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MBRG Publications (last five years)


Click here for direct access to supplemental material for selected papers

 

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