J. Masel

发表

Topological structures for 4-dimensional geographic information systems

N. Hazelton, L. M. Bennett, J. Masel, 1992 .

Robustness and evolvability.

Meredith V. Trotter, J. Masel, 2010, Trends in genetics : TIG.

Robustness: mechanisms and consequences.

M. Siegal, J. Masel, 2009, Trends in genetics : TIG.

Evolution of molecular error rates and the consequences for evolvability

J. Masel, E. Rajon, Etienne Rajon, 2011, Proceedings of the National Academy of Sciences.

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

C. Schlichting, E. Snell-Rood, J. Masel, 2015, Heredity.

Compensatory Evolution and the Origins of Innovations

J. Masel, E. Rajon, 2012, Genetics.

Quantitative prediction of molecular clock and ka/ks at short timescales.

Joanna Masel, J. Masel, Grant I Peterson, 2009, Molecular biology and evolution.

Amino acids that are well tolerated in random peptides in E. coli are enriched in young animal but not young plant genes

J. Masel, Luke J Kosinski, Nathan Aviles, 2020 .

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

Joanna Masel, C. W. Birky, W. Nicholson, 2006, Evolution; international journal of organic evolution.

The evolution of bet-hedging adaptations to rare scenarios.

Joanna Masel, J. Masel, Oliver D. King, 2007, Theoretical population biology.

Answering evolutionary questions: A guide for mechanistic biologists

D. Promislow, J. Masel, 2016, BioEssays : news and reviews in molecular, cellular and developmental biology.

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

M. Siegal, J. Masel, A. Lancaster, 2019, Nature Communications.

Adaptive evolution of feed-forward loops versus diamonds to filter out short spurious signals

M. Siegal, J. Masel, A. Lancaster, 2018, bioRxiv.

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

J. Masel, Luke J Kosinski, J. James, 2021, eLife.

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

J. Masel, Luke J Kosinski, J. James, 2020, bioRxiv.

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

J. Masel, B. A. Wilson, M. Cordes, 2019, Genetics.

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

J. Masel, B. A. Wilson, M. Cordes, 2017, Genetics.

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

Ashley I. Teufel, J. Masel, D. Liberles, 2015, Genome biology and evolution.

Evolutionary Capacitance Emerges Spontaneously during Adaptation to Environmental Changes.

J. Masel, P. Nelson, Paul G. Nelson, 2018, Cell reports.

Evolutionary capacitance emerges spontaneously during adaptation to environmental changes

J. Masel, P. Nelson, Paul G. Nelson, 2017, bioRxiv.

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

J. Masel, Y. Wurm, C. Dessimoz, 2020, Genome biology and evolution.

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

J. Masel, J. Bertram, K. Gomez, 2018, Genetics.

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

J. Masel, C. Griswold, 2009, PLoS genetics.

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

J. Masel, J. James, S. Willis, 2020, bioRxiv.

The kinetics of proteinase K digestion of linear prion polymers

V. Jansen, J. Masel, Joanna Masel, 1999, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Differential retention of Pfam domains creates long-term evolutionary trends

J. Masel, J. James, P. Nelson, 2022, bioRxiv.

CHANCE, PURPOSE, AND PROGRESS IN EVOLUTION AND CHRISTIANITY

J. Masel, L. Mix, 2014, Evolution; international journal of organic evolution.

Genetic drift

Joanna Masel, J. Masel, 2011, Current Biology.

Foldability of a Natural De Novo Evolved Protein.

J. Masel, V. Wysocki, Jing Yan, 2017, Structure.

The timing of COVID-19 transmission

R. Hinch, A. Nurtay, M. Kendall, 2020, medRxiv.

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

M. Gerstein, J. Masel, K. Xiong, 2020, bioRxiv.

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

M. Siegal, J. Masel, A. Lancaster, 2019, Nature Communications.

Quantifying SARS‐CoV‐2 Infection Risk Within the Google/Apple Exposure Notification Framework to Inform Quarantine Recommendations

Y. Son, J. Masel, P. Beamer, 2021, Risk analysis : an official publication of the Society for Risk Analysis.

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

Sameer Halai, Joanna Masel, Tina White, 2020, medRxiv.

Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth

J. Masel, B. A. Wilson, Rafik Neme, 2017, Nature Ecology &Evolution.

Putatively Noncoding Transcripts Show Extensive Association with Ribosomes

J. Masel, B. A. Wilson, Benjamin A. Wilson, 2011, Genome biology and evolution.

Cryptic Genetic Variation Is Enriched for Potential Adaptations

J. Masel, 2006, Genetics.

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

J. Masel, Luke J Kosinski, 2019, bioRxiv.

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

J. Masel, Luke J Kosinski, Nathan Aviles, 2022, bioRxiv.

More benign random peptides in E. coli are enriched for similar amino acids as young animal but not plant genes

J. Masel, Luke J Kosinski, Nathan Aviles, 2020 .

Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes

J. Masel, S. Willis, 2017, Genetics.

The conversion of 3' UTRs into coding regions.

J. Masel, M. Giacomelli, Adam Hancock, 2007, Molecular biology and evolution.

Differential retention of Pfam domains creates long-term evolutionary trends

J. Masel, J. James, P. Nelson, 2023, bioRxiv.

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

Aviv Bergman, Joanna Masel, A. Bergman, 2003, Evolution; international journal of organic evolution.

Eco-evolutionary "fitness" in 3 dimensions: absolute growth, absolute efficiency, and relative competitiveness

J. Masel, 2014, 1407.1024.

Drift Barriers to Quality Control When Genes Are Expressed at Different Levels Running Title: Drift Barriers to Quality Control

Jay P. McEntee, J. Masel, K. Xiong, 2022 .

Drift barriers for the proofreading of genes expressed at different levels

Jay P. McEntee, J. Masel, K. Xiong, 2016 .

The Effects of Selection Against Translational Errors on the Evolution of Protein Evolvability

Meredith V. Trotter, J. Masel, Kayla M. Peck, 2010 .

Substitution load revisited: reproductive excess, the proportion of deaths that are selective, and adaptation’s speed limit

J. Masel, Moisés Expósito-Alonso, J. Matheson, 2021, bioRxiv.

Q&A: Evolutionary capacitance

J. Masel, 2013, BMC Biology.

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

H. True, J. Masel, A. Lancaster, 2010, Genetics.

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

J. Masel, C. Griswold, 2009, Genetics.

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

Joanna Masel, J. Masel, H. Maughan, 2007, Genetics.

The Loss of Adaptive Plasticity during Long Periods of Environmental Stasis

J. Masel, H. Maughan, Oliver D. King, 2006, The American Naturalist.

Evolutionary Capacitance May Be Favored by Natural Selection

J. Masel, 2005, Genetics.

Intercellular competition and the inevitability of multicellular aging

J. Masel, P. Nelson, Paul G. Nelson, 2017, Proceedings of the National Academy of Sciences.

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

Daniel B. Weissman, Meredith V. Trotter, J. Masel, 2013, Evolution; international journal of organic evolution.

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

D. Promislow, J. Masel, P. Nelson, 2019, bioRxiv.

Efficient inhibition of prion replication by PrP-Fc(2) suggests that the prion is a PrP(Sc) oligomer.

A. Aguzzi, J. Masel, N. Genoud, 2005, Journal of molecular biology.

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

J. Masel, J. Bertram, K. Gomez, 2020, bioRxiv.

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

Jason Bertram, Joanna Masel, J. Masel, 2019, Genetics.

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

M. Gerstein, J. Masel, K. Xiong, 2020, bioRxiv.

Rethinking Hardy–Weinberg and genetic drift in undergraduate biology

Joanna Masel, J. Masel, 2012, BioEssays : news and reviews in molecular, cellular and developmental biology.

The Recent De Novo Origin of Protein C-Termini

J. Masel, M. Cordes, L. Guzman, 2015, Genome biology and evolution.

Fluctuations in HIV-1 viral load are correlated to CD4+ T-lymphocyte count during the natural course of infection.

J. Goedert, A. Lloyd, T. O'Brien, 2000 .

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

J. Masel, K. Xiong, P. Nelson, 2019, bioRxiv.

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

J. Masel, J. James, Catherine Weibel, 2023, bioRxiv.

Gene Birth Contributes to Structural Disorder Encoded by Overlapping Genes

J. Masel, S. Willis, 2017, Genetics.

A clean partition of "fitness" into three incommensurable dimensions: growth, efficiency, and competitiveness

J. Masel, 2014 .

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

J. Masel, J. Bertram, K. Gomez, 2018, Genetics.

The Roles of Mutation Accumulation and Selection in Loss of Sporulation in Experimental Populations of Bacillus subtilis

W. Nicholson, J. Masel, H. Maughan, 2007, Genetics.

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

W. Nicholson, J. Masel, H. Maughan, 2006, Evolution; international journal of organic evolution.

A lottery model of density-dependent selection in evolutionary genetics

J. Masel, J. Bertram, J. Bertram, 2017 .

Density-dependent selection in evolutionary genetics: a lottery model of Grime's triangle

J. Masel, J. Bertram, 2017 .

Quantifying the kinetic parameters of prion replication.

