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Items: 35

1.

Investigating Instructor Talk in Novel Contexts: Widespread Use, Unexpected Categories, and an Emergent Sampling Strategy.

Harrison CD, Nguyen TA, Seidel SB, Escobedo AM, Hartman C, Lam K, Liang KS, Martens M, Acker GN, Akana SF, Balukjian B, Benton HP, Blair JR, Boaz SM, Boyer KE, Bram JB, Burrus LW, Byrd DT, Caporale N, Carpenter EJ, Chan YM, Chen L, Chovnick A, Chu DS, Clarkson BK, Cooper SE, Creech CJ, de la Torre JR, Denetclaw WF, Duncan K, Edwards AS, Erickson K, Fuse M, Gorga JJ, Govindan B, Green LJ, Hankamp PZ, Harris HE, He ZH, Ingalls SB, Ingmire PD, Jacobs JR, Kamakea M, Kimpo RR, Knight JD, Krause SK, Krueger LE, Light TL, Lund L, Márquez-Magaña LM, McCarthy BK, McPheron L, Miller-Sims VC, Moffatt CA, Muick PC, Nagami PH, Nusse G, Okimura KM, Pasion SG, Patterson R, Pennings PS, Riggs B, Romeo JM, Roy SW, Russo-Tait T, Schultheis LM, Sengupta L, Spicer GS, Swei A, Wade JM, Willsie JK, Kelley LA, Owens MT, Trujillo G, Domingo C, Schinske JN, Tanner KD.

CBE Life Sci Educ. 2019 Sep;18(3):ar47. doi: 10.1187/cbe.18-10-0215.

2.

Evolutionary Dynamics in Structured Populations Under Strong Population Genetic Forces.

Feder AF, Pennings PS, Hermisson J, Petrov DA.

G3 (Bethesda). 2019 Oct 7;9(10):3395-3407. doi: 10.1534/g3.119.400605.

3.

Inferring population genetics parameters of evolving viruses using time-series data.

Zinger T, Gelbart M, Miller D, Pennings PS, Stern A.

Virus Evol. 2019 Jun 8;5(1):vez011. doi: 10.1093/ve/vez011. eCollection 2019 Jan.

4.

Polygenic adaptation: From sweeps to subtle frequency shifts.

Höllinger I, Pennings PS, Hermisson J.

PLoS Genet. 2019 Mar 20;15(3):e1008035. doi: 10.1371/journal.pgen.1008035. eCollection 2019 Mar.

5.

Correction: Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV.

Theys K, Feder AF, Gelbart M, Hartl M, Stern A, Pennings PS.

PLoS Genet. 2018 Dec 10;14(12):e1007855. doi: 10.1371/journal.pgen.1007855. eCollection 2018 Dec.

6.

Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV.

Theys K, Feder AF, Gelbart M, Hartl M, Stern A, Pennings PS.

PLoS Genet. 2018 Jun 28;14(6):e1007420. doi: 10.1371/journal.pgen.1007420. eCollection 2018 Jun. Erratum in: PLoS Genet. 2018 Dec 10;14(12):e1007855.

7.

Collectively Improving Our Teaching: Attempting Biology Department-wide Professional Development in Scientific Teaching.

Owens MT, Trujillo G, Seidel SB, Harrison CD, Farrar KM, Benton HP, Blair JR, Boyer KE, Breckler JL, Burrus LW, Byrd DT, Caporale N, Carpenter EJ, Chan YM, Chen JC, Chen L, Chen LH, Chu DS, Cochlan WP, Crook RJ, Crow KD, de la Torre JR, Denetclaw WF, Dowdy LM, Franklin D, Fuse M, Goldman MA, Govindan B, Green M, Harris HE, He ZH, Ingalls SB, Ingmire P, Johnson ARB, Knight JD, LeBuhn G, Light TL, Low C, Lund L, Márquez-Magaña LM, Miller-Sims VC, Moffatt CA, Murdock H, Nusse GL, Parker VT, Pasion SG, Patterson R, Pennings PS, Ramirez JC, Ramirez RM, Riggs B, Rohlfs RV, Romeo JM, Rothman BS, Roy SW, Russo-Tait T, Sehgal RNM, Simonin KA, Spicer GS, Stillman JH, Swei A, Timpe LC, Vredenburg VT, Weinstein SL, Zink AG, Kelley LA, Domingo CR, Tanner KD.

