-
1
-
-
84975742565
-
A map of human genome variation from population-scale sequencing
-
1000 Genomes Proj Consort
-
1000 Genomes Proj. Consort. 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061-73
-
(2010)
Nature
, vol.467
, pp. 1061-1073
-
-
-
2
-
-
0034708480
-
The genome sequence of Drosophila melanogaster
-
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, et al. 2000. The genome sequence of Drosophila melanogaster. Science 287:2185-95
-
(2000)
Science
, vol.287
, pp. 2185-2195
-
-
Adams, M.D.1
Celniker, S.E.2
Holt, R.A.3
Evans, C.A.4
Gocayne, J.D.5
-
3
-
-
27744525806
-
Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp Nipponbare) genome sequence: Sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome
-
Ammiraju JS, Yu Y, Luo M, Kudrna D, Kim H, et al. 2005. Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Nipponbare) genome sequence: sequencing of gap-specific fosmid clones uncovers new euchromatic portions of the genome. Theor. Appl. Genet. 111:1596-607
-
(2005)
Theor. Appl. Genet
, vol.111
, pp. 1596-1607
-
-
Ammiraju, J.S.1
Yu, Y.2
Luo, M.3
Kudrna, D.4
Kim, H.5
-
4
-
-
84860771820
-
SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich A, Nurk S, Antipov D, Gurevich AA, DvorkinM, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19:455-77
-
(2012)
J. Comput. Biol
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
-
5
-
-
84922706733
-
String graph construction using incremental hashing
-
Ben-Bassat I,Chor B. 2014. String graph construction using incremental hashing. Bioinformatics 30:3515-23
-
(2014)
Bioinformatics
, vol.30
, pp. 3515-3523
-
-
Ben-Bassat, I.1
Chor, B.2
-
6
-
-
84930851165
-
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
-
Berlin K, Koren S, Chin C-S, Drake JP, Landolin JM, Phillippy AM. 2015. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33:623-30
-
(2015)
Nat. Biotechnol
, vol.33
, pp. 623-630
-
-
Berlin, K.1
Koren, S.2
Chin, C.-S.3
Drake, J.P.4
Landolin, J.M.5
Phillippy, A.M.6
-
7
-
-
0014814325
-
Space/time trade-offs in hash coding with allowable errors
-
Bloom BH. 1970. Space/time trade-offs in hash coding with allowable errors. Commun. ACM 13:422-26
-
(1970)
Commun. ACM
, vol.13
, pp. 422-426
-
-
Bloom, B.H.1
-
8
-
-
79951530130
-
Scaffolding pre-assembled contigs using SSPACE
-
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27:578-79
-
(2011)
Bioinformatics
, vol.27
, pp. 578-579
-
-
Boetzer, M.1
Henkel, C.V.2
Jansen, H.J.3
Butler, D.4
Pirovano, W.5
-
9
-
-
84866656074
-
Succinct de Bruijn graphs
-
ed. B Raphael, J Tang Lect. Notes Bioinform. 7534. Berlin: Springer
-
Bowe A, Onodera T, Sadakane K, Shibuya T. 2012. Succinct de Bruijn graphs. In Algorithms in Bioinformatics, ed. B Raphael, J Tang, pp. 225-35. Lect. Notes Bioinform. 7534. Berlin: Springer
-
(2012)
Algorithms in Bioinformatics
, pp. 225-235
-
-
Bowe, A.1
Onodera, T.2
Sadakane, K.3
Shibuya, T.4
-
10
-
-
84958523793
-
GAML: Genome assembly by maximum likelihood
-
ed. D Brown, B Morgenstern, pp. Lect. Notes Bioinform. 8701. Berlin Springer
-
Boža V, Brejová B, Vinař T. 2014. GAML: genome assembly by maximum likelihood. In Algorithms in Bioinformatics, ed. D Brown, B Morgenstern, pp. 122-34. Lect.Notes Bioinform. 8701. Berlin: Springer
-
(2014)
Algorithms in Bioinformatics
, pp. 122-134
-
-
Boža, V.1
Brejová, B.2
Vinař, T.3
-
11
-
-
84991528460
-
Assemblathon 2: Evaluating de novo methods of genome assembly in three vertebrate species
-
Bradnam KR, Fass JN, Alexandrov A, Baranay P, BechnerM, et al. 2013. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience 2:10
-
(2013)
GigaScience
, vol.2
, pp. 10
-
-
Bradnam, K.R.1
Fass, J.N.2
Alexandrov, A.3
Baranay, P.4
Bechner, M.5
-
12
-
-
84870260198
-
Analysis of the bread wheat genome using whole-genome shotgun sequencing
-
Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, et al. 2012. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491:705-10
-
(2012)
Nature
, vol.491
, pp. 705-710
-
-
Brenchley, R.1
Spannagl, M.2
Pfeifer, M.3
Barker, G.L.4
D'Amore, R.5
-
13
-
-
43149086380
-
ALLPATHS: De novo assembly of whole-genome shotgun microreads
-
Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, et al. 2008. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18:810-20
