RWRtoolkit Narrative

Kainer, David; Lane, Matthew; Sullivan, Kyle; Miller, J. Izaak; Cashman, Mikaela; Morgan, Mallory; Cliff, Ashley; Romero, Jonathon; Walker, Angelica; Blair, D. Dakota; Chhetri, Hari; Wang, Yongqin; Pavicic, Mirko; Furches, Anna; Noshay, Jaclyn; Drake, Meghan; Landry, Natalie; Ireland, AJ; Missaoui, Ali; Kang, Yun; Sedbrook, John; Dehal, Paramvir; Canon, Shane; Jacobson, Daniel

doi:10.25982/165213.26/2519695

Title: RWRtoolkit Narrative

Dataset
Other Related Research

Abstract

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) to identify single nucleotide polymorphisms (SNPs) associated with Switchgrass shoot biomass. We then assigned these SNPs to Switchgrass genes, and using Phytozome (Goodstein et al., 2012), assigned these 38 Switchgrass GWAS genes to 32 Arabidopsis orthologs. These 32 genes are the starting set of genes (i.e. the seed gene set) for this demo narrative.

Authors:

Kainer, David; Lane, Matthew; Sullivan, Kyle; Miller, J. Izaak; Cashman, Mikaela; Morgan, Mallory; Cliff, Ashley; Romero, Jonathon; Walker, Angelica; Blair, D. Dakota; Chhetri, Hari; Wang, Yongqin; Pavicic, Mirko; Furches, Anna; Noshay, Jaclyn; Drake, Meghan; Landry, Natalie; Ireland, AJ; Missaoui, Ali; Kang, Yun more »

Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, QLD, Australia; DOE Systems Biology Knowledgebase
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Univ. of Tennessee, Knoxville, TN (United States). Bredesen Center for Interdisciplinary Research and Graduate Education
Brookhaven National Laboratory (BNL), Upton, NY (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Noble Research Institute, Ardmore, OK (United States)
Illinois State University (ISU), Normal, IL (United States)

Publication Date:: Tue Jul 16 00:00:00 EDT 2024

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Subject:: 59 BASIC BIOLOGICAL SCIENCES

OSTI Identifier:: 2519695

DOI:: https://doi.org/10.25982/165213.26/2519695

Citation Formats


                    Kainer, David, Lane, Matthew, Sullivan, Kyle, Miller, J. Izaak, Cashman, Mikaela, Morgan, Mallory, Cliff, Ashley, Romero, Jonathon, Walker, Angelica, Blair, D. Dakota, Chhetri, Hari, Wang, Yongqin, Pavicic, Mirko, Furches, Anna, Noshay, Jaclyn, Drake, Meghan, Landry, Natalie, Ireland, AJ, Missaoui, Ali, Kang, Yun, Sedbrook, John, Dehal, Paramvir, Canon, Shane, and Jacobson, Daniel. RWRtoolkit Narrative.  United States: N. p., 2024. 
        Web.  doi:10.25982/165213.26/2519695.

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                    Kainer, David, Lane, Matthew, Sullivan, Kyle, Miller, J. Izaak, Cashman, Mikaela, Morgan, Mallory, Cliff, Ashley, Romero, Jonathon, Walker, Angelica, Blair, D. Dakota, Chhetri, Hari, Wang, Yongqin, Pavicic, Mirko, Furches, Anna, Noshay, Jaclyn, Drake, Meghan, Landry, Natalie, Ireland, AJ, Missaoui, Ali, Kang, Yun, Sedbrook, John, Dehal, Paramvir, Canon, Shane, & Jacobson, Daniel. RWRtoolkit Narrative.  United States.  doi:https://doi.org/10.25982/165213.26/2519695

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                    Kainer, David, Lane, Matthew, Sullivan, Kyle, Miller, J. Izaak, Cashman, Mikaela, Morgan, Mallory, Cliff, Ashley, Romero, Jonathon, Walker, Angelica, Blair, D. Dakota, Chhetri, Hari, Wang, Yongqin, Pavicic, Mirko, Furches, Anna, Noshay, Jaclyn, Drake, Meghan, Landry, Natalie, Ireland, AJ, Missaoui, Ali, Kang, Yun, Sedbrook, John, Dehal, Paramvir, Canon, Shane, and Jacobson, Daniel. 2024.  
"RWRtoolkit Narrative".  United States.  doi:https://doi.org/10.25982/165213.26/2519695.  https://www.osti.gov/servlets/purl/2519695. Pub date:Tue Jul 16 00:00:00 EDT 2024

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@article{osti_2519695,

  title        = {RWRtoolkit Narrative},

  author       = {Kainer, David and Lane, Matthew and Sullivan, Kyle and Miller, J. Izaak and Cashman, Mikaela and Morgan, Mallory and Cliff, Ashley and Romero, Jonathon and Walker, Angelica and Blair, D. Dakota and Chhetri, Hari and Wang, Yongqin and Pavicic, Mirko and Furches, Anna and Noshay, Jaclyn and Drake, Meghan and Landry, Natalie and Ireland, AJ and Missaoui, Ali and Kang, Yun and Sedbrook, John and Dehal, Paramvir and Canon, Shane and Jacobson, Daniel},

  abstractNote = {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) to identify single nucleotide polymorphisms (SNPs) associated with Switchgrass shoot biomass. We then assigned these SNPs to Switchgrass genes, and using Phytozome (Goodstein et al., 2012), assigned these 38 Switchgrass GWAS genes to 32 Arabidopsis orthologs. These 32 genes are the starting set of genes (i.e. the seed gene set) for this demo narrative.},

  doi          = {10.25982/165213.26/2519695},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Tue Jul 16 00:00:00 EDT 2024},

  month        = {Tue Jul 16 00:00:00 EDT 2024}

}

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DOI: https://doi.org/10.25982/165213.26/2519695

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