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Jonathan Friedman

 https://orcid.org/0000-0001-8476-8030
    Calculated based on number of publications stored in Pure and citations from Scopus
    20092024

    Research activity per year

    Search results

    • 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 journal › Article › peer-review

      Open Access

    • Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species

      Meroz, N., Livny, T., Toledano, G., Sorokin, Y., Tovi, N. & Friedman, J., 16 Oct 2024, In: Cell Systems. 15, 10, p. 930-940 11 p.

      Research output: Contribution to journal › Article › peer-review

    • 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 journal › Article › peer-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 journal › Article › peer-review

      Open Access
      1 Scopus citations

    • Quantifying microbial interactions: concepts, caveats, and applications

      Meroz, N., Livny, T. & Friedman, J., Aug 2024, In: Current Opinion in Microbiology. 80, 102511.

      Research output: Contribution to journal › Review article › peer-review

    • 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 journal › Article › peer-review

      Open Access
      10 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 journal › Article › peer-review

      Open Access
      7 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 journal › Article › peer-review

      41 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 journal › Article › peer-review

      Open Access
      28 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 journal › Article › peer-review

      37 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 journal › Article › peer-review

      Open Access
      20 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 journal › Article › peer-review

      Open Access
      26 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 journal › Article › peer-review

      Open Access
      101 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 journal › Article › peer-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 journal › Article › peer-review

      Open Access
      142 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 journal › Article › peer-review

      Open Access
      19 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 journal › Article › peer-review

      112 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 journal › Article › peer-review

      Open Access
      154 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 journal › Article › peer-review

      Open Access
      51 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 journal › Article › peer-review

      Open Access
      243 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 journal › Article › peer-review

      Open Access
      317 Scopus citations

    • Ecological systems biology: The dynamics of interacting populations

      Friedman, J. & Gore, J., Feb 2017, In: Current Opinion in Systems Biology. 1, p. 114-121 8 p.

      Research output: Contribution to journal › Review article › peer-review

      42 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 journal › Article › peer-review

      Open Access
      109 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 journal › Article › peer-review

      Open Access
      504 Scopus citations

    • Erratum: Host lifestyle affects human microbiota on daily timescales(Genome Biology (2014) 15 (R89) DOI: 10.1186/gb-2014-15-7-r89)

      David, L. A., Materna, A. C., Friedman, J., Baptista, M. I. C., Blackburn, M. C., Perrotta, A., Erdman, S. E. & Alm, E. J., 2016, In: Genome Biology. 17, 1, 117.

      Research output: Contribution to journal › Comment/debate

      Open Access
      5 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 journal › Article › peer-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 journal › Article › peer-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 journal › Article › peer-review

      Open Access
      184 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 journal › Article › peer-review

      Open Access
      662 Scopus citations
    • 2013

      Computational methods for high-throughput comparative analyses of natural microbial communities

      Preheim, S. P., Perrotta, A. R., Friedman, J., Smilie, C., Brito, I., Smith, M. B. & Alm, E., 2013, Microbial Metagenomics, Metatranscriptomics, and Metaproteomics. Academic Press Inc., p. 353-370 18 p. (Methods in Enzymology; vol. 531).

      Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

      31 Scopus citations

    • 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 journal › Article › peer-review

      Open Access
      33 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 journal › Article › peer-review

      Open Access
      2012 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 journal › Article › peer-review

      Open Access
      1621 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 journal › Article › peer-review

      Open Access
      362 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 journal › Article › peer-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 journal › Article › peer-review

      Open Access
      8478 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 journal › Article › peer-review

      646 Scopus citations
    • 2009

      Looking for Darwin's footprints in the microbial world

      Shapiro, B. J., David, L. A., Friedman, J. & Alm, E. J., May 2009, In: Trends in Microbiology. 17, 5, p. 196-204 9 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      66 Scopus citations
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