| Year |
Citation |
Score |
| 2024 |
Mitchell DG, Edgar A, Mateu JR, Ryan JF, Martindale MQ. The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor. Communications Biology. 7: 203. PMID 38374160 DOI: 10.1038/s42003-024-05901-7 |
0.594 |
|
| 2023 |
Rouhana L, Edgar A, Hugosson F, Dountcheva V, Martindale MQ, Ryan JF. Cytoplasmic polyadenylation is an ancestral hallmark of early development in animals. Molecular Biology and Evolution. PMID 37288606 DOI: 10.1093/molbev/msad137 |
0.598 |
|
| 2023 |
Babonis LS, Enjolras C, Reft AJ, Foster BM, Hugosson F, Ryan JF, Daly M, Martindale MQ. Single-cell atavism reveals an ancient mechanism of cell type diversification in a sea anemone. Nature Communications. 14: 885. PMID 36797294 DOI: 10.1038/s41467-023-36615-9 |
0.505 |
|
| 2023 |
Ortiz J, Bobkov YV, DeBiasse MB, Mitchell DG, Edgar A, Martindale MQ, Moss AG, Babonis LS, Ryan JF. Independent innexin radiation shaped signaling in ctenophores. Molecular Biology and Evolution. PMID 36740225 DOI: 10.1093/molbev/msad025 |
0.597 |
|
| 2022 |
Steinworth BM, Martindale MQ, Ryan JF. Gene loss may have shaped the cnidarian and bilaterian Hox and ParaHox complement. Genome Biology and Evolution. PMID 36508343 DOI: 10.1093/gbe/evac172 |
0.62 |
|
| 2022 |
Ketchum RN, Davidson PL, Smith EG, Wray GA, Burt JA, Ryan JF, Reitzel AM. A chromosome-level 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. PMID 36161313 DOI: 10.1093/gbe/evac144 |
0.692 |
|
| 2022 |
Tekle YI, Wang F, Tran H, Hayes TD, Ryan JF. The draft genome of Cochliopodium minus reveals a complete meiosis toolkit and provides insight into the evolution of sexual mechanisms in Amoebozoa. Scientific Reports. 12: 9841. PMID 35701521 DOI: 10.1038/s41598-022-14131-y |
0.361 |
|
| 2022 |
Santander MD, Maronna MM, Ryan JF, Andrade SCS. The state of Medusozoa genomics: current evidence and future challenges. Gigascience. 11. PMID 35579552 DOI: 10.1093/gigascience/giac036 |
0.356 |
|
| 2022 |
Babonis LS, Enjolras C, Ryan JF, Martindale MQ. A novel regulatory gene promotes novel cell fate by suppressing ancestral fate in the sea anemone . Proceedings of the National Academy of Sciences of the United States of America. 119: e2113701119. PMID 35500123 DOI: 10.1073/pnas.2113701119 |
0.487 |
|
| 2020 |
Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderón LA, Grombacher L, Roller M, Barlow LD, Camilli S, Ryan JF, Wörheide G, Hill AL, et al. Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. Nature Communications. 11: 3676. PMID 32719321 DOI: 10.1038/S41467-020-17397-W |
0.486 |
|
| 2020 |
Ketchum RN, Smith EG, DeBiasse MB, Vaughan GO, McParland D, Leach WB, Al-Mansoori N, Ryan JF, Burt JA, Reitzel AM. Population genomic analyses of the sea urchin Echinometra sp. EZ across an extreme environmental gradient. Genome Biology and Evolution. PMID 32697837 DOI: 10.1093/Gbe/Evaa150 |
0.664 |
|
| 2020 |
Moreland RT, Nguyen AD, Ryan JF, Baxevanis AD. The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization. Database : the Journal of Biological Databases and Curation. 2020. PMID 32386298 DOI: 10.1093/Database/Baaa029 |
0.49 |
|
| 2020 |
DeBiasse MB, Colgan WN, Harris L, Davidson B, Ryan JF. Inferring tunicate relationships and the evolution of the tunicate Hox cluster with the genome of Corella inflata. Genome Biology and Evolution. PMID 32211845 DOI: 10.1093/Gbe/Evaa060 |
