Joseph F. Ryan
Whitney Laboratory for Marine Bioscience
GeneGenomeGeneticsEvolutionary biologyBiology
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Publications 69
#1Joshua G Medina-Feliciano (UPR-RP: University of Puerto Rico, Río Piedras)
#2Stacy PirroH-Index: 3
Last. Joseph F. Ryan (Whitney Laboratory for Marine Bioscience)H-Index: 25
view all 5 authors...
Regeneration is one of the most fascinating and yet least understood processes of animals. Echinoderms, one of the closest related invertebrate groups to humans, can contribute to our understanding of the genetic basis of regenerative processes. Amongst echinoderms, sea cucumbers have the ability to grow back most of their body parts following injury, including the intestine and nervous tissue. The cellular and molecular events underlying these abilities in sea cucumbers have been most extensive...
#1Melissa B. DeBiasse (Whitney Laboratory for Marine Bioscience)H-Index: 9
#2William N Colgan (Swarthmore College)
Last. Joseph F. Ryan (Whitney Laboratory for Marine Bioscience)H-Index: 25
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Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Towards this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, "inflated" atrial chamber. Combin...
#1Nathan J. Kenny (Natural History Museum)H-Index: 13
#2Warren R. Francis (University of Southern Denmark)H-Index: 10
Last. Maša Roller (EMBL-EBI: European Bioinformatics Institute)H-Index: 4
view all 17 authors...
The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits such as nervous systems arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here we present its 326 Mbp genome, assembled to high contiguity (N50: 9.88 Mbp) with 23 chromosomes on 24 scaffolds. Our an...
#1Moreland Rt (NIH: National Institutes of Health)
#1R. Travis Moreland (NIH: National Institutes of Health)H-Index: 6
Last. Andreas D. Baxevanis (NIH: National Institutes of Health)H-Index: 43
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: Following the completion of the genome sequencing and gene prediction of Mnemiopsis leidyi, a lobate ctenophore that is native to the coastal waters of the western Atlantic Ocean, we developed and implemented the Mnemiopsis Genome Project Portal (MGP Portal), a comprehensive Web-based data portal for navigating the genome sequence and gene annotations. In the years following the first release of the MGP Portal, it has become evident that the inclusion of data from significant published studies...
1 CitationsSource
#1Justine Dardaillon (University of Montpellier)H-Index: 2
#2Delphine DaugaH-Index: 6
Last. Patrick Lemaire (University of Montpellier)H-Index: 44
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ANISEED ( is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression pro...
#1Michal Levin (Technion – Israel Institute of Technology)H-Index: 7
#2Leon Anavy (Technion – Israel Institute of Technology)H-Index: 6
Last. Itai Yanai (Technion – Israel Institute of Technology)H-Index: 34
view all 26 authors...
In this Letter, affiliation number 1 was incorrectly listed as ‘Department of Biology, Technion – Israel Institute of Technion, Haifa 32000, Israel’ instead of ‘Department of Biology, Technion- Israel Institute of Technology, Haifa 32000, Israel’. The original Letter has not been corrected.
#1William N Colgan (Broad Institute)
#1William Colgan (Broad Institute)
Last. Brad Davidson (Swarthmore College)H-Index: 21
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Background Mutations in gene regulatory networks often lead to genetic divergence without impacting gene expression or developmental patterning. The rules governing this process of developmental systems drift, including the variable impact of selective constraints on different nodes in a gene regulatory network, remain poorly delineated.
#1Alexandra M. Hernandez (UF: University of Florida)H-Index: 1
#2Joseph F. Ryan (UF: University of Florida)H-Index: 25
Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of 6-state recoding approaches by comparing the performance of analyses on recoded and non-recoded datasets that have been simulated under gradients of compositional heterogen...
3 CitationsSource
#1Melissa B. DeBiasse (UF: University of Florida)H-Index: 9
#2Joseph F. Ryan (UF: University of Florida)H-Index: 25
The integrity of science requires that the process be based on sound experimental design and objective methodology. Strategies that increase reproducibility and transparency in science protect this integrity by reducing conscious and unconscious biases. Given the large number of analysis options and the constant development of new methodologies in phylogenetics, this field is one that would particularly benefit from more transparent research design. Herein, we introduce phylotocol (fi lō ’ta kol...
2 CitationsSource
#1Aki Ohdera (PSU: Pennsylvania State University)H-Index: 5
#2Cheryl Lewis Ames (National Museum of Natural History)H-Index: 6
Last. Joseph F. Ryan (UF: University of Florida)H-Index: 25
view all 11 authors...
BACKGROUND: Anthozoa, Endocnidozoa, and Medusozoa are the 3 major clades of Cnidaria. Medusozoa is further divided into 4 clades, Hydrozoa, Staurozoa, Cubozoa, and Scyphozoa-the latter 3 lineages make up the clade Acraspeda. Acraspeda encompasses extraordinary diversity in terms of life history, numerous nuisance species, taxa with complex eyes rivaling other animals, and some of the most venomous organisms on the planet. Genomes have recently become available within Scyphozoa and Cubozoa, but t...