-
(2008)
Genome Res
, vol.18
, pp. 810-820
-
-
Butler, J.1
MacCallum, I.2
Kleber, M.3
Shlyakhter, I.A.4
Belmonte, M.K.5
-
14
-
-
84859319800
-
Computational techniques for human genome resequencing using mated gapped reads
-
Carnevali P, Baccash J, Halpern AL, Nazarenko I, Nilsen GB, et al. 2012. Computational techniques for human genome resequencing using mated gapped reads. J. Comput. Biol. 19:279-92
-
(2012)
J. Comput. Biol
, vol.19
, pp. 279-292
-
-
Carnevali, P.1
Baccash, J.2
Halpern, A.L.3
Nazarenko, I.4
Nilsen, G.B.5
-
15
-
-
39049156065
-
Short read fragment assembly of bacterial genomes
-
ChaissonMJ, Pevzner PA. 2008. Short read fragment assembly of bacterial genomes. Genome Res. 18:324-30
-
(2008)
Genome Res
, vol.18
, pp. 324-330
-
-
Chaisson, M.J.1
Pevzner, P.A.2
-
16
-
-
84866687164
-
Space-efficient and exact de Bruijn graph representation based on a bloom filter
-
ed. B Raphael, J Tang, pp. 236-48. Lect. Notes Bioinform. 7534. Berlin: Springer
-
Chikhi R, Rizk G. 2012. Space-efficient and exact de Bruijn graph representation based on a bloom filter. In Algorithms in Bioinformatics, ed. B Raphael, J Tang, pp. 236-48. Lect. Notes Bioinform. 7534. Berlin: Springer
-
(2012)
Algorithms in Bioinformatics
-
-
Chikhi, R.1
Rizk, G.2
-
17
-
-
84880798154
-
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
-
Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563-69
-
(2013)
Nat. Methods
, vol.10
, pp. 563-569
-
-
Chin, C.S.1
Alexander, D.H.2
Marks, P.3
Klammer, A.A.4
Drake, J.5
-
18
-
-
84874322149
-
ALE: A generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
-
Clark SC, Egan R, Frazier PI, Wang Z. 2013. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics 29:435-43
-
(2013)
Bioinformatics
, vol.29
, pp. 435-443
-
-
Clark, S.C.1
Egan, R.2
Frazier, P.I.3
Wang, Z.4
-
19
-
-
79951526698
-
Succinct data structures for assembling large genomes
-
Conway TC, Bromage AJ. 2011. Succinct data structures for assembling large genomes. Bioinformatics 27:479-86
-
(2011)
Bioinformatics
, vol.27
, pp. 479-486
-
-
Conway, T.C.1
Bromage, A.J.2
-
20
-
-
84957005432
-
Pooled genomic indexing (PGI):mathematical analysis and experiment design
-
ed. R Guigó, D Gusfield, pp. 10-28. Lect. Notes Comput. Sci. 2452. Berlin: Springer
-
Csurös M, Milosavljevic A. 2002. Pooled genomic indexing (PGI):mathematical analysis and experiment design. In Algorithms in Bioinformatics, ed. R Guigó, D Gusfield, pp. 10-28. Lect. Notes Comput. Sci. 2452. Berlin: Springer
-
(2002)
Algorithms in Bioinformatics
-
-
Csurös, M.1
Milosavljevic, A.2
-
21
-
-
77954324418
-
SOPRA: Scaffolding algorithm for paired reads via statistical optimization
-
Dayarian A, Michael TP, Sengupta AM. 2010. SOPRA: scaffolding algorithm for paired reads via statistical optimization. BMC Bioinform. 11:345
-
(2010)
BMC Bioinform
, vol.11
, pp. 345
-
-
Dayarian, A.1
Michael, T.P.2
Sengupta, A.M.3
-
22
-
-
21044451909
-
A tool for analyzing mate pairs in assemblies (TAMPA
-
Dew IM, Walenz B, Sutton G. 2005. A tool for analyzing mate pairs in assemblies (TAMPA). J. Comput. Biol. 12:497-513
-
(2005)
J. Comput. Biol
, vol.12
, pp. 497-513
-
-
Dew, I.M.1
Walenz, B.2
Sutton, G.3
-
23
-
-
79960120736
-
Amemory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly
-
Dinh H, Rajasekaran S. 2011.Amemory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly. Bioinformatics 27:1901-7
-
(2011)
Bioinformatics
, vol.27
, pp. 1901-1907
-
-
Dinh, H.1
Rajasekaran, S.2
-
24
-
-
84874330144
-
SCARPA: Scaffolding reads with practical algorithms
-
Donmez N, Brudno M. 2013. SCARPA: scaffolding reads with practical algorithms. Bioinformatics 29:428-34
-
(2013)
Bioinformatics
, vol.29
, pp. 428-434
-
-
Donmez, N.1
Brudno, M.2
-
25
-
-
83055181941
-
Assemblathon 1: A competitive assessment of de novo short read assembly methods
-
Earl D, Bradnam K, St. John J, Darling A, Lin D, et al. 2011. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 21:2224-41
-
(2011)
Genome Res
, vol.21
, pp. 2224-2241
-
-
Earl, D.1
Bradnam, K.2
St. John, J.3
Darling, A.4
Lin, D.5
-
26
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
Eid J, Fehr A, Gray J, Luong K, Lyle J, et al. 2009. Real-time DNA sequencing from single polymerase molecules. Science 323:133-38
