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MBRG Publications (last six years)


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2019

Manuscripts

Boswell, M., Lu, Y., Boswell, W., Hildreth, K., Salinas, R., Walter, C.A., Walter, R.B (2019). Fluorescent Light Incites a Conserved Immune and Inflammatory Genetic Response within Vertebrate Organs (Danio rerioOryzias latipes, and Mus musculus).Genes,10:271 https://doi.org/10.3390/genes10040271

2018

Manuscripts

Klotz, B., Kneitz, S., Regensburger, M., Dannemann, M., Kelso, J., Lu, Y., Boswell W., Postlethwait, J., Warren, W., Kunz, M., Walter, R.B. and M. Schartl (2018). Expression signatures of early-stage and advanced medaka melanomas. Comp. Biochem. & Physiology, Part C, 208:20-28 https://doi.org/10.1016/j.cbpc.2017.11.005

Lu, Yuan, Reyes, J., Walter, S., Gonzalez, T., Medrano, G., Boswell, M., Boswell, W., Savage, S. and R.B. Walter (2018). Characterization of Basal Gene Expression Trends Over a Diurnal Cycle in Xiphophorus maculatus Skin, Brain and Liver. Comp. Biochem. & Physiology, Part C, 208:2-11, https://doi.org/10.1016/j.cbpc.2017.11.013

Wise, J.P. Jr., Wise, T.F., Wise, C.F., Wise, S.S., Gianos, C. Jr. , , Xie, H., Walter, R.B., Boswell, M., Zhu, C., Zheng, T., Perins, C., and J.P. Sr.,Wise. (2018).  A three-year study of metal levels in skin biopsies of whales in the Gulf of Mexico after the Deepwater Horizon oil crisis.  Comp. Biochem. & Physiology, Part C, 205:15-25, https://doi.org/10.1016/j.cbpc.2017.12.003

Warren, W.C., Kuderna, L., Alexander, A., Catchen, J., Pérez-Silva, J.G., López-Otín, Víctor Quesada, C., Minx, P., Tomlinson, C., Montague, M., Farias, F.H.G., Walter, R.B., Marques-Bonet, T., Glenn, T., Kieran, T.J., Wise, S.S., Wise Jr., J.P., Waterhouse, R.M., and J.P. Wise, Sr. (2018). The novel evolution of the sperm whale genome.  Genome Biol. Evololution 9(12):3260-3264. https://doi.org/10.1093/gbe/evx187

Lu, Y., Boswell, M., Boswell, W., Kneitz, S., Hausmann, M., Klotz, B., Regneri, J., Savage, M., Amores, A., Postlethwait, J., Warren, W., Schartl, M., and R. B. Walter (2018). Comparison of Xiphophorus and Human Melanoma  Transcriptomes Reveals Conserved Pathway Interactions, Pigment Cell Melanoma Res., 2018:1-13, https://doi.org/10.1111/pcmr.12686  (Cover photo selection)

Warren, W., García-Pérez, R., Xu, S., Lampert, K., Chalopin, D., Stöck, M., Loewe, L., Lu, Y., Kuderna, L., Minx, P., Montague, M., Tomlinson, C., Hillier, L., Murphy, D., Wang, J., Wang, Z., Garcia, C.M., Thomas, G., Volff, J-N., Farias, F., Aken, B., Walter, R.B., Pruitt, K., Marques-Bonet, T., Hahn, M., Kneitz, S., Lynch, M., and M. Schartl (2018).  Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly, Nature - Evolution and Ecology, 2:669–679, https://doi.org/ 10.1038/s41559-018-0473-y

Walter, R.B., Boswell, M, Chang, J., Boswell, W.T., Lu, Y., Navarro, K, Walter, S.M., Walter, D.J., Salinas, R. and M. Savage (2018).  Waveband Specific Transcriptional Control of Select Genetic Pathways in Vertebrate Skin. BMC Genomics, 19:355-373.  https://doi.org/10.1186/s12864-018-4735-5

