Explanipedia

Global distribution patterns of an ocean-surface dwelling animal are associated with organismal mirror asymmetry Open

Tom Iwanicki, Nikolai Maximenko, Casey W. Dunn, Samuel H. Church, Deborah Goodwin , et al. · 2025

Organismal mirror asymmetry is common in nature, where an individual may have either a left- or right-handed form; however, the causes and consequences of this asymmetry have long fascinated and perplexed biologists. The cnidarian by-the-w…

Examination of Germline and Somatic Intercellular Bridges in <i>Hydra vulgaris</i> Reveals Insights into the Evolutionarily Conserved Mechanism of Intercellular Bridge Formation Open

Kari L. Price, Dyuthi M. Tharakan, Willi Salvenmoser, Kathleen Ayers, Jennifer Mah , et al. · 2025

Incomplete cytokinesis results in the formation of stable intercellular bridges that have been extensively studied in bilaterians, where they play essential roles in cell-cell communication and coordination of differentiation. However, lit…

From surfacing to stranding: The origins and dispersal dynamics of a neustonic siphonophore Open

River B. Abedon, Mary Beth Decker, Casey W. Dunn, Samuel H. Church · 2025

The siphonophore Physalia physalis regularly strands along the US East Coast, yet the dynamics driving its seasonal and geographic distribution in this region remain poorly understood. Building on a new understanding of Physalia population…

Correction: Zooid arrangement and colony growth in Porpita porpita Open

Kohei Oguchi, Akiteru Maeno, Keita Yoshida, Gaku Yamamoto, Hisanori Kohtsuka , et al. · 2025

Zooid arrangement and colony growth in Porpita porpita Open

Kohei Oguchi, Akiteru Maeno, Keita Yoshida, Gaku Yamamoto, Hisanori Kohtsuka , et al. · 2025

Background The blue button, Porpita porpita (Porpitidae), is a highly integrated colonial animal—i.e., a superorganism. It has multiple genetically identical bodies (zooids) that arise from the same embryo and are functionally specialized …

Population genomics of a sailing siphonophore reveals genetic structure in the open ocean Open

Samuel H. Church, River B. Abedon, Namrata Ahuja, Colin J. Anthony, Dalila Destanović , et al. · 2025

The open ocean is a vast, highly connected environment, and the organisms found there have been hypothesized to represent massive, well-mixed populations. Of these, the man-o'-war or bluebottle (Physalia) is uniquely suited to long-distanc…

A Chromosome-Scale Genome of Nanomia septata Reveals Extensive Rearrangement But No Clear Driver of the Unique Colony-Level Organization of Siphonophores Open

Namrata Ahuja, Darrin T. Schultz, Dalila Destanović, Samuel H. Church, Natasha Picciani , et al. · 2025

Siphonophores (Cnidaria:Hydrozoa) are pelagic colonial marine invertebrates with many highly specialized bodies (zooids) within a single colony. Their unique biology and ecological importance have made them of particular interest. Recent w…

Examination of germline and somatic intercellular bridges in <i>Hydra vulgaris</i> reveals insights into the evolutionarily conserved mechanism of intercellular bridge formation Open

Kari L. Price, Dyuthi M. Tharakan, Willi Salvenmoser, Kathleen Ayers, Jennifer Mah , et al. · 2025

Incomplete cytokinesis results in the formation of stable intercellular bridges that have been extensively studied in bilaterians, where they play essential roles in cell-cell communication and coordination of differentiation. However, lit…

Global Genomics of Man-O'-War (Physalia) Reveals Ocean Surface Biodiversity Open

Samuel H. Church, River B. Abedon, Namrata Ahuja, Colin J. Anthony, Dalila Destanović , et al. · 2025

Physalia gonodendra are not yet sexually mature when released Open

Kohei Oguchi, Gaku Yamamoto, Hisanori Kohtsuka, Casey W. Dunn · 2024

The blue bottle genus Physalia is one of the well-known siphonophore belonging to the Cnidaria, Hydrozoa. Physalia is also known as a ferocious predator, occasionally stinging and fatally wounding humans, but key details of its life cycle …

Prospective Evaluation of Routine Statewide Integration of Molecular Epidemiology and Contact Tracing to Disrupt Human Immunodeficiency Virus Transmission Open

Rami Kantor, Jon A. Steingrimsson, John P Fulton, Vladimir Novitsky, Mark Howison , et al. · 2024

Background Human immunodeficiency virus (HIV) remains a global challenge and novel measures for transmission disruption are needed. Contact tracing is limited by reluctance or inability of newly diagnosed individuals to name at-risk contac…

Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells Open

Samuel H. Church, Jasmine L. Mah, Casey W. Dunn · 2024

Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons evoke evolutionary histories, as d…

Vertical trophic structure and niche partitioning of gelatinous predators in a pelagic food web: Insights from stable isotopes of siphonophores Open

Elizabeth D. Hetherington, Hilary G. Close, Steven H. D. Haddock, Alejandro Damian‐Serrano, Casey W. Dunn , et al. · 2024

Gelatinous zooplankton are increasingly recognized as key components of pelagic ecosystems, and there have been many recent insights into their ecology and roles in food webs. To examine the trophic ecology of siphonophores (Cnidaria, Hydr…

Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores Open

Namrata Ahuja, Xuwen Cao, Darrin T. Schultz, Natasha Picciani, Arianna Lord , et al. · 2024

Siphonophores (Cnidaria: Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fr…

Referee report. For: The genome sequence of a hydroid, Candelabrum cocksii (Cocks, 1854) [version 1; peer review: 2 approved] Open

