Visualization of a neutral network
Visualization of a fitness landscape (McCandlish, 2011).

Joining Cold Spring Harbor Laboratory as Assistant Professor in January 2017. Watch for new website!

Research Interests

My research is focused on developing new mathematical tools for understanding both the structure of the genotype-phenotype map and its effects on evolving populations.

I am also broadly interested in theoretical population genetics, reversible Markov chains, non-linear dimensionality reduction, and the philosophy of biology.

Publications

Bienvenu, F., Akcay, E., Legendre, S., and McCandlish, D.M. The genealogical decomposition of a matrix population model with applications to the aggregation of stages. bioRxiv preprint. doi: 10.1101/067793

Newberry, M., McCandlish, D.M., and Plotkin, J.B. 2016. Assortative mating can impede or facilitate fixation of underdominant alleles. Theoretical Population Biology. 112: 14-21. doi: 10.1016/j.tpb.2016.07.003

McCandlish, D.M., Shah, P., and Plotkin, J.B. 2016. Epistasis and the dynamics of reversion in molecular evolution. Genetics. 203: 1335-1351. doi: 10.1534/genetics.116.188961

McCandlish, D.M., and Plotkin, J.B. 2016. Transcriptional errors and the drift barrier. PNAS 113: 3136–3138. doi: 10.1073/pnas.1601785113

Stoltzfus, A. and McCandlish, D.M. 2015. Mutation-biased adaptation in Andean house wrens. PNAS. 112: 13753-13754. doi: 10.1073/pnas.1518490112

McCandlish, D.M., Otwinowski, J., and Plotkin, J.B. 2015. Detecting epistasis from an ensemble of adapting populations. Evolution 69:2359-2370. doi: 10.1111/evo.12735

Shah, P.*, McCandlish, D.M.*, and Plotkin, J.B. 2015. Historical contingency and entrenchment in protein evolution under purifying selection. PNAS 112:E3226-E3235. doi: 10.1073/pnas.1412933112

McCandlish, D.M., Epstein, C.L., and Plotkin, J.B. 2015. Formal properties of the probability of fixation: identities, inequalities and approximations. Theoretical Population Biology 99:98-113. doi: 10.1016/j.tpb.2014.11.004

Norris, R.W., Strope, C.L., McCandlish, D.M., and Stoltzfus, A. 2015. Bayesian priors for tree calibration: evaluating two new approaches based on fossil intervals. bioRxiv preprint. doi: 10.1101/014340

McCandlish, D.M., and Stolzfus, A. 2014. Modeling evolution using the probability of fixation: history and implications. Quarterly Review of Biology 89:225-252. www.jstor.org/stable/10.1086/677571

McCandlish, D.M., Epstein, C.L., and Plotkin, J.B. 2014. The inevitability of deleterious substitutions during adaptation. Evolution 68:1351-1364. doi: 10.1111/evo.12350

McCandlish, D.M. 2013. On the findability of genotypes. Evolution 67:2592-2603. doi: 10.1111/evo.12128

McCandlish, D.M. Rajon E., Shah P., Ding Y. and Plotkin J.B. 2013. The role of epistasis in protein evolution. Nature: 497: E1-E2. doi: 10.1038/nature12219

McCandlish, D.M. 2011. Visualizing fitness landscapes. Evolution 65:1544-1588. doi: 10.1111/j.1558-5646.2011.01236.x

Tolstorukov, M.Y., Colasanti, A.V., McCandlish, D.M., Olson, W.K., and Zhurkin, V.B. 2007. A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. Journal of Molecular Biology 371: 725-738. doi: 10.1016/j.jmb.2007.05.048

* = co-first authors