Regneri, J., Klotz, B., Wilde, B., Kottler, V., Hausmann, M., Kneitz, S., Regensburger, M., Maurus, K., Götz, R., Lu, Y., Walter, R., Herpin, A., and M. Schartl (2018). Analysis of the putative tumor suppressor gene cdkn2ab in pigment cells and melanoma of Xiphophorus and medaka, Pigment Cell Melanoma Res. 2018;00:1–11, https://doi.org/10.1111/pcmr.12729  (Cover photo selection)

Zavadil, J., Herzig, M., Hildreth, K., Foroushani, A., Boswell, W., Walter, R.B., Reddick, R., White, H., Zare, H., and C. Walter (2018). C3HeB/FeJ Mice Mimic Gene Expression and Pathobiological Features of Human Hepatocellular Carcinoma, Molecular Carcinogenesis. 2018;1–12, https://doi.org/10.1002/mc.22929

Franchini, P., Jones, J., Xiong, P., Kneitz, S., Gompert, Z., Warren, W.C., Walter, R.B., Meyer, A., Schartl. M. (2018).  Long-term experimental hybridisation results in a heterologous transition and the evolution of a new sex chromosome in swordtail fish, Nature Commumncation. 9:5136, https://doi.org/10.1038/s41467-018-07648-2

Book Chapters/Monographs

Hagedorn, M., Varga, Z., Walter, R.B, Tiersch, T.R. (2018).  Workshop Report: Cryopreservation of Aquatic Biomedical Models, Cryobiology, 2018:110.264. https://doi.org/10.1016/j.cryobiol.2018.10.264

Walter, R.B., LU, Y., Savage, M. (2018) The Xiphophorus Genetic Stock Center. “Genetic Resources of Model Organisms – Strategies for Conservation”, R. Jarret (ed.), CRC Press/Taylor and Francis Publishing, In press.

2017

Manuscripts

Boswell, M., Boswell, W., Lu, Y., Savage, M., Mazurek, Z., Chang, J., Muster, J., and Walter, R. (2017). The transcriptional response of skin to fluorescent light exposure in viviparous (Xiphophorus) and oviparous (Danio, Oryzias) fishes. Comp Biochem Physiol C Toxicol Pharmacol. 2017 Oct 7. pii: S1532-0456(17)30169-2. doi: 10.1016/j.cbpc.2017.10.003.

Boswell, W. T., Boswell, M., Walter, D. J., Navarro, K. L., Chang, J., Lu, Y., Savage, M. G., Shen, J., and Walter, R. B. (2017). Exposure to 4100K fluorescent light elicits sex specific transcriptional responses in Xiphophorus maculatus skin. Comp Biochem Physiol C Toxicol Pharmacol. 2017 Sep 29. pii: S1532-0456(17)30163-1. doi: 10.1016/j.cbpc.2017.09.008.

Gonzalez, T. J., Lu, Y., Boswell, M., Boswell, W., Medrano, G., Walter, S., Ellis, S., Savage, M., Varga, Z. M., Lawrence, C., Sanders, G., and Walter, R. B. (2017). Fluorescent light exposure incites acute and prolonged immune responses in zebrafish (Danio rerio) skin. Comp Biochem Physiol C Toxicol Pharmacol. 2017 Sep 29. pii: S1532-0456(17)30164-3. doi: 10.1016/j.cbpc.2017.09.009.

Lu, Y., Boswell, M., Boswell, W., Kneitz, S., Hausmann, M., Klotz, B., Regneri, J., Savage, M., Amores, A., Postlethwait, J., Warren, W., Schartl, M., and Walter, R. (2017). Molecular genetic analysis of the melanoma regulatory locus in Xiphophorus interspecies hybrids. Mol Carcinog. 2017 Aug;56(8):1935-1944. doi: 10.1002/mc.22651. Epub 2017 Apr 13.

