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Articles
 
Albright, M. B. N., Louca, S., Winkler, D. E., Feeser, K. L., Haig, S. J., Whiteson, K. L., Emerson, J. B., Dunbar, J. (2021) - Solutions in microbiome engineering: prioritizing barriers to organism establishment
ISME Journal. DOI:10.1038/s41396-021-01088-5
Louca, S. (2021) - The rates of global bacterial and archaeal dispersal
ISME Journal. DOI:10.1038/s41396-021-01069-8
MacPherson, A., Louca, S., McLaughlin, A., Joy, J. B., Pennell, M. W. (2021) - Unifying phylogenetic birth-death models in epidemiology and macroevolution
Systematic Biology. DOI:10.1093/sysbio/syab049
Louca, S., McLaughlin, A., MacPherson, A., Joy, J. B., Pennell, M. W. (2021) - Fundamental identifiability limits in molecular epidemiology
Molecular Biology and Evolution 38:4010-4024. DOI:10.1093/molbev/msab149
Louca, S. (2021) - SARS-CoV-2 infections in 165 countries over time
International Journal of Infectious Diseases 111:336-346. DOI:10.1016/j.ijid.2021.08.067
Louca, S., Pennell, M.W. (2021) - Why extinction estimates from extant phylogenies are so often zero
Current Biology 31:3168-3173. DOI:10.1016/j.cub.2021.04.066
Louca, S. (2021) - Phylogeographic estimation and simulation of global diffusive dispersal
Systematic Biology 70:340-359. DOI:10.1093/sysbio/syaa061
Louca, S., Mazel, F., Doebeli, M., Parfrey, W. L. (2021) - Response to "Vast (but avoidable) underestimation of global biodiversity"
PLOS Biology 19:e3001362. DOI:10.1371/journal.pbio.3001362
Louca, S., Pennell, M.W. (2020) - A general and efficient algorithm for the likelihood of diversification and discrete-trait evolutionary models
Systematic Biology 69:545-556. DOI:10.1093/sysbio/syz055
Louca, S., Pennell, M.W. (2020) - Extant timetrees are consistent with a myriad of diversification histories
Nature 580:502-505. DOI:10.1038/s41586-020-2176-1.
Commentary by Mark Pagel.
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
Environmental Microbiology Reports 12:514-524. DOI:10.1111/1758-2229.12866
Louca, S. (2020) - Simulating trees with millions of species
Bioinformatics 36:2907-2908. DOI:10.1093/bioinformatics/btaa031
Louca, S., Mazel, F., Doebeli, M., Parfrey, W. L. (2019) - A census-based estimate of Earth's bacterial and archaeal diversity
PLOS Biology 17:e3000106. DOI:10.1371/journal.pbio.3000106. Associated data: GPC
Louca, S., Astor, Y. M., Doebeli, M., Taylor, G. T., Scranton, M. I. (2019) - Microbial metabolite fluxes in a model marine anoxic ecosystem
Geobiology 17:628-642. DOI:10.1111/gbi.12357. Supporting MATLAB code.
Louca, S., Scranton, M. I., Taylor, G. T., Astor, Y. M., Crowe, S. A., Doebeli, M. (2019) - Circumventing kinetics in biogeochemical modeling
PNAS 116:11329-11338. DOI:10.1073/pnas.1819883116. Supporting MATLAB code.
Louca, S., Shih, P. M., Pennell, M. W., Fischer, W. W., Parfrey, L. W., Doebeli, M. (2018) - Bacterial diversification through geological time
Nature Ecology & Evolution 2:1458-1467. DOI:10.1038/s41559-018-0625-0. Science Friday radio interview.
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
Nature Ecology & Evolution 2:936-943. DOI:10.1038/s41559-018-0519-1
Louca, S., Doebeli, M., Parfrey, L. W. (2018) - Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem
Microbiome 6:41. DOI:10.1186/s40168-018-0420-9
Louca, S., Doebeli, M. (2018) - Efficient comparative phylogenetics on large trees
Bioinformatics 34:1053-1055. DOI:10.1093/bioinformatics/btx701. Associated software: castor R package
