-
1
-
-
36448948250
-
Extending assembly of short DNA sequences to handle error
-
W. R. Jeck, J. A. Reinhardt, D. A. Baltrus, M. T. Hickenbotham, V. Magrini, E. R. Mardis, J. L. Dangl, and C. D. Jones, "Extending assembly of short DNA sequences to handle error," Bioinformatics, vol. 23, no. 21, p. 2942, 2007.
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, pp. 2942
-
-
Jeck, W.R.1
Reinhardt, J.A.2
Baltrus, D.A.3
Hickenbotham, M.T.4
Magrini, V.5
Mardis, E.R.6
Dangl, J.L.7
Jones, C.D.8
-
2
-
-
0035859921
-
An eulerian path approach to DNA fragment assembly
-
P. A. Pevzner, H. Tang, and M. S. Waterman, "An eulerian path approach to DNA fragment assembly," Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 17, p. 9748, 2001.
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.17
, pp. 9748
-
-
Pevzner, P.A.1
Tang, H.2
Waterman, M.S.3
-
3
-
-
27544497879
-
The fragment assembly string graph
-
[Online]. Available
-
E. W. Myers, "The fragment assembly string graph," Bioinformatics, vol. 21, no. suppl-2, pp. ii79-ii85, 2005. [Online]. Available: http://www.bioinformatics.oxfordjournals.org/cgi/ doi/10.1093/bioinformatics/ bti1114
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL.-2
-
-
Myers, E.W.1
-
4
-
-
66449136667
-
ABySS: A parallel assembler for short read sequence data
-
[Online]. Available
-
J. T. Simpson, K. Wong, S. D. Jackman, J. E. Schein, S. J. Jones, and I. Birol, "ABySS: a parallel assembler for short read sequence data," Genome Research, vol. 19, no. 6, pp. 1117-1123, 2009. [Online]. Available: http://genome.cshlp.org/cgi/doi/10.1101/gr.089532.108
-
(2009)
Genome Research
, vol.19
, Issue.6
, pp. 1117-1123
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.5
Birol, I.6
-
5
-
-
60849111957
-
Parallel short sequence assembly of transcriptomes
-
B. Jackson, P. Schnable, and S. Aluru, "Parallel short sequence assembly of transcriptomes," BMC bioinformatics, vol. 10, no. Suppl 1, p. S14,2009.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 1
-
-
Jackson, B.1
Schnable, P.2
Aluru, S.3
-
6
-
-
55849103219
-
Parallel construction of bidirected string graphs for genome assembly
-
[Online]. Available
-
B. G. Jackson and S. Aluru, "Parallel construction of bidirected string graphs for genome assembly," in 2008 37th International Conference on Parallel Processing, Portland, Oregon, USA, 2008, pp. 346-353. [Online]. Available: http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4625868
-
2008 37th International Conference on Parallel Processing, Portland, Oregon, USA, 2008
, pp. 346-353
-
-
Jackson, B.G.1
Aluru, S.2
-
7
-
-
0034833132
-
A new approach to fragment assembly in DNA sequencing
-
P. A. Pevzner, H. Tang, and M. S. Waterman, "A new approach to fragment assembly in DNA sequencing," in Proceedings of the fifth annual international conference on Computational biology, 2001, pp. 256-267.
