Publications

 
Rest, J. S., K. Bullaughey, G. P. Morris, W. H. Li. 2012. Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast. PLoS ONE. 7(2): e32274.
Rest, J.S. 2010. The expansion of molecular data in evolutionary biology. In Bell, M.A., W.F. Eanes, D.J. Futuyma, and J.S. Levinton (eds.), Evolution Since Darwin: the First 150 Years. Sinauer Associates, Sunderland.
Jiang, Y., I. Lucas, D.J. Young, E.M. Davis, T. Karrison, J.S. Rest, M.M. LeBeau. 2009. Common fragile sites are characterized by histone hypoacetylation. Human Molecular Genetics. 18:4501-4512
Bradley, M.E., J.S. Rest, W.S. Li, and N.B. Schwartz. 2008. Sulfate activation enzymes: phylogeny and association with pyrophosphatase. Journal of Molecular Evolution. 68(1):1-13.
Brown, J.W., J.S. Rest, J. Garcia-Moreno, M.D. Sorenson, and D.P. Mindell. 2008. Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. BMC Biology. 6:6.
Rest, J.S. and D.P. Mindell. 2003. Retroids in Archaea: phylogeny and lateral origins. Molecular Biology and Evolution. 20: 1134-1142.
Qiu, Y.-L., L. Li, B. Wang, Z. Chen, V. Knoop, M. Groth-Malonek, O. Dombrovska, J. Lee, L. Kent, J.S. Rest, G. F. Estabrook, T. A. Hendry, D. W. Taylor, C. M. Testa, M. Ambros, B. Crandall-Stotler, R. J. Duff, M. Stech, W. Frey, D. Quandt, and C. C. Davis. 2006. The deepest divergences in land plants inferred from phylogenomic evidence. PNAS. 103: 15511-15516.
Qiu, Y.-L., O. Dombrovska, J. H. Lee, L.B. Li, B. A. Whitlock, F. Bernasconi-Quadroni, J. S. Rest, C. C. Davis, T. Borsch, K. W. Hilu, S. S. Renner, D. E. Soltis, P. S. Soltis, M. J. Zanis, J. J. Cannone, R. R. Gutell, M. Powell, V. Savolainen, L. W. Chatrou, M. W. Chase. 2005. Phylogenetic analyses of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes. International Journal of Plant Science. 166(5): 815-842.
Xiankui S., J.M. Fontaine, J.S. Rest, E.A. Shelden, M.J. Welsh, and R. Benndorf. 2004. Interaction of human HSP22 (HSPB8) with other small heat shock proteins. Journal of Biological Chemistry. 279(4):2394-2402.
Mindell, D.P., J.S. Rest, and L.P. Villarreal. 2004. Viruses and the tree of life. In Cracraft, J. and M. J. Donoghue (eds.), Assembling the Tree of Life. Oxford University Press, New York. (Book Chapter).
Rest, J.S. and D.P. Mindell. 2003. SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host shifting. Infection, Genetics and Evolution 3: 219-225.
Rest, J.S., J.C. Ast, C.C. Austin, P.J. Waddell, E.A. Tibbetts, J.M. Hay, and D.P. Mindell. 2003. Molecular systematics of Reptilia and the tuatara mitochondrial genome. Molecular Phylogenetics and Evolution. 29: 289-297.
Tucker, P.K., R.M. Adkins, and J.S. Rest. 2003. Differential rates of evolution for the ZFY-related zinc finger genes, Zfy, Zfx and Zfa in the mouse genus Mus. Molecular Biology and Evolution. 20:999-1005.
Fontaine, J.M., J.S. Rest, M.J. Walsh and R. Benndorf. 2003. The sperm outer dense fiber protein is the 10th member of the superfamily of mammalian small stress proteins. Cell Stress and Chaperones. 8:62-69.
Dimmic M.W., J.S. Rest, D.P. Mindell, and R. Goldstein. 2002. rtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. Journal of Molecular Evolution. 55: 65-73.
Liu Y., Y. Shen, J.S. Rest, P.A. Raymond, D.J. Zack. 2001. Isolation and characterization of a zebrafish homologue of the cone rod homeobox gene. Investigative Ophthalmology and Visual Science. 42:481-7.
Meshnick S.R., P.A. Hossler, K.S. Enger, P. Kazanjian, J.S. Rest, D. Mindell, B.Z. Li, C.H. Lee, L.F. Nimri, J.L. Carter, C.B. Beard, L. Huang. 2001 Distribution of DHPS mutations among ITS subtypes of P-carinii f. sp hominis. Journal of Eukaryotic Microbiology. 126S-128S Suppl. S.
 