0.54 |
|
| 2019 |
Dardaillon J, Dauga D, Simion P, Faure E, Onuma TA, DeBiasse MB, Louis A, Nitta KR, Naville M, Besnardeau L, Reeves W, Wang K, Fagotto M, Guéroult-Bellone M, Fujiwara S, ... ... Ryan JF, et al. ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. Nucleic Acids Research. PMID 31680137 DOI: 10.1093/Nar/Gkz955 |
0.509 |
|
| 2019 |
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, ... ... Ryan JF, et al. Author Correction: The mid-developmental transition and the evolution of animal body plans. Nature. PMID 31673121 DOI: 10.1038/S41586-019-1698-X |
0.519 |
|
| 2019 |
Colgan W, Leanza A, Hwang A, DeBiasse MB, Llosa I, Rodrigues D, Adhikari H, Barreto Corona G, Bock S, Carillo-Perez A, Currie M, Darkoa-Larbi S, Dellal D, Gutow H, Hokama P, ... ... Ryan JF, et al. Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements. Evodevo. 10: 24. PMID 31632631 DOI: 10.1186/S13227-019-0137-2 |
0.397 |
|
| 2019 |
Babonis LS, Ryan JF, Enjolras C, Martindale MQ. Genomic analysis of the tryptome reveals molecular mechanisms of gland cell evolution. Evodevo. 10: 23. PMID 31583070 DOI: 10.1186/S13227-019-0138-1 |
0.617 |
|
| 2019 |
Ohdera A, Ames CL, Dikow RB, Kayal E, Chiodin M, Busby B, La S, Pirro S, Collins AG, Medina M, Ryan JF. Box, stalked, and upside-down? Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Alatina alata (Cubozoa), Calvadosia cruxmelitensis (Staurozoa), and Cassiopea xamachana (Scyphozoa). Gigascience. 8. PMID 31257419 DOI: 10.1093/Gigascience/Giz069 |
0.47 |
|
| 2019 |
Jiang JB, Quattrini AM, Francis WR, Ryan JF, Rodríguez E, McFadden CS. A hybrid de novo assembly of the sea pansy (Renilla muelleri) genome. Gigascience. 8. PMID 30942866 DOI: 10.1093/Gigascience/Giz026 |
0.525 |
|
| 2019 |
Pastrana CC, DeBiasse MB, Ryan JF. Sponges lack ParaHox genes. Genome Biology and Evolution. PMID 30859199 DOI: 10.1093/Gbe/Evz052 |
0.516 |
|
| 2019 |
DuBuc TQ, Ryan J, Martindale MQ. "Dorsal-ventral" genes are part of an ancient axial patterning system: evidence from Trichoplax adhaerens (Placozoa). Molecular Biology and Evolution. PMID 30726986 DOI: 10.1093/Molbev/Msz025 |
0.676 |
|
| 2018 |
Ketchum RN, DeBiasse MB, Ryan JF, Burt JA, Reitzel AM. The complete mitochondrial genome of the sea urchin, sp. EZ. Mitochondrial Dna. Part B, Resources. 3: 1225-1227. PMID 33474471 DOI: 10.1080/23802359.2018.1532335 |
0.617 |
|
| 2018 |
Babonis LS, DeBiasse MB, Francis WR, Christianson LM, Moss AG, Haddock SHD, Martindale MQ, Ryan JF. Integrating embryonic development and evolutionary history to characterize tentacle-specific cell types in a ctenophore. Molecular Biology and Evolution. PMID 30169705 DOI: 10.1093/Molbev/Msy171 |
0.629 |
|
| 2018 |
Hernandez AM, Ryan JF. Horizontally transferred genes in the ctenophore . Peerj. 6: e5067. PMID 29922518 DOI: 10.7717/Peerj.5067 |
0.465 |
|
| 2018 |
Kayal E, Bentlage B, Sabrina Pankey M, Ohdera AH, Medina M, Plachetzki DC, Collins AG, Ryan JF. Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits Bmc Evolutionary Biology. 18. DOI: 10.1186/S12862-018-1142-0 |
0.457 |
|
| 2018 |
Ketchum RN, DeBiasse MB, Ryan JF, Burt JA, Reitzel AM. The complete mitochondrial genome of the sea urchin, Echinometra sp. EZ Mitochondrial Dna Part B. 3: 1225-1227. DOI: 10.1080/23802359.2018.1532335 |
