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

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Meta-analysis of gut microbiome studies identifies disease-specific and shared responses von Duvallet, Claire, Gibbons, Sean M., Gurry, Thomas, Irizarry, Rafael A., Alm, Eric J.

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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 von Bolyen, Evan, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J., Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, 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, Kosciolek, Tomasz, Kreps, Jorden, Lee, Joslynn, Ley, Ruth, Liu, Yong-Xin, Loftfield, Erikka, Lozupone, Catherine, Maher, Massoud, Marotz, Clarisse, Martin, Bryan D., McDonald, Daniel, McIver, Lauren J., Melnik, Alexey V., Metcalf, Jessica L., Morgan, Sydney C., Naimey, Ahmad Turan, Navas-Molina, Jose A., Nothias, Louis Felix, Peoples, Samuel L., Petras, Daniel, Rasmussen, Lasse Buur, Rivers, Adam, Robeson, Michael S., Segata, Nicola, Shaffer, Michael, Shiffer, Arron, Sinha, Rashmi, 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, von Hippel, Max, Walters, William, Wan, Yunhu, Wang, Mingxun, Warren, Jonathan, Weber, Kyle C., Williamson, Charles H. D., Willis, Amy D., Zaneveld, Jesse R., Zhang, Yilong, Zhu, Qiyun, Knight, Rob, Caporaso, J. Gregory

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Unraveling the processes shaping mammalian gut microbiomes over evolutionary time von Groussin, Mathieu, Mazel, Florent, Sanders, Jon G., Smillie, Chris S., Lavergne, Sébastien, Thuiller, Wilfried, Alm, Eric J.

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

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Rapid evolutionary innovation during an Archaean genetic expansion von David, Lawrence A., Alm, Eric J.

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A practical guide to methods controlling false discoveries in computational biology von 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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Horizontal gene transfer and the evolution of bacterial and archaeal population structure von Polz, Martin F, Alm, Eric J, Hanage, William P

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Framework for rational donor selection in fecal microbiota transplant clinical trials von Duvallet, Claire, Zellmer, Caroline, Panchal, Pratik, Budree, Shrish, Osman, Majdi, Alm, Eric J

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

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An omics-based framework for assessing the health risk of antimicrobial resistance genes von 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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Microbial symbionts accelerate wound healing via the neuropeptide hormone oxytocin von 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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Population Genomics of Early Events in the Ecological Differentiation of Bacteria von 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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Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools von Jiang, Xiaofang, Hall, Andrew Brantley, Xavier, Ramnik J, Alm, Eric J

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Salt-responsive gut commensal modulates TH17 axis and disease von 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.

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Making waves: Wastewater surveillance of SARS-CoV-2 for population-based health management von 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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SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases von 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, Chai, Peter, Thompson, Janelle, Alm, Eric

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

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Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning von Cleary, Brian, Brito, Ilana Lauren, Huang, Katherine, Gevers, Dirk, Shea, Terrance, Young, Sarah, Alm, Eric J

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Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation von 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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