Franks, S.J., N.C. Kane, N.B. O’Hara, S. Tittes, J.S. Rest. 2016. Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendent gene pools. Molecular Ecology 25: 2622-3631.




Rest, J.S, O. Wilkins, W. Yuan, M. Purugganan, J. Gurevitch. 2016. Meta-analysis and meta-regression of transcriptomic response to water stress in Arabidopsis. The Plant Journal 85: 548-560.
O’Hara, N.B., J.S. Rest, S.J. Franks. 2016. Factors affecting the disease severity of Alternaria blackspot in natural Brassica rapa populations on the California and Oregon coasts. Madroño 63: 249-257.
O’Hara, N.B., J.S. Rest, S.J. Franks. 2015. Increased susceptibility to fungal disease accompanies adaptation to drought in Brassica rapa. Evolution 70(1): 241-248.
Xi, Z., L. Liu, J.S. Rest,  C.C. Davis. 2014. Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies. Systematic Biology. 63(6): 919-932.
Martinez, C.A., J.S. Rest, A-R. Kim, M.Z. Ludwig, M. Kreitman, K.P. White, J. Reinitz. 2014. Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change. Molecular Biology and Evolution. 31(4): 903-916.
Rest, J. S., C. M. Morales, J. B. Waldron, D. A. Opulente, J. Fisher, S. Moon, K. Bullaughey, L. Carey, D. Dedousis. 2013. Nonlinear fitness consequences of variation in expression level of a eukaryotic gene. Molecular Biology and Evolution. 30 (2): 448-456.
Opulente, D. A., C. M. Morales, L. Carey, J. S. Rest. 2013. Coevolution trumps pleiotropy: Carbon assimilation traits are independent of metabolic network structure in budding yeast. PLoS ONE. 8(1): e54403.
Xi, Z., Y. Wang, R. K. Bradley, M. Sugumaran, C. J. Marx, J. S. Rest, C. C. Davis. 2013. Massive mitochondrial gene transfer in a parasitic flowering plant clade. PLoS Genetics. 9(2): e1003265.
Xi Z, J.S. Rest, C.C. Davis CC. 2013. Phylogenomics and coalescent analyses resolve extant seed plant relationships. PLoS ONE. 8(11): e80870.

Xi, Z., R. K. Bradley, K. J. Wurdack, K. M. Wong, M. Sugumaran, K. Bomblies, J. S. Rest*, C. C. Davis. 2012. Horizontal transfer of expressed genes in a parasitic flowering plant. BMC Genomics. 13:227.
*Co-corresponding author
 

Featured in the news:

A gene thief. The Economist. 16 June 2012, print edition

SBU's Joshua Rest studies a unique parasitic plant. Times Beacon Record. 24 July 2012

Mysterious Asian "corpse flower" parasite actually steals huge chunks of its host's DNA - but what does it do with it? Daily Mail. 7 June 2012

"Stealing" life's building blocks. Harvard Gazette. 8 June 2012

Parasitic flower pirates genes from its host. Scientific American. 8 June 2012

 

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Featured in the news:

The Molecular Ecologist, Popular Science, Huffington Post, and Environment360.
Highlighted in a Perspectives article in Molecular Ecology.