Selected Lab Publications

Dunn, CW (2014) Reconsidering the phylogenetic utility of miRNA in animals. PNAS. doi:10.1073/pnas.1413545111.

Zapata, F, NG Wilson, M Howison, SCS Andrade, KM Jörger, Michael Schrödl, Freya E Goetz, Gonzalo Giribet, Casey W Dunn (preprint) Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. BioRxiv. bioRxiv preprint: doi:10.1101/007039. Git code repository:

Church, SH, JF Ryan, CW Dunn (preprint) Automation and Evaluation of the SOWH Test of Phylogenetic Topologies with SOWHAT. BioRxiv. bioRxiv preprint: doi:10.1101/005264. Git code repository:

Siebert, S, FE Goetz, SH Church, P Bhattacharyya, F Zapata, SHD Haddock, and CW Dunn. (preprint) Stem Cells in a Colonial Animal with Localized Growth Zones. bioRxiv preprint: doi:10.1101/001685. Git code repository:

Howison, M, F Zapata, EJ Edwards, and CW Dunn (2014) Bayesian genome assembly and assessment by Markov Chain Monte Carlo sampling. PLoS One 9:e99497. doi:10.1371/journal.pone.0099497. arXiv preprint: 1308.1388. Git code repository: Example analysis report:

Lopez, J, H Bracken-Grissom, A Collins, T Collins, K Crandall, D Distel, C Dunn, et al. (2014) Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes. Journal of Heredity 105:1-18. doi:10.1093/jhered/est084

Ryan, JF, K Pang, CE Schnitzler, A Nguyen, RT Moreland, DK Simmons, BJ Koch, WR Francis, P Havlak, NISC Comparative Sequencing Program, SA Smith, NH Putnam, SHD Haddock, CW Dunn, TG Wolfsberg, JC Mullikin, MQ Martindale, AD Baxevanis (2013) The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 432:1242592. doi:10.1126/science.1242592, PMC3920664

(Photo by Stefan Siebert)

CW Dunn, M Howison, and F Zapata (2013) Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14:330. doi:10.1186/1471-2105-14-330. arXiv preprint: 1307.6432. Git code repository: (software), (analyses).

Howison, M, F Zapata, CW Dunn (2013) Toward a statistically explicit understanding of de novo sequence assembly. Bioinformatics 29:2959-2963. doi:10.1093/bioinformatics/btt525.

Siebert, S, PR Pugh, SHD Haddock, CW Dunn (2013) Re-evaluation of characters in Apolemiidae (Siphonophora), with description of two new species from Monterey Bay, California. Zootaxa 3702: 201–232. doi:10.11646/zootaxa.3702.3.1 (pdf)

Dunn, CW, X Luo, Z Wu (2013) Phylogenetic analysis of gene expression. Integrative and Comparative Biology 53:847-856. doi:10.1093/icb/ict068. arXiv preprint: 1302.2978. Git code repository:

Helm, RR, S Siebert, S Tulin, J Smith, CW Dunn (2013) Characterization of differential transcript abundance through time during Nematostella vectensis development. BMC Genomics 14:266. doi:10.1186/1471-2164-14-266. Git code repository:

Dunn, CW (2013) Evolution: Out of the Ocean. Current Biology 23:R242-R243. doi:10.1038/10.1016/j.cub.2013.01.06

Howison, M, N Sinnott-Armstrong, CW Dunn (2012) BioLite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance. 4th USENIX Workshop on the Theory and Practice of Provenance (TaPP12). video, pdf. Git code repository:

Smith, SA, NG Wilson, F Goetz, C Feehery, SCS Andrade, GW Rouse, G Giribet, CW Dunn (2011) Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature 480:364-367. doi:10.1038/nature10526

Siebert, S, MD Robinson, SC Tintori, F Goetz, RR Helm, SA Smith, N Shaner, SHD Haddock, CW Dunn (2011) Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows. PLoS One 6(7): e22953. doi:10.1371/journal.pone.0022953 (pdf)

Edgecombe, GD, G Giribet, CW Dunn, A Hejnol, RM Kristensen, RC Neves, GW Rouse, K Worsaae, and MV Sørensen (2011) Higher-level metazoan relationships: recent progress and remaining questions. Organisms, Diversity, and Evolution. doi:10.1007/s13127-011-0044-4 (pdf)

Haddock, SHD and CW Dunn (2011) Practical Computing for Biologists. Sinauer Associates (Sunderland, MA). Book Site, Read more at the publisher's site

Hejnol, A, M Obst, A Stamatakis, M Ott, G Rouse, G Edgecombe, P Martinez, J Baguñà, X Bailly, U Jondelius, M Wiens, WEG Müller, Elaine Seaver, WC Wheeler, MQ Martindale, G Giribet, and CW Dunn (2009) Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. R. Soc. B. 276:4261-4270 doi:10.1098/rspb.2009.0896

Dunn, CW (2009) Siphonophores. Current Biology 19:R233-R234. doi:10.1016/j.cub.2009.02.009

Giribet, G, CW Dunn, GD Edgecombe, A Hejnol, MQ Martindale, and GW Rouse (2009) Assembling the spiralian tree of life (p 52-64) In: Animal Evolution. MJ Telford and DTJ Littlewood (eds). Oxford University Press.