M A Nowak, M. Nowak, V. Jansen, 1999, Biophysical chemistry.

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

J. Masel, J. Bertram, 2019, Evolution; international journal of organic evolution.

A central role for boom-bust cycles in maintaining genetic variation in fluctuating environments

J. Masel, J. Bertram, 2017, bioRxiv.

Unlinked background selection reduces neutral diversity more than linked background selection

J. Masel, J. Matheson, 2023 .

Background selection theory overestimates effective population size for high mutation rates

J. Masel, J. Matheson, 2022 .

Hsp90 depletion goes wild

M. Siegal, J. Masel, 2012, BMC Biology.

Commentary Hsp90 Depletion Goes Wild Co M M E N Ta R Y Open Blockinaccess

M. Siegal, J. Masel, 2022 .

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

David N. Lyttle, J. Masel, 2011, Theoretical population biology.

The Evolution of Reversible Switches in the Presence of Irreversible Mimics

J. Masel, A. Lancaster, 2009, Evolution; international journal of organic evolution.

Genetic assimilation can occur in the absence of selection for the assimilating phenotype, suggesting a role for the canalization heuristic

J. Masel, J. Masel, 2004, Journal of evolutionary biology.

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

V. Jansen, J. Masel, 2001, Biochimica et biophysica acta.

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

V. Jansen, J. Masel, V A Jansen, 2000, Biophysical chemistry.

Modelling the effectiveness and social costs of daily lateral flow antigen tests versus quarantine in preventing onward transmission of COVID-19 from traced contacts

C. Fraser, R. Hinch, A. Nurtay, 2021, medRxiv.

Predicting patterns of long‐term adaptation and extinction with population genetics

J. Masel, J. Bertram, K. Gomez, 2016, Evolution; international journal of organic evolution.

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

J. Masel, J. Petrie, 2020, Journal of the Royal Society Interface.

Evidence-Based Medicine as a Tool for Undergraduate Probability and Statistics Education

J. Masel, B. Blackburn, P. T. Humphrey, 2015, CBE life sciences education.

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

Joanna Masel, J. Masel, 2007 .

Digital contact tracing/notification for SARS-CoV-2: a retrospective of what went wrong

J. Masel, W. Ebbers, Sam Zimmerman, 2023 .

Outcome Orientation: A Misconception of Probability That Harms Medical Research and Practice

Joanna Masel, J. Masel, P. T. Humphrey, 2014, 1412.4604.

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

J. Masel, J. James, Catherine Weibel, 2023, bioRxiv.

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

J. Masel, J. James, S. Willis, 2023, bioRxiv.

nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models

R. Lanfear, J. Masel, L. Vinh, 2021, bioRxiv.

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

J. Masel, P. Nelson, 2018, Proceedings of the National Academy of Sciences.

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

Joanna Masel, Leandra M. Brettner, J. Masel, 2012, BMC Systems Biology.

Density-dependent selection and the limits of relative fitness.

J. Masel, J. Bertram, 2019, Theoretical population biology.

Density-dependent selection and the limits of relative fitness

J. Masel, J. Bertram, 2018, bioRxiv.

The cost of selection in selective deaths paid out of reproductive excess

J. Masel, Moisés Expósito-Alonso, J. Matheson, 2023, bioRxiv.

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

J. Masel, Kacey C. Ernst, Bruce Helming, 2021 .

Digital contact tracing/notification for SARS-CoV-2: navigating six points of failure

J. Masel, W. Ebbers, Sam Zimmerman, 2023, 2306.00873.

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

J. Masel, J. Matheson, Joseph Matheson, 2023, bioRxiv.

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

J. Masel, Jennifer E. James, Paul G. Nelson, 2023, Molecular biology and evolution.

Compensatory Evolution and the Origins of Innovations

J. Masel, Etienne Rajon, 2012, Genetics.

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

Jay P. McEntee, J. Masel, D. Porfirio, 2016, Genetics.

Density-dependent selection and the limits of relative fitness

J. Masel, J. Bertram, 2017, bioRxiv.

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

J. Masel, J. Bertram, J. Matheson, 2023, bioRxiv.