Publications

Alejandro Gil-Gomez, Joshua S Rest (2024). Wiring between close nodes in molecular networks evolves more quickly than between distant nodes. Molecular Biology and Evolution.

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Mariana Rius, Joshua S Rest, Gina V Filloramo, Anna M G Novák Vanclová, John M Archibald, Jackie L Collier (2023). Horizontal gene transfer and fusion spread carotenogenesis among diverse heterotrophic protists. Genome Biology and Evolution.

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Jackie L. Collier, Joshua S. Rest, Lucie Gallot-Lavallée, Erik Lavington, Alan Kuo, Jerry Jenkins, Chris Plott, Jasmyn Pangilinan, Chris Daum, Igor V. Grigoriev, Gina V. Filloramo, Anna M. G. Novák Vanclová, John M. Archibald (2023). The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses. Current Biology.

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Elena Hamann, Christopher S Pauli, Zoé Joly-Lopez, Simon C Groen, Joshua S Rest, Nolan C Kane, Michael D Purugganan, Steven J Franks (2021). Rapid evolutionary changes in gene expression in response to climate fluctuations. Molecular ecology.

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Joanne Figueiredo, Joshua Rest, Sarah Adamo, Rebecca Grella, James Dilger (2021). Nicotine Stimulates Peristalsis in N. Vectensis: From Behavior to Nicotinic Receptor Genes.

Niamh B O’Hara, Steven J Franks, Nolan C Kane, Silas Tittes, Joshua S Rest (2021). Evolution of pathogen response genes associated with increased disease susceptibility during adaptation to an extreme drought in a Brassica rapa plant population. BMC Ecology and Evolution.

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Drahomı́ra Faktorová, R Ellen R Nisbet, José A Fernández Robledo, Elena Casacuberta, Lisa Sudek, Andrew E Allen, Manuel Ares, Cristina Aresté, Cecilia Balestreri, Adrian C Barbrook, Joshua S Rest, Mariana Rius, others (2020). Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature methods.

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Liming Cai, Zhenxiang Xi, André M Amorim, Manickam Sugumaran, Joshua Rest, Liang Liu, Charles C Davis (2019). Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval. New Phytologist.

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Sonya M Hanson, George Georghiou, Manish K Thakur, W Todd Miller, Joshua S Rest, John D Chodera, Markus A Seeliger (2019). What makes a kinase promiscuous for inhibitors?. Cell chemical biology.

Jackie L Collier, Joshua Rest (2019). Swimming, gliding, and rolling toward the mainstream: cell biology of marine protists. Molecular biology of the cell.

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Steven J Franks, Nolan C Kane, Niamh B O'Hara, Silas Tittes, Joshua S Rest (2016). Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools. Molecular Ecology.

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Joshua S Rest, Olivia Wilkins, Wei Yuan, Michael D Purugganan, Jessica Gurevitch (2016). Meta-analysis and meta-regression of transcriptomic responses to water stress in Arabidopsis. The Plant Journal.

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Niamh O'Hara, Joshua Rest, Steven J Franks (2016). Increased susceptibility to fungal disease accompanies adaptation to drought in Brassica rapa. Evolution.

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Niamh O'Hara, Joshua Rest, Steven J Franks (2016). Factors affecting the disease severity of Alternaria blackspot in natural Brassica rapa populations on the California and Oregon coasts. Madroño.

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Zhenxiang Xi, Liang Liu, Joshua S Rest, Charles C Davis (2014). Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies. Systematic biology.

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Carlos Martinez, Joshua S Rest, Ah-Ram Kim, Michael Ludwig, Martin Kreitman, Kevin White, John Reinitz (2014). Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change. Molecular biology and evolution.

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Zhenxiang Xi, Joshua S Rest, Charles C Davis (2013). Phylogenomics and coalescent analyses resolve extant seed plant relationships. PLoS One.

Zhenxiang Xi, Yuguo Wang, Robert K Bradley, M Sugumaran, Christopher J Marx, Joshua S Rest, Charles C Davis (2013). Massive mitochondrial gene transfer in a parasitic flowering plant clade. PLoS Genet.