CBE Life Sci Educ. 2018 Spring;17(1). pii: ar2. doi: 10.1187/cbe.17-06-0106. Erratum in: CBE Life Sci Educ. 2018 Spring;17 (1):.

8.

A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host.

Feder AF, Kline C, Polacino P, Cottrell M, Kashuba ADM, Keele BF, Hu SL, Petrov DA, Pennings PS, Ambrose Z.

PLoS Pathog. 2017 May 25;13(5):e1006358. doi: 10.1371/journal.ppat.1006358. eCollection 2017 May.

9.

Classroom sound can be used to classify teaching practices in college science courses.

Owens MT, Seidel SB, Wong M, Bejines TE, Lietz S, Perez JR, Sit S, Subedar ZS, Acker GN, Akana SF, Balukjian B, Benton HP, Blair JR, Boaz SM, Boyer KE, Bram JB, Burrus LW, Byrd DT, Caporale N, Carpenter EJ, Chan YM, Chen L, Chovnick A, Chu DS, Clarkson BK, Cooper SE, Creech C, Crow KD, de la Torre JR, Denetclaw WF, Duncan KE, Edwards AS, Erickson KL, Fuse M, Gorga JJ, Govindan B, Green LJ, Hankamp PZ, Harris HE, He ZH, Ingalls S, Ingmire PD, Jacobs JR, Kamakea M, Kimpo RR, Knight JD, Krause SK, Krueger LE, Light TL, Lund L, Márquez-Magaña LM, McCarthy BK, McPheron LJ, Miller-Sims VC, Moffatt CA, Muick PC, Nagami PH, Nusse GL, Okimura KM, Pasion SG, Patterson R, Pennings PS, Riggs B, Romeo J, Roy SW, Russo-Tait T, Schultheis LM, Sengupta L, Small R, Spicer GS, Stillman JH, Swei A, Wade JM, Waters SB, Weinstein SL, Willsie JK, Wright DW, Harrison CD, Kelley LA, Trujillo G, Domingo CR, Schinske JN, Tanner KD.

Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):3085-3090. doi: 10.1073/pnas.1618693114. Epub 2017 Mar 6.

10.

Soft Selective Sweeps in Evolutionary Rescue.

Wilson BA, Pennings PS, Petrov DA.

Genetics. 2017 Apr;205(4):1573-1586. doi: 10.1534/genetics.116.191478. Epub 2017 Feb 17.

11.

Correction: More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.

Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS.

Elife. 2017 Jan 19;6. pii: e24879. doi: 10.7554/eLife.24879. No abstract available.

12.

More effective drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1.

Feder AF, Rhee SY, Holmes SP, Shafer RW, Petrov DA, Pennings PS.

Elife. 2016 Feb 15;5. pii: e10670. doi: 10.7554/eLife.10670. Erratum in: Elife. 2017 Jan 19;6:.

13.

The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens.

Wilson BA, Garud NR, Feder AF, Assaf ZJ, Pennings PS.

Mol Ecol. 2016 Jan;25(1):42-66. doi: 10.1111/mec.13474. Epub 2015 Dec 17. Review.

14.

The singing vortex.

Arndt R, Pennings P, Bosschers J, van Terwisga T.

Interface Focus. 2015 Oct 6;5(5):20150025. doi: 10.1098/rsfs.2015.0025.

15.

Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multidrug resistance.

Moreno-Gamez S, Hill AL, Rosenbloom DI, Petrov DA, Nowak MA, Pennings PS.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):E2874-83. doi: 10.1073/pnas.1424184112. Epub 2015 May 18.

16.

Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health.

Perron GG, Inglis RF, Pennings PS, Cobey S.

Evol Appl. 2015 Mar;8(3):211-22. doi: 10.1111/eva.12254. Epub 2015 Mar 23.

17.

Oh sister, where art thou? Spatial population structure and the evolution of an altruistic defence trait.

Pamminger T, Foitzik S, Metzler D, Pennings PS.

J Evol Biol. 2014 Nov;27(11):2443-56. doi: 10.1111/jeb.12496. Epub 2014 Sep 28.

18.

HIV Drug Resistance: Problems and Perspectives.

Pennings PS.

Infect Dis Rep. 2013 Jun 6;5(Suppl 1):e5. doi: 10.4081/idr.2013.s1.e5. eCollection 2013 Jun 6. Review.

19.

Loss and recovery of genetic diversity in adapting populations of HIV.

Pennings PS, Kryazhimskiy S, Wakeley J.