-
(2009)
Science
, vol.323
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
Luong, K.4
Lyle, J.5
-
27
-
-
36949007183
-
Strainer: Software for analysis of population variation in community genomic datasets
-
Eppley JM, Tyson GW, Getz WM, Banfield JF. 2007. Strainer: software for analysis of population variation in community genomic datasets. BMC Bioinform. 8:398
-
(2007)
BMC Bioinform
, vol.8
, pp. 398
-
-
Eppley, J.M.1
Tyson, G.W.2
Getz, W.M.3
Banfield, J.F.4
-
28
-
-
0034506014
-
Opportunistic data structures with applications
-
41st, Redondo Beach, CA, Nov. 12-14
-
Ferragina P, Manzini G. 2000. Opportunistic data structures with applications. Presented at Annu. Symp. Found. Comput. Sci., 41st, Redondo Beach, CA, Nov. 12-14
-
(2000)
Presented at Annu. Symp. Found. Comput. Sci
-
-
Ferragina, P.1
Manzini, G.2
-
29
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
-
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
Clayton, R.A.4
Kirkness, E.F.5
-
30
-
-
80955159932
-
Opera: Reconstructing optimal genomic scaffolds with highthroughput paired-end sequences
-
Gao S, Sung WK, Nagarajan N. 2011. Opera: reconstructing optimal genomic scaffolds with highthroughput paired-end sequences. J. Comput. Biol. 18:1681-91
-
(2011)
J. Comput. Biol
, vol.18
, pp. 1681-1691
-
-
Gao, S.1
Sung, W.K.2
Nagarajan, N.3
-
31
-
-
84882295406
-
De novo likelihood-basedmeasures for comparing genome assemblies
-
GhodsiM,Hill CM, Astrovskaya I, LinH, Sommer DD, et al. 2013. De novo likelihood-basedmeasures for comparing genome assemblies. BMC Res. Notes 6:334
-
(2013)
BMC Res. Notes
, vol.6
, pp. 334
-
-
Ghodsi, M.1
Hill, C.M.2
Astrovskaya, I.3
Lin, H.4
Sommer, D.D.5
-
32
-
-
79952178131
-
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
-
Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, et al. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. PNAS 108:1513-18
-
(2011)
PNAS
, vol.108
, pp. 1513-1518
-
-
Gnerre, S.1
MacCallum, I.2
Przybylski, D.3
Ribeiro, F.J.4
Burton, J.N.5
-
33
-
-
84860523681
-
Readjoiner: A fast and memory efficient string graph-based sequence assembler
-
Gonnella G, Kurtz S. 2012. Readjoiner: a fast and memory efficient string graph-based sequence assembler. BMC Bioinform. 13:82
-
(2012)
BMC Bioinform
, vol.13
, pp. 82
-
-
Gonnella, G.1
Kurtz, S.2
-
35
-
-
0030972827
-
Against a whole-genome shotgun
-
Green P. 1997. Against a whole-genome shotgun. Genome Res. 7:410-17
-
(1997)
Genome Res
, vol.7
, pp. 410-417
-
-
Green, P.1
-
36
-
-
43149085041
-
De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
-
HernandezD, Francois P, Farinelli L, Osteras M, Schrenzel J. 2008. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res. 18:802-9
-
(2008)
Genome Res
, vol.18
, pp. 802-809
-
-
Hernandez, D.1
Francois, P.2
Farinelli, L.3
Osteras, M.4
Schrenzel, J.5
-
37
-
-
0032849859
-
CAP3: A DNA sequence assembly program
-
Huang X, Madan A. 1999. CAP3: a DNA sequence assembly program. Genome Res. 9:868-77
-
(1999)
Genome Res
, vol.9
, pp. 868-877
-
-
Huang, X.1
Madan, A.2
-
38
-
-
84878076144
-
REAPR: A universal tool for genome assembly evaluation
-
Hunt M, Kikuchi T, Sanders M, Newbold C, BerrimanM, Otto TD. 2013. REAPR: a universal tool for genome assembly evaluation. Genome Biol. 14:R47
-
(2013)
Genome Biol
, vol.14
, pp. R47
-
-
Hunt, M.1
Kikuchi, T.2
Sanders, M.3
Newbold, C.4
Berriman, M.5
Otto, T.D.6
-
40
-
-
0029312687
-
A new algorithm for DNA sequence assembly
-
Idury RM, Waterman MS. 1995. A new algorithm for DNA sequence assembly. J. Comput. Biol. 2:291-306
-
(1995)
J. Comput. Biol
, vol.2
, pp. 291-306
-
-
Idury, R.M.1
Waterman, M.S.2
-
41
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
Int. Hum. Genome Seq. Consort
-
Int. Hum. Genome Seq. Consort. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
-
42
-
-
84856246802
-
De novo assembly and genotyping of variants using colored de Bruijn graphs
-
Iqbal Z, CaccamoM, Turner I, Flicek P,McVean G. 2012. De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat. Genet. 44:226-32
-
(2012)
Nat. Genet
, vol.44
, pp. 226-232
-
-
Iqbal, Z.1
Caccamo, M.2
Turner, I.3
Flicek, P.4
McVean, G.5
-
43
-
-
0037267048
-
Whole-genome sequence assembly for mammalian genomes: Arachne 2
