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Items: 1 to 50 of 66

1.

Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum.

Lindsey ARI, Kelkar YD, Wu X, Sun D, Martinson EO, Yan Z, Rugman-Jones PF, Hughes DST, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni HV, Worley KC, Muzny DM, Ye G, Gibbs RA, Richards S, Yi SV, Stouthamer R, Werren JH.

BMC Biol. 2018 May 18;16(1):54. doi: 10.1186/s12915-018-0520-9.

2.

Selection on the regulation of sympathetic nervous activity in humans and chimpanzees.

Lee KS, Chatterjee P, Choi EY, Sung MK, Oh J, Won H, Park SM, Kim YJ, Yi SV, Choi JK.

PLoS Genet. 2018 Apr 19;14(4):e1007311. doi: 10.1371/journal.pgen.1007311. eCollection 2018 Apr.

3.

Development of novel EST-SSR markers for ploidy identification based on de novo transcriptome assembly for Misgurnus anguillicaudatus.

Feng B, Yi SV, Zhang M, Zhou X.

PLoS One. 2018 Apr 12;13(4):e0195829. doi: 10.1371/journal.pone.0195829. eCollection 2018.

4.

Rapid regulatory evolution of a nonrecombining autosome linked to divergent behavioral phenotypes.

Sun D, Huh I, Zinzow-Kramer WM, Maney DL, Yi SV.

Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):2794-2799. doi: 10.1073/pnas.1717721115. Epub 2018 Feb 26.

5.

Insights into Epigenome Evolution from Animal and Plant Methylomes.

Yi SV.

Genome Biol Evol. 2017 Nov 1;9(11):3189-3201. doi: 10.1093/gbe/evx203.

6.

Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species.

Huh I, Wu X, Park T, Yi SV.

Brief Bioinform. 2017 Jul 21. doi: 10.1093/bib/bbx077. [Epub ahead of print]

PMID:
28981571
7.

Body-hypomethylated human genes harbor extensive intragenic transcriptional activity and are prone to cancer-associated dysregulation.

Mendizabal I, Zeng J, Keller TE, Yi SV.

Nucleic Acids Res. 2017 May 5;45(8):4390-4400. doi: 10.1093/nar/gkx020.

8.

Evaluation of Possible Proximate Mechanisms Underlying the Kinship Theory of Intragenomic Conflict in Social Insects.

Galbraith DA, Yi SV, Grozinger CM.

Integr Comp Biol. 2016 Dec;56(6):1206-1214.

PMID:
27940613
9.

What Signatures Dominantly Associate with Gene Age?

Yin H, Wang G, Ma L, Yi SV, Zhang Z.

Genome Biol Evol. 2016 Oct 13;8(10):3083-3089.

10.

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution.

Mendizabal I, Shi L, Keller TE, Konopka G, Preuss TM, Hsieh TF, Hu E, Zhang Z, Su B, Yi SV.

Mol Biol Evol. 2016 Nov;33(11):2947-2959. Epub 2016 Aug 25.

11.

The multivariate association between genomewide DNA methylation and climate across the range of Arabidopsis thaliana.

Keller TE, Lasky JR, Yi SV.

Mol Ecol. 2016 Apr;25(8):1823-37. doi: 10.1111/mec.13573. Epub 2016 Mar 14.

PMID:
26850505
12.

Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate-Vertebrate Boundary.

Keller TE, Han P, Yi SV.

Mol Biol Evol. 2016 Apr;33(4):1019-28. doi: 10.1093/molbev/msv345. Epub 2015 Dec 29.

13.

Effects of DNA Methylation and Chromatin State on Rates of Molecular Evolution in Insects.

Glastad KM, Goodisman MA, Yi SV, Hunt BG.

G3 (Bethesda). 2015 Dec 4;6(2):357-63. doi: 10.1534/g3.115.023499.

14.

Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation.

Mendizabal I, Yi SV.

