-
1
-
-
84856736515
-
Genome sequencing reveals agronomically important loci in rice using MutMap
-
Abe, A., S. Kosugi, K. Yoshida, S. Natsume, H. Takagi et al., 2012. Genome sequencing reveals agronomically important loci in rice using MutMap. Nat. Biotechnol. 30: 174-178
-
(2012)
Nat. Biotechnol
, vol.30
, pp. 174-178
-
-
Abe, A.1
Kosugi, S.2
Yoshida, K.3
Natsume, S.4
Takagi, H.5
-
2
-
-
80755125553
-
Harnessing cloud computing with Galaxy Cloud
-
Afgan, E., D. Baker, N. Coraor, H. Goto, I. M. Paul et al., 2011. Harnessing cloud computing with Galaxy Cloud. Nat. Biotechnol. 29: 972-974
-
(2011)
Nat. Biotechnol
, vol.29
, pp. 972-974
-
-
Afgan, E.1
Baker, D.2
Coraor, N.3
Goto, H.4
Paul, I.M.5
-
3
-
-
68349104949
-
MAQGene: Software to facilitate C elegans mutant genome sequence analysis
-
Bigelow, H., M. Doitsidou, S. Sarin, and O. Hobert, 2009. MAQGene: software to facilitate C. elegans mutant genome sequence analysis. Nat. Methods 6: 549
-
(2009)
Nat. Methods
, vol.6
, pp. 549
-
-
Bigelow, H.1
Doitsidou, M.2
Sarin, S.3
Hobert, O.4
-
4
-
-
77954489376
-
Manipulation of FASTQ data with Galaxy
-
Blankenberg, D., A. Gordon, G. Von Kuster, N. Coraor, J. Taylor et al., 2010. Manipulation of FASTQ data with Galaxy. Bioinformatics 26: 1783-1785
-
(2010)
Bioinformatics
, vol.26
, pp. 1783-1785
-
-
Blankenberg, D.1
Gordon, A.2
von Kuster, G.3
Coraor, N.4
Taylor, J.5
-
5
-
-
84862506964
-
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
-
Cingolani, P., and A. Platts, L. Wang le, M. Coon, T. Nguyen et al., 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6: 80-92
-
(2012)
Fly (Austin)
, vol.6
, pp. 80-92
-
-
Cingolani, P.1
Platts, A.2
le Wang, L.3
Coon, M.4
Nguyen, T.5
-
6
-
-
4243709036
-
-
in S, edited by J. M. Chambers, and T. J. Hastie. CRC Press, Boca Raton, FL
-
Cleveland, W. S., E. Grosse, and W. M. Shyu, 1992. Local regression models, Statistical Models in S, edited by J. M. Chambers, and T. J. Hastie. CRC Press, Boca Raton, FL
-
(1992)
Local regression models, Statistical Models
-
-
Cleveland, W.S.1
Grosse, E.2
Shyu, W.M.3
-
7
-
-
79960405019
-
The variant call format and VCFtools
-
Danecek, P., A. Auton, G. Abecasis, C. A. Albers, E. Banks et al., 2011. The variant call format and VCFtools. Bioinformatics 27: 2156-2158
-
(2011)
Bioinformatics
, vol.27
, pp. 2156-2158
-
-
Danecek, P.1
Auton, A.2
Abecasis, G.3
Albers, C.A.4
Banks, E.5
-
8
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo, M. A., E. Banks, R. Poplin, K. V. Garimella, J. R. Maguire et al., 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43: 491-498
-
(2011)
Nat. Genet
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
Banks, E.2
Poplin, R.3
Garimella, K.V.4
Maguire, J.R.5
-
9
-
-
53249115177
-
Automated screening for mutants affecting dopaminergic-neuron specification in C elegans
-
Doitsidou, M., N. Flames, A. C. Lee, A. Boyanov, and O. Hobert, 2008. Automated screening for mutants affecting dopaminergic-neuron specification in C. elegans. Nat. Methods 5: 869-872
-
(2008)
Nat. Methods
, vol.5
, pp. 869-872
-
-
Doitsidou, M.1
Flames, N.2
Lee, A.C.3
Boyanov, A.4
Hobert, O.5
-
10
-
-
78149477199
-
C elegans mutant identification with a one-step wholegenome-sequencing and SNP mapping strategy
-
Doitsidou, M., R. J. Poole, S. Sarin, H. Bigelow, and O. Hobert, 2010. C. elegans mutant identification with a one-step wholegenome-sequencing and SNP mapping strategy. PLoS ONE 5: e15435
