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

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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 by Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R, Bokulich, Nicholas A, Abnet, Christian C, Al-Ghalith, Gabriel A, Alexander, Harriet, Alm, Eric J, Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J, Brown, C Titus, Callahan, Benjamin J, Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K, Diener, Christian, Dorrestein, Pieter C, Douglas, Gavin M, Durall, Daniel M, Duvallet, Claire, Edwardson, Christian F, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M, Gibson, Deanna L, Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A, Janssen, Stefan, Jarmusch, Alan K, Jiang, Lingjing, Kaehler, Benjamin D, Kang, Kyo Bin, Keefe, Christopher R, Keim, Paul, Kelley, Scott T, Knights, Dan, Koester, Irina, Kosciolek, Tomasz, Kreps, Jorden, Langille, Morgan G I, Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D, McDonald, Daniel, Melnik, Alexey V, Morgan, Sydney C, Morton, Jamie T, Naimey, Ahmad Turan, Navas-Molina, Jose A, Nothias, Louis Felix, Orchanian, Stephanie B, Pearson, Talima, Peoples, Samuel L, Petras, Daniel, Preuss, Mary Lai, Rasmussen, Lasse Buur, Robeson, 2nd, Michael S, Rosenthal, Patrick, Segata, Nicola, Shaffer, Michael, Song, Se Jin, Spear, John R, Swafford, Austin D, Thompson, Luke R, Torres, Pedro J, Trinh, Pauline, Tripathi, Anupriya, Turnbaugh, Peter J, Ul-Hasan, Sabah, van der Hooft, Justin J J, Vargas, Fernando, Vázquez-Baeza, Yoshiki, Vogtmann, Emily, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Weber, Kyle C, Williamson, Charles H D, Willis, Amy D, Xu, Zhenjiang Zech, Zaneveld, Jesse R, Zhang, Yilong, Zhu, Qiyun, Knight, Rob, Caporaso, J Gregory

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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

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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

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Correcting for batch effects in case-control microbiome studies by Gibbons, Sean M, Duvallet, Claire, Alm, Eric J

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Rapid evolutionary innovation during an Archaean genetic expansion by DAVID, Lawrence A, ALM, Eric J

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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

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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

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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

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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

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Random sequences rapidly evolve into de novo promoters by Yona, Avihu H, Alm, Eric J, Gore, Jeff

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Mobile genes in the human microbiome are structured from global to individual scales by Brito, I L, Yilmaz, S, Huang, K, Xu, L, Jupiter, S D, Jenkins, A P, Naisilisili, W, Tamminen, M, Smillie, C S, Wortman, J R, Birren, B W, Xavier, R J, Blainey, P C, Singh, A K, Gevers, D, Alm, E J

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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

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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

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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

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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.

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Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations by Chu, Nathaniel D, Smith, Mark B, Perrotta, Allison R, Kassam, Zain, Alm, Eric J

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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

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Do Cryopreserved Mesenchymal Stromal Cells Display Impaired Immunomodulatory and Therapeutic Properties? by Moll, Guido, Alm, Jessica J., Davies, Lindsay C., von Bahr, Lena, Heldring, Nina, Stenbeck‐Funke, Lillemor, Hamad, Osama A., Hinsch, Robin, Ignatowicz, Lech, Locke, Matthew, Lönnies, Helena, Lambris, John D., Teramura, Yuji, Nilsson‐Ekdahl, Kristina, Nilsson, Bo, Blanc, Katarina

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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.

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