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Louca, S., McLaughlin, A., MacPherson, A., Joy, J. B., Pennell, M. W. (in press) - Fundamental identifiability limits in molecular epidemiology
Molecular Biology and Evolution. DOI:10.1101/2021.01.18.427170
Louca, S., Pennell, M.W. (in press) - Why extinction estimates from extant phylogenies are so often zero
Current Biology. DOI:10.1101/2021.01.04.425256
Louca, S. (2021) - Phylogeographic estimation and simulation of global diffusive dispersal
Systematic Biology 70:340-359. DOI:10.1093/sysbio/syaa061
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., 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., 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., 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
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., 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., 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., 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. (2017) - Probing the metabolism of microorganisms
Science 358:1264-1265. DOI:10.1126/science.aar2000
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
Advanced Modeling in Biology
This book introduces advanced modeling concepts in biology, focusing on differential equation models and stochastic processes.
Author: Stilianos Louca
Stilianos Louca (2016) - The ecology of microbial metabolic pathways
University of British Columbia, Institute of Applied Mathematics, PhD thesis
Stilianos Louca (2012) - Collective dynamics in infinite networks of pulse-coupled phase oscillators
Friedrich-Schiller Universität, Physikalisch-Astronomische Fakultät, Diplom thesis
Stilianos Louca (2010) - Additive set functions as linear functionals
Friedrich-Schiller Universität, Fakultät für Mathematik und Informatik, Bachelor thesis

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