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| Articles
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| Albright, S., Louca, S. (2023) - Trait biases in microbial reference genomes |
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| Scientific Data 10:84. DOI:10.1038/s41597-023-01994-7 |
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| Louca, S., Henao-Diaz, L. F., Pennell, M.W. (2022) - The scaling of diversification rates with age is likely explained by sampling bias |
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| Evolution 76:1625-1637. DOI:10.1111/evo.14515 |
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| Albright, M. B. N., Louca, S., Winkler, D. E., Feeser, K. L., Haig, S. J., Whiteson, K. L., Emerson, J. B., Dunbar, J. (2022) - Solutions in microbiome engineering: prioritizing barriers to organism establishment |
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| ISME Journal 16:331-338. DOI:10.1038/s41396-021-01088-5 |
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| Louca, S., Taylor, G. T, Astor, Y. M., Buck, K., Muller-Karger, F. E. (2022) - Transport-limited reactions in microbial systems |
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| Environmental Microbiology 25:268-282. DOI:10.1111/1462-2920.16275 |
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| MacPherson, A., Louca, S., McLaughlin, A., Joy, J. B., Pennell, M. W. (2022) - Unifying phylogenetic birth-death models in epidemiology and macroevolution |
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| Systematic Biology 71:172-189. DOI:10.1093/sysbio/syab049 |
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| Louca, S. (2021) - SARS-CoV-2 infections in 165 countries over time |
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| International Journal of Infectious Diseases 111:336-346. DOI:10.1016/j.ijid.2021.08.067 |
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| Louca, S. (2021) - Phylogeographic estimation and simulation of global diffusive dispersal |
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| Systematic Biology 70:340-359. DOI:10.1093/sysbio/syaa061 |
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| Louca, S., Pennell, M.W. (2021) - Why extinction estimates from extant phylogenies are so often zero |
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| Current Biology 31:3168-3173. DOI:10.1016/j.cub.2021.04.066 |
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| Louca, S., McLaughlin, A., MacPherson, A., Joy, J. B., Pennell, M. W. (2021) - Fundamental identifiability limits in molecular epidemiology |
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| Molecular Biology and Evolution 38:4010-4024. DOI:10.1093/molbev/msab149 |
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| Louca, S. (2021) - The rates of global bacterial and archaeal dispersal |
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| ISME Journal 16:159-167. DOI:10.1038/s41396-021-01069-8 |
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| Louca, S., Mazel, F., Doebeli, M., Parfrey, W. L. (2021) - Response to "Vast (but avoidable) underestimation of global biodiversity" |
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| PLOS Biology 19:e3001362. DOI:10.1371/journal.pbio.3001362 |
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| Louca, S., Rubin, I. N., Bohlmann, J., Madilao, L. L., Doebeli, M., Parfrey, L. W. (2020) - Effects of forced taxonomic transitions on metabolic structure and function in microbial microcosms |
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| Environmental Microbiology Reports 12:514-524. DOI:10.1111/1758-2229.12866 |
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| Louca, S. (2020) - Simulating trees with millions of species |
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| Bioinformatics 36:2907-2908. DOI:10.1093/bioinformatics/btaa031 |
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| Louca, S., Pennell, M.W. (2020) - Extant timetrees are consistent with a myriad of diversification histories |
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Nature 580:502-505. DOI:10.1038/s41586-020-2176-1.
Commentary by Mark Pagel. |
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| Louca, S., Pennell, M.W. (2020) - A general and efficient algorithm for the likelihood of diversification and discrete-trait evolutionary models |
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| Systematic Biology 69:545-556. DOI:10.1093/sysbio/syz055 |
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| Louca, S., Mazel, F., Doebeli, M., Parfrey, W. L. (2019) - A census-based estimate of Earth's bacterial and archaeal diversity |
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| PLOS Biology 17:e3000106. DOI:10.1371/journal.pbio.3000106. Associated data: GPC |
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| Louca, S., Astor, Y. M., Doebeli, M., Taylor, G. T., Scranton, M. I. (2019) - Microbial metabolite fluxes in a model marine anoxic ecosystem |
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| Geobiology 17:628-642. DOI:10.1111/gbi.12357. Supporting MATLAB code. |
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| Louca, S., Scranton, M. I., Taylor, G. T., Astor, Y. M., Crowe, S. A., Doebeli, M. (2019) - Circumventing kinetics in biogeochemical modeling |
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| PNAS 116:11329-11338. DOI:10.1073/pnas.1819883116. Supporting MATLAB code. |
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| Louca, S., Doebeli, M. (2018) - Efficient comparative phylogenetics on large trees |
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| Bioinformatics 34:1053-1055. DOI:10.1093/bioinformatics/btx701. Associated software: castor R package |
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| Louca, S., Doebeli, M., Parfrey, L. W. (2018) - Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem |
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| Microbiome 6:41. DOI:10.1186/s40168-018-0420-9 |
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| Louca, S., Polz, M. F., Mazel, F., Albright, M. B. N., Huber, J. A., O'Connor, M. I., Ackermann, M., Hahn, A. S., Srivastava, D. S., Crowe, S. A., Doebeli, M., Parfrey, L. W. (2018) - Function and functional redundancy in microbial systems |
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| Nature Ecology & Evolution 2:936-943. DOI:10.1038/s41559-018-0519-1 |
