Complete List of Published Work in MyBibliography: http://www.ncbi.nlm.nih.gov/sites/myncbi/amanda.larracuente.1/bibliography/40318594/public/?sort=date&direction=descending
ORCID: https://orcid.org/0000-0001-5944-5686
2024
Courret, C., Hemmer, L. , Wei,X. , Patel, P.D., Santinello, B., Geng,X., Chang, C-H, Mellone, B., Larracuente, A.M. 2023. Turnover of retroelements and satellite DNA drives centromere reorganization over short evolutionary timescales in Drosophila
BIORXIV.https://www.biorxiv.org/content/10.1101/2023.08.22.554357v1. In press. PLOS Biology
Santinello B, Sun R, Amjad A, Hoyt SJ, Ouyang L, Courret C, Drennan R, Leo L, Larracuente AM, Core L, O’Neill RJ, Mellone BG. Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape. BioRxiv. 2024 May. https://doi.org/10.1186/s13059-024-03433-1 Genome Biology. 25, 295.
2023
Courret, C.& and A.M. Larracuente. 2023. High levels of intra-strain structural variation in Drosophila simulans X pericentric heterochromatin. GENETICS. iyad176. https://doi.org/10.1093/genetics/iyad176.
Arkhipova, I.R, Burns, K.H., Chiappinelli, K. B., Chuong, E.B., Goubert, C., Guarné, A., Larracuente, A.M., and H.L. Levin. Meeting Report: Transposable Elements at the Crossroads of Evolution, Health and Disease 2023. Mobile DNA. Accepted. In press.
Courret, C., Wei, X., and Larracuente, A.M. 2023. New perspectives on the causes and consequences of male meiotic drive. Curr Opinion Gen & Dev. https://doi.org/10.1016/j.gde.2023.102111.
Martí, E. and A.M. Larracuente. 2023. Genetic conflict and the origin of multigene families: implications for sex chromosome evolution. Proc R. Soc. B. https://doi.org/10.1098/rspb.2023.1823.
Courret, C, Ogereau, G, Larracuente,A.M., and C. Montchamp-Moreau. 2023. The evolutionary history of Drosophila simulans Y chromosomes reveals molecular signatures of resistance to sex ratio meiotic drive. BioRxiv. https://doi.org/10.1101/2022.12.22.521550. Molecular Biology and Evolution 40(7):msad152. https://doi.org/10.1093/molbev/msad152
Sproul, J.S.S., Hotaling,S., Heckenhauer,J., Powell,A., Larracuente,A.M., Kelley,J.L., Pauls, S.U., Frandsen, P.B. 2023. Repetitive elements in the era of biodiversity genomics: insights from 600+ insect genomes. BioRxiv 2022.06.02.494618; Genome Research. https://doi.org/10.1101/gr.277387.122
2022
Lucas W Hemmer, Sherif Negm, Xuewen Geng, Cécile Courret, Beatriz Navarro-Domínguez, Iain Speece, Xiaolu Wei, Eddyson Altidor, James Chaffer, John S. Sproul, Amanda M Larracuente. 2022. Centromere-associated retroelement evolution in Drosophila melanogaster reveals an underlying conflict. BioRxiv https://doi.org/10.1101/2022.11.25.518008.
Hanlon, S.L., Larracuente, A.M. When it comes to genetics, cheaters do prosper. Chromosome Res (2022). https://doi.org/10.1007/s10577-022-09705-5
Navarro-Domínguez, B., Chang, C-H, Brand, C, Muirhead, C., Presgraves, D.C., and A.M. Larracuente. 2022 Epistatic selection on a selfish Segregation Distorter supergene: drive, recombination, and genetic load. BioRxiv 12/23/21 doi:10.1101/2021.12.22.473781. eLife 2022;11:e78981 DOI: 10.7554/eLife.78981
Chen, T., Wei, X., Courret, C., Cui, M., Cheng, L., Wu, J., Ahmad, K., Larracuente, A.M., Rong, Y. 2022. The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila. BIORXIV 4/22/22. PLoS Genet 18(9): e1010351. https://doi.org/10.1371/journal.pgen.1010351
Chang, C-H., Gregory, L.E., Gordon, K.E., Meiklejohn, C.D., Larracuente, A.M. 2022. Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes. eLife 2022;11:e75795 DOI: 10.7554/eLife.75795
2021
Wei,X., Eickbush,D.G., Speece,I., A.M. Larracuente. 2021. Heterochromatin-dependent transcription of satellite DNAs in the Drosophila melanogaster female germline. eLife 2021;10:e62375. doi: 10.7554/eLife.62375
Herbette M, X Wei, C-H Chang, A.M. Larracuente, B Loppin, R Dubruille. 2021. Distinct spermiogenic phenotypes underlie sperm elimination in the Segregation Distorter meiotic drive system. PLoS Genet 17(7): e1009662. https://doi.org/10.1371/journal.pgen.1009662
Heckenhauer, J., Frandsen, P.B., Sproul, J.S.&, Li, Z., Paule, J. Larracuente,A.M. ,Maughan, P.J., Barker, M.S.,Schneider, J.V., Pauls, S.V. 2021. Genome size evolution in the diverse insect order Trichoptera. BioRxiv 5/10/21. https://doi.org/10.1101/2021.05.10.443368.