-
(2010)
PLoS ONE
, vol.5
-
-
Doitsidou, M.1
Poole, R.J.2
Sarin, S.3
Bigelow, H.4
Hobert, O.5
-
11
-
-
0031978181
-
Base-calling of automated sequencer traces using phred II. Error probabilities
-
Ewing, B., and P. Green, 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194
-
(1998)
Genome Res
, vol.8
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
12
-
-
77955499817
-
Whole-genome profiling of mutagenesis in Caenorhabditis elegans
-
Flibotte, S., M. L. Edgley, I. Chaudhry, J. Taylor, S. E. Neil et al., 2010. Whole-genome profiling of mutagenesis in Caenorhabditis elegans. Genetics 185: 431-441
-
(2010)
Genetics
, vol.185
, pp. 431-441
-
-
Flibotte, S.1
Edgley, M.L.2
Chaudhry, I.3
Taylor, J.4
Neil, S.E.5
-
13
-
-
77952214725
-
The Groucho ortholog UNC-37interacts with the short Groucho-like protein LSY-22 to control developmental decisions in C elegans
-
Flowers, E. B., R. J. Poole, B. Tursun, E. Bashllari, I. Pe'er et al., 2010. The Groucho ortholog UNC-37interacts with the short Groucho-like protein LSY-22 to control developmental decisions in C. elegans. Development 137: 1799-1805
-
(2010)
Development
, vol.137
, pp. 1799-1805
-
-
Flowers, E.B.1
Poole, R.J.2
Tursun, B.3
Bashllari, E.4
Pe'er, I.5
-
14
-
-
84864477464
-
Synteny-based mapping-by-sequencing enabled by targeted enrichment
-
Galvao, V. C., K. J. Nordstrom, C. Lanz, P. Sulz, J. Mathieu et al., 2012. Synteny-based mapping-by-sequencing enabled by targeted enrichment. Plant J. 71: 517-526
-
(2012)
Plant J
, vol.71
, pp. 517-526
-
-
Galvao, V.C.1
Nordstrom, K.J.2
Lanz, C.3
Sulz, P.4
Mathieu, J.5
-
15
-
-
0346494826
-
WormBase: A multi-species resource for nematode biology and genomics
-
DATABASE ISSUE
-
Harris, T. W., N. Chen, F. Cunningham, M. Tello-Ruiz, I. Antoshechkin et al., 2004. WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res. 32(Database issue): D411-D417
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Harris, T.W.1
Chen, N.2
Cunningham, F.3
Tello-Ruiz, M.4
Antoshechkin, I.5
-
16
-
-
38749149152
-
Whole-genome sequencing and variant discovery in C elegans
-
Hillier, L. W., G. T. Marth, A. R. Quinlan, D. Dooling, G. Fewell et al., 2008. Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods 5: 183-188
-
(2008)
Nat. Methods
, vol.5
, pp. 183-188
-
-
Hillier, L.W.1
Marth, G.T.2
Quinlan, A.R.3
Dooling, D.4
Fewell, G.5
-
17
-
-
77749274428
-
The impact of whole genome sequencing on model system genetics: Get ready for the ride
-
Hobert, O., 2010. The impact of whole genome sequencing on model system genetics: get ready for the ride. Genetics 184: 317-319
-
(2010)
Genetics
, vol.184
, pp. 317-319
-
-
Hobert, O.1
-
19
-
-
77954595318
-
Coevolution of neuropeptidergic signaling systems: From worm to man
-
Janssen, T., M. Lindemans, E. Meelkop, L. Temmerman, and L. Schoofs, 2010. Coevolution of neuropeptidergic signaling systems: from worm to man. Ann. N. Y. Acad. Sci. 1200: 1-14
-
(2010)
Ann. N. Y. Acad. Sci
, vol.1200
, pp. 1-14
-
-
Janssen, T.1
Lindemans, M.2
Meelkop, E.3
Temmerman, L.4
Schoofs, L.5
-
20
-
-
0036079158
-
The human genome browser at UCSC
-
Kent, W. J., C. W. Sugnet, T. S. Furey, K. M. Roskin, T. H. Pringle et al., 2002. The human genome browser at UCSC. Genome Res. 12: 996-1006
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
