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pIRS: Profile-based Illumina pair-end reads simulator.

Hu X, Yuan J, Shi Y, et al. pIRS: Profile-based Illumina pair-end reads simulator. Bioinformatics. 2012;28(11):1533-5. doi:10.1093/bioinformatics/bts187

High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data.

Chao MC, Pritchard JR, Zhang YJ, et al. High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data. Nucleic Acids Res. 2013;41(19):9033-48. doi:10.1093/nar/gkt654

Cosi2: an efficient simulator of exact and approximate coalescent with selection.

Shlyakhter I, Sabeti PC, Schaffner SF. Cosi2: an efficient simulator of exact and approximate coalescent with selection. Bioinformatics. 2014;30(23):3427-9. doi:10.1093/bioinformatics/btu562

Building human genome maps with radiation hybrids.

Slonim D, Kruglyak L, Stein L, Lander E. Building human genome maps with radiation hybrids. J Comput Biol. 1997;4(4):487-504. doi:10.1089/cmb.1997.4.487

Faster multipoint linkage analysis using Fourier transforms.

Kruglyak L, Lander ES. Faster multipoint linkage analysis using Fourier transforms. J Comput Biol. 1998;5(1):1-7. doi:10.1089/cmb.1998.5.1

High-resolution haplotype structure in the human genome.

Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. High-resolution haplotype structure in the human genome. Nat Genet. 2001;29(2):229-32. doi:10.1038/ng1001-229