Community structure follows simple assembly rules in microbial microcosms

The rhizosphere microbiome and plant health

Berendsen, R. L., Pieterse, C. M. J., & Bakker, P. A. H. M. (2012) · Trends in Plant Science · doi:10.1016/j.tplants.2012.04.001 · Cited by 5,347

Microbial interactions: from networks to models

Faust, K., & Raes, J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2832 · Cited by 4,268

The Microbial Engines That Drive Earth's Biogeochemical Cycles

Falkowski, P. G., Fenchel, T., & Delong, E. F. (2008) · Science · doi:10.1126/science.1153213 · Cited by 3,379

The role of the gut microbiota in nutrition and health

Flint, H. J., Scott, K. P., Louis, P., & Duncan, S. H. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2012.156 · Cited by 2,283

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

Berry, D., & Stefanie Widder, A. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00219 · Cited by 1,812

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

Fukami, T. (2015) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110411-160340 · Cited by 1,724

Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors

Kerr, B., Riley, M. A., Feldman, M. W., & Bohannan, B. J. M. (2002) · Nature · doi:10.1038/nature00823 · Cited by 1,593

THE NATURE AND CONSEQUENCES OF INDIRECT EFFECTS IN ECOLOGICAL COMMUNITIES

Wootton, J. T. (1994) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.es.25.110194.002303 · Cited by 1,192

Competitive Exclusion

Armstrong, R. A., & McGehee, R. (1980) · The American Naturalist · doi:10.1086/283553 · Cited by 1,016

Biodiversity of plankton by species oscillations and chaos

Huisman, J., & Weissing, F. J. (1999) · Nature · doi:10.1038/46540 · Cited by 1,004

Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes

Arya, S., George, A. B., & O’Dwyer, J. P. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2307313120 · Cited by 31

Many broadly-shared mycobionts characterize mycorrhizal interactions of two coexisting epiphytic orchids in a high elevation tropical forest

Herrera, P., Suárez, J. P., Sánchez‐Rodríguez, A., Molina, M. D. C., Prieto, M., & Méndez, M. (2018) · Fungal ecology · doi:10.1016/j.funeco.2018.11.003 · Cited by 29

How competitive intransitivity and niche overlap affect spatial coexistence

Yang, Y., & Hui, C. (2020) · Oikos · doi:10.1111/oik.07735 · Cited by 28

Interactions between metabolism and growth can determine the co-existence of Staphylococcus aureus and Pseudomonas aeruginosa

Pajon, C., Fortoul, M. C., Diaz-Tang, G., Meneses, E. M., Kalifa, A. R., Sevy, E., Mariah, T., Toscan, B., Marcelin, M., Hernandez, D. M., et al. (2023) · eLife · doi:10.7554/elife.83664 · Cited by 28

Growth tradeoffs produce complex microbial communities on a single limiting resource

Manhart, M., & Shakhnovich, E. I. (2018) · RePEc: Research Papers in Economics · Cited by 28

Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation

Čaušević, S., Tackmann, J., Sentchilo, V., von Mering, C., & van der Meer, J. R. (2022) · mSystems · doi:10.1128/msystems.00160-22 · Cited by 27

Interactions between Culturable Bacteria Are Predicted by Individual Species’ Growth

Nestor, E., Toledano, G., & Friedman, J. (2023) · mSystems · doi:10.1128/msystems.00836-22 · Cited by 27

Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities

Cao, X., Hamilton, J. J., & Venturelli, O. S. (2018) · Biochemistry · doi:10.1021/acs.biochem.8b01006 · Cited by 31

Experimental evolution reveals microbial traits for association with the host gut

Vega, N. M. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000129 · Cited by 26

Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa

Luo, N., Wang, S., Lu, J. G., Ouyang, X., & You, L. (2021) · Molecular Systems Biology · doi:10.15252/msb.202010089 · Cited by 26

Coexistence holes characterize the assembly and disassembly of multispecies systems

Angulo, M. T., Kelley, A., Montejano, L., Song, C., & Saavedra, S. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01462-8 · Cited by 24

Designing Probiotic Therapies With Broad-Spectrum Activity Against a Wildlife Pathogen

