Publications

Featured publications


  • Gutaker, R.M., Weiss, C.L., Ellis, D., Anglin, N.L., Knapp, S., Fernández-Alonso J.L., Prat, S., Burbano, H.A. 2019. The origins and adaptation of European potatoes reconstructed from historical genomes. Nat Ecol Evol 3:1093-1101 (doi: 10.1038/s41559-019-0921-3).

  • Exposito-Alonso M., Becker C., Schuenemann V.J., Reiter E., Setzer C., Slovak R., Brachi B., Hagmann J., Grimm D., Jiahui C., Busch, W., Bergelson, J., Ness, R.W., Krause, J., Burbano, H.A.*, Weigel, D.* 2018. The rate and potential relevance of new mutations in a colonizing plant lineage. PLoS Genetics. 14(2):e1007155. (doi: 10.137/journal.pgen.1007155) (*Contributed equally as supervisors).

  • Swarts K., Gutaker R. M., Benz B., Blake M., Bukowski R., Holland J., Kruse-Peeples M., Lepak M., Prim L., Romay M.C., Ross-Ibarra J., Sanchez-Gonzales J.J., Schmidt C., Schuenemann V.J., Krause J., Matson R.G., Weigel D., Buckler E.S., Burbano, H.A. 2017. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 357(6350):512-515 (doi:10.1126/science.aam9425).

  • Yoshida K., Schuenemann V.J., Cano L.M., Pais M., Mishra B., Sharma R., Lanz C., Martin F.N., Kamoun S., Krause J., Thines M., Weigel D., Burbano H.A. 2013. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. eLife 2, e00731. (doi:10.7554/eLife.00731).

  • Burbano H.A., Hodges E., Green R.E., Briggs A.W., Krause J., Meyer M., Good J.M., Maricic T., Johnson P.L., Xuan Z., [others], Pääbo S. 2010. Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328, 723-725. (doi:10.1126/science.1188046).


Preprints


  • Latorre, S.M, Burbano, H.A. 2021. The emergence of wheat blast in Zambia and Bangladesh was caused by the same genetic lineage of Magnaporthe oryzae. Zenodo (doi:10.5281/zenodo.4619405).

  • Shirsekar, G., Devos, J., Latorre, S.M., Blaha, A., Queiros Dias, M., González-Hernando, A., Lundberg, D.S, Burbano, H.A., Fenster, C.B., Weigel D. 2021. Fine-scale Population Structure of North American Arabidopsis thaliana Reveals Multiple Sources of Introduction from Across Eurasia. bioRxiv (doi:10.1101/2021.01.22.427575).

  • Win, J., Harant, A., Malmgrem, A., Langner, T., Shrestha, R-M., Latorre, S.M., Were, V., Talbot, N.J., Burbano, H.A., Picco, A.M., Kamoun, S. 2020. Large scale genome assemblies of Magnaporthe oryzae rice isolates from Italy. Zenodo (doi:10.5281/zenodo.4326823).

  • Latorre, S.M., Hermann, M., Paulsen, M.J., Roedelsperger, C., Dréau, A., Roeseler, W., Sommer, R.J., Burbano, H.A. 2020. Museum phylogenomics of extinct Oryctes beetles from the Mascarene Islands. bioRxiv (doi:10.1101/2020.02.19.954339).


2021

  • Lagner, T., Harant, A., Gomez-Luciano, L.B., Shresta, R.K., Malmgren, A., Latorre, S.M., Burbano, H.A., Win, J., Kamoun S. 2021. Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus. PLoS Genet 17(2): e1009386 (doi:10.1371/journal.pgen.1009386 ).

2020

  • Latorre, S.M., Lang, P.L.M., Burbano, H.A., Gutaker, R.M. 2020. Isolation, Library Preparation and Bioinformatic Analysis of Historical and Ancient Plant DNA. Curr. Protoc. Plant Biol. 5(4):e20121 (doi: 10.1002/cppb.20121).

  • Latorre, S.M., Reyes-Avila, C.S., Malmgren, A., Win, J., Kamoun, S. , Burbano, H.A. 2020. Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus BMC Biology 18 (88) (doi:10.1186/s12915-020-00818-z).