Cartwright, P, NM Evans, CW Dunn, AC Marques, MP Miglietta, P Schuchert, and AG Collins (2008) Phylogenetics of Hydroidolina (Hydrozoa: Cnidaria). Journal of the Marine Biological Association of the United Kingdom. 88:1663-1672. doi:10.1017/S0025315408002257 (pdf)

Dunn, CW, A Hejnol, DQ Matus, K Pang, WE Browne, SA Smith, E Seaver, GW Rouse, M Obst, GD Edgecombe, MV Sorensen, SHD Haddock, A Schmidt-Rhaesa, A Okusu, RM Kristensen, WC Wheeler, MQ Martindale, and G Giribet (2008) Broad phylogenomic sampling improves resolution of the Animal Tree of Life. Nature. 452:745-749. doi:10.1038/nature06614

Smith, SA and CW Dunn (2008) Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics. 24:715-716. doi:10.1093/bioinformatics/btm619 (pdf). Code repository:

Giribet, G, CW Dunn, GD Edgecombe, and GW Rouse (2007) A modern look at the Animal Tree of Life. Zootaxa 1668:61-79. (pdf)

Oota, H, CW Dunn, WC Speed, AJ Pakstis, MA Palmatier, JR Kidd and KK Kidd (2007) Conservative evolution in duplicated genes of the primate Class I ADH cluster. Gene. 392:64-76. doi:10.1016/j.gene.2006.11.008 (pdf)

Mills, CE, AC Marques, AE Migotto, DR Calder, C Hand, JT Rees, SHD Haddock, CW Dunn, and PR Pugh. (2007) Hydrozoa: Polyps, Hydromedusae, and Siphonophora. In: The Light & Smith manual: intertidal invertebrates from central California to Oregon, 4th edition. JT Carlton (ed). University of California Press.

Dunn, CW and GP Wagner (2006) The evolution of colony-level development in the Siphonophora (Cnidaria:Hydrozoa). Development, Genes, and Evolution. 216:743-754. doi:10.1007/s00427-006-0101-8 (pdf)

Matus, DQ, K Pang, H Marlow, CW Dunn, GH Thomsen, and MQ Martindale (2006) Deep evolutionary roots for bilaterality in the metazoa. Proceedings of the National Academy of Sciences USA 103:11195-11200. doi:10.1073/pnas.0601257103 (pdf)

Matus, DQ, RR Copley, CW Dunn, A Hejnol, H Eccleston, KM Halanych, MQ Martindale, and MJ Telford (2006) Broad Taxon and Gene Sampling Indicate that Chaetognaths Are Protostomes. Current Biology 16:R575-R576 doi:10.1016/j.cub.2006.07.017 (pdf)

Dunn, CW, PR Pugh, and SHD Haddock (2005) Molecular phylogenetics of the Siphonophora (Cnidaria), with implications for the evolution of functional specialization. Systematic Biology 54:916-935. doi:10.1080/10635150500354837 (pdf)

Dunn, CW (2005) The complex colony-level organization of the deep-sea siphonophore Bargmannia elongata (Cnidaria, Hydrozoa) is directionally asymmetric and arises by the subdivision of pro-buds. Developmental Dynamics. 234:835-834. doi:10.1002/dvdy.20483 (pdf)

Dunn, CW, PR Pugh, and SHD Haddock (2005) Marrus claudanielis, a new species of deep-sea physonect siphonophore (Siphonophora, Physonectae). Bull. Mar. Sci. 76:699-714. (pdf)

Haddock, SHD, CW Dunn, PR Pugh. and C.E. Schnitzler. (2005) Bioluminescent and red-fluorescent lures in a deep-sea siphonophore. Science. 309:263. doi:10.1126/science.1110441 (pdf)

Haddock, SHD, CW Dunn, and PR Pugh (2005) A reexamination of siphonophore terminology and morphology, applied to the description of two new prayine species with remarkable bio-optical properties. J. Mar. Biol. Assoc. U.K. 85:695-707. doi:10.1017/S0025315405011616 (pdf)

Haddock, SHD and CW Dunn (2005) The complex world of siphonohpores. JMBA Global Marine Environment 2005(2):24-25. (pdf)

Lynch, VJ, JJ Roth, K Takahashi, CW Dunn, DF Nonaka, G Stopper and GP Wagner (2004) Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society B: Biological Sciences 271:2201-2207. doi:10.1098/rspb.2004.2848 (pdf)