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Items: 34

1.

Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear.

Jansen HT, Trojahn S, Saxton MW, Quackenbush CR, Evans Hutzenbiler BD, Nelson OL, Cornejo OE, Robbins CT, Kelley JL.

Commun Biol. 2019 Sep 13;2:336. doi: 10.1038/s42003-019-0574-4. eCollection 2019.

2.

Insights from transcriptome profiling on the non-photosynthetic and stomatal signaling response of maize carbonic anhydrase mutants to low CO2.

Kolbe AR, Studer AJ, Cornejo OE, Cousins AB.

BMC Genomics. 2019 Feb 15;20(1):138. doi: 10.1186/s12864-019-5522-7.

3.

Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process.

Cornejo OE, Yee MC, Dominguez V, Andrews M, Sockell A, Strandberg E, Livingstone D 3rd, Stack C, Romero A, Umaharan P, Royaert S, Tawari NR, Ng P, Gutierrez O, Phillips W, Mockaitis K, Bustamante CD, Motamayor JC.

Commun Biol. 2018 Oct 16;1:167. doi: 10.1038/s42003-018-0168-6. eCollection 2018.

4.

Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao.

Osorio-Guarín JA, Quackenbush CR, Cornejo OE.

PLoS One. 2018 Oct 17;13(10):e0203973. doi: 10.1371/journal.pone.0203973. eCollection 2018.

5.
6.

Corrigendum: A Larger Chocolate Chip-Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps.

Livingstone Iii D, Stack C, Mustiga GM, Rodezno DC, Suarez C, Amores F, Feltus FA, Mockaitis K, Cornejo OE, Motamayor JC.

Front Plant Sci. 2018 Jul 16;9:948. doi: 10.3389/fpls.2018.00948. eCollection 2018.

7.

Genome Sequence Resources for the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) and the Barley Stripe Rust Pathogen (Puccinia striiformis f. sp. hordei).

Xia C, Wang M, Yin C, Cornejo OE, Hulbert SH, Chen X.

Mol Plant Microbe Interact. 2018 Nov;31(11):1117-1120. doi: 10.1094/MPMI-04-18-0107-A. Epub 2018 Sep 7.

8.

Tripolar chromosome segregation drives the association between maternal genotype at variants spanning PLK4 and aneuploidy in human preimplantation embryos.

McCoy RC, Newnham LJ, Ottolini CS, Hoffmann ER, Chatzimeletiou K, Cornejo OE, Zhan Q, Zaninovic N, Rosenwaks Z, Petrov DA, Demko ZP, Sigurjonsson S, Handyside AH.

Hum Mol Genet. 2018 Jul 15;27(14):2573-2585. doi: 10.1093/hmg/ddy147.

9.

Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes.

Cornejo OE, Hickey RJ, Suzuki H, Forney LJ.

Evol Appl. 2017 Nov 16;11(3):312-324. doi: 10.1111/eva.12555. eCollection 2018 Mar.

10.
11.

A Larger Chocolate Chip-Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps.

Livingstone D 3rd, Stack C, Mustiga GM, Rodezno DC, Suarez C, Amores F, Feltus FA, Mockaitis K, Cornejo OE, Motamayor JC.

Front Plant Sci. 2017 Dec 5;8:2008. doi: 10.3389/fpls.2017.02008. eCollection 2017. Erratum in: Front Plant Sci. 2018 Jul 16;9:948.

12.

Pherotype Polymorphism in Streptococcus pneumoniae Has No Obvious Effects on Population Structure and Recombination.

Miller EL, Evans BA, Cornejo OE, Roberts IS, Rozen DE.

Genome Biol Evol. 2017 Oct 1;9(10):2546-2559. doi: 10.1093/gbe/evx188.

13.

Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans.

McManus KF, Taravella AM, Henn BM, Bustamante CD, Sikora M, Cornejo OE.

PLoS Genet. 2017 Mar 10;13(3):e1006560. doi: 10.1371/journal.pgen.1006560. eCollection 2017 Mar.

14.

Geographic Differentiation and Population Genetic Structure of Moniliophthora roreri in the Principal Cocoa Production Areas in Colombia.

