Preprint
88. Bucao, C.F., Aletti, C., Moretti, S., Thompson, A.W., Racicot, B.L., Wilson, C.A., Bobe, J., Braasch, I., Guigen, Y., Postlethwait, J.H., and Robinson-Rechavi, M. (2024) Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs. bioRxiv 2024.11.11.623020. Link
87. Barker, A.V., Carlson, K.B., Wcisel, D.J., Birchler De Allende, I., Braasch, I., Fisk, M., Dornburg, A., and Yoder, J.A. (2024) Holostean genomes reveal evolutionary novelty in the vertebrate immunoproteasome that have implications for MHCI function. bioRxiv 2024.11.01.621518. Link
86. Yuan, H., Mancuso, C.A., Johnson, K., Braasch, I., and Krishnan, A. (2024) Computational strategies for cross-species knowledge transfer and translational biomedicine. arXiv:2408.08503. Link
85. Wei, J., Wood, T.W.P., Flaherty, K., Enny, A., Andrescavage, A., Brazer, D., Navon, D., Stewart, T.A., Cohen, H., Shanabag, A., Kuroda, S., Braasch, I., and Nakamura, T. (2023) Distinct ossification trade-offs illuminate the shoulder girdle reconfiguration at the water-to-land transition. bioRxiv 2023.07.17.547998. Link
87. Barker, A.V., Carlson, K.B., Wcisel, D.J., Birchler De Allende, I., Braasch, I., Fisk, M., Dornburg, A., and Yoder, J.A. (2024) Holostean genomes reveal evolutionary novelty in the vertebrate immunoproteasome that have implications for MHCI function. bioRxiv 2024.11.01.621518. Link
86. Yuan, H., Mancuso, C.A., Johnson, K., Braasch, I., and Krishnan, A. (2024) Computational strategies for cross-species knowledge transfer and translational biomedicine. arXiv:2408.08503. Link
85. Wei, J., Wood, T.W.P., Flaherty, K., Enny, A., Andrescavage, A., Brazer, D., Navon, D., Stewart, T.A., Cohen, H., Shanabag, A., Kuroda, S., Braasch, I., and Nakamura, T. (2023) Distinct ossification trade-offs illuminate the shoulder girdle reconfiguration at the water-to-land transition. bioRxiv 2023.07.17.547998. Link
2024
84. Thompson, A.W., Black, A.C., Huang, Y., Shi, Q., Furness, A.I., Braasch, I., Hoffmann, F.G., and Ortí, G. (2024) Transcriptomic data support phylogenetic congruence and reveal genomic changes associated with the repeated evolution of annualism in aplocheiloid killifishes (Cyprinodontiformes). Molecular Phylogenetics and Evolution 201, 108209. Link
83. Shah, M.A., Xie, X., Rodina, M., Stundl, J., Braasch, I., Šindelka, R., Rzepkowska, M., Saito, T., and Pšenička, M. (2024) Sturgeon Gut Development: A Unique Yolk Utilization Strategy Among Vertebrates. Frontiers in Cell and Developmental Biology 12, 1358702. Link
82. Mathavarajah, S., Thompson, A.W., Stoyek, M.R., Quinn, T.A., Roy, S., Braasch, I., Roger, A. J., Langelaan, D. N., and Dellaire, G. (2024) Suppressors of cGAS-STING are downregulated during fin-limb regeneration and aging in aquatic vertebrates. Journal of Experimental Zoology B: Molecular and Developmental Evolution 342, 241-251. Link
81. Schneider, P.N., Seemann, F., Harris, M.P., and Braasch, I. (2024) Trawling aquatic life for new models in biomedical research and evolutionary developmental biology. Journal of Experimental Zoology B: Molecular and Developmental Evolution 342, 123-125. Link
80. Braasch, I. (2024) In the Spotlight - Established Researcher. Journal of Experimental Zoology B: Molecular and Developmental Evolution 342, 121-122. Link
79. Valentini, P., Akula, S., Alvarado-Vazquez, A., Hallgren, J., Fu, Z., Racicot, B., Braasch, I., Thorpe, M., and Hellman, L. (2024). Extended Cleavage Specificity of Two Hematopoietic Serine Proteases from a Ray-Finned Fish, the Spotted Gar (Lepisosteus oculatus). International Journal of Molecular Sciences 25, 1669. Link
78. Imaizumi, G., Ushio, K., Nishihara, H., Braasch, I., Watanabe, E., Kumagai, S., Furuta, T., Matsuzaki, K., Romero, M.F., Kato, A., and Nagashima, A. (2024) Functional divergence in solute permeability between ray-finned fish-specific paralogs of aqp10. Genome Biology and Evolution 16, evad221. Link
