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2021
Saputra E, Kowalczyk A, Cusick L, Clark NL, Chikina M. Phylogenetic Permulations: a statistically rigorous approach to measure confidence in associations between phenotypes and genetic elements in a phylogenetic context . Molecular Biology and Evolution. 2021; msab068.
Furman CM, Elbashir R, Pannafino G, Clark NL, Alani E. Experimental exchange of paralogous domains in the MLH family provides evidence of sub-functionalization after gene duplication. G3 Genes|Genomes|Genetics . 2021. jkab111.
Keeble S, Firman RC, Sarver BAJ, Clark NL, Simmons LW, Dean MD. Evolutionary, proteomic, and experimental evidence that the extracellular matrix of cumulus cells impacts fertilization outcomes. Biology of Reproduction . 2021.
Kowalczyk A, Gbadamosi O, Kolor K Sosa Jahree, St Croix C, Gibson G, Chikina M, Aizenman E, Clark NL, Kiselyov K. Evolutionary rate covariation identifies SLC30A9 (ZnT9) as a mitochondrial zinc transporter . bioRxiv. 2021.
2020
Kowalczyk, A, Partha R, Clark NL, and Chikina M. Pan-mammalian analysis of molecular constraints underlying extended lifespan . eLife . 2020; 9: e51089.
Talsness DM, Owings KG, Coelho E, Mercenne G, Pleinis JM, Partha R, Hope KA, Zuberi AR, Clark NL, Lutz CM, Rodan AR, Chow CY. A Drosophila screen identifies NKCC1 as a modifier of NGLY1 deficiency . eLife . 2020;9 e57831.
Jen-Wei Huang, Ananya Acharya, Angelo Taglialatela, Tarun Nambiar, Raquel Cuella-Martin, Giuseppe Leuzzi, Samuel Hayward, Sarah Joseph, Gregory Brunette, Roopesh Anand, Rajesh Soni, Nathan Clark, Kara Bernstein, Petr Cejka, and Alberto Ciccia. MCM8IP activates the MCM8-9 helicase to promote DNA synthesis and homologous recombination upon DNA damage . Nature Communications . 2020; 11: 2928
2019
Sackton TB and Clark NL. Convergent evolution in the genomics era: new insights and directions . Philosophical Transactions of the Royal Society B. 2019; 374(1777): Article ID 20190102. PDF
Kowalczyk A, Meyer WK, Partha R, Mao W, Clark NL, Chikina M. RERconverge: an R package for associating evolutionary rates with convergent traits . Bioinformatics . 2019; 1-3: btz468. PDF
Partha R, Kowalczyk A, Clark NL, Chikina M. Robust methods for detecting convergent shifts in evolutionary rates . Molecular Biology and Evolution . 2019; 36(8): 1817-1830. PDF
Raza Q, Choi JY, Li Y, O’Dowd RM, Watkins SC, Hong Y, Clark NL, Kwiatkowski AV. Evolutionary rate covariation identifies the GTPase activating protein Raskol as a signaling component of the cadherin adhesion network in Drosophila . PLOS Genetics . 2019; 15(2): e1007720. Featured in Perspective by Jeffrey Colgren and Scott Nichols . Evolution as a guide for experimental cell biology.
Brunette GJ, Jamalruddin MA, Baldock RA, Clark NL, Bernstein KA. Evolution-based screening enables genome-wide prioritization and discovery of DNA repair genes . Proceedings of the National Academy of Sciences, USA. 2019; 116(39): 19593-19599. PDF
Hill JA, Neethiraj R, Rastas P, Clark NL, Morehouse NI, de la Paz Celorio-Mancera M, Cols JC, Dircksen H, Meslin C, Sikkink K, Vives M, Vogel H, Wiklund C, Boggs CL, Nylin, Wheat CW. A butterfly chromonome reveals selection dynamics during extensive and cryptic chromosomal reshuffling . Science Advances. 2019; 12:5(6):eaau3648. PDF
Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark NL, Chen V, Lu S Chen L, Yu L, Hochheiser HS, Jiang X, Wang J, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference . PLOS Computational Biology . 2019; 15(7): e1007088.
2018
Wynn K. Meyer, Jerrica Jamison, Rebecca Richter, Stacy E. Woods, Charles Kronk, Raghavendran Partha, Amanda Kowalczyk, Maria Chikina, Robert K. Bonde, Joseph Gaspard, Janet M. Lanyon, Clement E. Furlong, and Nathan L. Clark. Ancient convergent losses of Paraoxonase 1 yield deleterious consequences for modern marine mammals . Science . 2018; 361(6402): 591-594. PDF
Sumitha Nallu, Jason Hill, Kristine Don, Carlos Sahagun, Wei Zhang, Camille Meslin, Emilie Snell-Rood, Nathan L. Clark, Nathan I. Morehouse, Joy Bergelson, Christopher W. Wheat and Marcus R. Kronforst. The molecular genetic basis of herbivory between butterflies and their host-plants . Nature: Ecology and Evolution . 2018; 2: 1418-1427. PDF
2017
Partha R, Chauhan BK, Worman-Ferreria Z, Robinson JD, Lathrop K, Nischal KK, Chikina M*, Clark NL*. Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling . eLife . 2017; 6: e25884.
Meslin C, Cherwin TS, Plakke MS, Small BS, Goetz BJ, Morehouse NI, Clark NL. Structural complexity and molecular heterogeneity of a butterfly ejaculate reflect a complex history of selection . Proceedings of the National Academy of Sciences, USA . 2017; 114(27): E5406–E5413. Featured in The Atlantic. PDF
2016
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 drainageOpen Forum Infectious Diseases . 2016; 3(3):ofw120. PDF
Chikina M, Robinson JD, Clark NL. Hundreds of genes experienced convergent shifts in selective pressure in marine mammals . Molecular Biology and Evolution . 2016. 33(9): 2182-2192. PDF
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 . Journal of Biological Chemistry . 2016; 291(9): 4442-52. PDF
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. PDF
2015
Wolfe NW, Clark NL. ERC Analysis: web-based inference of gene function via Evolutionary Rate Covariation. Bioinformatics . 2015. doi:10.1093/bioinformatics/btv454. PDF
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. 115, 496-502. PDF
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. PDF
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
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. PDF
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. PDF
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.
2014
2013
2012
2011
2010
2009
Clark NL, Gasper J, Sekino M, Springer SA, Aquadro CF, Swanson WJ. Coevolution of interacting fertilization proteins . PLOS Genetics 2009; 5(7): e1000570.
Dean MD, Clark NL, Findlay GD, Karn RC, Yi X, Swanson WJ, MacCoss MJ, Nachman MJ. Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus ) . Molecular Biology and Evolution . 2009; 26(8): 1733. PDF
2008
Clark NL. Adaptive evolution of primate sperm proteins. In: Encyclopedia of Life Sciences (ELS). 2008. John Wiley and Sons, Ltd: Chichester.
Karn RC, Clark NL, Nguyen ED, Swanson WJ. Adaptive evolution in rodent seminal vesicle proteins. Molecular Biology and Evolution . 2008; 25(11): 2301. PDF
2007
2006
2005
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