Category: Papers by CGEB labs

TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets

STAR Protoc. 2022 Feb 15;3(1):101175. doi: 10.1016/j.xpro.2022.101175. eCollection 2022 Mar 18. ABSTRACT Various bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semiautomated pipeline that allows both coarse and fine-scale tuning of large protein sequence …

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Novel Application of Survival Models for Predicting Microbial Community Transitions with Variable Selection for Environmental DNA

Survival analysis is a prolific statistical tool in medicine for inferring risk and time to disease-related events. However, it is underutilized in microbiome research to predict microbial community-mediated events, partly due to the sparsity and high-dimensional nature of the data. We advance the application of Cox proportional hazards (Cox PH) survival models to environmental DNA …

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Novel application of survival models for predicting microbial community transitions with variable selection for eDNA

Appl Environ Microbiol. 2022 Feb 9:AEM0214621. doi: 10.1128/AEM.02146-21. Online ahead of print. ABSTRACT Survival analysis is a prolific statistical tool in medicine for inferring risk and time to disease-related events. However, it is under-utilized in microbiome research to predict microbial community mediated events, partly due to the sparsity and high dimensional nature of the data. …

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Evolution of amino acid propensities under stability-mediated epistasis

Mol Biol Evol. 2022 Feb 4:msac030. doi: 10.1093/molbev/msac030. Online ahead of print. ABSTRACT Site-specific amino acid preferences are influenced by the genetic background of the protein. The preferences for resident amino acids are expected to, on average, increase over time because of replacements at other sites – a nonadaptive phenomenon referred to as the ‘evolutionary …

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Author Correction: Microbiome differential abundance methods produce different results across 38 datasets

Nat Commun. 2022 Feb 3;13(1):777. doi: 10.1038/s41467-022-28401-w. NO ABSTRACT PMID:35115546 | DOI:10.1038/s41467-022-28401-w

Standards recommendations for the Earth BioGenome Project

Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115639118. doi: 10.1073/pnas.2115639118. ABSTRACT A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer …

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Why sequence all eukaryotes?

Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115636118. doi: 10.1073/pnas.2115636118. ABSTRACT Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there …

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The Earth BioGenome Project 2020: Starting the clock

Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115635118. doi: 10.1073/pnas.2115635118. NO ABSTRACT PMID:35042800 | DOI:10.1073/pnas.2115635118

Microbiome differential abundance methods produce different results across 38 datasets

Nat Commun. 2022 Jan 17;13(1):342. doi: 10.1038/s41467-022-28034-z. ABSTRACT Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale studies systematically exploring the appropriateness of using these tools interchangeably, and the scale and significance of the differences between them. …

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Microbiota of Crassostrea virginica larvae during a hatchery crash and under normal production: Amplicon sequence data

Data Brief. 2021 Dec 23;40:107755. doi: 10.1016/j.dib.2021.107755. eCollection 2022 Feb. ABSTRACT We present oyster larval microbiota from two feeding studies, in which wild type and low-salinity tolerant lines were either fed or starved. In one study, all larvae unexpectedly died, which was concurrent with an event in which all larvae in an adjoining oyster hatchery …

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