Ryan, Joseph F.

The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

Ryan, J. F., Pang, K., Schnitzler, C. E., Nguyen, A.-D., Moreland, R. T., Simmons, D. K., Koch, B. J., Francis, W. R., Havlak, P., Program, N. C. S., et al. (2013) · Science

Marine Invertebrate Physiology and EcologyDevelopmental Biology and Gene Regulation

Cited by 682

Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits

Kayal, E., Bentlage, B., Sabrina Pankey, M., Ohdera, A. H., Medina, M., Plachetzki, D. C., Collins, A. G., & Ryan, J. F. (2018) · BMC Evolutionary Biology

Marine Invertebrate Physiology and EcologyGenomics and Phylogenetic Studies

Cited by 255

The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa

Ryan, J. F., Pang, K., Program, N. C. S., Mullikin, J. C., Martindale, M. Q., & Baxevanis, A. D. (2010) · EvoDevo

Marine Invertebrate Physiology and EcologyDevelopmental Biology and Gene Regulation

Cited by 160

Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes

Schnitzler, C. E., Pang, K., Powers, M. L., Reitzel, A. M., Ryan, J. F., Simmons, D., Tada, T., Park, M., Gupta, J., Brooks, S. Y., et al. (2012) · BMC Biology

bioluminescence and chemiluminescence researchMarine Invertebrate Physiology and Ecology

Cited by 132

Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

Kenny, N. J., Francis, W. R., Rivera-Vicéns, R. E., Juravel, K., de Mendoza, A., Díez-Vives, C., Lister, R., Bezares-Calderón, L. A., Grombacher, L., Roller, M., et al. (2020) · Nature Communications

Marine Invertebrate Physiology and EcologyGenomics and Phylogenetic Studies

Cited by 129

Genomic insights into Wnt signaling in an early diverging metazoan, the ctenophore Mnemiopsis leidyi

Pang, K., Ryan, J. F., Program, N. C. S., Mullikin, J. C., Baxevanis, A. D., & Martindale, M. Q. (2010) · EvoDevo

Developmental Biology and Gene RegulationMarine Invertebrate Physiology and Ecology

Cited by 115

Evolution of the TGF-β Signaling Pathway and Its Potential Role in the Ctenophore, Mnemiopsis leidyi

Pang, K., Ryan, J. F., Baxevanis, A. D., & Martindale, M. Q. (2011) · PLoS ONE

Developmental Biology and Gene RegulationMarine Invertebrate Physiology and Ecology

Cited by 93

Where is my mind? How sponges and placozoans may have lost neural cell types

Ryan, J. F., & Chiodin, M. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences

Marine Invertebrate Physiology and EcologyMarine Sponges and Natural Products

Cited by 73

A new transcriptome and transcriptome profiling of adult and larval tissue in the box jellyfish Alatina alata: an emerging model for studying venom, vision and sex

Lewis Ames, C., Ryan, J. F., Bely, A. E., Cartwright, P., & Collins, A. G. (2016) · BMC Genomics

Marine Invertebrate Physiology and EcologyGenomics and Phylogenetic Studies

Cited by 63

Did the ctenophore nervous system evolve independently?

Ryan, J. F. (2014) · Zoology

Marine Invertebrate Physiology and EcologyDevelopmental Biology and Gene Regulation

Cited by 55

Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses

Hernandez, A. M., & Ryan, J. F. (2019) · Systematic Biology

Genomics and Phylogenetic StudiesRNA and protein synthesis mechanisms

Cited by 52

Automation and evaluation of the SOWH Test with SOWHAT

Church, S. H., Ryan, J. F., & Dunn, C. W. (2015) · Systematic Biology

Genomics and Phylogenetic StudiesEvolution and Paleontology Studies

Cited by 50

Nuclear receptors from the ctenophore Mnemiopsis leidyi lack a zinc-finger DNA-binding domain: lineage-specific loss or ancestral condition in the emergence of the nuclear receptor superfamily?

Reitzel, A. M., Pang, K., Ryan, J. F., Mullikin, J. C., Martindale, M. Q., Baxevanis, A. D., & Tarrant, A. M. (2011) · EvoDevo

Marine Invertebrate Physiology and EcologyDevelopmental Biology and Gene Regulation

Cited by 36

Baa.pl: A tool to evaluate de novo genome assemblies with RNA transcripts

Ryan, J. F. (2013) · arXiv

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 12