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Items: 1 to 50 of 82

1.

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, Tempe 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):.

2.
3.

Genomic and Transcriptomic Analysis Reveals Spliced Leader Trans-Splicing in Cryptomonads.

Roy SW.

Genome Biol Evol. 2017 Mar 1;9(3):468-473. doi: 10.1093/gbe/evx012.

4.

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.

5.

The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell.

Slabodnick MM, Ruby JG, Reiff SB, Swart EC, Gosai S, Prabakaran S, Witkowska E, Larue GE, Fisher S, Freeman RM Jr, Gunawardena J, Chu W, Stover NA, Gregory BD, Nowacki M, Derisi J, Roy SW, Marshall WF, Sood P.

Curr Biol. 2017 Feb 20;27(4):569-575. doi: 10.1016/j.cub.2016.12.057. Epub 2017 Feb 9.

6.
7.

Mechanism for DNA transposons to generate introns on genomic scales.

Huff JT, Zilberman D, Roy SW.

Nature. 2016 Oct 27;538(7626):533-536. doi: 10.1038/nature20110. Epub 2016 Oct 19.

8.
9.

Is Mutation Random or Targeted?: No Evidence for Hypermutability in Snail Toxin Genes.

Roy SW.

Mol Biol Evol. 2016 Oct;33(10):2642-7. doi: 10.1093/molbev/msw140. Epub 2016 Aug 2.

PMID:
27486220
10.

How Common Is Parallel Intron Gain? Rapid Evolution Versus Independent Creation in Recently Created Introns in Daphnia.

Roy SW.

Mol Biol Evol. 2016 Aug;33(8):1902-6. doi: 10.1093/molbev/msw091. Epub 2016 May 10.

PMID:
27189562
11.

HAPCAD: An open-source tool to detect PCR crossovers in next-generation sequencing generated HLA data.

McDevitt SL, Bredeson JV, Roy SW, Lane JA, Noble JA.

Hum Immunol. 2016 Mar;77(3):257-263. doi: 10.1016/j.humimm.2016.01.013. Epub 2016 Jan 20.

12.

The Plasmodium gaboni genome illuminates allelic dimorphism of immunologically important surface antigens in P. falciparum.

Roy SW.

Infect Genet Evol. 2015 Dec;36:441-449. doi: 10.1016/j.meegid.2015.08.014. Epub 2015 Aug 18.

PMID:
26296605
13.
14.

Transcriptome sequencing and analysis of Plasmodium gallinaceum reveals polymorphisms and selection on the apical membrane antigen-1.

Lauron EJ, Oakgrove KS, Tell LA, Biskar K, Roy SW, Sehgal RN.

Malar J. 2014 Sep 26;13:382. doi: 10.1186/1475-2875-13-382.

15.

A new model for the origins of allelic dimorphism in Plasmodium falciparum.

Roy SW, Ferreira MU.

Parasitol Int. 2015 Jun;64(3):229-37. doi: 10.1016/j.parint.2014.09.008. Epub 2014 Sep 22.

PMID:
25251164
16.

Origin of spliceosomal introns and alternative splicing.

Irimia M, Roy SW.

Cold Spring Harb Perspect Biol. 2014 Jun 2;6(6). pii: a016071. doi: 10.1101/cshperspect.a016071.

17.

Diversity and evolution of spliceosomal systems.

Roy SW, Irimia M.

Methods Mol Biol. 2014;1126:13-33. doi: 10.1007/978-1-62703-980-2_2.

PMID:
24549653
18.

Elephant shark genome provides unique insights into gnathostome evolution.

Venkatesh B, Lee AP, Ravi V, Maurya AK, Lian MM, Swann JB, Ohta Y, Flajnik MF, Sutoh Y, Kasahara M, Hoon S, Gangu V, Roy SW, Irimia M, Korzh V, Kondrychyn I, Lim ZW, Tay BH, Tohari S, Kong KW, Ho S, Lorente-Galdos B, Quilez J, Marques-Bonet T, Raney BJ, Ingham PW, Tay A, Hillier LW, Minx P, Boehm T, Wilson RK, Brenner S, Warren WC.

Nature. 2014 Jan 9;505(7482):174-9. doi: 10.1038/nature12826. Erratum in: Nature. 2014 Sep 25;513(7519):574.

19.

Ancient cis-regulatory constraints and the evolution of genome architecture.

Irimia M, Maeso I, Roy SW, Fraser HB.

Trends Genet. 2013 Sep;29(9):521-8. doi: 10.1016/j.tig.2013.05.008. Epub 2013 Jun 18. Review.

PMID:
23791467
20.

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.

Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJ, Herman EK, Klute MJ, Nakayama T, Oborník M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale CJ, Hempel F, Henrissat B, Höppner MP, Ishida K, Kim E, Kořený L, Kroth PG, Liu Y, Malik SB, Maier UG, McRose D, Mock T, Neilson JA, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV, Archibald JM.

Nature. 2012 Dec 6;492(7427):59-65. doi: 10.1038/nature11681. Epub 2012 Nov 28.

PMID:
23201678
21.

Genome evolution: where do new introns come from?

Roy SW, Irimia M.

Curr Biol. 2012 Jul 10;22(13):R529-31. doi: 10.1016/j.cub.2012.05.017.

22.

Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.

Irimia M, Tena JJ, Alexis MS, Fernandez-Miñan A, Maeso I, Bogdanovic O, de la Calle-Mustienes E, Roy SW, Gómez-Skarmeta JL, Fraser HB.

Genome Res. 2012 Dec;22(12):2356-67. doi: 10.1101/gr.139725.112. Epub 2012 Jun 21.

23.

Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans.

Zhou Q, Zhu HM, Huang QF, Zhao L, Zhang GJ, Roy SW, Vicoso B, Xuan ZL, Ruan J, Zhang Y, Zhao RP, Ye C, Zhang XQ, Wang J, Wang W, Bachtrog D.

BMC Genomics. 2012 Mar 22;13:109. doi: 10.1186/1471-2164-13-109.

24.

Widespread recurrent evolution of genomic features.

Maeso I, Roy SW, Irimia M.

Genome Biol Evol. 2012;4(4):486-500. doi: 10.1093/gbe/evs022. Epub 2012 Mar 13. Review.

25.

Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1.

Irimia M, Denuc A, Ferran JL, Pernaute B, Puelles L, Roy SW, Garcia-Fernàndez J, Marfany G.

RNA Biol. 2012 Jan;9(1):12-21. doi: 10.4161/rna.9.1.18387. Epub 2012 Jan 1.

PMID:
22258141
26.

Contrasting 5' and 3' evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures.

Irimia M, Maeso I, Burguera D, Hidalgo-Sánchez M, Puelles L, Roy SW, Garcia-Fernàndez J, Ferran JL.

Genome Biol Evol. 2011;3:551-64. doi: 10.1093/gbe/evr056. Epub 2011 Jun 16.

27.

Numerous fragmented spliceosomal introns, AT-AC splicing, and an unusual dynein gene expression pathway in Giardia lamblia.

Roy SW, Hudson AJ, Joseph J, Yee J, Russell AG.

Mol Biol Evol. 2012 Jan;29(1):43-9. doi: 10.1093/molbev/msr063. Epub 2011 Apr 11.

PMID:
21482665
28.

Stepwise assembly of the Nova-regulated alternative splicing network in the vertebrate brain.

Irimia M, Denuc A, Burguera D, Somorjai I, Martín-Durán JM, Genikhovich G, Jimenez-Delgado S, Technau U, Roy SW, Marfany G, Garcia-Fernàndez J.

Proc Natl Acad Sci U S A. 2011 Mar 29;108(13):5319-24. doi: 10.1073/pnas.1012333108. Epub 2011 Mar 9.

29.

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.

Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C, Bouquet JM, Danks G, Poulain J, Campsteijn C, Adamski M, Cross I, Yadetie F, Muffato M, Louis A, Butcher S, Tsagkogeorga G, Konrad A, Singh S, Jensen MF, Huynh Cong E, Eikeseth-Otteraa H, Noel B, Anthouard V, Porcel BM, Kachouri-Lafond R, Nishino A, Ugolini M, Chourrout P, Nishida H, Aasland R, Huzurbazar S, Westhof E, Delsuc F, Lehrach H, Reinhardt R, Weissenbach J, Roy SW, Artiguenave F, Postlethwait JH, Manak JR, Thompson EM, Jaillon O, Du Pasquier L, Boudinot P, Liberles DA, Volff JN, Philippe H, Lenhard B, Roest Crollius H, Wincker P, Chourrout D.

Science. 2010 Dec 3;330(6009):1381-5. doi: 10.1126/science.1194167. Epub 2010 Nov 18.

30.

Molecular characterization of Myostatin gene from Zhikong scallop Chlamys farreri (Jones et Preston 1904).

Hu X, Guo H, He Y, Wang S, Zhang L, Wang S, Huang X, Roy SW, Lu W, Hu J, Bao Z.

Genes Genet Syst. 2010;85(3):207-18.

31.

Constrained intron structures in a microsporidian.

Lee RC, Gill EE, Roy SW, Fast NM.

