complete publications

PARICHY LAB

Complete publications and preprints

Aman AJ, Saunders LM, Carr AA, Srivatsan SR, Eberhard CD, Carrington B, Watkins-Chow D, Pavan WJ, Trapnell C, Parichy DM. 2023. Transcriptomic proﬁling of tissue environments critical for post-embryonic patterning and morphogenesis of zebraﬁsh skin. eLife 10.7554/eLife.86670.1. PDF WEB
Huang D, Lewis VM, Toomey MB, Corbo JC, Parichy DM. 2021. Development and genetics of red coloration in the zebrafish relative Danio albolineatus. eLife 10:e70253. PDF WEB
Lalonde RL, Kemmler CL, Riemslagh FW, Aman AJ, Kresoja-Rakic J, Moran HR, Nieuwenhuize S, Parichy DM, Burger A, Mosimann M. 2022. Heterogeneity and genomic loci of ubiquitous Cre reporter transgenes in zebrafish. Developmental Dynamics doi.org/10.1002/dvdy.499
Aman AJ, Kim M, Saunders LM, Parichy DM. 2021. Thyroid hormone couples skin morphogenesis to body growth during post-embryonic zebrafish development. Developmental Biology 477:205–218. PDF WEB
McCluskey, B. M., Liang, Y., Lewis, V. M., Patterson, L. B. and Parichy, D. M. 2021. Pigment pattern morphospace of Danio fishes: evolutionary diversification and mutational effects. Biology Open bio.058814. PDF WEB
McCluskey BM, Uji S, Mancusi JL, Postlethwait JH, Parichy DM. 2021. A complex genetic architecture in zebrafish relatives Danio quagga and D. kyathit underlies development of stripes and spots. PLoS Genetics 17:e1009364. PDF WEB
Salis P, Roux N, Huang D, Marcionetti A, Mouginot P, Reynaud M, Salles O, Salamin N, Pujol B, Parichy DM, Planes S, Laudet V. 2021. Thyroid hormones regulate the formation and environmental plasticity of white bars in clownfishes. Proc. Natl Acad. Sci. USA 118:e2101634118. PDF WEB
Eom DS, Patterson LB, Bostic RR, Parichy DM. 2021. Immunoglobulin superfamily receptor Junctional adhesion molecule 3 (Jam3) requirement for melanophore survival and patterning during formation of zebrafish stripes. Developmental Biology 476:314–327. PDF WEB
Parichy DM. 2021. Evolution of pigment cells and pattern: recent insights from teleost fishes. Current Opinion in Genetics and Development 69:88–96. PDF WEB
Gur D, Bain E, Johnson K, Aman AJ, Pasoili A, Flynn JD, Allen MC, Deheyn DD, Oron D, Levkowitz G, Lee JC, Lippincott-Schwartz J, Parichy DM. 2020. In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning. Nature Communications 11:6391. PDF WEB
Aman AJ, Parichy DM. 2020. “Zebrafish Integumentary System,” Chapter 4 in: Zebrafish in Biomedical Research (Cartner SC, Eisen J, Farmer S, Kent MS, Sanders GE, Guillemin K, Eds.). Elsevier. PDF
Parichy DM. 2020. “Zebrafish Pigmentation,” Chapter 21 in: Zebrafish in Biomedical Research (Cartner SC, Eisen J, Farmer S, Kent MS, Sanders GE, Guillemin K, Eds.). Elsevier. PDF
Parichy DM, Postlethwait J. 2020. “The Biotic and Abiotic Environment of Zebrafish,” in: Behavior and Neural Genetics of Zebrafish (Gerlai R, Ed.). Elsevier. PDF
Volkov LI, Kim-Han J, Saunders LM, Parichy DM, Corbo JC. 2020. Thyroid hormone regulates two mechanisms of long-wavelength vision with different transcription factor dependencies. Proc. Natl Acad. Sci. USA pnas.1920086117. WEB
Aman AJ, Parichy DM. 2020. “Zebrafish Integumentary System,” Chapter 4 in: Zebrafish in Biomedical Research (Cartner SC, Eisen J, Farmer S, Kent MS, Sanders GE, Guillemin K, Eds.). Elsevier. PDF
Patterson LB, Parichy DM. 2019. Zebraﬁsh pigment pattern formation: insights into the development and evolution of adult form. Annual Review of Genetics 53:505–530. PDF WEB