-
JaffeDB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, et al. 2003. Whole-genome sequence assembly for mammalian genomes: Arachne 2 Genome Res. 13:91-96
-
(2003)
Genome Res
, vol.13
, pp. 91-96
-
-
Jaffe, D.B.1
Butler, J.2
Gnerre, S.3
Mauceli, E.4
Lindblad-Toh, K.5
-
44
-
-
36448948250
-
Extending assembly of short DNA sequences to handle error
-
Jeck WR, Reinhardt JA, Baltrus DA, HickenbothamMT, Magrini V, et al. 2007. Extending assembly of short DNA sequences to handle error. Bioinformatics 23:2942-44
-
(2007)
Bioinformatics
, vol.23
, pp. 2942-2944
-
-
Jeck, W.R.1
Reinhardt, J.A.2
Baltrus, D.A.3
Hickenbotham, M.T.4
Magrini, V.5
-
45
-
-
0029197192
-
Combinatorial algorithms for DNA sequence assembly
-
Kececioglu JD, Myers EW. 1995. Combinatorial algorithms for DNA sequence assembly. Algorithmica 13:7-51
-
(1995)
Algorithmica
, vol.13
, pp. 7-51
-
-
Kececioglu, J.D.1
Myers, E.W.2
-
46
-
-
0034837599
-
Assembly of the working draft of the human genome with GigAssembler
-
Kent WJ, Haussler D. 2001. Assembly of the working draft of the human genome with GigAssembler. Genome Res. 11:1541-48
-
(2001)
Genome Res
, vol.11
, pp. 1541-1548
-
-
Kent, W.J.1
Haussler, D.2
-
47
-
-
76749117156
-
Assembly complexity of prokaryotic genomes using short reads
-
Kingsford C, SchatzMC, PopM. 2010. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinform. 11:21
-
(2010)
BMC Bioinform
, vol.11
, pp. 21
-
-
Kingsford, C.1
Schatz, M.C.2
Pop, M.3
-
48
-
-
84883664726
-
Reducing assembly complexity of microbial genomes with single-molecule sequencing
-
Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, et al. 2013. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biol. 14:R101
-
(2013)
Genome Biol
, vol.14
, pp. R101
-
-
Koren, S.1
Harhay, G.P.2
Smith, T.P.3
Bono, J.L.4
Harhay, D.M.5
-
49
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, et al. 2012. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30:693-700
-
(2012)
Nat. Biotechnol
, vol.30
, pp. 693-700
-
-
Koren, S.1
Schatz, M.C.2
Walenz, B.P.3
Martin, J.4
Howard, J.T.5
-
50
-
-
84901469882
-
Automated ensemble assembly and validation of microbial genomes
-
Koren S, Treangen TJ, Hill C, PopM, Phillippy A. 2014. Automated ensemble assembly and validation of microbial genomes. BMC Bioinform. 15:126
-
(2014)
BMC Bioinform
, vol.15
, pp. 126
-
-
Koren, S.1
Treangen, T.J.2
Hill, C.3
Pop, M.4
Phillippy, A.5
-
52
-
-
0023988195
-
Genomic mapping by fingerprinting random clones: A mathematical analysis
-
Lander ES, Waterman MS. 1988. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2:231-39
-
(1988)
Genomics
, vol.2
, pp. 231-239
-
-
Lander, E.S.1
Waterman, M.S.2
-
53
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, PopM, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
54
-
-
84864119729
-
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
-
Li H. 2012. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics 28:1838-44
-
(2012)
Bioinformatics
, vol.28
, pp. 1838-1844
-
-
Li, H.1
-
55
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-60
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
56
-
-
75149155568
-
The sequence and de novo assembly of the giant panda genome
-
Li R, FanW, Tian G, Zhu H, He L, et al. 2010. The sequence and de novo assembly of the giant panda genome. Nature 463:311-17
-
(2010)
Nature
, vol.463
, pp. 311-317
-
-
Li, R.1
Fan, W.2
Tian, G.3
Zhu, H.4
He, L.5
-
57
-
-
67650711615
-
SOAP2: An improved ultrafast tool for short read alignment
-
Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. 2009. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966-67
-
(2009)
Bioinformatics
, vol.25
, pp. 1966-1967
-
-
Li, R.1
Yu, C.2
Li, Y.3
Lam, T.W.4
Yiu, S.M.5
-
58
-
-
18844405663
-
Space-efficient whole genome comparisons with Burrows-Wheeler transforms
-
Lippert RA. 2005. Space-efficient whole genome comparisons with Burrows-Wheeler transforms. J. Comput. Biol. 12:407-15
-
(2005)
J. Comput. Biol
, vol.12
, pp. 407-415
-
-
Lippert, R.A.1
-
59
-
-
84876934998
-
Combinatorial pooling enables selective sequencing of the barley gene space
-
Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, et al. 2013. Combinatorial pooling enables selective sequencing of the barley gene space. PLOS Comput. Biol. 9:e1003010
