Lab Publications

• Nelson, J.T., Cornejo, O.E., Ag1000G Consortium. Evolutionary implications of recombination differences across diverging populations of Anopheles. bioRxiv 2021.02.04.429659; doi: https://doi.org/10.1101/2021.02.04.429659

• Saxton, M.W., Perry, B.W., Evans Hultzenbiler, B.D., Trojahn, S., Gee, A., Brown, A.P., Merrihew, G.E., Park, J., Cornejo, O.E., MacCoss, M.J., Robbins, C.T., Jansen, H.T., and Kelley, J.L. Serum plays an important role in reprogramming the seasonal transcriptional profile of brown bear adipocytes. iScience 2022 doi: https://doi.org/10.1016/j.isci.2022.105084

• Parikh VN, Ioannidis AG, Jimenez-Morales D, Gorzynski JE, De Jong HN, Liu X, Roque J, Cepeda-Espinoza VP, Osoegawa K, Hughes C, Sutton SC, Youlton N, Joshi R, Amar D, Tanigawa Y, Russo D, Wong J, Lauzon JT, Edelson J, Mas Montserrat D, Kwon Y, Rubinacci S, Delaneau O, Cappello L, Kim J, Shoura MJ, Raja AN, Watson N, Hammond N, Spiteri E, Mallempati KC, Montero-Martín G, Christle J, Kim J, Kirillova A, Seo K, Huang Y, Zhao C, Moreno-Grau S, Hershman SG, Dalton KP, Zhen J, Kamm J, Bhatt KD, Isakova A, Morri M, Ranganath T, Blish CA, Rogers AJ, Nadeau K, Yang S, Blomkalns A, O’Hara R, Neff NF, DeBoever C, Szalma S, Wheeler MT, Gates CM, Farh K, Schroth GP, Febbo P, deSouza F, Cornejo OE, Fernandez-Vina M, Kistler A, Palacios JA, Pinsky BA, Bustamante CD, Rivas MA, Ashley EA. Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy. Nat Commun. 2022 Aug 30;13(1):5107. doi: 10.1038/s41467-022-32397-8.

• Schwarzkopf, E.J. and Cornejo, O.E. PRDM9-directed recombination hotspots depleted near meiotically transcribed genes. Gene 2021 Mar 1;813:146123. doi: 10.1016/j.gene.2021.146123.

