Masel group

COVID-19

• Ferretti L., Wymant C., Nurtay A., Zhao L., Hinch R., Masel J., et al. (2021). Modelling the effectiveness and social costs of daily lateral flow antigen tests versus quarantine in preventing onward transmission of COVID-19 from traced contacts, medRxiv, preprint.
• Masel J., Shilen A., Helming B., Rutschman J., Windham G., Pogreba-Brown K., Ernst K. (2021). Quantifying meaningful adoption of a SARS-CoV-2 exposure notification app on the campus of the University of Arizona, medRxiv, preprint.
• Petrie J., Masel J. (2021). The economic value of quarantine is higher at lower case prevalence, with quarantine justified at lower risk of infection, Royal Society,18(182)
• Wilson A. M., Aviles N., Petire, J. I., Beamer P. I., Szabo Z., Ernst K. C., Masel J., et al. (2021). Quantifying SARS-CoV-2 infection risk within the Apple/Google exposure notification framework to inform quarantine recommendations, Risk Analysis.
• Ferretti L., Ledda A., Wymant C., Zhao L., Ledda V., Masel J., et al. (2020). The timing of COVID-19 Transmission, medRxiv, preprint.

Robustness, messy genotype-phenotype maps, and evolvability

• Xiong K., Gerstein M., Masel J. (2021). Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses, BioRxiv, preprint.
• Kosinski L. J., Masel J. (2020). Readthrough errors purge deleterious cryptic sequences, facilitating the birth of coding sequences, Molecular Biology and Evolution, 37(6), 1761-1774.
• Meer K. M., Nelson P. G., Xiong K., Masel J. (2019). High transcriptional error rates vary as a function of gene expression level, Genome Biology & Evolution, 12(1), 3754-3761.
• Xiong K., Lancaster A. K., Siegal M. L., & Masel J. (2019) Feed forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise, Nature Communications 10:2418.
• Nelson P., & Masel J. (2018) Evolutionary capacitance emerges spontaneously during adaptation to environmental changes, Cell Reports, 25(1): 249-258.
• Xiong K., McEntee J., Porfirio D., Masel J. (2017) Drift barriers to quality control when genes are expressed at different levels, Genetics 205: 397-407.
• Trotter, M. V.,Weissman, D. B., Peterson, G., Peck, K., & Masel, J. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation, Evolution, 68:3357–3367.
• Masel J. (2013) Q&A: Evolutionary capacitance, BMC Biology, 11:103.
• Brettner, L.M., & Masel, J. (2012) Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast , BMC Systems Biology, 6:128 
• Rajon, E., & Masel, J. (2013) Compensatory evolution and the origins of innovations, Genetics, 193(4):1209-20.
• Siegal M. L., & Masel J. (2012) Hsp90 depletion goes wild, BMC Biology 10:14 .
• Wilson, B. A., & Masel, J. (2011). Putatively noncoding transcripts show extensive association with ribosomes, Genome Biology & Evolution, 3, 1245-1252
• Masel, J. & Lyttle, D. N. (2011). The consequences of rare sexual reproduction by means of selfing in an otherwise clonally reproducing species. Theoretical Population Biology, 80(4), 317-322 .
• Rajon, E., & Masel, J. (2011). Evolution of molecular error rates and the consequences for evolvability. Proc. Natl. Acad. Sci. USA, 108(3), 1082-7.
• Masel, J., & Trotter, M. V. (2010). Robustness and Evolvability. Trends in Genetics, 26(9), 406-414.
• Lancaster, A. K., Bardill, J. P., True, H. L., & Masel, J. (2010). The Spontaneous Appearance Rate of the Yeast Prion [PSI+] and Its Implications For the Evolution of the Evolvability Properties of the [PSI+] System. Genetics, 184(2), 393-400.
• Masel, J., & Griswold, C. K. (2009). The strength of selection against the yeast prion [PSI+]. Genetics, 181(3), 1057-63.
• Masel, J., & Siegal, M. L. (2009). Robustness: mechanisms and consequences. Trends Genet.
• Griswold, C. K., & Masel, J. (2009). Complex adaptations can drive the evolution of the capacitor [PSI], even with realistic rates of yeast sex. PLoS Genet, 5(6), 1000517.
• Masel, J., & Maughan, H. (2007). Mutations leading to loss of sporulation ability in Bacillus subtilis are sufficiently frequent to favor genetic canalization. Genetics, 175(1), 453-7.
• Masel, J. (2006). Cryptic genetic variation is enriched for potential adaptations. Genetics, 172(3), 1985-91.
• Masel, J. (2005). Evolutionary capacitance may be favored by natural selection. Genetics, 170(3), 1359-71.
• Masel, J. (2004). Genetic assimilation can occur in the absence of selection for the assimilating phenotype, suggesting a role for the canalization heuristic. J Evol Biol, 17(5), 1106-10.
• Masel, J., & Bergman, A. (2003). The evolution of the evolvability properties of the yeast prion [PSI+]. Evolution, 57(7), 1498-512.

