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20092024

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  • 2024

    A Burkholderia cenocepacia-like environmental isolate strongly inhibits the plant fungal pathogen Zymoseptoria tritici

    Song, T., Gupta, S., Sorokin, Y., Frenkel, O., Cytryn, E. & Friedman, J., May 2024, In: Applied and Environmental Microbiology. 90, 5

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Multigenerational inheritance drives symbiotic interactions of the bacterium Bacillus subtilis with its plant host

    Gilhar, O., Ben-Navi, L. R., Olender, T., Aharoni, A., Friedman, J. & Kolodkin-Gal, I., Sep 2024, In: Microbiological Research. 286, 127814.

    Research output: Contribution to journalArticlepeer-review

  • Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases

    Zorea, A., Pellow, D., Levin, L., Pilosof, S., Friedman, J., Shamir, R. & Mizrahi, I., Dec 2024, In: Nature Communications. 15, 1, 3147.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • 2023

    Competitive interactions between culturable bacteria are highly non-additive

    Baichman-Kass, A., Song, T. & Friedman, J., Feb 2023, In: eLife. 12, e83398.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    7 Scopus citations
  • Interactions between Culturable Bacteria Are Predicted by Individual Species’ Growth

    Nestor, E., Toledano, G. & Friedman, J., Apr 2023, In: mSystems. 8, 2

    Research output: Contribution to journalArticlepeer-review

    Open Access
    6 Scopus citations
  • Metabolic exchanges are ubiquitous in natural microbial communities

    Kost, C., Patil, K. R., Friedman, J., Garcia, S. L. & Ralser, M., Dec 2023, In: Nature Microbiology. 8, 12, p. 2244-2252 9 p.

    Research output: Contribution to journalArticlepeer-review

    16 Scopus citations
  • 2022

    Antimicrobial Peptide Combination Can Hinder Resistance Evolution

    Maron, B., Rolff, J., Friedman, J. & Hayouka, Z., Aug 2022, In: Microbiology spectrum. 10, 4

    Research output: Contribution to journalArticlepeer-review

    Open Access
    21 Scopus citations
  • Complexity–stability trade-off in empirical microbial ecosystems

    Yonatan, Y., Amit, G., Friedman, J. & Bashan, A., Jun 2022, In: Nature Ecology and Evolution. 6, 6, p. 693-700 8 p.

    Research output: Contribution to journalArticlepeer-review

    33 Scopus citations
  • Resolving the conflict between antibiotic production and rapid growth by recognition of peptidoglycan of susceptible competitors

    Maan, H., Itkin, M., Malitsky, S., Friedman, J. & Kolodkin-Gal, I., Dec 2022, In: Nature Communications. 13, 1, 431.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    13 Scopus citations
  • 2021

    Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales

    Meroz, N., Tovi, N., Sorokin, Y. & Friedman, J., 1 Dec 2021, In: Nature Communications. 12, 1, 2891.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    22 Scopus citations
  • Positive interactions are common among culturable bacteria

    Kehe, J., Ortiz, A., Kulesa, A., Gore, J., Blainey, P. C. & Friedman, J., Nov 2021, In: Science advances. 7, 45, eabi7159.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    87 Scopus citations
  • Positive interactions within and between populations decrease the likelihood of evolutionary rescue

    Goldberg, Y. & Friedman, J., 18 Feb 2021, In: PLoS Computational Biology. 17, 2, 2.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    5 Scopus citations
  • 2020

    Deciphering functional redundancy in the human microbiome

    Tian, L., Wang, X. W., Wu, A. K., Fan, Y., Friedman, J., Dahlin, A., Waldor, M. K., Weinstock, G. M., Weiss, S. T. & Liu, Y. Y., Dec 2020, In: Nature Communications. 11, 1, 6217.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    128 Scopus citations
  • Microbial communities display alternative stable states in a fluctuating environment

    Abreu, C. I., Andersen Woltz, V. L., Friedman, J. & Gore, J., May 2020, In: PLoS Computational Biology. 16, 5, e1007934.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    17 Scopus citations
  • 2019

    Core gut microbial communities are maintained by beneficial interactions and strain variability in fish

    Kokou, F., Sasson, G., Friedman, J., Eyal, S., Ovadia, O., Harpaz, S., Cnaani, A. & Mizrahi, I., 1 Dec 2019, In: Nature Microbiology. 4, 12, p. 2456-2465 10 p.

