PopGen Theory & Methodology

lab members indicated

Matuszewski, M., M.E. Hildebrandt, G. Achaz, and J.D. Jensen. 2017. Coalescent processes with skewed offspring distributions and non-equilibrium demography. Accepted, Geneticsbiorxiv

Matuszewski, S., L. OrmondC. Bank, and J.D. Jensen. 2017. Two sides of the same coin: a population genetics perspective on lethal mutagenesis and mutational meltdownVirus Evol 3(1): 1-5pdf

Irwin, K.K., S. LaurentS. MatuszewskiS. VuilleumierL. OrmondH. ShimC. Bank, and J.D. Jensen. 2016. On the importance of skewed offspring distributions and background selection in viral population genetics. Heredity 117: 393-99. pdf

Matuszewski, S.(*), M.E. Hildebrandt(*), A.-H. Ghenu, J.D. Jensen, and C. Bank. 2016. A statistical guide to the design of deep mutational scanning experimentsGenetics 204: 77-87. pdf

Ferrer-Admetlla, A., C. Leuenberger, J.D. Jensen, and D. Wegmann. 2016. An approximate Markov model for the Wright-Fisher diffusion and its application to time series dataGenetics 203: 831-46. pdf

Shim, H., S. LaurentS. MatuszewskiM. Foll, and J.D. Jensen. 2016. Detecting and quantifying changing selection intensities from time-sampled polymorphism dataG3 6(4): 893-904pdf

Alcala, N., J.D. Jensen, A. Telenti, and S. Vuilleumier. 2016. The genomic signature of population reconnection following isolation: from theory to HIV. G3 6: 107-20pdf

Jensen, J.D.M. Foll, and L. Bernatchez. 2016. Introduction: the past, present, and future of genomic scans for selectionMol Ecol 25(1): 1-4. pdf

Ormond, L., M. FollG. EwingS. Pfeifer, and J.D. Jensen, 2016. Inferring the age of a fixed beneficial alleleMol Ecol 25(1): 157-9. pdf

Ewing, G. and J.D. Jensen, 2016. The consequences of not accounting for background selection in demographic inferenceMol Ecol 25(1): 135-141. pdf

Mathew, L. and J.D. Jensen, 2015. Evaluating the ability of the joint site frequency spectrum to co-estimate selection and demographyFront Genet. 6: 268. pdf

Mahajan, S.J. Crisci, A. Wong, S. Akbarian, M. Foll(#), and J.D. Jensen(#), 2015. Quantifying polymorphism and divergence from epigenetic data: a framework for inferring the action of selection. Front Genet. 6: 190. pdf

Ewing, G., P. Reiff, and J.D. Jensen, 2015. PopPlanner: Visually constructing demographic models for simulationFront Genet. 6: 150. pdf

Foll, M.(*)H. Shim(*), and J.D. Jensen, 2015. A Wright-Fisher ABC-based approach for inferring per-site effective population sizes and selection coefficients from time-sampled dataMol Ecol Res 15: 87-98. pdf

Bank, C.M. FollA. Ferrer-AdmetllaG. Ewing, and J.D. Jensen, 2014. Thinking too positive? Revisiting current methods in population genetic selection inferenceTrends Genet 30(12): 540-6. pdf

Poh, Y.-P., V. Domingues, H.E. Hoekstra, and J.D. Jensen, 2014. On the prospect of identifying adaptive loci in recently bottlenecked populations: a case study in beach micePLOS One 9(11): e110579. pdf

Jensen, J.D., 2014. On the unfounded enthusiasm for soft selective sweepsNat Comm 5: 5281. pdf

Bank, C., R.T. Hietpas, A. Wong, D.N.A. Bolon(#), and J.D. Jensen(#), 2014. A Bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environmentsGenetics 196: 841-52. pdf