Harrison, X. A., Sewell, T. R., Fisher, M. C., & Antwis, R. E. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.03134 · Cited by 26

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

Batsch, M., Guex, I., Todorov, H., Heiman, C. M., Vacheron, J., Vorholt, J. A., Keel, C., & van der Meer, J. R. (2024) · Nature Communications · doi:10.1038/s41467-024-51944-z · Cited by 27

Keystone concept revisited: insights into microbial community dynamics and control

Garza, D. R., Gonze, D., & Faust, K. (2026) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01266-8 · Cited by 26

Community assembly: perspectives from phytoplankton’s studies

Rojo, C. (2020) · Hydrobiologia · doi:10.1007/s10750-020-04249-3 · Cited by 25

Competition for nutrients increases invasion resistance during assembly of microbial communities

Wagner, A. (2022) · Molecular Ecology · doi:10.1111/mec.16565 · Cited by 23

Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions

Jo, C., Bernstein, D. B., Vaisman, N., Frydman, H. M., & Segrè, D. (2023) · mSystems · doi:10.1128/msystems.00017-21 · Cited by 25

Universal gut microbial relationships in the gut microbiome of wild baboons

Roche, K. E., Björk, J. R., Dasari, M. R., Grieneisen, L., Jansen, D., Gould, T. J., Gesquiere, L. R., Barreiro, L. B., Alberts, S. C., Blekhman, R., et al. (2023) · eLife · doi:10.7554/elife.83152 · Cited by 27

Oxidative stress changes interactions between 2 bacterial species from competitive to facilitative

Martino, R. D., Picot, A., & Mitri, S. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002482 · Cited by 25

Observed Ecological Communities Are Formed by Species Combinations That Are among the Most Likely to Persist under Changing Environments

Medeiros, L. P., Boege, K., del-Val, E., Zaldívar-Riverón, A., & Saavedra, S. (2021) · The American Naturalist · doi:10.1086/711663 · Cited by 25

Minimizing the number of optimizations for efficient community dynamic flux balance analysis

Brunner, J. D., & Chia, N. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007786 · Cited by 26

Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile

Sulaiman, J. E., Thompson, J. C., Cheung, P. L. K., Qian, Y., Mill, J., James, I., Im, H., Vivas, E. I., Simcox, J., & Venturelli, O. S. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.12.001 · Cited by 22

Analysis of productivity and stability of synthetic microbial communities

Di, S., & Yang, A. (2019) · Journal of The Royal Society Interface · doi:10.1098/rsif.2018.0859 · Cited by 23

Effect of Host, Environment and Fungal Growth on Fungal Leaf Endophyte Communities in Taiwan

Huang, Y. (2020) · Journal of Fungi · doi:10.3390/jof6040244 · Cited by 23

Merging dynamical and structural indicators to measure resilience in multispecies systems

Medeiros, L. P., Song, C., & Saavedra, S. (2021) · Journal of Animal Ecology · doi:10.1111/1365-2656.13421 · Cited by 23

The functional microbiome of grapevine throughout plant evolutionary history and lifetime

Fournier, P., Pellan, L., Barroso‐Bergadà, D., Bohan, D. A., Candresse, T., Delmotte, F., Dufour, M., Lauvergeat, V., Marrec, C. L., Marais, A., et al. (2022) · Advances in ecological research/Advances in Ecological Research · doi:10.1016/bs.aecr.2022.09.001 · Cited by 27

Designing More Informative Multiple-Driver Experiments

Thomas, M. K., & Ranjan, R. (2023) · Annual Review of Marine Science · doi:10.1146/annurev-marine-041823-095913 · Cited by 23

Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species–species modelling

Brunner, J. D., & Chia, N. (2019) · Journal of The Royal Society Interface · doi:10.1098/rsif.2019.0423 · Cited by 22

Effects of niche overlap on coexistence, fixation and invasion in a population of two interacting species

Badali, M., & Zilman, A. (2020) · Royal Society Open Science · doi:10.1098/rsos.192181 · Cited by 24

Formation, characterization and modeling of emergent synthetic microbial communities

