-
1
-
-
84975795680
-
An integrated map of genetic variation from 1,092 human genomes
-
An integrated map of genetic variation from 1,092 human genomes. Nature, 491(7422):56-65, Oct. 2012.
-
(2012)
Nature
, vol.491
, Issue.7422
, pp. 56-65
-
-
-
2
-
-
84975742565
-
[1000] Genomes Project Consortium. A map of human genome variation from population-scale sequencing
-
[1000] Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature, 467(7319):1061-1073, Oct. 2010.
-
(2010)
Nature
, vol.467
, Issue.7319
, pp. 1061-1073
-
-
-
3
-
-
0025183708
-
Basic local alignment search tool
-
S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. Basic local alignment search tool. Journal of Molecular Biology, 215(3):403-410, Oct. 1990.
-
(1990)
Journal of Molecular Biology
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
5
-
-
79959640102
-
Evaluation of next-generation sequencing software in mapping and assembly
-
S. Bao, R. Jiang, W. Kwan, B. Wang, X. Ma, and Y. Song. Evaluation of next-generation sequencing software in mapping and assembly. Journal of human genetics, 56(6):406-414, 2011.
-
(2011)
Journal of human genetics
, vol.56
, Issue.6
, pp. 406-414
-
-
Bao, S.1
Jiang, R.2
Kwan, W.3
Wang, B.4
Ma, X.5
Song, Y.6
-
6
-
-
58349097721
-
Human genomes as email attachments
-
S. Christley, Y. Lu, C. Li, and X. Xie. Human genomes as email attachments. Bioinformatics (Oxford, England), 25(2):274-275, Jan. 2009.
-
(2009)
Bioinformatics (Oxford, England)
, vol.25
, Issue.2
, pp. 274-275
-
-
Christley, S.1
Lu, Y.2
Li, C.3
Xie, X.4
-
7
-
-
4544388794
-
Dictionary matching and indexing with errors and don't cares. In
-
New York, NY, USA ACM.
-
R. Cole, L.-A. Gottlieb, and M. Lewenstein. Dictionary matching and indexing with errors and don't cares. In Proceedings of STOC, pages 91-100, New York, NY, USA, 2004. ACM.
-
(2004)
Proceedings of STOC
, pp. 91-100
-
-
Cole, R.1
Gottlieb, L.-A.2
Lewenstein, M.3
-
8
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
I. H. G. S. Consortium. Initial sequencing and analysis of the human genome. Nature, 409(6822):860-921, February 2001.
-
(2001)
Nature
, vol.409
, Issue.6822
, pp. 860-921
-
-
Consortium, I.H.G.S.1
-
9
-
-
77951115122
-
Consortium ICG. International network of cancer genome projects
-
Consortium ICG. International network of cancer genome projects. Nature, 464(7291):993-998, Apr. 2010.
-
(2010)
Nature
, vol.464
, Issue.7291
, pp. 993-998
-
-
-
10
-
-
79960405019
-
and 1000 Genomes Project Analysis Group. The variant call format and VCFtools
-
P. Danecek, A. Auton, G. Abecasis, and 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics (Oxford, England), 27(15):2156-2158, Aug. 2011.
-
(2011)
Bioinformatics (Oxford England)
, vol.27
, Issue.15
, pp. 2156-2158
-
-
Danecek, P.1
Auton, A.2
Abecasis, G.3
-
11
-
-
84855281420
-
Repetitive elements may comprise over two-thirds of the human genome
-
A. P. J. de Koning, W. Gu, T. A. Castoe, M. A. Batzer, and D. D. Pollock. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genetics, 7(12):e1002384, 12 2011.
-
(2011)
PLoS Genetics
, vol.7
, Issue.12
-
-
de Koning, A.P.J.1
Gu, W.2
Castoe, T.A.3
Batzer, M.A.4
Pollock, D.D.5
-
13
-
-
84861205393
-
Fast relative lempel-ziv self-index for similar sequences
-
Beijing, China, 2012
-
H. H. Do, J. Jansson, K. Sadakane, and W.-K. Sung. Fast relative lempel-ziv self-index for similar sequences. In Proceedings of FAW-AAIM 2012, Beijing, China, 2012., volume 7285 of LNCS, pages 291-302. Springer, 2012.