Saunders LM, Mishra AK, Aman AJ, Lewis VM, Toomey MB, Packer JS, Qiu X, McFaline-Figueroa JL, Corbo JC, Trapnell C, Parichy DM. 2019. Thyroid hormone regulates distinct paths to maturation in pigment cell lineages. eLife 8:e45181. PDF WEB
Lewis VM, Saunders LM, Larson TA, Bain EJ, Sturiale SL, Gur D, Chowdhury S, Flynn JD, Allen MC, Deheyn DD, Lee JC, Simon JA, Lippincott-Schwartz J, Raible DW, Parichy DM. 2019. Fate plasticity and reprogramming in genetically distinct populations of Danio leucophores. Proc. Natl Acad. Sci. USA pnas.1901021116. PDF WEB
Salis P, Lorin T, Lewis V, Rey C, Marcionetti A, Escande M-L, Toux N, Besseau L, Salamin N, Sémon M, Parichy DM, Volff J-N, Laudet V. 2019. Developmental and comparative transcriptomic identification of iridophore contribution to white barring in clownfish. Pigment Cell and Melanoma Research 32:391–402. PDF WEB
Spiewak JE, Bain EJ, Liu J, Kou K, Patterson LB, Kou K, Sturiale SL, Diba P, Eisen JS, Braasch I, Ganz J, Parichy DM. Evolution of endothelin signaling and diversification of adult pigment pattern in Danio fishes. PLoS Genetics 24:e1007538. PDF WEB
Aman AJ, Fulbright AN, Parichy DM. 2018. Wnt/β-catenin regulates an ancient signaling network during zebrafish scale development. eLife 10.7554/eLife.37001. PDF WEB
Eom DS, Parichy DM. 2017. A macrophage relay for long distance signaling during post-embryonic tissue remodeling. Science 355:1317–1320. PDF VIDEOS (115 Mb zip) WEB
Woodcock MR, Vaiugn-Wbolfe J, Elias A, Kump, DK, Kendall KD, Timoshevskaya N, Timoshevskiy V, Perrt DW, Smith JJ, Spiewak JE, Parichy DM, Voss SR. 2017. Identification of mutant genes and introgressed tiger salamander DNA in the laboratory axolotl, Ambystoma mexicanum. Scientific Reports 7:6 PDF
Hur M, Gistelinck CA, Huber P, Lee J, Thompson MH, Monstad-Rios AT, Watson CJ, McMenamin, SK, Willaert A, Parichy DM, Coucke P, Kwon RY. 2017. microCT-based skeletal phenomics in zebrafish reveals virtues of deep phenotyping at the whole-organism scale. eLife 6:e26014. PDF WEB
Parichy DM. 2016. News and Views: The gar is a fish...is a bird...is a mammal? Nature Genetics 48:344–345. PDF
McMenamin SK, Chandless MN, Parichy DM. 2016. Chapter 18. Working with post-embryonic zebrafish. Methods in Cell Biology: The Zebrafish: Cellular and Developmental Biology Part B, 4th Edition 134:587–607. PDF
Eom DS, Bain EJ, Patterson LB, Grout ME, Parichy DM. 2015. Long-distance communication by specialized cellular projections during pigment pattern development and evolution. eLife 10.7554/eLife.12401. PDF VIDEOS (65 Mb zip) WEB
Parichy DM. 2015. Advancing biology through a deeper understanding of zebrafish ecology and evolution. eLife 4:05636. PDF WEB
Patterson LB, Bain EJ, Parichy DM. 2014. Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution. Nature Communications 5:6299. PDF WEB
McMenamin SK, Bain EJ, McCann AE, Patterson LB, Eom DS, Waller ZP, Hamill JC, Kuhlman JA, Eisen JS, Parichy DM. 2014. Thyroid hormone-dependent adult pigment cell lineage and pattern in zebrafish. Science 345:1358–1361. PDF WEB
Parichy DM, Spiewak JE. 2014. Origins of adult pigmentation: developmental diversity in pigment stem cells and lineages and implications for pattern evolution. Pigment Cell and Melanoma Research 28:31–50. PDF WEB
Inouye S, Kondo S, Parichy DM, Watanabe S. 2014. Tetraspanin-3c requirement for pigment cell interactions and boundary formation in zebrafish adult pigment stripes. 2013. Pigment Cell and Melanoma Research 27:190–200. PDF
