Search Results - "Alm, Eric J"

Inferring correlation networks from genomic survey data by Friedman, Jonathan, Alm, Eric J

“…High-throughput sequencing based techniques, such as 16S rRNA gene profiling, have the potential to elucidate the complex inner workings of natural microbial…”
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Meta-analysis of gut microbiome studies identifies disease-specific and shared responses by Duvallet, Claire, Gibbons, Sean M., Gurry, Thomas, Irizarry, Rafael A., Alm, Eric J.

“…Hundreds of clinical studies have demonstrated associations between the human microbiome and disease, yet fundamental questions remain on how we can generalize…”
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Rapid evolutionary innovation during an Archaean genetic expansion by David, Lawrence A., Alm, Eric J.

“…Prehistory is in the genes Hidden in the modern-day genomes of today's living organisms are the imprints of ancient biogeochemical events. Lawrence David and…”
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A practical guide to methods controlling false discoveries in computational biology by Korthauer, Keegan, Kimes, Patrick K, Duvallet, Claire, Reyes, Alejandro, Subramanian, Ayshwarya, Teng, Mingxiang, Shukla, Chinmay, Alm, Eric J, Hicks, Stephanie C

“…In high-throughput studies, hundreds to millions of hypotheses are typically tested. Statistical methods that control the false discovery rate (FDR) have…”
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Horizontal gene transfer and the evolution of bacterial and archaeal population structure by Polz, Martin F, Alm, Eric J, Hanage, William P

“…Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome…”
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Random sequences rapidly evolve into de novo promoters by Yona, Avihu H., Alm, Eric J., Gore, Jeff

“…How new functions arise de novo is a fundamental question in evolution. We studied de novo evolution of promoters in Escherichia coli by replacing the lac…”
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Unraveling the processes shaping mammalian gut microbiomes over evolutionary time by Groussin, Mathieu, Mazel, Florent, Sanders, Jon G., Smillie, Chris S., Lavergne, Sébastien, Thuiller, Wilfried, Alm, Eric J.

“…Whether mammal–microbiome interactions are persistent and specific over evolutionary time is controversial. Here we show that host phylogeny and major dietary…”
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Correcting for batch effects in case-control microbiome studies by Gibbons, Sean M, Duvallet, Claire, Alm, Eric J

“…High-throughput data generation platforms, like mass-spectrometry, microarrays, and second-generation sequencing are susceptible to batch effects due to…”
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An omics-based framework for assessing the health risk of antimicrobial resistance genes by Zhang, An-Ni, Gaston, Jeffry M., Dai, Chengzhen L., Zhao, Shijie, Poyet, Mathilde, Groussin, Mathieu, Yin, Xiaole, Li, Li-Guan, van Loosdrecht, Mark C. M., Topp, Edward, Gillings, Michael R., Hanage, William P., Tiedje, James M., Moniz, Katya, Alm, Eric J., Zhang, Tong

“…Antibiotic resistance genes (ARGs) are widespread among bacteria. However, not all ARGs pose serious threats to public health, highlighting the importance of…”
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Salt-responsive gut commensal modulates TH17 axis and disease by Wilck, Nicola, Matus, Mariana G., Kearney, Sean M., Olesen, Scott W., Forslund, Kristoffer, Bartolomaeus, Hendrik, Haase, Stefanie, Mähler, Anja, Balogh, András, Markó, Lajos, Vvedenskaya, Olga, Kleiner, Friedrich H., Tsvetkov, Dmitry, Klug, Lars, Costea, Paul I., Sunagawa, Shinichi, Maier, Lisa, Rakova, Natalia, Schatz, Valentin, Neubert, Patrick, Frätzer, Christian, Krannich, Alexander, Gollasch, Maik, Grohme, Diana A., Côrte-Real, Beatriz F., Gerlach, Roman G., Basic, Marijana, Typas, Athanasios, Wu, Chuan, Titze, Jens M., Jantsch, Jonathan, Boschmann, Michael, Dechend, Ralf, Kleinewietfeld, Markus, Kempa, Stefan, Bork, Peer, Linker, Ralf A., Alm, Eric J., Müller, Dominik N.