-
(2013)
PLOS Comput. Biol
, vol.9
, pp. e1003010
-
-
Lonardi, S.1
Duma, D.2
Alpert, M.3
Cordero, F.4
Beccuti, M.5
-
60
-
-
84942887758
-
SOAPdenovo2: An empirically improved memoryefficient short-read de novo assembler
-
Luo R, Liu B, Xie Y, Li Z, Huang W, et al. 2012. SOAPdenovo2: an empirically improved memoryefficient short-read de novo assembler. GigaScience 1:18
-
(2012)
GigaScience
, vol.1
, pp. 18
-
-
Luo, R.1
Liu, B.2
Xie, Y.3
Li, Z.4
Huang, W.5
-
61
-
-
84976657294
-
The complexity of some problems on subsequences and supersequences
-
MaierD. 1978. The complexity of some problems on subsequences and supersequences. J. ACM25:322-36
-
(1978)
J. ACM25
, pp. 322-336
-
-
Maier, D.1
-
62
-
-
70349204183
-
Maximum likelihood genome assembly
-
Medvedev P, Brudno M. 2009. Maximum likelihood genome assembly. J. Comput. Biol. 16:1101-16
-
(2009)
J. Comput. Biol
, vol.16
, pp. 1101-1116
-
-
Medvedev, P.1
Brudno, M.2
-
63
-
-
37249080658
-
Computability of models for sequence assembly
-
ed. R Giancarlo, S Hannenhalli, pp. 289-301. Lect. Notes. Bioinform. 4645. Berlin: Springer
-
Medvedev P, Georgiou K, Myers G, Brudno M. 2007. Computability of models for sequence assembly. In Algorithms in Bioinformatics, ed. R Giancarlo, S Hannenhalli, pp. 289-301. Lect. Notes. Bioinform. 4645. Berlin: Springer
-
(2007)
Algorithms in Bioinformatics
-
-
Medvedev, P.1
Georgiou, K.2
Myers, G.3
Brudno, M.4
-
64
-
-
80955139667
-
Paired de Bruijn graphs: A novel approach for incorporating mate pair information into genome assemblers
-
Medvedev P, Pham S, ChaissonM,TeslerG, Pevzner P. 2011. Paired de Bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. J. Comput. Biol. 18:1625-34
-
(2011)
J. Comput. Biol
, vol.18
, pp. 1625-1634
-
-
Medvedev, P.1
Pham, S.2
Chaisson, M.3
Tesler, G.4
Pevzner, P.5
-
65
-
-
81155158421
-
Efficient counting of k-mers in DNA sequences using a bloom filter
-
Melsted P, Pritchard JK. 2011. Efficient counting of k-mers in DNA sequences using a bloom filter. BMC Bioinform. 12:333
-
(2011)
BMC Bioinform
, vol.12
, pp. 333
-
-
Melsted, P.1
Pritchard, J.K.2
-
66
-
-
84936754552
-
Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads
-
Moncunill V, Gonzalez S, Bea S, Andrieux LO, Salaverria I, et al. 2014. Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads. Nat. Biotechnol. 32:1106-12
-
(2014)
Nat. Biotechnol
, vol.32
, pp. 1106-1112
-
-
Moncunill, V.1
Gonzalez, S.2
Bea, S.3
Andrieux, L.O.4
Salaverria, I.5
-
67
-
-
79551622954
-
Strain-resolved community genomic analysis of gut microbial colonization in a premature infant
-
Morowitz MJ, Denef VJ, Costello EK, Thomas BC, Poroyko V, et al. 2011. Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. PNAS 108:1128-33
-
(2011)
PNAS
, vol.108
, pp. 1128-1133
-
-
Morowitz, M.J.1
Denef, V.J.2
Costello, E.K.3
Thomas, B.C.4
Poroyko, V.5
-
68
-
-
0029312158
-
Toward simplifying and accurately formulating fragment assembly
-
Myers EW. 1995. Toward simplifying and accurately formulating fragment assembly. J. Comput. Biol. 2:275-90
-
(1995)
J. Comput. Biol
, vol.2
, pp. 275-290
-
-
Myers, E.W.1
-
69
-
-
27544497879
-
The fragment assembly string graph
-
Myers EW. 2005. The fragment assembly string graph. Bioinformatics 21(Suppl. 2):ii79-85
-
(2005)
Bioinformatics
, vol.21
, pp. ii79-85
-
-
Myers, E.W.1
-
70
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, et al. 2000. A whole-genome assembly of Drosophila. Science 287:2196-204
-
(2000)
Science
, vol.287
, pp. 2196-2204
-
-
Myers, E.W.1
Sutton, G.G.2
Delcher, A.L.3
Dew, I.M.4
Fasulo, D.P.5
-
72
-
-
84958554065
-
Efficient local alignment discovery amongst noisy long reads
-
ed. D Brown, B Morgenstern,. Lect. Notes Bioinform. 8701. Berlin: Springer
-
Myers G. 2014. Efficient local alignment discovery amongst noisy long reads. In Algorithms in Bioinformatics, ed. D Brown, B Morgenstern, pp. 52-67. Lect. Notes Bioinform. 8701. Berlin: Springer
-
(2014)
Algorithms in Bioinformatics
, pp. 52-67
-
-
Myers, G.1
-
73
-
-
70349212271
-
Parametric complexity of sequence assembly: Theory and applications to next generation sequencing
-