Hamada H, Watanabe M, Lau HE, Nishida T, Hasegawa T, Parichy DM, Kondo S. 2014. Involvement of Delta–Notch signaling in zebrafish adult stripe patterning. Development 141:1–7. PDF
Patterson LB, Parichy DM. 2013. Interactions with iridophores and the tissue environment required for patterning melanophores and xanthophores during zebrafish adult pigment stripe formation. PLoS Genetics 9:e1003561. PDF WEB
McMenamin SK, Minchin JEN, Gordon TN, Rawls JF, Parichy DM. 2013. Dwarfism and increased adiposity in the gh1 mutant zebrafish vizzini. Endocrinology 154:1476–1487. PDF WEB
Eom DS, Inouye S, Patterson LB, Gordon TG, Kondo S, Watanabe M, Parichy DM. 2012. Melanophore migration and survival during zebrafish adult pigment stripe development require the immunoglobulin superfamily adhesion molecule, Igsf11. PLoS Genetics 8:e1002899. 154:1476–1487. PDF WEB
McMennamin SK, Parichy DM. 2012. Metamorphosis in teleosts. Current Topics in Cell and Developmental Biology 103:128–165. PDF WEB
Roeselers G, Mittge EK, Stevens WZ, Parichy DM, Cavanauh CM, Guillemin K, Rawls JF. 2011. Evidence for a core gut microbiota in the zebrafish. ISME J 5:1595–1608. PDF
Budi EH, Patterson LB, Parichy DM. 2011. Post-embryonic nerve-associated precursors to adult pigment cells: genetic requirements and dynamics of morphogenesis and differentiation. PLoS Genetics 7:e1002044. PDF WEB
Elizondo MR, Budi EH, Parichy DM. 2010. trpm7 regulation of in vivo cation homeostasis and kidney function involves stanniocalcin1 and fgf23. Endocrinology 151:5700–5709. PDF WEB
Larson TA, Gordon TN, Lau E, Parichy DM. 2010. Defects in oligodendrocyte and Schwann cell development, pigment pattern, and craniofacial morphology in puma mutant zebrafish having an alpha tubulin mutation. Developmental Biology 346:296–309. PDF
Curran K, Lister JA, Kunkel GR, Prendergast, Parichy DM, Raible DW. 2010. Interplay between Foxd3 and Mitf regulate cell fate plasticity in the zebraﬁsh neural crest. Developmental Biology 344:107–118. PDF
Christiansen HE, Lang MR, Pace JM, Parichy DM. 2009. Critical roles for col27a1a and col27a1b in notochord morphogenesis, vertebral mineralization and post-embryonic axial growth. PLoS One 4e:8481. PDF WEB
Lang MR, Gordon TN, Patterson LB, Johnson SL, Parichy DM. 2009. Basonuclin-2 functions in adult pigment pattern formation and female fertility. PLoS Genetics 5:e1000744. PDF WEB
Parichy DM, Elizondo MR, Mills MG, Gordon TN, Engeszer RE. 2009. Normal table of post-embryonic zebrafish development: staging by externally visible anatomy of the living fish. Developmental Dynamics 238:2975–3015. PDF WEB
Hultman KA, Budi EH, Teasley DC, Gottleib AY, Parichy DM, Johnson SL. 2009. Defects in ErbB-dependent establishment of adult melanocyte stem cells reveals independent origins for embryonic and regeneration melanocytes. PLoS Genetics 5:e1000544. PDF
Budi EH, Patterson LB, Parichy DM. 2008. Embryonic requirements for Erbb signaling in neural crest development and adult pigment pattern formation. Development 135:2603–2614. PDF WEB
Engeszer RE, Wang G, Ryan MJ, Parichy DM. 2008. Sex-specific perceptual space for a vertebrate basal social aggregative behavior. Proc. Natl Acad. Sci. USA 105:929–933. PDF WEB
Kelsh RN, Parichy DM. 2007. “Pigmentation.” In: Fish Larval Physiology (Finn RN, Kapoor BG, Eds.). Science Publishers Inc.