Casey W. Dunn · 2024

2899. Integrating HIV Partner Services and Molecular Epidemiology Data to Enhance HIV Transmission Disruption in Rhode Island: Findings from a Public Health-Academic Partnership Open

Aditya Khanna, Vladimir Novitsky, August Guang, Mark Howison, Fizza S. Gillani , et al. · 2023

Background HIV remains a significant public health concern. Both contact tracing (identifying and notifying partners of people diagnosed with HIV) and molecular epidemiology (phylogenetic inference and cluster detection), are used to disru…

Unification of species, gene, and cell trees for single-cell expression analyses Open

Samuel H. Church, Jasmine L. Mah, Casey W. Dunn · 2023

Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as …

Reconstructing cell type evolution across species through cell phylogenies of single-cell RNAseq data Open

Jasmine L. Mah, Casey W. Dunn · 2023

The origin and evolution of cell types has emerged as a key topic in evolutionary biology. Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type evolution have largely been limited to pairwise comparisons …

Giants among Cnidaria: large nuclear genomes and rearranged mitochondrial genomes in siphonophores Open

Namrata Ahuja, Xuwen Cao, Darrin T. Schultz, Natasha Picciani, Arianna Lord , et al. · 2023

Siphonophores (Cnidaria:Hydrozoa) are abundant predators found throughout the ocean and are important components in worldwide zooplankton. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and dif…

An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic Open

Mark Howison, Fizza S. Gillani, Vlad Novitsky, Jon A. Steingrimsson, John P Fulton , et al. · 2023

Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a co…

The evolution of ovary-biased gene expression in Hawaiian Drosophila Open

Samuel H. Church, Catriona Munro, Casey W. Dunn, Cassandra G. Extavour · 2023

With detailed data on gene expression accessible from an increasingly broad array of species, we can test the extent to which our developmental genetic knowledge from model organisms predicts expression patterns and variation across specie…

Integrating HIV Cluster Analysis in Routine Public Health Prevention Efforts: Lessons Learned from a Statewide Public Health – Academic Partnership Open

John P Fulton, Vladimir Novitsky, Fizza S. Gillani, August Guang, Jon A. Steingrimsson , et al. · 2023

Not all clusters are equal: dynamics of molecular HIV-1 clusters in a statewide Rhode Island epidemic Open

Vlad Novitsky, Jon A. Steingrimsson, Mark Howison, Casey W. Dunn, Fizza S. Gillani , et al. · 2022

Objectives: Molecular epidemiology is a powerful tool to characterize HIV epidemics and prioritize public health interventions. Typically, HIV clusters are assumed to have uniform patterns over time. We hypothesized that assessment of clus…

Normalizing need not be the norm: count-based math for analyzing single-cell data Open

Samuel H. Church, Jasmine L. Mah, Günter P. Wagner, Casey W. Dunn · 2022

Counting transcripts of mRNA is a key method of observation in modern biology. With advances in counting transcripts in single cells (single-cell RNA sequencing or scRNA-seq), these data are routinely used to identify cells by their transc…

Characterizing the secret diets of siphonophores (Cnidaria: Hydrozoa) using DNA metabarcoding Open

Alejandro Damian‐Serrano, Elizabeth D. Hetherington, C. Anela Choy, Steven H. D. Haddock, A. A. Lapides , et al. · 2022

Siphonophores (Cnidaria: Hydrozoa) are abundant and diverse gelatinous predators in open-ocean ecosystems. Due to limited access to the midwater, little is known about the diets of most deep-dwelling gelatinous species, which constrains ou…

Beyond HIV outbreaks: protocol, rationale and implementation of a prospective study quantifying the benefit of incorporating viral sequence clustering analysis into routine public health interventions Open

Jon A. Steingrimsson, John P Fulton, Mark Howison, Vlad Novitsky, Fizza S. Gillani , et al. · 2022

Introduction HIV continues to have great impact on millions of lives. Novel methods are needed to disrupt HIV transmission networks. In the USA, public health departments routinely conduct contact tracing and partner services and interview…

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses Open

August Guang, Mark Howison, Lauren Ledingham, Matthew D’Antuono, Philip A. Chan , et al. · 2022

Background Phylogenetic analyses of HIV sequences are used to detect clusters and inform public health interventions. Conventional approaches summarize within-host HIV diversity with a single consensus sequence per host of the pol gene, ob…

Integrating siphonophores into marine food‐web ecology Open

Elizabeth D. Hetherington, Alejandro Damian‐Serrano, Steven H. D. Haddock, Casey W. Dunn, C. Anela Choy · 2022

Siphonophores are a clade of understudied colonial hydrozoans (Cnidaria) that are abundant predators in oceanic ecosystems, with species present across the water column. We (1) synthesize current knowledge about siphonophore trophic ecolog…

Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora Open

Catriona Munro, Felipe Zapata, Mark Howison, Stefan Siebert, Casey W. Dunn · 2022

Siphonophores are complex colonial animals, consisting of asexually produced bodies (zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional special…

Statewide Longitudinal Trends in Transmitted HIV-1 Drug Resistance in Rhode Island, USA Open

Vlad Novitsky, Jon A. Steingrimsson, Fizza S. Gillani, Mark Howison, Su Aung , et al. · 2021

Background HIV-1 transmitted drug resistance (TDR) remains a global challenge that can impact care, yet its comprehensive assessment is limited and heterogenous. We longitudinally characterized statewide TDR in Rhode Island. Methods Demogr…

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