-
21
-
-
21044446786
-
Functional genomic analysis of RNA interference in C elegans
-
Kim, J. K., H. W. Gabel, R. S. Kamath, M. Tewari, A. Pasquinelli et al., 2005. Functional genomic analysis of RNA interference in C. elegans. Science 308: 1164-1167
-
(2005)
Science
, vol.308
, pp. 1164-1167
-
-
Kim, J.K.1
Gabel, H.W.2
Kamath, R.S.3
Tewari, M.4
Pasquinelli, A.5
-
22
-
-
84869037809
-
The SACY-1 DEAD-box helicase links the somatic control of oocyte meiotic maturation to the sperm-to-oocyte switch and gamete maintenance in Caenorhabditis elegans
-
(in press)
-
Kim, S., J. A. Govindan, Z. J. Tu, and D. Greenstein, 2012. The SACY-1 DEAD-box helicase links the somatic control of oocyte meiotic maturation to the sperm-to-oocyte switch and gamete maintenance in Caenorhabditis elegans. Genetics (in press)
-
(2012)
Genetics
-
-
Kim, S.1
Govindan, J.A.2
Tu, Z.J.3
Greenstein, D.4
-
23
-
-
84858651046
-
The pseudokinase NIPI-4 is a novel regulator of antimicrobial peptide gene expression
-
Labed, S. A., S. Omi, M. Gut, J. J. Ewbank, and N. Pujol, 2012. The pseudokinase NIPI-4 is a novel regulator of antimicrobial peptide gene expression. PLoS ONE 7: e33887
-
(2012)
PLoS ONE
, vol.7
-
-
Labed, S.A.1
Omi, S.2
Gut, M.3
Ewbank, J.J.4
Pujol, N.5
-
24
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., C. Trapnell, M. Pop, and S. L. Salzberg, 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
25
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
Li, H., and R. Durbin, 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589-595
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
26
-
-
77957272611
-
A survey of sequence alignment algorithms for next-generation sequencing
-
Li, H., and N. Homer, 2010. A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform. 11: 473-483
-
(2010)
Brief. Bioinform
, vol.11
, pp. 473-483
-
-
Li, H.1
Homer, N.2
-
27
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li, H., J. Ruan, and R. Durbin, 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18: 1851-1858
-
(2008)
Genome Res
, vol.18
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
28
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
-
29
-
-
70349739736
-
The Integrated Genome Browser: Free software for distribution and exploration of genome-scale datasets
-
Nicol, J. W., G. A. Helt, S. G. Blanchard Jr., A. Raja, and A. E. Loraine, 2009. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25: 2730-2731
-
(2009)
Bioinformatics
, vol.25
, pp. 2730-2731
-
-
Nicol, J.W.1
Helt, G.A.2
Blanchard Jr., S.G.3
Raja, A.4
Loraine, A.E.5
-
30
-
-
79956314887
-
Genotype and SNP calling from next-generation sequencing data
-
Nielsen, R., J. S. Paul, A. Albrechtsen, and Y. S. Song, 2011. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12: 443-451
-
(2011)
Nat. Rev. Genet
, vol.12
, pp. 443-451
-
-
Nielsen, R.1
Paul, J.S.2
Albrechtsen, A.3
Song, Y.S.4
-
31
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan, A. R., and I. M. Hall, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
32
-
-
82355175168
-
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping
-
Reece-Hoyes, J. S., A. Diallo, B. Lajoie, A. Kent, S. Shrestha et al., 2011. Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat. Methods 8: 1059-1064
-
(2011)
Nat. Methods
, vol.8
, pp. 1059-1064
-
-
Reece-Hoyes, J.S.1
Diallo, A.2
