Search Results - "Wandro, Stephen"

The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis by Wandro, Stephen, Osborne, Stephanie, Enriquez, Claudia, Bixby, Christine, Arrieta, Antonio, Whiteson, Katrine

“…The assembly and development of the gut microbiome in infants have important consequences for immediate and long-term health. Preterm infants represent an…”
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Predictable Molecular Adaptation of Coevolving Enterococcus faecium and Lytic Phage EfV12-phi1 by Wandro, Stephen, Oliver, Andrew, Gallagher, Tara, Weihe, Claudia, England, Whitney, Martiny, Jennifer B H, Whiteson, Katrine

“…Bacteriophages are highly abundant in human microbiota where they coevolve with resident bacteria. Phage predation can drive the evolution of bacterial…”
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A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities by Shaffer, Justin P, Marotz, Clarisse, Belda-Ferre, Pedro, Martino, Cameron, Wandro, Stephen, Estaki, Mehrbod, Salido, Rodolfo A, Carpenter, Carolina S, Zaramela, Livia S, Minich, Jeremiah J, Bryant, MacKenzie, Sanders, Karenina, Fraraccio, Serena, Ackermann, Gail, Humphrey, Gregory, Swafford, Austin D, Miller-Montgomery, Sandrine, Knight, Rob

“…One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused…”
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Cervicovaginal Microbiome Composition Is Associated with Metabolic Profiles in Healthy Pregnancy by Oliver, Andrew, LaMere, Brandon, Weihe, Claudia, Wandro, Stephen, Lindsay, Karen L, Wadhwa, Pathik D, Mills, David A, Pride, David T, Fiehn, Oliver, Northen, Trent, de Raad, Markus, Li, Huiying, Martiny, Jennifer B H, Lynch, Susan, Whiteson, Katrine

“…Microbes and their metabolic products influence early-life immune and microbiome development, yet remain understudied during pregnancy. Vaginal microbial…”
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Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition by Marotz, Clarisse, Cavagnero, Kellen J, Song, Se Jin, McDonald, Daniel, Wandro, Stephen, Humphrey, Greg, Bryant, MacKenzie, Ackermann, Gail, Diaz, Edgar, Knight, Rob

“…As the number of human microbiome studies expand, it is increasingly important to identify cost-effective, practical preservatives that allow for room…”
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Phage Cocktails Constrain the Growth of Enterococcus by Wandro, Stephen, Ghatbale, Pooja, Attai, Hedieh, Hendrickson, Clark, Samillano, Cyril, Suh, Joy, Dunham, Sage J B, Pride, David T, Whiteson, Katrine

“…Phages that infect pathogenic bacteria present a valuable resource for treating antibiotic-resistant infections. We isolated and developed a collection of 19…”
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Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References by Hakim, Daniel, Wandro, Stephen, Zengler, Karsten, Zaramela, Livia S, Nowinski, Brent, Swafford, Austin, Zhu, Qiyun, Song, Se Jin, Gonzalez, Antonio, McDonald, Daniel, Knight, Rob

“…Assigning taxonomy remains a challenging topic in microbiome studies, due largely to ambiguity of reads which overlap multiple reference genomes. With the Web…”
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Signatures of HIV and Major Depressive Disorder in the Plasma Microbiome by Taylor, Bryn C, Sheikh Andalibi, Mohammadsobhan, Wandro, Stephen, Weldon, Kelly C, Sepich-Poore, Gregory D, Carpenter, Carolina S, Fraraccio, Serena, Franklin, Donald, Iudicello, Jennifer E, Letendre, Scott, Gianella, Sara, Grant, Igor, Ellis, Ronald J, Heaton, Robert K, Knight, Rob, Swafford, Austin D

“…Inter-individual differences in the gut microbiome are linked to alterations in inflammation and blood-brain barrier permeability, which may increase the risk…”
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Dosing and Re-Administration of Lentiviral Vector for In Vivo Gene Therapy in Rhesus Monkeys and ADA-Deficient Mice by Carbonaro-Sarracino, Denise A., Tarantal, Alice F., Lee, C. Chang I., Kaufman, Michael L., Wandro, Stephen, Jin, Xiangyang, Martinez, Michele, Clark, Danielle N., Chun, Krista, Koziol, Colin, Hardee, Cinnamon L., Wang, Xiaoyan, Kohn, Donald B.

“…Adenosine deaminase (ADA)-deficient mice and healthy rhesus monkeys were studied to determine the impact of age at treatment, vector dosage, dosing schedule,…”
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Making It Last: Storage Time and Temperature Have Differential Impacts on Metabolite Profiles of Airway Samples from Cystic Fibrosis Patients by Wandro, Stephen, Carmody, Lisa, Gallagher, Tara, LiPuma, John J, Whiteson, Katrine

“…Metabolites of human or microbial origin have the potential to be important biomarkers of the disease state in cystic fibrosis (CF). Clinical sample collection…”
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Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases by Armstrong, George, Martino, Cameron, Morris, Justin, Khaleghi, Behnam, Kang, Jaeyoung, DeReus, Jeff, Zhu, Qiyun, Roush, Daniel, McDonald, Daniel, Gonazlez, Antonio, Shaffer, Justin P, Carpenter, Carolina, Estaki, Mehrbod, Wandro, Stephen, Eilert, Sean, Akel, Ameen, Eno, Justin, Curewitz, Ken, Swafford, Austin D, Moshiri, Niema, Rosing, Tajana, Knight, Rob

