Selected Publications

Evolutionary Genetic Engineering, Gene Drive, and Genetic Pest Management

• Bryk, J., Reeves, R. G., Reed, F. A., & Denton, J. A. (2017). Transcriptional effects of a positive feedback circuit in Drosophila melanogaster. BMC Genomics, 18(1), 990. https://doi.org/10.1186/s12864-017-4385-z
• Reed, F. A. (2017). Evolutionary Genetic Engineering in the Indo-Pacific: Conservation, Humanitarian, and Social Issues. arXiv preprint arXiv:1706.01710. https://arxiv.org/abs/1706.01710
• Reed, F. A. (2017). CRISPR/Cas9 gene drive: Growing pains for a new technology. Genetics, 205(3), 1037-1039. https://doi.org/10.1534/genetics.116.198887
• Láruson, Á. J., & Reed, F. A. (2016). Stability of underdominant genetic polymorphisms in population networks. Journal of Theoretical Biology, 390, 156-163. https://doi.org/10.1016/j.jtbi.2015.11.023
• Gokhale, C. S., Reeves, R. G., & Reed, F. A. (2014). Dynamics of a combined medea-underdominant population transformation system. BMC Evolutionary Biology, 14(1), 98. https://doi.org/10.1186/1471-2148-14-98
• Reeves, R. G., Bryk, J., Altrock, P. M., Denton, J. A., & Reed, F. A. (2014). First steps towards underdominant genetic transformation of insect populations. PLoS One, 9(5), e97557. https://doi.org/10.1371/journal.pone.0097557
• Reeves, R. G., Denton, J. A., Santucci, F., Bryk, J., & Reed, F. A. (2012). Scientific standards and the regulation of genetically modified insects. PLoS Neglected Tropical Diseases, 6(1), e1502. https://doi.org/10.1371/journal.pntd.0001502
• Altrock, P. M., Traulsen, A., & Reed, F. A. (2011). Stability properties of underdominance in finite subdivided populations. PLoS computational Biology, 7(11), e1002260. https://doi.org/10.1371/journal.pcbi.1002260
• Altrock, P. M., Traulsen, A., Reeves, R. G., & Reed, F. A. (2010). Using underdominance to bi-stably transform local populations. Journal of Theoretical Biology, 267(1), 62-75. https://doi.org/10.1016/j.jtbi.2010.08.004

Human Genetics

• Tishkoff, S. A., Reed, F. A., Friedlaender, F. R., Ehret, C., Ranciaro, A., Froment, A., ... & Ibrahim, M. (2009). The genetic structure and history of Africans and African Americans. Science, 324(5930), 1035-1044. https://doi.org/10.1126/science.1172257
• Friedlaender, J. S., Friedlaender, F. R., Reed, F. A., Kidd, K. K., Kidd, J. R., Chambers, G. K., ... & Merriwether, D. A. (2008). The genetic structure of Pacific Islanders. PLoS Genetics, 4(1), e19. https://doi.org/10.1371/journal.pgen.0040019
• Tishkoff, S. A., Gonder, M. K., Henn, B. M., Mortensen, H., Knight, A., Gignoux, C., ... & Reed, F. A. (2007). History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation. Molecular Biology and Evolution, 24(10), 2180-2195. https://doi.org/10.1093/molbev/msm155
• Tishkoff, S. A., Reed, F. A., Ranciaro, A., Voight, B. F., Babbitt, C. C., Silverman, J. S., ... & Ibrahim, M. (2007). Convergent adaptation of human lactase persistence in Africa and Europe. Nature Genetics, 39(1), 31. https://doi.org/10.1038/ng1946
• Reed, F. A., & Tishkoff, S. A. (2006). African human diversity, origins and migrations. Current Opinion in Genetics & Development, 16(6), 597-605. https://doi.org/10.1016/j.gde.2006.10.008
• Gonder, M. K., Mortensen, H. M., Reed, F. A., de Sousa, A., & Tishkoff, S. A. (2006). Whole-mtDNA genome sequence analysis of ancient African lineages. Molecular Biology and Evolution, 24(3), 757-768. https://doi.org/10.1093/molbev/msl209
• Reed, F. A., & Aquadro, C. F. (2006). Mutation, selection and the future of human evolution. TRENDS in Genetics, 22(9), 479-484. https://doi.org/10.1016/j.tig.2006.07.005
• Reed, F. A., Akey, J. M., & Aquadro, C. F. (2005). Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes. Genome Research, 15(9), 1211-1221. https://doi.org/10.1101/gr.3413205
• Reed, F. A., Kontanis, E. J., Kennedy, K. A., & Aquadro, C. F. (2003). Brief communication: ancient DNA prospects from Sri Lankan highland dry caves support an emerging global pattern. American Journal of Physical Anthropology, 121(2), 112-116. https://doi.org/10.1002/ajpa.10211
• Aquadro, C. F., DuMont, V. B., & Reed, F. A. (2001). Genome-wide variation in the human and fruitfly: a comparison. Current Opinion in Genetics & Development, 11(6), 627-634. https://doi.org/10.1016/S0959-437X(00)00245-8

Book

• Láruson, Á. J., and F. A. Reed. (book contract signed 2018). Population Genetics with R: A Practical Guide, ISBN 9780198829539, Oxford University Press.