Hum Mol Genet. 2016 Jan 1;25(1):69-82. doi: 10.1093/hmg/ddv449. Epub 2015 Oct 28.

15.

Impacts of Chromatin States and Long-Range Genomic Segments on Aging and DNA Methylation.

Sun D, Yi SV.

PLoS One. 2015 Jun 19;10(6):e0128517. doi: 10.1371/journal.pone.0128517. eCollection 2015.

16.

Erratum to: The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes.

Kocher SD, Li C, Yang W, Tan H, Yi SV, Yang X, Hoekstra HE, Zhang G, Pierce NE, Yu DW.

Genome Biol. 2015 Feb 12;16:34. doi: 10.1186/s13059-014-0574-0.

17.
18.

Bis-class: a new classification tool of methylation status using bayes classifier and local methylation information.

Huh I, Yang X, Park T, Yi SV.

BMC Genomics. 2014 Jul 18;15:608. doi: 10.1186/1471-2164-15-608.

19.

Epigenetics and evolution.

Mendizabal I, Keller TE, Zeng J, Yi SV.

Integr Comp Biol. 2014 Jul;54(1):31-42. doi: 10.1093/icb/icu040. Epub 2014 May 16. Review.

PMID:
24838745
20.

The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis.

Jameson Kiesling NM, Yi SV, Xu K, Gianluca Sperone F, Wildman DE.

Mol Phylogenet Evol. 2015 Jan;82 Pt B:386-99. doi: 10.1016/j.ympev.2014.03.027. Epub 2014 Apr 30.

PMID:
24792088
21.

Epigenetic inheritance and genome regulation: is DNA methylation linked to ploidy in haplodiploid insects?

Glastad KM, Hunt BG, Yi SV, Goodisman MA.

Proc Biol Sci. 2014 Apr 30;281(1785):20140411. doi: 10.1098/rspb.2014.0411. Print 2014 Jun 22.

22.

DNA methylation and evolution of duplicate genes.

Keller TE, Yi SV.

Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5932-7. doi: 10.1073/pnas.1321420111. Epub 2014 Apr 7.

23.

Fundamental diversity of human CpG islands at multiple biological levels.

Zeng J, Nagrajan HK, Yi SV.

Epigenetics. 2014 Apr;9(4):483-91. doi: 10.4161/epi.27654. Epub 2014 Jan 13.

24.

The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes.

Kocher SD, Li C, Yang W, Tan H, Yi SV, Yang X, Hoekstra HE, Zhang G, Pierce NE, Yu DW.

Genome Biol. 2013 Dec 20;14(12):R142. doi: 10.1186/gb-2013-14-12-r142. Erratum in: Genome Biol. 2015;16:34.

25.

Obligate mutualism within a host drives the extreme specialization of a fig wasp genome.

Xiao JH, Yue Z, Jia LY, Yang XH, Niu LH, Wang Z, Zhang P, Sun BF, He SM, Li Z, Xiong TL, Xin W, Gu HF, Wang B, Werren JH, Murphy RW, Wheeler D, Niu LM, Ma GC, Tang T, Bian SN, Wang NX, Yang CY, Wang N, Fu YG, Li WZ, Yi SV, Yang XY, Zhou Q, Lu CX, Xu CY, He LJ, Yu LL, Chen M, Zheng Y, Wang SW, Zhao S, Li YH, Yu YY, Qian XJ, Cai Y, Bian LL, Zhang S, Wang JY, Yin Y, Xiao H, Wang GH, Yu H, Wu WS, Cook JM, Wang J, Huang DW.

Genome Biol. 2013 Dec 20;14(12):R141. doi: 10.1186/gb-2013-14-12-r141.

26.

Kin selection, genomics and caste-antagonistic pleiotropy.

Hall DW, Yi SV, Goodisman MA.

Biol Lett. 2013 Oct 16;9(6):20130309. doi: 10.1098/rsbl.2013.0309. Print 2013.

27.

The evolution of lineage-specific clusters of single nucleotide substitutions in the human genome.

