PUBLICATIONS

Pre-prints

Lea, A.J., Vilgalys, T.P., Durst, P.A.P., and Tung, J. Maximizing ecological and evolutionary insight from bisulfite sequencing data sets. bioRxiv: dx.doi.org/10.1101/091488 [Link]

Sun, S., Hood, M., Scott, L., Peng, Q., Mukherjee, S., Tung, J., and Zhou, X. Differential expression analysis for RNAseq using Poisson mixed models. bioRxiv: dx.doi.org/10.1101/073403 [Link]


2017

Miller, E.A., Livermore, J.A., Alberts, S.C., Tung, J., and Archie, E.A. 2017. Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons. Microbiome 5: 8. [Open Access]


2016

Snyder-Mackler, N.+, Sanz, J.+, Kohn, J.N., Brinkworth, J.F., Morrow, S., Shaver, A.O., Grenier, J., Pique-Regi, R., Johnson, Z.P., Wilson, M.E., Barreiro, L.B.*, and Tung, J.* 2016. Social status alters immune regulation and response to infection in macaques. Science 354: 1041-1045. [Link]. See also the related Perspective by Robert Sapolsky.

Nédélec, Y., Sanz, J., Baharian, G., Szpiech, Z.A., Pacis, A., Dumaine, A., Grenier, J., Freiman, A., Sams, A.J.,  Hebert, S., Sabourin, A.P., Luca, F., Blekhman, R., Hernandez, R.D., Pique-Regi, R., Tung, J., Yotova, V., and Barreiro, L.B. 2016. Genetic ancestry and natural selection drive population differences in immune responses to infection in humans. Cell 167: 657-669. [Link]

Kohn, J.N., Snyder-Mackler, N., Barreiro, L.B., Johnson, Z.P., Tung, J.*, and Wilson, M.E.* Dominance rank causally affects personality and glucocorticoid regulation in female rhesus macaques. Psychoneuroendocrinology 74: 179-188 [Link]).

Blekhman, R., Tang, K., Archie, E.A., Barreiro, L.B., Johnson, Z.P., Wilson, M.E., Kohn, J., Yuan, M.L., Gesquiere, L., Grieneisen, L.E., and Tung, J. Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data. Scientific Reports 6: 31519 [Open Access]

Wall, J.D., Schlebusch, S.A., Alberts, S.C., Cox, L.A., Snyder-Mackler, N., Nevonen, K., Carbone, L., and Tung, J. 2016. Genome-wide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons. Molecular Ecology 25: 3469-3483. [Link] [Download accepted version]

Snyder-Mackler, N., Majoros, W.H., Yuan, M.L., Shaver, A.O., Gordon, J.B., Kopp, G.H., Schlebusch, S.A., Wall, J.D., Alberts, S.C., Mukherjee, S., Zhou, X., and Tung, J. 2016. Efficient genome-wide sequencing and low coverage pedigree analysis from non-invasively collected samples. Genetics 203: 699-714. [Open Access] [Software available here]

Charruau, P., Johnston, R., Stahler, D.R., Lea, A.J., Snyder-Mackler, N., Smith, D.W., vonHoldt, B., Cole, S.W., Tung, J., and Wayne, R.K. 2016. Pervasive effects of aging on gene expression in wild wolves. Molecular Biology and Evolution 33: 1967-1978. [Link]

Tung, J.*, Archie, E.A.*, Altmann, J., and Alberts, S.C. 2016. Cumulative early adversity predicts longevity in wild baboons. Nature Communications 7: 11181. [Open Access]

Snyder-Mackler, N., Kohn, J.N., Barreiro, L.B., Johnson, Z.P., Wilson, M.E., and Tung, J. 2016. Social status drives social relationships in groups of unrelated female rhesus macaques. Animal Behaviour 111: 207-317. [Link]

Lea, A.J., Altmann, J., Alberts, S.C., and Tung, J. 2016. Resource base influences genome-wide DNA methylation levels in wild baboons (Papio cynocephalus). Molecular Ecology 25: 1681-1696. [Link]


