-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
0037162885
-
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
-
Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-1310.
-
(2002)
Science
, vol.297
, pp. 1301-1310
-
-
Aparicio, S.1
Chapman, J.2
Stupka, E.3
Putnam, N.4
Chia, J.M.5
Dehal, P.6
Christoffels, A.7
Rash, S.8
Hoon, S.9
Smit, A.10
-
3
-
-
61849109937
-
Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
-
Barriere A, Yang SP, Pekarek E, Thomas CG, Haag ES, Ruvinsky I. 2009. Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes. Genome Res 19: 470-480.
-
(2009)
Genome Res
, vol.19
, pp. 470-480
-
-
Barriere, A.1
Yang, S.P.2
Pekarek, E.3
Thomas, C.G.4
Haag, E.S.5
Ruvinsky, I.6
-
4
-
-
2242464840
-
The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins
-
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, et al. 2002. The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science 298: 2157-2167.
-
(2002)
Science
, vol.298
, pp. 2157-2167
-
-
Dehal, P.1
Satou, Y.2
Campbell, R.K.3
Chapman, J.4
Degnan, B.5
De Tomaso, A.6
Davidson, B.7
Di Gregorio, A.8
Gelpke, M.9
Goodstein, D.M.10
-
5
-
-
78649705889
-
Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate
-
Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Canestro C, et al. 2010. Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 330: 1381-1385.
-
(2010)
Science
, vol.330
, pp. 1381-1385
-
-
Denoeud, F.1
Henriet, S.2
Mungpakdee, S.3
Aury, J.M.4
Da Silva, C.5
Brinkmann, H.6
Mikhaleva, J.7
Olsen, L.C.8
Jubin, C.9
Canestro, C.10
-
6
-
-
79953175254
-
Hapsembler: An assembler for highly polymorphic genomes
-
ed. V Bafna and CS Sahinalp, Springer- Verlag, Berlin, Germany
-
Donmez N, Brudno M. 2011. Hapsembler: An assembler for highly polymorphic genomes. In RECOMB (ed. V Bafna and CS Sahinalp), Vol. 6577, pp. 38-52. Springer-Verlag, Berlin, Germany.
-
(2011)
RECOMB
, vol.6577
, pp. 38-52
-
-
Donmez, N.1
Brudno, M.2
-
7
-
-
79551624472
-
Considering transposable element diversification in de novo annotation approaches
-
doi: 10.1371/journal.pone.0016526
-
Flutre T, Duprat E, Feuillet C, Quesneville H. 2011. Considering transposable element diversification in de novo annotation approaches. PLoS ONE 6: e16526. doi: 10.1371/journal.pone.0016526.
-
(2011)
PLoS ONE
, vol.6
-
-
Flutre, T.1
Duprat, E.2
Feuillet, C.3
Quesneville, H.4
-
8
-
-
61449124151
-
FrameDP: Sensitive peptide detection on noisy matured sequences
-
Gouzy J, Carrere S, Schiex T. 2009. FrameDP: Sensitive peptide detection on noisy matured sequences. Bioinformatics 25: 670-671.
-
(2009)
Bioinformatics
, vol.25
, pp. 670-671
-
-
Gouzy, J.1
Carrere, S.2
Schiex, T.3
-
10
-
-
0037020114
-
The genome sequence of the malaria mosquito Anopheles gambiae
-
Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR,Wincker P, Clark AG, Ribeiro JM,Wides R, et al. 2002. The genome sequence of the malaria mosquito Anopheles gambiae . Science 298: 129-149.
-
(2002)
Science
, vol.298
, pp. 129-149
-
-
Holt, R.A.1
Subramanian, G.M.2
Halpern, A.3
Sutton, G.G.4
Charlab, R.5
Nusskern, D.R.6
Wincker, P.7
Clark, A.G.8
Ribeiro, J.M.9
Wides, R.10
-
11
-
-
2442629464
-
The diploid genome sequence of Candida albicans
-
Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, Magee BB, Newport G, Thorstenson YR, Agabian N, Magee PT, et al. 2004. The diploid genome sequence of Candida albicans. Proc Natl Acad Sci 101: 7329-7334.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 7329-7334
-
-
Jones, T.1
Federspiel, N.A.2
Chibana, H.3
Dungan, J.4
Kalman, S.5
Magee, B.B.6
Newport, G.7
Thorstenson, Y.R.8
Agabian, N.9
Magee, P.T.10
-
12
-
-
78649358717
-
Quake: Quality-aware detection and correction of sequencing errors
-
doi: 10.1186/gb-2010-11-11-r116.
-
Kelley DR, Schatz MC, Salzberg SL. 2010. Quake: Quality-aware detection and correction of sequencing errors. Genome Biol 11: R116. doi: 10.1186/gb-2010-11-11-r116.
-
(2010)
Genome Biol
, vol.11
-
-
Kelley, D.R.1
Schatz, M.C.2
Salzberg, S.L.3
-
13
-
-
0141815478
-
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
-
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. 2003. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci 100: 11484-11489.
