H. Wichman

发表

Evolutionary reversals during viral adaptation to alternating hosts.

J. Bull, W. Crill, H. Wichman, 2000, Genetics.

Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models

Craig R. Miller, Paul Joyce, Craig R Miller, 2011, Genetics.

Testing the Extreme Value Domain of Attraction for Distributions of Beneficial Fitness Effects

Paul Joyce, Holly A Wichman, P. Joyce, 2007, Genetics.

X Chromosome Inactivation and Xist Evolution in a Rodent Lacking LINE-1 Activity

B. Carstens, H. Wichman, M. Cantrell, 2009, PloS one.

ΦX174 Attenuation by Whole-Genome Codon Deoptimization

Craig R. Miller, James T. Van Leuven, R. A. Hughes, 2020, bioRxiv.

Positive Selection and Multiple Losses of the LINE-1-Derived L1TD1 Gene in Mammals Suggest a Dual Role in Genome Defense and Pluripotency

Janet M. Young, R. McLaughlin, Rafik Neme, 2014, PLoS genetics.

Initiating a watch list for Ebola virus antibody escape mutations

Craig R. Miller, Erin L. Johnson, F. M. Ytreberg, 2016, PeerJ.

Love the one you’re with: replicate viral adaptations converge on the same phenotypic change

Craig R. Miller, P. Joyce, Anna C Nagel, 2016, PeerJ.

EPISTATIC EFFECTS BETWEEN MUTATIONS AT HOST RECOGNITION SITES IN X 174 BACTERIOPHAGE

K. Pepin, H. Wichman, 2007 .

Rapidly evolving repetitive DNAs in a conservative genome: A test of factors that affect chromosomal evolution

R. Bradley, H. Wichman, 1994, Chromosome Research.

Mys, a family of mammalian transposable elements isolated by phylogenetic screening

S. Potter, H. Wichman, D. S. Pine, 1985, Nature.

First-Step Mutations for Adaptation at Elevated Temperature Increase Capsid Stability in a Virus

Craig R. Miller, P. Joyce, K. Lee, 2011, PloS one.

Two persistent LINE-1 lineages in Peromyscus have unequal rates of evolution.

N. C. Casavant, A. Sherman, H. Wichman, 1996, Genetics.

Molecular evolution of two lineages of L1 (LINE-1) retrotransposons in the california mouse, Peromyscus californicus.

N. C. Casavant, A. Sherman, H. Wichman, 1998, Genetics.

RETROTRANSPOSON MYS IS CONCENTRATED ON THE SEX CHROMOSOMES: IMPLICATIONS FOR COPY NUMBER CONTAINMENT

R. Baker, H. Wichman, 1990, Evolution; international journal of organic evolution.

IMPLICATIONS FOR COPY NUMBER CONTAINMENT

R. Baker, H. Wichman, 1990 .

SINE extinction preceded LINE extinction in sigmodontine rodents: implications for retrotranspositional dynamics and mechanisms

H. Wichman, T. Rinehart, R. Grahn, 2005, Cytogenetic and Genome Research.

Flying Around in the Genome: Characterization of LINE-1 in Chiroptera.

R. Baker, H. Wichman, Lei Yang, 2019, Special publications.

The Impact of Spatial Structure on Viral Genomic Diversity Generated during Adaptation to Thermal Stress

Stephen M. Krone, S. Krone, H. Wichman, 2014, PloS one.

In search of retrotransposons: exploring the potential of the PCR.

R. A. Van Den Bussche, H. Wichman, 1992, BioTechniques.

Modeling the Directed Evolution of Broad Host Range Phages

J. Bull, S. Krone, H. Wichman, 2022, bioRxiv.

Extinction of LINE-1 activity coincident with a major mammalian radiation in rodents

H. Wichman, M. Cantrell, T. Rinehart, 2005, Cytogenetic and Genome Research.

VARIABLE EPISTATIC EFFECTS BETWEEN MUTATIONS AT HOST RECOGNITION SITES IN φX174 BACTERIOPHAGE

K. Pepin, H. Wichman, 2007, Evolution; international journal of organic evolution.

Variable Pleiotropic Effects From Mutations at the Same Locus Hamper Prediction of Fitness From a Fitness Component

K. Pepin, Melanie A. Samuel, H. Wichman, 2006, Genetics.

Reproduction and thermoregulation in Peromyscus: Effects of chronic short days

G. Lynch, H. Wichman, 1981, Physiology & Behavior.

An ancient retrovirus-like element contains hot spots for SINE insertion.

