-
1
-
-
84884407337
-
Tumour heterogeneity in the clinic
-
Bedard, P. L., Hansen, A. R., Ratain, M. J. and Siu, L. L. (2013) Tumour heterogeneity in the clinic. Nature, 501, 355–364.
-
(2013)
Nature
, vol.501
, pp. 355-364
-
-
Bedard, P.L.1
Hansen, A.R.2
Ratain, M.J.3
Siu, L.L.4
-
2
-
-
84876592083
-
A genomic view of mosaicism and human disease
-
Biesecker, L. G. and Spinner, N. B. (2013) A genomic view of mosaicism and human disease. Nat. Rev. Genet., 14, 307–320.
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 307-320
-
-
Biesecker, L.G.1
Spinner, N.B.2
-
3
-
-
84885340966
-
Cluster and feature modeling from combinatorial stochastic processes
-
Broderick, T., Jordan, M. I. and Pitman, J. (2013) Cluster and feature modeling from combinatorial stochastic processes. Statist. Sci., 28, 289–312.
-
(2013)
Statist. Sci.
, vol.28
, pp. 289-312
-
-
Broderick, T.1
Jordan, M.I.2
Pitman, J.3
-
4
-
-
85059423352
-
-
and, Boca Raton, CRC Press
-
Brooks, S., Gelman, A., Jones, G. and Meng, X.-L. (2011) Handbook of Markov Chain Monte Carlo. Boca Raton: CRC Press.
-
(2011)
Handbook of Markov Chain Monte Carlo
-
-
Brooks, S.1
Gelman, A.2
Jones, G.3
Meng, X.-L.4
-
5
-
-
79960925372
-
Modernizing reference genome assemblies
-
Church, D. M., Schneider, V. A., Graves, T., Auger, K., Cunningham, F., Bouk, N., Chen, H.-C., Agarwala, R., McLaren, W. M., Ritchie, G. R., Albracht, D., Kremitzki, M., Rock, S., Kotkiewicz, H., Kremitzki, C., Wollam, A., Trani, L., Fulton, L., Fulton, R., Matthews, L., Whitehead, S., Chow, W., Torrance, J., Dunn, M., Harden, G., Threadgold, G., Wood, J., Collins, J., Heath, P., Griffiths, G., Pelan, S., Grafham, D., Eichler, E. E., Weinstock, G., Mardis, E. R., Wilson, R. K., Howe, K., Flicek, P. and Hubbard, T. (2011) Modernizing reference genome assemblies. PLOS Biol., 9, no. 7, article e1001091.
-
(2011)
PLOS Biol
, vol.9
, Issue.7
-
-
Church, D.M.1
Schneider, V.A.2
Graves, T.3
Auger, K.4
Cunningham, F.5
Bouk, N.6
Chen, H.-C.7
Agarwala, R.8
McLaren, W.M.9
Ritchie, G.R.10
Albracht, D.11
Kremitzki, M.12
Rock, S.13
Kotkiewicz, H.14
Kremitzki, C.15
Wollam, A.16
Trani, L.17
Fulton, L.18
Fulton, R.19
Matthews, L.20
Whitehead, S.21
Chow, W.22
Torrance, J.23
Dunn, M.24
Harden, G.25
Threadgold, G.26
Wood, J.27
Collins, J.28
Heath, P.29
Griffiths, G.30
Pelan, S.31
Grafham, D.32
Eichler, E.E.33
Weinstock, G.34
Mardis, E.R.35
Wilson, R.K.36
Howe, K.37
Flicek, P.38
Hubbard, T.39
more..
-
6
-
-
79956329337
-
Somatic mosaicism in healthy human tissues
-
De, S. (2011) Somatic mosaicism in healthy human tissues. Trends Genet., 27, 217–223.
-
(2011)
Trends Genet.