    Research output: Contribution to journalArticlepeer-review

    95 Scopus citations
  • Massively parallel screening of synthetic microbial communities

    Kehe, J., Kulesa, A., Ortiz, A., Ackerman, C. M., Thakku, S. G., Sellers, D., Kuehn, S., Gore, J., Friedman, J. & Blainey, P. C., 2019, In: Proceedings of the National Academy of Sciences of the United States of America. 116, 26, p. 12804-12809 6 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    144 Scopus citations
  • Mortality causes universal changes in microbial community composition

    Abreu, C. I., Friedman, J., Andersen Woltz, V. L. & Gore, J., 1 Dec 2019, In: Nature Communications. 10, 1, 2120.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    47 Scopus citations
  • 2018

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

    Smillie, C. S., Sauk, J., Gevers, D., Friedman, J., Sung, J., Youngster, I., Hohmann, E. L., Staley, C., Khoruts, A., Sadowsky, M. J., Allegretti, J. R., Smith, M. B., Xavier, R. J. & Alm, E. J., 14 Feb 2018, In: Cell Host and Microbe. 23, 2, p. 229-240.e5

    Research output: Contribution to journalArticlepeer-review

    Open Access
    235 Scopus citations
  • 2017

    Community structure follows simple assembly rules in microbial microcosms

    Friedman, J., Higgins, L. M. & Gore, J., 27 Mar 2017, In: Nature Ecology and Evolution. 1, 5, 0109.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    307 Scopus citations
  • Mapping the ecological networks of microbial communities

    Xiao, Y., Angulo, M. T., Friedman, J., Waldor, M. K., Weiss, S. T. & Liu, Y. Y., 1 Dec 2017, In: Nature Communications. 8, 1, 2042.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    100 Scopus citations
  • 2016

    Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

    Weiss, S., Van Treuren, W., Lozupone, C., Faust, K., Friedman, J., Deng, Y., Xia, L. C., Xu, Z. Z., Ursell, L., Alm, E. J., Birmingham, A., Cram, J. A., Fuhrman, J. A., Raes, J., Sun, F., Zhou, J. & Knight, R., 1 Jul 2016, In: ISME Journal. 10, 7, p. 1669-1681 13 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    470 Scopus citations
  • Preferential interactions promote blind cooperation and informed defection

    Pérez-Escudero, A., Friedman, J. & Gore, J., 6 Dec 2016, In: Proceedings of the National Academy of Sciences of the United States of America. 113, 49, p. 13995-14000 6 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    3 Scopus citations
  • Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem

    Preheim, S. P., Olesen, S. W., Spencer, S. J., Materna, A., Varadharajan, C., Blackburn, M., Friedman, J., Rodríguez, J., Hemond, H. & Alm, E. J., 15 Aug 2016, In: Nature Microbiology. 1, 16130.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    30 Scopus citations
  • Universality of human microbial dynamics

    Bashan, A., Gibson, T. E., Friedman, J., Carey, V. J., Weiss, S. T., Hohmann, E. L. & Liu, Y. Y., 8 Jun 2016, In: Nature. 534, 7606, p. 259-262 4 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    176 Scopus citations
  • 2014

    Host lifestyle affects human microbiota on daily timescales

    David, L. A., Materna, A. C., Friedman, J., Campos-Baptista, M. I., Blackburn, M. C., Perrotta, A., Erdman, S. E. & Alm, E. J., 2014, In: Genome Biology. 15, 7, R89.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    635 Scopus citations
  • 2013

    Sympatric Speciation: When Is It Possible in Bacteria?