K. Olsson, H. Wichman, A. Ingermann, 2001, Genetics.

X accumulation of LINE-1 retrotransposons in Tokudaia osimensis, a spiny rat with the karyotype XO

Y. Matsuda, A. Kuroiwa, H. Wichman, 2006, Cytogenetic and Genome Research.

Transposable elements and the evolution of genome organization in mammals

R. Baker, R. Bussche, H. Wichman, 2004, Genetica.

An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus

Paul Joyce, Holly A Wichman, P. Joyce, 2005, Nature Genetics.

Reviving the Dead: History and Reactivation of an Extinct L1

H. Wichman, Lei Yang, L. Scott, 2014, PLoS genetics.

Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development

R. Mueller, Cheng Sun, H. Wichman, 2014, BMC Genomics.

Adaptive Molecular Evolution for 13,000 Phage Generations

J. Bull, H. Wichman, J. Millstein, 2005, Genetics.

MysTR: an Endogenous Retrovirus Family in Mammals That Is Undergoing Recent Amplifications to Unprecedented Copy Numbers

R. Baker, H. Wichman, M. Cantrell, 2005, Journal of Virology.

Retrofitting the Genome: L1 Extinction Follows Endogenous Retroviral Expansion in a Group of Muroid Rodents

H. Wichman, M. Cantrell, L. Scott, 2011, Journal of Virology.

Loss of LINE-1 Activity in the Megabats

H. Wichman, M. Cantrell, L. Scott, 2008, Genetics.

Isolation of markers from recently transposed LINE-1 retrotransposons.

H. Wichman, M. Cantrell, L. Scott, 2000, BioTechniques.

The end of the LINE?: lack of recent L1 activity in a group of South American rodents.

N. C. Casavant, R. Baker, H. Wichman, 2000, Genetics.

Analysis of Orthologous Retrovirus-Like Elements in the White-Footed Mouse, Peromyscus leucopus

H. Wichman, R. Sawby, 1997, Journal of Molecular Evolution.

Stickbreaking: A Novel Fitness Landscape Model That Harbors Epistasis and Is Consistent with Commonly Observed Patterns of Adaptive Evolution

Craig R. Miller, P. Joyce, Anna C Nagel, 2012, Genetics.

Retrotransposon Mys was active during evolution of the Peromyscus leucopus-maniculatus complex

R. Baker, R. Bussche, H. Wichman, 2004, Journal of Molecular Evolution.

Experimental evolution recapitulates natural evolution.

J. Bull, H. Wichman, L. Scott, 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

Different trajectories of parallel evolution during viral adaptation.

J. Bull, H. Wichman, C. M. Boulianne, 1999, Science.

Tracing the history of LINE and SINE extinction in sigmodontine rodents

H. Wichman, Lei Yang, L. Scott, 2018, Mobile DNA.

Distribution of LINEs and other repetitive elements in the karyotype of the bat Carollia: implications for X-chromosome inactivation

R. Baker, H. Wichman, D. Parish, 2002, Cytogenetic and Genome Research.

Molecular phylogenetics of Stenodermatini bat genera: congruence of data from nuclear and mitochondrial DNA.

R. Baker, R. A. Van Den Bussche, H. Wichman, 1993, Molecular biology and evolution.

Genome organization of repetitive elements in the rodent, Peromyscus leucopus

J. Longmire, R. Baker, H. Wichman, 2004, Mammalian Genome.

Intragenomic movement and concerted evolution of satellite DNA in Peromyscus: evidence from in situ hybridization.

H. Wichman, G. Hong, M. Hamilton, 1992, Cytogenetics and cell genetics.

Evolutionary Feedback Mediated through Population Density, Illustrated with Viruses in Chemostats

H. Wichman, J. Bull, J. Millstein, 2005, The American Naturalist.

Integration of molecular cytogenetics, dated molecular phylogeny, and model-based predictions to understand the extreme chromosome reorganization in the Neotropical genus Tonatia (Chiroptera: Phyllostomidae)

Fengtang Yang, R. Baker, F. Hoffmann, 2015, BMC Evolutionary Biology.