, vol.27
, pp. 217-223
-
-
De, S.1
-
7
-
-
84935825808
-
-
and, Genome Biol
-
Deshwar, A., Vembu, S., Yung, C. K., Jang, G. H., Stein, L. and Morris, Q. (2015) PhyloWGS: Reconstructing subclonal composition and evolution from whole genome sequencing of tumors. Genome Biol., 16, article 35.
-
(2015)
PhyloWGS: Reconstructing subclonal composition and evolution from whole genome sequencing of tumors
, vol.16
-
-
Deshwar, A.1
Vembu, S.2
Yung, C.K.3
Jang, G.H.4
Stein, L.5
Morris, Q.6
-
8
-
-
84862776906
-
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
-
Ding, L., Ley, T. J., Larson, D. E., Miller, C. A., Koboldt, D. C., Welch, J. S., Ritchey, J. K., Young, M. A., Lamprecht, T., McLellan, M. D., McMichael, J. F., Wallis, J. W., Lu, C., Shen, D., Harris, C. C., Dooling, D. J., Fulton, R. S., Fulton, L. L., Chen, K., Schmidt, H., Kalicki-Veizer, J., Magrini, V. J., Cook, L., McGrath, S. D., Vickery, T. L., Wendl, M. C., Heath, S., Watson, M. A., Link, D. C., Tomasson, M. H., Shannon, W. D., Payton, J. E., Kulkarni, S., Westervelt, P., Walter, M. J., Graubert, T. A., Mardis, E. R., Wilson, R. K. and DiPersio, J. F. (2012) Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature, 481, 506–510.
-
(2012)
Nature
, vol.481
, pp. 506-510
-
-
Ding, L.1
Ley, T.J.2
Larson, D.E.3
Miller, C.A.4
Koboldt, D.C.5
Welch, J.S.6
Ritchey, J.K.7
Young, M.A.8
Lamprecht, T.9
McLellan, M.D.10
McMichael, J.F.11
Wallis, J.W.12
Lu, C.13
Shen, D.14
Harris, C.C.15
Dooling, D.J.16
Fulton, R.S.17
Fulton, L.L.18
Chen, K.19
Schmidt, H.,.20
Kalicki-Veizer, J.,.21
Magrini, V.J.22
Cook, L.,.23
McGrath, S.D.24
Vickery, T.L.25
Wendl, M.C.26
Heath, S.27
Watson, M.A.28
Link, D.C.29
Tomasson, M.H.30
Shannon, W.D.31
Payton, J.E.32
Kulkarni, S.33
Westervelt, P.34
Walter, M.J.35
Graubert, T.A.36
Mardis, E.R.37
Wilson, R.K.38
DiPersio, J.F.39
more..
-
9
-
-
84902315822
-
High-definition reconstruction of clonal composition in cancer
-
Fischer, A., Vázquez-García, I., Illingworth, C. J. and Mustonen, V. (2014) High-definition reconstruction of clonal composition in cancer. Cell Rep., 7, 1740–1752.
-
(2014)
Cell Rep.
, vol.7
, pp. 1740-1752
-
-
Fischer, A.1
Vázquez-García, I.2
Illingworth, C.J.3
Mustonen, V.4
-
10
-
-
0242416667
-
Cell biology: developmental predisposition to cancer
-
Frank, S. A. and Nowak, M. A. (2003) Cell biology: developmental predisposition to cancer. Nature, 422, 494.
-
(2003)
Nature
, vol.422
, Issue.494
-
-
Frank, S.A.1
Nowak, M.A.2
-
11
-
-
1542374198
-
Problems of somatic mutation and cancer
-
Frank, S. A. and Nowak, M. A. (2004) Problems of somatic mutation and cancer. Bioessays, 26, 291–299.
-
(2004)
Bioessays
, vol.26
, pp. 291-299
-
-
Frank, S.A.1
Nowak, M.A.2
-
12
-
-
84856013431
-
Clonal evolution in cancer
-
Greaves, M. and Maley, C. C. (2012) Clonal evolution in cancer. Nature, 481, 306–313.
