Publications

For up to date citation information, see my Google Scholar page.

Freedman AH, Gaspar JM, Sackton TB. In press. Short paired-end reads trump long single end reads for expression analysis. BMC Bioinformatics 21:149. [link]

Freedman AH, Clamp M, Sackton TB. In press. Error, noise and bias in de novo transcriptome assemblies. Molecular Ecology Resources doi: 10.1111/1755-0998.13156. *“From the cover” featured article, recommended by Faculty Opinions [link]

Yuan FL, Freedman AH, Chirio L, Lebreton M, Bonebrake TC. 2018. Thermal performance across a forest-ecotone gradient produces divergent climate change vulnerability within species. Ecography 41:1-11. [link]

Ostrander EA, Wayne RK, Freedman AH, Davis BW. 2017. Demographic history, selection and functional diversity of the canine genome. Nature Reviews Genetics 18: 705-720. [link]

Serres-Armero A, Povolotskaya IS, Quillez J, Twigg D, Ramirez O, Santpere G, Kuderna LFK, Hernandez-Rodriguez J, Fernandez-Callejo M, Gomez-Sanchez D, Sirakov S, Freedman AH, Fan Z, Novembre J, Navarro A, Boyko A, Kidd JM, Wayne R, Vilà C, Lorente-Galdos B, Marques-Bonet T. 2017. Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. BMC Genomics 18:977. [link]

Freedman AH, Wayne RK. 2017. Deciphering the origin of dogs: from fossils to genomes. Annual Review of Animal Biosciences 5:281-307. [link]

Freedman AH, Lohmueller KE, and Wayne RK. 2016. Evolutionary history, selective sweeps, and deleterious variation in the dog. Annual Review of Ecology, Evolution and Systematics 47:73-96. [link]

Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Silva P, Han E, Galaverni M, Fan Z, Gronau I, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker H, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins T, Nelson SF, Ostrander EA , Marques-Bonet T, Wayne RK, Novembre J. 2016 Demographically-based evaluation of genomic regions under selection in domestic dogs. PLoS Genetics: e1005851. [link]

Hendricks S, Sesink Clee PR, Harrigan RH, Pollinger JP, Freedman AH, Callas R, Figura PJ, Wayne RK. 2016. Re-defining historical geographic range in species with sparse records: implications for the Mexican wolf reintroduction program. Biological Conservation 194:48-57. [link]

Anthony NM, Atteke C, Bruford MW, Dallmeier F, Freedman A, et al. 2015. Evolution and conservation of Central African biodiversity: priorities for future research and education in the Congo Basin and Gulf of Guinea. Biotropica 47:6-17. [link]

Freedman AH, Gronau I, Schweizer RM, Han E, Ortega-Del Vecchyo D, Silva P, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker H, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins T, Nelson SF, Ostrander EA , Marques-Bonet T, Wayne RK, Novembre J. 2014. Genome sequencing highlights the dynamic early history of dogs. PLoS Genetics 10: e1004016. *Selected by Faculty of 1000. Rated one of the top 20 stories of 2013 by Science News. [link]

Thalmann O, Shapiro B, Cui P, Schuenemann VJ, Sawyer SK, Greenfield DL, Germonpré MB, Sablin MV, López-Giráldez F, Napierala H, Uerpmann H-P, Loponte DM, Acosta AA, Giemsch L, Schmitz RW, Worthington B, Buikstra JE, Druzhkova A, Graphodatsky AS, Ovodov ND, Wahlberg N, Freedman AH, Schweizer RM, Koepfli K-P, Leonard JA, Meyer M, Krause J, Pääbo S, Green RE, Wayne RK. 2013. Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science 342:871-874. [link]

Thomassen HA, Freedman AH, Brown DM, Buermann W, Jacobs DK. 2013. Seasonal timing of rainfall sustains reproductive isolation in East African giraffes. PLoS ONE 8:e77191. [link]

Anthony NM, Mickala P, Abernethy KA, Atteke C, Bissiengou P, Bruford MW, Dallmeier F, Decaëns T, Dudu A, Freedman A, et al. 2012. Biodiversity and conservation genetics research in Central Africa: new approaches and avenues for international collaboration. Conservation Genetics Resources 4:523-525. [link]

Smith TB, Thomassen HA, Freedman AH, Sehgal RNM, Buermann W, Saatchi S, Pollinger J, Milá B, Pires D, Valkiunas G, Wayne RK. 2011. Patterns of divergence in the olive sunbird Cyanomitra olivacea (Aves:Nectariniidae) across the African rainforest-savanna ecotone. Biological Jounal of the Linnean Society 103:821-835. [link]

Freedman AH, Buermann W, Mitchard ETA, DeFries RS, Smith TB. 2010. Human impacts flatten rainforest-savanna gradient and reduce adaptive diversity. PLoS ONE 5:1-9. *Selected by Faculty of 1000. [link]

Freedman AH, Thomassen HA, Buermann W, Smith TB. 2010. Genomic signals of adaptive diversification in a rainforest lizard. Molecular Ecology 19:3773-3788. [link]

Thomassen HA, Cheviron Z, Freedman AH, Harrigan R, Wayne RK, Smith TB. 2010. Spatial modeling and landscape-level approaches for visualizing intra-specific variation. Molecular Ecology 19:3532-3548. [link]

Pease KM, Freedman AH, Pollinger J, McCormack JE, Buermann W, Rodzen J, Banks J , Meredith E, Bleich VC, Schaefer RJ, Jones K, Wayne RK. 2009. Landscape genetic structure of Calfornia mule deer (Odocoileus hemionus): the role of contemporary ecological and historical factors. Molecular Ecology 18:1848-1862. [link]

Freedman AH, Buermann W, Lebreton M, Chirio L, Smith TB. 2009. Modeling the effects of anthropogenic habitat change on savanna snake invasions into African rainforest. Conservation Biology 23:81-92. [link]

Funk DW, Noel LE, Freedman AH. 2004. Environmental gradients, plant distribution and species richness in Arctic salt marsh near Prudhoe Bay, Alaska. Wetlands Ecology and Management 12:215-233. [link]

Freedman AH, Portier KM, Sunquist ME. 2003. Life history analysis for black bears (Ursus americanus) in a changing demographic landscape. Ecological Modelling 167:47-64. [link]

Hamilton AM, Freedman AH, Franz R. 2002. Influence of deer feeders, habitat, and sensory cues on predation rates on artificial turtle nests. American Midland Naturalist 147:123-13. [link]