-
1
-
-
84866662716
-
Understanding pathogens in the era of next generation sequencing
-
Methot, P. O., Understanding pathogens in the era of next generation sequencing. J. Infect. Dev. Countries 2012, 6, 689-691.
-
(2012)
J. Infect. Dev. Countries
, vol.6
, pp. 689-691
-
-
Methot, P.O.1
-
2
-
-
84907483586
-
Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals
-
Cheng, A. Y., Teo, Y. Y., Ong, R. T., Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals. Bioinformatics 2014, 30, 1707-1713.
-
(2014)
Bioinformatics
, vol.30
, pp. 1707-1713
-
-
Cheng, A.Y.1
Teo, Y.Y.2
Ong, R.T.3
-
3
-
-
84879043343
-
Quantifying single nucleotide variant detection sensitivity in exome sequencing
-
Meynert, A. M., Bicknell, L. S., Hurles, M. E., Jackson, A. P., Taylor, M. S., Quantifying single nucleotide variant detection sensitivity in exome sequencing. BMC Bioinformatics 2013, 14, 195.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 195
-
-
Meynert, A.M.1
Bicknell, L.S.2
Hurles, M.E.3
Jackson, A.P.4
Taylor, M.S.5
-
4
-
-
84885300845
-
Reliable identification of genomic variants from RNA-seq data
-
Piskol, R., Ramaswami, G., Li, J. B., Reliable identification of genomic variants from RNA-seq data. Am. J. Hum. Genet. 2013, 93, 641-651.
-
(2013)
Am. J. Hum. Genet.
, vol.93
, pp. 641-651
-
-
Piskol, R.1
Ramaswami, G.2
Li, J.B.3
-
5
-
-
34249807325
-
A mass spectrometry-friendly database for cSNP identification
-
Schandorff, S., Olsen, J. V., Bunkenborg, J., Blagoev, B. et al., A mass spectrometry-friendly database for cSNP identification. Nat. Methods 2007, 4, 465-466.
-
(2007)
Nat. Methods
, vol.4
, pp. 465-466
-
-
Schandorff, S.1
Olsen, J.V.2
Bunkenborg, J.3
Blagoev, B.4
-
6
-
-
79955765660
-
A bioinformatics workflow for variant peptide detection in shotgun proteomics
-
Li, J., Su, Z., Ma, Z. Q., Slebos, R. J. et al., A bioinformatics workflow for variant peptide detection in shotgun proteomics. Mol. Cell. Proteomics 2011, 10, M110 006536.
-
(2011)
Mol. Cell. Proteomics
, vol.10
-
-
Li, J.1
Su, Z.2
Ma, Z.Q.3
Slebos, R.J.4
-
7
-
-
84891818263
-
Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences
-
Sheynkman, G. M., Shortreed, M. R., Frey, B. L., Scalf, M., Smith, L. M., Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. J. Proteome Res. 2014, 13, 228-240.
-
(2014)
J. Proteome Res.
, vol.13
, pp. 228-240
-
-
Sheynkman, G.M.1
Shortreed, M.R.2
Frey, B.L.3
Scalf, M.4
Smith, L.M.5
-
8
-
-
84891810621
-
Large-scale quantification of single amino-acid variations by a variation-associated database search strategy
-
Song, C., Wang, F., Cheng, K., Wei, X. et al., Large-scale quantification of single amino-acid variations by a variation-associated database search strategy. J. Proteome Res. 2014, 13, 241-248.
-
(2014)
J. Proteome Res.
, vol.13
, pp. 241-248
-
-
Song, C.1
Wang, F.2
Cheng, K.3
Wei, X.4
-
9
-
-
80855128254
-
Deep proteome and transcriptome mapping of a human cancer cell line
-
Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J. et al., Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Systems Biol. 2011, 7, 548.
-
(2011)
Mol. Systems Biol.
, vol.7
, pp. 548
-
-
Nagaraj, N.1
Wisniewski, J.R.2
Geiger, T.3
Cox, J.4
-
10
-
-
0035173378
-
dbSNP: the NCBI database of genetic variation
-
Sherry, S. T., Ward, M. H., Kholodov, M., Baker, J. et al., dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29, 308-311.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 308-311
-
-
Sherry, S.T.1
Ward, M.H.2
Kholodov, M.3
Baker, J.4
-
11
-
-
0036081078
-
DNA Data Bank of Japan (DDBJ) for genome scale research in life science
-
Tateno, Y., Imanishi, T., Miyazaki, S., Fukami-Kobayashi, K. et al., DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res. 2002, 30, 27-30.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 27-30
-
-
Tateno, Y.1
Imanishi, T.2
Miyazaki, S.3
Fukami-Kobayashi, K.4
-
12
-
-
70349866687
-
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data
-
Morgan, M., Anders, S., Lawrence, M., Aboyoun, P. et al., ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 2009, 25, 2607-2608.
