-
1
-
-
65549109397
-
Visualisation of genomic data with the Hilbert curve
-
Anders S (2009) Visualisation of genomic data with the Hilbert curve. Bioinformatics 25: 1231-1235.
-
(2009)
Bioinformatics
, vol.25
, pp. 1231-1235
-
-
Anders, S.1
-
2
-
-
54949147307
-
F-Seq: A feature density estimator for high-throughput sequence tags
-
Boyle AP, Guinney J, Crawford GE, Furey TS (2008) F-Seq: A feature density estimator for high-throughput sequence tags. Bioinformatics 24: 2537-2538.
-
(2008)
Bioinformatics
, vol.24
, pp. 2537-2538
-
-
Boyle, A.P.1
Guinney, J.2
Crawford, G.E.3
Furey, T.S.4
-
4
-
-
77954363385
-
Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data
-
[Epub ahead of print]
-
Bravo HC, Irizarry RA (2009) Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data. Biometrics [Epub ahead of print].
-
(2009)
Biometrics
-
-
Bravo, H.C.1
Irizarry, R.A.2
-
5
-
-
77949481052
-
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
-
Bullard JH, Purdom E, Hansen KD, Dudoit S (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11: 94
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 94
-
-
Bullard, J.H.1
Purdom, E.2
Hansen, K.D.3
Dudoit, S.4
-
6
-
-
67649866313
-
Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data
-
Choi H, Nesvizhskii A, Ghosh D, Qin ZS (2009) Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. Bioinformatics 25:1715-1721.
-
(2009)
Bioinformatics
, vol.25
, pp. 1715-1721
-
-
Choi, H.1
Nesvizhskii, A.2
Ghosh, D.3
Qin, Z.S.4
-
7
-
-
65549102180
-
Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease
-
Chu T, Bunce K, Hogge WA, Peters DG (2009) Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease. Bioinformatics 25: 1244-1250.
-
(2009)
Bioinformatics
, vol.25
, pp. 1244-1250
-
-
Chu, T.1
Bunce, K.2
Hogge, W.A.3
Peters, D.G.4
-
8
-
-
46249103973
-
Stem cell transcriptome profiling via massive-scale mRNA sequencing
-
Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5: 613-619.
-
(2008)
Nat Methods
, vol.5
, pp. 613-619
-
-
Cloonan, N.1
Forrest, A.R.2
Kolle, G.3
Gardiner, B.B.4
Faulkner, G.J.5
-
9
-
-
40749109894
-
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
-
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215-219.
-
(2008)
Nature
, vol.452
, pp. 215-219
-
-
Cokus, S.J.1
Feng, S.2
Zhang, X.3
Chen, Z.4
Merriman, B.5
-
10
-
-
49549125680
-
Annotation of metagenome short reads using proxygenes
-
Dalevi D, Ivanova NN, Mavromatis K, Hooper SD, Szeto E, et al. (2008) Annotation of metagenome short reads using proxygenes. Bioinformatics 24: i7-i13.
-
(2008)
Bioinformatics
, vol.24
-
-
Dalevi, D.1
Ivanova, N.N.2
Mavromatis, K.3
Hooper, S.D.4
Szeto, E.5
-
11
-
-
52649157765
-
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
-
Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36: e105.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
12
-
-
47149111640
-
TileQC: A system for tile-based quality control of the Solexa data
-
Dolan PC, Denver DR (2009) TileQC: A system for tile-based quality control of the Solexa data. BMC Bioinformatics 9: 250.
-
(2009)
BMC Bioinformatics
, vol.9
, pp. 250
-
-
Dolan, P.C.1
Denver, D.R.2
-
13
-
-
0042307371
-
Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations
-
Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B (2003) Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci USA 100: 8817-8822.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 8817-8822
-
-
Dressman, D.1
Yan, H.2
Traverso, G.3
Kinzler, K.W.4
Vogelstein, B.5
-
16
-
-
24044522270
-
BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis
-
Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, et al. (2006) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21: 3439-3440.