-
(2012)
Nature
, vol.481
, pp. 306-313
-
-
Greaves, M.1
Maley, C.C.2
-
14
-
-
84893164721
-
Inferring clonal evolution of tumors from single nucleotide somatic mutations
-
Jiao, W., Vembu, S., Deshwar, A., Stein, L. and Morris, Q. (2014) Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC Bioinform., 15, article 35.
-
(2014)
BMC Bioinform.
, vol.15
, pp. 35
-
-
Jiao, W.1
Vembu, S.2
Deshwar, A.3
Stein, L.4
Morris, Q.5
-
15
-
-
84863242156
-
Bayesian analysis of multistate event history data: beta-dirichlet process prior
-
Kim, Y., James, L. and Weissbach, R. (2012) Bayesian analysis of multistate event history data: beta-dirichlet process prior. Biometrika, 99, 127–140.
-
(2012)
Biometrika
, vol.99
, pp. 127-140
-
-
Kim, Y.1
James, L.2
Weissbach, R.3
-
16
-
-
84861400043
-
cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate
-
Klambauer, G., Schwarzbauer, K., Mayr, A., Clevert, D.-A., Mitterecker, A., Bodenhofer, U. and Hochreiter, S. (2012) cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res., 40, no. 9, article e69.
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.9
-
-
Klambauer, G.1
Schwarzbauer, K.2
Mayr, A.3
Clevert, D.-A.4
Mitterecker, A.5
Bodenhofer, U.6
Hochreiter, S.7
-
17
-
-
84938507617
-
A bayesian feature allocation model for tumor heterogeneity
-
Lee, J., Müller, P., Gulukota, K. and Ji, Y. (2015) A bayesian feature allocation model for tumor heterogeneity. Ann. Appl. Statist., 9, 621–639.
-
(2015)
Ann. Appl. Statist.
, vol.9
, pp. 621-639
-
-
Lee, J.1
Müller, P.2
Gulukota, K.3
Ji, Y.4
-
18
-
-
67649884743
-
Fast and accurate short read alignment with Burrows–Wheeler transform
-
Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25, 1754–1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
19
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
and 1000 Genome Project Data Processing Subgroup
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. and 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078–2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
20
-
-
84964313312
-
A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data
-
Li, B. and Li, J. Z. (2014) A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data. Genome Biol., 15, article473.
-
(2014)
Genome Biol.
, vol.15
-
-
Li, B.1
Li, J.Z.2
-
21
-
-
77956295988
-
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M. and DePristo, M. A. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297–1303.
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
Kernytsky, A.6
Garimella, K.7
Altshuler, D.8
Gabriel, S.9
Daly, M.10
DePristo, M.A.11
-
22
-
-
84952310964
-
Sciclone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution
-
Miller, C. A., White, B. S., Dees, N. D., Griffith, M., Welch, J. S., Griffith, O. L., Vij, R., Tomasson, M. H., Graubert, T. A., Walter, M. J., Ellis, M. J., Schierding, W., DiPersio, J. F., Ley, T. J., Mardis, E. R., Wilson, R. K. and Ding, L. (2014) Sciclone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLOS Computnl Biol., 10, no. 8, article e1003665.
-
(2014)
PLOS Computnl Biol.
, vol.10
, Issue.8
-
-
Miller, C.A.1
White, B.S.2
Dees, N.D.3
Griffith, M.4
Welch, J.S.5
Griffith, O.L.6
Vij, R.7
Tomasson, M.H.8
Graubert, T.A.9
Walter, M.J.10
Ellis, M.J.11
Schierding, W.12
DiPersio, J.F.13
Ley, T.J.14
Mardis, E.R.15
Wilson, R.K.16
Ding, L.17
-
23
-
-
79953766940
-
Tumour evolution inferred by single-cell sequencing
-
Navin, N., Kendall, J., Troge, J., Andrews, P., Rodgers, L., McIndoo, J., Cook, K., Stepansky, A., Levy, D., Esposito, D., Muthuswamy, L., Krasnitz, A., McCombie, W. R., Hicks, J. and Wigler, M. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472, 90–94.