83. Shah, M.A., Xie, X., Rodina, M., Stundl, J., Braasch, I., Šindelka, R., Rzepkowska, M., Saito, T., and Pšenička, M. (2024) Sturgeon Gut Development: A Unique Yolk Utilization Strategy Among Vertebrates. Frontiers in Cell and Developmental Biology 12, 1358702. Link
82. Mathavarajah, S., Thompson, A.W., Stoyek, M.R., Quinn, T.A., Roy, S., Braasch, I., Roger, A. J., Langelaan, D. N., and Dellaire, G. (2024) Suppressors of cGAS-STING are downregulated during fin-limb regeneration and aging in aquatic vertebrates. Journal of Experimental Zoology B: Molecular and Developmental Evolution 342, 241-251. Link
81. Schneider, P.N., Seemann, F., Harris, M.P., and Braasch, I. (2024) Trawling aquatic life for new models in biomedical research and evolutionary developmental biology. Journal of Experimental Zoology B: Molecular and Developmental Evolution 342, 123-125. Link
80. Braasch, I. (2024) In the Spotlight - Established Researcher. Journal of Experimental Zoology B: Molecular and Developmental Evolution 342, 121-122. Link
79. Valentini, P., Akula, S., Alvarado-Vazquez, A., Hallgren, J., Fu, Z., Racicot, B., Braasch, I., Thorpe, M., and Hellman, L. (2024). Extended Cleavage Specificity of Two Hematopoietic Serine Proteases from a Ray-Finned Fish, the Spotted Gar (Lepisosteus oculatus). International Journal of Molecular Sciences 25, 1669. Link
78. Imaizumi, G., Ushio, K., Nishihara, H., Braasch, I., Watanabe, E., Kumagai, S., Furuta, T., Matsuzaki, K., Romero, M.F., Kato, A., and Nagashima, A. (2024) Functional divergence in solute permeability between ray-finned fish-specific paralogs of aqp10. Genome Biology and Evolution 16, evad221. Link
2023
77. Xu, M.R.X, Liao,Z.Y., Brock, J.R., Kang, D., Li, G.Y., Chen, Z.Q., Wang, Y.H., Gao, Z.N. , Agarwal, G. , Wei, K.H.C, Shao, F., Pang, S., Platts, A.E., van de Velde, J., Lin. H.M., Teresi, S.J., Bird, K., Niederhuth, C.E., Xu, J.G., Yu, G.H., Yang, J.Y., Dai, S.F., Nelson, A., Braasch, I., Zhang, X.G., Schartl, M., Edger, P.P., Han, M.J., and Zhang, H.H. (2023) Maternal dominance contributes to subgenome differentiation in allopolyploid fishes. Nature Communications 14, 8357. Link
76. Kemmler, C.L., Smolikova, J., Moran, H., Mannion, B.J., Knapp, D., Lim, F., Czarkwiani, A., Aguayo, V.H., Rapp, V., Fitch, O.E., Bötschi, S., Selleri, L., Farley, E., Braasch, I., Yun, M., Visel, A., Osterwalder, M., Mosimann, C., Kozmik, Z., and Burger A (2023) Conserved enhancers control notochord expression of vertebrate Brachyury. Nature Communications 14, 6594. Link
75. Stundl, J., Martik, M., Chen, D., Raja, D.A., Franěk, R., Pospisilova, A., Pšenička, M., Metscher, B. D., Braasch, I., Haitina, T., Cerny, R., Ahlberg, P., and Bronner, M. E. (2023) Ancient vertebrate dermal armor evolved from trunk neural crest. Proceedings of the National Academy of Sciences 120, e2221120120. Link
74. Mathavarajah, S., Vergunst, K. L., Williams, S. K., He, R., Maliougina, M., Habib, E. B., Park, M., Salsman, J., Roy, S., Braasch, I., Roger, A. J., Langelaan, D. N., and Dellaire, G. (2023) PML and PML-like exonucleases restrict retrotransposons in jawed vertebrates. Nucleic Acids Research 51, 3185-3204. Link
73. Parey, E., Louis, A., Montfort, J., Bouchez, O., Roques, C., Iampietro, C., Lluch, J., Castinel, A., Donnadieu, C., Desvignes, T., Floi Bucao, C., Jouanno, E., Wen, M., Mejri, S., Dirks, R., Jansen, H., Henkel, C., Chen, W.-J., Zahm, M., Cabau, C., Klopp, C., Thompson, A.W., Robinson-Rechavi, R., Braasch, I., Lecointre, G., Bobe, J., Postlethwait, J.H., Berthelot, C., Roest Crollius, H., and Guiguen, Y. (2023) Genome structures resolve the early diversification of teleost fishes. Science 379, 572–575. Link