Jaimes YY, Gonzalez C, Rojas J, Cornejo OE, Mideros MF, Restrepo S, Cilas C, Furtado EL.

Plant Dis. 2016 Aug;100(8):1548-1558. doi: 10.1094/PDIS-12-15-1498-RE. Epub 2016 May 27.

PMID:
30686241
15.

Evolution of the Transmission-Blocking Vaccine Candidates Pvs28 and Pvs25 in Plasmodium vivax: Geographic Differentiation and Evidence of Positive Selection.

Chaurio RA, Pacheco MA, Cornejo OE, Durrego E, Stanley CE Jr, Castillo AI, Herrera S, Escalante AA.

PLoS Negl Trop Dis. 2016 Jun 27;10(6):e0004786. doi: 10.1371/journal.pntd.0004786. eCollection 2016 Jun.

16.

GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data.

Cooke TF, Yee MC, Muzzio M, Sockell A, Bell R, Cornejo OE, Kelley JL, Bailliet G, Bravi CM, Bustamante CD, Kenny EE.

PLoS Genet. 2016 Feb 1;12(2):e1005631. doi: 10.1371/journal.pgen.1005631. eCollection 2016 Feb.

17.

POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, de Barros Damgaard P, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T Jr, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CPE, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E.

Science. 2015 Aug 21;349(6250):aab3884. doi: 10.1126/science.aab3884. Epub 2015 Jul 21.

18.

Genome-wide patterns of genetic polymorphism and signatures of selection in Plasmodium vivax.

Cornejo OE, Fisher D, Escalante AA.

Genome Biol Evol. 2014 Dec 17;7(1):106-19. doi: 10.1093/gbe/evu267.

19.

The genetic prehistory of the New World Arctic.

Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P, Korneliussen TS, Grønnow B, Appelt M, Gulløv HC, Friesen TM, Fitzhugh W, Malmström H, Rasmussen S, Olsen J, Melchior L, Fuller BT, Fahrni SM, Stafford T Jr, Grimes V, Renouf MA, Cybulski J, Lynnerup N, Lahr MM, Britton K, Knecht R, Arneborg J, Metspalu M, Cornejo OE, Malaspinas AS, Wang Y, Rasmussen M, Raghavan V, Hansen TV, Khusnutdinova E, Pierre T, Dneprovsky K, Andreasen C, Lange H, Hayes MG, Coltrain J, Spitsyn VA, Götherström A, Orlando L, Kivisild T, Villems R, Crawford MH, Nielsen FC, Dissing J, Heinemeier J, Meldgaard M, Bustamante C, O'Rourke DH, Jakobsson M, Gilbert MT, Nielsen R, Willerslev E.

Science. 2014 Aug 29;345(6200):1255832. doi: 10.1126/science.1255832.

20.

The genome of a Late Pleistocene human from a Clovis burial site in western Montana.

Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW Jr, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS 5th, Allentoft ME, Cornejo OE, Tambets K, Eriksson A, Heintzman PD, Karmin M, Korneliussen TS, Meltzer DJ, Pierre TL, Stenderup J, Saag L, Warmuth VM, Lopes MC, Malhi RS, Brunak S, Sicheritz-Ponten T, Barnes I, Collins M, Orlando L, Balloux F, Manica A, Gupta R, Metspalu M, Bustamante CD, Jakobsson M, Nielsen R, Willerslev E.

Nature. 2014 Feb 13;506(7487):225-9. doi: 10.1038/nature13025.

21.

The role of selection in shaping diversity of natural M. tuberculosis populations.

Pepperell CS, Casto AM, Kitchen A, Granka JM, Cornejo OE, Holmes EC, Birren B, Galagan J, Feldman MW.

PLoS Pathog. 2013 Aug;9(8):e1003543. doi: 10.1371/journal.ppat.1003543. Epub 2013 Aug 15. Erratum in: PLoS Pathog. 2013 Aug;9(8). doi:10.1371/annotation/cff22061-44d5-4301-b853-41702d160203. Holmes, Eddie C [corrected to Holmes, Edward C].

