Recent Publications (2011-Present):
Babonis, L.S., Enjolras, C., Ryan, J.F., Martindale, M.Q. 2022. A novel regulatory gene promotes novel cell fate by suppressing ancestral fate in the sea anemone Nematostella vectensis. Proceedings of the National Academy of Sciences, doi:10.1073/pnas.2113701119
Ortiz, J., Bobkov, Y.V., DeBiasse, M.B., Mitchell, D.G., Edgar, A., Martindale, M.Q., Moss, A.G., Babonis, L.S., Ryan, J.F. 2022. Independent
innexin radiation shaped signaling in ctenophores. bioRxiv, https://doi.org/10.1101/2022.10.11.511657
Tekle, Y.I., Wang, F., Tran, H., Hayes, D., Ryan, J.F. 2022. The Draft Genome of Cochliopodium minus reveals a complete meiosis toolkit and provides insight into the evolution of sexual mechanisms in Amoebozoa. Scientific Reports. doi:10.1038/s41598-022-14131-y
Santander, M.D., Maronna, M.M., Ryan, J.F., da Silva, S.C. 2022. The state of Medusozoa genomics: current evidence and future challenges. GigaScience. doi:10.1093/gigascience/giac036
Ketchum, R.N., Davidson, P.L., Smith, E.G., Wray, G.A., Burt, J.A., Ryan, J.F., Reitzel, A.M. 2022. A chromosomelevel genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes. Genome Biology and Evolution, doi:10.1093/gbe/evac144
Steinworth, B., Martindale, M.Q., Ryan, J.F. 2022. Gene Loss may have Shaped the Cnidarian and Bilaterian Hox and ParaHox Complement. Genome Biology and Evolution, Volume 15, Issue 1, January 2023, evac172, https://doi.org/10.1093/gbe/evac172
Almazan, E.M.P., Ryan, J.F., Rouhana, L. 2021. Regeneration of planarian auricles and reestablishment of chemotactic ability. Frontier in Cell and Developmental Biology. doi:10.3389/fcell.2021.777951
Hernandez, A.M., Ryan, J.F. 2021. Six-state Amino Acid Recoding is not an Effective Strategy to Offset Compositional Heterogeneity and Saturation in Phylogenetic Analyses. Society of Systematic Biologists. doi:10.1093/sysbio/syab027
Medina-Feliciano, J.G., Pirro, S., Garcia-Arraras, J.E., Mashanov, V., Ryan, J.F. 2021. Draft genome of the sea cucumber Holothuria glaberrima, a model for the study of regeneration. Frontiers in Marine Science. doi:10.3389/fmars.2021.603410
Ketchum, R.N., Smith, E.G., DeBiasse, M.B., Vaughan, G.O., McParland, D., Leach, W.B., AlMansoori, N., Ryan, J.F., Burt, J.A., Reitzel, A.M. 2020. Population genomic analysis of a sea urchin across an extreme environmental gradient. Genome Biology and Evolution. 12(10):1819-29.
Kenny, N.J., Francis, W.R., Rivera-Vicéns, R.E., Juravel, K., de Mendoza, A., Díez-Vives, C., Lister, R., Bezares-Calderon, L., Grombacher, L., Roller, M., Barlow, L.D., Camilli, S., Ryan, J.F., Wörheide, G., Hill, A.L., Riesgo, A., Leys, S. 2020. Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. Nature Communications. 11(1):3676.
DeBiasse, M.B., Colgan, W.N., Harris, L., Davidson, B., Ryan, J.F. 2020. Inferring tunicate relationships and the evolution of the tunicate Hox cluster with the genome of Corella inflata. Genome Biology and Evolution. 12(6):948-964.
Moreland, M.T., Nguyen, A.D., Ryan, J.F., Baxevanis, A.D. 2020. The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization. Database (Oxford). 2020:baaa029.