0.632 |
|
| 2017 |
Sasson DA, Ryan JF. A reconstruction of sexual modes throughout animal evolution. Bmc Evolutionary Biology. 17: 242. PMID 29207942 DOI: 10.1186/S12862-017-1071-3 |
0.333 |
|
| 2017 |
Martin-Duran JM, Ryan JF, Vellutini B, Pang K, Hejnol A. Increased taxon sampling reveals thousands of hidden orthologs in flatworms. Genome Research. PMID 28400424 DOI: 10.1101/Gr.216226.116 |
0.8 |
|
| 2016 |
Lewis Ames C, Ryan JF, Bely AE, Cartwright P, Collins AG. 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. 17: 650. PMID 27535656 DOI: 10.1186/S12864-016-2944-3 |
0.335 |
|
| 2016 |
Babonis LS, Martindale MQ, Ryan JF. Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis. Bmc Evolutionary Biology. 16: 114. PMID 27216622 DOI: 10.1186/S12862-016-0683-3 |
0.643 |
|
| 2016 |
Battelle BA, Ryan JF, Kempler KE, Saraf SR, Marten CE, Warren WC, Minx P, Montague MJ, Green PJ, Schmidt SA, Fulton L, Patel NH, Protas ME, Wilson RK, Porter ML. Opsin repertoire and expression patterns in horseshoe crabs: evidence from the genome of Limulus polyphemus (Arthropoda: Chelicerata). Genome Biology and Evolution. PMID 27189985 DOI: 10.1093/Gbe/Evw100 |
0.515 |
|
| 2016 |
Long KA, Nossa CW, Sewell MA, Putnam NH, 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. 5: 20. PMID 27175279 DOI: 10.1186/S13742-016-0125-6 |
0.408 |
|
| 2016 |
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, ... ... Ryan JF, et al. The mid-developmental transition and the evolution of animal body plans. Nature. PMID 26886793 DOI: 10.1038/Nature16994 |
0.609 |
|
| 2015 |
Zwarycz AS, Nossa CW, Putnam NH, 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. PMID 26659921 DOI: 10.1093/Gbe/Evv243 |
0.513 |
|
| 2015 |
Ryan JF, Chiodin M. Where is my mind? How sponges and placozoans may have lost neural cell types. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370. PMID 26554046 DOI: 10.1098/Rstb.2015.0059 |
0.316 |
|
| 2015 |
Dunn CW, Ryan JF. The evolution of animal genomes. Current Opinion in Genetics & Development. 35: 25-32. PMID 26363125 DOI: 10.1016/J.Gde.2015.08.006 |
0.481 |
|
| 2014 |
Ryan JF. Did the ctenophore nervous system evolve independently? Zoology (Jena, Germany). 117: 225-6. PMID 24986234 DOI: 10.1016/J.Zool.2014.06.001 |
0.347 |
|
| 2014 |
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. 15: 316. PMID 24773765 DOI: 10.1186/1471-2164-15-316 |
0.459 |
|
| 2014 |
Bracken-Grissom H, Collins AG, Collins T, Crandall K, Distel D, Dunn C, Giribet G, Haddock S, Knowlton N, Martindale M, Medina M, Messing C, O'Brien SJ, Paulay G, ... ... Ryan JF, et al. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes. The Journal of Heredity. 105: 1-18. PMID 24336862 DOI: 10.1093/jhered/est084 |
0.614 |
|
| 2013 |
Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P, Smith SA, Putnam NH, Haddock SH, Dunn CW, Wolfsberg TG, et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science (New York, N.Y.). 342: 1242592. PMID 24337300 DOI: 10.1126/Science.1242592 |
0.747 |
|
| 2013 |
Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EG, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémy RM, Bast J, Bazykin GA, Chabrol O, ... ... Ryan JF, et al. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature. 500: 453-7. PMID 23873043 DOI: 10.1038/Nature12326 |