“…Increasing data volumes on high-throughput sequencing instruments such as the NovaSeq 6000 leads to long computational bottlenecks for common metagenomics data…”
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Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition by Marotz, Clarisse, Cavagnero, Kellen J., Song, Se Jin, McDonald, Daniel, Wandro, Stephen, Humphrey, Greg, Bryant, MacKenzie, Ackermann, Gail, Diaz, Edgar, Knight, Rob

“…As the number of human microbiome studies expand, it is increasingly important to identify cost-effective, practical preservatives that allow for room…”
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Microbiome analyses of blood and tissues suggest cancer diagnostic approach by Poore, Gregory D, Kopylova, Evguenia, Zhu, Qiyun, Carpenter, Carolina, Fraraccio, Serena, Wandro, Stephen, Kosciolek, Tomasz, Janssen, Stefan, Metcalf, Jessica, Song, Se Jin, Kanbar, Jad, Miller-Montgomery, Sandrine, Heaton, Robert, Mckay, Rana, Patel, Sandip Pravin, Swafford, Austin D, Knight, Rob

“…Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in…”
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Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions by Narunsky-Haziza, Lian, Sepich-Poore, Gregory D, Livyatan, Ilana, Asraf, Omer, Martino, Cameron, Nejman, Deborah, Gavert, Nancy, Stajich, Jason E, Amit, Guy, González, Antonio, Wandro, Stephen, Perry, Gili, Ariel, Ruthie, Meltser, Arnon, Shaffer, Justin P, Zhu, Qiyun, Balint-Lahat, Nora, Barshack, Iris, Dadiani, Maya, Gal-Yam, Einav N, Patel, Sandip Pravin, Bashan, Amir, Swafford, Austin D, Pilpel, Yitzhak, Knight, Rob, Straussman, Ravid

“…Cancer-microbe associations have been explored for centuries, but cancer-associated fungi have rarely been examined. Here, we comprehensively characterize the…”
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Robustness of cancer microbiome signals over a broad range of methodological variation by Sepich-Poore, Gregory D., McDonald, Daniel, Kopylova, Evguenia, Guccione, Caitlin, Zhu, Qiyun, Austin, George, Carpenter, Carolina, Fraraccio, Serena, Wandro, Stephen, Kosciolek, Tomasz, Janssen, Stefan, Metcalf, Jessica L., Song, Se Jin, Kanbar, Jad, Miller-Montgomery, Sandrine, Heaton, Robert, Mckay, Rana, Patel, Sandip Pravin, Swafford, Austin D., Korem, Tal, Knight, Rob

“…In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas (TCGA) [ 1 ]. Multiple peer-reviewed papers independently verified or…”
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Retraction Note: Microbiome analyses of blood and tissues suggest cancer diagnostic approach by Poore, Gregory D., Kopylova, Evguenia, Zhu, Qiyun, Carpenter, Carolina, Fraraccio, Serena, Wandro, Stephen, Kosciolek, Tomasz, Janssen, Stefan, Metcalf, Jessica, Song, Se Jin, Kanbar, Jad, Miller-Montgomery, Sandrine, Heaton, Robert, Mckay, Rana, Patel, Sandip Pravin, Swafford, Austin D., Knight, Rob

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Correction: Robustness of cancer microbiome signals over a broad range of methodological variation by Sepich-Poore, Gregory D., McDonald, Daniel, Kopylova, Evguenia, Guccione, Caitlin, Zhu, Qiyun, Austin, George, Carpenter, Carolina, Fraraccio, Serena, Wandro, Stephen, Kosciolek, Tomasz, Janssen, Stefan, Metcalf, Jessica L., Song, Se Jin, Kanbar, Jad, Miller-Montgomery, Sandrine, Heaton, Robert, Mckay, Rana, Patel, Sandip Pravin, Swafford, Austin D., Korem, Tal, Knight, Rob

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Cystic Fibrosis-Associated Stenotrophomonas maltophilia Strain-Specific Adaptations and Responses to pH by Gallagher, Tara, Phan, Joann, Oliver, Andrew, Chase, Alexander B, England, Whitney E, Wandro, Stephen, Hendrickson, Clark, Riedel, Stefan F, Whiteson, Katrine

“…The airway fluids of cystic fibrosis (CF) patients contain local pH gradients and are more acidic than those of healthy individuals. pH is a critical factor…”
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RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach by Poore, Gregory D., Kopylova, Evguenia, Zhu, Qiyun, Carpenter, Carolina, Fraraccio, Serena, Wandro, Stephen, Kosciolek, Tomasz, Janssen, Stefan, Metcalf, Jessica, Song, Se Jin, Kanbar, Jad, Miller-Montgomery, Sandrine, Heaton, Robert, Mckay, Rana, Patel, Sandip Pravin, Swafford, Austin D., Knight, Rob

“…Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in…”
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Abstract 1184: Early-stage lung cancer detection via circulating microbial DNA biomarkers and machine learning classification by Sepich-Poore, Gregory D., Fraraccio, Serena, Wandro, Stephen, Knight, Rob, Miller-Montgomery, Sandrine, Adams, Eddie

“…Abstract Introduction: Human tissues, including tumors, are extensively colonized by taxonomically diverse microbes. Intra-tumoral microbial activity and…”
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