All Stories

  1. The order in which amino acids were added to the genetic code in ancient life

    Article • Proceedings of the National Academy of Sciences, December 2024, Proceedings of the National Academy of Sciences

    Joanna Masel

  2. Extinction vortices are driven more by a shortage of beneficial mutations than by deleterious mutation accumulation

    Article • October 2024, Cold Spring Harbor Laboratory Press

    Joanna Masel

  3. The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder

    Article • eLife, September 2024, eLife

    Joanna Masel

  4. The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder

    Article • eLife, September 2024, eLife

    Joanna Masel

  5. The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder

    Article • July 2024, eLife

    Joanna Masel

  6. Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor’s protein domains

    Article • April 2024, Cold Spring Harbor Laboratory Press

    Joanna Masel

  7. Background Selection From Unlinked Sites Causes Nonindependent Evolution of Deleterious Mutations

    Article • Genome Biology and Evolution, March 2024, Oxford University Press (OUP)

    Joanna Masel

  8. Enhanced testing can substantially improve defence against several types of respiratory virus pandemic

    Article • February 2024, Cold Spring Harbor Laboratory Press

    Joanna Masel

  9. Combatting SARS-CoV-2 With Digital Contact Tracing and Notification: Navigating Six Points of Failure

    Article • JMIR Public Health and Surveillance, December 2023, JMIR Publications Inc.

    Joanna Masel

  10. Optimal targeting of interventions uses estimated risk of infectiousness to control a pandemic with minimal collateral damage

    Article • October 2023, Cold Spring Harbor Laboratory Press

    Joanna Masel

  11. A Mechanistically Integrated Model of Exploitative and Interference Competition over a Single Resource Produces Widespread Coexistence

    Article • September 2023, Cold Spring Harbor Laboratory Press

    Joanna Masel

  12. Human deleterious mutation rate implies high fitness variance, with declining mean fitness compensated by rarer beneficial mutations of larger effect

    Article • September 2023, Cold Spring Harbor Laboratory Press

    Joanna Masel

  13. A new codon adaptation metric predicts vertebrate body size and tendency to protein disorder

    Article • July 2023, eLife

    Joanna Masel

  14. Combatting SARS-CoV-2 With Digital Contact Tracing and Notification: Navigating Six Points of Failure (Preprint)

    Article • June 2023, JMIR Publications Inc.

    Joanna Masel

  15. Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends

    Article • Molecular Biology and Evolution, March 2023, Oxford University Press (OUP)

    Joanna Masel

  16. The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder

    Article • March 2023, Cold Spring Harbor Laboratory Press

    Joanna Masel

  17. The effectiveness of selection in a species affects the direction of amino acid frequency evolution

    Article • February 2023, Cold Spring Harbor Laboratory Press

    Joanna Masel

  18. Differential retention of Pfam domains creates long-term evolutionary trends

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Joanna Masel

  19. Random Peptides Rich in Small and Disorder-Promoting Amino Acids Are Less Likely to Be Harmful

    Article • Genome Biology and Evolution, May 2022, Oxford University Press (OUP)

    Joanna Masel

  20. Genetics of adaptation and fitness landscapes: From toy models to testable quantitative predictions

    Article • Evolution, May 2022, Wiley

    Joanna Masel

  21. nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models

    Article • Systematic Biology, February 2022, Oxford University Press (OUP)

    Joanna Masel

  22. Background selection from unlinked sites causes non-independent evolution of deleterious mutations

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Joanna Masel

  23. Substitution load revisited: a high proportion of deaths can be selective

    Article • November 2021, Cold Spring Harbor Laboratory Press

    Joanna Masel

  24. The economic value of quarantine is higher at lower case prevalence, with quarantine justified at lower risk of infection

    Article • Journal of The Royal Society Interface, September 2021, Royal Society Publishing

    Joanna Masel

  25. Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses

    Article • Genetics, August 2021, Oxford University Press (OUP)

    Joanna Masel

  26. Quantifying meaningful usage of a SARS-CoV-2 exposure notification app on the campus of the University of Arizona

    Article • February 2021, Cold Spring Harbor Laboratory Press

    Joanna Masel

  27. Universal and taxon-specific trends in protein sequences as a function of age

    Article • eLife, January 2021, eLife

    Joanna Masel

  28. Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Joanna Masel

  29. The economic value of quarantine is higher at lower case prevalence, with quarantine justified at lower risk of infection

    Article • November 2020, Cold Spring Harbor Laboratory Press

    Joanna Masel

  30. Mutation bias can shape adaptation in large asexual populations experiencing clonal interference

    Article • Proceedings of the Royal Society B Biological Sciences, October 2020, Royal Society Publishing

    Joanna Masel

  31. The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder

    Article • October 2020, Cold Spring Harbor Laboratory Press

    Joanna Masel

  32. Quantifying SARS-CoV-2 infection risk within the Google/Apple exposure notification framework to inform quarantine recommendations

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Joanna Masel

  33. Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence

    Article • Genome Biology and Evolution, June 2020, Oxford University Press (OUP)