-
(2011)
Nature
, vol.472
, pp. 90-94
-
-
Navin, N.1
Kendall, J.2
Troge, J.3
Andrews, P.4
Rodgers, L.5
McIndoo, J.6
Cook, K.7
Stepansky, A.8
Levy, D.9
Esposito, D.10
Muthuswamy, L.11
Krasnitz, A.12
McCombie, W.R.13
Hicks, J.14
Wigler, M.15
-
24
-
-
84880934918
-
THetA: inferring intra-tumor heterogeneity from high-throughput dna sequencing data
-
Oesper, L., Mahmoody, A. and Raphael, B. J. (2013) THetA: inferring intra-tumor heterogeneity from high-throughput dna sequencing data. Genome Biol., 14, article R80.
-
(2013)
Genome Biol.
, vol.14
, pp. R80
-
-
Oesper, L.1
Mahmoody, A.2
Raphael, B.J.3
-
25
-
-
84897954204
-
PyClone: statistical inference of clonal population structure in cancer
-
Roth, A., Khattra, J., Yap, D., Wan, A., Laks, E., Biele, J., Ha, G., Aparicio, S., Bouchard-Côté, A. and Shah, S. P. (2014) PyClone: statistical inference of clonal population structure in cancer. Nat. Meth., 11, 396–398.
-
(2014)
Nat. Meth.
, vol.11
, pp. 396-398
-
-
Roth, A.1
Khattra, J.2
Yap, D.3
Wan, A.4
Laks, E.5
Biele, J.6
Ha, G.7
Aparicio, S.8
Bouchard-Côté, A.9
Shah, S.P.10
-
26
-
-
80053393750
-
Insight into the heterogeneity of breast cancer through next-generation sequencing
-
Russnes, H. G., Navin, N., Hicks, J. and Borresen-Dale, A.-L. (2011) Insight into the heterogeneity of breast cancer through next-generation sequencing. J. Clin. Investgn, 121, 3810–3818.
-
(2011)
J. Clin. Investgn
, vol.121
, pp. 3810-3818
-
-
Russnes, H.G.1
Navin, N.2
Hicks, J.3
Borresen-Dale, A.-L.4
-
28
-
-
84971311457
-
Bayclone: Bayesian nonparametric inference of tumor subclones using ngs data
-
Sengupta, S., Gulukota, K., Lee, J., Müller, P. and Ji, Y. (2015) Bayclone: Bayesian nonparametric inference of tumor subclones using ngs data. Proc. Pacif. Symp. Biocomput., 20, 467–478.
-
(2015)
Proc. Pacif. Symp. Biocomput.
, vol.20
, pp. 467-478
-
-
Sengupta, S.1
Gulukota, K.2
Lee, J.3
Müller, P.4
Ji, Y.5
-
29
-
-
84884963475
-
Trap: a tree approach for fingerprinting subclonal tumor composition
-
Strino, F., Parisi, F., Micsinai, M. and Kluger, Y. (2013) Trap: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Res., 41, no. 17, article e165.
-
(2013)
Nucleic Acids Res.
, vol.41
, Issue.17
-
-
Strino, F.1
Parisi, F.2
Micsinai, M.3
Kluger, Y.4
-
30
-
-
84905474730
-
Inferring clonal composition from multiple sections of a breast cancer
-
Zare, H., Wang, J., Hu, A., Weber, K., Smith, J., Nickerson, D., Song, C., Witten, D., Blau, C. A. and Noble, W. S. (2014) Inferring clonal composition from multiple sections of a breast cancer. PLOS Computnl Biol., 10, no. 7, article e1003703.
-
(2014)
PLOS Computnl Biol.
, vol.10
, Issue.7
-
-
Zare, H.1
Wang, J.2
Hu, A.3
Weber, K.4
Smith, J.5
Nickerson, D.6
Song, C.7
Witten, D.8
Blau, C.A.9
Noble, W.S.10
|