Search Results - "Weighill, Deborah"

Fungal-Bacterial Networks in the Populus Rhizobiome Are Impacted by Soil Properties and Host Genotype by Bonito, Gregory, Benucci, Gian Maria Niccolò, Hameed, Khalid, Weighill, Deborah, Jones, Piet, Chen, Ko-Hsuan, Jacobson, Daniel, Schadt, Christopher, Vilgalys, Rytas

“…Plant root-associated microbial symbionts comprise the plant rhizobiome. These microbes function in provisioning nutrients and water to their hosts, impacting…”
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Linking crop traits to transcriptome differences in a progeny population of tetraploid potato by Alexandersson, Erik, Kushwaha, Sandeep, Subedi, Aastha, Weighill, Deborah, Climer, Sharlee, Jacobson, Daniel, Andreasson, Erik

“…Potato is the third most consumed crop in the world. Breeding for traits such as yield, product quality and pathogen resistance are main priorities…”
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3-way networks: application of hypergraphs for modelling increased complexity in comparative genomics by Weighill, Deborah A, Jacobson, Daniel A

“…We present and develop the theory of 3-way networks, a type of hypergraph in which each edge models relationships between triplets of objects as opposed to…”
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Data Integration in Poplar: ‘Omics Layers and Integration Strategies by Weighill, Deborah, Tschaplinski, Timothy J., Tuskan, Gerald A., Jacobson, Daniel

“…Populus trichocarpa is an important biofuel feedstock that has been the target of extensive research and is emerging as a model organism for plants, especially…”
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Defining the genetic components of callus formation: A GWAS approach by Tuskan, Gerald A, Mewalal, Ritesh, Gunter, Lee E, Palla, Kaitlin J, Carter, Kelsey, Jacobson, Daniel A, Jones, Piet C, Garcia, Benjamin J, Weighill, Deborah A, Hyatt, Philip D, Yang, Yongil, Zhang, Jin, Reis, Nicholas, Chen, Jin-Gui, Muchero, Wellington

“…A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture…”
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Gene Targeting in Disease Networks by Weighill, Deborah, Ben Guebila, Marouen, Glass, Kimberly, Platig, John, Yeh, Jen Jen, Quackenbush, John

“…Profiling of whole transcriptomes has become a cornerstone of molecular biology and an invaluable tool for the characterization of clinical phenotypes and the…”
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Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses by Lee, Laura L, Blumer-Schuette, Sara E, Izquierdo, Javier A, Zurawski, Jeffrey V, Loder, Andrew J, Conway, Jonathan M, Elkins, James G, Podar, Mircea, Clum, Alicia, Jones, Piet C, Piatek, Marek J, Weighill, Deborah A, Jacobson, Daniel A, Adams, Michael W W, Kelly, Robert M

“…Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely…”
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Multi-Phenotype Association Decomposition: Unraveling Complex Gene-Phenotype Relationships by Weighill, Deborah, Jones, Piet, Bleker, Carissa, Ranjan, Priya, Shah, Manesh, Zhao, Nan, Martin, Madhavi, DiFazio, Stephen, Macaya-Sanz, David, Schmutz, Jeremy, Sreedasyam, Avinash, Tschaplinski, Timothy, Tuskan, Gerald, Jacobson, Daniel

“…Various patterns of multi-phenotype associations (MPAs) exist in the results of Genome Wide Association Studies (GWAS) involving different topologies of single…”
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Characterization of DWARF14 Genes in Populus by Zheng, Kaijie, Wang, Xiaoping, Weighill, Deborah A., Guo, Hao-Bo, Xie, Meng, Yang, Yongil, Yang, Jun, Wang, Shucai, Jacobson, Daniel A., Guo, Hong, Muchero, Wellington, Tuskan, Gerald A., Chen, Jin-Gui

“…Strigolactones are a new class of plant hormones regulating shoot branching and symbiotic interactions with arbuscular mycorrhizal fungi. Studies of branching…”
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Network Metamodeling: Effect of Correlation Metric Choice on Phylogenomic and Transcriptomic Network Topology by Weighill, Deborah A, Jacobson, Daniel