  • Weiss, C.L., Gansauge M-T., Aximu-Petri, A., Meyer, M., Burbano, H.A. 2020. Mining ancient microbiomes using selective enrichment of damaged DNA molecules. BMC Genomics 21 (432) (doi:10.1186/s12864-020-06820-7 ).

  • Lang, P.L.M., Weiss, C.L., Kersten, S., Latorre, S.M., Nagel, S., Nickel, B., Meyer, M., Burbano, H.A. 2020. Hybridization ddRAD-sequencing for population genomics of non-model plants using highly degraded historical specimen DNA. 2020. Molecular Ecology Resources 20:1228-1247 (doi:10.1111/1755-0998.13168.).

  • Exposito-Alonso, M., Drost, H-G., Burbano, H.A., Weigel, D. 2020. The Earth BioGenome Project: Opportunities and Challenges for Plant Genomics and Conservation. Plant J. 102(2):222-229 (doi: 10.1111/tpj.14631).

2019

  • Exposito-Alonso, M., 500 Genomes Field Experiment Team, Burbano, H.A., Bossdorf, O. , Nielsen, R., Weigel, D. 2019. Natural Selection on the Arabidopsis thaliana genome in present and future climates. Nature 573(7772):126-129 (doi:10.1038/s41586-019-1520-9).

  • Gutaker, R.M., Weiss, C.L., Ellis, D., Anglin, N.L., Knapp, S., Fernández-Alonso J.L., Prat, S., Burbano, H.A. 2019. The origins and adaptation of European potatoes reconstructed from historical genomes. Nat Ecol Evol 3:1093-1101 (doi: 10.1038/s41559-019-0921-3).

  • Lang, P.L.M., Willems, F.M., Scheepens, J.F., Burbano, H.A.*, Bossdorf, O.* 2019. Using herbaria to study global environmental change. New Phytologist 221(1):110/122 (doi:10.1111/nph.15401). (*Contributed equally as supervisors).

2018

  • Weiss C.L., Pais M., Cano L.M., Kamoun S. Burbano H.A. 2018. nQuire: A statistical framework for ploidy estimation using next generation sequencing. BMC Bioinformatics. 19:122 (doi:10.1186/s12859-018-2128-z).

  • Exposito-Alonso M., Becker C., Schuenemann V.J., Reiter E., Setzer C., Slovak R., Brachi B., Hagmann J., Grimm D., Jiahui C., Busch, W., Bergelson, J., Ness, R.W., Krause, J., Burbano, H.A.*, Weigel, D.* 2018. The rate and potential relevance of new mutations in a colonizing plant lineage. PLoS Genetics. 14(2):e1007155. (doi: 10.137/journal.pgen.1007155) (*Contributed equally as supervisors).

  • Exposito-Alonso, M., Vasseur, F., Ding, W., Wang, G., Burbano, H.A., Weigel, D. 2018. Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana. Nat Ecol Evol. 2:352-358 (doi: 10.1038/s41559-017-0423-0).

2017

  • Swarts K., Gutaker R. M., Benz B., Blake M., Bukowski R., Holland J., Kruse-Peeples M., Lepak M., Prim L., Romay M.C., Ross-Ibarra J., Sanchez-Gonzales J.J., Schmidt C., Schuenemann V.J., Krause J., Matson R.G., Weigel D., Buckler E.S., Burbano, H.A. 2017. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 357(6350):512-515 (doi:10.1126/science.aam9425).

  • Durvasula A., Fulgione A., Gutaker R.M., Alacakaptan S.I., Flood P.J., Neto C., Tsuchimatsu T., Burbano H.A., Pico F.X., Alonso-Blanco C., et al. 2017. African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. PNAS 114(20):5213-5218 (doi:10.1073/pnas.1616736114).

  • Slon, V., Hopfe, C., Weiss, C.L., [25 others], Burbano, H.A., Päabo, S., Meyer. M. 2017 Neandertal and Denisovan DNA from pleistocene sediments. Science 356(6338):605-608 (doi:10.1126/science.aam9695).