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| Louca, S., Shih, P. M., Pennell, M. W., Fischer, W. W., Parfrey, L. W., Doebeli, M. (2018) - Bacterial diversification through geological time |
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| Nature Ecology & Evolution 2:1458-1467. DOI:10.1038/s41559-018-0625-0. Science Friday radio interview. |
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| Louca, S. (2017) - Probing the metabolism of microorganisms |
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| Science 358:1264-1265. DOI:10.1126/science.aar2000 |
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| Barraquand, F., Louca, S., Abbott, K. C., Cobbold, C. A., Cordoleani, F., DeAngelis, D. L., Elderd, B. D., Fox, J. W., Greenwood, P., Hilker, F. M., Murray, D. L., Stieha, C. R., Taylor, R. A., Vitense, K., Wolkowicz, G. S. K., Tyson, R. C. (2017) - Moving forward in circles: challenges and opportunities in modeling population cycles |
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| Ecology Letters 20:1074-1092. DOI:10.1111/ele.12789 |
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| Louca, S., Jacques, S. M. S., Pires, A. P. F., Leal, J. S., González, A. L, Doebeli, M., Farjalla, V. F. (2017) - Functional structure of the bromeliad tank microbiome is strongly shaped by local geochemical conditions |
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| Environmental Microbiology 19:3132-3151. DOI:10.1111/1462-2920.13788 |
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| Louca, S., Doebeli, S. (2017) - Taxonomic variability and functional stability in microbial communities infected by phages |
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| Environmental Microbiology 19:3863-3878. DOI:10.1111/1462-2920.13743 |
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| Louca, S., Crowe, S. A. (2017) - Microscale reservoir effects on microbial sulfur isotope fractionation |
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| Geochimica et Cosmochimica Acta 203:117-139. DOI:10.1016/j.gca.2017.01.007. Supporting MATLAB code. |
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| Louca, S., Jacques, S. M. S., Pires, A. P. F., Leal, J. S., Srivastava, D. S., Parfrey, L. W., Farjalla, V. F., Doebeli, M. (2016) - High taxonomic variability despite stable functional structure across microbial communities |
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Nature Ecology & Evolution 1:0015. DOI:10.1038/s41559-016-0015.
Blog post: Behind the paper. Commentary: By S. Gibbons |
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| Louca, S., Parfrey, L. W., Doebeli, M. (2016) - Decoupling function and taxonomy in the global ocean microbiome |
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| Science 353:1272-1277. DOI:10.1126/science.aaf4507. Associated software: FAPROTAX |
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| Louca, S., Hawley, A. K., Katsev, S., Torres-Beltran, M., Bhatia, M. P., Kheirandish, S., Michiels, C. C., Capelle, D., Lavik, G., Doebeli, M., Crowe, S. A., Hallam, S. J (2016) - Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone |
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| PNAS 113:E5925-E5933. DOI:10.1073/pnas.1602897113. Supporting MATLAB code. |
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| Hahn, A. S., Konwar, K., Louca, S., Hanson, N. W., Hallam, S. J. (2016) - The information science of microbial ecology |
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| Current Opinion in Microbiology 31:209-216. DOI:10.1016/j.mib.2016.04.014 |
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| Louca, S., Doebeli, M. (2016) - Reaction-centric modeling of microbial ecosystems |
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| Ecological Modelling 335:74-86. DOI:10.1016/j.ecolmodel.2016.05.011 |
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| Louca, S., Doebeli, M. (2015) - Transient dynamics of competitive exclusion in microbial communities |
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| Environmental Microbiology 18:1863-1874. DOI:10.1111/1462-2920.13058 |
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| Louca, S., Doebeli, M. (2015) - Calibration and analysis of genome-based models for microbial ecology |
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| eLife 4:e08208. DOI:10.7554/eLife.08208. Associated software: Microbial Community Modeler |
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| Louca, S., Doebeli, M. (2015) - Detecting cyclicity in ecological time series |
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| Ecology 96:1724-1732. DOI:10.1890/14-0126.1. Associated software: peacots R package |
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| Louca, S., Doebeli, M. (2014) - Distinguishing intrinsic limit cycles from forced oscillations in ecological time series |
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| Theoretical Ecology 7:381-390. DOI:10.1007/s12080-014-0225-9 |
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| Louca, S., Lampo, M., Doebeli, M. (2014) - Assessing host extinction risk following exposure to Batrachochytrium dendrobatidis |
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| Proceedings of the Royal Society B 281:20132783. DOI:10.1098/rspb.2013.2783 |
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| Louca, S., Atay, F. M. (2014) - Spatially structured networks of pulse-coupled phase oscillators on metric spaces |
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| AIMS Journal of Discrete and Continuous Dynamical Systems - A 34:3703-3745. DOI:10.3934/dcds.2014.34.3703 |
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| Louca, S., Atay, F. M. (2013) - Stationary states in infinite networks of spiking oscillators with noise |
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| SIAM Journal on Applied Dynamical Systems 12:415-449. DOI:10.1137/120880264 |
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| Louca, S., Ibanez, S., Piau, D., Després, L. (2012) - Specialized nursery pollination mutualisms as evolutionary traps stabilized by antagonistic traits |
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| Journal of Theoretical Biology 296:65-83. DOI:10.1016/j.jtbi.2011.11.028 |
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Louca lab. Department of Biology, University of Oregon, Eugene, USA
© 2023 Stilianos Louca all rights reserved
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