-
1
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies,M., Egholm,M., Altman,W.E., Attiya,S., Bader,J.S., Bemben,L.A., Berka,J., Braverman,M.S., Chen,Y.J., Chen,Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.J.9
Chen, Z.10
-
2
-
-
84975742565
-
A map of human genome variation from population-scale sequencing
-
1000 Genomes Project Consortium
-
1000 Genomes Project Consortium (2005) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
-
(2005)
Nature
, vol.467
, pp. 1061-1073
-
-
-
3
-
-
84975795680
-
An integrated map of genetic variation from 1,092 human genomes
-
1000 Genomes Project Consortium
-
1000 Genomes Project Consortium (2005) An integrated map of genetic variation from 1,092 human genomes. Nature, 491, 56-65.
-
(2005)
Nature
, vol.491
, pp. 56-65
-
-
-
4
-
-
79957589237
-
Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations
-
O'Roak,B.J., Deriziotis,P., Lee,C., Vives,L., Schwartz,J.J., Girirajan,S., Karakoc,E.,Mackenzie,A.P., Ng,S.B., Baker,C. et al. (2005) Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat. Genet., 43, 585-589.
-
(2005)
Nat. Genet.
, vol.43
, pp. 585-589
-
-
O'roak, B.J.1
Deriziotis, P.2
Lee, C.3
Vives, L.4
Schwartz, J.J.5
Girirajan, S.6
Karakoc, E.7
Mackenzie, A.P.8
Ng, S.B.9
Baker, C.10
-
5
-
-
79952178131
-
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
-
Gnerre,S., Maccallum,I., Przybylski,D., Ribeiro,F.J., Burton,J.N., Walker,B.J., Sharpe,T., Hall,G., Shea,T.P., Sykes,S. et al. (2005) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl. Acad. Sci. U.S.A., 108, 1513-1518.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 1513-1518
-
-
Gnerre, S.1
Maccallum, I.2
Przybylski, D.3
Ribeiro, F.J.4
Burton, J.N.5
Walker, B.J.6
Sharpe, T.7
Hall, G.8
Shea, T.P.9
Sykes, S.10
-
7
-
-
0034506014
-
Opportunistic data structures with applications
-
Ferragina,P. and Manzini,G. (2005) Opportunistic data structures with applications. In: FOCS, pp. 390-398.
-
(2005)
FOCS
, pp. 390-398
-
-
Ferragina, P.1
Manzini, G.2
-
8
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li,H. and Durbin,R. (2005) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
-
(2005)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
9
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead,B., Trapnell,C., Pop,M. and Salzberg,S.L. (2005) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
-
(2005)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
10
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead,B. and Salzberg,S.L. (2005) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
-
(2005)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
11
-
-
67650711615
-
SOAP2: An improved ultrafast tool for short read alignment
-
Li,R., Yu,C., Li,Y., Lam,T.W., Yiu,S.M., Kristiansen,K. and Wang,J. (2005) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
-
(2005)
Bioinformatics
, vol.25
, pp. 1966-1967
-
-
Li, R.1
Yu, C.2
Li, Y.3
Lam, T.W.4
Yiu, S.M.5
Kristiansen, K.6
Wang, J.7
-
12
-
-
70349556543
-
Personalized copy number and segmental duplication maps using next-generation sequencing
-
Alkan,C., Kidd,J.M., Marques-Bonet,T., Aksay,G., Antonacci,F., Hormozdiari,F., Kitzman,J.O., Baker,C., Malig,M., Mutlu,O. et al. (2005) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet., 41, 1061-1067.
-
(2005)
Nat. Genet.
, vol.41
, pp. 1061-1067
-
-
Alkan, C.1
Kidd, J.M.2
Marques-Bonet, T.3
Aksay, G.4
Antonacci, F.5
Hormozdiari, F.6
Kitzman, J.O.7
Baker, C.8
Malig, M.9
Mutlu, O.10
-
13
-
-
84881278275
-
Accelerating read mapping with FastHASH
-
Xin,H., Lee,D., Hormozdiari,F., Yedkar,S., Mutlu,O. and Alkan,C. (2005) Accelerating read mapping with FastHASH. BMC Genomics, 14(Suppl.1), S13.