Mol Biol Evol. 2010 Sep;27(9):1979-82. doi: 10.1093/molbev/msq087. Epub 2010 Apr 1.

32.

Internal and external paralogy in the evolution of tropomyosin genes in metazoans.

Irimia M, Maeso I, Gunning PW, Garcia-Fernàndez J, Roy SW.

Mol Biol Evol. 2010 Jul;27(7):1504-17. doi: 10.1093/molbev/msq018. Epub 2010 Feb 10.

33.

Complex selection on 5' splice sites in intron-rich organisms.

Irimia M, Roy SW, Neafsey DE, Abril JF, Garcia-Fernandez J, Koonin EV.

Genome Res. 2009 Nov;19(11):2021-7. doi: 10.1101/gr.089276.108. Epub 2009 Sep 10.

34.

Intronization, de-intronization and intron sliding are rare in Cryptococcus.

Roy SW.

BMC Evol Biol. 2009 Aug 7;9:192. doi: 10.1186/1471-2148-9-192.

35.

Splicing in the eukaryotic ancestor: form, function and dysfunction.

Roy SW, Irimia M.

Trends Ecol Evol. 2009 Aug;24(8):447-55. doi: 10.1016/j.tree.2009.04.005. Epub 2009 Jul 1.

PMID:
19576657
37.

Sequence diversity and evolutionary dynamics of the dimorphic antigen merozoite surface protein-6 and other Msp genes of Plasmodium falciparum.

Roy SW, Weedall GD, da Silva RL, Polley SD, Ferreira MU.

Gene. 2009 Aug 15;443(1-2):12-21. doi: 10.1016/j.gene.2009.05.007. Epub 2009 May 20.

PMID:
19463923
38.

Probing evolutionary repeatability: neutral and double changes and the predictability of evolutionary adaptation.

Roy SW.

PLoS One. 2009;4(2):e4500. doi: 10.1371/journal.pone.0004500. Epub 2009 Feb 23.

39.

Phylogenomics: gene duplication, unrecognized paralogy and outgroup choice.

Roy SW.

PLoS One. 2009;4(2):e4568. doi: 10.1371/journal.pone.0004568. Epub 2009 Feb 23.

40.

Quantitative regulation of alternative splicing in evolution and development.

Irimia M, Rukov JL, Roy SW, Vinther J, Garcia-Fernandez J.

Bioessays. 2009 Jan;31(1):40-50. doi: 10.1002/bies.080092. Review.

PMID:
19154001
41.

Mystery of intron gain: new data and new models.

Roy SW, Irimia M.

Trends Genet. 2009 Feb;25(2):67-73. doi: 10.1016/j.tig.2008.11.004. Epub 2008 Dec 11.

PMID:
19070397
42.

The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification.

Hoogewijs D, De Henau S, Dewilde S, Moens L, Couvreur M, Borgonie G, Vinogradov SN, Roy SW, Vanfleteren JR.

BMC Evol Biol. 2008 Oct 9;8:279. doi: 10.1186/1471-2148-8-279.

43.
44.

Origin of introns by 'intronization' of exonic sequences.

Irimia M, Rukov JL, Penny D, Vinther J, Garcia-Fernandez J, Roy SW.

Trends Genet. 2008 Aug;24(8):378-81. doi: 10.1016/j.tig.2008.05.007. Epub 2008 Jul 1.

PMID:
18597887
45.

When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis.

Roy SW, Irimia M.

Bioessays. 2008 Jun;30(6):601-5. doi: 10.1002/bies.20749. Review.

PMID:
18478540
47.

Rare genomic characters do not support Coelomata: RGC_CAMs.

Roy SW, Irimia M.

J Mol Evol. 2008 Mar;66(3):308-15. doi: 10.1007/s00239-008-9077-5. Epub 2008 Mar 5.

PMID:
18320261
48.

Intron mis-splicing: no alternative?

Roy SW, Irimia M.

Genome Biol. 2008;9(2):208. doi: 10.1186/gb-2008-9-2-208. Epub 2008 Feb 19. Review.

49.

Patterns of polymorphism in genomic regions flanking three highly polymorphic surface antigens in Plasmodium falciparum.

Amodu OK, Hartl DL, Roy SW.

Mol Biochem Parasitol. 2008 May;159(1):1-6. doi: 10.1016/j.molbiopara.2007.12.004. Epub 2007 Dec 15.

PMID:
18291540
50.

Rare genomic characters do not support Coelomata: intron loss/gain.

Roy SW, Irimia M.

Mol Biol Evol. 2008 Apr;25(4):620-3. doi: 10.1093/molbev/msn035. Epub 2008 Feb 14.

PMID:
18281272

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