22.

iXora: exact haplotype inferencing and trait association.

Utro F, Haiminen N, Livingstone D 3rd, Cornejo OE, Royaert S, Schnell RJ, Motamayor JC, Kuhn DN, Parida L.

BMC Genet. 2013 Jun 6;14:48. doi: 10.1186/1471-2156-14-48.

23.

ARG-based genome-wide analysis of cacao cultivars.

Utro F, Cornejo OE, Livingstone D, Motamayor JC, Parida L.

BMC Bioinformatics. 2012;13 Suppl 19:S17. doi: 10.1186/1471-2105-13-S19-S17. Epub 2012 Dec 19.

24.

Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans.

Cornejo OE, Lefébure T, Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, Burne RA, Siepel A, Bustamante CD, Stanhope MJ.

Mol Biol Evol. 2013 Apr;30(4):881-93. doi: 10.1093/molbev/mss278. Epub 2012 Dec 10.

25.

Timing the origin of human malarias: the lemur puzzle.

Pacheco MA, Battistuzzi FU, Junge RE, Cornejo OE, Williams CV, Landau I, Rabetafika L, Snounou G, Jones-Engel L, Escalante AA.

BMC Evol Biol. 2011 Oct 12;11:299. doi: 10.1186/1471-2148-11-299.

26.

Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.

Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA.

PLoS Genet. 2011 Sep;7(9):e1002280. doi: 10.1371/journal.pgen.1002280. Epub 2011 Sep 15.

27.

On the diversity of malaria parasites in African apes and the origin of Plasmodium falciparum from Bonobos.

Krief S, Escalante AA, Pacheco MA, Mugisha L, André C, Halbwax M, Fischer A, Krief JM, Kasenene JM, Crandfield M, Cornejo OE, Chavatte JM, Lin C, Letourneur F, Grüner AC, McCutchan TF, Rénia L, Snounou G.

PLoS Pathog. 2010 Feb 12;6(2):e1000765. doi: 10.1371/journal.ppat.1000765.

28.

Polymorphic competence peptides do not restrict recombination in Streptococcus pneumoniae.

Cornejo OE, McGee L, Rozen DE.

Mol Biol Evol. 2010 Mar;27(3):694-702. doi: 10.1093/molbev/msp287. Epub 2009 Nov 25. Erratum in: Mol Biol Evol. 2010 Nov;27(11):2667.

PMID:
19942613
29.

The population and evolutionary dynamics of homologous gene recombination in bacterial populations.

Levin BR, Cornejo OE.

PLoS Genet. 2009 Aug;5(8):e1000601. doi: 10.1371/journal.pgen.1000601. Epub 2009 Aug 14.

30.

Splice variants of the human ZC3H14 gene generate multiple isoforms of a zinc finger polyadenosine RNA binding protein.

Leung SW, Apponi LH, Cornejo OE, Kitchen CM, Valentini SR, Pavlath GK, Dunham CM, Corbett AH.

Gene. 2009 Jun 15;439(1-2):71-8. doi: 10.1016/j.gene.2009.02.022. Epub 2009 Mar 18.

31.

Oscillations in continuous culture populations of Streptococcus pneumoniae: population dynamics and the evolution of clonal suicide.

Cornejo OE, Rozen DE, May RM, Levin BR.

Proc Biol Sci. 2009 Mar 22;276(1659):999-1008. doi: 10.1098/rspb.2008.1415.

32.

The origin and age of Plasmodium vivax.

Cornejo OE, Escalante AA.

Trends Parasitol. 2006 Dec;22(12):558-63. Epub 2006 Oct 10.

33.

A monkey's tale: the origin of Plasmodium vivax as a human malaria parasite.

Escalante AA, Cornejo OE, Freeland DE, Poe AC, Durrego E, Collins WE, Lal AA.

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1980-5. Epub 2005 Jan 31.

34.

Assessing the effect of natural selection in malaria parasites.

Escalante AA, Cornejo OE, Rojas A, Udhayakumar V, Lal AA.

Trends Parasitol. 2004 Aug;20(8):388-95. Review.

PMID:
15246323

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