Beroukhim et al., 2006
Beroukhim, R., Lin, M., Park, Y., Hao, K., Zhao, X., Garraway, L. A., Fox, E. A., Hochberg, E. P., Mellinghoff, I. K., Hofer, M. D., et al. (2006).
Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide snp arrays.
PLoS Comput Biol, 2(5):e41.

Chao, 1987
Chao, A. (1987).
Estimating the population size for capture-recapture data with unequal catchability.
Biometrics, pages 783-791.

Chao et al., 2014
Chao, A., Gotelli, N. J., Hsieh, T., Sander, E. L., Ma, K., Colwell, R. K., and Ellison, A. M. (2014).
Rarefaction and extrapolation with hill numbers: a framework for sampling and estimation in species diversity studies.
Ecological monographs, 84(1):45-67.

Chao et al., 2013
Chao, A., Wang, Y., and Jost, L. (2013).
Entropy and the species accumulation curve: a novel entropy estimator via discovery rates of new species.
Methods in Ecology and Evolution, 4(11):1091-1100.

Choi et al., 2009
Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., Nayir, A., Bakkaloglu, A., Özen, S., Sanjad, S., Nelson-Williams, C., Farhi, A., Mane, S., and Lifton, R. P. (2009).
Genetic diagnosis by whole exome capture and massively parallel DNA sequencing.
Proc Natl Acad Sci U S A, 106(45):19096-19101.

He and Ecker, 2016
He, Y. and Ecker, J. (2016).
Non-cg methylation in the human genome.
Annual Review of Genom.

Heap et al., 2010
Heap, G. A., Yang, J. H. M., Downes, K., Healy, B. C., Hunt, K. A., Bockett, N., Franke, L., Dubois, P. C., Mein, C. A., Dobson, R. J., Albert, T. J., Rodesch, M. J., Clayton, D. G., Todd, J. A., van Heel, D. A., and Plagnol, V. (2010).
Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing.
Hum Mol Genet, 19(1):122-134.

Hiatt et al., 2013
Hiatt, J., Pritchard, C., Salipante, S., O'Roak, B., and Shendure, J. (2013).
Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation.
Genome Research, (23):843-854.

Kuchenbecker et al., 2015
Kuchenbecker, L., Nienen, M., Hecht, J., Neumann, A. U., Babel, N., Reinert, K., and Robinson, P. N. (2015).
Imseq-a fast and error aware approach to immunogenetic sequence analysis.
Bioinformatics, 31(18):2963-2971.

Li et al., 2012
Li, J., Lupat, R., Amarasinghe, K. C., Thompson, E. R., Doyle, M. A., Ryland, G. L., Tothill, R. W., Halgamuge, S. K., Campbell, I. G., and Gorringe, K. L. (2012).
Contra: copy number analysis for targeted resequencing.
Bioinformatics, 28(10):1307-1313.

Martin and Wang, 2011
Martin, J. A. and Wang, Z. (2011).
Next-generation transcriptome assembly.
Nat Rev Genet, 12(10):671-682.

Ng et al., 2009
Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E. E., Bamshad, M., Nickerson, D. A., and Shendure, J. (2009).
Targeted capture and massively parallel sequencing of 12 human exomes.
Nature, 461(7261):272-276.

Niu and Zhang, 2012
Niu, Y. S. and Zhang, H. (2012).
The screening and ranking algorithm to detect dna copy number variations.
Ann Appl Stat, 6(3):1306-1326.

Peng et al., 2015
Peng, Q., Satya, R. V., Lewis, M., Randad, P., and Wang, Y. (2015).
Reducing amplification artifacts in high multiplex amplicon sequencing by using molecular barcodes.
BMC Genomics, (16):589.

Wang et al., 2009
Wang, Z., Gerstein, M., and Snyder, M. (2009).
RNA-Seq: a revolutionary tool for transcriptomics.
Nat Rev Genet, 10(1):57-63.

Yoon et al., 2009
Yoon, S., Xuan, Z., Makarov, V., Ye, K., and Sebat, J. (2009).
Sensitive and accurate detection of copy number variants using read depth of coverage.
Genome Res., 19:1586-1592.