-
(2006)
Bioinformatics
, vol.21
, pp. 3439-3440
-
-
Durinck, S.1
Moreau, Y.2
Kasprzyk, A.3
Davis, S.4
de Moor, B.5
-
17
-
-
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: 133-138.
-
(2009)
Science
, vol.323
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
Luong, K.4
Lyle, J.5
-
18
-
-
48449094744
-
Alta-Cyclic: A self-optimizing base caller for next-generation sequencing
-
Erlich Y, Mitra PP, delaBastide M, McCombie WR, Hannon GJ (2008) Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods 5: 679-682.
-
(2008)
Nat Methods
, vol.5
, pp. 679-682
-
-
Erlich, Y.1
Mitra, P.P.2
Delabastide, M.3
McCombie, W.R.4
Hannon, G.J.5
-
19
-
-
48249140621
-
FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology
-
Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, et al. (2008) FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24: 1729-1730.
-
(2008)
Bioinformatics
, vol.24
, pp. 1729-1730
-
-
Fejes, A.P.1
Robertson, G.2
Bilenky, M.3
Varhol, R.4
Bainbridge, M.5
-
20
-
-
73949090104
-
Applications of ultra-high-throughput sequencing
-
Fox S, Filichkin S, Mockler TC (2009) Applications of ultra-high-throughput sequencing. Methods Mol Biol 553: 79-108.
-
(2009)
Methods Mol Biol
, vol.553
, pp. 79-108
-
-
Fox, S.1
Filichkin, S.2
Mockler, T.C.3
-
21
-
-
41849084855
-
Discovering microRNAS from deep sequencing data using miRDeep
-
Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, et al. (2008) Discovering microRNAS from deep sequencing data using miRDeep. Nat Biotechnol 26: 407-415.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 407-415
-
-
Friedländer, M.R.1
Chen, W.2
Adamidi, C.3
Maaskola, J.4
Einspanier, R.5
-
22
-
-
65649083411
-
Estimating accuracy of RNA-Sequencing and microarray with proteomics
-
Fu X, Fu N, Guo S, Yan Z, Xu Y, et al. (2009) Estimating accuracy of RNA-Sequencing and microarray with proteomics. BMC Genomics 10: 161.
-
(2009)
BMC Genomics
, vol.10
, pp. 161
-
-
Fu, X.1
Fu, N.2
Guo, S.3
Yan, Z.4
Xu, Y.5
-
23
-
-
77951957381
-
SNVMix: Predicting single nucleotide variants from next-generation sequencing of tumors
-
Goya R, Sun MG, Morin RD, Leung G, Ha G, et al. (2010) SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics 26: 730-736.
-
(2010)
Bioinformatics
, vol.26
, pp. 730-736
-
-
Goya, R.1
Sun, M.G.2
Morin, R.D.3
Leung, G.4
Ha, G.5
-
24
-
-
41749104588
-
Single-Molecule DNA Sequencing of a Viral Genome
-
Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, et al. (2008) Single-Molecule DNA Sequencing of a Viral Genome. Science 320: 106-109.
-
(2008)
Science
, vol.320
, pp. 106-109
-
-
Harris, T.D.1
Buzby, P.R.2
Babcock, H.3
Beer, E.4
Bowers, J.5
-
25
-
-
52049119933
-
Parameter estimation for robust HMM analysis of ChIP-chip data
-
Humburg P, Bulger D, Stone G (2008) Parameter estimation for robust HMM analysis of ChIP-chip data. BMC Bioinformatics 9: 343.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 343
-
-
Humburg, P.1
Bulger, D.2
Stone, G.3
-
26
-
-
55749094855
-
An integrated software system for analyzing ChIP-chip and ChIP-seq data
-
Ji H, Jiang H, Ma W, Johnson DS, Myers RM, et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26: 1293-1300.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1293-1300
-
-
Ji, H.1
Jiang, H.2
Ma, W.3
Johnson, D.S.4
Myers, R.M.5
-
27
-
-
64549119707
-
Statistical inferences for isoform expression in RNA-Seq
-
Jiang H, Wong W (2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25: 1026-1032.
