Ryan Lab Publications

Journal titles have been removed to encourage the reading of manuscript titles!  
Names in bold indicate members of Ryan Lab. Superscript key: p=postdoc, g=graduate student, u=undergraduate

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Hernandez AMg & Ryan JF.
Six-state Amino Acid Recoding is not an Effective Strategy to Offset the Effects of Compositional Heterogeneity and Saturation in Phylogenetic Analyses. 2021, doi:10.1093/sysbio/syab027
supplement analyses / supplement figures / supplement commands / supplement pseudocode / GitHub / Dryad

Medina-Feliciano JG, Pirro S, García-Arrarás JE, Mashanov V, Ryan JF.
Draft genome of the sea cucumber Holothuria glaberrima, a model for the study of regeneration. 2021, doi:10.3389/fmars.2021.603410
GitHub / Genome portal

Ketchum RN, Smith EG, DeBiasse MBp, Vaughan GO, McParland D, Leach WB, Al-Mansoori N, Ryan JF, Burt JA, Reitzel AM.
Population genomic analysis of a sea urchin across an extreme environmental gradient. 2020, doi:10.1093/gbe/evaa150

Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderon L, Grombacher L, Roller M, Barlow LD, Camilli S, Ryan JF, Wörheide G, Hill AL, Riesgo A, Leys S.
Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. 2020, doi:10.1038/s41467-020-17397-w

DeBiasse MBp, Colgan WNu, Harris Lu, Davidson B, Ryan JF.
Inferring tunicate relationships and the evolution of the tunicate Hox cluster with the genome of Corella inflata. 2020, doi:10.1093/gbe/evaa060
GitHub / Genome portal

Moreland MT, Nguyen AD, Ryan JF, Baxevanis AD.
The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization. 2020, doi:10.1093/database/baaa029
Mnemiopsis leidyi genome portal

Dardaillon J, Dauga D, Simion P, Faure E, Onuma T, DeBiasse MP, Louis A, Nitta K, Naville M, Besnardeau L, Reeves W, Wang K, Fagotto M, Guéroult-Bellone M, Fujiwara S, Dumollard R, Veeman M, Volff JN, Roest Crollius H, Douzery E, Ryan J, Davidson B, Nishida H, Dantec C, Lemaire P.
ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. 2019, doi:10.1093/nar/gkz955

Babonis LS, Ryan JF, Enjolras C, Martindale MQ.
Genomic analysis of the tryptome reveals molecular mechanisms of gland cell evolution. 2019, doi:10.1186/s13227-019-0138-1
GitHub

Colgan Wu, Leanza Au, Hwang Au, DeBiasse MBp, Llosa Iu, Rodrigues Du, Adhikari Hu, Corona GBu, Bock Su, Carillo-Perez Au, Currie Mu, Darkoa-Larbi Su, Dellal Du, Gutow Hu, Hokama Pu, Kibby Eu, Linhart Nu, Moody Su, Naganuma Au, Nguyen Du, Stanton Ru, Stark Su, Tumey Cu, Velleca Au, Ryan JF, Davidson B.
Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements. 2019, doi:10.1186/s13227-019-0137-2

Ohdera AH, Ames CL, Dikow RB, Kayal E, Chiodin Mp, 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). 2019, doi:10.1093/gigascience/giz069
GitHub / GigaDB / Alatina genome portal / Calvadosia genome portal / Cassiopea genome portal

Jiang J, Quattrini AM, Francis WR, Ryan JF, Rodriguez E, McFadden CS.
A hybrid de novo assembly of the sea pansy (Renilla muelleri) Genome. 2019, doi:10.1093/gigascience/giz026

Pastrana CCu*, DeBiasse MBp*, Ryan JF.
Sponges lack ParaHox genes. 2019, doi:10.1093/gbe/evz052
* authors contributed equally
GitHub

Dubuc TQ, Ryan JF, Martindale MQ.
"Dorsal-ventral" genes are part of an ancient axial patterning system: evidence from Trichoplax adhaerens (Placozoa). 2019, doi:10.1093/molbev/msz025

DeBiasse MBp & Ryan JF.
Phylotocol: Promoting transparency and overcoming bias in phylogenetics. 2018, doi:10.1093/sysbio/syy090
GitHub

Ketchum RN, DeBiasse MBp, Ryan JF, Burt JA, Reitzel AM.
The complete mitochondrial genome of the sea urchin, Echinometra sp. EZ. 2018, doi:10.1080/23802359.2018.1532335

Babonis LS, DeBiasse MBp, 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. 2018, doi:10.1093/molbev/msy171
GitHub

Hernandez AMG, Ryan JF.
Horizontally transferred genes in the ctenophore Mnemiopsis leidyi. 2018, doi:10.7717/peerj.5067
GitHub

Kayal E, Bentlage B, Pankey MS, 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. 2018, doi:10.1186/s12862-018-1142-0
GitHub

Sasson DAp, Jacquez AAu, Ryan JF.
The ctenophore Mnemiopsis leidyi regulates egg production via conspecific communication. 2018, doi:10.1186_s12898-018-0169-9
GitHub

Haddock SHD, Christianson LM, Francis WR, Martini S, Dunn CW, Pugh PR, Mills CE, Osborn KJ, Seibel BA, Choy CA, Schnitzler CE, Matsumoto GI, Messié M, Schultz DT, Winnikoff JR, Powers ML, Gasca R, Browne WE, Johnsen S, Schlining KL, Thun SV, Erwin BE, Ryan JF, Thuesen EV.
Insights into the Biodiversity, Behavior, and Bioluminescence of Deep-Sea Organisms Using Molecular and Maritime Technology. 2018, doi:10.5670/oceanog.2017.422

Sasson DSp & Ryan JF.
A reconstruction of sexual modes throughout animal evolution. 2017, doi:10.1186/s12862-017-1071-3
GitHub

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
GitHub

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

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

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.

