-
1
-
-
0037286212
-
Computation and analysis of multiple structural change models
-
BAI, J. and PERRON, P. (2003). Computation and analysis of multiple structural change models. J. Appl. Econometrics 18 1-22.
-
(2003)
J. Appl. Econometrics
, vol.18
, pp. 1-22
-
-
Bai, J.1
Perron, P.2
-
2
-
-
84945709924
-
On the approximation of curves by line segments using dynamic programming
-
BELLMAN, R. (1961). On the approximation of curves by line segments using dynamic programming. Commun. ACM 4 284.
-
(1961)
Commun. ACM
, vol.4
, pp. 284
-
-
Bellman, R.1
-
3
-
-
82955198919
-
-
Technical Report 804, Dept. Statistics, Univ. California, Berkeley
-
BENJAMINI, Y. and SPEED, T. (2011). Estimation and correction for GC-content bias in high throughput sequencing. Technical Report 804, Dept. Statistics, Univ. California, Berkeley.
-
(2011)
Estimation and Correction For GC-content Bias In High Throughput Sequencing
-
-
Benjamini, Y.1
Speed, T.2
-
4
-
-
78651430230
-
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
-
Boeva, V., Zinovyev, A., Bleakley, K., Vert, J.-P., Janoueix-Lerosey, I., Delattre, O. and Barillot, E. (2011). Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics 27 268-269.
-
(2011)
Bioinformatics
, vol.27
, pp. 268-269
-
-
Boeva, V.1
Zinovyev, A.2
Bleakley, K.3
Vert, J.-P.4
Janoueix-Lerosey, I.5
Delattre, O.6
Barillot, E.7
-
5
-
-
44349191457
-
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing
-
Campbell, P. J., Stephens, P. J., Pleasance, E. D., O'meara, S., Li, H., Santarius, T., Stebbings, L. A., Leroy, C., Edkins, S., Hardy, C., Teague, J. W., Menzies, A., Goodhead, I., Turner, D. J., Clee, C.M., Quail, M. A., Cox, A., Brown, C., Durbin, R., Hurles, M. E., Edwards, P. A. W., Bignell, G. R., Stratton, M. R. and Futreal, P. A. (2008). Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nature Genetics 40 722-729.
-
(2008)
Nature Genetics
, vol.40
, pp. 722-729
-
-
Campbell, P.J.1
Stephens, P.J.2
Pleasance, E.D.3
O'Meara, S.4
Li, H.5
Santarius, T.6
Stebbings, L.A.7
Leroy, C.8
Edkins, S.9
Hardy, C.10
Teague, J.W.11
Menzies, A.12
Goodhead, I.13
Turner, D.J.14
Clee, C.M.15
Quail, M.A.16
Cox, A.17
Brown, C.18
Durbin, R.19
Hurles, M.E.20
Edwards, P.A.W.21
Bignell, G.R.22
Stratton, M.R.23
Futreal, P.A.24
more..
-
6
-
-
79551522261
-
Estimation of parent specific DNA copy number in tumors using high-density genotyping arrays
-
MR2776334
-
CHEN, H., XING, H. and ZHANG, N. R. (2011). Estimation of parent specific DNA copy number in tumors using high-density genotyping arrays. PLoS Comput. Biol. 7 e1001060, 15. MR2776334
-
(2011)
PLoS Comput. Biol
, vol.7
, Issue.15
-
-
Chen, H.1
Xing, H.2
Zhang, N.R.3
-
7
-
-
80052990473
-
Systematic bias in highthroughput sequencing data and its correction by BEADS
-
CHEUNG, M.-S., DOWN, T. A., LATORRE, I. and AHRINGER, J. (2011). Systematic bias in highthroughput sequencing data and its correction by BEADS. Nucleic Acids Res. 39 e103.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Cheung, M.-S.1
Down, T.A.2
Latorre, I.3
Ahringer, J.4
-
8
-
-
58149218240
-
High-resolution mapping of copynumber alterations with massively parallel sequencing
-
Chiang, D. Y., Getz, G., Jaffe, D. B., O'kelly, M. J., Zhao, X., Carter, S. L., Russ, C., Nusbaum, C., Meyerson, M. and Lander, E. S. (2009). High-resolution mapping of copynumber alterations with massively parallel sequencing. Nature Methods 6 99-103.
