Casey W. Dunn, Ph.D. - Publications

Ecology and Evolutionary Biology Yale University, New Haven, CT 
 Ecology and Evolutionary Biology Brown University, Providence, RI 

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Church SH, Mah JL, Dunn CW. Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells. Plos Biology. 22: e3002633. PMID 38787797 DOI: 10.1371/journal.pbio.3002633  0.783
2024 Ahuja N, Cao X, Schultz DT, Picciani N, Lord A, Shao S, Jia K, Burdick DR, Haddock SHD, Li Y, Dunn CW. Giants among Cnidaria: large nuclear genomes and rearranged mitochondrial genomes in siphonophores. Genome Biology and Evolution. PMID 38502059 DOI: 10.1093/gbe/evae048  0.663
2024 Mah JL, Dunn CW. Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data. Nature Ecology & Evolution. PMID 38182680 DOI: 10.1038/s41559-023-02281-9  0.765
2023 Church SH, Mah JL, Wagner G, Dunn CW. Normalizing need not be the norm: count-based math for analyzing single-cell data. Theory in Biosciences = Theorie in Den Biowissenschaften. PMID 37947999 DOI: 10.1007/s12064-023-00408-x  0.745
2023 Church SH, Munro C, Dunn CW, Extavour CG. The evolution of ovary-biased gene expression in Hawaiian Drosophila. Plos Genetics. 19: e1010607. PMID 36689550 DOI: 10.1371/journal.pgen.1010607  0.303
2022 Munro C, Zapata F, Howison M, Siebert S, Dunn CW. Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora. Molecular Biology and Evolution. 39. PMID 35134205 DOI: 10.1093/molbev/msac027  0.317
2021 Li Y, Steenwyk JL, Chang Y, Wang Y, James TY, Stajich JE, Spatafora JW, Groenewald M, Dunn CW, Hittinger CT, Shen XX, Rokas A. A genome-scale phylogeny of the kingdom Fungi. Current Biology : Cb. PMID 33607033 DOI: 10.1016/j.cub.2021.01.074  0.416
2020 Smith SD, Pennell MW, Dunn CW, Edwards SV. Phylogenetics is the New Genetics (for Most of Biodiversity). Trends in Ecology & Evolution. 35: 415-425. PMID 32294423 DOI: 10.1016/J.Tree.2020.01.005  0.395
2019 Munro C, Vue Z, Behringer RR, Dunn CW. Morphology and development of the Portuguese man of war, Physalia physalis. Scientific Reports. 9: 15522. PMID 31664071 DOI: 10.1038/S41598-019-51842-1  0.329
2019 Wang LG, Lam TT, Xu S, Dai Z, Zhou L, Feng T, Guo P, Dunn CW, Jones BR, Bradley T, Zhu H, Guan Y, Jiang Y, Yu G. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. PMID 31633786 DOI: 10.1093/Molbev/Msz240  0.347
2018 Pugh PR, Dunn CW, Haddock SHD. Description of Tottonophyes enigmatica gen. nov., sp. nov. (Hydrozoa, Siphonophora, Calycophorae), with a reappraisal of the function and homology of nectophoral canals Zootaxa. 4415: 452-472. PMID 30313611 DOI: 10.11646/Zootaxa.4415.3.3  0.386
2018 Lewis ZR, Dunn CW. We are not so special. Elife. 7. PMID 29969097 DOI: 10.7554/Elife.38726  0.387
2018 Munro C, Siebert S, Zapata F, Howison M, Damian Serrano A, Church SH, Goetz FE, Pugh PR, Haddock SHD, Dunn CW. Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution. Molecular Phylogenetics and Evolution. PMID 29940256 DOI: 10.1016/J.Ympev.2018.06.030  0.777
2018 Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A. Pairwise comparisons across species are problematic when analyzing functional genomic data. Proceedings of the National Academy of Sciences of the United States of America. PMID 29301966 DOI: 10.1073/Pnas.1707515115  0.517
2017 Helm RR, Dunn CW. Indoles induce metamorphosis in a broad diversity of jellyfish, but not in a crown jelly (Coronatae). Plos One. 12: e0188601. PMID 29281657 DOI: 10.1371/Journal.Pone.0188601  0.358
2016 Hejnol A, Dunn CW. Animal Evolution: Are Phyla Real? Current Biology : Cb. 26: R424-R426. PMID 27218852 DOI: 10.1016/J.Cub.2016.03.058  0.391
2016 Guang A, Zapata F, Howison M, Lawrence CE, Dunn CW. An Integrated Perspective on Phylogenetic Workflows. Trends in Ecology & Evolution. PMID 26775796 DOI: 10.1016/J.Tree.2015.12.007  0.444
2016 Dunn CW, Munro C. Comparative genomics and the diversity of life Zoologica Scripta. 45: 5-13. DOI: 10.1111/Zsc.12211  0.478
2015 Dunn CW. Genomics: Acorn worms in a nutshell. Nature. 527: 448-9. PMID 26580019 DOI: 10.1038/Nature16315  0.446
2015 Zapata F, Goetz FE, Smith SA, Howison M, Siebert S, Church SH, Sanders SM, Ames CL, McFadden CS, France SC, Daly M, Collins AG, Haddock SH, Dunn CW, Cartwright P. Phylogenomic Analyses Support Traditional Relationships within Cnidaria. Plos One. 10: e0139068. PMID 26465609 DOI: 10.1371/Journal.Pone.0139068  0.778