Xu K, Wang J, Elango N, Yi SV.

Mol Phylogenet Evol. 2013 Oct;69(1):276-85. doi: 10.1016/j.ympev.2013.06.003. Epub 2013 Jun 14.

PMID:
23770436
28.

DNA methylation and transcriptional noise.

Huh I, Zeng J, Park T, Yi SV.

Epigenetics Chromatin. 2013 Apr 26;6(1):9. doi: 10.1186/1756-8935-6-9. Erratum in: Epigenetics Chromatin. 2014;7:13.

29.

The function of intragenic DNA methylation: insights from insect epigenomes.

Hunt BG, Glastad KM, Yi SV, Goodisman MA.

Integr Comp Biol. 2013 Aug;53(2):319-28. doi: 10.1093/icb/ict003. Epub 2013 Mar 18. Review.

PMID:
23509238
30.

Patterning and regulatory associations of DNA methylation are mirrored by histone modifications in insects.

Hunt BG, Glastad KM, Yi SV, Goodisman MA.

Genome Biol Evol. 2013;5(3):591-8. doi: 10.1093/gbe/evt030.

31.

Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution.

Zeng J, Konopka G, Hunt BG, Preuss TM, Geschwind D, Yi SV.

Am J Hum Genet. 2012 Sep 7;91(3):455-65. doi: 10.1016/j.ajhg.2012.07.024. Epub 2012 Aug 23.

32.

Morris Goodman's hominoid rate slowdown: the importance of being neutral.

Yi SV.

Mol Phylogenet Evol. 2013 Feb;66(2):569-74. doi: 10.1016/j.ympev.2012.07.031. Epub 2012 Aug 10. Review.

PMID:
22902941
33.

Development and annotation of shotgun sequence libraries from New World monkeys.

Jameson NM, Xu K, Yi SV, Wildman DE.

Mol Ecol Resour. 2012 Sep;12(5):950-5. doi: 10.1111/j.1755-0998.2012.03162.x. Epub 2012 Jun 21.

PMID:
22715851
34.

Lineage-specific variation in slow- and fast-X evolution in primates.

Xu K, Oh S, Park T, Presgraves DC, Yi SV.

Evolution. 2012 Jun;66(6):1751-61. doi: 10.1111/j.1558-5646.2011.01556.x. Epub 2012 Feb 2.

PMID:
22671544
35.

On the presence and role of human gene-body DNA methylation.

Jjingo D, Conley AB, Yi SV, Lunyak VV, Jordan IK.

Oncotarget. 2012 Apr;3(4):462-74.

36.

The evolution of invertebrate gene body methylation.

Sarda S, Zeng J, Hunt BG, Yi SV.

Mol Biol Evol. 2012 Aug;29(8):1907-16. doi: 10.1093/molbev/mss062. Epub 2012 Feb 10.

PMID:
22328716
37.

The genome of Tetranychus urticae reveals herbivorous pest adaptations.

Grbić M, Van Leeuwen T, Clark RM, Rombauts S, Rouzé P, Grbić V, Osborne EJ, Dermauw W, Ngoc PC, Ortego F, Hernández-Crespo P, Diaz I, Martinez M, Navajas M, Sucena É, Magalhães S, Nagy L, Pace RM, Djuranović S, Smagghe G, Iga M, Christiaens O, Veenstra JA, Ewer J, Villalobos RM, Hutter JL, Hudson SD, Velez M, Yi SV, Zeng J, Pires-daSilva A, Roch F, Cazaux M, Navarro M, Zhurov V, Acevedo G, Bjelica A, Fawcett JA, Bonnet E, Martens C, Baele G, Wissler L, Sanchez-Rodriguez A, Tirry L, Blais C, Demeestere K, Henz SR, Gregory TR, Mathieu J, Verdon L, Farinelli L, Schmutz J, Lindquist E, Feyereisen R, Van de Peer Y.

Nature. 2011 Nov 23;479(7374):487-92. doi: 10.1038/nature10640.