“…We explore the use of a network meta-modeling approach to compare the effects of similarity metrics used to construct biological networks on the topology of…”
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Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence by Furches, Anna, Kainer, David, Weighill, Deborah, Large, Annabel, Jones, Piet, Walker, Angelica M., Romero, Jonathon, Gazolla, Joao Gabriel Felipe Machado, Joubert, Wayne, Shah, Manesh, Streich, Jared, Ranjan, Priya, Schmutz, Jeremy, Sreedasyam, Avinash, Macaya-Sanz, David, Zhao, Nan, Martin, Madhavi Z., Rao, Xiaolan, Dixon, Richard A., DiFazio, Stephen, Tschaplinski, Timothy J., Chen, Jin-Gui, Tuskan, Gerald A., Jacobson, Daniel

“…Understanding the regulatory network controlling cell wall biosynthesis is of great interest in Populus trichocarpa, both because of its status as a model…”
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Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation by Weighill, Deborah, Macaya-Sanz, David, DiFazio, Stephen Paul, Joubert, Wayne, Shah, Manesh, Schmutz, Jeremy, Sreedasyam, Avinash, Tuskan, Gerald, Jacobson, Daniel

“…Various 'omics data types have been generated for , each providing a layer of information which can be represented as a density signal across a chromosome. We…”
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High Throughput Screening Technologies in Biomass Characterization by Decker, Stephen R., Harman-Ware, Anne E., Happs, Renee M., Wolfrum, Edward J., Tuskan, Gerald A., Kainer, David, Oguntimein, Gbekeloluwa B., Rodriguez, Miguel, Weighill, Deborah, Jones, Piet, Jacobson, Daniel

“…Biomass analysis is a slow and tedious process and not solely due to the long generation time for most plant species. Screening large numbers of plant variants…”
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Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery by Weighill, Deborah, Jones, Piet, Shah, Manesh, Ranjan, Priya, Muchero, Wellington, Schmutz, Jeremy, Sreedasyam, Avinash, Macaya-Sanz, David, Sykes, Robert, Zhao, Nan, Martin, Madhavi Z., DiFazio, Stephen, Tschaplinski, Timothy J., Tuskan, Gerald, Jacobson, Daniel

“…Biological organisms are complex systems that are composed of functional networks of interacting molecules and macro-molecules. Complex phenotypes are the…”
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Predicting genotype-specific gene regulatory networks by Weighill, Deborah, Ben Guebila, Marouen, Glass, Kimberly, Quackenbush, John, Platig, John

“…Understanding how each person's unique genotype influences their individual patterns of gene regulation has the potential to improve our understanding of human…”
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Promise of bile circulating tumor DNA in biliary tract cancers by Kearney, Joseph F., Weighill, Deborah, Yeh, Jen Jen

“…An explosion of technological advances has facilitated the unprecedented use of liquid biopsy methods to isolate and interrogate circulating tumor DNA for…”
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GRAND: a database of gene regulatory network models across human conditions by Ben Guebila, Marouen, Lopes-Ramos, Camila M, Weighill, Deborah, Sonawane, Abhijeet Rajendra, Burkholz, Rebekka, Shamsaei, Behrouz, Platig, John, Glass, Kimberly, Kuijjer, Marieke L, Quackenbush, John

“…Abstract Gene regulation plays a fundamental role in shaping tissue identity, function, and response to perturbation. Regulatory processes are controlled by…”
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Parallel accelerated Custom Correlation Coefficient calculations for genomics applications by Joubert, Wayne, Nance, James, Climer, Sharlee, Weighill, Deborah, Jacobson, Daniel

“…•A novel mapping of 2-way and 3-way CCC calculations to GPUs is presented.•A parallel algorithm scaling to thousands of compute nodes is developed.•Near-ideal…”
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Parallel accelerated vector similarity calculations for genomics applications by Joubert, Wayne, Nance, James, Weighill, Deborah, Jacobson, Daniel

“…•A novel mapping of 2-way / 3-way vector similarity calculations to GPUs is presented.•A parallel algorithm scaling to thousands of compute nodes is…”
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DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks by Shutta, Katherine H, Weighill, Deborah, Burkholz, Rebekka, Guebila, Marouen Ben, DeMeo, Dawn L, Zacharias, Helena U, Quackenbush, John, Altenbuchinger, Michael

“…The increasing quantity of multi-omic data, such as methylomic and transcriptomic profiles collected on the same specimen or even on the same cell, provides a…”
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