2015

Lea, A.J., Tung, J.*, and Zhou, X.* 2015. A flexible, efficient binomial mixed model for identifying differential DNA methylation in bisulfite sequencing data. PLoS Genetics 11: e1005650. [Open Access] [Software available here]

Pacis, A., Tailleux, L., Morin, A.M., Lambourne, J., MacIsaac, J., Yotova, V., Dumaine, A., Danckaert, A., Luca, F., Grenier, J.C., Hansen, K.D., Gicquel, B., Yu, M., Pai, A., He, C., Tung, J., Pastinen, T., Kobor, M.S., Pique-Regi, R., Gilad, Y., and Barreiro, L.B. 2015. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Research 25: 1801-1811. [Open Access]

Franz, M., McLean, E., Tung, J., Altmann, J., and Alberts, S.C. 2015. Self-organizing dominance hierarchies in a wild primate population. Proceedings of the Royal Society B 282: 20151512. [Link]

Archie, E.A. and Tung, J. 2015. Social behavior and the microbiome. Current Opinions in Behavioral Sciences 6: 28-34. [Open Access]. See the related Insight by Jack Gilbert.

Galbany, J., Tung, J., Altmann, J., Alberts, S.C. 2015. Canine length in wild male baboons: maturation, aging, and social dominance rank. PLoS ONE 10: e0126415. [Open Access]

Tung, J., Barreiro, L.B., Burns, M., Grenier, J.C., Lynch, J., Grieneisen, L., Altmann, J., Alberts, S.C., Blekhman, R., and Archie, E.A. 2015. Social networks predict gut microbiome composition in wild baboons. eLife 4: e05224. [Open Access]

Lea, A.J., Altmann, J., Alberts, S.C.*, and Tung, J.* 2015. Developmental constraints in a wild primate. American Naturalist 185: 809-821. [Link]

Tung, J.*, Zhou, X.*, Alberts, S.C., Stephens, M., and Gilad, Y. 2015. The genetic architecture of gene expression levels in wild baboons. eLife 4: e04729. [Open Access]


2014

Archie, E.A., Tung, J., Clark, M., Altmann, J., and Alberts, S.C. 2014. Social affiliation matters: both same-sex and opposite-sex relationships predict survival in wild female baboons. Proceedings of the Royal Society B. 281: 20141261. [Link]

Tung, J. 2014. Genes revisited: the biodemography of social environmental variation through a functional genomic lens. In: Lane, M. and Weinstein, M., eds. Sociality, Hierarchy, Health: Comparative Biodemography. Washington, DC: The National Academies Press: 39 - 64. [Link]

Snyder-Mackler, N.M., Somel, M., and Tung, J. 2014. Shared signatures of social stress and aging in PBMC gene expression profiles. Aging Cell 13: 954-957 [Open Access]

Gallego Romero, I., Pai., A.A., Tung, J., and Gilad, Y. 2014. RNA-seq: impact of RNA degradation on transcript quantification. BMC Biology 12: 42. [Open Access]


2013

Tung, J. and Gilad, Y. 2013. Social environmental effects on gene regulation. Cellular and Molecular Life Sciences 70: 4323-4339. [Open Access]

Runcie, D.E., Wiedmann, R.T., Archie, E.A., Altmann, J., Wray, G.A., Alberts, S.C., and Tung, J. 2013. Social environment influences the relationship between genotype and gene expression in wild baboons. Philosophical Transactions of the Royal Society B 368: 20120345. [Free full text]

Loisel, D.A. and Tung, J. 2013. Genetic variation in the immune system of old world monkeys: functional and selective effects. In: Brinkworth, J.F. and Pechenkina, E.A., eds. Primates, Pathogens, and Evolution: A Context for Understanding Emerging Disease. New York, NY: Springer: 65 - 90.

