Search Results - "PeerJ (San Francisco, CA)"

A brief introduction to mixed effects modelling and multi-model inference in ecology by Harrison, Xavier A, Donaldson, Lynda, Correa-Cano, Maria Eugenia, Evans, Julian, Fisher, David N, Goodwin, Cecily E D, Robinson, Beth S, Hodgson, David J, Inger, Richard

“…The use of linear mixed effects models (LMMs) is increasingly common in the analysis of biological data. Whilst LMMs offer a flexible approach to modelling a…”
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MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies by Kang, Dongwan D, Li, Feng, Kirton, Edward, Thomas, Ashleigh, Egan, Rob, An, Hong, Wang, Zhong

“…We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent…”
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partR2: partitioning R2 in generalized linear mixed models by Stoffel, Martin A, Nakagawa, Shinichi, Schielzeth, Holger

“…The coefficient of determination R2 quantifies the amount of variance explained by regression coefficients in a linear model. It can be seen as the…”
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Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection by Saçar Demirci, Müserref Duygu, Adan, Aysun

“…MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression found in more than 200 diverse organisms. Although it is still not fully established…”
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VSEARCH: a versatile open source tool for metagenomics by Rognes, Torbjørn, Flouri, Tomáš, Nichols, Ben, Quince, Christopher, Mahé, Frédéric

“…VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide…”
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Hierarchical generalized additive models in ecology: an introduction with mgcv by Pedersen, Eric J, Miller, David L, Simpson, Gavin L, Ross, Noam

“…In this paper, we discuss an extension to two popular approaches to modeling complex structures in ecological data: the generalized additive model (GAM) and…”
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kuenm: an R package for detailed development of ecological niche models using Maxent by Cobos, Marlon E, Peterson, A Townsend, Barve, Narayani, Osorio-Olvera, Luis

“…Ecological niche modeling is a set of analytical tools with applications in diverse disciplines, yet creating these models rigorously is now a challenging…”
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Analyzing mixing systems using a new generation of Bayesian tracer mixing models by Stock, Brian C, Jackson, Andrew L, Ward, Eric J, Parnell, Andrew C, Phillips, Donald L, Semmens, Brice X

“…The ongoing evolution of tracer mixing models has resulted in a confusing array of software tools that differ in terms of data inputs, model assumptions, and…”
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Swarm v2: highly-scalable and high-resolution amplicon clustering by Mahé, Frédéric, Rognes, Torbjørn, Quince, Christopher, de Vargas, Colomban, Dunthorn, Micah

“…Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs),…”
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phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things) by Revell, Liam J

“…Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about…”
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Impact of COVID-19 outbreak on the mental health status of undergraduate medical students in a COVID-19 treating medical college: a prospective longitudinal study by Saraswathi, Ilango, Saikarthik, Jayakumar, Senthil Kumar, K, Madhan Srinivasan, Kumar, Ardhanaari, M, Gunapriya, Raghunath

“…The COVID-19 pandemic is found to affect the mental health of the population. Undergraduate medical students are especially prone to mental health disorders…”
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Random forest as a generic framework for predictive modeling of spatial and spatio-temporal variables by Hengl, Tomislav, Nussbaum, Madlene, Wright, Marvin N, Heuvelink, Gerard B M, Gräler, Benedikt

“…Random forest and similar Machine Learning techniques are already used to generate spatial predictions, but spatial location of points (geography) is often…”
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The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles by Piwowar, Heather, Priem, Jason, Larivière, Vincent, Alperin, Juan Pablo, Matthias, Lisa, Norlander, Bree, Farley, Ashley, West, Jevin, Haustein, Stefanie

“…Despite growing interest in Open Access (OA) to scholarly literature, there is an unmet need for large-scale, up-to-date, and reproducible studies assessing…”
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Factors affecting the composition of the gut microbiota, and its modulation by Hasan, Nihal, Yang, Hongyi

“…Gut microbiota have important functions in the body, and imbalances in the composition and diversity of those microbiota can cause several diseases. The host…”
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The timing mega-study: comparing a range of experiment generators, both lab-based and online by Bridges, David, Pitiot, Alain, MacAskill, Michael R, Peirce, Jonathan W

“…Many researchers in the behavioral sciences depend on research software that presents stimuli, and records response times, with sub-millisecond precision…”
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The impact of artificial intelligence in medicine on the future role of the physician by Ahuja, Abhimanyu S

“…The practice of medicine is changing with the development of new Artificial Intelligence (AI) methods of machine learning. Coupled with rapid improvements in…”
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Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences by Rideout, Jai Ram, He, Yan, Navas-Molina, Jose A, Walters, William A, Ursell, Luke K, Gibbons, Sean M, Chase, John, McDonald, Daniel, Gonzalez, Antonio, Robbins-Pianka, Adam, Clemente, Jose C, Gilbert, Jack A, Huse, Susan M, Zhou, Hong-Wei, Knight, Rob, Caporaso, J Gregory

“…We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on…”
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Continent-wide survey reveals massive decline in African savannah elephants by Chase, Michael J, Schlossberg, Scott, Griffin, Curtice R, Bouché, Philippe J C, Djene, Sintayehu W, Elkan, Paul W, Ferreira, Sam, Grossman, Falk, Kohi, Edward Mtarima, Landen, Kelly, Omondi, Patrick, Peltier, Alexis, Selier, S A Jeanetta, Sutcliffe, Robert

“…African elephants (Loxodonta africana) are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes…”
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SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses by Brown, Jason L, Bennett, Joseph R, French, Connor M

“…SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most…”
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DNA metabarcoding of littoral hardbottom communities: high diversity and database gaps revealed by two molecular markers by Wangensteen Fuentes, Owen Simon, Palacín, Creu, Guardiola, Magdalena, Turon, Xavier

“…Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA…”
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