Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis von Weber, Nick, Liou, David, Dommer, Jennifer, MacMenamin, Philip, Quiñones, Mariam, Misner, Ian, Oler, Andrew J, Wan, Joe, Kim, Lewis, Coakley McCarthy, Meghan, Ezeji, Samuel, Noble, Karlynn, Hurt, Darrell E

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Composition of the intestinal microbiota in extended-spectrum β-lactamase-producing Enterobacteriaceae carriers and non-carriers in Thailand von Piewngam, Pipat, Quiñones, Mariam, Thirakittiwatthana, Witoon, Yungyuen, Thitiya, Otto, Michael, Kiratisin, Pattarachai

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Compartmentalized Control of Skin Immunity by Resident Commensals von Naik, Shruti, Bouladoux, Nicolas, Wilhelm, Christoph, Molloy, Michael J., Salcedo, Rosalba, Kastenmuller, Wolfgang, Deming, Clayton, Quinones, Mariam, Koo, Lily, Conlan, Sean, Spencer, Sean, Hall, Jason A., Dzutsev, Amiran, Kong, Heidi, Campbell, Daniel J., Trinchieri, Giorgio, Segre, Julia A., Belkaid, Yasmine

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"METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI's sequence read archive" von Quinones, Mariam, Liou, David T., Shyu, Conrad, Kim, Wongyu, Vujkovic-Cvijin, Ivan, Belkaid, Yasmine, Hurt, Darrell E.

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The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya von Easton, Alice V, Quiñones, Mariam, Vujkovic-Cvijin, Ivan, Oliveira, Rita G, Kepha, Stella, Odiere, Maurice R, Anderson, Roy M, Belkaid, Yasmine, Nutman, Thomas B

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Long-term antibiotic exposure promotes mortality after systemic fungal infection by driving lymphocyte dysfunction and systemic escape of commensal bacteria von Drummond, Rebecca A, Desai, Jigar V, Ricotta, Emily E, Swamydas, Muthulekha, Deming, Clay, Conlan, Sean, Quinones, Mariam, Matei-Rascu, Veronika, Sherif, Lozan, Lecky, David, Lee, Chyi-Chia R, Green, Nathaniel M, Collins, Nicholas, Zelazny, Adrian M, Prevots, D Rebecca, Bending, David, Withers, David, Belkaid, Yasmine, Segre, Julia A, Lionakis, Michail S

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Probiotic/prebiotic supplementation of antiretrovirals improves gastrointestinal immunity in SIV-infected macaques von Klatt, Nichole R, Canary, Lauren A, Sun, Xiaoyong, Vinton, Carol L, Funderburg, Nicholas T, Morcock, David R, Quiñones, Mariam, Deming, Clayton B, Perkins, Molly, Hazuda, Daria J, Miller, Michael D, Lederman, Michael M, Segre, Julie A, Lifson, Jeffrey D, Haddad, Elias K, Estes, Jacob D, Brenchley, Jason M

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Intraluminal Containment of Commensal Outgrowth in the Gut during Infection-Induced Dysbiosis von Molloy, Michael J., Grainger, John R., Bouladoux, Nicolas, Hand, Timothy W., Koo, Lily Y., Naik, Shruti, Quinones, Mariam, Dzutsev, Amiran K., Gao, Ji-Liang, Trinchieri, Giorgio, Murphy, Philip M., Belkaid, Yasmine

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Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus von Wollenberg, Kurt R, Desjardins, Christopher A, Zalutskaya, Aksana, Slodovnikova, Vervara, Oler, Andrew J, Quiñones, Mariam, Abeel, Thomas, Chapman, Sinead B, Tartakovsky, Michael, Gabrielian, Andrei, Hoffner, Sven, Skrahin, Aliaksandr, Birren, Bruce W, Rosenthal, Alexander, Skrahina, Alena, Earl, Ashlee M

