-
1
-
-
52949096084
-
Next-generation DNA, sequencing methods
-
Mardis ER. Next-generation DNA, sequencing methods. Annu Rev Genomics Hum Genet. 2008;9:387-402.
-
(2008)
Annu Rev Genomics Hum Genet.
, vol.9
, pp. 387-402
-
-
Mardis, E.R.1
-
2
-
-
84857859359
-
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets
-
Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res. 2012;40:e31.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Thomas-Chollier, M.1
Herrmann, C.2
Defrance, M.3
Sand, O.4
Thieffry, D.5
Helden, J.6
-
3
-
-
84863887694
-
Studying and modelling dynamic biological processes using time-series gene expression data
-
Bar-Joseph Z, Gitter A, Simon I. Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Genet. 2012;13:552-64.
-
(2012)
Nat Rev Genet.
, vol.13
, pp. 552-564
-
-
Bar-Joseph, Z.1
Gitter, A.2
Simon, I.3
-
4
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010;330:1787-97.
-
(2010)
Science
, vol.330
, pp. 1787-1797
-
-
Roy, S.1
Ernst, J.2
Kharchenko, P.V.3
Kheradpour, P.4
Negre, N.5
-
5
-
-
84555179177
-
Identifying differential histone modification sites from ChIP-seq data
-
Xu H, Sung WK. Identifying differential histone modification sites from ChIP-seq data. Methods Mol Biol. 2012;802:293-303.
-
(2012)
Methods Mol Biol.
, vol.802
, pp. 293-303
-
-
Xu, H.1
Sung, W.K.2
-
6
-
-
84869502241
-
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions
-
Furey TS. ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet. 2012;13:840-52.
-
(2012)
Nat Rev Genet.
, vol.13
, pp. 840-852
-
-
Furey, T.S.1
-
7
-
-
84969416529
-
-
NCBI Genome. Available at: http://www.ncbi.nlm.nih.gov/genome.
-
-
-
-
8
-
-
0036500609
-
A genomic regulatory network for development
-
Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, et al. A genomic regulatory network for development. Science. 2002;295:1669-78.
-
(2002)
Science.
, vol.295
, pp. 1669-1678
-
-
Davidson, E.H.1
Rast, J.P.2
Oliveri, P.3
Ransick, A.4
Calestani, C.5
Yuh, C.H.6
-
9
-
-
46149104377
-
Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution
-
Carroll SB. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell. 2008;134:25-36.
-
(2008)
Cell.
, vol.134
, pp. 25-36
-
-
Carroll, S.B.1
-
10
-
-
33847057226
-
The evolutionary significance of cis-regulatory mutations
-
Wray GA. The evolutionary significance of cis-regulatory mutations. Nat Rev Genet. 2007;8:206-16.
-
(2007)
Nat Rev Genet.
, vol.8
, pp. 206-216
-
-
Wray, G.A.1
-
11
-
-
51549097146
-
Resurrecting the role of transcription factor change in developmental evolution
-
Lynch VJ, Wagner GP. Resurrecting the role of transcription factor change in developmental evolution. Evolution. 2008;62:2131-54.
-
(2008)
Evolution.
, vol.62
, pp. 2131-2154
-
-
Lynch, V.J.1
Wagner, G.P.2
-
12
-
-
18844374522
-
Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast
-
Tanay A, Regev A, Shamir R. Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci U S A. 2005;102:7203-8.
-
(2005)
Proc Natl Acad Sci U S A.
, vol.102
, pp. 7203-7208
-
-
Tanay, A.1
Regev, A.2
Shamir, R.3
-
13
-
-
84922499223
-
Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks
-
Cheatle Jarvela AM, Brubaker L, Vedenko A, Gupta A, Armitage BA, Bulyk ML, et al. Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks. Mol Biol Evol. 2014;31:2672-88.
-
(2014)
Mol Biol Evol.
, vol.31
, pp. 2672-2688
-
-
Cheatle Jarvela, A.M.1
Brubaker, L.2
Vedenko, A.3
Gupta, A.4
Armitage, B.A.5
Bulyk, M.L.6
-
14
-
-
72949119310
-
Complex landscapes of somatic rearrangement in human breast cancer genomes
-
Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature. 2009;462:1005-10.
-
(2009)
Nature.
, vol.462
, pp. 1005-1010
-
-
Stephens, P.J.1
McBride, D.J.2
Lin, M.L.3
Varela, I.4
Pleasance, E.D.5
Simpson, J.T.6
-
15
-
-
0034682523
-
Distinct spectra of somatic mutations accumulated with age in mouse heart and small intestine
-
Dollé ME, Snyder WK, Gossen JA, Lohman PH, Vijg J. Distinct spectra of somatic mutations accumulated with age in mouse heart and small intestine. Proc Natl Acad Sci U S A. 2000;97:8403-8.
-
(2000)
Proc Natl Acad Sci U S A.