-
(2012)
Proceedings of FAW-AAIM 2012
, vol.7285
, pp. 291-302
-
-
Do, H.H.1
Jansson, J.2
Sadakane, K.3
Sung, W.-K.4
-
14
-
-
84883296101
-
String algorithms and data structures
-
abs/0801.2378, 2008
-
P. Ferragina. String algorithms and data structures. CoRR, abs/0801.2378, 2008.
-
CoRR
-
-
Ferragina, P.1
-
15
-
-
45849125008
-
An(other) entropy-bounded compressed suffix tree
-
J. Fischer, V. Mäkinen, and G. Navarro. An(other) entropy-bounded compressed suffix tree. In Proceedings of 19th Annual Symposium on Combinatorial Pattern Matching (CPM), LNCS 5029, pages 152-165, 2008.
-
(2008)
In Proceedings of 19th Annual Symposium on Combinatorial Pattern Matching (CPM), LNCS
, vol.5029
, pp. 152-165
-
-
Fischer, J.1
Mäkinen, V.2
Navarro, G.3
-
16
-
-
84857847846
-
A faster grammar-based self-index. In LATA'12
-
Berlin, Heidelberg, Springer
-
T. Gagie, P. Gawrychowski, J. Kärkkäinen, and Y. Nekrich. A faster grammar-based self-index. In LATA'12, pages 240-251, Berlin, Heidelberg, 2012. Springer.
-
(2012)
, pp. 240-251
-
-
Gagie, T.1
Gawrychowski, P.2
Kärkkäinen, J.3
Nekrich, Y.4
-
17
-
-
0034592914
-
Deformable markov model templates for time-series pattern matching. In
-
New York, NY, USA, ACM
-
X. Ge and P. Smyth. Deformable markov model templates for time-series pattern matching. In Proceedings of SIGKDD, pages 81-90, New York, NY, USA, 2000. ACM.
-
(2000)
Proceedings of SIGKDD
, pp. 81-90
-
-
Ge, X.1
Smyth, P.2
-
19
-
-
0004137004
-
-
Cambridge University Press, New York, NY, USA
-
D. Gusfield. Algorithms on strings, trees, and sequences: computer science and computational biology. Cambridge University Press, New York, NY, USA, 1997.
-
(1997)
Algorithms on strings, trees, and sequences: computer science and computational biology
-
-
Gusfield, D.1
-
20
-
-
65449144325
-
Evaluation of next generation sequencing platforms for population targeted sequencing studies
-
O. Harismendy, P. Ng, et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biology, 10(3):R32+, 2009.
-
(2009)
Genome Biology
, vol.10
, Issue.3
-
-
Harismendy, O.1
Ng, P.2
-
21
-
-
0036226603
-
BLAT-The BLAST-Like Alignment Tool
-
W. J. Kent. BLAT-The BLAST-Like Alignment Tool. Genome Research, 12(4):656-664, Apr. 2002.
-
(2002)
Genome Research
, vol.12
, Issue.4
, pp. 656-664
-
-
Kent, W.J.1
-
22
-
-
0036079158
-
The human genome browser at UCSC
-
W. J. Kent, C. W. Sugnet, T. S. Furey, K. M. Roskin, T. H. Pringle, A. M. Zahler, and D. Haussler. The human genome browser at UCSC. Genome Research, 12(6):996-1006, 2002.
-
(2002)
Genome Research
, vol.12
, Issue.6
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
23
-
-
77952780999
-
Efficient processing of substring match queries with inverted q-gram indexes. In
-
Y. Kim, K.-G. Woo, H. Park, and K. Shim. Efficient processing of substring match queries with inverted q-gram indexes. In Proceedings of ICDE 2010,Long Beach, California, USA, pages 721-732.
-
(2010)
Proceedings of ICDE Long Beach, California, USA
, pp. 721-732
-
-
Kim, Y.1
Woo, K.-G.2
Park, H.3
Shim, K.4
-
24
-
-
84876408746
-
On compressing and indexing repetitive sequences
-
S. Kreft and G. Navarro. On compressing and indexing repetitive sequences. Theoretical Computer Science, 483:115-133, 2013.
-
(2013)
Theoretical Computer Science
, vol.483
, pp. 115-133
-
-
Kreft, S.1
Navarro, G.2
-
25
-
-
84859210032
-
Fast gapped-read alignment with bowtie 2
-
B. Langmead and S. L. Salzberg. Fast gapped-read alignment with bowtie 2. Nat Meth, 9(4):357-359, Apr. 2012.
-
(2012)
Nat Meth
, vol.9
, Issue.4
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
26
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
B. Langmead, C. Trapnell, M. Pop, and S. Salzberg. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10(3):R25-10, Mar. 2009.