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  0.464
2015 Church SH, Ryan JF, Dunn CW. Automation and Evaluation of the SOWH Test with SOWHAT. Systematic Biology. 64: 1048-58. PMID 26231182 DOI: 10.1093/Sysbio/Syv055  0.715
2015 Laumer CE, Bekkouche N, Kerbl A, Goetz F, Neves RC, Sørensen MV, Kristensen RM, Hejnol A, Dunn CW, Giribet G, Worsaae K. Spiralian Phylogeny Informs the Evolution of Microscopic Lineages. Current Biology : Cb. 25: 2000-6. PMID 26212884 DOI: 10.1016/J.Cub.2015.06.068  0.443
2015 Siebert S, Goetz FE, Church SH, Bhattacharyya P, Zapata F, Haddock SH, Dunn CW. Stem cells in Nanomia bijuga (Siphonophora), a colonial animal with localized growth zones. Evodevo. 6: 22. PMID 26090088 DOI: 10.1186/S13227-015-0018-2  0.709
2015 Church SH, Siebert S, Bhattacharyya P, Dunn CW. The histology of Nanomia bijuga (Hydrozoa: Siphonophora). Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 324: 435-49. PMID 26036693 DOI: 10.1002/Jez.B.22629  0.749
2015 Dunn CW, Leys SP, Haddock SH. The hidden biology of sponges and ctenophores. Trends in Ecology & Evolution. 30: 282-91. PMID 25840473 DOI: 10.1016/J.Tree.2015.03.003  0.639
2015 Reich A, Dunn C, Akasaka K, Wessel G. Phylogenomic analyses of Echinodermata support the sister groups of Asterozoa and Echinozoa. Plos One. 10: e0119627. PMID 25794146 DOI: 10.1371/journal.pone.0119627  0.339
2015 González VL, Andrade SC, Bieler R, Collins TM, Dunn CW, Mikkelsen PM, Taylor JD, Giribet G. A phylogenetic backbone for Bivalvia: an RNA-seq approach. Proceedings. Biological Sciences / the Royal Society. 282: 20142332. PMID 25589608 DOI: 10.1098/Rspb.2014.2332  0.472
2015 Reich A, Dunn C, Akasaka K, Wessel G. Phylogenomic analyses of echinodermata support the sister groups of Asterozoa and Echinozoa Plos One. 10. DOI: 10.1371/Journal.Pone.0119627  0.439
2015 Zapata F, Wilson NG, Howison M, Andrade SCS, Jörger KM, Schrödl M, Goetz FE, Giribet G, Dunn CW. Correction to Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda Proceedings of the Royal Society B: Biological Sciences. 282: 20142941. DOI: 10.1098/Rspb.2014.2941  0.432
2014 Zapata F, Wilson NG, Howison M, Andrade SC, Jörger KM, Schrödl M, Goetz FE, Giribet G, Dunn CW. Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. Proceedings. Biological Sciences / the Royal Society. 281: 20141739. PMID 25232139 DOI: 10.1098/Rspb.2014.1739  0.496
2014 Dunn CW. Reconsidering the phylogenetic utility of miRNA in animals. Proceedings of the National Academy of Sciences of the United States of America. 111: 12576-7. PMID 25122678 DOI: 10.1073/Pnas.1413545111  0.36
2014 Howison M, Zapata F, Edwards EJ, Dunn CW. Bayesian genome assembly and assessment by markov chain monte carlo sampling. Plos One. 9: e99497. PMID 24968249 DOI: 10.1371/Journal.Pone.0099497  0.365
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, 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  0.66
2014 Dunn CW, Giribet G, Edgecombe GD, Hejnol A. Animal phylogeny and its evolutionary implications Annual Review of Ecology, Evolution, and Systematics. 45: 371-395. DOI: 10.1146/Annurev-Ecolsys-120213-091627  0.405
2013 Siebert S, Pugh PR, Haddock SH, Dunn CW. Re-evaluation of characters in Apolemiidae (Siphonophora), with description of two new species from Monterey Bay, California. Zootaxa. 3702: 201-32. PMID 26146720 DOI: 10.11646/Zootaxa.3702.3.1  0.393
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  0.468
2013 Dunn CW, Howison M, Zapata F. Agalma: an automated phylogenomics workflow. Bmc Bioinformatics. 14: 330. PMID 24252138 DOI: 10.1186/1471-2105-14-330  0.437
2013 Howison M, Zapata F, Dunn CW. Toward a statistically explicit understanding of de novo sequence assembly. Bioinformatics (Oxford, England). 29: 2959-63. PMID 24021385 DOI: 10.1093/Bioinformatics/Btt525  0.379
2013 Dunn CW, Luo X, Wu Z. Phylogenetic analysis of gene expression. Integrative and Comparative Biology. 53: 847-56. PMID 23748631 DOI: 10.1093/Icb/Ict068  0.425
2013 Helm RR, Siebert S, Tulin S, Smith J, Dunn CW. Characterization of differential transcript abundance through time during Nematostella vectensis development. Bmc Genomics. 14: 266. PMID 23601508 DOI: 10.1186/1471-2164-14-266  0.356