-
(2009)
Bioinformatics
, vol.25
, pp. 1026-1032
-
-
Jiang, H.1
Wong, W.2
-
28
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
29
-
-
33845940688
-
Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators
-
Ju J, Kim DH, Bi L, Meng Q, Bai X, et al. (2006) Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci USA 103: 19635-19640.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 19635-19640
-
-
Ju, J.1
Kim, D.H.2
Bi, L.3
Meng, Q.4
Bai, X.5
-
30
-
-
70349646530
-
Bayes Call: A model-based basecalling algorithm for high-throughput short-read sequencing
-
Kao W, Stevens C, Song Y (2009) Bayes Call: A model-based basecalling algorithm for high-throughput short-read sequencing. Genome Res 19: 1884-1895.
-
(2009)
Genome Res
, vol.19
, pp. 1884-1895
-
-
Kao, W.1
Stevens, C.2
Song, Y.3
-
31
-
-
57449100870
-
Design and analysis of ChIP-seq experiments for DNA-binding proteins
-
Kharchenko PV, Tolstorukov MY, Park PJ (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 26: 1351-1359.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1351-1359
-
-
Kharchenko, P.V.1
Tolstorukov, M.Y.2
Park, P.J.3
-
32
-
-
70350023532
-
Improved base calling for the Illumina Genome Analyzer using machine learning strategies
-
Kircher M, Stenzel U, Kelso J (2009) Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol 10: R83.
-
(2009)
Genome Biol
, vol.10
-
-
Kircher, M.1
Stenzel, U.2
Kelso, J.3
-
34
-
-
62349130698
-
Ultrafast and memory efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, 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
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
35
-
-
67649837030
-
Rtracklayer: An R package for interfacing with genome browsers
-
Lawrence M, Gentleman R, Carey V (2009) rtracklayer: an R package for interfacing with genome browsers. Bioinformatics 25: 1841-1842.
-
(2009)
Bioinformatics
, vol.25
, pp. 1841-1842
-
-
Lawrence, M.1
Gentleman, R.2
Carey, V.3
-
36
-
-
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: 1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
37
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li H, Ruan J, Durbin R (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
-
38
-
-
52949096084
-
Next generation DNA sequencing methods
-
Mardis ER (2008) Next generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9: 387-402.
-
(2008)
Annu Rev Genomics Hum Genet
, vol.9
, pp. 387-402
-
-
Mardis, E.R.1
-
39
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, 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
-
40
-
-
50649089207
-
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
-
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genom Res 18: 1509-1517.
-
(2008)
Genom Res
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.E.2
Mane, S.M.3
Stephens, M.4
Gilad, Y.5
-
41
-
-
34548682537
-
Pyrosequencing applications
-
Marsh S (2007) Pyrosequencing applications. Methods Mol Biol 373: 15-24.
-
(2007)
Methods Mol Biol
, vol.373
, pp. 15-24
-
-
Marsh, S.1
-
42
-
-
70449704529
-
Computational methods for discovering structural variation with next-generation sequencing
-
Medvedev P, Stanciu M, Brudno M (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat Methods 6: S13-S20.
-
(2009)
Nat Methods
, vol.6
-
-
Medvedev, P.1
Stanciu, M.2
Brudno, M.3
-
43
-
-
44949162060
-
Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases
-
Meng X, Noyes MB, Zhu LJ, Lawson ND, Wolfe SA (2008) Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol 26: 695-701.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 695-701
-
-
Meng, X.1
Noyes, M.B.2
Zhu, L.J.3
Lawson, N.D.4
Wolfe, S.A.5
-
44
-
-
0000251971
-
Maximum likelihood estimation via the ECM algorithm: A general framework
-
Meng XL, Rubin DB (1993) Maximum likelihood estimation via the ECM algorithm: A general framework. Biometrika 80: 267-278.
-
(1993)
Biometrika
, vol.80
, pp. 267-278
-
-
Meng, X.L.1
Rubin, D.B.2
-
45
-
-
72849144434
-
Sequencing technologies - the next generation
-
Metzker ML (2010) Sequencing technologies - the next generation. Nat Rev Genet 11: 31-46.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 31-46
-
-
Metzker, M.L.1
-
46
-
-
70349866687
-
Shortread: A Bioconductor package for input, quality assessment and exploration of high throughput sequence data
-
Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, et al. (2009) Shortread: a Bioconductor package for input, quality assessment and exploration of high throughput sequence data. Bioinformatics 25: 2607-2608.