Wang, J., Carper, D. L., Burdick, L. H., Shrestha, H. K., Appidi, M. R., Abraham, P. E., Timm, C. M., Hettich, R. L., Pelletier, D. A., & Doktycz, M. J. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.03.034 · Cited by 22

Symbiosis and the Anthropocene

Hom, E. F. Y., & Penn, A. S. (2021) · Symbiosis · doi:10.1007/s13199-021-00794-0 · Cited by 27

Local and collective transitions in sparsely-interacting ecological communities

Marcus, S., Turner, A. M., & Bunin, G. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010274 · Cited by 25

Metabolic model-based ecological modeling for probiotic design

Brunner, J. D., & Chia, N. (2024) · eLife · doi:10.7554/elife.83690 · Cited by 20

Biodiversity Loss Threatens the Current Functional Similarity of Beta Diversity in Benthic Diatom Communities

Virta, L., Soininen, J., & Norkko, A. M. (2020) · Microbial Ecology · doi:10.1007/s00248-020-01576-9 · Cited by 21

Why is cyclic dominance so rare?

Park, H. J., Pichugin, Y., & Traulsen, A. (2020) · eLife · doi:10.7554/elife.57857 · Cited by 20

Fluorescent Protein Expression as a Proxy for Bacterial Fitness in a High-Throughput Assay

Schlechter, R. O., Kear, E. J., Remus, D. M., & Remus‐Emsermann, M. N. P. (2021) · Applied and Environmental Microbiology · doi:10.1128/aem.00982-21 · Cited by 20

Understanding the impact of third-party species on pairwise coexistence

Deng, J., Taylor, W., & Saavedra, S. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010630 · Cited by 20

Transitivity and intransitivity in soil bacterial networks

Verdú, M., Alcántara, J. M., Navarro‐Cano, J. A., & Goberna, M. (2023) · The ISME Journal · doi:10.1038/s41396-023-01540-8 · Cited by 20

Spatial coordination in a mutually beneficial bacterial community enhances its antibiotic resistance

Li, L., Wu, T., Wang, Y., Ran, M., Kang, Y., Ouyang, Q., & Luo, C. (2019) · Communications Biology · doi:10.1038/s42003-019-0533-0 · Cited by 19

Microbiological stability and sensorial valorization of thyme and oregano essential oils alone or combined with ethanolic pomegranate extracts in wine marinated pork meat

Mantzourani, I., Daoutidou, M., Nikolaou, A., Kourkoutas, Y., Alexopoulos, A., Tzavellas, I. F., Dasenaki, M. E., Τhomaidis, Ν. S., & Plessas, S. (2022) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2022.110022 · Cited by 22

Ecological landscapes guide the assembly of optimal microbial communities

George, A. B., & Korolev, K. S. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010570 · Cited by 20

The effects of chemical fungicides and salicylic acid on the apple microbiome and fungal disease incidence under changing environmental conditions

McLaughlin, M. S., Yurgel, S. N., Abbasi, P. A., & Ali, S. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1342407 · Cited by 19

Environment‐Organism Feedbacks Drive Changes in Ecological Interactions

Meacock, O. J., & Mitri, S. (2024) · Ecology Letters · doi:10.1111/ele.70027 · Cited by 19

Spatiotemporal ecological chaos enables gradual evolutionary diversification without niches or tradeoffs

Mahadevan, A., Pearce, M. T., & Fisher, D. S. (2023) · eLife · doi:10.7554/elife.82734 · Cited by 18

Predicting bacterial interaction outcomes from monoculture growth and supernatant assays

Schmitz, D. A., Wechsler, T., Mignot, I., & Kümmerli, R. (2024) · ISME Communications · doi:10.1093/ismeco/ycae045 · Cited by 18

Experimental and computational approaches to unravel microbial community assembly

de Cárcer, D. A. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.11.031 · Cited by 18

High-dimensional microbiome interactions shape host fitnessPreprint

Gould, A. L., Zhang, V., Lamberti, L., Jones, E. W., Obadia, B., Gavryushkin, A., Korasidis, N., Carlson, J. M., Beerenwinkel, N., & Ludington, W. B. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/232959 · Cited by 18