-
Proceedings of the Fifth Annual International Conference on Computational Biology, 2001
, pp. 256-267
-
-
Pevzner, P.A.1
Tang, H.2
Waterman, M.S.3
-
8
-
-
39049156065
-
Short read fragment assembly of bacterial genomes
-
[Online]. Available
-
M. J. Chaisson and P. A. Pevzner, "Short read fragment assembly of bacterial genomes," Genome Research, vol. 18, no. 2, pp. 324-330, 2008. [Online]. Available: http://www.genome.org/cgi/doi/10.1101/gr.7088808
-
(2008)
Genome Research
, vol.18
, Issue.2
, pp. 324-330
-
-
Chaisson, M.J.1
Pevzner, P.A.2
-
9
-
-
0029955205
-
A new strategy for genome sequencing
-
May [Online]. Available
-
J. C. Venter, H. O. Smith, and L. Hood, "A new strategy for genome sequencing," Nature, vol. 381, no. 6581, pp. 364-366, May 1996. [Online]. Available: http://dx.doi.org/10.1038/381364a0
-
(1996)
Nature
, vol.381
, Issue.6581
, pp. 364-366
-
-
Venter, J.C.1
Smith, H.O.2
Hood, L.3
-
10
-
-
67449095888
-
Genome assembly reborn: Recent computational challenges
-
[Online]. Available
-
M. Pop, "Genome assembly reborn: recent computational challenges," Briefings in Bioinformatics, vol. 10, no. 4, pp. 354-366, 2009. [Online]. Available: http://bib.oxfordjournals.org/cgi/doi/10.1093/bib/ bbp026
-
(2009)
Briefings in Bioinformatics
, vol.10
, Issue.4
, pp. 354-366
-
-
Pop, M.1
-
11
-
-
37249080658
-
Computability of models for sequence assembly
-
P. Medvedev, K. Georgiou, G. Myers, and M. Brudno, "Computability of models for sequence assembly," Algorithms in Bioinformatics, pp. 289-301, 2007.
-
(2007)
Algorithms in Bioinformatics
, pp. 289-301
-
-
Medvedev, P.1
Georgiou, K.2
Myers, G.3
Brudno, M.4
-
12
-
-
43149085041
-
De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
-
[Online]. Available
-
D. Hernandez, P. Francois, L. Farinelli, M. Osteras, and J. Schrenzel, "De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer," Genome Research, vol. 18, no. 5, pp. 802-809, 2008. [Online]. Available: http://www.genome.org/cgi/ doi/10.1101/gr.072033.107
-
(2008)
Genome Research
, vol.18
, Issue.5
, pp. 802-809
-
-
Hernandez, D.1
Francois, P.2
Farinelli, L.3
Osteras, M.4
Schrenzel, J.5
-
14
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de bruijn graphs
-
[Online]. Available
-
D. R. Zerbino and E. Birney, "Velvet: Algorithms for de novo short read assembly using de bruijn graphs," Genome Research, vol. 18, no. 5, pp. 821-829, 2008. [Online]. Available: http: //www.genome.org/cgi/doi/10.1101/gr. 074492.107
-
(2008)
Genome Research
, vol.18
, Issue.5
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
15
-
-
60949086787
-
Crystallizing short- read assemblies around seeds
-
[Online]. Available
-
M. Hossain, N. Azimi, and S. Skiena, "Crystallizing short- read assemblies around seeds," BMC Bioinformatics, vol. 10, no. Suppl 1, p. S16, 2009. [Online]. Available: http://www.biomedcentral.com/ 1471-2105/10/S1/S16
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 1
-
-
Hossain, M.1
Azimi, N.2
Skiena, S.3
-
16
-
-
43149086380
-
ALLPATHS: De novo assembly of whole-genome shotgun microreads
-
J. Butler, I. MacCallum, M. Kleber, I. A. Shlyakhter, M. K. Belmonte, E. S. Lander, C. Nusbaum, and D. B. Jaffe, "ALLPATHS: de novo assembly of whole-genome shotgun microreads," Genome Research, vol. 18, no. 5, p. 810, 2008.