Nagarajan N, Pop M. 2009. Parametric complexity of sequence assembly: theory and applications to next generation sequencing. J. Comput. Biol. 16:897-908
-
(2009)
J. Comput. Biol
, vol.16
, pp. 897-908
-
-
Nagarajan, N.1
Pop, M.2
-
74
-
-
43349084767
-
Scaffolding and validation of bacterial genome assemblies using optical restriction maps
-
Nagarajan N, Read TD, Pop M. 2008. Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics 24:1229-35
-
(2008)
Bioinformatics
, vol.24
, pp. 1229-1235
-
-
Nagarajan, N.1
Read, T.D.2
Pop, M.3
-
75
-
-
84858992875
-
MetaVelvet: An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
-
New York ACM
-
Namiki T, Hachiya T, Tanaka H, Sakakibara Y. 2011. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. In Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pp. 116-24. New York: ACM
-
(2011)
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
, pp. 116-124
-
-
Namiki, T.1
Hachiya, T.2
Tanaka, H.3
Sakakibara, Y.4
-
76
-
-
84921783122
-
Accurate de novo and transmitted indel detection in exome-capture data using microassembly
-
Narzisi G, O'Rawe JA, Iossifov I, Fang H, Lee YH, et al. 2014. Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nat. Methods 11:1033-36
-
(2014)
Nat. Methods
, vol.11
, pp. 1033-1036
-
-
Narzisi, G.1
O'Rawe, J.A.2
Iossifov, I.3
Fang, H.4
Lee, Y.H.5
-
77
-
-
84890060577
-
Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold
-
Nijkamp JF, Pop M, Reinders MJ, de Ridder D. 2013. Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold. Bioinformatics 29:2826-34
-
(2013)
Bioinformatics
, vol.29
, pp. 2826-2834
-
-
Nijkamp, J.F.1
Pop, M.2
Reinders, M.J.3
De Ridder, D.4
-
78
-
-
0034764307
-
SSAHA: A fast search method for large DNA databases
-
Ning Z, Cox AJ, Mullikin JC. 2001. SSAHA: a fast search method for large DNA databases. Genome Res. 11:1725-29
-
(2001)
Genome Res
, vol.11
, pp. 1725-1729
-
-
Ning, Z.1
Cox, A.J.2
Mullikin, J.C.3
-
80
-
-
84865176493
-
Scalingmetagenome sequence assembly with probabilistic de Bruijn graphs
-
Pell J, Hintze A, Canino-KoningR,HoweA,Tiedje JM, BrownCT. 2012. Scalingmetagenome sequence assembly with probabilistic de Bruijn graphs. PNAS 109:13272-77
-
(2012)
PNAS
, vol.109
, pp. 13272-13277
-
-
Pell, J.1
Hintze, A.2
Canino-Koning, R.3
Howe, A.4
Tiedje, J.M.5
Brown, C.T.6
-
82
-
-
84861760530
-
IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
-
Peng Y, Leung HC, Yiu SM, Chin FY. 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420-28
-
(2012)
Bioinformatics
, vol.28
, pp. 1420-1428
-
-
Peng, Y.1
Leung, H.C.2
Yiu, S.M.3
Chin, F.Y.4
-
83
-
-
78449313673
-
Identifying SNPs without a reference genome by comparing raw reads
-
ed. E Chavez, S Lonardi,. Lect. Notes. Comput. Sci. 6393. Berlin: Springer
-
Peterlongo P, Schnel N, Pisanti N, Sagot M-F, Lacroix V. 2010. Identifying SNPs without a reference genome by comparing raw reads. In String Processing and Information Retrieval, ed. E Chavez, S Lonardi, pp. 147-58. Lect. Notes. Comput. Sci. 6393. Berlin: Springer
-
(2010)
String Processing and Information Retrieval
, pp. 147-158
-
-
Peterlongo, P.1
Schnel, N.2
Pisanti, N.3
Sagot, M.-F.4
LaCroix, V.5
-
84
-
-
0024474332
-
1-Tuple DNA sequencing: Computer analysis
-
Pevzner PA. 1989. 1-Tuple DNA sequencing: computer analysis. J. Biomol. Struct. Dyn. 7:63-73
-
(1989)
J. Biomol. Struct. Dyn
, vol.7
, pp. 63-73
-
-
Pevzner, P.A.1
-
85
-
-
0035232164
-
Fragment assembly with double-barreled data
-
Pevzner PA, Tang H. 2001. Fragment assembly with double-barreled data. Bioinformatics 17(Suppl. 1):S225-33
-
(2001)
Bioinformatics
, vol.17
, pp. S225-S233
-
-
Pevzner, P.A.1
Tang, H.2
-
86
-
-
0035859921
-
An Eulerian path approach to DNA fragment assembly
-
Pevzner PA, Tang H, Waterman MS. 2001. An Eulerian path approach to DNA fragment assembly. PNAS 98:9748-53
-
(2001)
PNAS
, vol.98
, pp. 9748-9753
-
-
Pevzner, P.A.1
Tang, H.2
Waterman, M.S.3
-
87
-
-
84874192171
-
Pathset graphs: A novel approach for comprehensive utilization of paired reads in genome assembly
-
Pham SK, Antipov D, Sirotkin A, Tesler G, Pevzner PA, Alekseyev MA. 2013. Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly. J. Comput. Biol. 20:359-71
-
(2013)
J. Comput. Biol
, vol.20
, pp. 359-371
-
-
Pham, S.K.1
Antipov, D.2
Sirotkin, A.3
Tesler, G.4