Louca, S., Doebeli, S. (2017) - Taxonomic variability and functional stability in microbial communities infected by phages
Environmental Microbiology 19:3863-3878. DOI:10.1111/1462-2920.13743
Louca, S., Crowe, S. A. (2017) - Microscale reservoir effects on microbial sulfur isotope fractionation
Geochimica et Cosmochimica Acta 203:117-139. DOI:10.1016/j.gca.2017.01.007. Supporting MATLAB code.
Louca, S. (2017) - Probing the metabolism of microorganisms
Science 358:1264-1265. DOI:10.1126/science.aar2000
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
Environmental Microbiology 19:3132-3151. DOI:10.1111/1462-2920.13788
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
Ecology Letters 20:1074-1092. DOI:10.1111/ele.12789
Louca, S., Doebeli, M. (2016) - Reaction-centric modeling of microbial ecosystems
Ecological Modelling 335:74-86. DOI:10.1016/j.ecolmodel.2016.05.011
Hahn, A. S., Konwar, K., Louca, S., Hanson, N. W., Hallam, S. J. (2016) - The information science of microbial ecology
Current Opinion in Microbiology 31:209-216. DOI:10.1016/j.mib.2016.04.014
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
PNAS 113:E5925-E5933. DOI:10.1073/pnas.1602897113. Supporting MATLAB code.
Louca, S., Parfrey, L. W., Doebeli, M. (2016) - Decoupling function and taxonomy in the global ocean microbiome
Science 353:1272-1277. DOI:10.1126/science.aaf4507. Associated software: FAPROTAX
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
Nature Ecology & Evolution 1:0015. DOI:10.1038/s41559-016-0015.
Blog post: Behind the paper. Commentary: By S. Gibbons
Louca, S., Doebeli, M. (2015) - Transient dynamics of competitive exclusion in microbial communities
Environmental Microbiology 18:1863-1874. DOI:10.1111/1462-2920.13058
Louca, S., Doebeli, M. (2015) - Calibration and analysis of genome-based models for microbial ecology
eLife 4:e08208. DOI:10.7554/eLife.08208. Associated software: Microbial Community Modeler
Louca, S., Doebeli, M. (2015) - Detecting cyclicity in ecological time series
Ecology 96:1724-1732. DOI:10.1890/14-0126.1. Associated software: peacots R package
Louca, S., Doebeli, M. (2014) - Distinguishing intrinsic limit cycles from forced oscillations in ecological time series
Theoretical Ecology 7:381-390. DOI:10.1007/s12080-014-0225-9
Louca, S., Lampo, M., Doebeli, M. (2014) - Assessing host extinction risk following exposure to Batrachochytrium dendrobatidis
Proceedings of the Royal Society B 281:20132783. DOI:10.1098/rspb.2013.2783
Louca, S., Atay, F. M. (2014) - Spatially structured networks of pulse-coupled phase oscillators on metric spaces
AIMS Journal of Discrete and Continuous Dynamical Systems - A 34:3703-3745. DOI:10.3934/dcds.2014.34.3703
Louca, S., Atay, F. M. (2013) - Stationary states in infinite networks of spiking oscillators with noise
SIAM Journal on Applied Dynamical Systems 12:415-449. DOI:10.1137/120880264
Louca, S., Ibanez, S., Piau, D., Després, L. (2012) - Specialized nursery pollination mutualisms as evolutionary traps stabilized by antagonistic traits
Journal of Theoretical Biology 296:65-83. DOI:10.1016/j.jtbi.2011.11.028
 
 
Books
 
Dynamical Modeling in Biology
This book introduces advanced dynamical modeling concepts in biology, focusing on differential equations, iterative maps and stochastic processes.
 

Louca lab. Department of Biology, University of Oregon, Eugene, USA
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