72. Motoshima, T., Nagashima, A., Ota, C., Oka, H., Hosono, K., Braasch, I., Nishihara, H., Kato, A. (2023) Na+/Cl- cotransporter 2 is not fish-specific and widely found in amphibians, non-avian reptiles, and select mammals. Physiological Genomics 55, 113-131. Link
76. Kemmler, C.L., Smolikova, J., Moran, H., Mannion, B.J., Knapp, D., Lim, F., Czarkwiani, A., Aguayo, V.H., Rapp, V., Fitch, O.E., Bötschi, S., Selleri, L., Farley, E., Braasch, I., Yun, M., Visel, A., Osterwalder, M., Mosimann, C., Kozmik, Z., and Burger A (2023) Conserved enhancers control notochord expression of vertebrate Brachyury. Nature Communications 14, 6594. Link
75. Stundl, J., Martik, M., Chen, D., Raja, D.A., Franěk, R., Pospisilova, A., Pšenička, M., Metscher, B. D., Braasch, I., Haitina, T., Cerny, R., Ahlberg, P., and Bronner, M. E. (2023) Ancient vertebrate dermal armor evolved from trunk neural crest. Proceedings of the National Academy of Sciences 120, e2221120120. Link
74. Mathavarajah, S., Vergunst, K. L., Williams, S. K., He, R., Maliougina, M., Habib, E. B., Park, M., Salsman, J., Roy, S., Braasch, I., Roger, A. J., Langelaan, D. N., and Dellaire, G. (2023) PML and PML-like exonucleases restrict retrotransposons in jawed vertebrates. Nucleic Acids Research 51, 3185-3204. Link
73. Parey, E., Louis, A., Montfort, J., Bouchez, O., Roques, C., Iampietro, C., Lluch, J., Castinel, A., Donnadieu, C., Desvignes, T., Floi Bucao, C., Jouanno, E., Wen, M., Mejri, S., Dirks, R., Jansen, H., Henkel, C., Chen, W.-J., Zahm, M., Cabau, C., Klopp, C., Thompson, A.W., Robinson-Rechavi, R., Braasch, I., Lecointre, G., Bobe, J., Postlethwait, J.H., Berthelot, C., Roest Crollius, H., and Guiguen, Y. (2023) Genome structures resolve the early diversification of teleost fishes. Science 379, 572–575. Link
72. Motoshima, T., Nagashima, A., Ota, C., Oka, H., Hosono, K., Braasch, I., Nishihara, H., Kato, A. (2023) Na+/Cl- cotransporter 2 is not fish-specific and widely found in amphibians, non-avian reptiles, and select mammals. Physiological Genomics 55, 113-131. Link
2022
71. Annona, G., Sato, I., Pascual-Anaya, J., Braasch, I., Voss, R., Stundl, J., Soukup, V., Kuratani, S., Postlethwait, J.H., and D'Aniello, S. (2021) Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development. Proceedings of the Royal Society B: Biological Sciences 289, 20220667. Link
70. Thompson, A.W., Wojtas, H., Davoll, M., and Braasch, I. (2022) Genome of the Rio Pearlfish (Nematolebias whitei), a bi-annual killifish model for Eco-Evo-Devo in extreme environments. G3 Genes|Genomes|Genetics 12, jkac045. Link
69. Mikami, M., Ineno, T., Thompson, A.W., Braasch, I., Ishiyama, M., and Kawasaki, K. (2022) Convergent losses of SCPP genes and ganoid scales among non-teleost actinopterygians. Gene 811, 146091. Link
70. Thompson, A.W., Wojtas, H., Davoll, M., and Braasch, I. (2022) Genome of the Rio Pearlfish (Nematolebias whitei), a bi-annual killifish model for Eco-Evo-Devo in extreme environments. G3 Genes|Genomes|Genetics 12, jkac045. Link
69. Mikami, M., Ineno, T., Thompson, A.W., Braasch, I., Ishiyama, M., and Kawasaki, K. (2022) Convergent losses of SCPP genes and ganoid scales among non-teleost actinopterygians. Gene 811, 146091. Link
2021
68. Dornburg, A., Wcisel, D.W., Zapfe, K., Ferraro, E., Roupe-Abrams, L., Thompson, A.W., Braasch, I., Ota, T., Yoder, J.A. (2021) Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system. Immunogenetics 73, 479-497. Link
67. Thompson, A.W., Hawkins, M.B., Parey, E., Wcisel, D., Ota, T., Kawasaki, K., Funk, E., Losilla, M., Fitch, O.E., Pan, Q., Feron, R., Louis, A., Montfort, J., Milhes, M., Racicot, B., Childs, K., Fontenot, Q., Ferrara, A., David, S.R., McCune, A., Dornburg, A., Yoder, J., Guiguen, Y., Roest Crollius, H., Berthelot, C., Harris, M., and Braasch, I. (2021) The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nature Genetics 53, 1373–1384. Link