PLoS Genet. 2014 Jan;10(1):e1004000. doi: 10.1371/journal.pgen.1004000. Epub 2014 Jan 23.

20.

HIV-1 transmission networks in a small world.

Pennings PS, Holmes SP, Shafer RW.

J Infect Dis. 2014 Jan 15;209(2):180-2. doi: 10.1093/infdis/jit525. Epub 2013 Oct 22. No abstract available.

21.

Evidence of adaptation from ancestral variation in young populations of beach mice.

Domingues VS, Poh YP, Peterson BK, Pennings PS, Jensen JD, Hoekstra HE.

Evolution. 2012 Oct;66(10):3209-23. doi: 10.1111/j.1558-5646.2012.01669.x. Epub 2012 May 4.

PMID:
23025610
22.

Raiders from the sky: slavemaker founding queens select for aggressive host colonies.

Pamminger T, Modlmeier AP, Suette S, Pennings PS, Foitzik S.

Biol Lett. 2012 Oct 23;8(5):748-50. doi: 10.1098/rsbl.2012.0499. Epub 2012 Jul 18.

23.

Standing genetic variation and the evolution of drug resistance in HIV.

Pennings PS.

PLoS Comput Biol. 2012;8(6):e1002527. doi: 10.1371/journal.pcbi.1002527. Epub 2012 Jun 7.

24.

Increased host aggression as an induced defense against slave-making ants.

Pamminger T, Scharf I, Pennings PS, Foitzik S.

Behav Ecol. 2011 Mar;22(2):255-260. Epub 2011 Jan 6.

25.

Similar evolutionary potentials in an obligate ant parasite and its two host species.

Pennings PS, Achenbach A, Foitzik S.

J Evol Biol. 2011 Apr;24(4):871-86. doi: 10.1111/j.1420-9101.2010.02223.x. Epub 2011 Feb 16.

26.

Genetic diversity, population structure and sex-biased dispersal in three co-evolving species.

Foitzik S, Bauer S, Laurent S, Pennings PS.

J Evol Biol. 2009 Dec;22(12):2470-80. doi: 10.1111/j.1420-9101.2009.01863.x. Epub 2009 Nov 3.

27.

Association of orthodenticle with natural variation for early embryonic patterning in Drosophila melanogaster.

Goering LM, Hunt PK, Heighington C, Busick C, Pennings PS, Hermisson J, Kumar S, Gibson G.

J Exp Zool B Mol Dev Evol. 2009 Dec 15;312(8):841-54. doi: 10.1002/jez.b.21299.

28.

An analytically tractable model for competitive speciation.

Pennings PS, Kopp M, Meszéna G, Dieckmann U, Hermisson J.

Am Nat. 2008 Jan;171(1):E44-71. doi: 10.1086/523952.

PMID:
18171142
29.

Specialization and local adaptation of a fungal parasite on two host plant species as revealed by two fitness traits.

Sicard D, Pennings PS, Grandclément C, Acosta J, Kaltz O, Shykoff JA.

Evolution. 2007 Jan;61(1):27-41.

PMID:
17300425
30.

Soft sweeps III: the signature of positive selection from recurrent mutation.

Pennings PS, Hermisson J.

PLoS Genet. 2006 Dec 15;2(12):e186. Epub 2006 Sep 14.

31.

Soft sweeps II--molecular population genetics of adaptation from recurrent mutation or migration.

Pennings PS, Hermisson J.

Mol Biol Evol. 2006 May;23(5):1076-84. Epub 2006 Mar 6.

PMID:
16520336
32.

Soft sweeps: molecular population genetics of adaptation from standing genetic variation.

Hermisson J, Pennings PS.

Genetics. 2005 Apr;169(4):2335-52. Epub 2005 Feb 16.

33.

Natural enemies and sex: how seed predators and pathogens contribute to sex-differential reproductive success in a gynodioecious plant.

Collin C, Pennings P, Rueffler C, Widmer A, Shykoff J.

Oecologia. 2002 Mar;131(1):94-102. doi: 10.1007/s00442-001-0854-8. Epub 2002 Mar 1.

PMID:
28547517
34.

Wolbachia bacteria effects after experimental interspecific transfers in terrestrial isopods.

Rigaud T, Pennings PS, Juchault P.

J Invertebr Pathol. 2001 May;77(4):251-7.

PMID:
11437528
35.

Dylan's lesson.

Pennings PT.

Nursing. 1992 Aug;22(8):84-5. No abstract available.

PMID:
1495618

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