-
(2005)
BMC Genomics
, vol.14
, Issue.SUPPL.1
-
-
Xin, H.1
Lee, D.2
Hormozdiari, F.3
Yedkar, S.4
Mutlu, O.5
Alkan, C.6
-
14
-
-
77955163329
-
MrsFAST: A cache-oblivious algorithm for short-read mapping
-
Hach,F., Hormozdiari,F., Alkan,C., Hormozdiari,F., Birol,I., Eichler,E.E. and Sahinalp,S.C. (2005) mrsFAST: a cache-oblivious algorithm for short-read mapping. Nat. Methods, 7, 576-577.
-
(2005)
Nat. Methods
, vol.7
, pp. 576-577
-
-
Hach, F.1
Hormozdiari, F.2
Alkan, C.3
Hormozdiari, F.4
Birol, I.5
Eichler, E.E.6
Sahinalp, S.C.7
-
15
-
-
79960122547
-
Sensitive and fast mapping of di-base encoded reads
-
Hormozdiari,F., Hach,F., Sahinalp,S.C. and Alkan,C. (2005) Sensitive and fast mapping of di-base encoded reads. Bioinformatics, 27, 1915-1921.
-
(2005)
Bioinformatics
, vol.27
, pp. 1915-1921
-
-
Hormozdiari, F.1
Hach, F.2
Sahinalp, S.C.3
Alkan, C.4
-
16
-
-
69749106334
-
RazerS-fast read mapping with sensitivity control
-
Weese,D., Emde,A.K., Rausch,T., Doring,A. and Reinert,K. (2005) RazerS-fast read mapping with sensitivity control. Genome Res., 19, 1646-1654.
-
(2005)
Genome Res.
, vol.19
, pp. 1646-1654
-
-
Weese, D.1
Emde, A.K.2
Rausch, T.3
Doring, A.4
Reinert, K.5
-
17
-
-
84870471176
-
RazerS 3: Faster, fully sensitive read mapping
-
Weese,D., Holtgrewe,M. and Reinert,K. (2005) RazerS 3: faster, fully sensitive read mapping. Bioinformatics, 28, 2592-2599.
-
(2005)
Bioinformatics
, vol.28
, pp. 2592-2599
-
-
Weese, D.1
Holtgrewe, M.2
Reinert, K.3
-
18
-
-
67049159825
-
SHRiMP: Accurate mapping of short color-space reads
-
Rumble,S.M., Lacroute,P., Dalca,A.V., Fiume,M., Sidow,A. and Brudno,M. (2005) SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol., 5, 11.
-
(2005)
PLoS Comput. Biol.
, vol.5
, pp. 11
-
-
Rumble, S.M.1
Lacroute, P.2
Dalca, A.V.3
Fiume, M.4
Sidow, A.5
Brudno, M.6
-
19
-
-
79953310937
-
SHRiMP2: Sensitive yet practical short read mapping
-
David,M., Dzamba,M., Lister,D., Ilie,L. and Brudno,M. (2005) SHRiMP2: sensitive yet practical short read mapping. Bioinformatics,27, 1011-1012.
-
(2005)
Bioinformatics
, vol.27
, pp. 1011-1012
-
-
David, M.1
Dzamba, M.2
Lister, D.3
Ilie, L.4
Brudno, M.5
-
20
-
-
54949110994
-
ZOOM! Zillions of oligos mapped
-
Lin,H., Zhang,Z., Zhang,M.Q., Ma,B. and Li,M. (2005) ZOOM! Zillions of oligos mapped. Bioinformatics, 24, 2431-2437.
-
(2005)
Bioinformatics
, vol.24
, pp. 2431-2437
-
-
Lin, H.1
Zhang, Z.2
Zhang, M.Q.3
Ma, B.4
Li, M.5
-
21
-
-
84873312972
-
SRmapper: A fast and sensitive genome-hashing alignment tool
-
Gontarz,P.M., Berger,J. and Wong,C.F. (2013) SRmapper: a fast and sensitive genome-hashing alignment tool. Bioinformatics, 29, 316-321.
-
(2013)
Bioinformatics
, vol.29
, pp. 316-321
-
-
Gontarz, P.M.1
Berger, J.2
Wong, C.F.3
-
22
-
-
77951820899
-
Fast and SNP-tolerant detection of complex variants and splicing in short reads
-
Wu,T.D. and Nacu,S. (2005) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics, 26, 873-881.