-
(2008)
Genome Research
, vol.18
, Issue.5
, pp. 810
-
-
Butler, J.1
MacCallum, I.2
Kleber, M.3
Shlyakhter, I.A.4
Belmonte, M.K.5
Lander, E.S.6
Nusbaum, C.7
Jaffe, D.B.8
-
17
-
-
0012999647
-
A comparison of parallel algorithms for connected components
-
[Online]. Available
-
J. Greiner, "A comparison of parallel algorithms for connected components," in Proceedings of the sixth annual ACM symposium on Parallel algorithms and architectures - SPAA '94, Cape May, New Jersey, United States, 1994, pp. 16-25. [Online]. Available: http://portal.acm.org/citation.cfm?doid= 181014.181021
-
Proceedings of the Sixth Annual ACM Symposium on Parallel Algorithms and Architectures - SPAA '94, Cape May, New Jersey, United States, 1994
, pp. 16-25
-
-
Greiner, J.1
-
18
-
-
38149048421
-
Techniques for designing efficient parallel graph algorithms for SMPs and multicore processors
-
G. Cong and D. A. Bader, "Techniques for designing efficient parallel graph algorithms for SMPs and multicore processors," Lecture Notes in Computer Science, vol. 4742, p. 137, 2007.
-
(2007)
Lecture Notes in Computer Science
, vol.4742
, pp. 137
-
-
Cong, G.1
Bader, D.A.2
-
19
-
-
0020183349
-
Efficient parallel algorithms for some graph problems
-
F. Y. Chin, J. Lam, I. Chen et al., "Efficient parallel algorithms for some graph problems," Communications of the ACM, vol. 25, no. 9, p. 665,1982.
-
(1982)
Communications of the ACM
, vol.25
, Issue.9
, pp. 665
-
-
Chin, F.Y.1
Lam, J.2
Chen, I.3
-
21
-
-
0030646267
-
A distributed algorithm for constructing an Eulerian tour
-
IEEE
-
S. Makki, "A distributed algorithm for constructing an Eulerian tour," in Performance, Computing, and Communications Conference, 1997. IPCCC 1997., IEEE International. IEEE, 1997, pp. 94-100.
-
(1997)
Performance, Computing, and Communications Conference, 1997. IPCCC 1997., IEEE International
, pp. 94-100
-
-
Makki, S.1
-
22
-
-
85034217228
-
Finding euler circuits in logarithmic parallel time
-
Not Known, [Online]. Available
-
B. Awerbuch, A. Israeli, and Y. Shiloach, "Finding euler circuits in logarithmic parallel time," in Proceedings of the sixteenth annual ACM symposium on Theory of computing - STOC '84, Not Known, 1984, pp. 249-257. [Online]. Available: http://portal.acm.org/citation.cfm?doid= 800057.808688
-
(1984)
Proceedings of the Sixteenth Annual ACM Symposium on Theory of Computing - STOC '84
, pp. 249-257
-
-
Awerbuch, B.1
Israeli, A.2
Shiloach, Y.3
-
23
-
-
0000019758
-
New connectivity and MSF algorithms for Shuffle-Exchange network and PRAM
-
[Online]. Available
-
Awerbuch and Shiloach, "New connectivity and MSF algorithms for Shuffle-Exchange network and PRAM," IEEE Transactions on Computers, vol. C-36, no. 10, pp. 1258-1263, 1987. [Online]. Available: http://ieeexplore.ieee. org/lpdocs/epic03/wrapper.htm?arnumber=1676869
-
(1987)
IEEE Transactions on Computers
, vol.C-36
, Issue.10
, pp. 1258-1263
-
-
Awerbuch1
Shiloach2
-
24
-
-
78650600092
-
-
Proceedings of the
-
J. Siek, L. Lee, A. Lumsdaine, L. Lee, L. Blackford, J. Demmel, J. Dongarra, I. Duff, S. Hammarling, M. Heroux et al., "The boost graph library: User guide and reference manual," in Proceedings of the, vol. 243, 2002, pp. 112-121.