Pevzner, P.A.5
Alekseyev, M.A.6
-
88
-
-
45549109750
-
Genome assembly forensics: Finding the elusive mis-assembly
-
Phillippy AM, SchatzMC, PopM. 2008. Genome assembly forensics: finding the elusive mis-assembly. Genome Biol. 9:R55
-
(2008)
Genome Biol
, vol.9
, pp. R55
-
-
Phillippy, A.M.1
Schatz, M.C.2
Pop, M.3
-
90
-
-
84894167959
-
-
Presented at IEEE Int. Conf. Bioinform. Bioeng. , 13th, Chania, Greece, Nov. 10-13
-
Price J, Ward J, Udall J, Snell Q, Clement M. 2013. Identification and correction of substitution errors in Moleculo long reads. Presented at IEEE Int. Conf. Bioinform. Bioeng., 13th, Chania, Greece, Nov. 10-13
-
(2013)
Identification and Correction of Substitution Errors in Moleculo Long Reads
-
-
Price, J.1
Ward, J.2
Udall, J.3
Snell, Q.4
Clement, M.5
-
91
-
-
84872968454
-
CGAL: Computing genome assembly likelihoods
-
Rahman A, Pachter L. 2013. CGAL: computing genome assembly likelihoods. Genome Biol. 14:R8
-
(2013)
Genome Biol
, vol.14
, pp. R8
-
-
Rahman, A.1
Pachter, L.2
-
92
-
-
0004460195
-
The shortest common supersequence problem over binary alphabet is NP-complete
-
Räihä K-J, Ukkonen E. 1981. The shortest common supersequence problem over binary alphabet is NP-complete. Theor. Comput. Sci. 16:187-98
-
(1981)
Theor. Comput. Sci
, vol.16
, pp. 187-198
-
-
Räihä, K.-J.1
Ukkonen, E.2
-
93
-
-
84905576523
-
Integrating mapping-, assembly-and haplotype-based approaches for calling variants in clinical sequencing applications
-
Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SR, et al. 2014. Integrating mapping-, assembly-and haplotype-based approaches for calling variants in clinical sequencing applications. Nat. Genet. 46:912-18
-
(2014)
Nat. Genet
, vol.46
, pp. 912-918
-
-
Rimmer, A.1
Phan, H.2
Mathieson, I.3
Iqbal, Z.4
Twigg, S.R.5
-
94
-
-
84886036945
-
Compact representation of k-mer de Bruijn graphs for genome read assembly
-
Rodland EA. 2013. Compact representation of k-mer de Bruijn graphs for genome read assembly. BMC Bioinform. 14:313
-
(2013)
BMC Bioinform
, vol.14
, pp. 313
-
-
Rodland, E.A.1
-
95
-
-
82255185486
-
Fast scaffolding with small independent mixed integer programs
-
Salmela L,Makinen V, ValimakiN, Ylinen J, Ukkonen E. 2011. Fast scaffolding with small independent mixed integer programs. Bioinformatics 27:3259-65
-
(2011)
Bioinformatics
, vol.27
, pp. 3259-3265
-
-
Salmela, L.1
Makinen, V.2
Valimaki, N.3
Ylinen, J.4
Ukkonen, E.5
-
96
-
-
84857893016
-
GAGE: A critical evaluation of genome assemblies and assembly algorithms
-
Salzberg SL, Phillippy AM, Zimin AV, Puiu D, Magoc T, et al. 2012. GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res. 22:557-67
-
(2012)
Genome Res
, vol.22
, pp. 557-567
-
-
Salzberg, S.L.1
Phillippy, A.M.2
Zimin, A.V.3
Puiu, D.4
Magoc, T.5
-
97
-
-
0016678133
-
The Croonian Lecture, 1975: Nucleotide sequences in DNA
-
Sanger F. 1975. The Croonian Lecture, 1975: Nucleotide sequences in DNA. Proc. R. Soc. Lond. B 191:317-33
-
(1975)
Proc. R. Soc. Lond. B
, vol.191
, pp. 317-333
-
-
Sanger, F.1
-
98
-
-
0027485082
-
Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping
-
Schwartz DC, Li X, Hernandez LI, Ramnarain SP, Huff EJ, Wang YK. 1993. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262:110-14
-
(1993)
Science
, vol.262
, pp. 110-114
-
-
Schwartz, D.C.1
Li, X.2
Hernandez, L.I.3
Ramnarain, S.P.4
Huff, E.J.5
Wang, Y.K.6
-
99
-
-
84897108483
-
Exploring genome characteristics and sequence quality without a reference
-
Simpson JT. 2014. Exploring genome characteristics and sequence quality without a reference. Bioinformatics 30:1228-35
-
(2014)
Bioinformatics
, vol.30
, pp. 1228-1235
-
-
Simpson, J.T.1
-
100
-
-
77954238055
-
Efficient construction of an assembly string graph using the FM-index
-
Simpson JT, Durbin R. 2010. Efficient construction of an assembly string graph using the FM-index. Bioinformatics 26:i367-73
-
(2010)
Bioinformatics
, vol.26
, pp. i367-i373
-
-
Simpson, J.T.1
Durbin, R.2
-
101
-
-
84857838310
-
Efficient de novo assembly of large genomes using compressed data structures
-
Simpson JT, Durbin R. 2012. Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 22:549-56
-
(2012)
Genome Res
, vol.22
, pp. 549-556
-
-
Simpson, J.T.1
Durbin, R.2