0.701 |
|
| 2012 |
Schnitzler CE, Pang K, Powers ML, Reitzel AM, Ryan JF, Simmons D, Tada T, Park M, Gupta J, Brooks SY, Blakesley RW, Yokoyama S, Haddock SH, Martindale MQ, Baxevanis AD. Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes. Bmc Biology. 10: 107. PMID 23259493 DOI: 10.1186/1741-7007-10-107 |
0.807 |
|
| 2012 |
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. 13: 714. PMID 23256903 DOI: 10.1186/1471-2164-13-714 |
0.488 |
|
| 2012 |
DuBuc TQ, Ryan JF, Shinzato C, Satoh N, Martindale MQ. Coral comparative genomics reveal expanded Hox cluster in the cnidarian-bilaterian ancestor. Integrative and Comparative Biology. 52: 835-41. PMID 22767488 DOI: 10.1093/Icb/Ics098 |
0.645 |
|
| 2012 |
Koch BJ, 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. 7: e33261. PMID 22438907 DOI: 10.1371/Journal.Pone.0033261 |
0.34 |
|
| 2012 |
Kelada SN, Aylor DL, Peck BC, Ryan JF, Tavarez U, Buus RJ, Miller DR, Chesler EJ, Threadgill DW, Churchill GA, Pardo-Manuel de Villena F, Collins FS. Genetic analysis of hematological parameters in incipient lines of the collaborative cross. G3 (Bethesda, Md.). 2: 157-65. PMID 22384394 DOI: 10.1534/G3.111.001776 |
0.334 |
|
| 2012 |
Reitzel AM, Ryan JF, Tarrant AM. Establishing a model organism: a report from the first annual Nematostella meeting. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 34: 158-61. PMID 22102371 DOI: 10.1002/Bies.201100145 |
0.649 |
|
| 2011 |
Pett W, Ryan JF, Pang K, Mullikin JC, Martindale MQ, Baxevanis AD, Lavrov DV. Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome. Mitochondrial Dna. 22: 130-42. PMID 21985407 DOI: 10.3109/19401736.2011.624611 |
0.737 |
|
| 2011 |
Pang K, Ryan JF, Baxevanis AD, Martindale MQ. Evolution of the TGF-β signaling pathway and its potential role in the ctenophore, Mnemiopsis leidyi. Plos One. 6: e24152. PMID 21931657 DOI: 10.1371/Journal.Pone.0024152 |
0.697 |
|
| 2011 |
Reitzel AM, Pang K, Ryan JF, Mullikin JC, Martindale MQ, Baxevanis AD, 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? Evodevo. 2: 3. PMID 21291545 DOI: 10.1186/2041-9139-2-3 |
0.753 |
|
| 2011 |
Hurle B, Marques-Bonet T, Antonacci F, Hughes I, Ryan JF, Eichler EE, Ornitz DM, Green ED. Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses. Bmc Evolutionary Biology. 11: 23. PMID 21261979 DOI: 10.1186/1471-2148-11-23 |
0.532 |
|
| 2010 |
Pang K, Ryan JF, Mullikin JC, Baxevanis AD, Martindale MQ. Genomic insights into Wnt signaling in an early diverging metazoan, the ctenophore Mnemiopsis leidyi. Evodevo. 1: 10. PMID 20920349 DOI: 10.1186/2041-9139-1-10 |
0.712 |
|
| 2010 |
Ryan JF, Pang K, Mullikin JC, Martindale MQ, Baxevanis AD. The homeodomain complement of the ctenophore Mnemiopsis leidyi suggests that Ctenophora and Porifera diverged prior to the ParaHoxozoa. Evodevo. 1: 9. PMID 20920347 DOI: 10.1186/2041-9139-1-9 |
0.785 |
|
| 2009 |
Moreland RT, Ryan JF, Pan C, Baxevanis AD. The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family. Database : the Journal of Biological Databases and Curation. 2009: bap004. PMID 20157477 DOI: 10.1093/Database/Bap004 |
0.397 |
|
| 2007 |
Ryan JF, Baxevanis AD. Hox, Wnt, and the evolution of the primary body axis: insights from the early-divergent phyla. Biology Direct. 2: 37. PMID 18078518 DOI: 10.1186/1745-6150-2-37 |