-
(2002)
The Boost Graph Library: User Guide and Reference Manual
, vol.243
, pp. 112-121
-
-
Siek, J.1
Lee, L.2
Lumsdaine, A.3
Lee, L.4
Blackford, L.5
Demmel, J.6
Dongarra, J.7
Duff, I.8
Hammarling, S.9
Heroux, M.10
-
25
-
-
49049132956
-
An (log) parallel connectivity algorithm
-
[Online]. Available
-
Y. Shiloach and U. Vishkin, "An (log) parallel connectivity algorithm," Journal of Algorithms, vol. 3, no. 1, pp. 57-67, 1982. [Online]. Available: http://linkinghub.elsevier.com/retrieve/pii/ 0196677482900086
-
(1982)
Journal of Algorithms
, vol.3
, Issue.1
, pp. 57-67
-
-
Shiloach, Y.1
Vishkin, U.2
-
26
-
-
77749295512
-
Realtime parallel hashing on the GPU
-
[Online]. Available
-
D. A. Alcantara, A. Sharf, F. Abbasinejad, S. Sengupta, M. Mitzenmacher, J. D. Owens, and N. Amenta, "Realtime parallel hashing on the GPU," ACM Transactions on Graphics, vol. 28, no. 5, p. 1, 2009. [Online]. Available: http://portal.acm.org/citation.cfm?doid=1618452.1618500
-
(2009)
ACM Transactions on Graphics
, vol.28
, Issue.5
, pp. 1
-
-
Alcantara, D.A.1
Sharf, A.2
Abbasinejad, F.3
Sengupta, S.4
Mitzenmacher, M.5
Owens, J.D.6
Amenta, N.7
-
27
-
-
36049035884
-
Parallel prefix sum (scan) with cuda
-
H. Nguyen, Ed. Addison Wesley, Aug.
-
M. Harris, S. Sengupta, and J. D. Owens, "Parallel prefix sum (scan) with cuda," in GPU Gems 3, H. Nguyen, Ed. Addison Wesley, Aug.2007.
-
(2007)
GPU Gems
, vol.3
-
-
Harris, M.1
Sengupta, S.2
Owens, J.D.3
-
28
-
-
77952833958
-
-
Citeseer, Tech. Rep.
-
S. Sengupta, M. Harris, and M. Garland, "Efficient parallel scan algorithms for GPUs," Citeseer, Tech. Rep., 2008.
-
(2008)
Efficient Parallel Scan Algorithms for GPUs
-
-
Sengupta, S.1
Harris, M.2
Garland, M.3
-
29
-
-
78651284120
-
Scan primitives for gpu computing
-
ACM, Aug.
-
S. Sengupta, M. Harris, Y. Zhang, and J. D. Owens, "Scan primitives for gpu computing," in Graphics Hardware 2007. ACM, Aug. 2007,pp. 97-106.
-
(2007)
Graphics Hardware 2007
, pp. 97-106
-
-
Sengupta, S.1
Harris, M.2
Zhang, Y.3
Owens, J.D.4
-
31
-
-
54949137701
-
MetaSim- A sequencing simulator for genomics and metagenomics
-
D. C. Richter, F. Ott, A. F. Auch, R. Schmid, and D. H. Huson, "MetaSim- a sequencing simulator for genomics and metagenomics," PLoS One, vol. 3, no. 10, p. 3373, 2008.
-
(2008)
PLoS One
, vol.3
, Issue.10
, pp. 3373
-
-
Richter, D.C.1
Ott, F.2
Auch, A.F.3
Schmid, R.4
Huson, D.H.5
-
32
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
S. Kurtz, A. Phillippy, A. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S. Salzberg, "Versatile and open software for comparing large genomes," Genome biology, vol. 5, no. 2, p. R12, 2004.
-
(2004)
Genome Biology
, vol.5
, Issue.2
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
Salzberg, S.7
-
33
-
-
77953984180
-
Parallel de novo assembly of large genomes from high-throughput short reads
-
B. G. Jackson, M. Regennitter, X. Yang, P. S. Schnable, and S. Aluru, "Parallel de novo assembly of large genomes from high-throughput short reads," in Parallel & Distributed Processing (IPDPS), 2010 IEEE International Symposium on, 2010, pp. 1-10.
-
Parallel & Distributed Processing (IPDPS), 2010 IEEE International Symposium On, 2010
, pp. 1-10
-
-
Jackson, B.G.1
Regennitter, M.2
Yang, X.3
Schnable, P.S.4
Aluru, S.5
|