Hotaling S, Sproul J.S.&, Heckenhauer J., Powell A., Larracuente A.M., Pauls S.U., Kelley J.L., and P.B. Frandsen. 2021. Long-reads are revolutionizing 20 years of insect genome sequencing. BioRxiv 2/15/21. https://doi.org/10.1101/2021.02.14.431146. Accepted, Genome Biology and Evolution.
Chakraborty, C-H Chang, D. E. Khost, J. Vedanayagam, J.R. Adrion, Y. Liao, K. Montooth, C.D. Meiklejohn, A.M. Larracuente, J.J. Emerson. 2021. Evolution of genome structure in the Drosophila simulans species complex. Genome Research. 31: 380-396. doi: 10.1101/gr.263442.120 
2020
Sherif Negm, Anya D. Greenberg, Amanda M. Larracuente, John S. Sproul. 2020. RepeatProfiler: a pipeline for visualization and comparative analysis of repetitive DNA profiles. Molecular Ecology Resources, 2020;00:1–13. https://doi.org/10.1111/1755-0998.13305.
Price, T.A.R., Windbichler, N., Unckless, R.L., Sutter, A., Runge, J-N, Ross P.A., Pomiankowski, A., Nuckolls,N., Montchamp-Moreau, C., Mideo, N., Martin, O.Y., Manser, A., Larracuente, A.M., Holman, L., Godwin, J., Gemmell, N., Courret, C.&,Buchman, A, Lindholm, A.K. 2020. Resistance to Natural and Synthetic Gene Drive Systems. Journal of Evolutionary Biology. 33(10): 1345-1360. https://doi.org/10.1111/jeb.13693.
Sproul, J., Khost, D.E.*, Eickbush, D.G., Negm, S., Wei, X., Wong, I., and A.M. Larracuente 2020. Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade. BIORXIV/2019/846238, Molecular Biology and Evolution. 37(8)2241-2256, https://doi.org/10.1093/molbev/msaa078
2019
Courret, C. , Chang, C-H., Wei, K., Montchamp-Moreau, C., Larracuente, A.M. 2019.Meiotic drive mechanisms: lessons from Drosophila. In press. Proceedings of the Royal Society B.
Chang, C-H, Chavan, A, Palladino, J., Wei, X., Martins, N.M.C., Santinello, B., Chen, C-C, Erceg, J., Beliveau, B.J., Wu, C-T, Larracuente, A.M., and Mellone, B.G. 2019. Islands of retroelements are major components of Drosophila melanogaster centromeres. BioRxiv Epub 2/1/2019. PLoS Biology https://doi.org/10.1371/journal.pbio.3000241.
Chang, C-H. and A.M. Larracuente. 2019. Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome. GENETICS 211: 333-348. doi: 10.1534/genetics.118.301765. BioRxiv 07/25/2018.
-featured in GENETICS highlights 1/1/2019 http://www.genetics.org/content/211/1/NP
2018
Fallon, T.R., Lower, S.E., Chang, C-H, Bessho-Uehara, M., Martin, G.J., Bewick, A.J., Behringer, M., Debat, H.J., Wong, I., Day, J.C. , Suvorov, A., Silva, C.J., Hall, D.W., Schmitz, R.J., Nelson, D.R., Lewis, S., Shigenobu,S., Bybee, S.M., Larracuente, A.M., Oba, Y., Weng, J-K. 2017. Firefly genomes illuminate the origin and evolution of bioluminescence. BioRxiv 12/21/17. Elife Oct 16;7. pii: e36495. doi: 10.7554/eLife.36495.
2017
Khost, D.E., D. Eickbush, A.M. Larracuente. 2017. Single molecule long read sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster. Genome Research . Advanced Access. 4/3/17. http://www.genome.org/cgi/doi/10.1101/gr.213512.116.
Chang, C-H. and A.M. Larracuente. 2017. Structural changes following the reversal of a Y chromosome to an autosome in Drosophila pseudoobscura. Evolution. 71-5:1285-1296. http://dx.doi.org/10.1111/evo.13229.
2016
Larracuente, A.M. 2016. FISH in Drosophila in Fluorescence in situ Hybridization (FISH) – Application Guide, T Liehr (Editor), 2nd Ed., Springer, Berlin, 2017, ISBN: 978-3662529577.