• Osorio-Guarín JA, Gopaulchan D, Quanckenbush C, Lennon AM, Umaharan P, Cornejo OE. Comparative transcriptomic analysis reveals key components controlling spathe color in Anthurium andraeanum (Hort.). PLoS ONE (2021) 16(12): e0261364. https://doi.org/10.1371/journal.pone.0261364
• Nelson, J.T., Motamayor, J.C. and Cornejo, O.E. Environment and pathogens shape local and regional adaptations to global change in the chocolate tree, Theobroma cacao L. Molecular Ecology 30(3): 656-669. https://doi.org/10.1111/mec.15754.
• Nelson, J.T. and Cornejo, O.E. CoMICS: an R package for the identification of outliers across multiple selection scans (in review at Molecular Ecology Resources, available in the biorXiv) [It has been incorporated in https://doi.org/10.1111/mec.15754.].
• Jimenez Schwarzkopf, E., Motamayor, J.C., and Cornejo, O.E. Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations. BMC Genomics 21: 332. doi: 10.1186/s12864-020-6746-2
• Jansen HT, Trojahn S, Saxton MW, Quackenbush CR, Evans Hutzenbiler BD, Nelson OL, Cornejo OE, Robbins CT, Kelley JL. Hibernation induces widespread transcriptional remodeling in metabolic tissues of the grizzly bear. Commun Biol. 2019 Sep 13;2:336. doi: 10.1038/s42003-019-0574-4
• Osorio-Guarín, J.A., Garzón-Martínez, G.A., Delgadillo-Duran, P. Bastidas, S., Moreno, L.P., Enciso-Rodríguez, F.E., Cornejo, O.E.* and L.S. Barrero*. Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population. BMC Plant Biol 19, 533 (2019) doi:10.1186/s12870-019-2153-8
• Kolbe AR, Studer AJ, Cornejo OE, Cousins AB. (2019) Insights from transcriptome profiling on the non-photosynthetic and stomatal signaling response of maize carbonic anhydrase mutants to low CO₂. BMC Genomics. 2019;20(1):138. doi:10.1186/s12864-019-5522-7
• Osorio J, Quackenbush CR, Cornejo O.E.  (2018) Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao. PLOS One 13(10): e0203973.
• Cornejo OE, Yee M-C, Mockaitis K, Adams A, Strandberg R, Livingston D, Stack C, Umaharan P, Royaert S, Tawari NR, Ng P, Schnell R, Phillips W, Bustamante CD, Motamayor JC. Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into the domestication process. Communications Biology 1. Article number: 167(2018)
• Xia, C., Wang, M., Yin , C., Cornejo, O.E., Hulbert, S.H., Chen. X. (2018) Genomic insights into host adaptationbetween the wheat stripe rust pathogen(Puccinia striiformisf. sp.tritici) andthe barley stripe rust pathogen(Puccinia striiformisf. sp.hordei) BMC Genomics 19(1):664.
• Xia C, Wang M, Yin C, Cornejo O.E., Hulbert S, Chen X. (2018) 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). Mol Plant Microbe Interact. doi: 10.1094/MPMI-04-18-0107-A.
• McCoy, R.C., Newnham, L.J., Ottolini, C., Hoffmann, E., Chatzimeletiou, K., Cornejo, O.E., Petrov, D.A., Demko, Z.P., Sigurjonsson, S., Handyside, A.H. (2018). Tripolar mitosis drives the association between maternal genotypes of PLK4 and aneuploidy in human preimplantation embryos. Human Molecular Genetics doi:https://doi.org/10.1093/hmg/ddy147
• Xia, C., Wang, M., Cornejo, O.E., Jiwan, D.A., See, D.R., Chen, X. (2017). Secretome characterization and correlation analysis reveal putative pathogenicity mechanisms in the wheat stripe rust fungus Puccinia striiformis f. sp. tritici. Frontiers in Microbiology 2017;00-12. doi: 10.3389/fmicb.2017.02394.
• Livingstone III, D., Stack, C., Mustiga, G., Rodezno, D., Suarez, C., Amores, F., Feltus, A., Mockaitis, K., Cornejo, O.E., Motamayor, JC. (2017). A large chocolate chip – development of a 15K Theobroma cacao L. SNP array to create high-density linkage maps. Frontiers in Plant Science 8:2008. doi.org/10.3389/fpls.2017.02008
• Miller EL, Evans BA, Cornejo OE, Roberts IS, Rozen DE. (2017). Pherotype polymorphism in Streptococcus pneumoniae has no obvious effects on population structure and recombination. Genome Biology and Evolution 9(10): 2546–2559. doi.org/10.1093/gbe/evx188
• Nelson, J.T., Wilson, R.E., McCracken, K.G., Cumming, G.S., Joseph, L., Guay, P-J., Peters, J.L. (2017). Divergence and gene flow in the globally distributed blue‐winged ducks.  Journal of Avian Biology 48(5): 640-649 (independent paper of my student Joel Nelson from his masters work)
• Cornejo OE*, Hickey RJ, Suzuki H, Forney LJ*. (2017). Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes. Evolutionary Applications 2017;00:1–13. https://doi.org/10.1111/eva.12555 (*co-corresponding authors)
• McManus KF, Tavarella A, Henn B, Bustamante CD, Sikora M*, Cornejo OE*. (2017) Population genetic analysis of the DARC locus (Duffy) reveals complex evolutionary history of a malaria resistance locus. PLOS Genetics 13(3): e1006560. doi:10.1371/journal.pgen.1006560. (Highlighted in Science, Mar 2017: Dramatic evolution within human genome may have been caused by malaria parasite)
• Chaurio RA, Pacheco MA, Cornejo OE, Stanley CE, Castillo AI, Herrera S, Escalante AA. (2016) Evolution of the transmission-blocking vaccine candidates Pvs28 and Pvs25 in Plasmodium vivax: differentiation of the parasite populations from The Americas. PLoS Neglected Tropical Diseases. 10(6): e0004786. doi:10.1371/journal.pntd.0004786
• Jaimes YY, Gonzalez C, Rojas J, Cornejo OE, Mideros MF, Restrepo S, Cilas C, Furtado EL. (2016) Geographic differentiation and genetic structure of Moniliophthora roreri in the principal Cocoa production areas in Colombia. Plant Disease. http://dx.doi.org/10.1094/PDIS-12-15-1498-RE