Lu, Y., Klimovich, C. M., Robeson, K. Z., Boswell, W., Rios-Cardenas, O., Walter, R. B., and Morris, M. R. (2017). Transcriptome assembly and candidate genes involved in nutritional programming in the swordtail fish Xiphophorus multilineatus. PeerJ. 2017 May 2;5:e3275. doi: 10.7717/peerj.3275. eCollection 2017.

2016 

Manuscripts

Shen, Y., Chalopin, D., Garcia, T., Boswell, M., Boswell, W., Shiryayev, S., Agarwala. R., Volff, J-N, Postlethwait, J.H., Schartl, M., Minx, P., Warren, W.C., and R.B. Walter. (2016).  X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species, BMC Genomics. doi: 10.1186/s12864-015-2361-z

2015 

Manuscripts

Schartl, M., Shen, Y., Maurus, K., Walter, R., Tomlinson, C., Wilson, R.K., Postlethwait, J., Warren, W.C. (2015). Whole Body Melanoma Transcriptome Response in Medaka. Plos One doi:10.1371/journal.pone.0143057

Chang, J., Lu, Y., Boswell, W.T., Boswell, M., Caballero, K.L., Walter, R.B. (2015) Molecular genetic response to varied wavelengths of light in Xiphophorus maculatus skin. Comp Biochem Physiol C Toxicol Pharmacol., 178:104-15. doi: 10.1016/j.cbpc.2015.10.002. PMID: 26460196

Boswell, W., Boswell, M., Titus, J., Savage, M., Lu, Y., Shen, J., Walter, R.B. (2015) Sex-specific molecular genetic response to UVB exposure in Xiphophorus maculatus skin. Comp Biochem Physiol C Toxicol Pharmacol., 178:76-85. doi: 10.1016/j.cbpc.2015.07.007. PMID: 26256120

Lu, Y., Boswell, M., Boswell, W., Yang, K., Schartl, M., Walter, R.B. (2015) Molecular genetic response of Xiphophorus maculatus-X. couchianus interspecies hybrid skin to UVB exposure. Comp Biochem Physiol C Toxicol Pharmacol., 178:86-92. doi: 10.1016/j.cbpc.2015.07.011 PMID: 26254713

Walter, R.B., Walter, D.J., Boswell, W.T., Caballero, K.L., Boswell, M., Lu, Y., Chang, J., Savage, M.G. (2015) Exposure to fluorescent light triggers down regulation of genes involved with mitotic progression in Xiphophorus skin. Comp Biochem Physiol C Toxicol Pharmacol., 178:93-103. doi: 10.1016/j.cbpc.2015.08.006

Book Chapters/Monographs
 

Lu, Y., Shen, Y., Warren, W., and R. B. Walter (2015) “Next Generation Sequencing in Aquatic Models”.  In: "Next Generation Sequencing – Advances, Applications, and Challenges", ISBN 978-953-51-4594-3. Jerrzy K. Kuliski, editor, INTECH publications. Janeza Trdine 9, 51000, Rijeka, Croatia. http://dx.doi.org/10.5772/61657

Walter, R.B., and T. Obara (2015).  Workshop Report: The Medaka Model for Comparative Assessment of Human Disease Mechanisms, Aquatic Animal Models of Human Disease: Selected Papers and Recommendations form the 7th Conference. Comparative Biochemistry and Physiology, Part C, 178: 156-162

2014

Manuscripts

Garcia T.I., Matos I., Shen, Y., Pabuwal V., Coelho, M.M., Wakamatsu, Y., Schartl, M., and R.B. Walter (2014). Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion. PLOS ONE, 9(6): e100250. doi: 10.1371/journal.pone.0100250, PMID 24945156

Amores, A., Catchen, C., Nanda, I., Warren, W., Walter, R.B., and M. Schartl and J.H. Postlethwait (2014).  A Rad-tag genetic map for the playtfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost fish. Genetics, 197 2):625-641. doi: 10.1534/genetics.114.164293, PMID 24700104

Contreras, A.J., Boswell, M., Downs, K.P., Pasquali, A., Mitchell, D.L. and R.B. Walter (2014) Cortisol Release in Response to UVB Exposure in Xiphophorus Fish. Comparative Biochemistry & Physiology, Part C, 163:95-101. doi: 10.1016/j.cbpc.2014.02.004, PMID 24625568