2013 Dunn CW. Evolution: out of the ocean. Current Biology : Cb. 23: R241-3. PMID 23518055 DOI: 10.1016/J.Cub.2013.01.067  0.304
2012 Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SCS, Rouse GW, Giribet G, Dunn CW. Correction: Corrigendum: Resolving the evolutionary relationships of molluscs with phylogenomic tools Nature. 493: 708-708. DOI: 10.1038/Nature11736  0.346
2011 Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SC, Rouse GW, Giribet G, Dunn CW. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature. 480: 364-7. PMID 22031330 DOI: 10.1038/Nature10526  0.446
2011 Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR, Smith SA, Shaner N, Haddock SH, Dunn CW. Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows. Plos One. 6: e22953. PMID 21829563 DOI: 10.1371/Journal.Pone.0022953  0.393
2011 Edgecombe GD, Giribet G, Dunn CW, Hejnol A, Kristensen RM, Neves RC, Rouse GW, Worsaae K, Sørensen MV. Higher-level metazoan relationships: Recent progress and remaining questions Organisms Diversity and Evolution. 11: 151-172. DOI: 10.1007/S13127-011-0044-4  0.496
2009 Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, Edgecombe GD, Martinez P, Baguñà J, Bailly X, Jondelius U, Wiens M, Müller WE, Seaver E, Wheeler WC, Martindale MQ, ... ... Dunn CW, et al. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proceedings. Biological Sciences / the Royal Society. 276: 4261-70. PMID 19759036 DOI: 10.1098/Rspb.2009.0896  0.486
2008 Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen MV, Haddock SH, Schmidt-Rhaesa A, Okusu A, Kristensen RM, et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 452: 745-9. PMID 18322464 DOI: 10.1038/Nature06614  0.467
2008 Smith SA, Dunn CW. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics (Oxford, England). 24: 715-6. PMID 18227120 DOI: 10.1093/Bioinformatics/Btm619  0.319
2008 Cartwright P, Evans NM, Dunn CW, Marques AC, Miglietta MP, Schuchert P, Collins AG. Phylogenetics of Hydroidolina (Hydrozoa: Cnidaria) Journal of the Marine Biological Association of the United Kingdom. 88: 1663-1672. DOI: 10.1017/S0025315408002257  0.395
2007 Oota H, Dunn CW, Speed WC, Pakstis AJ, Palmatier MA, Kidd JR, Kidd KK. Conservative evolution in duplicated genes of the primate Class I ADH cluster. Gene. 392: 64-76. PMID 17204375 DOI: 10.1016/J.Gene.2006.11.008  0.364
2007 Giribet G, Dunn CW, Edgecombe GD, Rouse GW. A modern look at the animal tree of life Zootaxa. 61-79. DOI: 10.11646/Zootaxa.1668.1.8  0.412
2006 Dunn CW, Wagner GP. The evolution of colony-level development in the Siphonophora (Cnidaria:Hydrozoa). Development Genes and Evolution. 216: 743-54. PMID 16983540 DOI: 10.1007/S00427-006-0101-8  0.562
2006 Matus DQ, Copley RR, Dunn CW, Hejnol A, Eccleston H, Halanych KM, Martindale MQ, Telford MJ. Broad taxon and gene sampling indicate that chaetognaths are protostomes. Current Biology : Cb. 16: R575-6. PMID 16890509 DOI: 10.1016/J.Cub.2006.07.017  0.418
2006 Matus DQ, Pang K, Marlow H, Dunn CW, Thomsen GH, Martindale MQ. Molecular evidence for deep evolutionary roots of bilaterality in animal development. Proceedings of the National Academy of Sciences of the United States of America. 103: 11195-200. PMID 16837574 DOI: 10.1073/Pnas.0601257103  0.311
2005 Dunn CW, Pugh PR, Haddock SH. Molecular phylogenetics of the siphonophora (Cnidaria), with implications for the evolution of functional specialization. Systematic Biology. 54: 916-35. PMID 16338764 DOI: 10.1080/10635150500354837  0.416
2005 Dunn CW. 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 : An Official Publication of the American Association of Anatomists. 234: 835-45. PMID 15986453 DOI: 10.1002/Dvdy.20483  0.395
2005 Haddock SHD, Dunn CW, Pugh PR. A re-examination of siphonophore terminology and morphology, applied to the description of two new prayine species with remarkable bio-optical properties Journal of the Marine Biological Association of the United Kingdom. 85: 695-707. DOI: 10.1017/S0025315405011616  0.338
2004 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP. Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings. Biological Sciences / the Royal Society. 271: 2201-7. PMID 15539344 DOI: 10.1098/Rspb.2004.2848  0.737
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