Akinyi, M.Y., Tung, J., Jeneby, M., Patel, N.B., Altmann, J., and Alberts, S.C. 2013. Role of grooming in reducing tick load in wild baboons (Papio cynocephalus). Animal Behaviour 85: 559-568. [Free full text]


2012

Harper, K.N., Fyumagwa, R.D., Hoare, R. Wambura, P.N., Coppenhaver, D.H., Sapolsky, R.M., Alberts, S.C., Tung, J., Kilewo, M., Batamuzi, E.K., Leendertz, F.H., Knauf, S., and Armelagos, G.J. 2012. Treponema pallidum infection in the wild baboons of East Africa: distribution and genetic characterization of the strains responsible. PLoS One 7: e50882. [Open Access]

Barreiro, L.B. and Tung, J. 2012. Perspective: Getting under--and through--the skin: ecological genomics of chytridiomycosis infection in frogs. Molecular Ecology 21: 3095-3097. [Free full text]

Tung, J., Barreiro, L.B., Johnson, Z.P., Hansen, K.D., Michopoulous, V., Toufexis, D., Michelini, K.M., Wilson, M.E., and Gilad, Y. 2012. Social environment is associated with gene regulatory variation in the rhesus macaque immune system. Proceedings of the National Academy of Sciences USA 109: 6490-6495 [Open Access]

Tung, J.*, Charpentier, M.J.E.*, Mukherjee, S., Altmann, J., and Alberts, S.C. 2012. Genetic effects on mating success and partner choice in a social mammal. American Naturalist 180: 113-129. [Free full text]

Charpentier, M.J.E.*, Fontaine, M.C.*, Cherel, E., Renoult, J.P., Jenkins, T., Benoit, L., Barthes, N., Alberts, S.C., Tung, J. 2012. Genetic structure in a dynamic baboon hybrid zone corroborates behavioral observations in a hybrid population. Molecular Ecology 21: 715-731. [Free full text]

Babbitt, C.C., Tung, J., Wray, G.A., and Alberts, S.C. 2012. Changes in gene expression associated with reproductive maturation in wild female baboons. Genome Biology and Evolution 4: 102-109.[Free full text]


2007 - 2011

Tung, J., Akinyi, M., Mutura, S., Altmann, J., Wray, G.A.*, and Alberts, S.C.* 2011. Allele specific gene expression in a wild nonhuman primate population. Molecular Ecology 20: 725-739. [Link]

Tung, J., Alberts, S.C.*, and Wray, G.A.* 2010. Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations. Trends in Genetics 26: 353-362. [Free full text]

Tung, J. and Wray, G.A. 2009. Evolution of traits deduced from genome comparisons. In: The Encyclopedia of Life Sciences: doi:10.1002/9780470015902.a0021746. [Link]

Tung, J., Fedrigo, O., Haygood, R., Mukherjee, S.*, and Wray, G.A.* 2009. Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation. Molecular Biology and Evolution 26: 2047-2059. [Free full text]

Tung, J., Primus, A., Bouley, A.J., Severson, T., Alberts, S.C.*, and Wray, G.A.* 2009. Evolution of a malaria resistance gene in wild primates. Nature 460: 388-392. [Link]

Leonhardt, S.*, Tung, J.*, Camden, J., Leal, M., and Drea, C.M. 2009. Seeing red: behavioral evidence of trichromatic color vision in strepsirrhine primates. Behavioral Ecology 20: 1-12. [Free full text]

Tung, J., Charpentier, M.J.E., Garfield, D.A., Altmann, J., and Alberts, S.C. 2008. Genetic evidence reveals dynamic patterns of hybridization in a wild baboon population. Molecular Ecology 17: 1998-2011. [Link]

Charpentier, M.J.E., Tung, J., Altmann, J., and Alberts, S.C. 2008. Age at maturity in wild baboons: genetic, demographic, and environmental influences. Molecular Ecology 17: 2026-2040. [Link]

Tung, J., Rudolph, J., Altmann, J., and Alberts, S.C. 2007. Parallel effects of genetic variation on ACE activity in baboons and humans. American Journal of Physical Anthropology 134: 1-8. [Link]