Engeszer RE, Alberici da Barbiano L, Ryan MJ, Parichy DM. 2007. Timing and plasticity of shoaling behaviour in the zebrafish, Danio rerio. Animal Behaviour 74:1269–1275. PDF
Parichy DM. 2007. Homology and the evolution of novelty during danio pigment pattern development. Molecular and Developmental Evolution (Journal of Experimental Zoology) 3-8:578–590. PDF
Mills MG, Nuckels RJ, Parichy DM. 2007. Deconstructing evolution of adult phenotypes: genetic analyses of kit reveal homology and evolutionary novelty during adult pigment pattern development of Danio fishes. Development 134:1081–1090. PDF WEB
Engeszer RE, Patterson LB, Rao AA, Parichy DM. 2007. Zebrafish in the wild: a review of natural history and new notes from the field. Zebrafish 4:21–40. PDF WEB
Streelman JT, Peichel C, Parichy DM. 2007. Developmental genetics of adaptation in fishes: the case for novelty. Annual Review of Ecology, Evolution, and Systematics 38:655–682. PDF
Parichy DM, Reedy MV, Erickson CA. 2006. “Regulation of melanoblast migration and differentiation.” Chapter 5, in: The Pigmentary System and its Disorders, 2nd Ed. (Nordland JJ, Boissy RE, Hearing VJ, King RA, Ortonne JP, Eds.). Oxford. PDF
Parichy DM. 2006. Evolution of danio pigment pattern development. Heredity 97:200–210. PDF
Smith JJ, Kump DK, Walker JA, Parichy DM, Voss SR. 2005. A comprehensive EST linkage map for tiger salamander and Mexican axolotl: enabling gene mapping and comparative genomics in Ambystoma. Genetics 171:1161–1171. PDF
Elizondo MR, Arduini BL, Paulsen J, Macdonald EL, Sabel JL, Henion PD, Cornell RA, Parichy DM. 2005. Defective skeletogenesis with kidney stone formation in dwarf zebrafish mutant for trpm7. Current Biology 15:667–671. PDF WEB
Parichy DM. 2005. “Variation and developmental biology: prospects for the future.” Chapter 19, in: Variation: A Hierarchical Examination of a Central Concept in Biology (Hallgrimsson B, Hall BK, Eds.). Academic Press. PDF
Quigley IK, Roberts R, Manuel JL, Nuckels RJ, Herrington E, MacDonald EL, Parichy DM. 2005. Evolutionary diversification of pigment pattern in Danio fishes: differential fms dependence and stripe loss in D. albolineatus. Development 132:89–104. PDF WEB
Quigley IK, Turner JM, Nuckels RJ, Manuel JL, Budi EH, MacDonald EL, Parichy DM. 2004. Pigment pattern evolution by differential deployment of neural crest and post-embryonic melanophore lineages in Danio fishes. Development 131:6053–6069. PDF WEB
Putta, S, Smith JJ, Walker J, Rondet M, Weisrock DW, Monaghan J, Samuels AK, Kump K, King DC, Maness NJ, Habermann B, Tanaka E, Bryant SV, Gardiner DM, Parichy DM, Voss SR. 2004. From biomedicine to natural history research: EST resources for ambystomatid salamanders. BMC Genomics 5:54. PDF
Engeszer RE, Ryan MJ, Parichy DM. 2004. Learned social preference in zebrafish. Current Biology 14:881–884. PDF WEB
Parichy DM, Turner JM, Parker NB. 2003. Essential role for puma in development of post-embryonic neural crest-derived cells in zebrafish. Developmental Biology 256:221–241. PDF WEB
Parichy DM, Turner JM. 2003. Zebrafish puma mutant decouples pigment pattern and somatic metamorphosis. Developmental Biology 256:242–257. PDF WEB
Parichy DM, Turner JM. 2003. Temporal and cellular requirements for Fms signaling during zebrafish adult pigment pattern development. Development 130:817–833. PDF WEB
Parichy DM. 2003. Pigment patterns: fish in stripes and spots. Current Biology 13:R947–R950. PDF
Quigley IK, Parichy DM. 2002. Pigment pattern formation in zebrafish: a model for developmental genetics and the evolution of form. Microsc. Res. Tech 58:442–455. PDF
Voss SR, Smith JJ, Gardiner D, Parichy DM. 2001. Conserved vertebrate chromosome segments in the large salamander genome. Genetics 158:735–746. PDF
Voss SR, Parichy DM. 2001. Salamander genome project. Axolotl Newsletter Issue 28.
