlling cyanobacterium <i>Microcystis flos‐aquae</i> blooms by coupled <span>CCM</span>–<span>ECCM</span> Bayesian networks Open
Cyanobacterial blooms in freshwater sources are a global concern, and gaining insight into their causes is crucial for effective resource management and control. In this study, we present a novel computational framework for the causal anal…
View article: A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants
A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants Open
The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other t…
View article: A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants
A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants Open
The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other t…
View article: Reviewer #2 (Public Review): A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants
Reviewer #2 (Public Review): A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants Open
The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other t…
View article: A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants
A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants Open
The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other t…
View article: OMG-ATTACK: Self-Supervised On-Manifold Generation of Transferable Evasion Attacks
OMG-ATTACK: Self-Supervised On-Manifold Generation of Transferable Evasion Attacks Open
Evasion Attacks (EA) are used to test the robustness of trained neural networks by distorting input data to misguide the model into incorrect classifications. Creating these attacks is a challenging task, especially with the ever-increasin…
View article: A framework for identifying factors controlling cyanobacterium Microcystis flos-aquae blooms by coupled CCM-ECCM Bayesian networks
A framework for identifying factors controlling cyanobacterium Microcystis flos-aquae blooms by coupled CCM-ECCM Bayesian networks Open
1. Cyanobacterial blooms in freshwater sources are a global concern, and gaining insight into their causes is crucial for effective resource management and control. 2. In this study, we present a computational framework for the causal anal…
View article: A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data Open
Background The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous …
View article: Additional file 5 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
Additional file 5 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data Open
Additional file 5. Lists of taxa-dominated enzymes. Analysis is based on samples from treatments with G210 apple rootstocks.
View article: Additional file 4 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
Additional file 4 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data Open
Additional file 4. Differentially abundant functional groups (KO & EC functional schemes).
View article: Two independent loss‐of‐function mutations in <i>anthocyanidin synthase</i> homeologous genes are responsible for the all‐green phenotype of sweet basil
Two independent loss‐of‐function mutations in <i>anthocyanidin synthase</i> homeologous genes are responsible for the all‐green phenotype of sweet basil Open
Sweet basil, Ocimum basilicum L., is an important culinary herb grown worldwide. Although basil is green, many landraces, breeding lines, and exotic cultivars have purple stems and flowers. This anthocyanin pigmentation is unacceptable in …
View article: Additional file 6 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
Additional file 6 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data Open
Additional file 6. Topological properties of enzymes (network degree) vs their score of taxonomic dominance. Analysis is based on samples from treatments with G210 apple rootstocks.
View article: Additional file 1 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
Additional file 1 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data Open
Additional file 1. A summary of the number of sequenced reads per library.
View article: Additional file 8 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
Additional file 8 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data Open
Additional file 8. Lists of taxa-dependent compounds. Analysis is based on samples from treatments with G210 apple rootstocks.
View article: Additional file 9 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
Additional file 9 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data Open
Additional file 9. Distribution of the number of reads, taxa-dominated enzymes and taxa-dependent compounds across taxonomic groups in different treatments. The analysis is based on samples from treatments with G210 apple rootstocks.
View article: Additional file 7 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
Additional file 7 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data Open
Additional file 7. Predicted environmental resources and network specific compounds in BjSa vs NTC.
View article: Additional file 3 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
Additional file 3 of A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data Open
Additional file 3. Differentially abundant taxonomic groups (genus and order levels).
View article: Two independent loss-of-function mutations in <i>anthocyanidin synthase</i> homeologous genes make sweet basil all green
Two independent loss-of-function mutations in <i>anthocyanidin synthase</i> homeologous genes make sweet basil all green Open
Sweet basil, Ocimum basilicum L., is an important culinary herb grown worldwide. Although basil is green, many landraces, breeding lines and exotic cultivars have purple stems and flowers. This anthocyanins pigmentation is unacceptable in …
View article: The Pomegranate Deciduous Trait Is Genetically Controlled by a PgPolyQ-MADS Gene
The Pomegranate Deciduous Trait Is Genetically Controlled by a PgPolyQ-MADS Gene Open
The pomegranate ( Punica granatum L.) is a deciduous fruit tree that grows worldwide. However, there are variants, which stay green in mild winter conditions and are determined evergreen. The evergreen trait is of commercial and scientific…
View article: Dual transcriptional analysis of Ocimum basilicum and Peronospora belbahrii in susceptible interactions
Dual transcriptional analysis of Ocimum basilicum and Peronospora belbahrii in susceptible interactions Open
Basil downy mildew, caused by the pathogen Peronospora belbahrii, is a major problem for sweet basil growers worldwide. The genome sequences of both Ocimum basilicum and P. belbahrii were recently completed but extensive transcriptome anal…
View article: The Meat Quality Characteristics of Holstein Calves: The Story of Israeli ‘Dairy Beef’
The Meat Quality Characteristics of Holstein Calves: The Story of Israeli ‘Dairy Beef’ Open
Global animal production systems are often criticized for their lack of sustainability and insufficient resilience to ensure food security. The ‘farm-to-fork’ approach aims at orienting food systems towards the creation of a positive envir…
View article: Dual transcriptional analysis of <i>Peronospora belbahrii</i> and <i>Ocimum basilicum</i> in susceptible interactions
Dual transcriptional analysis of <i>Peronospora belbahrii</i> and <i>Ocimum basilicum</i> in susceptible interactions Open
Basil downy mildew, caused by the pathogen Peronospora belbahrii , is a major problem for sweet basil growers worldwide. The genome sequences of both Ocimum basilicum and P. belbahrii were recently completed but extensive transcriptome ana…
View article: NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data
NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data Open
The study of microbial activity can be viewed as a triangle with three sides: environment (dominant resources in a specific habitat), community (species dictating a repertoire of metabolic conversions) and function (production and/or utili…
View article: Further Insights on the &lt;i&gt;Datura innoxia&lt;/i&gt; Hyoscyamine 6&lt;i&gt;β&lt;/i&gt;-Hydroxylase (DiH6H) Based on Biochemical Characterization and Molecular Modeling
Further Insights on the <i>Datura innoxia</i> Hyoscyamine 6<i>β</i>-Hydroxylase (DiH6H) Based on Biochemical Characterization and Molecular Modeling Open
Hyoscyamine, anisodamine and scopolamine are tropane alkaloids present in some Solanaceae species and used in modern medicine. L-Hyoscyamine is hydroxylated to 6β-hydroxyhyoscyamine (anisodamine) and then epoxidated to scopolamine by the d…