Protein evolution

• CC Dang, BQ Minh, H McShea, J Masel, JE James, LS Vinh, R Lanfear (2021). nQMkaer: estimating time non-reversible amino acid substitution models, BioRxiv, preprint
• L Kosinski, N Aviles, K Gomez, J Masel (2021). Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful, BioRxiv, preprint
• James J. E., Willis S. M., Nelson P. G., Weibel C., Kosinski L., Masel J. (2021). Universal and taxon-specific trends in protein sequences as a function of age, Elife, 10, e57347.
• Zile K., Dessimoz C., Wurm Y., Masel J. (2020). Only a single taxonomically restricted gene family in the Drosophila melanogaster subgroup can be identified with high confidence, Genome Biology and Evolution, 12(8), 1355-1366.
• Weibel C., James J. E., Willis S. M., Nelson P. G., Masel J. (2020). The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder, MedRxiv, preprint.
• Kosinski L., Aviles N., Gomez K., Masel J. (2020). More benign random peptides in E. coli are enriched for similar amino acids as young animal but not plant genes, BioRxiv, preprint.
• Bertram J., Masel J. (2020) Evolution rapidly optimizes stability and aggregation in lattice proteins despite pervasive landscape valleys and mazes, Genetics, 214(4), 1047-1057.
• Foy SG, Wilson BA, Bertram J, Cordes MHJ, Masel J. (2019) A shift in aggregation avoidance strategy marks a long-term direction to protein evolution, Genetics 211:1345-1355.
• Willis S., & Masel J. (2018) Gene birth contributes to structural disorder encoded by overlapping genes, Genetics 210(1): 303-313.
• Bungard D., Copple J. S., Yan J., Chhun J., Kumirov V. K., Foy S. G., Masel J., Wysocki V. H., & Cordes M. H. J. (2017) Foldability of a natural de novo evolved protein, Structure 25:1-10.
• Wilson B. A., Foy S. G., Neme R., & Masel J. (2017) Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth, Nature Ecology & Evolution, 1:0146.
• Andreatta, M. E., Levine, J.Al., Foy, S.G., Guzman, L., Kosinski, L., Cordes, M.H.J., & Masel, J. (2015) The recent de novo origin of protein C-termini, Genome Biology & Evolution 7(6):1686-1701.
• Giacomelli, M. G., Hancock, A. S., & Masel, J. (2007). The conversion of 3′ UTRs into coding regions. Mol Biol Evol, 24(2), 457-64.

Aging

• Nelson P., Promislow D., Masel J. (2019). Biomarkers for aging identified in cross-sectional studies tend to be non-causative, The Journals of Gerontology: Series A, 75(3), 466-472.
• Nelson P., Masel J. (2017) Intercellular competition and the inevitability of multicellular aging, PNAS 114: 12982–12987

Phenotypic switching

• Lancaster, A. K., & Masel, J. (2009). The evolution of reversible switches in the presence of irreversible mimics. Evolution, 63(9), 2350-62.
• King, O. D., & Masel, J. (2007). The evolution of bet-hedging adaptations to rare scenarios. Theor Pop Biol, 72, 560-575.

Trait loss

• Murren C. J., Auld J. R., Callahan H., Ghalambor C. K., Handelsman C. A., Heskel M. A., Kingsolver J. G., Maclean H. J., Masel J., Maughan H., Pfennig D. W., Relyea R. A., Seiter S., Snell-Rood E., Steiner U. K., & Schlichting C. D. (2015) Constraints on the evolution of phenotypic plasticity: costs of phenotype and costs of plasticity, Heredity, 115: 293-301
• Maughan, H., Masel, J., Birky Jr, C. W., & Nicholson, W. L. (2007). The roles of mutation accumulation and selection in loss of sporulation in experimental populations of Bacillus subtilis. Genetics, 177(2), 937-48. (PubMed) (doi)
• Masel, J., King, O. D., & Maughan, H. (2007). The loss of adaptive plasticity during long periods of environmental stasis. Am Nat, 169(1), 38-46. (PubMed) (doi)
• Maughan, H., Callicotte, V., Hancock, A., Birky Jr, C. W., Nicholson, W. L., & Masel, J. (2006). The population genetics of phenotypic deterioration in experimental populations of Bacillus subtilis. Evolution, 60(4), 686-95. (PubMed)

Relative vs. absolute competitions

• J Matheson, M Exposito-Alonso, J Masel (2021). Haldane's cost of selection imposes a mild constraint on adaptation, with a high proportion of deaths in A.thaliana being selective, BioRxiv, preprint
• Bertram J, Masel J. (2019) Different mechanisms drive the maintenance of polymorphism at loci subject to strong versus weak fluctuating selection, Evolution 73:883–896.
• Bertram J., & Masel J. (2019) Density-dependent selection and the limits of relative fitness, Theoretical Population Biology 129:81–92.
• Masel, J. (2016) Bypass Wall Street: A Biologist's Guide to the Rat Race, Perforce Publishing.
• Masel, J. (2016) How Your Savings Plan Fuels an Arms Race on Wall Street, Evonomics blog
• Masel J. Eco-evolutionary "fitness" in 3 dimensions: absolute growth, absolute efficiency, and relative competitiveness, unpublished manuscript.