-
(2009)
Nature Methods
, vol.6
, pp. 99-103
-
-
Chiang, D.Y.1
Getz, G.2
Jaffe, D.B.3
O'Kelly, M.J.4
Zhao, X.5
Carter, S.L.6
Russ, C.7
Nusbaum, C.8
Meyerson, M.9
Lander, E.S.10
-
9
-
-
0017875638
-
The problem of the Nile: Conditional solution to a changepoint problem
-
MR0513930
-
COBB, G. W. (1978). The problem of the Nile: Conditional solution to a changepoint problem. Biometrika 65 243-251. MR0513930
-
(1978)
Biometrika
, vol.65
, pp. 243-251
-
-
Cobb, G.W.1
-
10
-
-
29444441336
-
A high-resolution survey of deletion polymorphism in the human genome
-
CONRAD, D. F., ANDREWS, T. D., CARTER, N. P., HURLES, M. E. and PRITCHARD, J. K. (2006). A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38 75-81.
-
(2006)
Nat. Genet
, vol.38
, pp. 75-81
-
-
Conrad, D.F.1
Andrews, T.D.2
Carter, N.P.3
Hurles, M.E.4
Pritchard, J.K.5
-
11
-
-
52649157765
-
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
-
DOHM, J. C., LOTTAZ, C., BORODINA, T. and HIMMELBAUER, H. (2008). Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36 e105.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
12
-
-
77956887957
-
Inference about the change-point in a sequence of random variables
-
MR0273727
-
HINKLEY, D. V. (1970). Inference about the change-point in a sequence of random variables. Biometrika 57 1-17. MR0273727
-
(1970)
Biometrika
, vol.57
, pp. 1-17
-
-
Hinkley, D.V.1
-
15
-
-
79951748341
-
CNAseg-a novel framework for identification of copy number changes in cancer from secondgeneration sequencing data
-
IVAKHNO, S., ROYCE, T., COX, A. J., EVERS, D. J., CHEETHAM, R. K. and TAVARÉ, S. (2010). CNAseg-a novel framework for identification of copy number changes in cancer from secondgeneration sequencing data. Bioinformatics 26 3051-3058.
-
(2010)
Bioinformatics
, vol.26
, pp. 3051-3058
-
-
Ivakhno, S.1
Royce, T.2
Cox, A.J.3
Evers, D.J.4
Cheetham, R.K.5
Tavaré, S.6
-
16
-
-
33751340401
-
Genome assembly comparison to identify structural variants in the human genome
-
Khaja, R., Zhang, J., Macdonald, J. R., He, Y., Joseph-George, A. M., Wei, J., Rafiq, Q. C. M. A., Shago, M., Pantano, L., Aburatani, H., Jones, K., Redon, R., Hurles, M., Armengol, L., Estivill, X., Mural, R. J., Lee, C., Scherer, S. and Feuk, L. (2007). Genome assembly comparison to identify structural variants in the human genome. Nature Genetics 38 1413-1418.
-
(2007)
Nature Genetics
, vol.38
, pp. 1413-1418
-
-
Khaja, R.1
Zhang, J.2
Macdonald, J.R.3
He, Y.4
Joseph-George, A.M.5
Wei, J.6
Rafiq, Q.C.M.A.7
Shago, M.8
Pantano, L.9
Aburatani, H.10
Jones, K.11
Redon, R.12
Hurles, M.13
Armengol, L.14
Estivill, X.15
Mural, R.J.16
Lee, C.17
Scherer, S.18
Feuk, L.19
-
17
-
-
41149097010
-
Stochastic segmentation models for array-based comparative genomic hybridization data analysis
-
LAI, T. L., XING, H. and ZHANG, N. R. (2007). Stochastic segmentation models for array-based comparative genomic hybridization data analysis. Biostatistics 9 290-307.