Walter, D.J., Boswell, M., Volk de García, S., Walter, S.M., Breitenfeldt, E.W., Boswell W., and R. B. Walter (2014).  Characterization and Differential Expression of DNA Photolyases in Xiphophorus. Comparative Biochemistry & Physiology, Part C, 163: 77-85. doi: 10.1016/j.cbpc.2014.01.006, PMID 24496042

Yang, K., Boswell, M., Walter, D.J., Downs, K., Gaston-Pravia, Garcia, T., Shen, Y. Mitchell, D.L. and R.B. Walter (2014). UVB-induced Gene Expression in the Skin of Xiphophorus maculatus Jp163 B. Comparative Biochemistry & Physiology, Part C, 163:86-94.  doi: 10.1016/j.cbpc.2014.01.008, PMID 24496042

2013

Manuscripts

Cui, R., Schumer, M., Kruesi, K., Walter, R., Andolfatto, P., and G. Rosenthal (2013) Phylogenomics reveals extensive reticulate evolution in Xiphophorus fishes.  Evolution, 67(8): 216-2179. doi: 101111/evo.12099, PMID 23888843

Pabuwal, V., Boswell, M., Pasquali, A., Wise, S.S., Kumar, S., Shen, Y., Garcia, T., LaCerte, C., Wise, J.P. Jr, Wise, J.P. Sr., Warren, W., and R. B. Walter. (2013). Transcriptomic Analysis of Cultured Whale Skin Cells Exposed to Hexavalent Chromium [Cr(VI)], Aquatic Toxicology, 134-135:74-81. doi: 10.1016/ j.aquatox. 2013.03.003, PMID: 23584427

Kang Hyoun, J., Schartl,M., Walter, R.B., and A.  Meyer (2013) Comprehensive phylogenetic analyses of all species of swordtails and platies (genus Xiphophorus) uncover a hybrid origin of a swordtail fish, Xiphophorus monticolus.  BMC Evolutionary Biology, 13:25-44. doi: 10.1186/1471-2148-13-25. PMID: 23360326

Schumer, M.C., Cui, R., Boussau, B., Walter, R.B., Rosenthlal, G., and P. Andolfatto. (2013). An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences, Evolution, 67(4):1155-1168. doi: 10.1111/evo.12009. PMID: 23550763

Schartl, M.+, Walter, R. B.+, Shen. Y., Garcia, T., Catchen, J., Amores. A., Braasch. I., Chapolin D., Volff, J-N., Lesch, K-P., Bisazza, A., Minx P., Wilson. R.K., Fuerstenberg, S., Boore, J., Postlethwait, J. H. and W.C. Warren. (2013). The genome of the platyfish, Xiphophorus maculatus. (+These authors contributed equally to the work), Nature Genetics, 45(5):567-572. doi: 10.1038/ng.2604. PMID: 2354270

Shen, Y., Garcia, T., Pabuwal, V. Boswell, M., Pasqulai, A., Beldorth, I., Warren, W., Schartl, M, Cresko, W.A., and R.B. Walter (2013). Alternative strategies for development of a reference transcriptome for quantification of allele specific expression in organisms having sparse genomic resources. Comparative Biochemistry & Physiology, Part D, 8: 11-16. doi: 10.1016/j.cbd.2012.10.006. PMID: 23201534

2012

Manuscripts

Garcia, T.I., Shen, Y., Whitehead, A., Oleksiak, M., Crawford, D.C., and R.B. Walter (2012). RNA-Seq reveals complex genetic response to Deepwater Horizon oil release in Fundulus grandis. BMC Genomics, 13:474-483. 13:474-483. doi: 10.1186/1471-2164-13-474. PMID: 22971268