Lajoie, B.3
Kent, A.4
Shrestha, S.5
-
33
-
-
77955486655
-
Analysis of multiple ethyl methanesulfonate-mutagenized caenorhabditis elegans strains by whole-genome sequencing
-
Sarin, S., V. Bertrand, H. Bigelow, A. Boyanov, M. Doitsidou et al., 2010. Analysis of multiple ethyl methanesulfonate-mutagenized caenorhabditis elegans strains by whole-genome sequencing. Genetics 185: 417-430
-
(2010)
Genetics
, vol.185
, pp. 417-430
-
-
Sarin, S.1
Bertrand, V.2
Bigelow, H.3
Boyanov, A.4
Doitsidou, M.5
-
34
-
-
68349086946
-
SHOREmap: Simultaneous mapping and mutation identification by deep sequencing
-
Schneeberger, K., S. Ossowski, C. Lanz, T. Juul, A. H. Petersen et al., 2009. SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat. Methods 6: 550-551
-
(2009)
Nat. Methods
, vol.6
, pp. 550-551
-
-
Schneeberger, K.1
Ossowski, S.2
Lanz, C.3
Juul, T.4
Petersen, A.H.5
-
35
-
-
38849199286
-
Widespread genetic incompatibility in C elegans maintained by balancing selection
-
Seidel, H. S., M. V. Rockman, and L. Kruglyak, 2008. Widespread genetic incompatibility in C. elegans maintained by balancing selection. Science 319: 589-594
-
(2008)
Science
, vol.319
, pp. 589-594
-
-
Seidel, H.S.1
Rockman, M.V.2
Kruglyak, L.3
-
36
-
-
79957467830
-
OrthoList: A compendium of C elegans genes with human orthologs
-
Shaye, D. D., and I. Greenwald, 2011. OrthoList: a compendium of C. elegans genes with human orthologs. PLoS ONE 6: e20085
-
(2011)
PLoS ONE
, vol.6
-
-
Shaye, D.D.1
Greenwald, I.2
-
37
-
-
78751703892
-
Direct conversion of C elegans germ cells into specific neuron types
-
Tursun, B., T. Patel, P. Kratsios, and O. Hobert, 2011. Direct conversion of C. elegans germ cells into specific neuron types. Science 331: 304-308
-
(2011)
Science
, vol.331
, pp. 304-308
-
-
Tursun, B.1
Patel, T.2
Kratsios, P.3
Hobert, O.4
-
38
-
-
33747836205
-
Gene expression: Long-term gene silencing by RNAi
-
Vastenhouw, N. L., K. Brunschwig, K. L. Okihara, F. Muller, M. Tijsterman et al., 2006. Gene expression: long-term gene silencing by RNAi. Nature 442: 882
-
(2006)
Nature
, vol.442
, pp. 882
-
-
Vastenhouw, N.L.1
Brunschwig, K.2
Okihara, K.L.3
Muller, F.4
Tijsterman, M.5
-
39
-
-
23144462374
-
Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants
-
Wang, D., S. Kennedy, D. Conte Jr., J. K. Kim, H. W. Gabel et al., 2005. Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants. Nature 436: 593-597
-
(2005)
Nature
, vol.436
, pp. 593-597
-
-
Wang, D.1
Kennedy, S.2
Conte Jr., D.3
Kim, J.K.4
Gabel, H.W.5
-
40
-
-
79960150949
-
A left/right asymmetric neuronal differentiation program is controlled by the Caenorhabditis elegans lsy-27 zinc-finger transcription factor
-
Zhang, F., M. M. O'Meara, and O. Hobert, 2011. A left/right asymmetric neuronal differentiation program is controlled by the Caenorhabditis elegans lsy-27 zinc-finger transcription factor. Genetics 188: 753-759
-
(2011)
Genetics
, vol.188
, pp. 753-759
-
-
Zhang, F.1
O'Meara, M.M.2
Hobert, O.3
-
41
-
-
78751654713
-
A strategy for direct mapping and identification of mutations by wholegenome sequencing
-
Zuryn, S., S. Le Gras, K. Jamet, and S. Jarriault, 2010. A strategy for direct mapping and identification of mutations by wholegenome sequencing. Genetics 186: 427-430
-
(2010)
Genetics
, vol.186
, pp. 427-430
-
-
Zuryn, S.1
Le Gras, S.2
Jamet, K.3
Jarriault, S.4
|