Dardaillon, J., Dauga, D., Simion, P., Faure, E., Onuma, T.A., DeBiasse, M.B., Louis, A., Nitta, K.R., Naville, M., Besnardeau, L., Reeves, Wang, K., Fagotto, M., Guéroult-Bellone, M(g)., Fujiwara, S., Dumollard, R., Veeman, M., Volff, J.N., Roest, Crollius, H., Douzery, E., Ryan, J., Davidson, B., Nishida, H., Dantec, C., Lemaire, P. W. 2020. ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. Nucleic acids research. Jan 8;48(D1):D668-75.
Jiang, J.B., Quattrini, A.M., Francis, W.R., Ryan, J.F., Rodríguez, E., McFadden, C.S. 2019. A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome. GigaScience. Apr;8(4):giz026.
Pastrana, C.C., DeBiasse, M.B., Ryan, J.F. 2019. Sponges lack ParaHox genes. Genome biology and evolution. Apr;11(4):1250-7. Colgan, W., Leanza, A., Hwang, A., DeBiasse, M.B., Llosa, I., Rodrigues, D., Adhikari, H., Corona, G.B., Bock, S., Carillo-Perez, A., Currie, M., Colgan, W., Leanza, A., Hwang, A., DeBiasse, M.B.,
Llosa, I., Rodrigues, D., Adhikari, H., Corona, G.B., Bock, S., Carillo-Perez, A., Currie, M., Darkoa-Larbi, S., Dellal, D., Gutow, H., Hokama, P., Kibby, E., Linhart, N., Moody, S., Naganuma, A., Nguyen, D., Stanton, R., Stark, S., Tumey, C., Velleca, A., Ryan, J.F., Davidson, B. 2019. Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements. EvoDevo. Dec; 10(1):1-7.
Ohdera, A., Ames, C.L., Dikow, R.B., Kayal, E., Chiodin, M., Busby, B., La, S., Pirro, S., Collins, A.G., Medina, M., Ryan, J.F. 2019. Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa). GigaScience. Jul:8(7):giz069.
DeBiasse, M.B., Ryan, J.F. 2019. Phylotocol: Promoting transparency and overcoming bias in phylogenetics. Systematic biology. Jul 1;68(4):672-8.
Dubuc, T.Q., Bobkov, Y., Ryan, J., and Martindale, M.Q. (2018). The radial expression of dorsalventral patterning genes in placozoans, Trichoplax adhaerens, argues for an oral-aboral axis. BioRx, BIORXIV/2018/345777
Debiasse, M.B., Ryan, J.F., Phylotocol: Promoting transparency and overcoming bias in phylogenetics. Systematic Biology. 2018, doi:10.1093/sysbio/syy090
Ketchum, R.N., Debiasse, M.B., Ryan, J.F., Burt, J.A., Reitzel, A.M. The complete mitochondrial genome of the sea urchin, Echinometra sp. EZ. Mitochondrial DNA Part B. 2018, doi:10.1080/23802359.2018.1532335
Hernandez, A.M., Ryan, J.F. (2018). Horizontally transferred genes in the ctenophore Mnemiopsis leidyi. PeerJ,15;6:e5067.
Kayal, E., Bentlage, B., Pankey, M.S., Ohdera, A.H., Medina, M., Plachetzki, D.C., Collins, A.G., Ryan, J.F. (2018). Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits. BMC Evolutionary Biology, 18(1):68.
Sasson, D.A., Jacquez, A.A., Ryan, J.F. (2018). The ctenophore Mnemiopsis leidyi regulates egg production via conspecific communication. BMC ecology, 18(1):12.
