• Zapata F, Villarroel D. A new species of Escallonia (Escalloniaceae) from the inter-Andean tropical dry forests of Bolivia. PeerJ 7:e6328 doi repo


  • Munro C, Siebert S, Zapata F, Howison M, Damian-Serrano A, Church SH, Goetz FE, Pugh PR, Haddock SHD, Dunn CW (2018) Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution. Molecular Phylogenetics and Evolution. 127:823-833. doi repo
  • Huang A, Howison M, Zapata F, Lawrence CE, Dunn CW (2018) Revising transcriptome assemblies with phylogenetic information. doi repo
  • Dunn CW, Zapata F Munro C, Siebert S, Hejnol A. (2018) Pairwise comparisons are problematic when analyzing functional genomic data across species. Proceedings of the National Academy of Sciences, USA. 115(3):E409-E417 doi repo
  • Cadena CD, Zapata F, Jiménez I. (2018) Issues and Perspectives in Species Delimitation using Phenotypic Data - Atlantean Evolution in Darwin’s Finches. Systematic Biology. 67(2):181-194 doi repo


  • Guang A^, Zapata F^, Howison M, Dunn CW. (2016) An integrated perspective on phylogenetic workflows. Trends in Ecology & Evolution 31(2):116-126 (^ equal contribution) doi


  • 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 SHD, Dunn CW, and Cartwright P. (2015) Phylogenomic analyses support traditional relationships within Cnidaria. PLOS One 10(10): e0139068 doi repo
  • Siebert S, Goetz FE, Church SH, Bhattacharyya P, Zapata F, Haddock SHD , and Dunn CW. (2015) Stem Cells in a Colonial Animal with Localized Growth Zones. EvoDevo 6:22 doi repo


  • Weeks A, Zapata F, Pell SK , Daly DC, Mitchell J, and Fine PVA. (2014) To move or to evolve: contrasting patterns of intercontinental connectivity and climatic niche evolution in the Terebinthaceae (Anacardiaceae and Burseraceae). Frontiers in Genetics-Evolutionary and Population Genetics 5: 409 doi
  • Zapata F, Wilson NG, Howison M, Andrade SCS, Jörger KM, Schrödl M, Goetz FE, Giribet G, and Dunn CW. (2014) Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda. Proceedings of the Royal Society B: Biological Sciences 281:1471-2954 doi repo
  • Howison M, Zapata F, Edwards EJ, and Dunn CW. (2014) Bayesian genome assembly and assessment by Markov Chain Monte Carlo sampling. PLOS One 9:e99497 doi repo report
  • Fine PVA, Zapata F, Daly DC. (2014) Investigating processes of Neotropical rain forest tree diversification by examining the evolution and historical biogeography of the Protieae (Burseraceae). Evolution 68:1988-2004 doi repo


  • Dunn CW, Howison M, Zapata F. (2013) Agalma: an automated phylogenomics workflow. BMC Bioinformatics 14:330. doi repo report
  • Howison M, Zapata F, Dunn CW. (2013) Toward a statistically explicit understanding of de novo sequence assembly. Bioinformatics 29:2959-2963 doi
  • Sede SM, Dürnhöfer SI, Morello S, Zapata F. Phylogeny of Escallonia (Escalloniaceae) based on plastid DNA sequence data. Botanical Journal of the Linnean Society 173:442-451 doi
  • Zapata F, Fine PVA. (2013) Diversification of the monoterpene synthase gene family (TPSb) in Protium, a diverse genus of tropical trees: multiple copies under different selection regimes and consequences for functional diversity. Molecular Phylogenetics and Evolution 68:432-442 doi
  • Zapata F. (2013) A multilocus phylogenetic analysis of Escallonia: Diversification in montane South America. American Journal of Botany 100:526-545 doi
  • Fine PVA, Zapata F, Daly DC, Misiewicz TM, Mesones I, Cooper HF, Barbosa CE. (2013) The importance of environmental heterogeneity and spatial distance in generating phylogeographic structure in edaphic specialist and generalist tree species of Protium (Burseraceae) across the Amazon basin. Journal of Biogeography 40:646-661 doi


  • Zapata F, Jiménez I. (2012) Species delimitation: Inferring gaps in morphology across geography. Systematic Biology 61:179-194 doi repo (2013 Publisher’s Award for Excellence in Systematics Research)


  • Avraham S, Tung C-W, Ilic K, Jaiswal P, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens PF, Vincent L, Zapata F, Ware D. (2008) The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Research 36:D449-D454 doi


  • Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, Whitman NT, McCouch SR, Schaeffer ML, Ware DH, Stein LD, Rhee SY. The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiology 143:587-599 doi


  • Pujar A, Jaiswal P, Kellogg EA, Ilic K, Vincent L, Avraham S, Stevens PF, Zapata F, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Ware D, McCouch S. (2006) Whole-Plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology 142:414-428 doi


  • Jaiswal P, Avraham S, Ilic K, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens PF, Vincent L, Ware D, Zapata F. (2005) Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics 6:388-397 doi