Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA‐based census of soil biodiversity from a tropical forest
暂无分享,去创建一个
P. Taberlet | J. Chave | L. Zinger | E. Coissac | H. Schimann | A. Iribar | Guilhem Sommeria-Klein | Lucie Zinger | É. Coissac
[1] Alexander E. White,et al. Regional influences on community structure across the tropical-temperate divide , 2019, Nature Communications.
[2] Md Saydur Rahman,et al. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA , 2019, Global Ecology and Conservation.
[3] P. Taberlet,et al. Body size determines soil community assembly in a tropical forest. , 2018, Molecular ecology.
[4] Emmanuel Paradis,et al. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R , 2018, Bioinform..
[5] P. Legendre. Numerical Ecology , 2019, Encyclopedia of Ecology.
[6] R. Fletcher,et al. Extending the Latent Dirichlet Allocation model to presence/absence data: A case study on North American breeding birds and biogeographical shifts expected from climate change , 2018, Global change biology.
[7] M. Doebeli,et al. Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem , 2018, Microbiome.
[8] P. Taberlet,et al. Environmental DNA: For Biodiversity Research and Monitoring , 2018 .
[9] Kris Sankaran,et al. Latent variable modeling for the microbiome. , 2017, Biostatistics.
[10] Rick L. Stevens,et al. A communal catalogue reveals Earth’s multiscale microbial diversity , 2017, Nature.
[11] Anna Norberg,et al. How to make more out of community data? A conceptual framework and its implementation as models and software. , 2017, Ecology letters.
[12] J. Chave,et al. Quantifying micro-environmental variation in tropical rainforest understory at landscape scale by combining airborne LiDAR scanning and a sensor network , 2017, Annals of Forest Science.
[13] Ian Holmes,et al. Linking Statistical and Ecological Theory: Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process , 2014, Proceedings of the IEEE.
[14] Pierre Taberlet,et al. Inferring neutral biodiversity parameters using environmental DNA data sets , 2016, Scientific Reports.
[15] Shaowen Yao,et al. An overview of topic modeling and its current applications in bioinformatics , 2016, SpringerPlus.
[16] Wenjun Li,et al. Editorial: Actinobacteria in Special and Extreme Habitats: Diversity, Function Roles, and Environmental Adaptations , 2016, Front. Microbiol..
[17] Karoline Faust,et al. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. , 2016, FEMS microbiology reviews.
[18] Sophie J. Weiss,et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision , 2016, The ISME Journal.
[19] G. Kowalchuk,et al. The Ecology of Acidobacteria: Moving beyond Genes and Genomes , 2016, Front. Microbiol..
[20] Matthew Stephens,et al. Visualizing the structure of RNA-seq expression data using grade of membership models , 2016, bioRxiv.
[21] Francis K. C. Hui,et al. So Many Variables: Joint Modeling in Community Ecology. , 2015, Trends in ecology & evolution.
[22] O. Phillips,et al. Using repeated small-footprint LiDAR acquisitions to infer spatial and temporal variations of a high-biomass Neotropical forest , 2015 .
[23] Luis Pedro Coelho,et al. Structure and function of the global ocean microbiome , 2015, Science.
[24] Sara Taskinen,et al. Model‐based approaches to unconstrained ordination , 2015 .
[25] Hong Gu,et al. BioMiCo: a supervised Bayesian model for inference of microbial community structure , 2015, Microbiome.
[26] K. Peay,et al. Parsing ecological signal from noise in next generation amplicon sequencing. , 2015, The New phytologist.
[27] Eske Willerslev,et al. Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity , 2015 .
[28] Matthias Mauch,et al. The Minor fall, the Major lift: inferring emotional valence of musical chords through lyrics , 2015, Royal Society Open Science.
[29] R. Chazdon,et al. Decomposing biodiversity data using the Latent Dirichlet Allocation model, a probabilistic multivariate statistical method , 2014, Ecology letters.
[30] P. Schloss,et al. Dynamics and associations of microbial community types across the human body , 2014, Nature.
[31] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[32] Mihai Datcu,et al. Latent Dirichlet Allocation for Spatial Analysis of Satellite Images , 2013, IEEE Transactions on Geoscience and Remote Sensing.