Babonis, L.S., DeBiasse, M.B., Francis, W.R., Christianson, L.M., Moss, A.G., Haddock, S.H.D., Martindale, M.Q., Ryan, J.F. Integrating embryonic development and evolutionary history to characterize tentacle-specific cell types in a ctenophore. Molecular Biology and Evolution. 2018, doi:10.1093/molbev/msy171
Haddock, S.H.D., Christianson, L.M., Francis, W.R., Martini, S., Dunn, C.W., Pugh, P.R., Mills, C.E., Osborn, K.J., Seibel, B.A., Choy, C.A., Schnitzler, C.E., Matsumoto, G.I., Messié, M., Schultz, D.T., Winnikoff, J.R., Powers, M.L., Gasca, R., Browne, W.E., Johnsen, S., Schlining, K.L., Thun, S.V., Erwin, B.E., Ryan, J.F.,
Thuesen, E.V. BIODIVERSITY, BEHAVIOR, AND BIOLUMINESCENCE OF DEEP-SEA ORGANISMS. Oceanography.;30(4):38.
Sasson DS & Ryan JF. A reconstruction of sexual modes throughout animal evolution. (2017) BMC Evolutionary Biology, doi:10.1186/s12862-017-1071-3.
Martin-Duran JM*, Ryan JF*, Vellutini BCC, Pang K, and Hejnol A. Increased taxon sampling reveals thousands of hidden orthologs in flatworms. (2017) Genome Research doi:10.1101/gr.216226.116.
Ryan JF, Schnitzler CE, and Tamm SL, (2016) Meeting report of Ctenopalooza: The first international meeting of ctenophorologists. EvoDevo, doi:10.1186/s13227-016-0057-3
Ames CL, Ryan JF, Bely AE, Cartwright P, and Collins AG, (2016) 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. BMC Genomics, doi:10.1186/s12864-016-2944-3
Babonis LS, Martindale MQ, and Ryan JF, (2016) Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis. BMC Evolutionary Biology, 2016, doi:10.1186/s12862-016-0683-3.
Battelle BA, Ryan JF, Kempler K, Spencer S, Marten C, Warren W, Minx P, Montague M, Green P, Schmidt S, Fulton L, Patel N, Protas M, Wilson R, and Porter M. Opsin repertoire and expression patterns in horseshoe crabs: evidence from the genome of Limulus polyphemus. Genome Biology and Evolution, doi:10.1093/gbe/evw100.
Long KA, Nossa CW, Sewell MA, Putnam NH, and Ryan JF. Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis. GigaScience, 2016, doi:10.1186/s13742-016-0125-6.
Sasson DS and Ryan JF. The sex lives of ctenophores: the influence of light, body size, and self-fertilization on the reproductive output of the sea walnut, Mnemiopsis leidyi. PeerJ, 2016, doi.org/10.7717/peerj.1846.
Levin M, Anavy L, Cole AG, Winter E, Mostov N, Khair S, Senderovich N, Kovalev E, Silver DH, Feder M, Fernandez-Valverde SL, Nakanishi N, Simmons D, Simakov O, Larsson T, Liu SY, Jerafi-Vider A, Yaniv K, Ryan JF, Martindale MQ, Rink JC, Arendt D, Degnan SM, Degnan BM, Hashimshony T, & Yanai I. The mid-developmental transition and the evolution of animal body plans. Nature, 2016, doi:10.1038/nature16994.
Zwarycz AS, Nossa CW, Putnam N, & Ryan JF. Timing and scope of genomic expansion within Annelida: evidence from homeoboxes in the genome of the earthworm Eisenia fetida. Genome Biology and Evolution, 2016, doi:10.1093/gbe/evv243.
Ryan JF and Chiodin M. Where is my mind? How sponges and placozoans may have lost neural cell types. Philosophical Transactions of the Royal Society, Series B, 2015, doi:10.1098/rstb.2015.0059.
Dunn CW and Ryan JF. The evolution of animal genomes. Current Opinion in Genetics & Development, 2015, doi:10.1016/j.gde.2015.08.006
Church SH, Ryan JF and Dunn CW. Automation and Evaluation of the SOWH Test of Phylogenetic Topologies with SOWHAT. Systematic Biology 2015 doi:10.1093/sysbio/syv055.
Ryan JF. Did the ctenophore nervous system evolve independently?. Zoology, 2014, doi:10.1016/j.zool.2014.06.001.