Parichy DM, Johnson SL. 2001. Zebrafish hybrids suggest genetic mechanisms of pigment pattern diversification in Danio. Development, Genes and Evolution 211:319–328. PDF WEB
Parichy DM. 2001. “Pigment patterns of ectothermic vertebrates: heterochronic vs. non-heterochronic models for pigment pattern evolution.” In: Beyond Heterochrony (M. Zelditch, Ed.). Wiley. PDF
Parichy DM. 2001. Homology and evolutionary novelty in the deployment of extracellular matrix molecules during pigment pattern formation in salamanders (Taricha, Ambystoma). Molecular and Developmental Evolution (Journal of Experimental Zoology) 291:13–24. PDF
Parichy DM, Mellgren EM, Rawls JF, Lopes SS, Kelsh RN, Johnson SL. 2000. Mutational analysis of endothelin receptor b1 (rose) during neural crest and pigment pattern development in the zebrafish, Danio rerio. Developmental Biology, 227:294–306. PDF WEB
Parichy DM, Ransom DG, Paw B, Zon L, Johnson SL. 2000. An orthologue of the kit-related gene fms is required for development of neural crest–derived xanthophores and a subpopulation of adult melanocytes in the zebrafish, Danio rerio. Development, 127:3031–3044. PDF
Parichy DM, Rawls JF, Whitfield T, Pratt SJ, Johnson SL. 1999. Zebrafish sparse corresponds to an orthologue of c-kit and is required for the morphogenesis of a subpopulation of melanocytes, but is not essential for hematopoiesis or primordial germ cell development. Development 126:3425–3436. PDF
Parichy DM, Stigson M, Voss SR. 1999. Genetic analysis of steel and the PG-M/versican-encoding gene AxPG as candidate genes for the white (d) pigmentation mutant in the salamander Ambystoma mexicanum. Development, Genes and Evolution 209:349–356. PDF
Parichy DM. 1998. Experimental analysis of character coupling across a complex life cycle: pigment pattern metamorphosis in the tiger salamander, Ambystoma tigrinum tigrinum. Journal of Morphology 237:53–67. PDF
Reedy MV, Parichy DM, Erickson CA, Mason K, Frost-Mason SK. 1998. “Regulation of melanoblast migration and differentiation.” Chapter 5, in: The Pigmentary System and its Disorders (Nordland JJ, Boissy RE, Hearing VJ, King RA, Ortonne JP, Eds.). Oxford.
Parichy DM. 1996. Salamander pigment patterns: how can they be used to study developmental mechanisms and their evolutionary transformation? International Journal of Developmental Biology 40:871–884. PDF
Parichy DM. 1996. When neural crest and placodes collide: interactions between melanophores and the lateral lines that generate stripes in the salamander Ambystoma tigrinum tigrinum (Ambystomatidae). Developmental Biology 175:283–300. PDF
Parichy DM. 1996. Pigment patterns of larval salamanders (Ambystomatidae, Salamandridae): the role of the lateral line sensory system and the evolution of pattern-forming mechanisms. Developmental Biology 175:265–282. PDF
Parichy DM, Kaplan RH. 1995. Maternal investment and developmental plasticity: functional consequences for locomotor performance of hatchling frog larvae. Functional Ecology 9:606–617. PDF
Parichy DM, Kaplan RH. 1992. Maternal effects on offspring growth and development depend on environmental quality in the frog, Bombina orientalis. Oecologia 91:579–586.
Parichy DM, Kaplan RH. 1992. Developmental consequences of tail injury on the oriental fire-bellied toad, Bombina orientalis. Copeia 1992:129–137.
Parichy DM, Shaffer HB, Mangel M. 1992. Heterochrony as a unifying theme in evolution and development. Evolution 46:1252–1254.