Mobile genes in the human microbiome are structured from global to individual scales von 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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Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code von Fournier, G. P., Alm, E. J.

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MicrobesOnline: an integrated portal for comparative and functional genomics von Dehal, Paramvir S, Joachimiak, Marcin P, Price, Morgan N, Bates, John T, Baumohl, Jason K, Chivian, Dylan, Friedland, Greg D, Huang, Katherine H, Keller, Keith, Novichkov, Pavel S, Dubchak, Inna L, Alm, Eric J, Arkin, Adam P

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A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research von Poyet, M., Groussin, M., Gibbons, S. M., Avila-Pacheco, J., Jiang, X., Kearney, S. M., Perrotta, A. R., Berdy, B., Zhao, S., Lieberman, T. D., Swanson, P. K., Smith, M., Roesemann, S., Alexander, J. E., Rich, S. A., Livny, J., Vlamakis, H., Clish, C., Bullock, K., Deik, A., Scott, J., Pierce, K. A., Xavier, R. J., Alm, E. J.

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Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough von CHHABRA, S. R, HE, Q, ARKIN, A. P, SINGH, A. K, HUANG, K. H, GAUCHER, S. P, AIM, E. J, HE, Z, HADI, M. Z, HAZEN, T. C, WALL, J. D, ZHOU, J

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Temporal Transcriptomic Analysis as Desulfovibrio vulgaris Hildenborough Transitions into Stationary Phase during Electron Donor Depletion von Clark, M.E, He, Q, He, Z, Huang, K.H, Alm, E.J, Wan, X.-F, Hazen, T.C, Arkin, A.P, Wall, J.D, Zhou, J.-Z, Fields, M.W

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Clostridium difficile associated risk of death score (CARDS): a novel severity score to predict mortality among hospitalised patients with C. difficile infection von Kassam, Z., Cribb Fabersunne, C., Smith, M. B., Alm, E. J., Kaplan, G. G., Nguyen, G. C., Ananthakrishnan, A. N.

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Corrigendum: Mobile genes in the human microbiome are structured from global to individual scales von 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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Mechanisms of protein folding von Grantcharova, Viara, Alm, Eric J, Baker, David, Horwich, Arthur L

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Co-incidence of BA.1 and BA.2 at the start of Singapore's Omicron wave revealed by Community and University Campus wastewater surveillance von Chua, Feng Jun Desmond, Kim, Se Yeon, Hill, Eric, Cai, Jia Wei, Lee, Wei Lin, Gu, Xiaoqiong, Afri Affandi, Siti Aisyah, Kwok, Wee Chiew Germaine, Ng, Weijie, Leifels, Mats, Armas, Federica, Chandra, Franciscus, Chen, Hongjie, Alm, Eric J., Tay, Martin, Wong, Chui Ching Judith, Ng, Lee Ching, Wuertz, Stefan, Thompson, Janelle R.

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Multiomics Analyses to Deliver the Most Effective Treatment to Every Patient With Inflammatory Bowel Disease von Weersma, Rinse K., Xavier, Ramnik J., Weersma, R.K., Barrett, J.C., Vermeire, S., Xavier, R.J., Anderson, C.A., Wijmenga, C., Daly, M.J., Alm, E.J., Raes, J., Huttenhower, C., Stappenbeck, T., Netea, M., Kaser, A., Franke, A., McGovern, D.P., Colombel, J.F., van den Brink, G.R., Uhlig, H.H., Georges, M., Lees, C.W., Parkes, M., Giallourakis, C., Hart, A., Rioux, J.D., Sokol, H., Hurtado-Lorenzo, A., Yeretssian, G., Markus- de Kwaadsteniet, M.L., Festen, E.A., Rahmouni, S., Vieira-Silva, S., McIntyre, R.E., Moutsianas, L., Vermeire, Severine, Barrett, Jeffrey C.

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NMR characterization of residual structure in the denatured state of protein L von Yi, Qian, Scalley-Kim, Michelle L., Alm, Eric J., Baker, David

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DNA phosphorothioation is widespread and quantized in bacterial genomes von Wang, Lianrong, Chen, Shi, Vergin, Kevin L, Giovannoni, Stephen J, Chan, Simon W, DeMott, Michael S, Taghizadeh, Koli, Cordero, Otto X, Cutler, Michael, Timberlake, Sonia, Alm, Eric J, Polz, Martin F, Pinhassi, Jarone, Deng, Zixin, Dedon, Peter C

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Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles von Sinha, Trishla, Vich Vila, Arnau, Garmaeva, Sanzhima, Jankipersadsing, Soesma A., Imhann, Floris, Collij, Valerie, Bonder, Marc Jan, Jiang, Xiaofang, Gurry, Thomas, Alm, Eric J., D'Amato, Mauro, Weersma, Rinse K., Scherjon, Sicco, Wijmenga, Cisca, Fu, Jingyuan, Kurilshikov, Alexander, Zhernakova, Alexandra

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Looking for Darwin's footprints in the microbial world von Shapiro, B. Jesse, David, Lawrence A, Friedman, Jonathan, Alm, Eric J

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Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach von MUKHOPADHYAY, Aindrila, ZHILI HE, HUANG, Katherine, HUANG, Rick, JOYNER, Dominique C, KATZ, Natalie, KELLER, Martin, OELLER, Paul, REDDING, Alyssa, JUN SUN, WALL, Judy, JING WEI, ALM, Eric J, ZAMIN YANG, YEN, Huei-Che, JIZHONG ZHOU, KEASLING, Jay D, ARKIN, Adam P, BAIDOO, Edward E, BORGLIN, Sharon C, WENQIONG CHEN, HAZEN, Terry C, QIANG HE, HOLMAN, Hoi-Ying

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Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks von Rodionov, Dmitry A, Dubchak, Inna L, Arkin, Adam P, Alm, Eric J, Gelfand, Mikhail S

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Global Transcriptional, Physiological, and Metabolite Analyses of the Responses of Desulfovibrio vulgaris Hildenborough to Salt Adaptation von He, Zhili, Zhou, Aifen, Baidoo, Edward, He, Qiang, Joachimiak, Marcin P, Benke, Peter, Phan, Richard, Mukhopadhyay, Aindrila, Hemme, Christopher L, Huang, Katherine, Alm, Eric J, Fields, Matthew W, Wall, Judy, Stahl, David, Hazen, Terry C, Keasling, Jay D, Arkin, Adam P, Zhou, Jizhong

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Energetic Consequences of Nitrite Stress in Desulfovibrio vulgaris Hildenborough, Inferred from Global Transcriptional Analysis von He, Qiang, Huang, Katherine H, He, Zhili, Alm, Eric J, Fields, Matthew W, Hazen, Terry C, Arkin, Adam P, Wall, Judy D, Zhou, Jizhong

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A novel method for accurate operon predictions in all sequenced prokaryotes von Price, Morgan N., Huang, Katherine H., Alm, Eric J., Arkin, Adam P.

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