Search Results - "Swafford, Austin D."

Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults by de la Cuesta-Zuluaga, Jacobo, Kelley, Scott T, Chen, Yingfeng, Escobar, Juan S, Mueller, Noel T, Ley, Ruth E, McDonald, Daniel, Huang, Shi, Swafford, Austin D, Knight, Rob, Thackray, Varykina G

“…Gut microbial diversity changes throughout the human life span and is known to be associated with host sex. We investigated the association of age, sex, and…”
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Thermal ablation of tumor cells with antibody-functionalized single-walled carbon nanotubes by Chakravarty, Pavitra, Marches, Radu, Zimmerman, Neil S, Swafford, Austin D.-E, Bajaj, Pooja, Musselman, Inga H, Pantano, Paul, Draper, Rockford K, Vitetta, Ellen S

“…Single-walled carbon nanotubes (CNTs) emit heat when they absorb energy from near-infrared (NIR) light. Tissue is relatively transparent to NIR, which suggests…”
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A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities by Shaffer, Justin P, Carpenter, Carolina S, Martino, Cameron, Salido, Rodolfo A, Minich, Jeremiah J, Bryant, MacKenzie, Sanders, Karenina, Schwartz, Tara, Humphrey, Gregory, Swafford, Austin D, Knight, Rob

“…Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi…”
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Human Skin, Oral, and Gut Microbiomes Predict Chronological Age by Huang, Shi, Haiminen, Niina, Carrieri, Anna-Paola, Hu, Rebecca, Jiang, Lingjing, Parida, Laxmi, Russell, Baylee, Allaband, Celeste, Zarrinpar, Amir, Vázquez-Baeza, Yoshiki, Belda-Ferre, Pedro, Zhou, Hongwei, Kim, Ho-Cheol, Swafford, Austin D, Knight, Rob, Xu, Zhenjiang Zech

“…Human gut microbiomes are known to change with age, yet the relative value of human microbiomes across the body as predictors of age, and prediction robustness…”
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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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Salivary bacterial signatures in depression-obesity comorbidity are associated with neurotransmitters and neuroactive dipeptides by Aleti, Gajender, Kohn, Jordan N, Troyer, Emily A, Weldon, Kelly, Huang, Shi, Tripathi, Anupriya, Dorrestein, Pieter C, Swafford, Austin D, Knight, Rob, Hong, Suzi

“…Depression and obesity are highly prevalent, often co-occurring conditions marked by inflammation. Microbiome perturbations are implicated in…”
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Challenges in the construction of knowledge bases for human microbiome-disease associations by Badal, Varsha Dave, Wright, Dustin, Katsis, Yannis, Kim, Ho-Cheol, Swafford, Austin D, Knight, Rob, Hsu, Chun-Nan

“…The last few years have seen tremendous growth in human microbiome research, with a particular focus on the links to both mental and physical health and…”
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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy by Zhu, Qiyun, Huang, Shi, Gonzalez, Antonio, McGrath, Imran, McDonald, Daniel, Haiminen, Niina, Armstrong, George, Vázquez-Baeza, Yoshiki, Yu, Julian, Kuczynski, Justin, Sepich-Poore, Gregory D, Swafford, Austin D, Das, Promi, Shaffer, Justin P, Lejzerowicz, Franck, Belda-Ferre, Pedro, Havulinna, Aki S, Méric, Guillaume, Niiranen, Teemu, Lahti, Leo, Salomaa, Veikko, Kim, Ho-Cheol, Jain, Mohit, Inouye, Michael, Gilbert, Jack A, Knight, Rob

“…We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference…”
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An Allele of IKZF1 (Ikaros) Conferring Susceptibility to Childhood Acute Lymphoblastic Leukemia Protects Against Type 1 Diabetes by SWAFFORD, Austin D.-E, HOWSON, Joanna M. M, DAVISON, Lucy J, WALLACE, Chris, SMYTH, Deborah J, SCHUILENBURG, Helen, MAISURIA-ARMER, Meeta, MISTRY, Trupti, LENARDO, Michael J, TODD, John A

“…IKZF1 encoding Ikaros, an essential regulator of lymphopoiesis and immune homeostasis, has been implicated in the development of childhood acute lymphoblastic…”
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High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy by Raghuvanshi, Ruma, Vasco, Karla, Vázquez-Baeza, Yoshiki, Jiang, Lingjing, Morton, James T., Li, Danxun, Gonzalez, Antonio, DeRight Goldasich, Lindsay, Humphrey, Gregory, Ackermann, Gail, Swafford, Austin D., Conrad, Douglas, Knight, Rob, Dorrestein, Pieter C., Quinn, Robert A.

