-
1
-
-
7444260846
-
The ENCODE (ENCyclopedia Of DNA Elements) Project.
-
The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-640.
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
2
-
-
25844449770
-
Galaxy: a platform for interactive large-scale genome analysis.
-
1240089, 16169926
-
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. Galaxy: a platform for interactive large-scale genome analysis. Genome Res 2005, 15:1451-1455. 1240089, 16169926.
-
(2005)
Genome Res
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
Zhang, Y.7
Blankenberg, D.8
Albert, I.9
Taylor, J.10
Miller, W.11
Kent, W.J.12
Nekrutenko, A.13
-
3
-
-
22144452209
-
The Integr8 project--a resource for genomic and proteomic data.
-
Pruess M, Kersey P, Apweiler R. The Integr8 project--a resource for genomic and proteomic data. In Silico Biol 2005, 5:179-185.
-
(2005)
In Silico Biol
, vol.5
, pp. 179-185
-
-
Pruess, M.1
Kersey, P.2
Apweiler, R.3
-
4
-
-
61649123317
-
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.
-
2688269, 19208250
-
Bock C, Halachev K, Buch J, Lengauer T. EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biol 2009, 10:R14. 2688269, 19208250.
-
(2009)
Genome Biol
, vol.10
-
-
Bock, C.1
Halachev, K.2
Buch, J.3
Lengauer, T.4
-
5
-
-
63849301203
-
The UCSC Cancer Genomics Browser.
-
Zhu J, Sanborn JZ, Benz S, Szeto C, Hsu F, Kuhn RM, Karolchik D, Archie J, Lenburg ME, Esserman LJ, Kent WJ, Haussler D, Wang T. The UCSC Cancer Genomics Browser. Nat Methods 2009, 6:239-240.
-
(2009)
Nat Methods
, vol.6
, pp. 239-240
-
-
Zhu, J.1
Sanborn, J.Z.2
Benz, S.3
Szeto, C.4
Hsu, F.5
Kuhn, R.M.6
Karolchik, D.7
Archie, J.8
Lenburg, M.E.9
Esserman, L.J.10
Kent, W.J.11
Haussler, D.12
Wang, T.13
-
6
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome.
-
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
7
-
-
34249952425
-
Human T-cell leukemia virus type 1 integration target sites in the human genome: comparison with those of other retroviruses.
-
1900082, 17409138
-
Derse D, Crise B, Li Y, Princler G, Lum N, Stewart C, McGrath CF, Hughes SH, Munroe DJ, Wu X. Human T-cell leukemia virus type 1 integration target sites in the human genome: comparison with those of other retroviruses. J Virol 2007, 81:6731-6741. 1900082, 17409138.
-
(2007)
J Virol
, vol.81
, pp. 6731-6741
-
-
Derse, D.1
Crise, B.2
Li, Y.3
Princler, G.4
Lum, N.5
Stewart, C.6
McGrath, C.F.7
Hughes, S.H.8
Munroe, D.J.9
Wu, X.10
-
8
-
-
59949085939
-
H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome.
-
2652204, 19047520
-
Pauler FM, Sloane MA, Huang R, Regha K, Koerner MV, Tamir I, Sommer A, Aszodi A, Jenuwein T, Barlow DP. H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res 2009, 19:221-233. 2652204, 19047520.
-
(2009)
Genome Res
, vol.19
, pp. 221-233
-
-
Pauler, F.M.1
Sloane, M.A.2
Huang, R.3
Regha, K.4
Koerner, M.V.5
Tamir, I.6
Sommer, A.7
Aszodi, A.8
Jenuwein, T.9
Barlow, D.P.10
-
9
-
-
33751507060
-
Sequential Monte Carlo p-values.
-
Besag J, Clifford P. Sequential Monte Carlo p-values. Biometrika 1991, 78:301-304.
-
(1991)
Biometrika
, vol.78
, pp. 301-304
-
-
Besag, J.1
Clifford, P.2
-
11
-
-
63649083521
-
Genome wide application of DNA melting analysis.
-
Jost D, Everaers R. Genome wide application of DNA melting analysis. J Phys Condensed Matter 2009, 21:034108.