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Dana A Opulente, Christopher M Morales, Lucas B Carey, Joshua S Rest (2013). Coevolution trumps pleiotropy: carbon assimilation traits are independent of metabolic network structure in budding yeast. PloS one.

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Joshua S Rest, Christopher M Morales, John B Waldron, Dana A Opulente, Julius Fisher, Seungjae Moon, Kevin Bullaughey, Lucas B Carey, Demitri Dedousis (2012). Nonlinear fitness consequences of variation in expression level of a eukaryotic gene. Molecular biology and evolution.

Zhenxiang Xi, Robert K Bradley, Kenneth J Wurdack, KM Wong, M Sugumaran, Kirsten Bomblies, Joshua S Rest, Charles C Davis (2012). Horizontal transfer of expressed genes in a parasitic flowering plant. BMC genomics.

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Joshua S Rest, Kevin Bullaughey, Geoffrey P Morris, Wen-Hsiung Li (2012). Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast. PloS one.

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Michael E Bradley, Joshua Rest, Wen-Hsiung Li, Nancy B Schwartz (2009). Sulfate activation enzymes: phylogeny and association with pyrophosphatase. Journal of molecular evolution.

Yanwen Jiang, Isabelle Lucas, David J Young, Elizabeth M Davis, Theodore Karrison, Joshua S Rest, Michelle M Le Beau (2009). Common fragile sites are characterized by histone hypoacetylation. Human molecular genetics.

Joseph W Brown, Joshua Rest, Jaime Garcı́a-Moreno, Michael D Sorenson, David P Mindell (2008). Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. BMC biology.

Yin-Long Qiu, Libo Li, Bin Wang, Zhiduan Chen, Volker Knoop, Milena Groth-Malonek, Olena Dombrovska, Jungho Lee, Livija Kent, Joshua Rest, others (2006). The deepest divergences in land plants inferred from phylogenomic evidence. Proceedings of the National Academy of Sciences.

Yin-Long Qiu, Olena Dombrovska, Jungho Lee, Libo Li, Barbara A Whitlock, Fabiana Bernasconi-Quadroni, Joshua S Rest, Charles C Davis, Thomas Borsch, Khidir W Hilu, others (2005). Systematics-Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes. International Journal of Plant Sciences-Botanical Gazette.

David P Mindell, Joshua S Rest, Luis P Villarreal (2004). Viruses and the tree of life. Assembling the tree of life.

Joshua S Rest, Xiankui Sun, Jean-Marc Fontaine, Eric A Shelden, Michael J Welsh, Rainer Benndorf (2004). Interaction of human HSP22 (HSPB8) with other small heat shock proteins. Journal of biological chemistry.

Jean-Marc Fontaine, Joshua S Rest, Michael J Welsh, Rainer Benndorf (2003). The sperm outer dense fiber protein is the 10th member of the superfamily of mammalian small stress proteins. Cell stress & chaperones.

Joshua S Rest, David P Mindell (2003). SARS associated coronavirus has a recombinant polymerase and coronaviruses have a history of host-shifting. Infection, Genetics and Evolution.

Joshua S Rest, David P Mindell (2003). Retroids in archaea: phylogeny and lateral origins. Molecular biology and evolution.

Joshua Rest, Jennifer C Ast, Christopher C Austin, Peter J Waddell, Elizabeth A Tibbetts, Jennifer M Hay, David P Mindell (2003). Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome. Molecular Phylogenetics and Evolution.

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Priscilla K Tucker, Ronald M Adkins, Joshua 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.

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Matthew W Dimmic, Joshua Rest, David P Mindell, Richard A Goldstein (2002). rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. Journal of Molecular Evolution.

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Yuhui Liu, Yu-Chi Shen, Joshua Rest, Pamela A Raymond, Donald J Zack (2001). Isolation and characterization of a zebrafish homologue of the cone rod homeobox gene. Investigative ophthalmology & visual science.

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Steven R Meshnick, Paul A Hossler, Kyle S Enger, Powel Kazanjian, Joshua S Rest, David Mindell, Baozheng Li, Chao-hung Lee, Laila F Nimri, Jane L Carter, others (2001). Distribution of DHPS mutations among ITS subtypes of P. carinii f. sp. hominis. Blackwell Publishing Ltd.