Moreland RT, Nguyen AD, Ryan JF, Schnitzler CE, Koch BJ, Siewert K, Wolfsberg TG, Baxevanis AD. A customized Web portal for the genome of the ctenophore Mnemiopsis leidyi. BMC Genomics, 2014 Apr 28;15:316.
GIGA Community of Scientists.
Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes. Journal of Heredity, 2014 Jan-Feb;105(1):1-18.
Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P; NISC Comparative Sequencing Program, Smith SA, Putnam NH, Haddock SH, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD. The Genome of the Ctenophore Mnemiopsis leidyi and its implications on cell type evolution. Science, 2013 Dec 13;342(6164):1242592.
Flot JF, Aury J, Couloux A, Hespeels B, Xiang L, Arkhipova I, Bast J, Danchin E, da Rocha M, da Silva C, Gladyshev E, Gouret P, Hecox-Lea B, Henrissat B, Hejnol A, Manolis K, Kondrashov A, Koszul R, Mark Welch D, Noel B, Piskurek O, Pontarotti P, Ryan JF, Vakhrusheva O, Wincker P, Jaillon O, and Van Doninck K. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature, 2013 Aug 22;500(7463):453-7.
Schnitzler CE, Pang K, Powers M, Reitzel AM, Ryan JF, Simmons D, Tada T, Park M, Gupta J, Brooks SY, Blakesley RW, Yokoyama S, Haddock SHD, Martindale MQ, and Baxevanis AD. Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes. BMC Biology, 2012, Dec 21;10:107.
Maxwell EK, Ryan JF, Schnitzler CE, Browne WE, Baxevanis AD. MicroRNAs and essential components of the microRNA processing machinery are not encoded in the genome of the ctenophore Mnemiopsis leidyi. BMC Genomics, 2012, Dec 20;13:714.
Dubuc TQ*, Ryan JF*, Shinzato C, Satoh N, Martindale MQ. Coral comparative genomics reveal extensive Hox cluster in the cnidarian-bilaterian ancestor. Integrative and Comparative Biology, 2012 Jul 4.
Koch B*, Ryan JF*, Baxevanis AD. The Diversification of the LIM superclass at the Base of the Metazoa Increased Subcellular Complexity and Promoted Multicellular Specialization. PLoS One, 2012 March 15;7(3):e33261.
Kelada SN, Aylor DL, Peck Bailey CE, Ryan JF, Tavarez U, Buus RJ, Miller DR, Chesler EJ, Threadgill DW, Churchill GA, Pardo-Manuel de Villena F, and Collins FS. Genetic Analysis of Hematological Parameters in Incipient Lines of the Collaborative Cross. G3, 2012 Feb; 2:157-165.
Reitzel AM, Ryan JF, Tarrant AM. Establishing a model organism: A report from the first annual Nematostella meeting. Bioessays, 2011 Nov 18.
Pang K, Ryan JF, Baxevanis AD, and Martindale MQ. Evolution of the TGF-β signaling pathway and its potential role in the ctenophore Mnemiopsis leidyi. PLOS One, 2011 Sep 8;6(9):e24152.
Pett W, Ryan JF, Pang K, NISC Comparative Sequencing Program, Martindale MQ, Mullikin J, Baxevanis AD, and Lavrov D. Extreme Mitochondrial Genome Evolution in the Ctenophore Mnemiopsis leidyi. Mitochondrial DNA, 2011 Aug;22(4):130-42.
Reitzel AM, Pang K, Ryan JF, Mullikin JC, Baxevanis AD, Martindale MQ, and Tarrant AM. 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? BMC Evodevo, 2011, Feb 3;2(1):3.
Hurle B, Marques-Bonet T, Antonacci F, Hughes I, Ryan JF, NISC Comparative Sequencing Program, Eichler EE, Ornitz DM, and Green ED. Lineage-Specific Evolution of the Vertebrate Otopetrin Gene Family Revealed by Comparative Genomic Analyses. BMC Evolutionary Biology, 2011, Jan 24;11(1):23.