Foll, M.(*)Y.-P. Poh(*)N. RenzetteA. Ferrer-AdmetllaH. Shim, A.-S. Malaspinas, G. EwingC. Bank, P. Liu, D. Wegmann, D. R. Caffrey, K.B. Zeldovich, D.N.A. Bolon, J. Wang, T.F. Kowalik, C.A. Schiffer, R.W. Finberg, and J.D. Jensen, 2014. Influenza virus drug resistance: a time-sampled population genetics perspective. PLOS Genetics 10(2): e1004185. pdf

Ewing, G., and J.D. Jensen, 2014. Distinguishing neutral from deleterious mutations in growing populationsFront Genet. 5: 7. pdf

Crisci, J., Y.-P. PohS. Mahajan, and J.D. Jensen, 2013. On the impact of equilibrium assumptions on tests of selection. Front Genet. 4: 235. pdf

Joost, S., S. Vuilleumier, J.D. Jensen, S. Schoville, K. Leempoel, S. Stucki, C. Melo de Lima, J. Rolland, I. Widmer, and S. Manel, 2013. Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population geneticsMol Ecol 22(14): 3659-3665. pdf

Pavlidis, P., J.D. Jensen, W. Stephan, A. Stamatakis, 2012. A critical assessment of story-telling: GO categories and the importance of validating genomic scans. MBE 29(10): 3237-48. pdf

Crisci, J., Y.-P. PohA. BeanA. Simkin, and J.D. Jensen, 2012. Recent progress in polymorphism-based population genetic inferenceJ Hered 103: 287-96. pdf

Sinha, P., A. Dincer, D. Virgil, G. Xu, Y.-P. Poh, and J.D. Jensen, 2011. On detecting recent adaptive events using single genomesFront Genet. 2: 85-90. pdf

Crisci, J., A. Wong, J. Good, and J.D. Jensen, 2011. On characterizing adaptive events unique to modern humansGBE 3: 791-798. pdf

Jensen, J.D. and D. Bachtrog, 2011. Characterizing the influence of effective population size on the rate of adaptation: Gillespie’s Darwin Domain. GBE 3: 687-701. pdf

Cutler, D.J. and J.D. Jensen, 2010. To pool, or not to pool. Genetics 186: 41-3. pdf

Pavlidis, P., J.D. Jensen, and W. Stephan, 2010. Searching for footprints of positive selection in whole-genome SNP data from non-equilibrium populations. Genetics 185: 907-22. pdf

Jensen, J.D., and O.J. Rando, 2010. Recent evidence for pervasive adaptation targeting gene expression attributable to population size change. PNAS 107: E109-110. pdf

Pool, J. E., I. Hellmann, J.D. Jensen, and R. Nielsen. 2010, Population genomics and next-generation sequencing technologyGenome Res 20: 291-300. pdf

Jensen, J.D., 2009. On reconciling single and recurrent hitchhiking modelsGBE 1: 320-4. pdf

Jensen, J.D., K.R. Thornton, and P. Andolfatto, 2008. An approximate Bayesian estimator suggests strong recurrent selective sweeps in Drosophila. PLOS Genetics 4(9): e1000198. pdf

Jensen, J.D., K.R. Thornton, and C.F. Aquadro, 2008. Inferring selection in partially sequenced regionsMBE 25: 438-46. pdf

Jensen, J.D., K.R. Thornton, C.D. Bustamante, and C.F. Aquadro, 2007. On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in non-equilibrium populations. Genetics 176: 2371-2379pdf

Jensen, J.D., A. Wong, and C.F. Aquadro, 2007. On statistical and functional approaches for identifying targets of positive selectionTrends Genet 23: 484-491. pdf

Thornton, K.R. and J.D. Jensen, 2007. Controlling the false positive rate in multi-locus genome scans for selection. Genetics 175: 737-750. pdf

Thornton, K.R., J.D. Jensen, C. Bequet and P. Andolfatto, 2007. Progress and prospects in mapping recent selection in the genomeHeredity 98: 340-8. pdf

Jensen, J.D., Y. Kim, V. Bauer DuMont, C.F. Aquadro, and C.D. Bustamante, 2005. Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170: 1401-1410. pdf