Long KAu, 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.
Ophionereis fasciata genome portal / Australostichopus mollis genome portal / Patiriella regularis genome portal

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.
Genome portal

Sasson DSp & 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.

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.

Zwarycz ASu, 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.
GitHub / Genome portal

Ryan JF & Chiodin Mp.
Where is my mind? How sponges and placozoans may have lost neural cell types. 2015, doi:10.1098/rstb.2015.0059.

Dunn CW & Ryan JF.
The evolution of animal genomes. 2015, doi:10.1016/j.gde.2015.08.006

Church SH, Ryan JF & Dunn CW.
Automation and Evaluation of the SOWH Test of Phylogenetic Topologies with SOWHAT.
2015, doi:10.1093/sysbio/syv055.
GitHub

Ryan JF.
Did the ctenophore nervous system evolve independently? 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. 2014, doi:10.1186/1471-2164-15-316.
Mnemiopsis leidyi genome portal


Joseph Ryan’s pre-Whitney-Lab publications below.


 

GIGA Community of Scientists.
Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes. 2014, doi:10.1093/jhered/est084

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, doi:10.1126/science.1242592
supplement

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, doi:10.1038/nature12326

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, doi:10.1186/1741-7007-10-107

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. 2012, doi:10.1186/1471-2164-13-714

Dubuc TQ*, Ryan JF*, Shinzato C, Satoh N & Martindale MQ.
Coral comparative genomics reveal extensive Hox cluster in the cnidarian-bilaterian ancestor. 2012, doi:10.1093/icb/ics098
* authors contributed equally

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, doi:10.1371/journal.pone.0033261
* authors contributed equally

Kelada SN, Aylor DL, Peck BCE, 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, doi:10.1534/g3.111.001776

Reitzel AM, Ryan JF & Tarrant AM.
Establishing a model organism: A report from the first annual Nematostella meeting. 2011, doi:10.1002/bies.201100145

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, doi:10.1371/journal.pone.0024152

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, doi:10.3109/19401736.2011.624611

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, doi:10.1186/2041-9139-2-3

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, doi:10.1186/1471-2148-11-23

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, doi:10.1186/2041-9139-1-10

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, doi:10.1186/2041-9139-1-9

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, doi:10.1093/database/bap004
* authors contributed equally

Ryan JF & Baxevanis AD.
Hox, Wnt, and the Evolution of the Primary Body Axis: Insights from the Early-Divergent Phyla. 2007, doi:10.1186/1745-6150-2-37

Sullivan JC, Ryan JF, Mullikin JC & Finnerty JR.
Conserved and Novel Wnt Clusters in the Basal Eumetazoan Nematostella vectensis. 2007, doi:10.1007/s00427-007-0136-5

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, doi:10.1371/journal.pone.0000153

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, doi:10.1186/gb-2006-7-7-r64

Sullivan JC*, Ryan JF*, Watson JA, Webb J, Mullikin JC, Rokhsar D & Finnerty JR.
StellaBase: The Nematostella vectensis Genomics Database. 2006, doi:10.1093/nar/gkj020
* authors contributed equally

Darling JA, Reitzel AR, Burton PM, Mazza ME, Ryan JF, Sullivan JC & Finnerty JR.
Rising Starlet: the Starlet Sea Anemone, Nematostella vectensis. 2005, doi:10.1002/bies.20181

Ryan JF & Finnerty JR.
Cnidbase: The Cnidarian Evolutionary Genomics Database. 2003, doi:10.1093/nar/gkg116

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, doi:10.1101/gr.283202

Makalowska I, Ryan JF & Baxevanis AD.
GeneMachine: Gene Prediction and Sequence Annotation. 2001, doi:10.1093/bioinformatics/17.9.843

Szabo C, Masiello A, Ryan JF, BIC Consortium & Brody L.
The Breast Cancer Information Core: Database Design, Structure, and Scope. 2000, doi:10.1002/1098-1004(200008)16:2<123::AID-HUMU4>3.0.CO;2-Y

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, doi:10.1101/gr.10.5.624

Banerjee-Basu S, Ryan JF & Baxevanis AD.
The Homeodomain Resource: a Prototype Database for a Large Protein Family. 2000,doi:10.1093/nar/28.1.329

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, doi:10.1073/pnas.96.16.9277

Ferlanti ES, Ryan JF, Makalowska I & Baxevanis AD.
WebBLAST: An Integrated Solution for Organizing and Analyzing Sequence Data. 1999, doi:10.1093/bioinformatics/15.5.422

Banerjee-Basu S, Ferlanti ES, Ryan JF & Baxevanis AD.
The Homeodomain Resource: sequences, structures and genomic information. 1999, doi:10.1093/nar/27.1.336