-
(2009)
Genome Biology
, vol.10
, Issue.3
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.4
-
27
-
-
67649884743
-
Fast and accurate short read alignment with burrows-wheeler transform
-
H. Li and R. Durbin. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics (Oxford, England), 25(14):1754-1760, 2009.
-
(2009)
Bioinformatics (Oxford, England)
, vol.25
, Issue.14
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
28
-
-
79959927754
-
Wham: a high-throughput sequence alignment method
-
ACM
-
Y. Li, A. Terrell, and J. M. Patel. Wham: a high-throughput sequence alignment method. In Proceedings of the ACM SIGMOD International Conference on Management of Data, Athens, Greece, June 12-16, pages 445-456. ACM, 2011.
-
(2011)
In Proceedings of the ACM SIGMOD International Conference on Management of Data, Athens, Greece, June 12-16
, pp. 445-456
-
-
Li, Y.1
Terrell, A.2
Patel, J.M.3
-
29
-
-
84862661901
-
Online windowed subsequence matching over probabilistic sequences
-
New York, NY, USA ACM
-
Z. Li and T. Ge. Online windowed subsequence matching over probabilistic sequences. In Proceedings of the 2012 ACM SIGMOD International Conference on Management of Data, pages 277-288, New York, NY, USA, 2012. ACM.
-
(2012)
In Proceedings of the 2012 ACM SIGMOD International Conference on Management of Data
, pp. 277-288
-
-
Li, Z.1
Ge, T.2
-
30
-
-
84863702145
-
Compressive genomics
-
P.-R. Loh, M. Baym, and B. Berger. Compressive genomics. Nature Biotechnology, 30(7):627-630, July 2012.
-
(2012)
Nature Biotechnology
, vol.30
, Issue.7
, pp. 627-630
-
-
Loh, P.-R.1
Baym, M.2
Berger, B.3
-
31
-
-
0027681165
-
Suffix arrays: A new method for on-line string searches
-
U. Manber and E. W. Myers. Suffix arrays: A new method for on-line string searches. SIAM J. Comput., 22(5):935-948, 1993.
-
(1993)
SIAM J. Comput.
, vol.22
, Issue.5
, pp. 935-948
-
-
Manber, U.1
Myers, E.W.2
-
32
-
-
0345566149
-
A guided tour to approximate string matching
-
G. Navarro. A guided tour to approximate string matching. ACM Computing Surveys, 33(1):31-88, 2001.
-
(2001)
ACM Computing Surveys
, vol.33
, Issue.1
, pp. 31-88
-
-
Navarro, G.1
-
36
-
-
79959936774
-
Reference-based alignment in large sequence databases
-
P. Papapetrou, V. Athitsos, G. Kollios, and D. Gunopulos. Reference-based alignment in large sequence databases. Proceedings of the VLDB Endowment, 2(1):205-216, Aug. 2009.
-
(2009)
Proceedings of the VLDB Endowment
, vol.2
, Issue.1
, pp. 205-216
-
-
Papapetrou, P.1
Athitsos, V.2
Kollios, G.3
Gunopulos, D.4
-
38
-
-
0036725017
-
Human genome sequence variation and the influence of gene history, mutation and recombination
-
D. E. Reich, S. F. Schaffner, M. J. Daly, G. McVean, J. C. Mullikin, J. M. Higgins, D. J. Richter, E. S. Lander, and D. Altshuler. Human genome sequence variation and the influence of gene history, mutation and recombination. Nature Genetics, 32(1):135-142, Aug. 2002.
-
(2002)
Nature Genetics
, vol.32
, Issue.1
, pp. 135-142
-
-
Reich, D.E.1
Schaffner, S.F.2
Daly, M.J.3
Mcvean, G.4
Mullikin, J.C.5
Higgins, J.M.6
Richter, D.J.7
Lander, E.S.8
Altshuler, D.9
-
39
-
-
77955048001
-
Prefix tree indexing for similarity search and similarity joins on genomic data
-
Berlin, Heidelberg Springer
-
A. Rheinländer, M. Knobloch, N. Hochmuth, and U. Leser. Prefix tree indexing for similarity search and similarity joins on genomic data. In Proceedings of the 22nd SSDBM, pages 519-536, Berlin, Heidelberg, 2010. Springer.
-
(2010)
In Proceedings of the 22nd SSDBM
, pp. 519-536
-
-
Rheinländer, A.1
Knobloch, M.2
Hochmuth, N.3
Leser, U.4
-
40
-
-
78650868150
-
A window into third-generation sequencing. Human molecular genetics
-
E. E. Schadt, S. Turner, and A. Kasarskis. A window into third-generation sequencing. Human molecular genetics, 19(R2):R227-R240, Oct. 2010.