, vol.97
, pp. 8403-8408
-
-
Dollé, M.E.1
Snyder, W.K.2
Gossen, J.A.3
Lohman, P.H.4
Vijg, J.5
-
16
-
-
78650959663
-
Massive genomic rearrangement acquired in a single catastrophic event during cancer development
-
Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell. 2011;144:27-40.
-
(2011)
Cell.
, vol.144
, pp. 27-40
-
-
Stephens, P.J.1
Greenman, C.D.2
Fu, B.3
Yang, F.4
Bignell, G.R.5
Mudie, L.J.6
-
17
-
-
84880507665
-
Mutational heterogeneity in cancer and the search for new cancer-associated genes
-
Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499:214-8.
-
(2013)
Nature.
, vol.499
, pp. 214-218
-
-
Lawrence, M.S.1
Stojanov, P.2
Polak, P.3
Kryukov, G.V.4
Cibulskis, K.5
Sivachenko, A.6
-
18
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644-52.
-
(2011)
Nat Biotechnol.
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
-
19
-
-
84878558449
-
Probabilistic error correction for RNA sequencing
-
Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z. Probabilistic error correction for RNA sequencing. Nucleic Acids Res. 2013;41:e109.
-
(2013)
Nucleic Acids Res.
, vol.41
-
-
Le, H.S.1
Schulz, M.H.2
McCauley, B.M.3
Hinman, V.F.4
Bar-Joseph, Z.5
-
20
-
-
84859768479
-
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
-
Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012;28:1086-92.
-
(2012)
Bioinformatics.
, vol.28
, pp. 1086-1092
-
-
Schulz, M.H.1
Zerbino, D.R.2
Vingron, M.3
Birney, E.4
-
21
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008;133:1106-17.
-
(2008)
Cell.
, vol.133
, pp. 1106-1117
-
-
Chen, X.1
Xu, H.2
Yuan, P.3
Fang, F.4
Huss, M.5
Vega, V.B.6
-
22
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9:R137.
-
(2008)
Genome Biol.
, vol.9
, pp. R137
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
-
23
-
-
55749094855
-
An integrated software system for analyzing ChIP-chip and ChIP-seq data
-
Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH, et al. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol. 2008;26:1293-300.
-
(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
Wong, W.H.6
-
24
-
-
7444260846
-
The ENCODE (ENCyclopedia of DNA elements) project
-
ENCODE Project Consortium. The ENCODE (ENCyclopedia of DNA elements) project. Science. 2004;306:636-40.
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
25
-
-
84891808382
-
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
-
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014;42:D142-7.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D142-D147
-
-
Mathelier, A.1
Zhao, X.2
Zhang, A.W.3
Parcy, F.4
Worsley-Hunt, R.5
Arenillas, D.J.6
-
26
-
-
79958090979
-
DREME: motif discovery in transcription factor ChIP-seq data
-
Bailey TL. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics. 2011;27:1653-9.
-
(2011)
Bioinformatics.
, vol.27
, pp. 1653-1659
-
-
Bailey, T.L.1
-
28
-
-
33644877439
-
Human protein reference database-2006 update
-
Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, et al. Human protein reference database-2006 update. Nucleic Acids Res. 2006;34:411-4.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 411-414
-
-
Mishra, G.R.1
Suresh, M.2
Kumaran, K.3
Kannabiran, N.4
Suresh, S.5
Bala, P.6
-
29
-
-
84884698724
-
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression
-
Paris M, Kaplan T, Li XY, Villalta JE, Lott SE, Eisen MB. Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression. PLoS Genet. 2013;9:e1003748.
-
(2013)
PLoS Genet.
, vol.9
-
-
Paris, M.1
Kaplan, T.2
Li, X.Y.3
Villalta, J.E.4
Lott, S.E.5
Eisen, M.B.6
-
30
-
-
80052960863
-
Next-generation transcriptome assembly
-
Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet. 2011;12:671-82.
-
(2011)
Nat Rev Genet.
, vol.12
, pp. 671-682
-
-
Martin, J.A.1
Wang, Z.2
-
31
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821-9.
-
(2008)
Genome Res.
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
32
-
-
0041175648
-
Asymptotically efficient recursive estimation for incomplete data models using the observed information
-
Rydén T. Asymptotically efficient recursive estimation for incomplete data models using the observed information. Metrika. 1998;47:119-45.
-
(1998)
Metrika.
, vol.47
, pp. 119-145
-
-
Rydén, T.1
-
34
-
-
0001588636
-
Smooth on-line learning algorithms for hidden Markov models
-
Baldi P, Chauvin Y. Smooth on-line learning algorithms for hidden Markov models. Neural Comput. 1994;6:307-18.
-
(1994)
Neural Comput.
, vol.6
, pp. 307-318
-
-
Baldi, P.1
Chauvin, Y.2
-
35
-
-
33746829957
-
DNA microarray technologies for measuring protein-DNA interactions
-
Bulyk ML. DNA microarray technologies for measuring protein-DNA interactions. Curr Opin Biotechnol. 2006;17:422-30.
-
(2006)
Curr Opin Biotechnol.
, vol.17
, pp. 422-430
-
-
Bulyk, M.L.1
|