-
(2009)
J Phys Condensed Matter
, vol.21
, pp. 034108
-
-
Jost, D.1
Everaers, R.2
-
12
-
-
0027317073
-
Stability, structure and complexity of yeast chromosome III.
-
310056, 8414978
-
King GJ. Stability, structure and complexity of yeast chromosome III. Nucleic Acids Res 1993, 21:4239-4245. 310056, 8414978.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 4239-4245
-
-
King, G.J.1
-
13
-
-
34249723701
-
The human genomic melting map.
-
1868775, 17511513
-
Liu F, Tostesen E, Sundet JK, Jenssen TK, Bock C, Jerstad GI, Thilly WG, Hovig E. The human genomic melting map. PLoS Comput Biol 2007, 3:e93. 1868775, 17511513.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Liu, F.1
Tostesen, E.2
Sundet, J.K.3
Jenssen, T.K.4
Bock, C.5
Jerstad, G.I.6
Thilly, W.G.7
Hovig, E.8
-
14
-
-
0021014810
-
Correlation between thermal stability maps and genetic maps of double-stranded DNAs.
-
Suyama A, Wada A. Correlation between thermal stability maps and genetic maps of double-stranded DNAs. J Theor Biol 1983, 105:133-145.
-
(1983)
J Theor Biol
, vol.105
, pp. 133-145
-
-
Suyama, A.1
Wada, A.2
-
15
-
-
0034687143
-
Genes and the physics of the DNA double-helix.
-
Yeramian E. Genes and the physics of the DNA double-helix. Gene 2000, 255:139-150.
-
(2000)
Gene
, vol.255
, pp. 139-150
-
-
Yeramian, E.1
-
16
-
-
63649142183
-
Segmentation of DNA sequences into twostate regions and melting fork regions.
-
Tøstesen E, Sandve GK, Liu F, Hovig E. Segmentation of DNA sequences into twostate regions and melting fork regions. J Phys Condensed Matter 2009, 21:034109.
-
(2009)
J Phys Condensed Matter
, vol.21
, pp. 034109
-
-
Tøstesen, E.1
Sandve, G.K.2
Liu, F.3
Hovig, E.4
-
17
-
-
27144450646
-
Exons, introns, and DNA thermodynamics.
-
Carlon E, Malki ML, Blossey R. Exons, introns, and DNA thermodynamics. Phys Rev Lett 2005, 94:178101.
-
(2005)
Phys Rev Lett
, vol.94
, pp. 178101
-
-
Carlon, E.1
Malki, M.L.2
Blossey, R.3
-
18
-
-
0024277331
-
Vestiges of lost introns in the thermal stability map of DNA.
-
Hanai R, Suyama A, Wada A. Vestiges of lost introns in the thermal stability map of DNA. FEBS Lett 1988, 226:247-249.
-
(1988)
FEBS Lett
, vol.226
, pp. 247-249
-
-
Hanai, R.1
Suyama, A.2
Wada, A.3
-
21
-
-
0035042776
-
A literature network of human genes for high-throughput analysis of gene expression.
-
Jenssen TK, Laegreid A, Komorowski J, Hovig E. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 2001, 28:21-28.
-
(2001)
Nat Genet
, vol.28
, pp. 21-28
-
-
Jenssen, T.K.1
Laegreid, A.2
Komorowski, J.3
Hovig, E.4
-
22
-
-
0013153953
-
Python Reference Manual
-
Python Reference Manual. , http://docs.python.org/release/2.5.2/ref/ref.html
-
-
-
-
23
-
-
0036079158
-
The human genome browser at UCSC.
-
186604, 12045153
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12:996-1006. 186604, 12045153.
-
(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
Zahler, A.M.6
Haussler, D.7
-
25
-
-
78751606233
-
Galaxy
-
Galaxy. , http://main.g2.bx.psu.edu/
-
-
-
-
26
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
-
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
Amit, I.7
Lajoie, B.R.8
Sabo, P.J.9
Dorschner, M.O.10
Sandstrom, R.11
Bernstein, B.12
Bender, M.A.13
Groudine, M.14
Gnirke, A.15
Stamatoyannopoulos, J.16
Mirny, L.A.17
Lander, E.S.18
Dekker, J.19
-
27
-
-
46249112085
-
Combinatorial patterns of histone acetylations and methylations in the human genome.
