VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

por Espinoza, Josh L., Dupont, Chris L.
Publicado 2022

Identification of novel post-transcriptional features in olfactory receptor family mRNAs

por Shum, Eleen Y., Espinoza, Josh L., Ramaiah, Madhuvanthi, Wilkinson, Miles F.
Publicado 2015

Transcriptomic Study of Substrate-Specific Transport Mechanisms for Iron and Carbon in the Marine Copiotroph Alteromonas macleodii

por Manck, Lauren E., Espinoza, Josh L., Dupont, Christopher L., Barbeau, Katherine A.
Publicado 2020

The Airplane Cabin Microbiome

por Weiss, Howard, Hertzberg, Vicki Stover, Dupont, Chris, Espinoza, Josh L., Levy, Shawn, Nelson, Karen, Norris, Sharon
Publicado 2018

Influence of Substrate Concentration on the Culturability of Heterotrophic Soil Microbes Isolated by High-Throughput Dilution-to-Extinction Cultivation

por Bartelme, Ryan P., Custer, Joy M., Dupont, Christopher L., Espinoza, Josh L., Torralba, Manolito, Khalili, Banafshe, Carini, Paul
Publicado 2020

Genus-Wide Transcriptional Landscapes Reveal Correlated Gene Networks Underlying Microevolutionary Divergence in Diatoms

por Walworth, Nathan G, Espinoza, Josh L, Argyle, Phoebe A, Hinners, Jana, Levine, Naomi M, Doblin, Martina A, Dupont, Chris L, Collins, Sinéad
Publicado 2023

Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering

por Garza, Erin A., Bielinski, Vincent A., Espinoza, Josh L., Orlandi, Kona, Alfaro, Josefa Rivera, Bolt, Tayah M., Beeri, Karen, Weyman, Philip D., Dupont, Christopher L.
Publicado 2023

Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries

por Espinoza, Josh L, Torralba, Manolito, Leong, Pamela, Saffery, Richard, Bockmann, Michelle, Kuelbs, Claire, Singh, Suren, Hughes, Toby, Craig, Jeffrey M, Nelson, Karen E, Dupont, Chris L
Publicado 2022

Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures

por Badrane, Hassan, Cheng, Shaoji, Dupont, Christopher L, Hao, Binghua, Driscoll, Eileen, Morder, Kristin, Liu, Guojun, Newbrough, Anthony, Fleres, Giuseppe, Kaul, Drishti, Espinoza, Josh L, Clancy, Cornelius J, Nguyen, M. Hong
Publicado 2023

Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures

por Badrane, Hassan, Cheng, Shaoji, Dupont, Christopher L., Hao, Binghua, Driscoll, Eileen, Morder, Kristin, Liu, Guojun, Newbrough, Anthony, Fleres, Giuseppe, Kaul, Drishti, Espinoza, Josh L., Clancy, Cornelius J., Nguyen, M. Hong
Publicado 2023

Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling

por O’Rourke, Aubrie, Beyhan, Sinem, Choi, Yongwook, Morales, Pavel, Chan, Agnes P., Espinoza, Josh L., Dupont, Chris L., Meyer, Kirsten J., Spoering, Amy, Lewis, Kim, Nierman, William C., Nelson, Karen E.
Publicado 2020

Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach

por Espinoza, Josh L., Dupont, Chris L., O’Rourke, Aubrie, Beyhan, Sinem, Morales, Pavel, Spoering, Amy, Meyer, Kirsten J., Chan, Agnes P., Choi, Yongwook, Nierman, William C., Lewis, Kim, Nelson, Karen E.
Publicado 2021

A Silent Operon of Photorhabdus luminescens Encodes a Prodrug Mimic of GTP

por Shahsavari, Negar, Wang, Boyuan, Imai, Yu, Mori, Miho, Son, Sangkeun, Liang, Libang, Böhringer, Nils, Manuse, Sylvie, Gates, Michael F., Morrissette, Madeleine, Corsetti, Rachel, Espinoza, Josh L., Dupont, Chris L., Laub, Michael T., Lewis, Kim
Publicado 2022

Host-Microbiome Associations in Saliva Predict COVID-19 Severity

por Alqedari, Hend, Altabtbaei, Khaled, Espinoza, Josh L., Bin-Hasan, Saadoun, Alghounaim, Mohammad, Alawady, Abdullah, Altabtabae, Abdullah, AlJamaan, Sarah, Devarajan, Sriraman, AlShammari, Tahreer, Eid, Mohammed Ben, Matsuoka, Michele, Jang, Hyesun, Dupont, Christopher L., Freire, Marcelo
Publicado 2023

Competition between skin antimicrobial peptides and commensal bacteria in type 2 inflammation enables survival of S. aureus

por Nakatsuji, Teruaki, Brinton, Samantha L., Cavagnero, Kellen J., O’Neill, Alan M., Chen, Yang, Dokoshi, Tatsuya, Butcher, Anna M., Osuoji, Olive C., Shafiq, Faiza, Espinoza, Josh L., Dupont, Christopher L., Hata, Tissa R., Gallo, Richard L.
Publicado 2023

Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease

por Espinoza, Josh L., Harkins, Derek M., Torralba, Manolito, Gomez, Andres, Highlander, Sarah K., Jones, Marcus B., Leong, Pamela, Saffery, Richard, Bockmann, Michelle, Kuelbs, Claire, Inman, Jason M., Hughes, Toby, Craig, Jeffrey M., Nelson, Karen E., Dupont, Chris L.
Publicado 2018

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm

por Michaud, Jennifer M., Thompson, Luke R., Kaul, Drishti, Espinoza, Josh L., Richter, R. Alexander, Xu, Zhenjiang Zech, Lee, Christopher, Pham, Kevin M., Beall, Charlotte M., Malfatti, Francesca, Azam, Farooq, Knight, Rob, Burkart, Michael D., Dupont, Christopher L., Prather, Kimberly A.
Publicado 2018

Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant–cyanobacteria symbiosis

por Warshan, Denis, Espinoza, Josh L, Stuart, Rhona K, Richter, R Alexander, Kim, Sea-Yong, Shapiro, Nicole, Woyke, Tanja, C Kyrpides, Nikos, Barry, Kerrie, Singan, Vasanth, Lindquist, Erika, Ansong, Charles, Purvine, Samuel O, M Brewer, Heather, Weyman, Philip D, Dupont, Christopher L, Rasmussen, Ulla
Publicado 2017

Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children

por Nabwera, Helen M., Espinoza, Josh L., Worwui, Archibald, Betts, Modupeh, Okoi, Catherine, Sesay, Abdul K., Bancroft, Rowan, Agbla, Schadrac C., Jarju, Sheikh, Bradbury, Richard S., Colley, Mariama, Jallow, Amadou T., Liu, Jie, Houpt, Eric R, Prentice, Andrew M., Antonio, Martin, Bernstein, Robin M, Dupont, Christopher L., Kwambana-Adams, Brenda A.
Publicado 2021

Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality

por Santoro, Erika P., Borges, Ricardo M., Espinoza, Josh L., Freire, Marcelo, Messias, Camila S. M. A., Villela, Helena D. M., Pereira, Leandro M., Vilela, Caren L. S., Rosado, João G., Cardoso, Pedro M., Rosado, Phillipe M., Assis, Juliana M., Duarte, Gustavo A. S., Perna, Gabriela, Rosado, Alexandre S., Macrae, Andrew, Dupont, Christopher L., Nelson, Karen E., Sweet, Michael J., Voolstra, Christian R., Peixoto, Raquel S.
Publicado 2021