  • Warinner C., Herbig, A., Mann, A., Fellow-Yates, J.A., Weiss, C.L., Burbano, H.A., Orlando, L., Krause, J. 2017. A robust framework for microbial archaeology. Annu Rev Genomics Hum Genet 18:321-356 (doi:10.1146/annurev-genom-091416-035526).

  • Gutaker R.M., Burbano H.A. 2017. Reinforcing plant evolutionary genomics using ancient DNA. Curr Opin Plant Biol 36, 38-45. (doi:10.1016/j.pbi.2017.01.002).

  • Gutaker R.M., Reiter E., Furtwangler A., Schuenemann V.J., Burbano H.A. 2017. Extraction of ultrashort DNA molecules from herbarium specimens. Biotechniques 62, 76-79. (doi:10.2144/000114517).

2016

  • Weiss C.L., Schuenemann V.J., Devos J., Shirsekar G., Reiter E., Gould B.A., Stinchcombe J.R., Krause J., Burbano H.A. 2016. Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens. R Soc Open Sci 3, 160239. (doi:10.1098/rsos.160239).

  • Kuhlwilm M., Gronau I., Hubisz M.J., de Filippo C., Prado-Martinez J., Kircher M., Fu Q., Burbano H.A., Lalueza-Fox C., de la Rasilla M., et al. 2016. Ancient gene flow from early modern humans into Eastern Neanderthals. Nature. (doi:10.1038/nature16544).

2015

  • Weiss C.L., Dannemann M., Prufer K., Burbano H.A. 2015. Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data. eLife 4. (doi:10.7554/eLife.10005).

  • Smith L.M., Burbano H.A., Wang X., Fitz J., Wang G., Ural-Blimke Y., Weigel D. 2015. Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae. The Plant Journal 81, 597-610. (doi:10.1111/tpj.12754).

2014

  • Carneiro M., Rubin C.J., Di Palma F., Albert F.W., Alfoldi J., Barrio A.M., Pielberg G., Rafati N., Sayyab S., Turner-Maier J., [7 others], Burbano, H.A., et al. 2014. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 345, 1074-1079. (doi:10.1126/science.1253714).

  • Carneiro M., Albert F.W., Afonso S., Pereira R.J., Burbano H.A., Campos R., Melo-Ferreira J., Blanco-Aguiar J.A., Villafuerte R., Nachman M.W., et al. 2014. The genomic architecture of population divergence between subspecies of the European rabbit. PLoS Genetics 10 e1003519. (doi:10.1371/journal.pgen.1003519).

  • Castellano S., Parra G., Sanchez-Quinto F.A., Racimo F., Kuhlwilm M., Kircher M., Sawyer S., Fu Q., Heinze A., Nickel B., Dabney J., Siebauer M., White L., Burbano, H.A., et al. 2014. Patterns of coding variation in the complete exomes of three Neandertals. PNAS 111, 6666-6671. (doi:10.1073/pnas.1405138111).

  • Yoshida K., Burbano H.A. *, Krause J., Thines M., Weigel D.*, Kamoun S.* 2014. Mining herbaria for plant pathogen genomes: back to the future. PLoS Pathogens 10, e1004028. (doi:10.1371/journal.ppat.1004028). (*Contributed equally).

2013

  • Yoshida K., Schuenemann V.J., Cano L.M., Pais M., Mishra B., Sharma R., Lanz C., Martin F.N., Kamoun S., Krause J., Thines M., Weigel D., Burbano H.A. 2013. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. eLife 2, e00731. (doi:10.7554/eLife.00731).

  • Good J.M., Wiebe V., Albert F.W., Burbano H.A., Kircher M., Green R.E., Halbwax M., Andre C., Atencia R., Fischer A., et al. 2013. Comparative population genomics of the ejaculate in humans and the great apes. Mol Biol Evol, 964-976. (doi:10.1093/molbev/mst005

  • Maricic T., Gunther V., Georgiev O., Gehre S., Curlin M., Schreiweis C., Naumann R., Burbano H.A., Meyer M., Lalueza-Fox C., et al. 2013. A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Mol Biol Evol 30, 844-852. (doi:10.1093/molbev/mss271).