-
(2007)
Biostatistics
, vol.9
, pp. 290-307
-
-
Lai, T.L.1
Xing, H.2
Zhang, N.R.3
-
18
-
-
27544483495
-
Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data
-
LAI, W. R., JOHNSON, M. D., KUCHERLAPATI, R. and PARK, P. J. (2005). Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 21 3763-3770.
-
(2005)
Bioinformatics
, vol.21
, pp. 3763-3770
-
-
Lai, W.R.1
Johnson, M.D.2
Kucherlapati, R.3
Park, P.J.4
-
19
-
-
19844378139
-
Using penalized contrasts for the change-point problem
-
LAVIELLE, M. (2005). Using penalized contrasts for the change-point problem. Signal Processing 85 1501-1510.
-
(2005)
Signal Processing
, vol.85
, pp. 1501-1510
-
-
Lavielle, M.1
-
20
-
-
33645993906
-
Efficient calculation of interval scores for DNA copy number data analysis
-
electronic). MR2255255
-
Lipson, D., Aumann, Y., Ben-Dor, A., Linial, N. and Yakhini, Z. (2006). Efficient calculation of interval scores for DNA copy number data analysis. J. Comput. Biol. 13 215-228. (electronic). MR2255255
-
(2006)
J. Comput. Biol
, vol.13
, pp. 215-228
-
-
Lipson, D.1
Aumann, Y.2
Ben-Dor, A.3
Linial, N.4
Yakhini, Z.5
-
21
-
-
29444457877
-
Common deletion polymorphisms in the human genome
-
THE INTERNATIONAL HAPMAP CONSORTIUM
-
MCCARROLL, S. A., HADNOTT, T. N., PERRY, G. H., SABETI, P. C., ZODY, M. C., BARRETT, J. C., DALLAIRE, S., GABRIEL, S. B., LEE, C., DALY, M. J., ALTSHULER, D. M. and THE INTERNATIONAL HAPMAP CONSORTIUM (2006). Common deletion polymorphisms in the human genome. Nature Genetics 38 86-92.
-
(2006)
Nature Genetics
, vol.38
, pp. 86-92
-
-
McCarroll, S.A.1
Hadnott, T.N.2
Perry, G.H.3
Sabeti, P.C.4
Zody, M.C.5
Barrett, J.C.6
Dallaire, S.7
Gabriel, S.B.8
Lee, C.9
Daly, M.J.10
Altshuler, D.M.11
-
22
-
-
70449704529
-
Computational methods for discovering structural variation with next-generation sequencing
-
MEDVEDEV, P., STANCIU, M. and BRUDNO, M. (2009). Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods 6 S13-S20.
-
(2009)
Nat. Methods
, vol.6
-
-
Medvedev, P.1
Stanciu, M.2
Brudno, M.3
-
23
-
-
3543105225
-
Circular binary segmentation for the analysis of array-based DNA copy number data
-
OLSHEN, A. B., VENKATRAMAN, E. S., LUCITO, R. and WIGLER, M. (2004). Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5 557-572.
-
(2004)
Biostatistics
, vol.5
, pp. 557-572
-
-
Olshen, A.B.1
Venkatraman, E.S.2
Lucito, R.3
Wigler, M.4
-
24
-
-
79960393165
-
Parent-specific copy number in paired tumor-normal studies using circular binary segmentation
-
OLSHEN, A. B., BENGTSSON, H., NEUVIAL, P., SPELLMAN, P. T., OLSHEN, R. A. and SESHAN, V. E. (2011). Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics 27 2038-2046.