• Cook TF, Yee M-C, Muzzio M, Adams A, Bell R, Cornejo OE, Kelley JL, Bailliet G, Bravi CM, Bustamante CD, Kenny EE. (2016) GBStools: A unified approach for reduced representation sequencing and genotyping. PLoS Genetics. 12(2): e1005631. doi:10.1371/journal.pgen.1005631
• 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, Damgaard Pde B, 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 CP, 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. (2015) Genomic evidence for the Pleistocene and recent population history of Native Americans. Science. Vol. 349 no. 6250 DOI: 10.1126/science.aab3884
• Cornejo OE, Fisher D, Escalante AA. (2015) Genome-wide patterns of genetic polymorphism and signatures of selection in Plasmodium vivax. Genome Biology and Evolution. 7(1): 106-119. (Highlighted in Nature Reviews Microbiology in the News and Analysis – Genome Watchsection, March 2015)
• 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. (2014) The genetic prehistory of the New World Arctic. Science. 345 (6200) DOI: 10.1126/science.1255832
• 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. (2014) The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 506 (7487): 225 – 229 doi:10.1038/nature13025
• Pepperell CS, Casto AM, Kitchen A, Granka JM, Cornejo OE, Holmes EC, Birren B, Galagan J, Feldman MW (2013) The role of selection in shaping diversity of natural M. tuberculosis populations. PLoS Pathogens. 9(8): e1003543. doi: 10.1371/journal.ppat.1003543
• Utro F, Haiminen N, Livingstone D, Cornejo OE, Royaert S, Schnell RJ, Motamayor JC, Kuhn DN, Parida L. (2013) iXora: Exact Haplotype inferencing and trait association. BMC Genetics. 14: 48 (doi: 10.1186/1471-2156-14-48)
• Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, Livingstone D, Cornejo OE, Findley S, Zheng P, Utro F, Royaert S, Saski C, Jenkins J, Podicheti R, Zhao M, Scheffer B, Feltus A, Gutierrez O, Amores F, Phillips W, Marelli JP, May GD, Bretting P, Shapiro H, Ma J, Bustamante CD, Schnell RJ, Main D, Gilbert D, Parida L, Kuhn DN. (2013) The genome sequence of the most cultivated cacao type and its use in the mapping of oligogenic traits: pod color as an example. Genome Biology. 14:R53 (doi:10.1186/gb-2013-14-6-r53)
• 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. (2013) Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Molecular Biology and Evolution. 30(4): 881-893. [Highlighted in Science: “How Sweet it is: genes show how bacteria colonized human teeth” by Ann Gibbons]
• Utro F, Cornejo OE, Livingstone D, Motamayor JC, Parida L. (2012) ARG-Based genome-wide analysis of cacao cultivars. BMC Bioinformatics. 13 (Supp19): S17.
• Pacheco MA, Battistuzzi FU, Junge RE, Cornejo OE, Williams CV, Landau I, Rabetafika L, Snounou G, Jones-Engel L, Escalante AA. (2011) Timing the origin of human malarial: the lemur puzzle. BMC Evolutionary Biology. doi: 10.1186/1471-2148-11-299.
• 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. (2011) Phased whole genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genetics. 7(9): e1002280. doi:10.1371/journal.pgen.1002280
• Cornejo OE, McGee L, Rozen DE. (2010) Polymorphism in the competence peptide does not limit recombination in Streptococcus pneumoniae. Molecular Biology and Evolution. 27: 694-702.
• 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. On the diversity of malaria parasites in African Apes and the origin of Plasmodium falciparum from Bonobos. PLoS Pathogens 6(2): e1000765. doi:10.1371/journal.ppat.1000765.
• Levin BR, Cornejo OE. (2009) The Population and Evolutionary Dynamics of Homologous Gene Recombination in Bacteria. PLoS Genetics 5(8): e1000601. doi:10.1371/journal.pgen.1000601.
• Leung SW, Apponi LH, Cornejo OE, Kitchen CM, Valentini SR, Pavlath GK, Dunham CM, Corbett AH. (2009) Splice Variants of the Human ZC3H14 Gene Generate Multiple Isoforms of a Zinc Finger Polyadenosine RNA Binding Protein. Gene. 439(1-2):71-78.
• Cornejo OE, Rozen DE, May RM, Levin BR. (2009) Oscillations in Continuous Culture Populations of Streptococcus pneumoniae: Population Dynamics and the Evolution of Clonal Suicide. Proceedings of the Royal Society B. 276(1659):999-1008.
• Cornejo OE, Escalante AA. (2006) The origin and age of Plasmodium vivax. Trends in Parasitology. 22(12): 558-563.
• Escalante AA, Cornejo OE, Freeland DE, Poe AC, Durrego E, Collins WE, Lal AA. (2005) A monkey’s tale: The origin of Plasmodium vivax as a human malaria parasite. Proceedings of the National Academy of Sciences (USA) 102(6).
• Escalante AA, Cornejo OE, Rojas A, Udhayakumar V, Lal AA. (2004) Assessing the effect of natural selection in malaria parasites. Trends in Parasitology. 20(8): 388-395.
• Sebastiani M, Aponte C, Andara C, Cornejo OE, Esclasans D, Marquez E, Moscarella R, Ponte A, Vizcaino D. (2000) El enfoque de las evaluaciones de impacto ambiental en el ordenamiento territorial. Caso: Reserva Forestal Imataca, Venezuela (Impact assessment approach in land use ordering. Case study: Imataca Forstal Reserve in Venezuela). Revista Geografica Venezolana, 41(2): 187-213.

• McManus, KF. (2015) popRange: a highly flexible spatially and temporally explicit Wright-Fisher simulator. Source Code for Biology and Medicine 10:6 DOI: 10.1186/s13029-015-0036-4