66. Schwaner, M.J., Hsieh, S.T., Braasch, I., Bradley, S., Campos, C.B., Collins, C.E., Donatelli, C.M., Fish, F.E., Fitch, O.E., Flammang, B.E., Jackson, B.E., Jusufi, A., Mekdara, P.J., Patel, A., Swalla, B.J., Vickaryous, M., and McGowan, C.P. (2021) Future Tail Tales: A Forward-Looking, Integrative Perspective on Tail Research. Integrative and Comparative Biology 61, 521-537. Link
65. Enny, A., Shanabag, A., Thompson, A.W., Racicot, B., Braasch, I., and Nakamura, T. (2020) Cellular and molecular mechanisms of frontal bone development in spotted gar (Lepisosteus oculatus). Developmental Dynamics 250, 1668-1682. Link
64. Vigouroux, R.J., Duroure, K., Vougny, J., Albadri, S., Kozulin, P., Herrera, E., Nguyen-Ba-Charvet, K., Braasch, I., Suárez, R., Del Bene, F., and Chédotal, A. (2021) Bilateral visual projections exist in non-teleost bony fish and predate the emergence of tetrapods. Science 372, 150-156. Link
63. Feron, R., Pan, Q., Wen, M., Imarazene, B., Jouanno, E., Anderson, J., Herpin, A., Journot, L., Parrinello, H., Klopp, C., Kottler, V.A., Roco, A.S., Du, K., Kneitz, S., Adolfi, M., Wilson, C.A., McCluskey, B., Amores, A., Desvignes, T., Goetz, F.W., Takanashi, A., Kawaguchi, M., Detrich, H.W., Oliveira, M., Nobrega, R., Sakamoto, T., Nakamoto, M., Wargelius, A., Karlsen, Ø., Wang, Z., Stöck, M., Waterhouse, R.M., Braasch, I., Postlethwait, J.H., Schartl, M., and Guiguen, Y. (2021) RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data. Molecular Ecology Resources 21, 1715-1731. Link
67. Thompson, A.W., Hawkins, M.B., Parey, E., Wcisel, D., Ota, T., Kawasaki, K., Funk, E., Losilla, M., Fitch, O.E., Pan, Q., Feron, R., Louis, A., Montfort, J., Milhes, M., Racicot, B., Childs, K., Fontenot, Q., Ferrara, A., David, S.R., McCune, A., Dornburg, A., Yoder, J., Guiguen, Y., Roest Crollius, H., Berthelot, C., Harris, M., and Braasch, I. (2021) The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nature Genetics 53, 1373–1384. Link
66. Schwaner, M.J., Hsieh, S.T., Braasch, I., Bradley, S., Campos, C.B., Collins, C.E., Donatelli, C.M., Fish, F.E., Fitch, O.E., Flammang, B.E., Jackson, B.E., Jusufi, A., Mekdara, P.J., Patel, A., Swalla, B.J., Vickaryous, M., and McGowan, C.P. (2021) Future Tail Tales: A Forward-Looking, Integrative Perspective on Tail Research. Integrative and Comparative Biology 61, 521-537. Link
65. Enny, A., Shanabag, A., Thompson, A.W., Racicot, B., Braasch, I., and Nakamura, T. (2020) Cellular and molecular mechanisms of frontal bone development in spotted gar (Lepisosteus oculatus). Developmental Dynamics 250, 1668-1682. Link
64. Vigouroux, R.J., Duroure, K., Vougny, J., Albadri, S., Kozulin, P., Herrera, E., Nguyen-Ba-Charvet, K., Braasch, I., Suárez, R., Del Bene, F., and Chédotal, A. (2021) Bilateral visual projections exist in non-teleost bony fish and predate the emergence of tetrapods. Science 372, 150-156. Link
63. Feron, R., Pan, Q., Wen, M., Imarazene, B., Jouanno, E., Anderson, J., Herpin, A., Journot, L., Parrinello, H., Klopp, C., Kottler, V.A., Roco, A.S., Du, K., Kneitz, S., Adolfi, M., Wilson, C.A., McCluskey, B., Amores, A., Desvignes, T., Goetz, F.W., Takanashi, A., Kawaguchi, M., Detrich, H.W., Oliveira, M., Nobrega, R., Sakamoto, T., Nakamoto, M., Wargelius, A., Karlsen, Ø., Wang, Z., Stöck, M., Waterhouse, R.M., Braasch, I., Postlethwait, J.H., Schartl, M., and Guiguen, Y. (2021) RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data. Molecular Ecology Resources 21, 1715-1731. Link
2020
62. Braasch, I. (2020) Genome Evolution: Domestication of the allopolyploid goldfish. Current Biology 30, R812-R815. Link
