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Items: 1 to 50 of 66

1.

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

Miller CR, Van Leuven JT, Wichman HA, Joyce P.

Theor Popul Biol. 2018 Jul;122:97-109. doi: 10.1016/j.tpb.2017.10.006. Epub 2017 Dec 2.

PMID:
29198859
2.

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

Miller CR, Nagel AC, Scott L, Settles M, Joyce P, Wichman HA.

PeerJ. 2016 Jul 19;4:e2227. doi: 10.7717/peerj.2227. eCollection 2016.

3.

New Perspectives on Ebola Virus Evolution.

Brown CJ, Quates CJ, Mirabzadeh CA, Miller CR, Wichman HA, Miura TA, Ytreberg FM.

PLoS One. 2016 Aug 1;11(8):e0160410. doi: 10.1371/journal.pone.0160410. eCollection 2016.

4.

Obituary: Paul Joyce (1958-2016).

Miller CR, Wichman HA.

Biol Lett. 2016 May;12(5). pii: 20160396. doi: 10.1098/rsbl.2016.0396. No abstract available.

5.

Initiating a watch list for Ebola virus antibody escape mutations.

Miller CR, Johnson EL, Burke AZ, Martin KP, Miura TA, Wichman HA, Brown CJ, Ytreberg FM.

PeerJ. 2016 Feb 16;4:e1674. doi: 10.7717/peerj.1674. eCollection 2016.

6.
7.

Changing folding and binding stability in a viral coat protein: a comparison between substitutions accessible through mutation and those fixed by natural selection.

Miller CR, Lee KH, Wichman HA, Ytreberg FM.

PLoS One. 2014 Nov 18;9(11):e112988. doi: 10.1371/journal.pone.0112988. eCollection 2014.

8.

Positive selection and multiple losses of the LINE-1-derived L1TD1 gene in mammals suggest a dual role in genome defense and pluripotency.

McLaughlin RN Jr, Young JM, Yang L, Neme R, Wichman HA, Malik HS.

PLoS Genet. 2014 Sep 11;10(9):e1004531. doi: 10.1371/journal.pgen.1004531. eCollection 2014 Sep.

9.

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

Sun C, Wyngaard G, Walton DB, Wichman HA, Mueller RL.

BMC Genomics. 2014 Mar 11;15:186. doi: 10.1186/1471-2164-15-186.

10.

The impact of spatial structure on viral genomic diversity generated during adaptation to thermal stress.

Ally D, Wiss VR, Deckert GE, Green D, Roychoudhury P, Wichman HA, Brown CJ, Krone SM.

PLoS One. 2014 Feb 12;9(2):e88702. doi: 10.1371/journal.pone.0088702. eCollection 2014.

11.

Selection affects genes involved in replication during long-term evolution in experimental populations of the bacteriophage φX174.

Brown CJ, Millstein J, Williams CJ, Wichman HA.

PLoS One. 2013;8(3):e60401. doi: 10.1371/journal.pone.0060401. Epub 2013 Mar 22.

12.

Stickbreaking: a novel fitness landscape model that harbors epistasis and is consistent with commonly observed patterns of adaptive evolution.

Nagel AC, Joyce P, Wichman HA, Miller CR.

Genetics. 2012 Feb;190(2):655-67. doi: 10.1534/genetics.111.132134. Epub 2011 Nov 17.

13.

First-step mutations for adaptation at elevated temperature increase capsid stability in a virus.

Lee KH, Miller CR, Nagel AC, Wichman HA, Joyce P, Ytreberg FM.

PLoS One. 2011;6(9):e25640. doi: 10.1371/journal.pone.0025640. Epub 2011 Sep 29.

14.

Retrofitting the genome: L1 extinction follows endogenous retroviral expansion in a group of muroid rodents.

Erickson IK, Cantrell MA, Scott L, Wichman HA.

J Virol. 2011 Dec;85(23):12315-23. doi: 10.1128/JVI.05180-11. Epub 2011 Sep 28.

15.

Epistasis between beneficial mutations and the phenotype-to-fitness Map for a ssDNA virus.

Rokyta DR, Joyce P, Caudle SB, Miller C, Beisel CJ, Wichman HA.

PLoS Genet. 2011 Jun;7(6):e1002075. doi: 10.1371/journal.pgen.1002075. Epub 2011 Jun 2.

16.

Mutational effects and population dynamics during viral adaptation challenge current models.

Miller CR, Joyce P, Wichman HA.

Genetics. 2011 Jan;187(1):185-202. doi: 10.1534/genetics.110.121400. Epub 2010 Nov 1.

17.

Experimental evolution of viruses: Microviridae as a model system.

Wichman HA, Brown CJ.

Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2495-501. doi: 10.1098/rstb.2010.0053.

18.

Genic incompatibilities in two hybrid bacteriophages.

Rokyta DR, Wichman HA.

Mol Biol Evol. 2009 Dec;26(12):2831-9. doi: 10.1093/molbev/msp199. Epub 2009 Sep 2.

19.

Viral adaptation to an antiviral protein enhances the fitness level to above that of the uninhibited wild type.

Cherwa JE Jr, Sanchez-Soria P; Members of the University of Arizona Virology Laboratory Course 2007, Wichman HA, Fane BA.

J Virol. 2009 Nov;83(22):11746-50. doi: 10.1128/JVI.01297-09. Epub 2009 Sep 2.

20.

The genetics of adaptation for eight microvirid bacteriophages.

Rokyta DR, Abdo Z, Wichman HA.

