References¶
Barrick et al. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461:1243-1247.
Barrick, J.E., Lenski, R.E. (2009) Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb. Symp. Quant. Biol. 74:119-129.
Blount e al. (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 105:7899–7906.
Barrick, J.E., Lenski, R.E. (2009) Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb. Symp. Quant. Biol. 74:119-129.
McKenna et al. (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20:1297-1303.
Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151: 165–188.
Barrick, J.E., Colburn, G., Deatherage D.E., Traverse, C.C., Strand, M.D., Borges, J.J., Knoester, D.B., Reba, A., Meyer, A.G.(2014) Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics 15:1039.
Deatherage, D.E., Traverse, C.C., Wolf, L.N., Barrick, J.E. (2015) Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq. Front. Genet. 5:468.