61. Du, K., Stöck, M., Kneitz, S., Klopp, C., Woltering, J.M., Adolfi, M.C., Feron, R., Prokopov, D., Makunin, A., Kichigin, I., Schmidt, C., Fischer, P., Kuhl, H., Wuertz, S., Gessner, J., Kloas, W., Cabau, C., Iampietro, C., Parrinello, H., Tomlinson, C., Journot, L., Postlethwait, J.H., Braasch, I., Trifonov, V., Warren, W.C., Meyer, A., Guiguen, Y., and Schartl M. (2020) The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization. Nature Ecology & Evolution 4, 841-852. Link
60. Braasch, I., and McCluskey, B. M. (2020) Zebrafish Taxonomy and Evolution. In: The Zebrafish in Biomedical Research - Biology, Husbandry, Diseases, and Research Applications, Eds. Cartner, S., Eisen, J. S., Farmer, S., Guillemin, K., Kent, M., and Sanders, G. Link
59. Postlethwait, J. H., and Braasch, I. (2020) Zebrafish Genetics. In: The Zebrafish in Biomedical Research - Biology, Husbandry, Diseases, and Research Applications, Eds. Cartner, S., Eisen, J. S., Farmer, S., Guillemin, K., Kent, M., Sanders, G. Link
59. Postlethwait, J. H., and Braasch, I. (2020) Zebrafish Genetics. In: The Zebrafish in Biomedical Research - Biology, Husbandry, Diseases, and Research Applications, Eds. Cartner, S., Eisen, J. S., Farmer, S., Guillemin, K., Kent, M., Sanders, G. Link
2019
58. Cal, L., Suarez-Bregua, P., Braasch, I., Irion, U., Kelsh, R., Cerdá-Reverter, J. M., and Rotllant, J. (2019) Loss-of-function mutations in the melanocortin-1-receptor (Mc1r) cause disruption of dorso-ventral countershading in teleost fish. Pigment Cell and Melanoma Research 32, 817-828. Link
57. Ganz, J., Melancon, E., Wilson, C., Amores, A., Batzel, P., Strader, M., Braasch, I., Diba, P., Kuhlman, J. A., Postlethwait, J. H., and Eisen, J. S. (2019) Epigenetic factors Dnmt1 and Uhrf1 coordinate intestinal development. Developmental Biology 455, 473-484. Link
56. Darnet, S., Dragalzew, A. C., Amaral, D. B., Sousa, J. F., Thompson, A. W., Cass, A. N., Lorena, J., Pires, E. S., Costa, C. M., Sousa, M. P., Froebisch, N. B., Oliveira, G., Schneider, P. N., Davis, M. C., Braasch, I., and Schneider, I. (2019) Deep evolutionary origin of limb and fin regeneration. Proceedings of the National Academy of Sciences 116, 15106-1515. Link
55. Wolverton, E., Wong, M., Davis, P. E., Hoglin, B., Braasch, I., and Dores, R. (2019) Analyzing the pharmacological properties of gar (Lepisosteus oculatus) melanocortin receptors: Evaluating interactions with MRAP1 and MRAP2. General and Comparative Endocrinology 282, 113215. Link
54. Cal, L., Suarez-Bregua, P., Comesaña, P., Owen, J., Braasch, I., Kelsh, R., Cerdá-Reverter, J. M., and Rotllant, J. (2019) Countershading in zebrafish results from an Asip1 controlled dorsoventral gradient of pigment cell differentiation. Scientific Reports 9, 3449. Link
2018
53. Spiewak, J. E., Bain, E. J., Liu, J., Kou, K., Sturiale, S. L., Patterson, L. B., Diba, P., Eisen, J., Braasch, I., Ganz, J., and Parichy, D. M. (2018) Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes. PLoS Genetics 14, e1007538. Link
52. Braasch, I., Bobe, J., Guiguen, Y., and Postlethwait, J. H. (2018) Reply to: Sandve et al.: To sub- or neo-functionalize after whole genome duplication, that is the question. Nature Genetics 50, 910-911. Link
51. Desvignes, T., Carey, A., Braasch, I., Enright, T., and Postlethwait, J. H. (2018) Skeletal development in the heterocercal caudal fin of spotted gar (Lepisosteus oculatus) and other Lepisosteiformes. Developmental Dynamics 247, 724-740. Link
2017
50. Braasch, I., and Postlethwait, J. H. (2017) The Spotted Gar: Genomic Journeys into a Lost World. Journal of Experimental Zoology B: Molecular and Developmental Evolution 328, 593-595. Link
49. Kawasaki, K., Mikami, M., Nakatomi, M., Braasch, I., Batzel, P., Postlethwait, J. H., Sato, A., Sasagawa, I., and Ishiyama, M. (2017) SCPP Genes and Their Relatives in Gar: Rapid Expansion of Mineralization Genes in Osteichthyans. Journal of Experimental Zoology B: Molecular and Developmental Evolution 328, 645-665. Link
