Benjamin D. Kaehler
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Neutral mutation disequilibrium is common in prokaryotes and animals Open
Widely used models of sequence evolution assume DNA sequences are at equilibrium with respect to the processes that drive divergence, mutation and natural selection. Violations of this assumption have been shown to affect the conclusions f…
Network based differential abundance analysis: bridging community interactions and host microbiome dynamics Open
Differential abundance analysis is a critical task in microbiome research, aiming to identify microbial features (e.g., Amplicon Sequence Variant (ASV), Operational Taxonomic Unit (OTU), taxa) that vary across conditions. Despite significa…
New insights from modelling studies and molecular dynamics simulations of the <span>DI<sub>S5‐S6</sub></span> extracellular linker of the skeletal muscle sodium channel <i>NaV1.4</i> Open
In the CryoEM‐structure of the hSkMNaV1.4 ion channel (PDB:6AGF), the 59‐residue DI S5‐S6 linker peptide was omitted due to absence of electron density. This peptide is intriguing – comprised of unique sequence and found only in mammalian …
The Inherited Rate Matrix algorithm for phylogenetic model selection for non-stationary Markov processes Open
In phylogenetic reconstruction, substitution models that assume nucleotide frequencies do not change through time are in very widespread use. DNA sequences can exhibit marked compositional difference. Such compositional heterogeneity impli…
Silva 138.1 taxonomy classifiers for use with QIIME 2 q2-feature-classifier Open
Uniform and weighted naive Bayes classifiers trained on Silva 138.1 data for use with QIIME 2 q2-feature-classifier. full-length-average-classifier.qza and 515f-806r-average-classifier.qza are classifiers using weights averaged across 14 E…
Silva 138.1 taxonomy classifiers for use with QIIME 2 q2-feature-classifier Open
Uniform and weighted naive Bayes classifiers trained on Silva 138.1 data for use with QIIME 2 q2-feature-classifier. full-length-average-classifier.qza and 515f-806r-average-classifier.qza are classifiers using weights averaged across 14 E…
RESCRIPt: Reproducible sequence taxonomy reference database management Open
Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys. Repr…
View article: Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops Open
In October of 2020, in response to the Coronavirus Disease 2019 (COVID-19) pandemic, our team hosted our first fully online workshop teaching the QIIME 2 microbiome bioinformatics platform. We had 75 enrolled participants who joined from a…
Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences Open
Naive Bayes classifiers (NBC) have dominated the field of taxonomic classification of amplicon sequences for over a decade. Apart from having runtime requirements that allow them to be trained and used on modest laptops, they have persiste…
The inherited rate matrix algorithm for phylogenetic model selection for non-stationary Markov processes Open
all the data, results and analysis scripts
Beating Naive Bayes at Taxonomic Classification Open
QIIME 2 Artifacts containing microbiome samples, organised by EMPO 3 classification. Downloaded from Qiita.
Beating Naive Bayes at Taxonomic Classification Open
QIIME 2 Artifacts containing microbiome samples, organised by EMPO 3 classification. Downloaded from Qiita.
Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods Open
Microbiomes are integral components of diverse ecosystems, and increasingly recognized for their roles in the health of humans, animals, plants, and other hosts. Given their complexity (both in composition and function), the effective stud…
Species abundance information improves sequence taxonomy classification accuracy Open
Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which th…
redbiom: a Rapid Sample Discovery and Feature Characterization System Open
Although analyses that combine many microbiomes at the whole-community level have become routine, searching rapidly for microbiomes that contain a particular sequence has remained difficult. The software we present here, redbiom, dramatica…
Species-level microbial sequence classification is improved by source-environment information Open
Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which th…
Species abundance information improves sequence taxonomy classification accuracy - HMP and NCBI data Open
Data used to test q2-clawback using taxonomic weights derived from shotgun sequencing experiments. Includes reference sequences and taxonomies derived from the NCBI RefSeq database[1] and paired amplicon and shotgun sequencing results down…
Species abundance information improves sequence taxonomy classification accuracy - HMP and NCBI data Open
Data used to test q2-clawback using taxonomic weights derived from shotgun sequencing experiments. Includes reference sequences and taxonomies derived from the NCBI RefSeq database[1] and paired amplicon and shotgun sequencing results down…
Species abundance information improves sequence taxonomy classification accuracy - Qiita data Open
QIIME 2 Artifacts containing microbiome samples, organised by EMPO 3 classification. Used to test q2-clawback. Downloaded from Qiita. Draws from the following Qiita study ids: 11113[1], 11444, 1716, 10369[2], 990[3], 2080, 1713, 894, 1289,…
Species abundance information improves sequence taxonomy classification accuracy - Qiita data Open
QIIME 2 Artifacts containing microbiome samples, organised by EMPO 3 classification. Used to test q2-clawback. Downloaded from Qiita. Draws from the following Qiita study ids: 11113[1], 11444, 1716, 10369[2], 990[3], 2080, 1713, 894, 1289,…
View article: QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science Open
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will driv…
View article: QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science Open
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will driv…
View article: QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science Open
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will driv…
q2-sample-classifier: machine-learning tools for microbiome classification and regression Open
q2-sample-classifier is a plugin for the QIIME 2 microbiome bioinformatics platform that facilitates access, reproducibility, and interpretation of supervised learning (SL) methods for a broad audience of non-bioinformatics specialists.
Did aculeate silk evolve as an antifouling material? Open
Many of the challenges we currently face as an advanced society have been solved in unique ways by biological systems. One such challenge is developing strategies to avoid microbial infection. Social aculeates (wasps, bees and ants) mitiga…
Species abundance information improves sequence taxonomy classification accuracy Open
Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which th…