  • Fu Q., Meyer M., Gao X., Stenzel U., Burbano H.A., Kelso J., Päabo S. 2013. DNA analysis of an early modern human from Tianyuan Cave, China. PNAS 110(6), 2223-2227. (doi:10.1073/pnas.1221359110).

  • Manavella P.A., Koenig D., Rubio-Somoza I., Burbano H.A., Becker C., Weigel D. 2013. Tissue-specific silencing of Arabidopsis SU(VAR)3-9 HOMOLOG8 by miR171a. Plant Physiol 161, 805-812. (doi:10.1104/pp.112.207068).

2012

  • Dannemann M., Prufer K., Lizano E., Nickel B., Burbano H.A. *, Kelso J.* 2012. Transcription factors are targeted by differentially expressed miRNAs in primates. Genome Bio Evol 4, 552-564. (doi:10.1093/gbe/evs033). (*Contributed equally as supervisors).

  • Dannemann M., Nickel B., Lizano E., Burbano H.A. *, Kelso J.* 2012. Annotation of primate miRNAs by high throughput sequencing of small RNA libraries. BMC Genomics 13, 116. (doi:10.1186/1471-2164-13-116). (*Contributed equally as supervisors).

  • Burbano H.A., Green R.E., Maricic T., Lalueza-Fox C., de la Rasilla M., Rosas A., Kelso J., Pollard K.S., Lachmann M., Päabo S. 2012. Analysis of human accelerated DNA regions using archaic hominin genomes. PLoS One 7, e32877. (doi:10.1371/journal.pone.0032877).

2011

  • Bos K.I., Schuenemann V.J., Golding G.B., Burbano H.A., Waglechner N., Coombes B.K., McPhee J.B., DeWitte S.N., Meyer M., Schmedes S., et al. 2011. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506-510. (doi:10.1038/nature10549).

  • Albert F.W., Hodges E., Jensen J.D., Besnier F., Xuan Z., Rooks M., Bhattacharjee A., Brizuela L., Good J.M., Green R.E., Burbano H.A., et al. 2011. Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity 107, 205-214. (doi:10.1038/hdy.2011.4).

2010

  • Burbano H.A., Hodges E., Green R.E., Briggs A.W., Krause J., Meyer M., Good J.M., Maricic T., Johnson P.L., Xuan Z., et al. 2010. Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328, 723-725. (doi:10.1126/science.1188046).

  • Green R.E., Krause J., Briggs A.W., Maricic T., Stenzel U., Kircher M., Patterson N., Li H., Zhai W., Fritz M.H., [8 others], Burbano H.A., [others], Pääbo S.. 2010. A draft sequence of the Neandertal genome. Science 328, 710-722. (doi:10.1126/science.1188021).

2009

  • Green R.E., Briggs A.W., Krause J., Prufer K., Burbano H.A., Siebauer M., Lachmann M., Päabo S. 2009. The Neandertal genome and ancient DNA authenticity. EMBO J 28, 2494-2502. (doi:10.1038/emboj.2009.222).

2008

  • Green R.E., Malaspinas A.S., Krause J., Briggs A.W., Johnson P.L., Uhler C., Meyer M., Good J.M., Maricic T., Stenzel U., Prüfer K., Siebauer M., Burbano H.A., [11 others], Slatkin M, Pääbo S. 2008. A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing. Cell 134, 416-26 (doi:10.1016/j.cell.2008.06.021).

2007

  • Krause J., Lalueza-Fox C., Orlando L., Enard W., Green R.E., Burbano H.A., Hublin J.J., Hanni C., Fortea J., de la Rasilla M., et al. 2007. The derived FOXP2 variant of modern humans was shared with Neandertals. Curr Biol 17, 1908-1912. (doi:10.1016/j.cub.2007.10.008).

  • Burbano H.A., Andrade E. 2007. Analysis of tRNA abstract shapes of precursor/derivative amino acids in Archaea. Gene 396, 75-83. (doi:10.1016/j.gene.2007.02.024).