48. Cal, L.a, MegÍas, M., Cerdá-Reverter, J. M., Postlethwait, J. H., Braasch, I., and Rotllant J. (2017) BAC Recombineering of the Agouti Loci from Spotted Gar and Zebrafish Reveals the Evolutionary Ancestry of Dorsal-Ventral Pigment Asymmetry in Fish. Journal of Experimental Zoology B: Molecular and Developmental Evolution 328, 697-708. Link
47. Pasquier, J., Braasch, I., Batzel, P., Cabau, C., Montfort, J., Nguyen, T., Jouanno, E., Berthelot, C., Klopp, C., Journot, L., Postlethwait, J. H., Guiguen, Y., and Bobe, J. (2017) Evolution of gene expression after whole-genome duplication: New insights from the spotted gar genome. Journal of Experimental Zoology B: Molecular and Developmental Evolution 328, 709-721. Link
46. Cal, L., Suarez-Bregua, P., Cerdá-Reverter, J. M., Braasch, I., and Rotllant, J. (2017) Fish pigmentation and the melanocortin system. Comparative Biochemistry and Physiology A: Molecular and Integrative Physiology 211, 26-33. Link
45. Suárez-Bregua, P., Torres, E., Saxena, A., Guerreiro, P. M., Braasch, I., Prober, D., Morán, P., Cerda Reverter, J. M., Du, S., Adrio, F., Power, D., Canario, A., Postlethwait, J.H., Bronner, M., Cañestro, C., and Rotllant, J. (2017) Pth4, an ancient Parathyroid Hormone lost in eutherian mammals, reveals a new brain-to-bone signaling pathway. The FASEB Journal 31, 569-583. Link
2016
44. Sukeena, J. M., Galicia, C. A., Wilson, J. D., McGinn, T., Boughman, J. W., Robison, B. D., Postlethwait, J. H., Braasch, I., Stenkamp, D. L., and Fuerst, P. G. (2016) Characterization and Evolution of the Spotted Gar Retina. Journal of Experimental Zoology B: Molecular and Developmental Evolution 326, 403-421. Link
43. Askary, A., Smeeton, J., Paul, S., Schindler, S., Braasch, I., Ellis, N. A., Postlethwait, J., Miller, C. T., and Crump, J. G. (2016) Ancient origin of lubricated joints in bony vertebrates. eLife 5, e16415. Link
42. Braasch, I., Gar Genome Consortium (59 authors), and Postlethwait, J.H. (2016) The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics 48, 427-437. Link
41. Pasquier, J., Cabau, C., Nguyen, T., Jouanno, Severac, D., Braasch, I., Journot, L., Pontarotti, P., Klopp, C., Postlethwait, J.H., Guiguen, Y., and Bobe, J. (2016) Gene evolution and gene expression after whole genome duplication in fish: The PhyloFish database. BMC Genomics 17, 368. Link
2015
40. Braasch, I., Peterson, S. M., Desvignes, T., McCluskey, B. M., Batzel, P., and Postlethwait, J. H. (2015) A New Model Army: Emerging fish models to study the genomics of vertebrate Evo-Devo. Journal of Experimental Zoology B: Molecular and Developmental Evolution 324, 316-341. Link
39. Gehrke, A. R., Schneider, I., Tena, J.J., Gomez-Marin, C., Nakamura, T., Chandran, M., de la Calle-Mustienes, E., Braasch, I., Postlethwait, J.H., Gomez-Skarmeta, J.L., and Shubin, N.H. (2015) Deep conservation of wrist and digit enhancers in fish. Proceedings of the National Academy of Sciences 112, 803-808. Link
2014
38. Braasch, I., and Schartl, M. (2014) Evolution of endothelin receptors in vertebrates. General and Comparative Endocrinology 209, 21-34. Link
37. Ganz, J., Kroehne, V., Freudenreich, D., Machate, A., Geffarth, M., Braasch, I., Kaslin, J., and Brand, M. (2014) Subdivisions of the adult zebrafish pallium based on molecular marker analysis. F1000Research 3, 308. Link
36. Santos, M. E., Braasch, I., Boileau, N., Meyer, B. S., Sauteur, L., Böhne, A., Belting, H. G., Affolter, M., and Salzburger, W. (2014) The evolution of cichlid fish egg-spots is linked with a cis-regulatory change. Nature Communications 5, 5149. Link
35. Braasch, I., Guiguen, Y., Loker, R.c, Letaw, J. H., Ferrara, A., Bobe, J., and Postlethwait, J. H. (2014) Connectivity of vertebrate genomes: Paired-related homeobox (Prrx) genes in spotted gar, basal teleosts, and tetrapods. Comparative Biochemistry and Physiology C: Toxicology and Pharmacology 163, 24-36. Link
2013