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The extent of sequence complementarity correlates with the potency of cellular miRNA-mediated restriction of HIV-1 von Houzet, Laurent, Klase, Zachary, Yeung, Man Lung, Wu, Annie, Le, Shu-Yun, Quiñones, Mariam, Jeang, Kuan-Teh

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Dendritic cells expressing immunoreceptor CD300f are critical for controlling chronic gut inflammation von Lee, Ha-Na, Tian, Linjie, Bouladoux, Nicolas, Davis, Jacquice, Quinones, Mariam, Belkaid, Yasmine, Coligan, John E, Krzewski, Konrad

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Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum von López-Barragán, María J, Lemieux, Jacob, Quiñones, Mariam, Williamson, Kim C, Molina-Cruz, Alvaro, Cui, Kairong, Barillas-Mury, Carolina, Zhao, Keji, Su, Xin-zhuan

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UTR introns, antisense RNA and differentially spliced transcripts between Plasmodium yoelii subspecies von Li, Jian, Cai, Baowei, Qi, Yanwei, Zhao, Wenting, Liu, Jianwen, Xu, Ruixue, Pang, Qin, Tao, Zhiyong, Hong, Lingxian, Liu, Shengfa, Leerkes, Maarten, Quiñones, Mariam, Su, Xin-zhuan

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Patterns of microRNA expression in non-human primate cells correlate with neoplastic development in vitro von Teferedegne, Belete, Murata, Haruhiko, Quiñones, Mariam, Peden, Keith, Lewis, Andrew M

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Characterization of the Small Untranslated RNA RyhB and Its Regulon in Vibrio cholerae von DAVIS, Brigid M, QUINONES, Mariam, PRATT, Jason, YANPENG DING, WALDOR, Matthew K

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Colitis susceptibility in p47(phox-/-) mice is mediated by the microbiome von Falcone, E Liana, Abusleme, Loreto, Swamydas, Muthulekha, Lionakis, Michail S, Ding, Li, Hsu, Amy P, Zelazny, Adrian M, Moutsopoulos, Niki M, Kuhns, Douglas B, Deming, Clay, Quiñones, Mariam, Segre, Julia A, Bryant, Clare E, Holland, Steven M

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The normal breast microenvironment of premenopausal women differentially influences the behavior of breast cancer cells in vitro and in vivo von Fleming, Jodie M, Miller, Tyler C, Quinones, Mariam, Xiao, Zhen, Xu, Xia, Meyer, Matthew J, Ginsburg, Erika, Veenstra, Timothy D, Vonderhaar, Barbara K

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Impact of Acute HIV Infection and Early Antiretroviral Therapy on the Human Gut Microbiome von Sortino, Ornella, Phanuphak, Nittaya, Schuetz, Alexandra, Ortiz, Alexandra M, Chomchey, Nitiya, Belkaid, Yasmine, Davis, Jacquice, Mystakelis, Harry A, Quiñones, Mariam, Deleage, Claire, Ingram, Brian, Rerknimitr, Rungsun, Pinyakorn, Suteeraporn, Rupert, Adam, Robb, Merlin L, Ananworanich, Jintanat, Brenchley, Jason, Sereti, Irini

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Effect of PCR extension temperature on high-throughput sequencing von López-Barragán, María José, Quiñones, Mariam, Cui, Kairong, Lemieux, Jacob, Zhao, Keji, Su, Xin-zhuan

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Commensal–dendritic-cell interaction specifies a unique protective skin immune signature von Naik, Shruti, Bouladoux, Nicolas, Linehan, Jonathan L., Han, Seong-Ji, Harrison, Oliver J., Wilhelm, Christoph, Conlan, Sean, Himmelfarb, Sarah, Byrd, Allyson L., Deming, Clayton, Quinones, Mariam, Brenchley, Jason M., Kong, Heidi H., Tussiwand, Roxanne, Murphy, Kenneth M., Merad, Miriam, Segre, Julia A., Belkaid, Yasmine

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