38.

What are the determinants of gene expression levels and breadths in the human genome?

Park J, Xu K, Park T, Yi SV.

Hum Mol Genet. 2012 Jan 1;21(1):46-56. doi: 10.1093/hmg/ddr436. Epub 2011 Sep 26.

39.

Relaxed selection is a precursor to the evolution of phenotypic plasticity.

Hunt BG, Ometto L, Wurm Y, Shoemaker D, Yi SV, Keller L, Goodisman MA.

Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15936-41. doi: 10.1073/pnas.1104825108. Epub 2011 Sep 12.

40.

DNA methylation in insects: on the brink of the epigenomic era.

Glastad KM, Hunt BG, Yi SV, Goodisman MA.

Insect Mol Biol. 2011 Oct;20(5):553-65. doi: 10.1111/j.1365-2583.2011.01092.x. Epub 2011 Jun 24. Review.

PMID:
21699596
41.

Comparative analyses of DNA methylation and sequence evolution using Nasonia genomes.

Park J, Peng Z, Zeng J, Elango N, Park T, Wheeler D, Werren JH, Yi SV.

Mol Biol Evol. 2011 Dec;28(12):3345-54. doi: 10.1093/molbev/msr168. Epub 2011 Jun 20.

42.

Path lengths in protein-protein interaction networks and biological complexity.

Xu K, Bezakova I, Bunimovich L, Yi SV.

Proteomics. 2011 May;11(10):1857-67. doi: 10.1002/pmic.201000684. Epub 2011 Apr 8.

PMID:
21480527
43.

Functional relevance of CpG island length for regulation of gene expression.

Elango N, Yi SV.

Genetics. 2011 Apr;187(4):1077-83. doi: 10.1534/genetics.110.126094. Epub 2011 Feb 1.

44.

The genome of the fire ant Solenopsis invicta.

Wurm Y, Wang J, Riba-Grognuz O, Corona M, Nygaard S, Hunt BG, Ingram KK, Falquet L, Nipitwattanaphon M, Gotzek D, Dijkstra MB, Oettler J, Comtesse F, Shih CJ, Wu WJ, Yang CC, Thomas J, Beaudoing E, Pradervand S, Flegel V, Cook ED, Fabbretti R, Stockinger H, Long L, Farmerie WG, Oakey J, Boomsma JJ, Pamilo P, Yi SV, Heinze J, Goodisman MA, Farinelli L, Harshman K, Hulo N, Cerutti L, Xenarios I, Shoemaker D, Keller L.

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5679-84. doi: 10.1073/pnas.1009690108. Epub 2011 Jan 31.

45.

Evolution of microRNAs and the diversification of species.

Loh YH, Yi SV, Streelman JT.

Genome Biol Evol. 2011;3:55-65. doi: 10.1093/gbe/evq085. Epub 2010 Dec 15.

46.
47.

Functional conservation of DNA methylation in the pea aphid and the honeybee.

Hunt BG, Brisson JA, Yi SV, Goodisman MA.

Genome Biol Evol. 2010;2:719-28. doi: 10.1093/gbe/evq057. Epub 2010 Sep 20.

48.

Sociality is linked to rates of protein evolution in a highly social insect.

Hunt BG, Wyder S, Elango N, Werren JH, Zdobnov EM, Yi SV, Goodisman MA.

Mol Biol Evol. 2010 Mar;27(3):497-500. doi: 10.1093/molbev/msp225. Epub 2010 Jan 28.

PMID:
20110264
49.

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK; Nasonia Genome Working Group, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA.

Science. 2010 Jan 15;327(5963):343-8. doi: 10.1126/science.1178028. Erratum in: Science. 2010 Mar 26;327(5973):1577.

50.

Computational approaches for understanding the evolution of DNA methylation in animals.

Yi SV, Goodisman MA.

Epigenetics. 2009 Nov 16;4(8):551-6. Epub 2009 Nov 18. Review.

PMID:
20009525

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