Bibliography
- Abkevich et al., 2012
-
Abkevich, V., Timms, K. M., Hennessy, B. T., Potter, J., Carey, M. S., Meyer,
L. A., Smith-McCune, K., Broaddus, R., Lu, K. H., Chen, J., Tran, T. V.,
Williams, D., Iliev, D., Jammulapati, S., FitzGerald, L. M., Krivak, T.,
DeLoia, J. A., Gutin, A., Mills, G. B., and Lanchbury, J. S. (2012).
Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer.
British Journal of Cancer, 107(10):1776-1782. - 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. - Birkbak et al., 2012
-
Birkbak, N. J., Wang, Z. C., Kim, J.-Y., Eklund, A. C., Li, Q., Tian, R.,
Bowman-Colin, C., Li, Y., Greene-Colozzi, A., Iglehart, J. D., Tung, N.,
Ryan, P. D., Garber, J. E., Silver, D. P., Szallasi, Z., and Richardson,
A. L. (2012).
Telomeric allelic imbalance indicates defective dna repair and sensitivity to dna-damaging agents.
Cancer Discovery, 2(4):366-375. - 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. - de Luca et al., 2020
-
de Luca, X. M., Newell, F., Kazakoff, S. H., Hartel, G., McCart Reed, A. E.,
Holmes, O., Xu, Q., Wood, S., Leonard, C., Pearson, J. V., Lakhani, S. R.,
Waddell, N., Nones, K., and Simpson, P. T. (2020).
Using whole-genome sequencing data to derive the homologous recombination deficiency scores.
npj Breast Cancer, 6(1):33. - 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. - Lefranc et al., 2009
-
Lefranc, M.-P., Giudicelli, V., Ginestoux, C., Jabado-Michaloud, J., Folch, G.,
Bellahcene, F., Wu, Y., Gemrot, E., Brochet, X., Lane, J., et al. (2009).
Imgt®, the international immunogenetics information system®.
Nucleic acids research, 37(suppl_1):D1006-D1012. - 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. - 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. - Shugay et al., 2015
-
Shugay, M., Bagaev, D. V., Turchaninova, M. A., Bolotin, D. A., Britanova,
O. V., Putintseva, E. V., Pogorelyy, M. V., Nazarov, V. I., Zvyagin, I. V.,
Kirgizova, V. I., et al. (2015).
Vdjtools: unifying post-analysis of t cell receptor repertoires.
PLoS computational biology, 11(11):e1004503. - Shugay et al., 2017
-
Shugay, M., Zaretsky, A. R., Shagin, D. A., Shagina, I. A., Volchenkov, I. A.,
Shelenkov, A. A., Lebedin, M. Y., Bagaev, D. V., Lukyanov, S., and Chudakov,
D. M. (2017).
Mageri: Computational pipeline for molecular-barcoded targeted resequencing.
PLoS computational biology, 13(5):e1005480. - 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.