-
(2009)
Bioinformatics
, vol.25
, pp. 2607-2608
-
-
Morgan, M.1
Anders, S.2
Lawrence, M.3
Aboyoun, P.4
Pagès, H.5
-
47
-
-
41649106136
-
Application of massively parallel sequencing to micro RNA profiling and discovery in human embryonic stem cells
-
Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, et al. (2008) Application of massively parallel sequencing to micro RNA profiling and discovery in human embryonic stem cells. Genome Res 18: 610-621.
-
(2008)
Genome Res
, vol.18
, pp. 610-621
-
-
Morin, R.D.1
O'Connor, M.D.2
Griffith, M.3
Kuchenbauer, F.4
Delaney, A.5
-
48
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-seq
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 5: 621-628.
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
49
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
-
(2008)
Science
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
-
50
-
-
65649126066
-
Transcript length bias in RNA-sequencing data confounds systems biology
-
Oshlack A, Wakefield M (2009) Transcript length bias in RNA-sequencing data confounds systems biology. Biol Direct 4: 14.
-
(2009)
Biol Direct
, vol.4
, pp. 14
-
-
Oshlack, A.1
Wakefield, M.2
-
53
-
-
84879462012
-
String objects representing biological sequences, and matching algorithms
-
available at
-
Pages H, Aboyoun P, Gentleman R, DebRoy S (2009) String objects representing biological sequences, and matching algorithms. Biostrings available at: http://www.bioconductor.org/packages/bioc/html/Biostrings.html
-
(2009)
Biostrings
-
-
Pages, H.1
Aboyoun, P.2
Gentleman, R.3
Debroy, S.4
-
54
-
-
70449711243
-
Computation for ChIP-seq and RNA-seq studies
-
Pepke S, Wold B, Mortazavi A (2009) Computation for ChIP-seq and RNA-seq studies. Nat Methods 6: S22-S32.
-
(2009)
Nat Methods
, vol.6
-
-
Pepke, S.1
Wold, B.2
Mortazavi, A.3
-
56
-
-
70350697843
-
ISOLATE: A computational strategy for identifying the primary origin of cancers using high throughput sequencing
-
Quon G, Morris Q (2009) ISOLATE: A computational strategy for identifying the primary origin of cancers using high throughput sequencing. Bioinformatics 25: 2882-2889.
-
(2009)
Bioinformatics
, vol.25
, pp. 2882-2889
-
-
Quon, G.1
Morris, Q.2
-
57
-
-
55049090961
-
Probabilistic base calling of Solexa sequencing data
-
Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, et al. (2008) Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics 9: 431.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 431
-
-
Rougemont, J.1
Amzallag, A.2
Iseli, C.3
Farinelli, L.4
Xenarios, I.5
-
58
-
-
60149112271
-
Peakseq enables systematic scoring of ChIP-seq experiments relative to controls
-
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, et al. (2009) Peakseq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 27: 66-75.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
Euskirchen, G.2
Auerbach, R.K.3
Zhang, Z.D.4
Gibson, T.5
-
60
-
-
39449088572
-
Genome wide approaches to studying chromatin modifications
-
Schones DE, Zhao K (2008) Genome wide approaches to studying chromatin modifications. Nat Rev Genet 9: 179-191.
-
(2008)
Nat Rev Genet
, vol.9
, pp. 179-191
-
-
Schones, D.E.1
Zhao, K.2
-
61
-
-
50949097456
-
A feature-based approach to modeling protein-DNA interactions
-
e1000154
-
Sharon E, Lubliner S, Segal E (2008) A feature-based approach to modeling protein-DNA interactions. PLoS Comput Biol 4: e1000154.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Sharon, E.1
Lubliner, S.2
Segal, E.3
-
62
-
-
53649106195
-
Next-generation DNA sequencing
-
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nature Biotechnology 26: 1135-1145.