Experimental evolution in an era of molecular manipulation

Ascensao, J. A., & Desai, M. M. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00867-6 · Cited by 19

Designing a bioremediator: mechanistic models guide cellular and molecular specialization

Zaccaria, M., Dawson, W., Cristiglio, V., Reverberi, M., Ratcliff, L. E., Nakajima, T., Genovese, L., & Momeni, B. (2019) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2019.09.006 · Cited by 17

Determinism of microbial community assembly by drastic environmental change

Nishida, A., Nakagawa, M., & Yamamura, M. (2021) · PLoS ONE · doi:10.1371/journal.pone.0260591 · Cited by 17

Control points for design of taxonomic composition in synthetic human gut communities

Connors, B., Thompson, J. C., Sarah, E., Clark, R. L., Pfleger, B. F., & Venturelli, O. S. (2023) · Cell Systems · doi:10.1016/j.cels.2023.11.007 · Cited by 22

On the growth and form of bacterial colonies

Porter, R. L., Trenado-Yuste, C., Martínez-Calvo, A., Su, M., Wingreen, N. S., Datta, S. S., & Huang, K. C. (2025) · Nature Reviews Physics · doi:10.1038/s42254-025-00849-x · Cited by 20

Multi-stable bacterial communities exhibit extreme sensitivity to initial conditions

Wright, E. S., Gupta, R., & Vetsigian, K. (2021) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiab073 · Cited by 16

Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions

Doane, M. P., Ostrowski, M. D., Brown, M. V., Bramucci, A. R., Bodrossy, L., van de Kamp, J., Bissett, A. B., Steinberg, P. D., Doblin, M. A., & Seymour, J. R. (2023) · Environmental Microbiology · doi:10.1111/1462-2920.16341 · Cited by 16

Predicting N-Strain Coexistence from Co-colonization Interactions: Epidemiology Meets Ecology and the Replicator Equation

Madec, S., & Gjini, E. (2020) · Bulletin of Mathematical Biology · doi:10.1007/s11538-020-00816-w · Cited by 19

Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes

Blanchette, M. L., & Lund, M. A. (2021) · Microorganisms · doi:10.3390/microorganisms9061207 · Cited by 16

Cytokinin-microbiome interactions regulate developmental functions

Gupta, R., Elkabetz, D., Leibman‐Markus, M., Jami, E., & Bar, M. (2022) · Environmental Microbiome · doi:10.1186/s40793-022-00397-2 · Cited by 18

Coexistence Theory for Microbial Ecology, and Vice Versa

Orr, J. A., Armitage, D. W., & Letten, A. D. (2025) · Environmental Microbiology · doi:10.1111/1462-2920.70072 · Cited by 15

Enhancing nutritional niche and host defenses by modifying the gut microbiome

Sun, Q. H., Vega, N. M., Cervantes, B., Mancuso, C. P., Mao, N., Taylor, M. N., Collins, J. J., Khalil, A. S., Gore, J., & Lu, T. K. (2022) · Molecular Systems Biology · doi:10.15252/msb.20209933 · Cited by 17

Searching for Principles of Microbial Ecology Across Levels of Biological Organization

Gralka, M. (2023) · Integrative and Comparative Biology · doi:10.1093/icb/icad060 · Cited by 17

Mutualism reduces the severity of gene disruptions in predictable ways across microbial communities

Martinson, J. N. V., Chacón, J. M., Smith, B. A., Villarreal, A. R., Hunter, R. C., & Harcombe, W. R. (2023) · The ISME Journal · doi:10.1038/s41396-023-01534-6 · Cited by 19

Macroecological patterns in experimental microbial communities

Shoemaker, W. R., Sánchez, Á., & Grilli, J. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1013044 · Cited by 18

Successful microbial colonization of space in a more dispersed manner

Liu, X., Wang, M., Nie, Y., & Wu, X. (2021) · ISME Communications · doi:10.1038/s43705-021-00063-7 · Cited by 15

