Hi-C metagenome sequencing reveals soil phage–host interactions
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.
Published in Nature communications (23.11.2023)
Published in Nature communications (23.11.2023)
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Journal Article
Gene co-expression network analysis in zebrafish reveals chemical class specific modules
Shankar, Prarthana, McClure, Ryan S, Waters, Katrina M, Tanguay, Robyn L
Published in BMC genomics (13.09.2021)
Published in BMC genomics (13.09.2021)
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Journal Article
Coupling Genome-wide Transcriptomics and Developmental Toxicity Profiles in Zebrafish to Characterize Polycyclic Aromatic Hydrocarbon (PAH) Hazard
Shankar, Prarthana, Geier, Mitra C, Truong, Lisa, McClure, Ryan S, Pande, Paritosh, Waters, Katrina M, Tanguay, Robert L
Published in International journal of molecular sciences (25.05.2019)
Published in International journal of molecular sciences (25.05.2019)
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Journal Article
Tripogon loliiformis tolerates rapid desiccation after metabolic and transcriptional priming during initial drying
Okemo, Pauline A., Njaci, Isaac, Kim, Young-Mo, McClure, Ryan S., Peterson, Matthew J., Beliaev, Alexander S., Hixson, Kim K., Mundree, Sagadevan, Williams, Brett
Published in Scientific reports (23.11.2023)
Published in Scientific reports (23.11.2023)
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Journal Article
Unified feature association networks through integration of transcriptomic and proteomic data
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
Published in PLoS computational biology (17.09.2019)
Published in PLoS computational biology (17.09.2019)
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Journal Article
Selection, Succession, and Stabilization of Soil Microbial Consortia
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
Published in mSystems (01.07.2019)
Published in mSystems (01.07.2019)
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Journal Article
Improving network inference algorithms using resampling methods
Colby, Sean M, McClure, Ryan S, Overall, Christopher C, Renslow, Ryan S, McDermott, Jason E
Published in BMC bioinformatics (12.10.2018)
Published in BMC bioinformatics (12.10.2018)
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Journal Article
Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture
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.
Published in Scientific reports (10.01.2018)
Published in Scientific reports (10.01.2018)
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Journal Article
Unlocking the Constraints of Cyanobacterial Productivity: Acclimations Enabling Ultrafast Growth
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
Published in mBio (26.07.2016)
Published in mBio (26.07.2016)
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Journal Article
Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene
Wilson, Lindsay B., McClure, Ryan S., Waters, Katrina M., Simonich, Michael T., Tanguay, Robyn L.
Published in Frontiers in toxicology (25.08.2022)
Published in Frontiers in toxicology (25.08.2022)
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Journal Article
Indirect Interspecies Regulation: Transcriptional and Physiological Responses of a Cyanobacterium to Heterotrophic Partnership
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
Published in mSystems (01.03.2017)
Published in mSystems (01.03.2017)
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Journal Article
Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality
Song, Hyun-Seob, McClure, Ryan S, Bernstein, Hans C, Overall, Christopher C, Hill, Eric A, Beliaev, Alexander S
Published in Life (Basel, Switzerland) (27.03.2015)
Published in Life (Basel, Switzerland) (27.03.2015)
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Journal Article
Species-specific transcriptomic network inference of interspecies interactions
McClure, Ryan S., Overall, Christopher C., Hill, Eric A., Song, Hyun-Seob, Charania, Moiz, Bernstein, Hans C., McDermott, Jason E., Beliaev, Alexander S.
Published in The ISME Journal (01.08.2018)
Published in The ISME Journal (01.08.2018)
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Journal Article
Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations
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
Published in Scientific reports (02.07.2020)
Published in Scientific reports (02.07.2020)
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Journal Article
Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002
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
Published in Nucleic acids research (14.10.2016)
Published in Nucleic acids research (14.10.2016)
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Journal Article
Graphene oxide exposure alters gut microbial community composition and metabolism in an in vitro human model
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.
Published in NanoImpact (01.04.2023)
Published in NanoImpact (01.04.2023)
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Journal Article
Multi-Omic Dynamics Associate Oxygenic Photosynthesis with Nitrogenase-Mediated H2 Production in Cyanothece sp. ATCC 51142
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.
Published in Scientific reports (03.11.2015)
Published in Scientific reports (03.11.2015)
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Journal Article