Yang, H, Cuevas, R., Savage, M., Walter, R.B. and T. Tiersch. (2012) Sperm Cryopreservation in Live-bearing Xiphophorus Fishes: Offspring Production from Xiphophorus variatus and Strategies for Establishment of Sperm Repositories, Zebrafish, 9(3):126-134. doi: 10.1089/zeb.2012.0737

Garcia, T.I., Shen, Y., Catchen, J., Amores, A., Schartl, M., Postlethwait, J., and R.B. Walter (2012).  Effects of Short Read Quality and Quantity on a de novo Vertebrate Transcriptome Assembly. Comp. Biochem. & Physiology, Part C, 155:95-101. doi: 10.1016/j.cbpc.2011.05.012

Downs, K.P., Shen, Y., Pasquali, A., Beldorth, I., Savage, M., Gallier, K., Garcia, T., Booth, R.E. and R.B. Walter (2012) Characterization of Telomeres and Telomerase expression in Xiphophorus. Comparative Biochemistry & Physiology, Part C, 155:89-94. doi: 10.1016/j.cbpc.2011.05.005. PMID:21619941

Perez, A.N., Oehlers, L., Heater, S.J., Booth, R.E., Walter, R.B., and W.M. David (2012). Proteomic Analyses of the Xiphophorus Gordon-Kosswig Melanoma Model.  Comparative Biochemistry & Physiology, Part C, 81-88. doi: 10.1016/ j.cbpc. 2011.05.017. PMID: 21672637

Zhang, Z., Wells, M.C., Boswell, M.G., Beldorth, I., Kirk, L.M., Wang, Y., Wang, S., Savage, M., Walter, R.B., and R.E. Booth  (2012). Identification of Robust Hypoxia Biomarker Candidates from Fin and other Organs of Medaka (Oryzias latipes), Comparative Biochemistry & Physiology, Part C, 155:11-17. doi: 10.1016/ j.cbpc.2011.05.015. PMID: 21664487

Yang, H., Savage, M.G., Hazlewood, L., Walter, R.B., and T. R. Tiersch (2012). Offspring Production with Cryopreserved Sperm from a Live-bearing Fish Xiphophorus maculatus and Implications with Females. Comparative Biochemistry & Physiology, Part C, 155:55-63. doi: 10.1016/j.cbpc.2011.04.008

Shen, Y., Catchen, J., Garcia, T., Amores, T., Beldroth, I., Wagner, J.R., Zhang, Z., Postlethwait, J., Warren, W., Schartl, M., and R. B. Walter (2012).  Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F1 interspecies hybrids. Comparative Biochemistry & Physiology, Part C, 155:102-108. doi: 10.1016/j.cbpc.2011.03.012. PMID: 21466860

Yang, H., Walter, R.B., and T.R. Tiersch (2012). Current Status of Sperm Cryopreservation in the Genus Xiphophorus. In: Viviparous Fishes II, M. C. Uribe and H. Grier (eds.), New Life Publications (ISBN# 0-9645058-9-1), Homestead, Fl.  Pp 403-414.

Whitehead, A., Dubansky, B., Bodiner, C., Garcia, T., Miles, S., Pilley, C., Raghunathan, V., Roach, J., Walker, N., Walter, R.B., Rice, C.D., and F. Glavez  (2012).  Genomic and Physiological Footprint of the Deepwater Horizon Oil Spill on Resident Marsh Fishes. Proceedings of the National Academy of Sciences (USA), 109(50): 20298-20302. doi: 10.1073/pnas.1109545108, PMID:21949382

Book Chapters/Monographs

Fieber, L.A., Tanguay, R.L., Walter, R.B., and D. E. Williams (2012) Aquatic Animal Models of Human Disease: Selected Papers form the 5th Conference. Comparative Biochemistry and Physiology, Part C., 155:1-8, http://ijjkk.com/science/article/pii/S1532045611001165

Walter, R.B. (2012) “A Homage to Klaus D. Kallman: The Study of Beautiful Things” In: Viviparous Fishes II, M. C. Uribe and H. Grier (eds.), New Life Publications (ISBN# 0-9645058-9-1), Homestead, Fl. Pp 4-7