Generalizing game-changing species across microbial communities

Deng, J., Angulo, M. T., & Saavedra, S. (2021) · ISME Communications · doi:10.1038/s43705-021-00022-2 · Cited by 15

110th Anniversary: High-Order Interactions Can Eclipse Pairwise Interactions in Shaping the Structure of Microbial Communities

Ansari, A. F., Acharya, N. I. S., Kumaran, S., Ravindra, K., Reddy, Y. B. S., Dixit, N. M., & Raut, J. S. (2019) · Industrial & Engineering Chemistry Research · doi:10.1021/acs.iecr.9b03190 · Cited by 14

Competition and cooperation: The plasticity of bacterial interactions across environments

Solowiej-Wedderburn, J., Pentz, J. T., Lizana, L., Schroeder, B. O., Lind, P. A., & Libby, E. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1013213 · Cited by 14

Understanding the emergence of contingent and deterministic exclusion in multispecies communities

Song, C., Uricchio, L. H., Mordecai, E. A., & Saavedra, S. (2021) · Ecology Letters · doi:10.1111/ele.13846 · Cited by 15

Finding Core-Periphery Structures With Node Influences

Shen, X. Y., Aliko, S., Han, Y. J., Skipper, J. I., & Peng, C. (2021) · IEEE Transactions on Network Science and Engineering · doi:10.1109/tnse.2021.3138436 · Cited by 14

Periodic temporal environmental variations induce coexistence in resource competition models

Burkart, T., Willeke, J., & Frey, E. (2023) · Physical review. E · doi:10.1103/physreve.108.034404 · Cited by 14

Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media

Kleyer, H., Tecon, R., & Or, D. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.02057-19 · Cited by 14

Structured environments foster competitor coexistence by manipulating interspecies interfaces

Ursell, T. S. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007762 · Cited by 14

The potential to produce tropodithietic acid by Phaeobacter inhibens affects the assembly of microbial biofilm communities in natural seawater

Bech, P. K., Zhang, S., Henriksen, N. N. S. E., Bentzon‐Tilia, M., Strube, M. L., & Gram, L. (2023) · npj Biofilms and Microbiomes · doi:10.1038/s41522-023-00379-3 · Cited by 12

Single-cell mass distributions reveal simple rules for achieving steady-state growth

Roller, B. R. K., Hellerschmied, C., Wu, Y., Miettinen, T. P., Gomez, A. L., Manalis, S. R., & Polz, M. F. (2023) · mBio · doi:10.1128/mbio.01585-23 · Cited by 16

Ignoring social distancing: advances in understanding multi-species bacterial interactions

Ross, B. N., & Whiteley, M. (2020) · Faculty Reviews · doi:10.12703/r/9-23 · Cited by 13

The ratio of single to co‐colonization is key to complexity in interacting systems with multiple strains

Gjini, E., & Madec, S. (2021) · Ecology and Evolution · doi:10.1002/ece3.7259 · Cited by 14

Pairing off: a bottom‐up approach to the human gut microbiome

Abreu, C. I., Lopez, A. O., & Gore, J. (2018) · Molecular Systems Biology · doi:10.15252/msb.20188425 · Cited by 13

Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioningPreprint

Blasche, S., Kim, Y., Mars, R. A. T., Kafkia, E., Maansson, M., Machado, D., Teusink, B., Nielsen, J., Beneš, V., Neves, A. R., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/541870 · Cited by 13

Interspecies bacterial competition determines community assembly in the C. elegans intestinePreprint

Lopez, A. O., Vega, N. M., & Gore, J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/535633 · Cited by 13

Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community

Duxbury, S. J. N., Raguideau, S., Cremin, K., Richards, L., Medvecký, M., Rosko, J., Coates, M., Randall, K., Chen, J., Quince, C., et al. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf126 · Cited by 25

Ecological differentiation and assembly processes of abundant and rare bacterial subcommunities in karst groundwater

Zhong, S., Hou, B., Zhang, J., Wang, Y., Xu, X., Li, B., & Ni, J. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1111383 · Cited by 12

Understory vegetation restoration improves soil physicochemical properties, enzymatic activity, and changes diazotrophic communities in Cunninghamia lanceolata plantations but depends on site history