-
2769248, 18552846
-
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 2008, 40:897-903. 2769248, 18552846.
-
(2008)
Nat Genet
, vol.40
, pp. 897-903
-
-
Wang, Z.1
Zang, C.2
Rosenfeld, J.A.3
Schones, D.E.4
Barski, A.5
Cuddapah, S.6
Cui, K.7
Roh, T.Y.8
Peng, W.9
Zhang, M.Q.10
Zhao, K.11
-
28
-
-
84905572307
-
1000Genomes
-
1000Genomes. , http://www.1000genomes.org/
-
-
-
-
29
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
-
2858594, 19815776
-
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293. 2858594, 19815776.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
Amit, I.7
Lajoie, B.R.8
Sabo, P.J.9
Dorschner, M.O.10
Sandstrom, R.11
Bernstein, B.12
Bender, M.A.13
Groudine, M.14
Gnirke, A.15
Stamatoyannopoulos, J.16
Mirny, L.A.17
Lander, E.S.18
Dekker, J.19
-
30
-
-
77953572914
-
Integrating one-dimensional and three-dimensional maps of genomes.
-
Naumova N, Dekker J. Integrating one-dimensional and three-dimensional maps of genomes. J Cell Sci 123:1979-1988.
-
J Cell Sci
, vol.123
, pp. 1979-1988
-
-
Naumova, N.1
Dekker, J.2
-
31
-
-
67651152579
-
Fine-structured multi-scaling long-range correlations in completely sequenced genomes - features, origin, and classification.
-
2701493, 19533117
-
Knoch TA, Goker M, Lohner R, Abuseiris A, Grosveld FG. Fine-structured multi-scaling long-range correlations in completely sequenced genomes - features, origin, and classification. Eur Biophys J 2009, 38:757-779. 2701493, 19533117.
-
(2009)
Eur Biophys J
, vol.38
, pp. 757-779
-
-
Knoch, T.A.1
Goker, M.2
Lohner, R.3
Abuseiris, A.4
Grosveld, F.G.5
-
32
-
-
78751629346
-
Mako
-
Mako. , http://www.makotemplates.org
-
-
-
-
33
-
-
78751612307
-
JQuery
-
JQuery. , http://jquery.com
-
-
-
-
34
-
-
33750306080
-
-
Trelgol Publishing, Spanish Fork UT
-
Oliphant TE. Guide to NumPy 2006, Trelgol Publishing, Spanish Fork UT.
-
(2006)
Guide to NumPy
-
-
Oliphant, T.E.1
-
36
-
-
84885383187
-
RPy a robust Python interface to the R Programming Language
-
RPy a robust Python interface to the R Programming Language. , http://rpy.sf.net
-
-
-
-
37
-
-
78751622740
-
GPL
-
GPL. , http://www.gnu.org/copyleft/gpl.html
-
-
-
-
38
-
-
78751616047
-
Titan
-
Titan. , http://www.notur.no/hardware/titan/
-
-
-
-
39
-
-
66149186985
-
Genomic location analysis by ChIP-Seq.
-
Barski A, Zhao K. Genomic location analysis by ChIP-Seq. J Cell Biochem 2009, 107:11-18.
-
(2009)
J Cell Biochem
, vol.107
, pp. 11-18
-
-
Barski, A.1
Zhao, K.2
-
40
-
-
57449095143
-
Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.
-
2596141, 19014516
-
Zhang Y, Shin H, Song JS, Lei Y, Liu XS. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 2008, 9:537. 2596141, 19014516.
-
(2008)
BMC Genomics
, vol.9
, pp. 537
-
-
Zhang, Y.1
Shin, H.2
Song, J.S.3
Lei, Y.4
Liu, X.S.5
-
41
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes.
-
395923, 15075390
-
Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004, 101:6062-6067. 395923, 15075390.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.A.5
Block, D.6
Zhang, J.7
Soden, R.8
Hayakawa, M.9
Kreiman, G.10
Cooke, M.P.11
Walker, J.R.12
Hogenesch, J.B.13
-
42
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
-
2921165, 17603471
-
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560. 2921165, 17603471.