-
(2005)
Bioinformatics
, vol.26
, pp. 873-881
-
-
Wu, T.D.1
Nacu, S.2
-
23
-
-
84876548372
-
Fast and accurate read mapping with approximate seeds and multiple backtracking
-
Siragusa,E.,Weese,D. and Reinert,K. (2005) Fast and accurate read mapping with approximate seeds and multiple backtracking. Nucleic Acids Res., 41, e78.
-
(2005)
Nucleic Acids Res.
, vol.41
-
-
Siragusa, E.1
Weese, D.2
Reinert, K.3
-
24
-
-
84870837088
-
The GEM mapper: Fast, accurate and versatile alignment by filtration
-
Marco-Sola,S., Sammeth,M., Guigo,R. and Ribeca,P. (2005) The GEM mapper: fast, accurate and versatile alignment by filtration. Nat. Methods, 9, 1185-1188.
-
(2005)
Nat. Methods
, vol.9
, pp. 1185-1188
-
-
Marco-Sola, S.1
Sammeth, M.2
Guigo, R.3
Ribeca, P.4
-
25
-
-
80053978849
-
Comparative analysis of algorithms for next-generation sequencing read alignment
-
Ruffalo,M., LaFramboise,T. and Koyutrk,M. (2005) Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics, 27, 2790-2796.
-
(2005)
Bioinformatics
, vol.27
, pp. 2790-2796
-
-
Ruffalo, M.1
Laframboise, T.2
Koyutrk, M.3
-
26
-
-
84870822864
-
Tools for mapping high-throughput sequencing data
-
Fonseca,N.A., Rung,J., Brazma,A. and Marioni,J.C. (2005) Tools for mapping high-throughput sequencing data. Bioinformatics, 28, 3169-3177.
-
(2005)
Bioinformatics
, vol.28
, pp. 3169-3177
-
-
Fonseca, N.A.1
Rung, J.2
Brazma, A.3
Marioni, J.C.4
-
27
-
-
67650064593
-
Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
-
Hormozdiari,F., Alkan,C., Eichler,E.E. and Sahinalp,S.C. (2009) Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res., 19, 1270-1278.
-
(2009)
Genome Res.
, vol.19
, pp. 1270-1278
-
-
Hormozdiari, F.1
Alkan, C.2
Eichler, E.E.3
Sahinalp, S.C.4
-
28
-
-
77951860138
-
Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
-
Quinlan,A.R., Clark,R.A., Sokolova,S., Leibowitz,M.L., Zhang,Y., Hurles,M.E., Mell,J.C. and Hall,I.M. (2005) Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome Res., 20, 623-635.
-
(2005)
Genome Res.
, vol.20
, pp. 623-635
-
-
Quinlan, A.R.1
Clark, R.A.2
Sokolova, S.3
Leibowitz, M.L.4
Zhang, Y.5
Hurles, M.E.6
Mell, J.C.7
Hall, I.M.8
-
29
-
-
84874746879
-
CNVeM: Copy number variation detection using uncertainty of read mapping
-
Wang,Z., Hormozdiari,F., Yang,W.-Y., Halperin,E. and Eskin,E. (2005) CNVeM: copy number variation detection using uncertainty of read mapping. J. Comput. Biol., 20, 224-236.
-
(2005)
J. Comput. Biol.
, vol.20
, pp. 224-236
-
-
Wang, Z.1
Hormozdiari, F.2
Yang, W.-Y.3
Halperin, E.4
Eskin, E.5
-
31
-
-
79957967458
-
Natural genetic variation caused by small insertions and deletions in the human genome
-
Mills,R.E., Pittard,W.S., Mullaney,J.M., Farooq,U., Creasy,T.H., Mahurkar,A.A., Kemeza,D.M., Strassler,D.S., Ponting,C.P., Webber,C. and Devine,S.E. (2005) Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res., 21, 830-839.
-
(2005)
Genome Res.