Ding, K., Zhang, Y., Yang, A., Zhang, Y., Lu, M., Ge, S., Qiu, Y., Zhang, J., & Tong, Z. (2023) · Plant and Soil · doi:10.1007/s11104-023-06205-1 · Cited by 12

Filamentous prophage Pf4 promotes genetic exchange in Pseudomonas aeruginosa

Pei, T., Luo, H., Wang, Y., Li, H., Wang, X., Zhang, Y., An, Y., Wu, L., Ma, J., Liang, X., et al. (2024) · The ISME Journal · doi:10.1093/ismejo/wrad025 · Cited by 13

Bacteria, Fungi, and Protists Exhibit Distinct Responses to Managed Vegetation Restoration in the Karst Region

Xiao, C., Xiao, D., Sun, M., & Wang, K. (2024) · Microorganisms · doi:10.3390/microorganisms12061074 · Cited by 12

Characterizing a stable five-species microbial community for use in experimental evolution and ecology

Castledine, M., Pennycook, J., Newbury, A., Lear, L., Erdős, Z., Lewis, R., Kay, S., Sanders, D., Sünderhauf, D., Buckling, A. G. J., et al. (2024) · Microbiology · doi:10.1099/mic.0.001489 · Cited by 12

Assembly Graph as the Rosetta Stone of Ecological Assembly

Song, C. (2025) · Environmental Microbiology · doi:10.1111/1462-2920.70030 · Cited by 13

Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

Song, H., Lee, J., Haruta, S., Nelson, W. C., Lee, D., Lindemann, S. R., Fredrickson, J. K., & Bernstein, H. C. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01264 · Cited by 12

A neural network model predicts community-level signaling states in a diverse microbial community

Silva, K. P. T., & Boedicker, J. Q. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007166 · Cited by 11

Synthetic Mutualism and the Intervention Dilemma

Denton, J. A., & Gokhale, C. S. (2019) · Life · doi:10.3390/life9010015 · Cited by 13

Reconciling empirical interactions and species coexistence

Maynard, D. S., Wootton, J. T., Serván, C. A., & Stefano Allesina, A. (2019) · Ecology Letters · doi:10.1111/ele.13256 · Cited by 12

Tracking defined microbial communities by multicolor flow cytometry reveals tradeoffs between productivity and diversity

Midani, F. S., & David, L. A. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.910390 · Cited by 10

High-efficiency removal of rare earth elements from acid mine drainage by microbially induced carbonate precipitation process

Li, S., Wu, S., Wang, S., Liu, G., Zhan, Y., Tong, J., Zhou, K., & Xie, H. (2025) · Journal of Water Process Engineering · doi:10.1016/j.jwpe.2025.107134 · Cited by 11

SiGMoiD: A super-statistical generative model for binary data

Zhao, X., Plata, G., & Dixit, P. D. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009275 · Cited by 11

A competitive advantage through fast dead matter elimination in confined cellular aggregates

Pollack, Y. G., Bittihn, P., & Golestanian, R. (2021) · bioRxiv · doi:10.1088/1367-2630/ac788e · Cited by 13

State-Space-Based Framework for Predicting Microbial Interaction Variability in Wastewater Treatment Plants

Yu, Z., Huang, Y. L., Gan, Z., Meng, Y., & Meng, F. (2022) · Environmental Science & Technology · doi:10.1021/acs.est.2c02844 · Cited by 11

Master regulators of biological systems in higher dimensions

Eble, H., Joswig, M., Lamberti, L., & Ludington, W. B. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2300634120 · Cited by 15

Seasonal and short-term variations of bacteria and pathogenic bacteria on road deposited sediments

Wang, J., Huang‬‬‬‬, J. J., & Lynch, I. (2021) · Environmental Research · doi:10.1016/j.envres.2021.111903 · Cited by 11

Competition dynamics in long‐term propagations of Schizosaccharomyces pombe strain communities

Durão, P., Amicone, M., Perfeito, L., & Gordo, I. (2021) · Ecology and Evolution · doi:10.1002/ece3.8191 · Cited by 11

A density functional theory for ecology across scales

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