Genomic distribution of heterochromatic sequences in equids: implications to rapid chromosomal evolution.

O. Ryder, R. Baker, H. Wichman, 1991, The Journal of heredity.

Molecular approaches to mammalian retrotransposon isolation.

S. Martin, H. Wichman, 1993, Methods in enzymology.

Changing Folding and Binding Stability in a Viral Coat Protein: A Comparison between Substitutions Accessible through Mutation and Those Fixed by Natural Selection

Craig R. Miller, K. Lee, F. M. Ytreberg, 2014, PloS one.

Exceptional convergent evolution in a virus.

J. Bull, J. Huelsenbeck, D. Hillis, 1997, Genetics.

Selection Affects Genes Involved in Replication during Long-Term Evolution in Experimental Populations of the Bacteriophage φX174

Christopher J. Williams, H. Wichman, J. Millstein, 2013, PloS one.

Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage φX174

K. Pepin, H. Wichman, 2008, BMC Evolutionary Biology.

New Perspectives on Ebola Virus Evolution

Craig R. Miller, Christopher A. Mirabzadeh, F. M. Ytreberg, 2016, PloS one.

Big-benefit mutations in a bacteriophage inhibited with heat.

J. Bull, H. Wichman, J. Bull, 2000, Molecular biology and evolution.

Selecting among three basic fitness landscape models: additive, multiplicative and stickbreaking

Craig R. Miller, James T. Van Leuven, Paul Joyce, 2017, bioRxiv.

Epistasis between Beneficial Mutations and the Phenotype-to-Fitness Map for a ssDNA Virus

Craig R. Miller, Holly A. Wichman, Paul Joyce, 2011, PLoS genetics.

Selecting among three basic fitness landscape models: additive, multiplicative and stickbreaking

Craig R. Miller, James T. Van Leuven, Holly A. Wichman, 2017, bioRxiv.

Beneficial Fitness Effects Are Not Exponential for Two Viruses

Martin T. Ferris, C. Burch, P. Joyce, 2008, Journal of Molecular Evolution.

Experimental evolution of viruses: Microviridae as a model system

H. Wichman, C. Brown, 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

Space, Time, and Host Evolution Facilitate Coexistence of Competing Bacteriophages: Theory and Experiment

S. Krone, H. Wichman, J. Millstein, 2009, The American Naturalist.

The Genetics of Adaptation for Eight Microvirid Bacteriophages

Z. Abdo, D. Rokyta, H. Wichman, 2009, Journal of Molecular Evolution.

Genic incompatibilities in two hybrid bacteriophages.

D. Rokyta, H. Wichman, 2009, Molecular biology and evolution.

Horizontal Gene Transfer and the Evolution of Microvirid Coliphage Genomes

C. Burch, S. B. Caudle, D. Rokyta, 2006, Journal of bacteriology.

Bibliography of Karl Fredga

G. L. Bennett, J. B. Searle, K. Klinga-Levan, 2002, Cytogenetic and Genome Research.

Ecological Approach to Understanding Superinfection Inhibition in Bacteriophage

H. Wichman, E. J. Schwartz, L. Scott, 2021, Viruses.

Computer simulation of transposable element evolution: Random template and strict master models

J. Foster, H. Wichman, James E. Clough, 2004, Journal of Molecular Evolution.

Linear estimators for the evolution of transposable elements

L. Fox, P. Joyce, N. C. Casavant, 1999 .

Unusual pattern of bacterial ice nucleation gene evolution.

R. A. Van Den Bussche, H. Wichman, A R Edwards, 1994, Molecular biology and evolution.

Geographic variation in Peromyscus leucopus: short-day induced reproductive regression and spontaneous recrudescence.

G. Lynch, H. Wichman, H. Heath, 1982, Biology of reproduction.

Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades

Danna R. Gifford, M. DePristo, R. Lenski, 2022 .

Saturation mutagenesis genome engineering of infective ΦX174 bacteriophage via unamplified oligo pools and golden gate assembly

Craig R. Miller, James T. Van Leuven, Timothy A. Whitehead, 2019, bioRxiv.

Fengtang Yang, R. Baker, F. Hoffmann, 2015, BMC Evolutionary Biology.

Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models

Craig R. Miller, P. Joyce, H. Wichman, 2011, Genetics.