Travelling wave models in evolution

• Gomez K., Bertram J., Masel J. (2020). Mutation bias can shape adaptation in large asexual populations experiencing clonal interference, Proceedings of the Royal Society B, 287(1937), 20201503.
• Gomez K., Bertram J., & Masel J. (2019) Directional selection rather than functional constraints can shape the G matrix in rapidly adapting asexuals, Genetics 211: 715–729.
• Bertram J., Gomez K., & Masel J. (2017) Predicting patterns of long-term adaptation and extinction with population genetics, Evolution 71: 204–214.

Other topics in evolution

• J Matheson, J Masel (2022). Background selection theory overestimates effective population size for high mutation rates bioRxiv, preprint
• Teufel AI, Masel J, Liberles DA. (2015) What Fraction of Duplicates Observed in Recently Sequenced Genomes Is Segregating and Destined to Fail to Fix? Genome Biology and Evolution, 7(8): 2258-2264.
• Peterson, G. I., & Masel, J. (2009). Quantitative prediction of molecular clock and Ka/Ks at short timescales. Mol Biol Evol. 26(11): 2595-2603 (PubMed) (doi)

Prion biology

• Masel, J., Genoud, N., & Aguzzi, A. (2005). Efficient inhibition of prion replication by PrP-Fc₂ suggests that the prion is a PrP^Sc oligomer. J Mol Biol, 345(5), 1243-51. (PubMed) (doi)
• Masel, J., & Jansen, V. A. (2004). Prion kinetics. Biophys J, 87(1), 728. (PubMed) (doi)
• Masel, J., & Jansen, V. A. (2001). The measured level of prion infectivity varies in a predictable way according to the aggregation state of the infectious agent. Biochim Biophys Acta, 1535(2), 164-73. (PubMed)
• Masel, J., & Jansen, V. A. (2000). Designing drugs to stop the formation of prion aggregates and other amyloids. Biophys Chem, 88(1-3), 47-59. (PubMed)
• Masel, J., Jansen, V. A., & Nowak, M. A. (1999). Quantifying the kinetic parameters of prion replication. Biophys Chem, 77(2-3), 139-52. (PubMed)
• Masel, J., & Jansen, V. A. (1999). The kinetics of proteinase K digestion of linear prion polymers. Proc Biol Sci, 266(1431), 1927-31. (PubMed) (doi)

Teaching (defined broadly)

• Masel, J. and Promislow, D. E. L. (2016), Answering evolutionary questions: A guide for mechanistic biologists. BioEssays 38: 704–711 (PDF)
• Humphrey P. T., & Masel J. (2017) Outcome orientation — a misconception of probability that harms medical research and practice, Perspectives in Biology and Medicine, 59:147-155.
• Masel J., Humphrey P. T., Blackburn B., & Levine J. A. (2015) Evidence-based medicine as a tool for undergraduate probability and statistics education, CBE Life Sciences Education, 14:1-10.
• Mix L. J., & Masel J. (2014) Chance, purpose and progress in evolution and Christianity, Evolution, 68(8), 2441-2451.
• Masel, J. (2012) Rethinking Hardy-Weinberg and genetic drift in undergraduate biology. BioEssays 34:701-710
• Masel, J. (2011) Genetic drift. Current Biology, 21(20), R837-R838

Other

• Masel, J. (2007). A Bayesian model of quasi-magical thinking can explain observed co-operation in the public good game. J. Econ. Behav. Organ., 64, 216-231. (PDF) (doi)
• Bliss, T. M., Kelly, S., Shah, A. K., Foo, W. C., Kohli, P., & Stokes, C., et al. (2006). Transplantation of hNT neurons into the ischemic cortex: cell survival and effect on sensorimotor behavior. J Neurosci Res, 83(6), 1004-14. (PubMed) (doi)
• Kelly, S., Bliss, T. M., Shah, A. K., Sun, G. H., Ma, M., & Foo, W. C., et al. (2004). Transplanted human fetal neural stem cells survive, migrate, and differentiate in ischemic rat cerebral cortex. Proc Natl Acad Sci U S A, 101(32), 11839-44. (PubMed) (doi)
• Masel, J., Arnaout, R. A., O’Brien, T. R., Goedert, J. J., & Lloyd, A. L. (2000). Fluctuations in HIV-1 viral load are correlated to CD4+ T-lymphocyte count during the natural course of infection. J Acquir Immune Defic Syndr, 23(5), 375-9. (PubMed)
• Hazelton, N. W. J., Bennet, L. M., & Masel, J. (1992). Topological structures for 4-dimensional geographical information systems. Computers, Environment, and Urban Systems, 16, 227-237.