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
Giannoukos, G.6
Alvarez, P.7
Brockman, W.8
Kim, T.K.9
Koche, R.P.10
Lee, W.11
Mendenhall, E.12
O'Donovan, A.13
Presser, A.14
Russ, C.15
Xie, X.16
Meissner, A.17
Wernig, M.18
Jaenisch, R.19
Nusbaum, C.20
Lander, E.S.21
Bernstein, B.E.22
more..
-
43
-
-
67650711619
-
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.
-
2732366, 19505939
-
Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 2009, 25:1952-1958. 2732366, 19505939.
-
(2009)
Bioinformatics
, vol.25
, pp. 1952-1958
-
-
Zang, C.1
Schones, D.E.2
Zeng, C.3
Cui, K.4
Zhao, K.5
Peng, W.6
-
45
-
-
67650064594
-
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
-
2704439, 19498102
-
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res 2009, 19:1316-1323. 2704439, 19498102.
-
(2009)
Genome Res
, vol.19
, pp. 1316-1323
-
-
Pruitt, K.D.1
Harrow, J.2
Harte, R.A.3
Wallin, C.4
Diekhans, M.5
Maglott, D.R.6
Searle, S.7
Farrell, C.M.8
Loveland, J.E.9
Ruef, B.J.10
Hart, E.11
Suner, M.M.12
Landrum, M.J.13
Aken, B.14
Ayling, S.15
Baertsch, R.16
Fernandez-Banet, J.17
Cherry, J.L.18
Curwen, V.19
Dicuccio, M.20
Kellis, M.21
Lee, J.22
Lin, M.F.23
Schuster, M.24
Shkeda, A.25
Amid, C.26
Brown, G.27
Dukhanina, O.28
Frankish, A.29
Hart, J.30
more..
-
46
-
-
58149178579
-
NCBI Reference Sequences: current status, policy and new initiatives.
-
2686572, 18927115
-
Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 2009, 37:D32-36. 2686572, 18927115.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Pruitt, K.D.1
Tatusova, T.2
Klimke, W.3
Maglott, D.R.4
-
47
-
-
18444402182
-
The Ensembl genome database project.
-
99161, 11752248
-
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mongin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, et al. The Ensembl genome database project. Nucleic Acids Res 2002, 30:38-41. 99161, 11752248.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 38-41
-
-
Hubbard, T.1
Barker, D.2
Birney, E.3
Cameron, G.4
Chen, Y.5
Clark, L.6
Cox, T.7
Cuff, J.8
Curwen, V.9
Down, T.10
Durbin, R.11
Eyras, E.12
Gilbert, J.13
Hammond, M.14
Huminiecki, L.15
Kasprzyk, A.16
Lehvaslaiho, H.17
Lijnzaad, P.18
Melsopp, C.19
Mongin, E.20
Pettett, R.21
Pocock, M.22
Potter, S.23
Rust, A.24
Schmidt, E.25
Searle, S.26
Slater, G.27
Smith, J.28
Spooner, W.29
Stabenau, A.30
more..
-
48
-
-
38549148703
-
The vertebrate genome annotation (Vega) database.
-
2238886, 18003653
-
Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL. The vertebrate genome annotation (Vega) database. Nucleic Acids Res 2008, 36:D753-760. 2238886, 18003653.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Wilming, L.G.1
Gilbert, J.G.2
Howe, K.3
Trevanion, S.4
Hubbard, T.5
Harrow, J.L.6
-
49
-
-
38549163285
-
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
-
2238988, 18089548
-
Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, et al. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res 2008, 36:D793-799. 2238988, 18089548.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Yamasaki, C.1
Murakami, K.2
Fujii, Y.3
Sato, Y.4
Harada, E.5
Takeda, J.6
Taniya, T.7
Sakate, R.8
Kikugawa, S.9
Shimada, M.10
Tanino, M.11
Koyanagi, K.O.12
Barrero, R.A.13
Gough, C.14
Chun, H.W.15
Habara, T.16
Hanaoka, H.17
Hayakawa, Y.18
Hilton, P.B.19
Kaneko, Y.20
Kanno, M.21
Kawahara, Y.22
Kawamura, T.23
Matsuya, A.24
Nagata, N.25
Nishikata, K.26
Noda, A.O.27
Nurimoto, S.28
Saichi, N.29
Sakai, H.30
more..
|