-
(2003)
Proc Natl Acad Sci
, vol.100
, pp. 11484-11489
-
-
Kent, W.J.1
Baertsch, R.2
Hinrichs, A.3
Miller, W.4
Haussler, D.5
-
14
-
-
78651333227
-
Haplotype-resolved genome sequencing of a Gujarati Indian individual
-
Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, Patwardhan RP, Sudmant PH, Ng SB, Alkan C, Qiu R, Eichler EE, et al. 2011. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol 29: 59-63.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 59-63
-
-
Kitzman, J.O.1
Mackenzie, A.P.2
Adey, A.3
Hiatt, J.B.4
Patwardhan, R.P.5
Sudmant, P.H.6
Ng, S.B.7
Alkan, C.8
Qiu, R.9
Eichler, E.E.10
-
15
-
-
57249105124
-
Aggressive assembly of pyrosequencing reads with mates
-
Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G. 2008. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24: 2818-2824.
-
(2008)
Bioinformatics
, vol.24
, pp. 2818-2824
-
-
Miller, J.R.1
Delcher, A.L.2
Koren, S.3
Venter, E.4
Walenz, B.P.5
Brownley, A.6
Johnson, J.7
Li, K.8
Mobarry, C.9
Sutton, G.10
-
17
-
-
0034708758
-
A whole-genome assembly of Drosophila
-
Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, et al. 2000. A whole-genome assembly of Drosophila. Science 287: 2196-2204.
-
(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
Flanigan, M.J.6
Kravitz, S.A.7
Mobarry, C.M.8
Reinert, K.H.9
Remington, K.A.10
-
18
-
-
67449095888
-
Genome assembly reborn: Recent computational challenges
-
Pop M. 2009. Genome assembly reborn: Recent computational challenges. Brief Bioinform 10: 354-366.
-
(2009)
Brief Bioinform
, vol.10
, pp. 354-366
-
-
Pop, M.1
-
19
-
-
45749086679
-
The amphioxus genome and the evolution of the chordate karyotype
-
Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, et al. 2008. The amphioxus genome and the evolution of the chordate karyotype. Nature 453: 1064-1071.
-
(2008)
Nature
, vol.453
, pp. 1064-1071
-
-
Putnam, N.H.1
Butts, T.2
Ferrier, D.E.3
Furlong, R.F.4
Hellsten, U.5
Kawashima, T.6
Robinson-Rechavi, M.7
Shoguchi, E.8
Terry, A.9
Yu, J.K.10
-
20
-
-
0037267806
-
Human-mouse alignments with BLASTZ
-
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. 2003. Human-mouse alignments with BLASTZ. Genome Res 13: 103-107.
-
(2003)
Genome Res
, vol.13
, pp. 103-107
-
-
Schwartz, S.1
Kent, W.J.2
Smit, A.3
Zhang, Z.4
Baertsch, R.5
Hardison, R.C.6
Haussler, D.7
Miller, W.8
-
21
-
-
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: 1117-1123.
-
(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
-
22
-
-
34250206347
-
A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome
-
doi: 10.1186/gb-2007-8-3-r41
-
Small KS, Brudno M, Hill MM, Sidow A. 2007. A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol 8: R41. doi: 10.1186/gb-2007-8-3-r41.
-
(2007)
Genome Biol
, vol.8
-
-
Small, K.S.1
Brudno, M.2
Hill, M.M.3
Sidow, A.4
-
23
-
-
63049126614
-
Using RepeatMasker to identify repetitive elements in genomic sequences
-
Tarailo-Graovac M, ChenN. 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. Current Protoc Bioinformatics 25: 4.10.1-4.10.14.
-
(2009)
Current Protoc Bioinformatics
, vol.25
-
-
Tarailo-Graovac, M.1
Chen, N.2
-
24
-
-
23744446773
-
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
-
Vinson JP, Jaffe DB, O'Neill K, Karlsson EK, Stange-Thomann N, Anderson S, Mesirov JP, Satoh N, Satou Y, Nusbaum C, et al. 2005. Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi. Genome Res 15: 1127-1135.
-
(2005)
Genome Res
, vol.15
, pp. 1127-1135
-
-
Vinson, J.P.1
Jaffe, D.B.2
O'Neill, K.3
Karlsson, E.K.4
Stange-Thomann, N.5
Anderson, S.6
Mesirov, J.P.7
Satoh, N.8
Satou, Y.9
Nusbaum, C.10
-
25
-
-
79959385909
-
Sim4db and Leaff: Utilities for fast batch spliced alignment and sequence indexing
-
Walenz B, Florea L. 2011. Sim4db and Leaff: Utilities for fast batch spliced alignment and sequence indexing. Bioinformatics 27: 1869-1870.
-
(2011)
Bioinformatics
, vol.27
, pp. 1869-1870
-
-
Walenz, B.1
Florea, L.2
-
26
-
-
42249087308
-
The complete genome of an individual by massively parallel DNA sequencing
-
Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, et al. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452: 872-876.
-
(2008)
Nature
, vol.452
, pp. 872-876
-
-
Wheeler, D.A.1
Srinivasan, M.2
Egholm, M.3
Shen, Y.4
Chen, L.5
McGuire, A.6
He, W.7
Chen, Y.J.8
Makhijani, V.9
Roth, G.T.10
-
27
-
-
67649892606
-
Sim4cc: A cross-species spliced alignment program
-
doi: 10.1093.nar/gkp319
-
Zhou L, Pertea M, Delcher AL, Florea L. 2009. Sim4cc: A cross-species spliced alignment program. Nucleic Acids Res 37: e80. doi: 10.1093.nar/gkp319.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Zhou, L.1
Pertea, M.2
Delcher, A.L.3
Florea, L.4
|