    Joanna Masel

  34. Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Joanna Masel

  35. Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes

    Article • Genetics, April 2020, Oxford University Press (OUP)

    Joanna Masel

  36. Universal and taxon-specific trends in protein sequences as a function of age

    Article • March 2020, Cold Spring Harbor Laboratory Press

    Joanna Masel

  37. Mutation bias can shape adaptation in large asexual populations experiencing clonal interference

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Joanna Masel

  38. High Transcriptional Error Rates Vary as a Function of Gene Expression Level

    Article • Genome Biology and Evolution, December 2019, Oxford University Press (OUP)

    Joanna Masel

  39. Density-dependent selection and the limits of relative fitness

    Article • Theoretical Population Biology, October 2019, Elsevier

    Joanna Masel

  40. Evolution rapidly optimizes stability and aggregation in lattice proteins despite pervasive landscape valleys and mazes

    Article • September 2019, Cold Spring Harbor Laboratory Press

    Joanna Masel

  41. Readthrough errors purge deleterious cryptic sequences, facilitating the birth of coding sequences

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Joanna Masel

  42. Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise

    Article • Nature Communications, June 2019, Springer Science + Business Media

    Joanna Masel

  43. Biomarkers for aging identified in cross-sectional studies tend to be non-causative

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Joanna Masel

  44. Different mechanisms drive the maintenance of polymorphism at loci subject to strong versus weak fluctuating selection

    Article • Evolution, March 2019, Wiley

    Joanna Masel

  45. High transcriptional error rates vary as a function of gene expression level

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Joanna Masel

  46. A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution

    Article • Genetics, January 2019, Oxford University Press (OUP)

    Joanna Masel

  47. Directional Selection Rather Than Functional Constraints Can Shape the G Matrix in Rapidly Adapting Asexuals

    Article • Genetics, December 2018, Oxford University Press (OUP)

    Joanna Masel

  48. Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise

    Article • August 2018, Cold Spring Harbor Laboratory Press

    Joanna Masel

  49. Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes

    Article • Genetics, July 2018, Oxford University Press (OUP)

    Joanna Masel

  50. Directional selection rather than functional constraints can shape the G matrix in rapidly adapting asexuals

    Article • June 2018, Cold Spring Harbor Laboratory Press

    Joanna Masel

  51. Reply to Cheong et al.: Unicellular survival precludes Parrondo’s paradox

    Article • Proceedings of the National Academy of Sciences, May 2018, Proceedings of the National Academy of Sciences

    Joanna Masel

  52. Intercellular competition and the inevitability of multicellular aging

    Article • Proceedings of the National Academy of Sciences, October 2017, Proceedings of the National Academy of Sciences

    Joanna Masel

  53. A shift in aggregation avoidance strategy marks a long-term direction to protein evolution

    Article • August 2017, Cold Spring Harbor Laboratory Press

    Joanna Masel

  54. Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth

    Article • Nature Ecology & Evolution, April 2017, Springer Science + Business Media

    Joanna Masel

  55. Drift Barriers to Quality Control When Genes Are Expressed at Different Levels

    Article • Genetics, November 2016, Genetics Society of America

    Joanna Masel

  56. Drift barriers to quality control when genes are expressed at different levels

    Article • June 2016, Cold Spring Harbor Laboratory Press

    Joanna Masel

  57. Answering evolutionary questions: A guide for mechanistic biologists

    Article • BioEssays, May 2016, Wiley

    Joanna Masel

  58. What Fraction of Duplicates Observed in Recently Sequenced Genomes Is Segregating and Destined to Fail to Fix?

    Article • Genome Biology and Evolution, July 2015, Oxford University Press (OUP)

    Joanna Masel

  59. Constraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity

    Article • Heredity, February 2015, Nature

    Professor Cameron K Ghalambor, Joanna Masel

  60. Cryptic genetic variation can make “irreducible complexity” a common mode of adaptation in sexual populations

    Article • Evolution, September 2014, Wiley

    Joanna Masel

  61. CHANCE, PURPOSE, AND PROGRESS IN EVOLUTION AND CHRISTIANITY

    Article • Evolution, May 2014, Wiley

    Joanna Masel

  62. Q&A: Evolutionary capacitance

    Article • BMC Biology, September 2013, Springer Science + Business Media

    Joanna Masel

  63. Compensatory Evolution and the Origins of Innovations

    Article • Genetics, April 2013, Oxford University Press (OUP)

    Joanna Masel

  64. Rethinking Hardy–Weinberg and genetic drift in undergraduate biology

    Article • BioEssays, May 2012, Wiley

    Joanna Masel

  65. Hsp90 depletion goes wild

    Article • BMC Biology, February 2012, Springer Science + Business Media

    Joanna Masel

  66. Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast

    Article • BMC Systems Biology, January 2012, Springer Science + Business Media

    Joanna Masel

  67. The consequences of rare sexual reproduction by means of selfing in an otherwise clonally reproducing species

    Article • Theoretical Population Biology, December 2011, Elsevier

    Joanna Masel

  68. Genetic drift

    Article • Current Biology, October 2011, Elsevier

    Joanna Masel

  69. Evolution of molecular error rates and the consequences for evolvability

    Article • Proceedings of the National Academy of Sciences, January 2011, Proceedings of the National Academy of Sciences

