Search Results - "McClure, Ryan S"

Hi-C metagenome sequencing reveals soil phage–host interactions by Wu, Ruonan, Davison, Michelle R., Nelson, William C., Smith, Montana L., Lipton, Mary S., Jansson, Janet K., McClure, Ryan S., McDermott, Jason E., Hofmockel, Kirsten S.

“…Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome…”
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Gene co-expression network analysis in zebrafish reveals chemical class specific modules by Shankar, Prarthana, McClure, Ryan S, Waters, Katrina M, Tanguay, Robyn L

“…Abstract Background Zebrafish is a popular animal model used for high-throughput screening of chemical hazards, however, investigations of transcriptomic…”
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Coupling Genome-wide Transcriptomics and Developmental Toxicity Profiles in Zebrafish to Characterize Polycyclic Aromatic Hydrocarbon (PAH) Hazard by Shankar, Prarthana, Geier, Mitra C, Truong, Lisa, McClure, Ryan S, Pande, Paritosh, Waters, Katrina M, Tanguay, Robert L

“…Polycyclic Aromatic Hydrocarbons (PAHs) are diverse environmental pollutants associated with adverse human health effects. Many studies focus on the…”
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Tripogon loliiformis tolerates rapid desiccation after metabolic and transcriptional priming during initial drying by Okemo, Pauline A., Njaci, Isaac, Kim, Young-Mo, McClure, Ryan S., Peterson, Matthew J., Beliaev, Alexander S., Hixson, Kim K., Mundree, Sagadevan, Williams, Brett

“…Crop plants and undomesticated resilient species employ different strategies to regulate their energy resources and growth. Most crop species are sensitive to…”
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Toward a Better Understanding of Species Interactions through Network Biology by McClure, Ryan S

“…Within the last decade, there has been an explosion of multi-omics data generated for several microbial systems. At the same time, new methods of analysis have…”
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Unified feature association networks through integration of transcriptomic and proteomic data by McClure, Ryan S, Wendler, Jason P, Adkins, Joshua N, Swanstrom, Jesica, Baric, Ralph, Kaiser, Brooke L Deatherage, Oxford, Kristie L, Waters, Katrina M, McDermott, Jason E

“…High-throughput multi-omics studies and corresponding network analyses of multi-omic data have rapidly expanded their impact over the last 10 years. As…”
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Selection, Succession, and Stabilization of Soil Microbial Consortia by Zegeye, Elias K, Brislawn, Colin J, Farris, Yuliya, Fansler, Sarah J, Hofmockel, Kirsten S, Jansson, Janet K, Wright, Aaron T, Graham, Emily B, Naylor, Dan, McClure, Ryan S, Bernstein, Hans C

“…Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes…”
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Improving network inference algorithms using resampling methods by Colby, Sean M, McClure, Ryan S, Overall, Christopher C, Renslow, Ryan S, McDermott, Jason E

“…Relatively small changes to gene expression data dramatically affect co-expression networks inferred from that data which, in turn, can significantly alter the…”
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3' RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism by McClure, Ryan S, Rericha, Yvonne, Waters, Katrina M, Tanguay, Robyn L

“…The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these…”
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Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture by Khan, Nymul, Maezato, Yukari, McClure, Ryan S., Brislawn, Colin J., Mobberley, Jennifer M., Isern, Nancy, Chrisler, William B., Markillie, Lye Meng, Barney, Brett M., Song, Hyun-Seob, Nelson, William C., Bernstein, Hans C.

“…The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and…”
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Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth by Bernstein, Hans C, McClure, Ryan S, Hill, Eric A, Markillie, Lye Meng, Chrisler, William B, Romine, Margie F, McDermott, Jason E, Posewitz, Matthew C, Bryant, Donald A, Konopka, Allan E, Fredrickson, James K, Beliaev, Alexander S

“…Harnessing the metabolic potential of photosynthetic microbes for next-generation biotechnology objectives requires detailed scientific understanding of the…”
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Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene by Wilson, Lindsay B., McClure, Ryan S., Waters, Katrina M., Simonich, Michael T., Tanguay, Robyn L.

“…Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants and are associated with human disease. Canonically, many PAHs induce toxicity…”
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Indirect Interspecies Regulation: Transcriptional and Physiological Responses of a Cyanobacterium to Heterotrophic Partnership by Bernstein, Hans C, McClure, Ryan S, Thiel, Vera, Sadler, Natalie C, Kim, Young-Mo, Chrisler, William B, Hill, Eric A, Bryant, Donald A, Romine, Margaret F, Jansson, Janet K, Fredrickson, Jim K, Beliaev, Alexander S

“…The mechanisms by which microbes interact in communities remain poorly understood. Here, we interrogated specific interactions between photoautotrophic and…”
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Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality by Song, Hyun-Seob, McClure, Ryan S, Bernstein, Hans C, Overall, Christopher C, Hill, Eric A, Beliaev, Alexander S

“…Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon…”
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Computational Analysis of Interactions of the Oral Microbiota by McClure, Ryan S.

“…Purpose of Review The human oral microbiome is a complex site containing many hundreds of species with the community response of these species having a large…”
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Species-specific transcriptomic network inference of interspecies interactions by McClure, Ryan S., Overall, Christopher C., Hill, Eric A., Song, Hyun-Seob, Charania, Moiz, Bernstein, Hans C., McDermott, Jason E., Beliaev, Alexander S.

“…The advent of high-throughput ‘omics approaches coupled with computational analyses to reconstruct individual genomes from metagenomes provides a basis for…”
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Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations by McClure, Ryan S., Lee, Joon-Yong, Chowdhury, Taniya Roy, Bottos, Eric M., White, Richard Allen, Kim, Young-Mo, Nicora, Carrie D., Metz, Thomas O., Hofmockel, Kirsten S., Jansson, Janet K., Song, Hyun-Seob

“…The soil environment is constantly changing due to shifts in soil moisture, nutrient availability and other conditions. To contend with these changes, soil…”
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Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002 by McClure, Ryan S, Overall, Christopher C, McDermott, Jason E, Hill, Eric A, Markillie, Lye Meng, McCue, Lee Ann, Taylor, Ronald C, Ludwig, Marcus, Bryant, Donald A, Beliaev, Alexander S

“…Cyanobacterial regulation of gene expression must contend with a genome organization that lacks apparent functional context, as the majority of cellular…”
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Graphene oxide exposure alters gut microbial community composition and metabolism in an in vitro human model by Couvillion, Sneha P., Danczak, Robert E., Cao, Xiaoqiong, Yang, Qin, Keerthisinghe, Tharushi P., McClure, Ryan S., Bitounis, Dimitrios, Burnet, Meagan C., Fansler, Sarah J., Richardson, Rachel E., Fang, Mingliang, Qian, Wei-Jun, Demokritou, Philip, Thrall, Brian D.

“…Graphene oxide (GO) nanomaterials have unique physicochemical properties that make them highly promising for biomedical, environmental, and agricultural…”
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Multi-Omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-Mediated H2 Production in Cyanothece sp. ATCC 51142 by Bernstein, Hans C., Charania, Moiz A., McClure, Ryan S., Sadler, Natalie C., Melnicki, Matthew R., Hill, Eric A., Markillie, Lye Meng, Nicora, Carrie D., Wright, Aaron T., Romine, Margaret F., Beliaev, Alexander S.

“…To date, the proposed mechanisms of nitrogenase-driven photosynthetic H 2 production by the diazotrophic unicellular cyanobacterium Cyanothece sp . ATCC 51142…”
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