-
(2011)
Bioinformatics
, vol.27
, pp. 2038-2046
-
-
Olshen, A.B.1
Bengtsson, H.2
Neuvial, P.3
Spellman, P.T.4
Olshen, R.A.5
Seshan, V.E.6
-
25
-
-
0642360659
-
Detecting clusters in disease incidence
-
South Hadley, MA, Institute of Mathematical Statistics Lecture Notes-Monograph Series, IMS, Hayward, CA. MR1477929
-
RABINOWITZ, D. (1994). Detecting clusters in disease incidence. In Change-Point Problems (South Hadley, MA, 1992). Institute of Mathematical Statistics Lecture Notes-Monograph Series 23 255-275. IMS, Hayward, CA. MR1477929
-
(1994)
Change-Point Problems
, vol.23
, pp. 255-275
-
-
Rabinowitz, D.1
-
26
-
-
33751329250
-
Global variation in copy number in the human genome
-
Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, D. T., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., Cho, E. K., Dallaire, S., Freeman, J. L., Gonzalez, J. R., Gratacos, M., Huang, J., Kalaitzopoulos, D., Komura, D., Macdonald, J. R., Marshall, C. R., Mei, R., Montgomery, L., Nishimura, K., Okamura, K., Shen, F., Somerville, M. J., Tchinda, J., Valsesia, A., Woodwark, C., Yang, F., Zhang, J., Zerjal, T., Zhang, J., Armengol, L., Conrad, D. F., Estivill, X., Tyler-Smith, C., Carter, N. P., Aburatani, H., Lee, C., Jones, K. W., Scherer, S. W. and Hurles, M. E. (2006). Global variation in copy number in the human genome. Nature 444 444-454.
-
(2006)
Nature
, vol.444
, pp. 444-454
-
-
Redon, R.1
Ishikawa, S.2
Fitch, K.R.3
Feuk, L.4
Perry, G.H.5
Andrews, D.T.6
Fiegler, H.7
Shapero, M.H.8
Carson, A.R.9
Chen, W.10
Cho, E.K.11
Dallaire, S.12
Freeman, J.L.13
Gonzalez, J.R.14
Gratacos, M.15
Huang, J.16
Kalaitzopoulos, D.17
Komura, D.18
Macdonald, J.R.19
Marshall, C.R.20
Mei, R.21
Montgomery, L.22
Nishimura, K.23
Okamura, K.24
Shen, F.25
Somerville, M.J.26
Tchinda, J.27
Valsesia, A.28
Woodwark, C.29
Yang, F.30
Zhang, J.31
Zerjal, T.32
Zhang, J.33
Armengol, L.34
Conrad, D.F.35
Estivill, X.36
Tyler-Smith, C.37
Carter, N.P.38
Aburatani, H.39
Lee, C.40
Jones, K.W.41
Scherer, S.W.42
Hurles, M.E.43
more..
-
27
-
-
0000120766
-
Estimating the dimension of a model
-
MR0468014
-
SCHWARZ, G. (1978). Estimating the dimension of a model. Ann. Statist. 6 461-464. MR0468014
-
(1978)
Ann. Statist
, vol.6
, pp. 461-464
-
-
Schwarz, G.1
-
28
-
-
34547844126
-
Modeling recurrent DNA copy number alterations in array CGH data
-
SHAH, S. P., LAM, W. L., NG, R. T. and MURPHY, K. P. (2007). Modeling recurrent DNA copy number alterations in array CGH data. Bioinformatics 23 450-458.
-
(2007)
Bioinformatics
, vol.23
, pp. 450-458
-
-
Shah, S.P.1
Lam, W.L.2
Ng, R.T.3
Murphy, K.P.4
-
29
-
-
0012492891
-
Approximate tail probabilities for the maxima of some random fields
-
MR0929059
-
SIEGMUND, D. (1988a). Approximate tail probabilities for the maxima of some random fields. Ann. Probab. 16 487-501. MR0929059
-
(1988)
Ann. Probab
, vol.16
, pp. 487-501
-
-
Siegmund, D.1
-
30
-
-
0001793095
-
Confidence sets in change-point problems
-
MR0963139
-
SIEGMUND, D. (1988b). Confidence sets in change-point problems. Internat. Statist. Rev. 56 31-48. MR0963139
-
(1988)
Internat. Statist. Rev
, vol.56
, pp. 31-48
-
-
Siegmund, D.1
-
31
-
-
82255169896
-
Detecting simultaneous variant intervals in aligned sequences
-
MR2840169
-
SIEGMUND, D. O., YAKIR, B. and ZHANG, N. R. (2011). Detecting simultaneous variant intervals in aligned sequences. Ann. Appl. Stat. 5 645-668. MR2840169
-
(2011)
Ann. Appl. Stat
, vol.5
, pp. 645-668
-
-
Siegmund, D.O.1
Yakir, B.2
Zhang, N.R.3
-
32
-
-
34147104969
-
A faster circular binary segmentation algorithm for the analysis of array CGH data
-
VENKATRAMAN, E. S. and OLSHEN, A. B. (2007). A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23 657-663.
