David S. Clausen
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View article: Estimating Fold Changes from Partially Observed Outcomes with Applications in Microbial Metagenomics
Estimating Fold Changes from Partially Observed Outcomes with Applications in Microbial Metagenomics Open
We consider the problem of estimating fold-changes in the expected value of a multivariate outcome observed with unknown sample-specific and category-specific perturbations. This challenge arises in high-throughput sequencing studies of th…
View article: happi: a hierarchical approach to pangenomics inference
happi: a hierarchical approach to pangenomics inference Open
Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorgan…
View article: happi v0.8.7
happi v0.8.7 Open
This is happi version 0.8.7 which marks the version of happi at the time of manuscript acceptance. This is a static identifier for the version of the software used to produce the manuscript results.
View article: happi: a hierarchical approach to pangenomics inference
happi: a hierarchical approach to pangenomics inference Open
This contains supplementary materials, code, and data needed to reproduce the analyses and figures in the happi manuscript. You can also find more information on our GitHub page: https://github.com/statdivlab/happi_supplementary or the mai…
View article: Evaluating replicability in microbiome data.
Evaluating replicability in microbiome data. Open
High-throughput sequencing is widely used to study microbial communities. However, choice of laboratory protocol is known to affect the resulting microbiome data, which has an unquantified impact on many comparisons between communities of …
View article: Within-city variation in ambient carbon monoxide concentrations: Leveraging low-cost monitors in a spatiotemporal modeling framework
Within-city variation in ambient carbon monoxide concentrations: Leveraging low-cost monitors in a spatiotemporal modeling framework Open
Exposure to ambient carbon monoxide (CO) may be associated with cardiovascular disease outcomes based on human and animal experimental evidence, but current epidemiologic research is limited. The number and distribution of ground-level reg…
View article: Within-City Variation in Ambient Carbon Monoxide Concentrations: Leveraging Low-Cost Monitors in a Spatiotemporal Modeling Framework
Within-City Variation in Ambient Carbon Monoxide Concentrations: Leveraging Low-Cost Monitors in a Spatiotemporal Modeling Framework Open
The three novel parameters did not substantially improve model performance, suggesting that, on its own, our spatiotemporal modeling framework based on geographic features was reliable and robust. As low-cost air monitors become increasing…
View article: happi: a Hierarchical Approach to Pangenomics Inference
happi: a Hierarchical Approach to Pangenomics Inference Open
Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorgan…
View article: Modeling complex measurement error in microbiome experiments to estimate relative abundances and detection effects
Modeling complex measurement error in microbiome experiments to estimate relative abundances and detection effects Open
Accurate estimates of microbial species abundances are needed to advance our understanding of the role that microbiomes play in human and environmental health. However, artificially constructed microbiomes demonstrate that intuitive estima…
View article: Evaluating replicability in microbiome data
Evaluating replicability in microbiome data Open
Summary High-throughput sequencing is widely used to study microbial communities. However, choice of laboratory protocol is known to affect the resulting microbiome data, which has an unquantified impact on many comparisons between communi…
View article: Segment number threshold determines juvenile onset of germline cluster expansion in <i>Platynereis dumerilii</i>
Segment number threshold determines juvenile onset of germline cluster expansion in <i>Platynereis dumerilii</i> Open
Development of sexual characters and generation of gametes are tightly coupled with growth. Platynereis dumerilii is a marine annelid that has been used to study germline development and gametogenesis. P. dumerilii has germ cell clusters f…
View article: Author response for "Segment number threshold determines juvenile onset of germline cluster expansion in Platynereis dumerilii"
Author response for "Segment number threshold determines juvenile onset of germline cluster expansion in Platynereis dumerilii" Open
View article: Segment number threshold determines juvenile onset of germline cluster proliferation in<i>Platynereis dumerilii</i>
Segment number threshold determines juvenile onset of germline cluster proliferation in<i>Platynereis dumerilii</i> Open
Many animals rely on sexual reproduction to propagate by using gametes (oocytes and sperm). Development of sexual characters and generation of gametes are tightly coupled with the growth of an organism. Platynereis dumerilii is a marine se…
View article: A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants
A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants Open
Transcriptomic analyses from across eukaryotes indicate that most of the genome is transcribed at some point in the developmental trajectory of an organism. One class of these transcripts is termed long intergenic noncoding RNAs (lincRNAs)…