, vol.21
, pp. 830-839
-
-
Mills, R.E.1
Pittard, W.S.2
Mullaney, J.M.3
Farooq, U.4
Creasy, T.H.5
Mahurkar, A.A.6
Kemeza, D.M.7
Strassler, D.S.8
Ponting, C.P.9
Webber, C.10
Devine, S.E.11
-
32
-
-
84856409929
-
Detection of structural variants and indels within exome data
-
Karakoc,E., Alkan,C., O'Roak,B.J., Dennis,M.Y., Vives,L., Mark,K., Rieder,M.J., Nickerson,D.A. and Eichler,E.E. (2005) Detection of structural variants and indels within exome data. Nat. Methods, 9, 176-178.
-
(2005)
Nat. Methods
, vol.9
, pp. 176-178
-
-
Karakoc, E.1
Alkan, C.2
O'roak, B.J.3
Dennis, M.Y.4
Vives, L.5
Mark, K.6
Rieder, M.J.7
Nickerson, D.A.8
Eichler, E.E.9
-
33
-
-
79954672317
-
Genome structural variation discovery and genotyping
-
Alkan,C., Coe,B.P. and Eichler,E.E. (2005) Genome structural variation discovery and genotyping. Nat. Rev. Genet., 12, 363-376.
-
(2005)
Nat. Rev. Genet.
, vol.12
, pp. 363-376
-
-
Alkan, C.1
Coe, B.P.2
Eichler, E.E.3
-
34
-
-
77954205450
-
Next-generation VariationHunter: Combinatorial algorithms for transposon insertion discovery
-
Hormozdiari,F., Hajirasouliha,I., Dao,P., Hach,F., Yorukoglu,D., Alkan,C., Eichler,E.E. and Sahinalp,S.C. (2005) Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics, 26, i350-i357.
-
(2005)
Bioinformatics
, vol.26
-
-
Hormozdiari, F.1
Hajirasouliha, I.2
Dao, P.3
Hach, F.4
Yorukoglu, D.5
Alkan, C.6
Eichler, E.E.7
Sahinalp, S.C.8
-
35
-
-
79960405019
-
The variant call format and VCFtools
-
and 1000 Genomes Project Analysis Group
-
Danecek,P., Auton,A., Abecasis,G., Albers,C.A., Banks,E., DePristo,M.A., Handsaker,R.E., Lunter,G., Marth,G.T., Sherry,S.T., McVean,G., Durbin,R. and 1000 Genomes Project Analysis Group (2005) The variant call format and VCFtools. Bioinformatics, 27, 2156-2158.
-
(2005)
Bioinformatics
, vol.27
, pp. 2156-2158
-
-
Danecek, P.1
Auton, A.2
Abecasis, G.3
Albers, C.A.4
Banks, E.5
Depristo, M.A.6
Handsaker, R.E.7
Lunter, G.8
Marth, G.T.9
Sherry, S.T.10
McVean, G.11
Durbin, R.12
-
36
-
-
70349910898
-
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
-
Degner,J.F., Marioni,J.C., Pai,A.A., Pickrell,J.K., Nkadori,E., Gilad,Y. and Pritchard,J.K. (2005) Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics, 25, 3207-3212.
-
(2005)
Bioinformatics
, vol.25
, pp. 3207-3212
-
-
Degner, J.F.1
Marioni, J.C.2
Pai, A.A.3
Pickrell, J.K.4
Nkadori, E.5
Gilad, Y.6
Pritchard, J.K.7
-
37
-
-
80051489977
-
AlleleSeq: Analysis of allele-specific expression and binding in a network framework
-
Rozowsky,J., Abyzov,A., Wang,J., Alves,P., Raha,D., Harmanci,A., Leng,J., Bjornson,R., Kong,Y., Kitabayashi,N. et al. (2005) AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol. Syst. Biol., 7, 522.
-
(2005)
Mol. Syst. Biol.
, vol.7
, pp. 522
-
-
Rozowsky, J.1
Abyzov, A.2
Wang, J.3
Alves, P.4
Raha, D.5
Harmanci, A.6
Leng, J.7
Bjornson, R.8
Kong, Y.9
Kitabayashi, N.10
-
38
-
-
84870568092
-
A new strategy to reduce allelic bias in RNA-Seq readmapping
-
Satya,R.V., Zavaljevski,N. and Reifman,J. (2005) A new strategy to reduce allelic bias in RNA-Seq readmapping. Nucleic Acids Res., 40, e127.
-
(2005)
Nucleic Acids Res.
, vol.40
-
-
Satya, R.V.1
Zavaljevski, N.2
Reifman, J.3
|