[33] Susanne A. Fritz,et al. An Update of Wallace’s Zoogeographic Regions of the World , 2013, Science.
[34] Tu Bao Ho,et al. Fully Sparse Topic Models , 2012, ECML/PKDD.
[35] R. Knight,et al. Diversity, stability and resilience of the human gut microbiota , 2012, Nature.
[36] J. Raes,et al. Microbial interactions: from networks to models , 2012, Nature Reviews Microbiology.
[37] Dominik Olszewski. Employing Kullback-Leibler divergence and Latent Dirichlet Allocation for fraud detection in telecommunications , 2012, Intell. Data Anal..
[38] P. Taberlet,et al. Environmental DNA , 2012, Molecular ecology.
[39] R. Knight,et al. Sequencing our way towards understanding global eukaryotic biodiversity. , 2012, Trends in ecology & evolution.
[40] C. Quince,et al. Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics , 2012, PloS one.
[41] Arun Balagopalan. Improving Topic Reproducibility in Topic Models , 2012 .
[42] Rob Knight,et al. Bayesian community-wide culture-independent microbial source tracking , 2011, Nature Methods.
[43] Andrew McCallum,et al. Optimizing Semantic Coherence in Topic Models , 2011, EMNLP.
[44] Kurt Hornik,et al. topicmodels : An R Package for Fitting Topic Models , 2016 .
[45] Jonathan M. Chase,et al. Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist. , 2011, Ecology letters.
[46] Stephen E Fienberg,et al. Reconceptualizing the classification of PNAS articles , 2010, Proceedings of the National Academy of Sciences.
[47] David B. Dunson,et al. Probabilistic topic models , 2011, KDD '11 Tutorials.
[48] James Bailey,et al. Information Theoretic Measures for Clusterings Comparison: Variants, Properties, Normalization and Correction for Chance , 2010, J. Mach. Learn. Res..
[49] Carl T. Bergstrom,et al. The map equation , 2009, 0906.1405.
[50] Mollie E. Brooks,et al. Generalized linear mixed models: a practical guide for ecology and evolution. , 2009, Trends in ecology & evolution.
[51] P. Legendre,et al. Forward selection of explanatory variables. , 2008, Ecology.
[52] A. Kerkhoff,et al. Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity , 2008, Proceedings of the National Academy of Sciences.
[53] Andrew McCallum,et al. Topic Models Conditioned on Arbitrary Features with Dirichlet-multinomial Regression , 2008, UAI.
[54] Frans Bongers,et al. Above-ground biomass and productivity in a rain forest of eastern South America , 2008, Journal of Tropical Ecology.
[55] R. B. Jackson,et al. Toward an ecological classification of soil bacteria. , 2007, Ecology.
[56] M. Meilă. Comparing clusterings---an information based distance , 2007 .
[57] Robert I. McDonald,et al. The distance decay of similarity in ecological communities , 2007 .
[58] P. Legendre,et al. vegan : Community Ecology Package. R package version 1.8-5 , 2007 .
[59] W. Sloan,et al. Modeling Taxa-Abundance Distributions in Microbial Communities using Environmental Sequence Data , 2007, Microbial Ecology.
[60] Thomas L. Griffiths,et al. The Author-Topic Model for Authors and Documents , 2004, UAI.
[61] Mark Steyvers,et al. Finding scientific topics , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[62] Jean Thioulouse,et al. The ade4 package - I : One-table methods , 2004 .
[63] J. Thioulouse,et al. The ade 4 package-I : One-table methods by , 2004 .
[64] David R. Anderson,et al. Model Selection and Multimodel Inference , 2003 .
[65] Michael I. Jordan,et al. Latent Dirichlet Allocation , 2001, J. Mach. Learn. Res..
[66] G. Quinn,et al. Experimental Design and Data Analysis for Biologists , 2002 .
[67] P. Donnelly,et al. Inference of population structure using multilocus genotype data. , 2000, Genetics.
[68] K. Beven,et al. A physically based, variable contributing area model of basin hydrology , 1979 .