    Friedman, J., Alm, E. J. & Shapiro, B. J., 17 Jan 2013, In: PLoS ONE. 8, 1, e53539.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    32 Scopus citations
  • 2012

    A framework for human microbiome research

    Methé, B. A., Nelson, K. E., Pop, M., Creasy, H. H., Giglio, M. G., Huttenhower, C., Gevers, D., Petrosino, J. F., Abubucker, S., Badger, J. H., Chinwalla, A. T., Earl, A. M., Fitzgerald, M. G., Fulton, R. S., Hallsworth-Pepin, K., Lobos, E. A., Madupu, R., Magrini, V., Martin, J. C. & Mitreva, M. & 228 others, Muzny, D. M., Sodergren, E. J., Versalovic, J., Wollam, A. M., Worley, K. C., Wortman, J. R., Young, S. K., Zeng, Q., Aagaard, K. M., Abolude, O. O., Allen-Vercoe, E., Alm, E. J., Alvarado, L., Andersen, G. L., Anderson, S., Appelbaum, E., Arachchi, H. M., Armitage, G., Arze, C. A., Ayvaz, T., Baker, C. C., Begg, L., Belachew, T., Bhonagiri, V., Bihan, M., Blaser, M. J., Bloom, T., Bonazzi, V. R., Brooks, P., Buck, G. A., Buhay, C. J., Busam, D. A., Campbell, J. L., Canon, S. R., Cantarel, B. L., Chain, P. S., Chen, I. M. A., Chen, L., Chhibba, S., Chu, K., Ciulla, D. M., Clemente, J. C., Clifton, S. W., Conlan, S., Crabtree, J., Cutting, M. A., Davidovics, N. J., Davis, C. C., Desantis, T. Z., Deal, C., Delehaunty, K. D., Dewhirst, F. E., Deych, E., Ding, Y., Dooling, D. J., Dugan, S. P., Michael Dunne, W., Scott Durkin, A., Edgar, R. C., Erlich, R. L., Farmer, C. N., Farrell, R. M., Faust, K., Feldgarden, M., Felix, V. M., Fisher, S., Fodor, A. A., Forney, L., Foster, L., Di Francesco, V., Friedman, J., Friedrich, D. C., Fronick, C. C., Fulton, L. L., Gao, H., Garcia, N., Giannoukos, G., Giblin, C., Giovanni, M. Y., Goldberg, J. M., Goll, J., Gonzalez, A., Griggs, A., Gujja, S., Haas, B. J., Hamilton, H. A., Harris, E. L., Hepburn, T. A., Herter, B., Hoffmann, D. E., Holder, M. E., Howarth, C., Huang, K. H., Huse, S. M., Izard, J., Jansson, J. K., Jiang, H., Jordan, C., Joshi, V., Katancik, J. A., Keitel, W. A., Kelley, S. T., Kells, C., Kinder-Haake, S., King, N. B., Knight, R., Knights, D., Kong, H. H., Koren, O., Koren, S., Kota, K. C., Kovar, C. L., Kyrpides, N. C., La Rosa, P. S., Lee, S. L., Lemon, K. P., Lennon, N., Lewis, C. M., Lewis, L., Ley, R. E., Li, K., Liolios, K., Liu, B., Liu, Y., Lo, C. C., Lozupone, C. A., Dwayne Lunsford, R., Madden, T., Mahurkar, A. A., Mannon, P. J., Mardis, E. R., Markowitz, V. M., Mavrommatis, K., McCorrison, J. M., McDonald, D., McEwen, J., McGuire, A. L., McInnes, P., Mehta, T., Mihindukulasuriya, K. A., Miller, J. R., Minx, P. J., Newsham, I., Nusbaum, C., O'Laughlin, M., Orvis, J., Pagani, I., Palaniappan, K., Patel, S. M., Pearson, M., Peterson, J., Podar, M., Pohl, C., Pollard, K. S., Priest, M. E., Proctor, L. M., Qin, X., Raes, J., Ravel, J., Reid, J. G., Rho, M., Rhodes, R., Riehle, K. P., Rivera, M. C., Rodriguez-Mueller, B., Rogers, Y. H., Ross, M. C., Russ, C., Sanka, R. K., Sankar, P., Fah Sathirapongsasuti, J., Schloss, J. A., Schloss, P. D., Schmidt, T. M., Scholz, M., Schriml, L., Schubert, A. M., Segata, N., Segre, J. A., Shannon, W. D., Sharp, R. R., Sharpton, T. J., Shenoy, N., Sheth, N. U., Simone, G. A., Singh, I., Smillie, C. S., Sobel, J. D., Sommer, D. D., Spicer, P., Sutton, G. G., Sykes, S. M., Tabbaa, D. G., Thiagarajan, M., Tomlinson, C. M., Torralba, M., Treangen, T. J., Truty, R. M., Vishnivetskaya, T. A., Walker, J., Wang, L., Wang, Z., Ward, D. V., Warren, W., Watson, M. A., Wellington, C., Wetterstrand, K. A., White, J. R., Wilczek-Boney, K., Qing Wu, Y., Wylie, K. M., Wylie, T., Yandava, C., Ye, L., Ye, Y., Yooseph, S., Youmans, B. P., Zhang, L., Zhou, Y., Zhu, Y., Zoloth, L., Zucker, J. D., Birren, B. W., Gibbs, R. A., Highlander, S. K., Weinstock, G. M., Wilson, R. K. & White, O., 14 Jun 2012, In: Nature. 486, 7402, p. 215-221 7 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1968 Scopus citations
  • Inferring Correlation Networks from Genomic Survey Data