0.5 |
|
| 2007 |
Sullivan JC, Ryan JF, Mullikin JC, Finnerty JR. Conserved and novel Wnt clusters in the basal eumetazoan Nematostella vectensis. Development Genes and Evolution. 217: 235-9. PMID 17310352 DOI: 10.1007/S00427-007-0136-5 |
0.731 |
|
| 2007 |
Ryan JF, Mazza ME, Pang K, Matus DQ, Baxevanis AD, Martindale MQ, Finnerty JR. Pre-bilaterian origins of the Hox cluster and the Hox code: evidence from the sea anemone, Nematostella vectensis. Plos One. 2: e153. PMID 17252055 DOI: 10.1371/Journal.Pone.0000153 |
0.777 |
|
| 2006 |
Ryan JF, Burton PM, Mazza ME, Kwong GK, Mullikin JC, Finnerty JR. The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis. Genome Biology. 7: R64. PMID 16867185 DOI: 10.1186/Gb-2006-7-7-R64 |
0.758 |
|
| 2006 |
Sullivan JC, Ryan JF, Watson JA, Webb J, Mullikin JC, Rokhsar D, Finnerty JR. StellaBase: the Nematostella vectensis Genomics Database. Nucleic Acids Research. 34: D495-9. PMID 16381919 DOI: 10.1093/Nar/Gkj020 |
0.779 |
|
| 2005 |
Darling JA, Reitzel AR, Burton PM, Mazza ME, Ryan JF, Sullivan JC, Finnerty JR. Rising starlet: the starlet sea anemone, Nematostella vectensis. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 27: 211-21. PMID 15666346 DOI: 10.1002/Bies.20181 |
0.75 |
|
| 2003 |
Ryan JF, Finnerty JR. CnidBase: The Cnidarian Evolutionary Genomics Database. Nucleic Acids Research. 31: 159-63. PMID 12519972 DOI: 10.1093/Nar/Gkg116 |
0.735 |
|
| 2002 |
Thomas JW, Prasad AB, Summers TJ, Lee-Lin SQ, Maduro VV, Idol JR, Ryan JF, Thomas PJ, McDowell JC, Green ED. Parallel construction of orthologous sequence-ready clone contig maps in multiple species. Genome Research. 12: 1277-85. PMID 12176935 DOI: 10.1101/Gr.283202 |
0.414 |
|
| 2001 |
Makalowska I, Ryan JF, Baxevanis AD. GeneMachine: gene prediction and sequence annotation. Bioinformatics (Oxford, England). 17: 843-4. PMID 11590102 DOI: 10.1093/Bioinformatics/17.9.843 |
0.397 |
|
| 2000 |
Thomas JW, Summers TJ, Lee-Lin SQ, Maduro VV, Idol JR, Mastrian SD, Ryan JF, Jamison DC, Green ED. Comparative genome mapping in the sequence-based era: early experience with human chromosome 7. Genome Research. 10: 624-33. PMID 10810084 DOI: 10.1101/Gr.10.5.624 |
0.432 |
|
| 2000 |
Banerjee-Basu S, Ryan JF, Baxevanis AD. The homeodomain resource: a prototype database for a large protein family. Nucleic Acids Research. 28: 329-30. PMID 10592263 DOI: 10.1093/Nar/28.1.329 |
0.37 |
|
| 1999 |
Loftus SK, Chen Y, Gooden G, Ryan JF, Birznieks G, Hilliard M, Baxevanis AD, Bittner M, Meltzer P, Trent J, Pavan W. Informatic selection of a neural crest-melanocyte cDNA set for microarray analysis. Proceedings of the National Academy of Sciences of the United States of America. 96: 9277-80. PMID 10430933 DOI: 10.1038/14355 |
0.418 |
|
| 1999 |
Ferlanti ES, Ryan JF, Makalowska I, Baxevanis AD. WebBLAST 2.0: an integrated solution for organizing and analyzing sequence data. Bioinformatics (Oxford, England). 15: 422-3. PMID 10366662 DOI: 10.1093/Bioinformatics/15.5.422 |
0.34 |
|
| 1999 |
Banerjee-Basu S, Ferlanti ES, Ryan JF, Baxevanis AD. The Homeodomain Resource: sequences, structures and genomic information. Nucleic Acids Research. 27: 336-7. PMID 9847220 DOI: 10.1093/Nar/27.1.336 |
0.401 |
|
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