34. Meng, F., Braasch, I., Phillips, J. B., Lin, X., Titus, T., Zhang, C., and Postlethwait, J. H. (2013) Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish. Molecular Biology and Evolution 30, 1527-1543. Link
33. Amemiya, C. T., Alföldi, J., Lee A. P., Fan, S., Philippe H., MacCallum, I., Braasch, I., and 84 more authors (2013) Analysis of the African coelacanth genome sheds light on tetrapod evolution. Nature 496, 311-316. Link
32. Schartl, M., Walter, R. B., Shen, Y., Garcia, T., Catchen, J., Amores, A., Braasch, I., Chalopin, D., Volff, J. N., Lesch, K. P., Bisazza, A., Minx, P., Hillier, L., Wilson, R. K., Fuerstenberg, S., Boore, J., Searle S., Postlethwait, J. H., and Warren, W. C. (2013) The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nature Genetics 45, 567-572. Link
2012
31. Braasch, I., and Postlethwait, J. H. (2012) Fish polyploidy and the teleost genome duplication. In: Polyploidy and Genome Evolution, Eds. Soltis, P. S. and Soltis, D. E. Link
30. Anderson, J. L., Rodriguez Mari, A., Braasch, I., Amores, A., Hohenlohe, P., Batzel, P., and Postlethwait, J. H. (2012) Multiple Sex-Associated Regions and a Putative Sex Chromosome in Zebrafish Revealed by RAD Mapping and Population Genomics. PLoS One 7, e40701. Link
29. DeLaurier, A., Nakamura, Y., Braasch, I., Khanna, V., Kato, H., Wakitani, S., Postlethwait, J. H., and Kimmel, C. B. (2012) Histone deacetylase-4 is required during early cranial neural crest development for generation of the zebrafish palatal skeleton. BMC Developmental Biology 12, 16. Link
2011
28. Catchen, J. M., Braasch, I., and Postlethwait, J. H. (2011) Conserved synteny and the zebrafish genome. Methods in Cell Biology 104, 259-285. Link
27. Braasch, I., and Postlethwait, J. H. (2011) The teleost agouti related protein 2 gene is an ohnolog gone missing from the tetrapod genome. Proceedings of the National Academy of Sciences 108, E47-E48. Link
26. McFarlane, S., Svingen, T., Braasch, I., Koopman, P., Schartl, M., and Wilhelm, D. (2011) Expansion of the Ago gene family in the teleost clade. Development, Genes and Evolution 221, 95-104. Link
25. Braasch, I., and Liedtke, D. (2011) Pigment genes and cancer genes. In: Encyclopedia of Fish Physiology: From Genome to Environment, Eds. Farrell, A. P., Cech, J. J., Richards, J. G. and Stevens, E. D.
2010
24. Zhou, Q., Braasch, I., Froschauer A., Böhne A., Schultheis C., Schartl M., and Volff J.N. (2010) A novel marker for the platyfish (Xiphophorus maculatus) W chromosome is derived from a Polinton transposon. Journal of Genetics and Genomics 37, 181-188. Link
23. Herpin, A.●, Braasch, I.●, Kräussling, M., Schmidt, C., Thoma, E., Nakamura, S., Tanaka, M., and Schartl, M. (2010) Transcriptional rewiring of the sex determining dmrt1 gene duplicate by transposable elements. PLoS Genetics 6, e1000844.
● equal contribution Link
● equal contribution Link
22. Laisney, J., Braasch, I., Walter, R. B., Meierjohann, S., and Schartl, M. (2010) Lineage-specific co-evolution of the EGFR/EGF ligand signaling system. BMC Evolutionary Biology 10, 27. Link
2009
21. Braasch, I., Brunet, F., Volff, J. N., and Schartl, M. (2009) Pigmentation pathway evolution after whole genome duplication in fish. Genome Biology and Evolution 1, 479-493. Link
20. Braasch, I., Liedtke, D., Volff, J. N., and Schartl, M. (2009) Pigmentary function and evolution of tyrp1 gene duplicates in fish. Pigment Cell and Melanoma Research 22, 830-850. Link
19. Braasch, I., and Salzburger, W. (2009) In ovo omnia: diversification by duplication in fish and other vertebrates. Journal of Biology 8, 25. Link
18. Salzburger, W.●, Steinke, D.●, Braasch, I.●, and Meyer, A. (2009) Genome desertification in eutherians: can gene deserts explain the uneven distribution of genes in placental mammalian genomes? Journal of Molecular Evolution 69, 207-216.
