Microbial genes and pathways in inflammatory bowel disease von Schirmer, Melanie, Garner, Ashley, Vlamakis, Hera, Xavier, Ramnik J.

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Structure-based protein function prediction using graph convolutional networks von Gligorijević, Vladimir, Renfrew, P. Douglas, Kosciolek, Tomasz, Leman, Julia Koehler, Berenberg, Daniel, Vatanen, Tommi, Chandler, Chris, Taylor, Bryn C., Fisk, Ian M., Vlamakis, Hera, Xavier, Ramnik J., Knight, Rob, Cho, Kyunghyun, Bonneau, Richard

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Sticking together: building a biofilm the Bacillus subtilis way von Vlamakis, Hera, Chai, Yunrong, Beauregard, Pascale, Losick, Richard, Kolter, Roberto

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From cell differentiation to cell collectives: Bacillus subtilis uses division of labor to migrate von van Gestel, Jordi, Vlamakis, Hera, Kolter, Roberto

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Bacillus subtilis biofilm induction by plant polysaccharides von Beauregard, Pascale B, Chai, Yunrong, Vlamakis, Hera, Losick, Richard, Kolter, Roberto

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Control of cell fate by the formation of an architecturally complex bacterial community von Vlamakis, Hera, Aguilar, Claudio, Losick, Richard, Kolter, Roberto

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Akkermansia muciniphila phospholipid induces homeostatic immune responses von Bae, Munhyung, Cassilly, Chelsi D., Liu, Xiaoxi, Park, Sung-Moo, Tusi, Betsabeh Khoramian, Chen, Xiangjun, Kwon, Jaeyoung, Filipčík, Pavel, Bolze, Andrew S., Liu, Zehua, Vlamakis, Hera, Graham, Daniel B., Buhrlage, Sara J., Xavier, Ramnik J., Clardy, Jon

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Dynamic metabolic exchange governs a marine algal-bacterial interaction von Segev, Einat, Wyche, Thomas P, Kim, Ki Hyun, Petersen, Jörn, Ellebrandt, Claire, Vlamakis, Hera, Barteneva, Natasha, Paulson, Joseph N, Chai, Liraz, Clardy, Jon, Kolter, Roberto

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Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level von Kenny, Douglas J., Plichta, Damian R., Shungin, Dmitry, Koppel, Nitzan, Hall, A. Brantley, Fu, Beverly, Vasan, Ramachandran S., Shaw, Stanley Y., Vlamakis, Hera, Balskus, Emily P., Xavier, Ramnik J.

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Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity von Schirmer, Melanie, Smeekens, Sanne P., Vlamakis, Hera, Jaeger, Martin, Oosting, Marije, Franzosa, Eric A., ter Horst, Rob, Jansen, Trees, Jacobs, Liesbeth, Bonder, Marc Jan, Kurilshikov, Alexander, Fu, Jingyuan, Joosten, Leo A.B., Zhernakova, Alexandra, Huttenhower, Curtis, Wijmenga, Cisca, Netea, Mihai G., Xavier, Ramnik J.

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Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut von Jiang, Xiaofang, Hall, A Brantley, Arthur, Timothy D, Plichta, Damian R, Covington, Christian T, Poyet, Mathilde, Crothers, Jessica, Moses, Peter L, Tolonen, Andrew C, Vlamakis, Hera, Alm, Eric J, Xavier, Ramnik J

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Human gut bacteria produce ΤΗ17-modulating bile acid metabolites von Paik, Donggi, Yao, Lina, Zhang, Yancong, Bae, Sena, D’Agostino, Gabriel D., Zhang, Minghao, Kim, Eunha, Franzosa, Eric A., Avila-Pacheco, Julian, Bisanz, Jordan E., Rakowski, Christopher K., Vlamakis, Hera, Xavier, Ramnik J., Turnbaugh, Peter J., Longman, Randy S., Krout, Michael R., Clish, Clary B., Rastinejad, Fraydoon, Huttenhower, Curtis, Huh, Jun R., Devlin, A. Sloan

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The human gut microbiome in early-onset type 1 diabetes from the TEDDY study von Vatanen, Tommi, Franzosa, Eric A., Schwager, Randall, Tripathi, Surya, Arthur, Timothy D., Vehik, Kendra, Lernmark, Åke, Hagopian, William A., Rewers, Marian J., She, Jin-Xiong, Toppari, Jorma, Ziegler, Anette-G., Akolkar, Beena, Krischer, Jeffrey P., Stewart, Christopher J., Ajami, Nadim J., Petrosino, Joseph F., Gevers, Dirk, Lähdesmäki, Harri, Vlamakis, Hera, Huttenhower, Curtis, Xavier, Ramnik J.

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Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences von Mallick, Himel, Franzosa, Eric A., Mclver, Lauren J., Banerjee, Soumya, Sirota-Madi, Alexandra, Kostic, Aleksandar D., Clish, Clary B., Vlamakis, Hera, Xavier, Ramnik J., Huttenhower, Curtis

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Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life von Yassour, Moran, Jason, Eeva, Hogstrom, Larson J., Arthur, Timothy D., Tripathi, Surya, Siljander, Heli, Selvenius, Jenni, Oikarinen, Sami, Hyöty, Heikki, Virtanen, Suvi M., Ilonen, Jorma, Ferretti, Pamela, Pasolli, Edoardo, Tett, Adrian, Asnicar, Francesco, Segata, Nicola, Vlamakis, Hera, Lander, Eric S., Huttenhower, Curtis, Knip, Mikael, Xavier, Ramnik J.

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Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease von Lee, Jonathan Wei Jie, Plichta, Damian, Hogstrom, Larson, Borren, Nynke Z., Lau, Helena, Gregory, Sara M., Tan, William, Khalili, Hamed, Clish, Clary, Vlamakis, Hera, Xavier, Ramnik J., Ananthakrishnan, Ashwin N.

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Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation von Wlodarska, Marta, Luo, Chengwei, Kolde, Raivo, d’Hennezel, Eva, Annand, John W., Heim, Cortney E., Krastel, Philipp, Schmitt, Esther K., Omar, Abdifatah S., Creasey, Elizabeth A., Garner, Ashley L., Mohammadi, Sina, O’Connell, Daniel J., Abubucker, Sahar, Arthur, Timothy D., Franzosa, Eric A., Huttenhower, Curtis, Murphy, Leon O., Haiser, Henry J., Vlamakis, Hera, Porter, Jeffrey A., Xavier, Ramnik J.

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Bacterial flagella explore microscale hummocks and hollows to increase adhesion von Friedlander, Ronn S., Vlamakis, Hera, Kim, Philseok, Khan, Mughees, Kolter, Roberto, Aizenberg, Joanna

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Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis von Brown, Eric M., Ke, Xiaobo, Hitchcock, Daniel, Jeanfavre, Sarah, Avila-Pacheco, Julian, Nakata, Toru, Arthur, Timothy D., Fornelos, Nadine, Heim, Cortney, Franzosa, Eric A., Watson, Nicki, Huttenhower, Curtis, Haiser, Henry J., Dillow, Glen, Graham, Daniel B., Finlay, B. Brett, Kostic, Aleksandar D., Porter, Jeffrey A., Vlamakis, Hera, Clish, Clary B., Xavier, Ramnik J.

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Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations von Stražar, Martin, Temba, Godfrey S., Vlamakis, Hera, Kullaya, Vesla I., Lyamuya, Furaha, Mmbaga, Blandina T., Joosten, Leo A. B., van der Ven, Andre J. A. M., Netea, Mihai G., de Mast, Quirijn, Xavier, Ramnik J.

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