Anna Furches
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View article: Telomere-to-telomere assemblies reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in <i>Populus trichocarpa</i> likely driven by helitrons
Telomere-to-telomere assemblies reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in <i>Populus trichocarpa</i> likely driven by helitrons Open
Background The model woody plant Populus trichocarpa displays an atypical alkene-diverse wax cuticle likely driven by copy number variation (CNV) of 3-ketoacyl-CoA synthases ( KCS ), which has been difficult to confirm based on short-read …
View article: RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species Open
We introduce RWRtoolkit, a multiplex generation, exploration, and statistical package built for R and command-line users. RWRtoolkit enables the efficient exploration of large and highly complex biological networks generated from custom ex…
View article: RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species
RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species Open
Leveraging the use of multiplex multi-omic networks, key insights into genetic and epigenetic mechanisms supporting biofuel production have been uncovered. Here, we introduce RWRtoolkit, a multiplex generation, exploration, and statistical…
View article: Genetic underpinnings of arthropod community distributions in <i>Populus trichocarpa</i>
Genetic underpinnings of arthropod community distributions in <i>Populus trichocarpa</i> Open
Summary Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior stud…
View article: RWRtoolkit Narrative
RWRtoolkit Narrative Open
This narrative presents a demonstration of RWRtools methods to the important bioenergy feedstock Panicum virgatum (Switchgrass) by leveraging networks from the model plant Arabidopsis thaliana. We used a genome-wide association study (GWAS…
View article: Methods for controlling cell wall biosynthesis and genetically modified plants
Methods for controlling cell wall biosynthesis and genetically modified plants Open
The present disclosure provides methods of producing plants with preferred levels of cell wall biosynthesis; and uses of such plants. The inventors have identified that the GFR9, CCoAOMT and MYB41 genes are major regulators of the cell wal…
View article: Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases
Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases Open
Metabolite genome-wide association studies (mGWASs) are increasingly used to discover the genetic basis of target phenotypes in plants such as Populus trichocarpa , a biofuel feedstock and model woody plant species. Despite their growing i…
View article: Clustering the Planet: An Exascale Approach to Determining Global Climatype Zones
Clustering the Planet: An Exascale Approach to Determining Global Climatype Zones Open
We present an exascale approach for producing global scale, high resolution, longitudinally based geoclimate classifications. Using a GPU implementation of the DUO Similarity Metric on the Summit supercomputer, we calculated the pairwise e…
View article: A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes
A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes Open
Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been…
View article: A k-mer based approach for virus classification identifies coronavirus infections and viral associations in human and plant microbiomes
A k-mer based approach for virus classification identifies coronavirus infections and viral associations in human and plant microbiomes Open
Background Viruses are underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses h…
View article: Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa
Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa Open
To understand the genetic mechanisms underlying wood anatomical and morphological traits in Populus trichocarpa, we used 869 unrelated genotypes from a common garden in Clatskanie, Oregon that were previously collected from across the dist…
View article: A K-mer Based Approach for Virus Classification Identifies Coronavirus Infections and Viral Associations in Human and Plant Microbiomes
A K-mer Based Approach for Virus Classification Identifies Coronavirus Infections and Viral Associations in Human and Plant Microbiomes Open
BackgroundViruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses…
View article: Metabolic engineering of <i>Pseudomonas putida</i> for increased polyhydroxyalkanoate production from lignin
Metabolic engineering of <i>Pseudomonas putida</i> for increased polyhydroxyalkanoate production from lignin Open
Corrigendum: In the originally published article by Salvachua et al. (2019), the author Anna Furches was accidentally omitted from the byline of manuscript, ‘Metabolic engineering of Pseudomonas putida for increased polyhydroxyalkanoate pr…
View article: A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks
A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks Open
As time progresses and technology improves, biological data sets are continuously increasing in size. New methods and new implementations of existing methods are needed to keep pace with this increase. In this paper, we present a high-perf…
View article: Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence
Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence Open
Understanding the regulatory network controlling cell wall biosynthesis is of great interest in Populus trichocarpa, both because of its status as a model woody perennial and its importance for lignocellulosic products. We searched for gen…
View article: Metabolic engineering of <i>Pseudomonas putida</i> for increased polyhydroxyalkanoate production from lignin
Metabolic engineering of <i>Pseudomonas putida</i> for increased polyhydroxyalkanoate production from lignin Open
Summary Microbial conversion offers a promising strategy for overcoming the intrinsic heterogeneity of the plant biopolymer, lignin. Soil microbes that natively harbour aromatic‐catabolic pathways are natural choices for chassis strains, a…
View article: Plant Host-Associated Mechanisms for Microbial Selection
Plant Host-Associated Mechanisms for Microbial Selection Open
Plants serve as host to numerous microorganisms. The members of these microbial communities interact among each other and with the plant, and there is increasing evidence to suggest that the microbial community may promote plant growth, im…
View article: Scripts for Running Multiple Lines of Evidence Analysis
Scripts for Running Multiple Lines of Evidence Analysis Open
The software code titled “Scripts for Running Multiple Lunes of Evidence Analysis” enables high throughput network analysis; efficient analysis of large multi-omic networks in order to rank genes by connectivity. This code creates a set of…