“…Microbial diversity in the cystic fibrosis (CF) lung decreases over decades as pathogenic bacteria such as Pseudomonas aeruginosa take over. The dynamics of…”
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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets by Cantrell, Kalen, Fedarko, Marcus W, Rahman, Gibraan, McDonald, Daniel, Yang, Yimeng, Zaw, Thant, Gonzalez, Antonio, Janssen, Stefan, Estaki, Mehrbod, Haiminen, Niina, Beck, Kristen L, Zhu, Qiyun, Sayyari, Erfan, Morton, James T, Armstrong, George, Tripathi, Anupriya, Gauglitz, Julia M, Marotz, Clarisse, Matteson, Nathaniel L, Martino, Cameron, Sanders, Jon G, Carrieri, Anna Paola, Song, Se Jin, Swafford, Austin D, Dorrestein, Pieter C, Andersen, Kristian G, Parida, Laxmi, Kim, Ho-Cheol, Vázquez-Baeza, Yoshiki, Knight, Rob

“…Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool…”
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Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment by Minich, Jeremiah J, Ali, Farhana, Marotz, Clarisse, Belda-Ferre, Pedro, Chiang, Leslie, Shaffer, Justin P, Carpenter, Carolina S, McDonald, Daniel, Gilbert, Jack, Allard, Sarah M, Allen, Eric E, Knight, Rob, Sweeney, Daniel A, Swafford, Austin D

“…Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical…”
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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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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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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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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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Best practices for analysing microbiomes by Knight, Rob, Vrbanac, Alison, Taylor, Bryn C., Aksenov, Alexander, Callewaert, Chris, Debelius, Justine, Gonzalez, Antonio, Kosciolek, Tomasz, McCall, Laura-Isobel, McDonald, Daniel, Melnik, Alexey V., Morton, James T., Navas, Jose, Quinn, Robert A., Sanders, Jon G., Swafford, Austin D., Thompson, Luke R., Tripathi, Anupriya, Xu, Zhenjiang Z., Zaneveld, Jesse R., Zhu, Qiyun, Caporaso, J. Gregory, Dorrestein, Pieter C.

“…Complex microbial communities shape the dynamics of various environments, ranging from the mammalian gastrointestinal tract to the soil. Advances in DNA…”
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Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs by Gauglitz, Julia M, Morton, James T, Tripathi, Anupriya, Hansen, Shalisa, Gaffney, Michele, Carpenter, Carolina, Weldon, Kelly C, Shah, Riya, Parampil, Amy, Fidgett, Andrea L, Swafford, Austin D, Knight, Rob, Dorrestein, Pieter C

“…Even high-quality collection and reporting of study metadata in microbiome studies can lead to various forms of inadvertently missing or mischaracterized…”
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Qiita: rapid, web-enabled microbiome meta-analysis by Gonzalez, Antonio, Navas-Molina, Jose A., Kosciolek, Tomasz, McDonald, Daniel, Vázquez-Baeza, Yoshiki, Ackermann, Gail, DeReus, Jeff, Janssen, Stefan, Swafford, Austin D., Orchanian, Stephanie B., Sanders, Jon G., Shorenstein, Joshua, Holste, Hannes, Petrus, Semar, Robbins-Pianka, Adam, Brislawn, Colin J., Wang, Mingxun, Rideout, Jai Ram, Bolyen, Evan, Dillon, Matthew, Caporaso, J. Gregory, Dorrestein, Pieter C., Knight, Rob

“…Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be…”
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Mass spectrometry searches using MASST by Wang, Mingxun, Jarmusch, Alan K., Vargas, Fernando, Aksenov, Alexander A., Gauglitz, Julia M., Weldon, Kelly, Petras, Daniel, da Silva, Ricardo, Quinn, Robert, Melnik, Alexey V., van der Hooft, Justin J. J., Caraballo-Rodríguez, Andrés Mauricio, Nothias, Louis Felix, Aceves, Christine M., Panitchpakdi, Morgan, Brown, Elizabeth, Di Ottavio, Francesca, Sikora, Nicole, Elijah, Emmanuel O., Labarta-Bajo, Lara, Gentry, Emily C., Shalapour, Shabnam, Kyle, Kathleen E., Puckett, Sara P., Watrous, Jeramie D., Carpenter, Carolina S., Bouslimani, Amina, Ernst, Madeleine, Swafford, Austin D., Zúñiga, Elina I., Balunas, Marcy J., Klassen, Jonathan L., Loomba, Rohit, Knight, Rob, Bandeira, Nuno, Dorrestein, Pieter C.

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