-
(2008)
Nature Biotechnology
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
63
-
-
24644462173
-
Accurate multiplex polony sequencing of an evolved bacterial genome
-
Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728-1732.
-
(2005)
Science
, vol.309
, pp. 1728-1732
-
-
Shendure, J.1
Porreca, G.J.2
Reppas, N.B.3
Lin, X.4
McCutcheon, J.P.5
-
64
-
-
41149167170
-
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
-
Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, et al. (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17: 1636-1647.
-
(2008)
Mol Ecol
, vol.17
, pp. 1636-1647
-
-
Vera, J.C.1
Wheat, C.W.2
Fescemyer, H.W.3
Frilander, M.J.4
Crawford, D.L.5
-
65
-
-
69449099392
-
Comparison of next generation sequencing technologies for transcriptome characterization
-
Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, et al. (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 10: 347.
-
(2009)
BMC Genomics
, vol.10
, pp. 347
-
-
Wall, P.K.1
Leebens-Mack, J.2
Chanderbali, A.S.3
Barakat, A.4
Wolcott, E.5
-
66
-
-
84950432017
-
A Monte Carlo Implementation of the EM Algorithm and the Poor Man's Data Augmentation Algorithms
-
Wei GCG, Tanner MA (1990) A Monte Carlo Implementation of the EM Algorithm and the Poor Man's Data Augmentation Algorithms. J Am Stat Assoc 85: 699-704.
-
(1990)
J Am Stat Assoc
, vol.85
, pp. 699-704
-
-
Wei, G.C.G.1
Tanner, M.A.2
-
67
-
-
69949135779
-
Swift: Primary data analysis for the Illumina Solexa sequencing platform
-
Whiteford N, Skelly T, Curtis C, Ritchie ME, Löhr A, et al. (2009) Swift: primary data analysis for the Illumina Solexa sequencing platform. Bioinformatics 25: 2194-2199.
-
(2009)
Bioinformatics
, vol.25
, pp. 2194-2199
-
-
Whiteford, N.1
Skelly, T.2
Curtis, C.3
Ritchie, M.E.4
Löhr, A.5
-
68
-
-
64849083125
-
CNV-seq, a new method to detect copy number variation using high-throughput sequencing
-
Xie C, Tammi MT (2009) CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10: 80.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 80
-
-
Xie, C.1
Tammi, M.T.2
-
69
-
-
67650711619
-
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
-
Zang C, Schones DE, Zeng C, Cui K, Zhao K, et al. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25: 1952-1958.
-
(2009)
Bioinformatics
, vol.25
, pp. 1952-1958
-
-
Zang, C.1
Schones, D.E.2
Zeng, C.3
Cui, K.4
Zhao, K.5
-
70
-
-
77954382010
-
Probabilistic inference of ChIP-seq
-
available at
-
Zhang X, Gottardo R, Droit A (2010) Probabilistic inference of ChIP-seq. PICS available at: http://www.bioconductor.org/packages/2.6/bioc/html/PICS.html
-
(2010)
PICS
-
-
Zhang, X.1
Gottardo, R.2
Droit, A.3
-
71
-
-
53849146020
-
Model-based Analysis of ChIP-Seq (MACS)
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008a) Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
-
72
-
-
50949097455
-
Modelling ChIP Sequencing In Silico with Applications
-
e1000158
-
Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M, et al. (2008b) Modelling ChIP Sequencing In Silico with Applications. PLoS Comput Biol 4: e1000158.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Zhang, Z.D.1
Rozowsky, J.2
Snyder, M.3
Chang, J.4
Gerstein, M.5
-
73
-
-
84922353363
-
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments
-
available at
-
Zhu LJ, Pages H, Gazin C, Lawson N, Lin S, et al. (2009) Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments. Chippeak Anno available at: http://www.bioconductor.org/packages/2.5/bioc/html/ChIPpeakAnno.html
-
(2009)
Chippeak Anno
-
-
Zhu, L.J.1
Pages, H.2
Gazin, C.3
Lawson, N.4
Lin, S.5
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