J Mol Evol. 2009 Sep;69(3):229-39. doi: 10.1007/s00239-009-9267-9. Epub 2009 Aug 20.

21.

X chromosome inactivation and Xist evolution in a rodent lacking LINE-1 activity.

Cantrell MA, Carstens BC, Wichman HA.

PLoS One. 2009 Jul 15;4(7):e6252. doi: 10.1371/journal.pone.0006252.

22.

Space, time, and host evolution facilitate coexistence of competing bacteriophages: theory and experiment.

Coberly LC, Wei W, Sampson KY, Millstein J, Wichman HA, Krone SM.

Am Nat. 2009 Apr;173(4):E121-38. doi: 10.1086/597226.

23.

Beneficial fitness effects are not exponential for two viruses.

Rokyta DR, Beisel CJ, Joyce P, Ferris MT, Burch CL, Wichman HA.

J Mol Evol. 2008 Oct;67(4):368-76. doi: 10.1007/s00239-008-9153-x. Epub 2008 Sep 9.

24.
25.

Loss of LINE-1 activity in the megabats.

Cantrell MA, Scott L, Brown CJ, Martinez AR, Wichman HA.

Genetics. 2008 Jan;178(1):393-404. doi: 10.1534/genetics.107.080275.

26.
27.

Testing the extreme value domain of attraction for distributions of beneficial fitness effects.

Beisel CJ, Rokyta DR, Wichman HA, Joyce P.

Genetics. 2007 Aug;176(4):2441-9. Epub 2007 Jun 11.

28.

Evolutionary feedback mediated through population density, illustrated with viruses in chemostats.

Bull JJ, Millstein J, Orcutt J, Wichman HA.

Am Nat. 2006 Feb;167(2):E39-51. Epub 2005 Dec 12.

PMID:
16670974
29.

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

Scott LA, Kuroiwa A, Matsuda Y, Wichman HA.

Cytogenet Genome Res. 2006;112(3-4):261-9.

PMID:
16484782
30.

Horizontal gene transfer and the evolution of microvirid coliphage genomes.

Rokyta DR, Burch CL, Caudle SB, Wichman HA.

J Bacteriol. 2006 Feb;188(3):1134-42.

31.

Variable pleiotropic effects from mutations at the same locus hamper prediction of fitness from a fitness component.

Pepin KM, Samuel MA, Wichman HA.

Genetics. 2006 Apr;172(4):2047-56. Epub 2005 Dec 15.

32.

MysTR: an endogenous retrovirus family in mammals that is undergoing recent amplifications to unprecedented copy numbers.

Cantrell MA, Ederer MM, Erickson IK, Swier VJ, Baker RJ, Wichman HA.

J Virol. 2005 Dec;79(23):14698-707.

33.
34.

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

Grahn RA, Rinehart TA, Cantrell MA, Wichman HA.

Cytogenet Genome Res. 2005;110(1-4):407-15.

PMID:
16093693
35.

Behavioral and health implications of civilian spaceflight.

Wichman HA.

Aviat Space Environ Med. 2005 Jun;76(6 Suppl):B164-71.

PMID:
15943209
36.

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

Rokyta DR, Joyce P, Caudle SB, Wichman HA.

Nat Genet. 2005 Apr;37(4):441-4. Epub 2005 Mar 20.

PMID:
15778707
37.

Adaptive molecular evolution for 13,000 phage generations: a possible arms race.

Wichman HA, Millstein J, Bull JJ.

Genetics. 2005 May;170(1):19-31. Epub 2005 Jan 31.

38.

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

Parish DA, Vise P, Wichman HA, Bull JJ, Baker RJ.

Cytogenet Genome Res. 2002;96(1-4):191-7.

PMID:
12438798
39.

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

Cantrell MA, Filanoski BJ, Ingermann AR, Olsson K, DiLuglio N, Lister Z, Wichman HA.

Genetics. 2001 Jun;158(2):769-77.

40.

Experimental evolution recapitulates natural evolution.

Wichman HA, Scott LA, Yarber CD, Bull JJ.

Philos Trans R Soc Lond B Biol Sci. 2000 Nov 29;355(1403):1677-84.

41.

Isolation of markers from recently transposed LINE-1 retrotransposons.

Cantrell MA, Grahn RA, Scott L, Wichman HA.

Biotechniques. 2000 Dec;29(6):1310-6.

42.

Big-benefit mutations in a bacteriophage inhibited with heat.

Bull JJ, Badgett MR, Wichman HA.

Mol Biol Evol. 2000 Jun;17(6):942-50.

PMID:
10833201
43.

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

Casavant NC, Scott L, Cantrell MA, Wiggins LE, Baker RJ, Wichman HA.

Genetics. 2000 Apr;154(4):1809-17.

44.

Evolutionary reversals during viral adaptation to alternating hosts.

Crill WD, Wichman HA, Bull JJ.

Genetics. 2000 Jan;154(1):27-37.

45.

Different trajectories of parallel evolution during viral adaptation.

Wichman HA, Badgett MR, Scott LA, Boulianne CM, Bull JJ.

Science. 1999 Jul 16;285(5426):422-4.

46.
47.

Exceptional convergent evolution in a virus.

Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, Gulati A, Ho C, Molineux IJ.

Genetics. 1997 Dec;147(4):1497-507.

48.
49.

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

Casavant NC, Sherman AN, Wichman HA.

Genetics. 1996 Apr;142(4):1289-98.

50.

Remote ergonomic research in space: spacelab findings and a proposal.

Wichman HA, Donaldson SI.

Aviat Space Environ Med. 1996 Feb;67(2):171-5.

PMID:
8834945

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