● equal contribution Link
● equal contribution Link
17. Braasch, I., Volff, J. N., and Schartl, M. (2009) The endothelin system: evolution of vertebrate-specific ligand-receptor interactions by three rounds of genome duplication. Molecular Biology and Evolution 26, 783-799. Link
16. Klüver, N., Herpin, A., Braasch, I., Drießle, J., and Schartl, M. (2009) Regulatory back-up circuit of medaka wt1 co-orthologs ensures PGC maintenance. Developmental Biology 325, 179-188. Link
2008
15. Braasch, I., Volff, J. N., and Schartl, M. (2008) The evolution of teleost pigmentation and the fish-specific genome duplication. Journal of Fish Biology 73, 1891-1918. Link
14. Böhne, A., Schultheis, C., Zhou, Q., Froschauer, A., Schmidt, C., Selz, Y., Braasch, I., Ozouf-Costaz, C., Dettai, A., Ségurens, B., Couloux, A., Bernard-Samain, S., Chilmonczyk, S., Gannouni, A., Madani, K., Brunet, F., Galiana-Arnoux, D., Schartl, M., and Volff, J. N. (2008) Identification of new gene candidates on the sex chromosomes of the platyfish Xiphophorus maculatus. Cybium 32, 69-71. Link
13. Salzburger, W., Renn, S. C., Steinke, D., Braasch, I., Hofmann, H. A., and Meyer, A. (2008) Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs. BMC Genomics 9, 96. Link
2007
12. Salzburger, W.●, Braasch, I.●, and Meyer, A. (2007) Adaptive sequence evolution in a color gene involved in the formation of the characteristic egg-dummies of male haplochromine cichlid fishes. BMC Biology 5, 51. ● equal contribution Link
11. Siegel, N., Hoegg, S., Salzburger, W., Braasch, I., and Meyer, A. (2007) Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications. BMC Genomics 8, 312. Link
10. Braasch, I., Schartl, M., and Volff, J. N. (2007) Evolution of pigment synthesis pathways by gene and genome duplication in fish. BMC Evolutionary Biology 7, 74. Link
9. Selz, Y., Braasch, I., Hoffmann, C., Schmidt, C., Schultheis, C., Schartl, M., and Volff, J. N. (2007) Evolution of melanocortin receptors in teleost fish: The melanocortin type 1 receptor. Gene 401, 114-122. Link
2006
8. Schultheis, C., Zhou, Q., Froschauer, A., Nanda, I., Selz, Y., Schmidt, C., Matschl, S., Wenning, M., Veith, A.-M., Naciri, M., Hanel, R., Braasch, I., Dettai, A., Böhne, A., Ozouf-Costaz, C., Chilmonczyk, S., Ségurens, B., Couloux, A., Bernard-Samain, S., Schmid, M., Schartl, M., and Volff, J. N. (2006) Molecular analysis of the sex-determining region of the platyfish Xiphophorus maculatus. Zebrafish 3, 299-303. Link
7. Froschauer, A., Braasch, I., and Volff, J. N. (2006) Fish genomes, comparative genomics and vertebrate evolution. Current Genomics 7, 43-57. Link
6. Braasch, I., Salzburger, W., and Meyer, A. (2006) Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration. Molecular Biology and Evolution 23, 1192-1202. Link
5. Steinke, D., Salzburger, W., Braasch, I., and Meyer, A. (2006) Many genes in fish have species-specific asymmetric rates of molecular evolution. BMC Genomics 7, 20. Link
4. Lang, M., Miyake, T., Braasch, I., Tinnemore, D., Siegel, N.c, Salzburger, W., Amemiya, C. T., and Meyer, A. (2006) A BAC library of the East African haplochromine cichlid fish Astatotilapia burtoni. Journal of Experimental Zoology B: Molecular and Developmental Evolution 306, 35-44. Link
2001-2003
3. Taylor, J. S., Braasch, I., Frickey, T., Meyer, A., and Van de Peer, Y. (2003) Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Research 13, 382-390. Link
2. Van de Peer, Y., Taylor, J. S., Braasch, I., and Meyer, A. (2001) The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. Journal of Molecular Evolution 53, 436-446. Link
1. Taylor, J. S., Van de Peer, Y., Braasch, I., and Meyer, A. (2001) Comparative genomics provides evidence for an ancient genome duplication event in fish. Philosophical Transactions of the Royal Society London, Series B: Biological Sciences 356, 1661-1679. Link