“…A Western lifestyle with high salt consumption can lead to hypertension and cardiovascular disease. High salt may additionally drive autoimmunity by inducing T…”
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Making waves: Wastewater surveillance of SARS-CoV-2 for population-based health management by Thompson, Janelle R, Nancharaiah, Yarlagadda V, Gu, Xiaoqiong, Lee, Wei Lin, Rajal, Verónica B, Haines, Monamie B, Girones, Rosina, Ng, Lee Ching, Alm, Eric J, Wuertz, Stefan

“…•Wastewater surveillance cheaper and less invasive than massive testing of individuals.•Useful early alert of viral circulation to prevent outbreaks and inform…”
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Population Genomics of Early Events in the Ecological Differentiation of Bacteria by Shapiro, B. Jesse, Friedman, Jonathan, Cordero, Otto X., Preheim, Sarah P., Timberlake, Sonia C., Szabó, Gitta, Polz, Martin F., J. Alm, Eric

“…Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental…”
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Framework for rational donor selection in fecal microbiota transplant clinical trials by Duvallet, Claire, Zellmer, Caroline, Panchal, Pratik, Budree, Shrish, Osman, Majdi, Alm, Eric J

“…Early clinical successes are driving enthusiasm for fecal microbiota transplantation (FMT), the transfer of healthy gut bacteria through whole stool, as…”
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Correlation detection strategies in microbial data sets vary widely in sensitivity and precision by Weiss, Sophie, Van Treuren, Will, Lozupone, Catherine, Faust, Karoline, Friedman, Jonathan, Deng, Ye, Xia, Li Charlie, Xu, Zhenjiang Zech, Ursell, Luke, Alm, Eric J, Birmingham, Amanda, Cram, Jacob A, Fuhrman, Jed A, Raes, Jeroen, Sun, Fengzhu, Zhou, Jizhong, Knight, Rob

“…Disruption of healthy microbial communities has been linked to numerous diseases, yet microbial interactions are little understood. This is due in part to the…”
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Ecology drives a global network of gene exchange connecting the human microbiome by Smillie, Chris S., Smith, Mark B., Friedman, Jonathan, Cordero, Otto X., David, Lawrence A., Alm, Eric J.

“…Gene swapping in the human microbiome Horizontal gene transfer — the exchange of genetic material between different species or lineages — is an important…”
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Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation by Smillie, Christopher S., Sauk, Jenny, Gevers, Dirk, Friedman, Jonathan, Sung, Jaeyun, Youngster, Ilan, Hohmann, Elizabeth L., Staley, Christopher, Khoruts, Alexander, Sadowsky, Michael J., Allegretti, Jessica R., Smith, Mark B., Xavier, Ramnik J., Alm, Eric J.

“…Fecal microbiota transplantation (FMT) from healthy donor to patient is a treatment for microbiome-associated diseases. Although the success of FMT requires…”
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Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools by Jiang, Xiaofang, Hall, Andrew Brantley, Xavier, Ramnik J, Alm, Eric J

“…Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer could benefit human health by conferring new metabolic…”
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Fecal Microbiota Transplant for Relapsing Clostridium difficile Infection Using a Frozen Inoculum From Unrelated Donors: A Randomized, Open-Label, Controlled Pilot Study by Youngster, Ilan, Sauk, Jenny, Pindar, Christina, Wilson, Robin G., Kaplan, Jess L., Smith, Mark B., Alm, Eric J., Gevers, Dirk, Russell, George H., Hohmann, Elizabeth L.

“…Background. Recurrent Clostridium difficile infection (CDI) with poor response to standard antimicrobial therapy is a growing medical concern. We aimed to…”
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Microbial symbionts accelerate wound healing via the neuropeptide hormone oxytocin by Poutahidis, Theofilos, Kearney, Sean M, Levkovich, Tatiana, Qi, Peimin, Varian, Bernard J, Lakritz, Jessica R, Ibrahim, Yassin M, Chatzigiagkos, Antonis, Alm, Eric J, Erdman, Susan E

“…Wound healing capability is inextricably linked with diverse aspects of physical fitness ranging from recovery after minor injuries and surgery to diabetes and…”
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SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases by Wu, Fuqing, Zhang, Jianbo, Xiao, Amy, Gu, Xiaoqiong, Lee, Wei Lin, Armas, Federica, Kauffman, Kathryn, Hanage, William, Matus, Mariana, Ghaeli, Newsha, Endo, Noriko, Duvallet, Claire, Poyet, Mathilde, Moniz, Katya, Washburne, Alex D., Erickson, Timothy B., Chai, Peter R., Thompson, Janelle, Alm, Eric J.

“…Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a…”
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