-
(2010)
, vol.19
, Issue.R2
-
-
Schadt, E.E.1
Turner, S.2
Kasarskis, A.3
-
41
-
-
76249113666
-
Simultaneous alignment of short reads against multiple genomes
-
K. Schneeberger, J. Hagmann, S. Ossowski, N. Warthmann, S. Gesing, O. Kohlbacher, and D. Weigel. Simultaneous alignment of short reads against multiple genomes. Genome biology, 10(9):R98+, Sept. 2009.
-
(2009)
Genome biology
, vol.10
, Issue.9
-
-
Schneeberger, K.1
Hagmann, J.2
Ossowski, S.3
Warthmann, N.4
Gesing, S.5
Kohlbacher, O.6
Weigel, D.7
-
42
-
-
80052979900
-
Indexing finite language representation of population genotypes
-
WABI'11, Berlin, Heidelberg Springer
-
J. Siŕen, N. Välimäki, and V. Mäkinen. Indexing finite language representation of population genotypes. In Proceedings of the 11th international conference on Algorithms in bioinformatics, WABI'11, pages 270-281, Berlin, Heidelberg, 2011. Springer.
-
(2011)
In Proceedings of the 11th international conference on Algorithms in bioinformatics
, pp. 270-281
-
-
Siŕen, J.1
Välimäki, N.2
Mäkinen, V.3
-
43
-
-
84947737449
-
On using q-gram locations in approximate string matching
-
ESA '95, London, UK Springer
-
E. Sutinen and J. Tarhio. On using q-gram locations in approximate string matching. In Proceedings of the Third Annual European Symposium on Algorithms, ESA '95, pages 327-340, London, UK, 1995. Springer.
-
(1995)
Proceedings of the Third Annual European Symposium on Algorithms
, pp. 327-340
-
-
Sutinen, E.1
Tarhio, J.2
-
44
-
-
78449293693
-
Engineering a compressed suffix tree implementation
-
N. Vaelimaeki, V. Maekinen, W. Gerlach, and K. Dixit. Engineering a compressed suffix tree implementation. ACM Journal of Experimental Algorithmics, 14, 2009.
-
(2009)
ACM Journal of Experimental Algorithmics
, vol.14
-
-
Vaelimaeki, N.1
Maekinen, V.2
Gerlach, W.3
Dixit, K.4
-
47
-
-
84862702293
-
Can we beat the prefix filtering: an adaptive framework for similarity join and search
-
J. Wang, G. Li, and J. Feng. Can we beat the prefix filtering: an adaptive framework for similarity join and search. In SIGMOD Conference, pages 85-96, 2012.
-
(2012)
SIGMOD Conference
, pp. 85-96
-
-
Wang, J.1
Li, G.2
Feng, J.3
-
48
-
-
70849115286
-
Efficient approximate entity extraction with edit distance constraints
-
New York, NY, USA ACM
-
W. Wang, C. Xiao, X. Lin, and C. Zhang. Efficient approximate entity extraction with edit distance constraints. In Proceedings of the ACM SIGMOD International Conference on Management of data, pages 759-770, New York, NY, USA, 2009. ACM.
-
(2009)
Proceedings of the ACM SIGMOD International Conference on Management of data
, pp. 759-770
-
-
Wang, W.1
Xiao, C.2
Lin, X.3
Zhang, C.4
-
49
-
-
85039635408
-
Efficient direct search on compressed genomic data
-
X. Yang, B. Wang, C. Li, J. Wang, and X. Xie. Efficient direct search on compressed genomic data. In Proceedings of the IEEE International Conference on Data Engineering (ICDE), Australia (to appear; preprint at http://www.ics.uci.edu/xhx/publications/genomecompress.pdf).
-
In Proceedings of the IEEE International Conference on Data Engineering (ICDE), Australia (to appear; preprint at
-
-
Yang, X.1
Wang, B.2
Li, C.3
Wang, J.4
Xie, X.5
-
50
-
-
84873101180
-
A generic framework for efficient and effective subsequence retrieval
-
H. Zhu, G. Kollios, and V. Athitsos. A generic framework for efficient and effective subsequence retrieval. Proceedings VLDB Endow., 5(11):1579-1590, July 2012.
-
(2012)
Proceedings VLDB Endow
, vol.5
, Issue.11
, pp. 1579-1590
-
-
Zhu, H.1
Kollios, G.2
Athitsos, V.3
|