An old book

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Chikina M, Robinson JD, Clark NL. Hundreds of genes experienced convergent shifts in selective pressure in marine mammals. Molecular Biology and Evolution. 2016. Link

       A first demonstration of our method to identify convergent evolution associated with an environmental variable.

Böhm S, Szakal B, Herken BW, Sullivan MR, Mihalevic MJ, Kabbinavar FF, Branzei D, Clark NL, Bernstein KA. The budding yeast ubiquitin protease Ubp7 is a novel component involved in S-phase progression. Accepted for publication at Journal of Biological Chemistry. 2016. Link

Ziegler A, Augustin H, Clark NL, Berthelot-Grosjean M, Simonnet M, Steinert J, Geillon F, Maniere G, Featherstone D, and Grosjean Y. The Amino Acid Transporter JhI-21 Coevolves with Glutamate Receptors, Impacts NMJ Physiology, and Influences Locomotor Activity in Drosophila Larvae. Scientific Reports. 2016. 6:19692. Open Access link

Clancy CJ, Meslin C, Badrane H, Cheng S, Losada LC, Nierman WC, Vergidis P, Clark NL, Nguyen MH. Candida albicans transcriptional profiling within biliary fluid from a patient with cholangitis, before and after antifungal treatment and surgical drainage. Open Forum Infectious Diseases. 2016; 3(3):ofw120. Link


Meslin C, Plakke MS, Deutsch AB, Small BS, Morehouse NI*, Clark NL*. Digestive Organ in the Female Reproductive Tract Borrows Genes from Multiple Organ Systems to Adopt Critical Functions. Molecular Biology and Evolution. 2015. 32(6): 1567-1580. Open Access link

       " This is a well written and fascinating paper. " - Reviewer #1

       " I found the authors organ level approach refreshing in a field that can be very focused on individual genes. " - Reviewer #2

Priedigkeit NM, Wolfe NW, Clark NL. Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene networks. PLOS Genetics. 2015; 11(2): e1004967. Open Access link

       " This body of work had escaped my attention, and so I am grateful for the opportunity to review this manuscript, as I believe it is of general interest to the human-disease genetics field. In fact, I have the word "cool" written and underlined in the margins several times. " - Reviewer #1

Wolfe NW, Clark NL. ERC Analysis: web-based inference of gene function via Evolutionary Rate Covariation. Bioinformatics. 2015. doi:10.1093/bioinformatics/btv454. Open Access link

Mangels R, Young B, Keeble S, Ardekani R, Meslin C, Ferreira Z, Clark NL, Good JM, Dean MD. Genetic and phenotypic influences on copulatory plug survival in mice. Heredity. 2015. Link

Plakke MS, Deutsch AB, Meslin C, Clark NL, Morehouse NI. Dynamic digestive physiology of a female reproductive organ in a polyandrous butterfly. Journal of Experimental Biology. 2015. 218, 1548-1555. Link and Featured by JEB

Hancks DC, Hartley MK, Hagan C, Clark NL, Elde NC. Overlapping Patterns of Rapid Evolution in the Nucleic Acid Sensors cGAS and OAS1 Suggest a Common Mechanism of Pathogen Antagonism and Escape. PLOS Genetics. 2015. 11(5): e1005203. Open Access link

Godin SK, Meslin C, Bratton-Palmer DS, Hornack C, Mihalevic MJ, Yoshida K, Kabbinavar F, Sullivan M, Clark NL*, Bernstein KA*. Evolutionary and functional analysis of the invariant SWIM domain in the conserved Shu2/SWS1 protein family from Saccharomyces cerevisiae to Homo sapiens. Genetics. 2015. 199(4): 1023-1033. Link. Selected for issue highlight.


Findlay GD, Sitnik JL, Wang W, Aquadro CF, Clark NL, Wolfner MF. (2014) Evolutionary Rate Covariation Identifies New Members of a Protein Network Required for Drosophila melanogaster Female Post-Mating Responses. PLoS genetics 10(1): e1004108. Access the recommendation on F1000Prime pdf


Clark NL, Alani E, Aquadro CF. (2013) Evolutionary rate covariation involving meiotic proteins results from fluctuating evolutionary pressure in yeasts and mammals. Genetics 193(2): 529-538. pdf Selected for issue highlight.


Clark NL, Alani E, Aquadro CF. (2012) Evolutionary rate covariation reveals shared functionality and coexpression of genes. Genome Res 22(4): 714-720. pdf


Kelleher ES, Clark NL, Markow TA. 2011. Diversity Enhancing Selection Acts on a Female Reproductive Protease Family in Four Sub-Species of Drosophila mojavensis. Genetics. 187(3):865-76. pdf


Clark NL, Aquadro CF. 2010. A novel method to detect proteins evolving at correlated rates: Identifying new functional relationships between coevolving proteins. Molecular Biology and Evolution 27(5):1152-61. Access the recommendation on F1000Prime pdf


Clark NL, Gasper J, Sekino M, Springer SA, Aquadro CF, Swanson WJ. 2009. Coevolution of interacting fertilization proteins. PLoS Genetics 5(7): e1000570. pdf

Dean MD, Clark NL, Findlay GD, Karn RC, Yi X, Swanson WJ, MacCoss MJ, Nachman MJ. 2009. Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus). Molecular Biology and Evolution. 26(8): 1733. pdf


Karn RC, Clark NL, Nguyen ED, Swanson WJ. 2008. Adaptive evolution in rodent seminal vesicle proteins. Molecular Biology and Evolution. 25(11): 2301. pdf

Clark NL. 2008. Adaptive evolution of primate sperm proteins. In: Encyclopedia of Life Sciences (ELS). John Wiley and Sons, Ltd: Chichester. pdf


Clark NL, Findlay GD, Yi X, MacCoss MJ, Swanson WJ. 2007. Duplication and selection on abalone sperm lysin in an allopatric population. Molecular Biology and Evolution. 24(9): 2081. pdf


Clark NL, Aagaard JE, Swanson WJ. 2006. Evolution of reproductive proteins from animals and plants. Reproduction 131(1): 11-22. pdf

Panhuis, TM, Clark, NL & Swanson, WJ. 2006. Rapid evolution of reproductive proteins in abalone and Drosophila. Philosophical Transactions of the Royal Society B 361: 261-268. pdf


Clark NL, Swanson WJ. 2005. Pervasive adaptive evolution in primate seminal proteins. PLoS Genetics 1(3): e35. pdf

Stewart MK, Clark NL, Merrihew G, Galloway EM, Thomas JH. 2005. High genetic diversity in the chemoreceptor superfamily of Caenorhabditis elegans. Genetics 169(4): 1985-1996. pdf