-
(2009)
Bioinformatics
, vol.25
, pp. 2607-2608
-
-
Morgan, M.1
Anders, S.2
Lawrence, M.3
Aboyoun, P.4
-
13
-
-
0031955518
-
Base-calling of automated sequencer traces using phred. I. Accuracy assessment
-
Ewing, B., Hillier, L., Wendl, M. C., Green, P., Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998, 8, 175-185.
-
(1998)
Genome Res.
, vol.8
, pp. 175-185
-
-
Ewing, B.1
Hillier, L.2
Wendl, M.C.3
Green, P.4
-
14
-
-
0036079158
-
The human genome browser at UCSC
-
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M. et al., The human genome browser at UCSC. Genome Res. 2002, 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
-
15
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
Trapnell, C., Pachter, L., Salzberg, S. L., TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25, 1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
16
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M., Salzberg, S. L., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10, R25.
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
17
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T. et al., The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25, 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
-
18
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A. et al., Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 28, 511-515.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
-
19
-
-
28744458859
-
Bioconductor: open software development for computational biology and bioinformatics
-
Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B. et al., Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5, R80.
-
(2004)
Genome Biol.
, vol.5
, pp. R80
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
-
20
-
-
0034201441
-
EMBOSS: The European molecular biology open software suite
-
Rice, P., Longden, I., Bleasby, A., EMBOSS: The European molecular biology open software suite. Trends Genet. 2000, 16, 276-277.
-
(2000)
Trends Genet.
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
21
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z. et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29, 644-652.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
-
22
-
-
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., Platts, A., Wang le, L., Coon, M. et al., 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 2012, 6, 80-92.
-
(2012)
Fly
, vol.6
, pp. 80-92
-
-
Cingolani, P.1
Platts, A.2
Wang le, L.3
Coon, M.4
-
23
-
-
84891767394
-
RefSeq: an update on mammalian reference sequences
-
Pruitt, K. D., Brown, G. R., Hiatt, S. M., Thibaud-Nissen, F. et al., RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014, 42, D756-D763.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D756-D763
-
-
Pruitt, K.D.1
Brown, G.R.2
Hiatt, S.M.3
Thibaud-Nissen, F.4
-
24
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
-
Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
25
-
-
79953701087
-
Andromeda: a peptide search engine integrated into the MaxQuant environment
-
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A. et al., Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 2011, 10, 1794-1805.
-
(2011)
J. Proteome Res.
, vol.10
, pp. 1794-1805
-
-
Cox, J.1
Neuhauser, N.2
Michalski, A.3
Scheltema, R.A.4
-
26
-
-
33847630405
-
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
-
Elias, J. E., Gygi, S. P., Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 2007, 4, 207-214.
-
(2007)
Nat. Methods
, vol.4
, pp. 207-214
-
-
Elias, J.E.1
Gygi, S.P.2
-
27
-
-
71549117585
-
Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome
-
Wisniewski, J. R., Zougman, A., Mann, M., Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J. Proteome Res. 2009, 8, 5674-5678.
-
(2009)
J. Proteome Res.
, vol.8
, pp. 5674-5678
-
-
Wisniewski, J.R.1
Zougman, A.2
Mann, M.3
-
28
-
-
84891783174
-
Activities at the Universal Protein Resource (UniProt)
-
Apweiler, R., Bateman, A., Martin, M. J., O'Donovan, C. et al., Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014, 42, D191-D198.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D191-D198
-
-
Apweiler, R.1
Bateman, A.2
Martin, M.J.3
O'Donovan, C.4
-
29
-
-
84863393526
-
Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes
-
Michalski, A., Damoc, E., Lange, O., Denisov, E. et al., Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol. Cell. Proteomics 2012, 11, O111 013698.
-
(2012)
Mol. Cell. Proteomics
, vol.11
-
-
Michalski, A.1
Damoc, E.2
Lange, O.3
Denisov, E.4
-
30
-
-
78751653049
-
Mass spectrometry at the interface of proteomics and genomics
-
Krug, K., Nahnsen, S., Macek, B., Mass spectrometry at the interface of proteomics and genomics. Mol. Biosyst. 2011, 7, 284-291.
-
(2011)
Mol. Biosyst.
, vol.7
, pp. 284-291
-
-
Krug, K.1
Nahnsen, S.2
Macek, B.3
-
31
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey, J. D., Tibshirani, R., Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 2003, 100, 9440-9445.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
|