    Friedman, J. & Alm, E. J., Sep 2012, In: PLoS Computational Biology. 8, 9, e1002687.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1522 Scopus citations
  • Population genomics of early events in the ecological differentiation of bacteria

    Shapiro, B. J., Friedman, J., Cordero, O. X., Preheim, S. P., Timberlake, S. C., Szabó, G., Polz, M. F. & Alm, E. J., 6 Apr 2012, In: Science. 335, 6077, p. 48-51 4 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    356 Scopus citations
  • Shape and evolution of the fundamental niche in marine Vibrio

    Materna, A. C., Friedman, J., Bauer, C., David, C., Chen, S., Huang, I. B., Gillens, A., Clarke, S. A., Polz, M. F. & Alm, E. J., Dec 2012, In: ISME Journal. 6, 12, p. 2168-2177 10 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    23 Scopus citations
  • Structure, function and diversity of the healthy human microbiome

    Huttenhower, C., Gevers, D., Knight, R., Abubucker, S., Badger, J. H., Chinwalla, A. T., Creasy, H. H., Earl, A. M., Fitzgerald, M. G., Fulton, R. S., Giglio, M. G., Hallsworth-Pepin, K., Lobos, E. A., Madupu, R., Magrini, V., Martin, J. C., Mitreva, M., Muzny, D. M., Sodergren, E. J. & Versalovic, J. & 228 others, Wollam, A. M., Worley, K. C., Wortman, J. R., Young, S. K., Zeng, Q., Aagaard, K. M., Abolude, O. O., Allen-Vercoe, E., Alm, E. J., Alvarado, L., Andersen, G. L., Anderson, S., Appelbaum, E., Arachchi, H. M., Armitage, G., Arze, C. A., Ayvaz, T., Baker, C. C., Begg, L., Belachew, T., Bhonagiri, V., Bihan, M., Blaser, M. J., Bloom, T., Bonazzi, V., Paul Brooks, J., Buck, G. A., Buhay, C. J., Busam, D. A., Campbell, J. L., Canon, S. R., Cantarel, B. L., Chain, P. S. G., Chen, I. M. A., Chen, L., Chhibba, S., Chu, K., Ciulla, D. M., Clemente, J. C., Clifton, S. W., Conlan, S., Crabtree, J., Cutting, M. A., Davidovics, N. J., Davis, C. C., Desantis, T. Z., Deal, C., Delehaunty, K. D., Dewhirst, F. E., Deych, E., Ding, Y., Dooling, D. J., Dugan, S. P., Michael Dunne, W., Scott Durkin, A., Edgar, R. C., Erlich, R. L., Farmer, C. N., Farrell, R. M., Faust, K., Feldgarden, M., Felix, V. M., Fisher, S., Fodor, A. A., Forney, L. J., Foster, L., Di Francesco, V., Friedman, J., Friedrich, D. C., Fronick, C. C., Fulton, L. L., Gao, H., Garcia, N., Giannoukos, G., Giblin, C., Giovanni, M. Y., Goldberg, J. M., Goll, J., Gonzalez, A., Griggs, A., Gujja, S., Kinder