Larracuente, A.M. and V.H. Meller. 2016. Host–Symbiont Interactions: Male- Killers Exposed. Current Biology 26, R408–R431, May 23, 2016. http://dx.doi.org/10.1016/j.cub.2016.03.057
Lindholm, A. K., Dyer, K. A., Firman, R. C., Fishman, L., Forstmeier, W., Holman, L., Johannesson, H., Knief, U., Kokko, H., Larracuente, A. M., Manser, A., Montchamp-Moreau, C., Petrosyan, V. G., Pomiankowski, A., Presgraves, D. C., Safronova, L. D., Sutter, A., Unckless, R. L., Verspoor, R. L., Wedell, N., Wilkinson, G. S. & Price, T. A. R. 2016. The ecology and evolutionary dynamics of meiotic drive. Trends in Ecology & Evolution. http://dx.doi.org/10.1016/j.tree.2016.02.001
2015
Hales, K.G., C.A. Korey, A.M. Larracuente and D.M. Roberts. 2015. Genetics on the fly: a primer on the Drosophila model system. GENETICS. 201(3):815-842. doi: 10.1534/genetics.115.183392
Brand, C.B., A.M. Larracuente and D.C. Presgraves. 2015. Origin, evolution, and population genetics of the selfish Segregation distorter gene duplication in European and African populations of Drosophila melanogaster. Evolution. 69-5: 1271–1283. DOI: 10.1111/evo.12658. *
Unckless, R., A.M. Larracuente, and A.G. Clark. 2015. Sex-ratio meiotic drive and Y-linked resistance in Drosophila affinis. Genetics. Online 1/8/2015.10.1534/genetics.114.173948
Larracuente, A.M. and P.M. Ferree. 2015. Simple method for fluorescence DNA in situ hybridization to squashed chromosomes. J. Vis. Exp. 95, e52288. doi:10.3791/52288.
2014
Larracuente, A.M. 2014. The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive. BMC Evol. Biol.14:233. doi:10.1186/s12862-014-0233-9
Larracuente, A.M. and A.G. Clark. 2014. Recent selection on the Y-to-dot translocation in Drosophila pseudoobscura. Mol. Biol. Evol. 31(4):846-856. doi 10.1093/molbev/msu002.
2005-2013
Larracuente, A.M. and A.G. Clark. 2013. Surprising differences in the variability of Y chromosomes in African and Cosmopolitan populations of Drosophila melanogaster. Genetics. 193:201-214.
Larracuente, A.M. and D.C. Presgraves. 2012. The selfish Segregation Distorter gene complex of Drosophila melanogaster. Genetics. 192: 1-21.
Larracuente, A.M., M.A.F. Noor, A.G. Clark. 2010. Translocation of Y-linked genes to the dot chromosome in Drosophila pseudoobscura. Mol. Biol. Evol. 27(7): 1612-1620.
Singh, N.D., A.M. Larracuente, T.B. Sackton, A.G. Clark. 2009. Comparative genomics on the Drosophila Phylogenetic Tree. Annu. Rev. Ecol. Evol. Syst. 40:459–80.
Larracuente, A.M., T.B. Sackton*, A.J. Greenberg, A. Wong, N.D. Singh, D. Sturgill, Y. Zhang, B. Oliver, A.G. Clark. 2008. Evolution of protein-coding genes in Drosophila. Trends Genet. 24(3): 114-123.
Singh N.D., A.M. Larracuente*, A.G. Clark. 2008. Contrasting the efficacy of selection on the X and autosomes in Drosophila. Mol. Biol. Evol. 25(2):454-467.
Drosophila 12 Genomes Consortium: A.G. Clark, M.B. Eisen, D.R. Smith, C.M. Bergman, B. Oliver, T.A. Markow, T.C. Kaufman, M. Kellis, W. Gelbart, V.N. Iyer, D.A. Pollard, T.B. Sackton, A.M. Larracuente et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450(7167): 203-218.
Morris, S.R., A.M. Larracuente, K.M. Covino, M.S. Mustillo, K.E. Mattern, D.A. Liebner, H.D. Sheets. 2006. Limitations posed by parameter estimability in open population models: a case study using migratory stopover. Wilson Journal of Ornithology. 118(4): 513-526.
Morris, S.R., H.D. Sheets, E.M. Turner, D.A. Liebner, A.M. Larracuente. 2005. Problems associated with pooling mark-recapture data prior to estimating stopover length for migratory passerines. Pages 670-673 in Bird Conservation Implementation and Integration in the Americas: Proceedings of the Third International Partners in Flight Conference 2002 (C.J. Ralph and T.D. Rich, eds.). U.S.D.A. Forest Service Technical report, GTR-PSW-191, Albany, CA.
Morris, S.R., D.A. Liebner, A.M. Larracuente, E.M.Turner, H.D. Sheets. 2005. Multiple day constancy as an alternative to pooling for mark-recapture stopover estimates for nearctic-neotropical migrant landbirds. The Auk 122 (1):319-328.* indicates co-first author
Drosophila image in header taken by Mr.Checker.