-
(2007)
Bioinformatics
, vol.23
, pp. 657-663
-
-
Venkatraman, E.S.1
Olshen, A.B.2
-
33
-
-
77649323880
-
Optimal and fast detection of spatial clusters with scan statistics
-
MR2604703
-
WALTHER, G. (2010). Optimal and fast detection of spatial clusters with scan statistics. Ann. Statist. 38 1010-1033. MR2604703
-
(2010)
Ann. Statist
, vol.38
, pp. 1010-1033
-
-
Walther, G.1
-
34
-
-
12444256820
-
A method for calling gains and losses in array-CGH data
-
WANG, P., KIM, Y., POLLACK, J., NARASIMHAN, B. and TIBSHIRANI, R. (2005). A method for calling gains and losses in array-CGH data. Biostatistics 6 45-58.
-
(2005)
Biostatistics
, vol.6
, pp. 45-58
-
-
Wang, P.1
Kim, Y.2
Pollack, J.3
Narasimhan, B.4
Tibshirani, R.5
-
35
-
-
27944455289
-
A comparison study: Applying segmentation to arrayCGH data for downstream analyses
-
WILLENBROCK, H. and FRIDLYAND, J. (2005). A comparison study: Applying segmentation to arrayCGH data for downstream analyses. Bioinformatics 21 4084-4091.
-
(2005)
Bioinformatics
, vol.21
, pp. 4084-4091
-
-
Willenbrock, H.1
Fridlyand, J.2
-
36
-
-
64849083125
-
CNV-seq, a new method to detect copy number variation using high-throughput sequencing
-
XIE, C. and TAMMI, M. T. (2009). CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10 80.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 80
-
-
Xie, C.1
Tammi, M.T.2
-
37
-
-
69749122557
-
Sensitive and accurate detection of copy number variants using read depth of coverage
-
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.
-
(2009)
Genome Res
, vol.19
, pp. 1586-1592
-
-
Yoon, S.1
Xuan, Z.2
Makarov, V.3
Ye, K.4
Sebat, J.5
-
38
-
-
84866261102
-
DNA copy number profiling in normal and tumor genomes
-
J. Feng,W. Fu and F. Sun, eds.). Computational Biology, Springer, London
-
ZHANG, N. R. (2010). DNA copy number profiling in normal and tumor genomes. In Frontiers in Computational and Systems Biology (J. Feng,W. Fu and F. Sun, eds.). Computational Biology 15 259-281. Springer, London.
-
(2010)
Frontiers In Computational and Systems Biology
, vol.15
, pp. 259-281
-
-
Zhang, N.R.1
-
39
-
-
34247243220
-
A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data
-
MR2345571
-
ZHANG, N. R. and SIEGMUND, D. O. (2007). A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data. Biometrics 63 22-32, 309. MR2345571
-
(2007)
Biometrics
, vol.63
, Issue.309
, pp. 22-32
-
-
Zhang, N.R.1
Siegmund, D.O.2
-
40
-
-
77955883799
-
Detecting simultaneous changepoints in multiple sequences
-
MR2672488
-
ZHANG, N. R., SIEGMUND, D.O., JI, H. and LI, J. Z. (2010). Detecting simultaneous changepoints in multiple sequences. Biometrika 97 631-645. MR2672488
-
(2010)
Biometrika
, vol.97
, pp. 631-645
-
-
Zhang, N.R.1
Siegmund, D.O.2
Ji, H.3
Li, J.Z.4
|