Haake, S., Haas, B. J., Hamilton, H. A., Harris, E. L., Hepburn, T. A., Herter, B., Hoffmann, D. E., Holder, M. E., Howarth, C., Huang, K. H., Huse, S. M., Izard, J., Jansson, J. K., Jiang, H., Jordan, C., Joshi, V., Katancik, J. A., Keitel, W. A., Kelley, S. T., Kells, C., King, N. B., Knights, D., Kong, H. H., Koren, O., Koren, S., Kota, K. C., Kovar, C. L., Kyrpides, N. C., La Rosa, P. S., Lee, S. L., Lemon, K. P., Lennon, N., Lewis, C. M., Lewis, L., Ley, R. E., Li, K., Liolios, K., Liu, B., Liu, Y., Lo, C. C., Lozupone, C. A., Dwayne Lunsford, R., Madden, T., Mahurkar, A. A., Mannon, P. J., Mardis, E. R., Markowitz, V. M., Mavromatis, K., McCorrison, J. M., McDonald, D., McEwen, J., McGuire, A. L., McInnes, P., Mehta, T., Mihindukulasuriya, K. A., Miller, J. R., Minx, P. J., Newsham, I., Nusbaum, C., Oglaughlin, M., Orvis, J., Pagani, I., Palaniappan, K., Patel, S. M., Pearson, M., Peterson, J., Podar, M., Pohl, C., Pollard, K. S., Pop, M., Priest, M. E., Proctor, L. M., Qin, X., Raes, J., Ravel, J., Reid, J. G., Rho, M., Rhodes, R., Riehle, K. P., Rivera, M. C., Rodriguez-Mueller, B., Rogers, Y. H., Ross, M. C., Russ, C., Sanka, R. K., Sankar, P., Fah Sathirapongsasuti, J., Schloss, J. A., Schloss, P. D., Schmidt, T. M., Scholz, M., Schriml, L., Schubert, A. M., Segata, N., Segre, J. A., Shannon, W. D., Sharp, R. R., Sharpton, T. J., Shenoy, N., Sheth, N. U., Simone, G. A., Singh, I., Smillie, C. S., Sobel, J. D., Sommer, D. D., Spicer, P., Sutton, G. G., Sykes, S. M., Tabbaa, D. G., Thiagarajan, M., Tomlinson, C. M., Torralba, M., Treangen, T. J., Truty, R. M., Vishnivetskaya, T. A., Walker, J., Wang, L., Wang, Z., Ward, D. V., Warren, W., Watson, M. A., Wellington, C., Wetterstrand, K. A., White, J. R., Wilczek-Boney, K., Wu, Y., Wylie, K. M., Wylie, T., Yandava, C., Ye, L., Ye, Y., Yooseph, S., Youmans, B. P., Zhang, L., Zhou, Y., Zhu, Y., Zoloth, L., Zucker, J. D., Birren, B. W., Gibbs, R. A., Highlander, S. K., Methé, B. A., Nelson, K. E., Petrosino, J. F., Weinstock, G. M., Wilson, R. K. & White, O., 14 Jun 2012, In: Nature. 486, 7402, p. 207-214 8 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    8198 Scopus citations
  • 2011

    Ecology drives a global network of gene exchange connecting the human microbiome

    Smillie, C. S., Smith, M. B., Friedman, J., Cordero, O. X., David, L. A. & Alm, E. J., 8 Dec 2011, In: Nature. 480, 7376, p. 241-244 4 p.

    Research output: Contribution to journalArticlepeer-review

    624 Scopus citations
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