-
102
-
-
66449136667
-
ABySS: A parallel assembler for short read sequence data
-
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res. 19:1117-23
-
(2009)
Genome Res
, vol.19
, 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
-
103
-
-
66349083341
-
A geometric approach for classification and comparison of structural variants
-
Sindi S, Helman E, Bashir A, Raphael BJ. 2009. A geometric approach for classification and comparison of structural variants. Bioinformatics 25:i222-30
-
(2009)
Bioinformatics
, vol.25
, pp. i222-i230
-
-
Sindi, S.1
Helman, E.2
Bashir, A.3
Raphael, B.J.4
-
104
-
-
0018426987
-
A strategy ofDNAsequencing employing computer programs
-
Staden R. 1979. A strategy ofDNAsequencing employing computer programs. Nucleic Acids Res. 6:2601-10
-
(1979)
Nucleic Acids Res
, vol.6
, pp. 2601-2610
-
-
Staden, R.1
-
105
-
-
80052606169
-
The genome sequence of Atlantic cod reveals a unique immune system
-
Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrom M, et al. 2011. The genome sequence of Atlantic cod reveals a unique immune system. Nature 477:207-10
-
(2011)
Nature
, vol.477
, pp. 207-210
-
-
Star, B.1
Nederbragt, A.J.2
Jentoft, S.3
Grimholt, U.4
Malmstrom, M.5
-
107
-
-
0024135088
-
A greedy approximation algorithm for constructing shortest common superstrings
-
Tarhio J, Ukkonen E. 1988. A greedy approximation algorithm for constructing shortest common superstrings. Theor. Comput. Sci. 57:131-45
-
(1988)
Theor. Comput. Sci
, vol.57
, pp. 131-145
-
-
Tarhio, J.1
Ukkonen, E.2
-
108
-
-
84863693752
-
The tomato genome sequence provides insights into fleshy fruit evolution
-
Tomato Genome Consort
-
Tomato Genome Consort. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635-41
-
(2012)
Nature
, vol.485
, pp. 635-641
-
-
-
109
-
-
0035895505
-
The sequence of the human genome
-
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. 2001. The sequence of the human genome. Science 291:1304-51
-
(2001)
Science
, vol.291
, pp. 1304-1351
-
-
Venter, J.C.1
Adams, M.D.2
Myers, E.W.3
Li, P.W.4
Mural, R.J.5
-
110
-
-
84881496498
-
The genome sequence of the colonial chordate, Botryllus schlosseri
-
Voskoboynik A, Neff NF, Sahoo D, Newman AM, Pushkarev D, et al. 2013. The genome sequence of the colonial chordate, Botryllus schlosseri. eLife 2:e00569
-
(2013)
ELife
, vol.2
, pp. e00569
-
-
Voskoboynik, A.1
Neff, N.F.2
Sahoo, D.3
Newman, A.M.4
Pushkarev, D.5
-
112
-
-
84922584295
-
Comprehensive variation discovery in single human genomes
-
Weisenfeld NI, Yin S, Sharpe T, Lau B, Hegarty R, et al. 2014. Comprehensive variation discovery in single human genomes. Nat. Genet. 46:1350-55
-
(2014)
Nat. Genet
, vol.46
, pp. 1350-1355
-
-
Weisenfeld, N.I.1
Yin, S.2
Sharpe, T.3
Lau, B.4
Hegarty, R.5
-
113
-
-
84866712746
-
Exploiting sparseness in de novo genome assembly
-
Ye C, Ma ZS, Cannon CH, Pop M, Yu DW. 2012. Exploiting sparseness in de novo genome assembly. BMC Bioinform. 13(Suppl. 6):S1
-
(2012)
BMC Bioinform
, vol.13
, pp. S1
-
-
Ye, C.1
Ma, Z.S.2
Cannon, C.H.3
Pop, M.4
Yu, D.W.5
-
114
-
-
43149115851
-
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-29
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
115
-
-
73649103712
-
A single molecule scaffold for the maize genome
-
Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, et al. 2009. A single molecule scaffold for the maize genome. PLOS Genet. 5:e1000711
-
(2009)
PLOS Genet
, vol.5
, pp. e1000711
-
-
Zhou, S.1
Wei, F.2
Nguyen, J.3
Bechner, M.4
Potamousis, K.5
-
116
-
-
84885968059
-
The MaSuRCA genome assembler
-
Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. 2013. The MaSuRCA genome assembler. Bioinformatics 29:2669-77
-
(2013)
Bioinformatics
, vol.29
, pp. 2669-2677
-
-
Zimin, A.V.1
Marcais, G.2
Puiu, D.3
Roberts, M.4
Salzberg, S.L.5
Yorke, J.A.6
-
118
-
-
84899102003
-
Sequencing and assembly of the 22-Gb loblolly pine genome
-
Zimin AV, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, et al. 2014. Sequencing and assembly of the 22-Gb loblolly pine genome. Genetics 196:875-90
-
(2014)
Genetics
, vol.196
, pp. 875-890
-
-
Zimin, A.V.1
Stevens, K.A.2
Crepeau, M.W.3
Holtz-Morris, A.4
Koriabine, M.5
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