Search Results - "Wichman, Holly"

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  1. 1

    Epistasis between beneficial mutations and the phenotype-to-fitness Map for a ssDNA virus by Rokyta, Darin R, Joyce, Paul, Caudle, S Brian, Miller, Craig, Beisel, Craig J, Wichman, Holly A

    Published in PLoS genetics (01-06-2011)
    “…Epistatic interactions between genes and individual mutations are major determinants of the evolutionary properties of genetic systems and have therefore been…”
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  2. 2

    Mutational effects and population dynamics during viral adaptation challenge current models by Miller, Craig R, Joyce, Paul, Wichman, Holly A

    Published in Genetics (Austin) (01-01-2011)
    “…Adaptation in haploid organisms has been extensively modeled but little tested. Using a microvirid bacteriophage (ID11), we conducted serial passage…”
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  3. 3

    Genetic and functional basis of the reduction effect in bacteriophage ΦX174 by Bailes, Clayton L., Biggs, Karin R.H., Scott, LuAnn, Wichman, Holly A., Schwartz, Elissa J.

    Published in Virology (New York, N.Y.) (01-11-2023)
    “…The ΦX174 reduction effect describes a plasmid-based inhibitory phenomenon that mimics the superinfection inhibition found in wild phage populations. In this…”
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  4. 4

    Experimental evolution of viruses: Microviridae as a model system by Wichman, Holly A., Brown, Celeste J.

    “…φX174 was developed as a model system for experimental studies of evolution because of its small genome size and ease of cultivation. It has been used…”
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  5. 5

    Tracing the history of LINE and SINE extinction in sigmodontine rodents by Yang, Lei, Scott, LuAnn, Wichman, Holly A

    Published in Mobile DNA (21-05-2019)
    “…L1 retrotransposons have co-evolved with their mammalian hosts for the entire history of mammals and currently compose ~ 20% of a mammalian genome. B1…”
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  6. 6

    Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development by Sun, Cheng, Wyngaard, Grace, Walton, D Brian, Wichman, Holly A, Mueller, Rachel Lockridge

    Published in BMC genomics (11-03-2014)
    “…Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two…”
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  7. 7

    Modeling the Directed Evolution of Broad Host Range Phages by Bull, James J, Wichman, Holly A, Krone, Stephen M

    Published in Antibiotics (Basel) (27-11-2022)
    “…The host ranges of individual phages tend to be narrow, yet many applications of phages would benefit from expanded host ranges. Empirical methods have been…”
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  8. 8

    Positive selection and multiple losses of the LINE-1-derived L1TD1 gene in mammals suggest a dual role in genome defense and pluripotency by McLaughlin, Jr, Richard N, Young, Janet M, Yang, Lei, Neme, Rafik, Wichman, Holly A, Malik, Harmit S

    Published in PLoS genetics (01-09-2014)
    “…Mammalian genomes comprise many active and fossilized retroelements. The obligate requirement for retroelement integration affords host genomes an opportunity…”
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  9. 9

    Ecological Approach to Understanding Superinfection Inhibition in Bacteriophage by Biggs, Karin R H, Bailes, Clayton L, Scott, LuAnn, Wichman, Holly A, Schwartz, Elissa J

    Published in Viruses (17-07-2021)
    “…In microbial communities, viruses compete with each other for host cells to infect. As a consequence of competition for hosts, viruses evolve inhibitory…”
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  10. 10

    Controlling Recombination to Evolve Bacteriophages by Bull, James J, Wichman, Holly A, Krone, Stephen M, Molineux, Ian J

    Published in Cells (Basel, Switzerland) (01-04-2024)
    “…Recombination among different phages sometimes facilitates their ability to grow on new hosts. Protocols to direct the evolution of phage host range, as might…”
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  11. 11

    Changing folding and binding stability in a viral coat protein: a comparison between substitutions accessible through mutation and those fixed by natural selection by Miller, Craig R, Lee, Kuo Hao, Wichman, Holly A, Ytreberg, F Marty

    Published in PloS one (18-11-2014)
    “…Previous studies have shown that most random amino acid substitutions destabilize protein folding (i.e. increase the folding free energy). No analogous studies…”
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  12. 12

    New Perspectives on Ebola Virus Evolution by Brown, Celeste J, Quates, Caleb J, Mirabzadeh, Christopher A, Miller, Craig R, Wichman, Holly A, Miura, Tanya A, Ytreberg, F Marty

    Published in PloS one (01-08-2016)
    “…Since the recent devastating outbreak of Ebola virus disease in western Africa, there has been significant effort to understand the evolution of the deadly…”
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  13. 13

    Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking by Miller, Craig R., Van Leuven, James T., Wichman, Holly A., Joyce, Paul

    Published in Theoretical population biology (01-07-2018)
    “…Fitness landscapes map genotypes to organismal fitness. Their topographies depend on how mutational effects interact – epistasis – andare important for…”
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  14. 14

    The Genetics of Adaptation for Eight Microvirid Bacteriophages by Rokyta, Darin R., Abdo, Zaid, Wichman, Holly A.

    Published in Journal of molecular evolution (01-09-2009)
    “…Theories of adaptive molecular evolution have recently experienced significant expansion, and their predictions and assumptions have begun to be subjected to…”
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  15. 15

    Selection affects genes involved in replication during long-term evolution in experimental populations of the bacteriophage φX174 by Brown, Celeste J, Millstein, Jack, Williams, Christopher J, Wichman, Holly A

    Published in PloS one (22-03-2013)
    “…Observing organisms that evolve in response to strong selection over very short time scales allows the determination of the molecular mechanisms underlying…”
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  16. 16

    Reviving the dead: history and reactivation of an extinct l1 by Yang, Lei, Brunsfeld, John, Scott, LuAnn, Wichman, Holly

    Published in PLoS genetics (01-06-2014)
    “…Although L1 sequences are present in the genomes of all placental mammals and marsupials examined to date, their activity was lost in the megabat family,…”
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  17. 17

    First-step mutations for adaptation at elevated temperature increase capsid stability in a virus by Lee, Kuo Hao, Miller, Craig R, Nagel, Anna C, Wichman, Holly A, Joyce, Paul, Ytreberg, F Marty

    Published in PloS one (29-09-2011)
    “…The relationship between mutation, protein stability and protein function plays a central role in molecular evolution. Mutations tend to be destabilizing,…”
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  18. 18

    ΦX174 Attenuation by Whole-Genome Codon Deoptimization by Van Leuven, James T, Ederer, Martina M, Burleigh, Katelyn, Scott, LuAnn, Hughes, Randall A, Codrea, Vlad, Ellington, Andrew D, Wichman, Holly A, Miller, Craig R

    Published in Genome biology and evolution (03-02-2021)
    “…Abstract Natural selection acting on synonymous mutations in protein-coding genes influences genome composition and evolution. In viruses, introducing…”
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  19. 19

    The impact of spatial structure on viral genomic diversity generated during adaptation to thermal stress by Ally, Dilara, Wiss, Valorie R, Deckert, Gail E, Green, Danielle, Roychoudhury, Pavitra, Wichman, Holly A, Brown, Celeste J, Krone, Stephen M

    Published in PloS one (12-02-2014)
    “…Most clinical and natural microbial communities live and evolve in spatially structured environments. When changes in environmental conditions trigger…”
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  20. 20

    Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage φX174 by Pepin, Kim M, Wichman, Holly A

    Published in BMC evolutionary biology (17-03-2008)
    “…BACKGROUND: In large asexual populations where beneficial mutations may co-occur and recombination is absent, the fate of beneficial mutations can be…”
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