Journal titles have been removed to encourage the reading of titles!

Martin-Duran JM*, Ryan JF*, Vellutini BCC, Pang K, and Hejnol A.
Increased taxon sampling reveals thousands of hidden orthologs in flatworms. 2017, doi:10.1101/gr.216226.116
* authors contributed equally
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Ryan JF, Schnitzler CE, and Tamm SL.
Meeting report of Ctenopalooza: The first international meeting of ctenophorologists. 2016, doi:10.1186/s13227-016-0057-3
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Ames CL, Ryan JF, Bely AE, Cartwright P, and 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. 2016, doi:10.1186/s12864-016-2944-3
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Babonis LS, Martindale MQ, and Ryan JF.
Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis. 2016, doi:10.1186/s12862-016-0683-3.
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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. 2016, doi:10.1186/s13742-016-0125-6.
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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, and Porter ML.
Opsin repertoire and expression patterns in horseshoe crabs: evidence from the genome of Limulus polyphemus (Arthropoda: Chelicerata). 2016, doi:10.1093/gbe/evw100.
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Sasson DS & 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. 2016, doi.org/10.7717/peerj.1846.
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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. 2016, doi:10.1038/nature16994.
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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. 2016, doi:10.1093/gbe/evv243.
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Ryan JF & Chiodin M.
Where is my mind? How sponges and placozoans may have lost neural cell types. 2015, doi:10.1098/rstb.2015.0059.
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Dunn CW & Ryan JF.
The evolution of animal genomes. 2015, doi:10.1016/j.gde.2015.08.006
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Church SH, Ryan JF & Dunn CW.
Automation and Evaluation of the SOWH Test of Phylogenetic Topologies with SOWHAT.
2015 doi:10.1093/sysbio/syv055.
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Ryan JF.
Did the ctenophore nervous system evolve independently?. 2014, doi:10.1016/j.zool.2014.06.001.
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Names in bold indicate members of Ryan Lab. Joseph Ryan’s pre-Whitney-Lab publications below.


 

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. 2014 Apr 28;15:316. doi:10.1186/1471-2164-15-316.
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GIGA Community of Scientists.
Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes. Journal of 2014 Jan-Feb;105(1):1-18.
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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. 2013 Dec 13;342(6164):1242592.
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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 & Van Doninck K.
Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. 2013 Aug 22;500(7463):453-7. f1000

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 & Baxevanis AD.
Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes. 2012, Dec 21;10:107. highlyaccessed
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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. 2012, Dec 20;13:714. highlyaccessed
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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.
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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. 2012 March 15;7(3):e33261.
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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 & Collins FS.
Genetic Analysis of Hematological Parameters in Incipient Lines of the Collaborative Cross.
2012 Feb; 2:157-165.
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Reitzel AM, Ryan JF & Tarrant AM.
Establishing a model organism: A report from the first annual Nematostella meeting. 2011 Nov 18.
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Pang K, Ryan JF, Baxevanis AD & Martindale MQ.
Evolution of the TGF-Beta signaling pathway and its potential role in the ctenophore Mnemiopsis leidyi. 2011 Sep 8;6(9):e24152.
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Pett W, Ryan JF, Pang K, NISC Comparative Sequencing Program, Martindale MQ, Mullikin J, Baxevanis AD & Lavrov D.
Extreme Mitochondrial Genome Evolution in the Ctenophore Mnemiopsis leidyi. 2011 Aug;22(4):130-42.
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Reitzel AM, Pang K, Ryan JF, Mullikin JC, Baxevanis AD, Martindale MQ & 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? 2011, Feb 3;2(1):3.
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Hurle B, Marques-Bonet T, Antonacci F, Hughes I, Ryan JF, NISC Comparative Sequencing Program, Eichler EE, Ornitz DM & Green ED.
Lineage-Specific Evolution of the Vertebrate Otopetrin Gene Family Revealed by Comparative Genomic Analyses. 2011, Jan 24;11(1):23.
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Pang K, Ryan JF, NISC Comparative Sequencing Program, Mullikin JC, Baxevanis AD & Martindale MQ.
Genomic Insights into Wnt Signaling in an Early Diverging Metazoan, the Ctenophore Mnemiopsis leidyi.
2010 Oct 4;1(1):10. highlyaccessed
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Ryan JF, Pang K, NISC Comparative Sequencing Program, Mullikin JC, Martindale MQ & Baxevanis AD.
The Homeodomain Complement of the Ctenophore Mnemiopsis leidyi Suggests that Ctenophora and Porifera Diverged Prior to the ParaHoxozoa. 2010 Oct 4;1(1):9. f1000 highlyaccessed
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Moreland RT*, Ryan JF*, Pan CV & Baxevanis AD.
The Homeodomain Resource: A Comprehensive Collection of Sequence, Structure, Interaction, Genomic, and Functional Information on the Homeodomain Protein Family. 2009 Apr 28; bap004.
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Ryan JF & Baxevanis AD.
Hox, Wnt, and the Evolution of the Primary Body Axis: Insights from the Early-Divergent Phyla. 2007 Dec 13;2(1):37. highlyaccessed
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Sullivan JC, Ryan JF, Mullikin JC & Finnerty JR.
Conserved and Novel Wnt Clusters in the Basal Eumetazoan Nematostella vectensis. 2007 Mar;217(3):235-9.
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Ryan JF, Mazza TM, 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. 2007 Jan 24;2:e153.
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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. 2006 Jul 24;7(7):R64. highlyaccessed
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Sullivan JC*, Ryan JF*, Watson JA, Webb J, Mullikin JC, Rokhsar D & Finnerty JR.
StellaBase: The Nematostella vectensis Genomics Database. 2006 Jan 1;34(Database issue):D495-9.
* authors contributed equally
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Darling JA, Reitzel AR, Burton PM, Mazza ME, Ryan JF, Sullivan JC & Finnerty JR.
Rising Starlet: the Starlet Sea Anemone, Nematostella vectensis. 2005 Feb;27(2):211-21.
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Ryan JF & Finnerty JR.
Cnidbase: The Cnidarian Evolutionary Genomics Database. 2003 Jan 1;31(1):159-63.
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Thomas JW, Prasad AB, Lee-Lin SQ, Maduro VV, Idol JR, Ryan JF & Green ED.
Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species. 2002 Aug;12(8):1277-85.
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Makalowska I, Ryan JF & Baxevanis AD.
GeneMachine: Gene Prediction and Sequence Annotation. 2001 Sep;17(9):843-4.
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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. 2000 May;10(5):624-633.
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Szabo C, Masiello A, Ryan JF, BIC Consortium & Brody L.
The Breast Cancer Information Core: Database Design, Structure, and Scope. 2000;16(2):123-31.
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Banerjee-Basu S, Ryan JF & Baxevanis AD.
The Homeodomain Resource: a Prototype Database for a Large Protein Family. 2000 Jan 1;28(1):329-30.
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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. 1999 Aug 3;96(16):9277-80.
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Ferlanti ES, Ryan JF, Makalowska I & Baxevanis AD.
WebBLAST: An Integrated Solution for Organizing and Analyzing Sequence Data. 1999 May;15(5):422-423.
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