Book Chapters

• Reed, F. A., Traulsen, A., & Altrock, P. M. (2013). Underdominance. In Brenner's Encyclopedia of Genetics (pp. 247-249). Elsevier. https://doi.org/10.1016/j.jtbi.2011.04.032
• Reed, F. A. (2012). Modern Human Migrations: The First 200,000 Years. In Migrations: Interdisciplinary Perspectives (pp. 315-326). Springer, Vienna. https://doi.org/10.1007/978-3-7091-0950-2_29
• Allaby, R. G., Friedlaender, F. R., Reed, F. A., Kidd, K. K., Kidd, J. R., Chambers, G. K., ... & Merriwether, D. A. (2010). Prehistoric Pacific Population Movements. In The Global Origins and Development of Seafaring, 143-157. ISBN: 978-1-902937-52-6, McDonald Institute for Archaeological Research.
• Reed, F. A. (2008). Are Humans Still Evolving?. eLS. https://doi.org/10.1002/9780470015902.a0020794

Patent Applications

• Reeves, G. and Reed, F., Max-Planck-Gesellschaft zur Forderung der Wissenschaften, (2015). Stable transformation of a population and a method of biocontainment using haploinsufficiency and underdominance principles. U.S. Patent Application 14/654,450. https://patents.google.com/patent/US20150373937A1
• Tishkoff, S.A. and Reed, F.A., University of Maryland, (2008). Single nucleotide polymorphisms and the identification of lactose intolerance. U.S. Patent Application 11/976,676. https://patents.google.com/patent/WO2008057265A2

Other Publications

• Evolutionary Game Theory and Dynamical Systems

  • Traulsen, A., & Reed, F. A. (2012). From genes to games: cooperation and cyclic dominance in meiotic drive. Journal of Theoretical Biology, 299, 120-125. https://doi.org/10.1016/j.jtbi.2011.04.032
  • Milinski, M., Sommerfeld, R. D., Krambeck, H. J., Reed, F. A., & Marotzke, J. (2008). The collective-risk social dilemma and the prevention of simulated dangerous climate change. Proceedings of the National Academy of Sciences, 105(7), 2291-2294. https://doi.org/10.1073/pnas.0709546105
  • Reed, F. A. (2007). Two-locus epistasis with sexually antagonistic selection: a genetic Parrondo's paradox. Genetics, 176(3), 1923-1929. https://doi.org/10.1534/genetics.106.069997
  • in addition to publications in other categories above

• Conservation Genetics, Invasive Species, Genetics of Harvested Species

  • Kingston, S. E., Martino, P., Melendy, M., Reed, F. A., & Carlon, D. B. (2017). Linking genotype to phenotype in a changing ocean: inferring the genomic architecture of a blue mussel stress response with genome‐wide association. Journal of Evolutionary Biology. 31(3): 346–361. http://dx.doi.org/10.1111/jeb.13224
  • Shafer, A. B., Wolf, J. B., Alves, P. C., De Meester, L., Ekblom, R., Fior, S., ... & Norman, A. J. (2016). Reply to Garner et al. Proc. Natl. Acad. Sci. USA, 108, 12348. https://doi.org/10.1016/j.tree.2015.11.010
  • Shafer, A. B., Wolf, J. B., Alves, P. C., Bergström, L., Bruford, M. W., Brännström, I., ... & Fawcett, K. D. (2015). Genomics and the challenging translation into conservation practice. Trends in Ecology & Evolution, 30(2), 78-87. https://doi.org/10.1016/j.tree.2014.11.009
  • Stemshorn, K. C., Reed, F. A., Nolte, A. W., & Tautz, D. (2011). Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.). Molecular Ecology, 20(7), 1475-1491. https://doi.org/10.1111/j.1365-294X.2010.04997.x

• Population Genetics

  • Haubold, B., Reed, F. A., & Pfaffelhuber, P. (2010). Alignment-free estimation of nucleotide diversity. Bioinformatics, 27(4), 449-455. https://doi.org/10.1093/bioinformatics/btq689
  • Reed, F. A., & Tishkoff, S. A. (2006). Positive selection can create false hotspots of recombination. Genetics, 172(3), 2011-2014. https://doi.org/10.1534/genetics.105.052183
  • in addition to publications in other categories above

• Classical and Molecular Genetics

  • Tabios, M., L. Boell, and F. A. Reed. (2014) A new mutation of PDA synthase, sepia, isolated from wild Drosophila melanogaster. Drosophila Information Service 97, 176–177. http://www.ou.edu/journals/dis/DIS97/Tabios%20176.pdf
  • Kontanis, E. J., & Reed, F. A. (2006). Evaluation of Real‐Time PCR Amplification Efficiencies to Detect PCR Inhibitors. Journal of Forensic Sciences, 51(4), 795-804. https://doi.org/10.1111/j.1556-4029.2006.00182.x
  • Reed, F. A., Reeves, R. G., & Aquadro, C. F. (2005). Evidence of susceptibility and resistance to cryptic X-linked meiotic drive in natural populations of Drosophila melanogaster. Evolution, 59(6), 1280-1291. https://doi.org/10.1554/05-021