    Joanna Masel

  70. Putatively Noncoding Transcripts Show Extensive Association with Ribosomes

    Article • Genome Biology and Evolution, January 2011, Oxford University Press (OUP)

    Joanna Masel

  71. Robustness and Evolvability

    Article • Trends in Genetics, September 2010, Elsevier

    Joanna Masel

  72. The Spontaneous Appearance Rate of the Yeast Prion [PSI+] and Its Implications for the Evolution of the Evolvability Properties of the [PSI+] System

    Article • Genetics, February 2010, Oxford University Press (OUP)

    Joanna Masel

  73. Robustness: mechanisms and consequences

    Article • Trends in Genetics, September 2009, Elsevier

    Joanna Masel

  74. THE EVOLUTION OF REVERSIBLE SWITCHES IN THE PRESENCE OF IRREVERSIBLE MIMICS

    Article • Evolution, September 2009, Wiley

    Joanna Masel

  75. Quantitative Prediction of Molecular Clock and Ka/Ks at Short Timescales

    Article • Molecular Biology and Evolution, August 2009, Oxford University Press (OUP)

    Joanna Masel

  76. Complex Adaptations Can Drive the Evolution of the Capacitor [PSI+], Even with Realistic Rates of Yeast Sex

    Article • PLoS Genetics, June 2009, PLOS

    Joanna Masel

  77. The Strength of Selection Against the Yeast Prion [PSI+]

    Article • Genetics, March 2009, Oxford University Press (OUP)

    Joanna Masel

  78. The evolution of bet-hedging adaptations to rare scenarios

    Article • Theoretical Population Biology, December 2007, Elsevier

    Joanna Masel

  79. A Bayesian model of quasi-magical thinking can explain observed cooperation in the public good game

    Article • Journal of Economic Behavior & Organization, October 2007, Elsevier

    Joanna Masel

  80. The Roles of Mutation Accumulation and Selection in Loss of Sporulation in Experimental Populations ofBacillus subtilis

    Article • Genetics, October 2007, Oxford University Press (OUP)

    Joanna Masel

  81. The Loss of Adaptive Plasticity during Long Periods of Environmental Stasis

    Article • The American Naturalist, January 2007, University of Chicago Press

    Joanna Masel

  82. Mutations Leading to Loss of Sporulation Ability in Bacillus subtilis Are Sufficiently Frequent to Favor Genetic Canalization

    Article • Genetics, January 2007, Oxford University Press (OUP)

    Joanna Masel

  83. The Conversion of 3′ UTRs into Coding Regions

    Article • Molecular Biology and Evolution, November 2006, Oxford University Press (OUP)

    Joanna Masel

  84. THE POPULATION GENETICS OF PHENOTYPIC DETERIORATION IN EXPERIMENTAL POPULATIONS OF BACILLUS SUBTILIS

    Article • Evolution, April 2006, Wiley

    Joanna Masel

  85. Cryptic Genetic Variation Is Enriched for Potential Adaptations

    Article • Genetics, March 2006, Oxford University Press (OUP)

    Joanna Masel

  86. THE POPULATION GENETICS OF PHENOTYPIC DETERIORATION IN EXPERIMENTAL POPULATIONS OF BACILLUS SUBTILIS

    Article • Evolution, January 2006, The Society for the Study of Evolution

    Joanna Masel

  87. Evolutionary Capacitance May Be Favored by Natural Selection

    Article • Genetics, July 2005, Oxford University Press (OUP)

    Joanna Masel

  88. Efficient Inhibition of Prion Replication by PrP-Fc2 Suggests that the Prion is a PrPSc Oligomer

    Article • Journal of Molecular Biology, February 2005, Elsevier

    Joanna Masel

  89. Prion Kinetics

    Article • Biophysical Journal, July 2004, Elsevier

    Joanna Masel

  90. THE EVOLUTION OF THE EVOLVABILITY PROPERTIES OF THE YEAST PRION [PSI+]

    Article • Evolution, July 2003, Wiley

    Joanna Masel

  91. THE EVOLUTION OF THE EVOLVABILITY PROPERTIES OF THE YEAST PRION [PSI+]

    Article • Evolution, January 2003, The Society for the Study of Evolution

    Joanna Masel

  92. The measured level of prion infectivity varies in a predictable way according to the aggregation state of the infectious agent

    Article • Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, February 2001, Elsevier

    Joanna Masel

  93. Designing drugs to stop the formation of prion aggregates and other amyloids

    Article • Biophysical Chemistry, December 2000, Elsevier

    Joanna Masel

  94. Quantifying the kinetic parameters of prion replication

    Article • Biophysical Chemistry, March 1999, Elsevier

    Joanna Masel

  95. Topological structures for 4-dimensional geographic information systems

    Article • Computers Environment and Urban Systems, May 1992, Elsevier

    Joanna Masel